Dec 10 2012

Truth in Education

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139 Responses to “Truth in Education”

  1. locutusbrgon 10 Dec 2012 at 11:05 am

    Outside of the obvious ridiculousness of trying to introduce dogma. I am worried that these battles will result in restrictions for science teachers that are trying to introduce new real scientific topics. Not saying give in or the battles do not need to be fought. I am just worried about another casualty of creation idiocy. Global warming, in the 80′s, was in my textbooks. I think they have a tougher time putting it in now. Makes me wonder what other new science is being avoided to reduce controversy.

  2. nybgruson 10 Dec 2012 at 12:40 pm

    I wouldn’t call AGW “new science” and would say it falls under the same umbrella of issues that evolution is currently facing as well.

    I would also say that “new science” should not even be an issue. Except for high school students of the highest caliber (i.e. those taking very advanced science courses) no pre-college students should be taught “new” science. Teaching the fundamentals and well accepted theories (like evolution) is what that education should be about. Defending science in elementary, middle, and high school should be no more complicated than pointing to the relevant chapters of the textbook they are using. Need to defend evolution to a questioning student? Point to the appropriate chapter of Campbell’s biology and that is it. High school is not the time to be pushing the limits of scientific discourse on the topic and discussing the role of proteomic, epigenetic, snRNA’s, or why Shapiro is wrong, etc in evolution. Learn the basics, then go on to that stuff in college. Perhaps one day we will settle those things to the point where they are high school level material. Not yet, and in no case can I see room or need for laws like this one to demand science teachers defend the science they teach. That is already settled by the committees on quality and standards of education and precisely why laws like these make no sense at all.

  3. locutusbrgon 10 Dec 2012 at 1:21 pm

    @ nybgrus
    AGW in the 80′s was a “new” science it was not even called AGW. That is the point. I was exposed to that in high school. I have no problem with pushing kids in high school. My high school had an excellent science department. We were taught subject matter that was duplicate to introductory physics, microbiology, botany and biology at the university level. Granted it was given in a year instead of a semester. The head of our department was a professor in microbiology at a Ivy league university. He headed that department because he like to get kids excited about science. I will admit that it was not a public school. There should be a way of pushing science beyond basics at high school level. IF you are incapable of expanding the discussion beyond the texts you are limiting the experience. When it comes to evolution textbooks are fine. If your kids teacher is saying “all you need to know is in the textbook and just follow the science textbook”. Then what if anything is the teacher teaching? How to read a textbook? I don’t want my kid at that school, anymore than one teaching intelligent design. It is just another way the creationists are hurting high school science education.

  4. nybgruson 10 Dec 2012 at 1:48 pm

    @locutus:

    I think we may be talking about different things. I went to a public HS and did organic chemistry, advanced statistics and calculus, etc. But those were the classes above and beyond what was needed to graduate and required meeting certain pre-req’s to take. That is where I learned a lot of “new” science and discussed such cutting edge ideas.

    I, however, am referring to the minimum standards for completion of high school. Those should reasonably not be more than imparting a basic understanding of the fundamental tenets of science and the scientific process. Besides the fact that the average high school student is simply not capable of succeeding in advanced classes like I took, there are many students who are not interested in a career in the sciences and should have the option to know the minimum there and take advanced courses in other areas (and some who are simply going to be the minimum achievers and that is OK… we just need to ensure that minimum is well taught, solid education).

    As for what do teachers teach… yeah, at the minimum level for completion of HS, most of what is taught is how to read a text book. That is not some innate skill we are born with, and (once again IMO), teaching beyond the book is not reasonable as a minumum requirement. There is also a convenient segregation of teachers – those teaching advanced classes should be well versed enough in the classes to adequately teach beyond the book. Those teaching the minimum should be well versed in teaching the average student how to understand and possibly apply the basics.

    If you don’t want your kid at a school that merely teaches the basics that way, more power to you. But that means you are putting in more effort and more of your own time educating your children than the average person and they are in a position to actually learn and benefit from these most advanced classes. In which case a private school may be a better fit. Or, in my case, my public school had (and still has) a very robust sciences curriculum with the opportunity for students like your children to take advanced classes whilst the rest of the school takes the minumum required to finish school.

  5. Zhankforon 10 Dec 2012 at 1:52 pm

    I think you mean by the turn of the 20th century?

  6. Zhankforon 10 Dec 2012 at 2:01 pm

    Oh… I see what you’ve done. Different interpretations of the phrase “turn of the nth century.” Sorry, everyone.

  7. tmac57on 10 Dec 2012 at 4:15 pm

    Kruse wants to mandate that teachers defend the truth of any science they teach which is challenged by a student. Again, very superficially this may seem benign. Teachers should explain to student how we know what we know.

    This doesn’t strike me as benign even superficially,due to the fact that a well rehearsed creationist raised student (or AGW denial indoctrinated one) could be very disruptive to the teacher’s lesson plan by endlessly citing contrarian points,leading to a black hole of doubt for those interested enough to listen to such an exchange.

  8. Steven Novellaon 10 Dec 2012 at 4:20 pm

    tmac – I agree, it’s benign totally out of context of the creationism, AGW, etc controversies.

    Regarding “turn of the 19th century” – apparently there is no consensus. It could be turn to or from the “nth” century. So it should only be used when obvious from the context, which it is here.

    http://www.chicagomanualofstyle.org/qanda/data/faq/topics/Numbers.html?old=Numbers17.html

  9. rezistnzisfutlon 10 Dec 2012 at 7:56 pm

    It wasn’t a year or two ago when it was in the news that 13% of high school biology teachers advocate creationism in class. I’ve seen video footage myself of teachers and students in public science classrooms basically condemning evolution and discussing the merits of the christian creation mythology as fact.

    Some teachers outright teach creationism in spite of laws, and many get away with it because, in their community, parents and other educators support them. A great many teachers, on the other hand (perhaps even the majority) either don’t want to become embroiled in controversy within their community, or don’t know enough about evolution to teach it effectively (or defend it), so most students leave high school knowing little about evolution, with only the impression left on them by their local church.

    It seems that creationists are winning the PR war with the general public on biology education, intellectualism, and scholarship in general. I hope I’m wrong, but there seems to be a large anti-intellectual and anti-science sentiment growing in the public sphere. It’s little wonder that the US is slipping so rapidly in science, math, and literacy compared to other developed nations.

    When proponents of science and science education are constantly defending the integrity of science, there’s something wrong. There just doesn’t seem to be enough emphasis on “offensively” advertising good science to the public.

  10. ccbowerson 10 Dec 2012 at 9:35 pm

    “Except for high school students of the highest caliber (i.e. those taking very advanced science courses) no pre-college students should be taught “new” science. Teaching the fundamentals and well accepted theories (like evolution) is what that education should be about. Defending science in elementary, middle, and high school should be no more complicated than pointing to the relevant chapters of the textbook they are using.”

    That is a bit simplistic, although I agree that the vast majority of science taught in those schools are settled/consensus science. In any classroom in which learning is happening there will be communication between teacher and student, and some students will have questions based upon what they have learned and been told during their lives. Such times could be important teaching moments, and responding something is true because the book says so is a bit dogmatic sounding (and with that there may be an impasse because that may set the perception of competing dogmas).

    Now perhaps that is not what you meant: perhaps you mean that the book will contain the rational or evidence for a given concept, but that may not always be the case. Also there is an implication in your response that implies that education at that level is just about supplying facts, but I disagree with that as well. Perhaps I am just misinterpreting what you meant.

    This reminds me (indirectly) of one of my more memorable classes in high school. It was an elective science class in my junior year of HS after earthscience, biology, chemistry and physics. The class introduced me to Carl Sagan (as 2 of his books were used in the class) and was filled with discussions and a ‘debate’ using the Drake equation. I probably learned the least amount of facts, but it made a lasting impression.

  11. nybgruson 10 Dec 2012 at 9:55 pm

    @CCbowers:

    Yes, I was being simplistic and of course I would love if classes, even at that level, truly taught critical analysis.

    I was merely arguing for the concept of the common denominator. What we should have as an absolute minimum to be considered a high school grad. I don’t think it is necessarily reasonable or possible to have the kind of education you and I both would like (and both experienced, to be honest) for absolutely everyone.

    And yes, I did mean that a good text (like Campbell’s) doesn’t just list facts but explains them. When I said that the teacher should be able to point to the text as justification for assertions was to mean that if a student questions the validity of a fact the textbook should be considered authoritative. This, of course, is part of the importance of textbook selection and especially vis-a-vis the near inception of creationist texts in Texas public schools. If a student asks why something occurs, then at a basic level the text should explain that as well and the teacher’s role should be to further explicate as necessary to help the student understand what the text is trying to say as well as reinforce with other examples and experiments/simulations. It is at the more advanced level that deeper questions can be answered and discussed. This also assumes a progression and building of scientific knowledge such that the age of the earth, for example, would be explained on principles the pupil has already been exposed to.

    And yes, I do think that it is only reasonable to teach consensus science to those in the pre-college years. They need to enter the adult world armed with a basic set of established facts, knowledge, and hopefully critical thinking and analysis skills. If they go on, they can then start learning more and more nuance.

    For example, when I first learned chemistry in middle school I was taught merely that reactions only go one direction. I developed a solid basis of the fundamentals of chemistry. Then at an older age I learned about how all reactions are reversible and that this is describe as a coefficient depending on the product(s) and solute called the Kd. And then so on and so forth.

    As our consensus knowledge grows, we may be able to cram more into the pre-college years, but I think it is reasonable that for the minimum graduation standards only consensus science is taught, with the opportunity for more advanced students to go further if they demonstrate desire and competence.

    Hopefully that clarifies my thoughts a bit.

  12. ccbowerson 10 Dec 2012 at 11:11 pm

    “What we should have as an absolute minimum to be considered a high school grad. I don’t think it is necessarily reasonable or possible to have the kind of education you and I both would like (and both experienced, to be honest) for absolutely everyone.”

    I had public education at all levels of schooling (elementary, middle, HS, college, and grad/professional), which has helped shaped my attachment to the concept of quality public education. Although I agree that not everyone needs or wants the same level of education, I’m not sure why we must restrict this conversation to the “bare minimum.” (Resisting an ‘Office Space’ joke here) Although I grew up, went to school, and lived in various cities in Upstate NY, this topic is bothersome because we are talking about messing with public education, which has enough obstacles as it is. Unfortunately, these creatonists are particularly active in states where public schools are already struggling.

    “And yes, I do think that it is only reasonable to teach consensus science to those in the pre-college years. They need to enter the adult world armed with a basic set of established facts, knowledge, and hopefully critical thinking and analysis skills. If they go on, they can then start learning more and more nuance.”

    Perhaps as a minimum standard this approach is fine, but I don’t think this is mutually exclusive of big picture understanding. For most people who do not pursue a career in the sciences, the facts that they learned in school about science become less and less important as they forget them, but the lessons learned will persist. To me, having a reasonable understanding how science works for the average person is far superior to remembering what they saw in the microscope 20 years ago. In addition I think there is a small role, even early on, about mentioning the frontiers of science (there will be questions asked in school that will make avoiding the topic impossible). It can pique a young students interest, and can give some perspective on the process of science. It already comes up with my 6 year old daughter

  13. nybgruson 11 Dec 2012 at 12:07 am

    I don’t disagree at all with you. I would love to see it happen across the board.

    As I said, I was just focusing on the minimums since that is where we have to set our standards. Above the minimum is, of course and by definition, always better. I am also considering the realities of the quality of teachers we have available.

    I’d like to focus on getting everyone at a good, acceptable, and reasonable standard of education. Once we get that taken care of – which yes, includes getting those interminable creationists out of all education – then we can work on raising that standard even more and concern ourselves with all the other extras we both agree are useful.

    And as for your 6 year old daughter, that is wonderful. But you should realize that is (in large part) because of who you (and your partner) are. Most people – the average – are not the same. We need to get those people at the minimum so their children can start out there and we can then raise the minimums (if that makes any sense).

  14. Jared Olsenon 11 Dec 2012 at 3:55 am

    Steve, your pendantry warms my heart! Of course you’ve got a link to an article about accepted use of ‘…the turn of’ !! :-)

  15. locutusbrgon 11 Dec 2012 at 10:24 am

    @ nybgrus

    I agree 100% with the basic standards, and your comments.

  16. ccbowerson 11 Dec 2012 at 12:10 pm

    “I agree 100% with the basic standards, and your comments.”

    I also agree with his comments (I usually do), but the minimum standards already get the most attention. I would like to see the discussion to extend beyond this more often. Its not like once we reach a certain threshold of a certain minimum, that we can then discuss beyond this. In reality, this is all happening in parallel, at the same time, and the excessive focus on the bare minimum standards may detract from the quality of education from a broader perspective. This is a big topic, and is perhaps beyond the scope of this blog

  17. sonicon 11 Dec 2012 at 1:10 pm

    I’ll relate this to teaching evolution in a moment as I there is a question to answer, but—

    The “Big Bang” is liked by theists and creationists, I believe.

    Arno Penzias, who won the Nobel Prize with Robert Wilson for the discovery of the cosmic background radiation that is seen as confirming the big bang model said this in an interview published by the New York Times–
    “The best data we have [concerning the Big Bang] are exactly what I would have predicted, had I nothing to go on but the five books of Moses, the Psalms, the bible as a whole.”

    What creationist wouldn’t like that? And would it be OK to include that in a study of the topic?

    As Stephen Hawking has pointed out- “So long as the universe had a beginning, we could suppose it had a creator.”

    The bigger point is covered here by this quote from Christopher Isham-
    “Perhaps the best argument in favor of the thesis that the Big Bang supports theism is the obvious unease with which it is greeted by some atheist physicists. At times this has led to scientific ideas, such as continuous creation or an oscillating universe, being advanced with a tenacity which so exceeds their intrinsic worth that one can only suspect the operation of psychological forces lying very much deeper than the usual academic desire of a theorist to support his or her theory.”

    And that relates to evolution as well–

    From Richard Lewontin a leader in developing the mathematical basis of population genetics author of numerous articles, textbooks and co-author with Gould:

    “Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door…”

    If this were included at the beginning of every section about evolution in biology texts I think it would be a good thing- it allows for the proper understanding of what follows:
    An argument based on an absolute prior commitment to a philosophical position.
    If one were to take away that commitment, than one might have different conclusions or give different weight to the evidence.

    Question- should a teacher be allowed to say what I just said???

  18. ccbowerson 11 Dec 2012 at 1:16 pm

    “Question- should a teacher be allowed to say what I just said???”

    Perhaps in a college level class, but I wouldn’t recommend it.

  19. BillyJoe7on 11 Dec 2012 at 3:51 pm

    I cannot remain silent and I cannot be accommodating, so please excuse the tone of this comment.

    Contrary to the pontification above from our erstwhile resident closet creationist (see the thread
    “Seeing with Touch” where his creationist credentials were exposed), science does not have an absolute prior commitment to the materialist philosophy.

    Materialism/naturalism is the assumption of science. If science were to assume supernaturalism, every mystery could stop at “the gods did it” (note: I always substitute ‘the gods’ for ‘God’ to nullify the nefarious christian bias). In other words, to make any sort of progress, science has to assume there are natural explanations. And, based on this assumption, science has for 400 years succeeded in displacing “the gods did it” with natural explanations. This is 400 years of evidence that the underlying assumption of science is true. Of course, truths in science are always conditional. Provide evidence of the supernatural and science will tune in. But the silence is deafening.

    As for placing that quote by Richard Lewontin “at the beginning of every section about evolution in biology texts”, all I can say is you have to be [expletive deleted, but it looks something like this: #v<|<!^g] kidding! Religion has no place in a science class.

  20. nybgruson 11 Dec 2012 at 4:22 pm

    @locutus of borg:

    Thank you for the kind words.

    @ccbowers:

    Also thank you for the kind words.

    I see where you are coming from and absolutely understand and agree. The ideas are indeed able to and should considered in parallel. Since this post, however, was about an attempt at using laws to subvert the the minimum standards, it seemed apropos for me to focus my discussion on that. Additionally, I would posit that one of the best ways to ensure, make easy, and make more available the sort of higher learning we both would certainly like is to ensure that a reasonable minimum is already met. If people en masse were genuinely educated well there would be simply no foothold for creationist thought to gain traction. More people would recognize and be willing to call it silliness and the culture would shift to make it an untenable position to hold (much like smoking is becoming in most developed nations). In other words, ensuring as many people actually achieve a minimum standard of science and general education means there will be fewer detractions and obstacles to higher education and allow the entirety of education to move forward. There is, after all, a reason why Scandinavian countries in particuler have a young population vastly more adept at math and science and overall much more educated than age and SES matched populations.

    As a corollary I would posit that while the two goals we speak of can and should run in tandem, that they are still tied to each other and thus neglecting the minumum drags down the progress of the maximum.

    @sonic:

    As CCbowerds said, perhaps at a college level as a point of discussion on the philosophy of science, but certainly not in the pre-college years when teaching consensus science should be the goal. Trust me, we have enough non-controversial (i.e. scientifically controversial, not manufactroversial like creationism/evolution) consensus science to spend all available time teaching that in the pre-college years. And that is what students need to know. IMO, education through high school is supposed to educate one enough to be a reasonable thoughtful, productive, and functional member of society. College is supposed to advance that education and obviously post-grad and post-doc work is where the frontiers of science and knowledge are supposed to be pushed and discussed.

    Also, Richard Lewontin is simply incorrect. The reason materialism stands is because there has been absolutely no credible challenge to it and it has demonstrated unequivocally, time and time again, its utility. To say otherwise – as Lewontin does – is akin to being a Scooby and Shaggy. No matter how many times they see there isn’t actually a ghost and every single mystery is always solved by demonstrated a perfectly natural criminal intent, they still insist that there must be ghosts. Don’t forget that humans can hold cognitive dissonance quite well and that many intelligent people can still desperately cling to their ideology in the face of contrary evidence, as Lewontin is doing. His explanation is a post-hoc rationalization of a fact he refuses to accept; materialism is the dominant philosophical underpinning to scientific inquiry because after hundreds of years there is not a single credible example of the universe working in any other way and in that same time frame all (minus the small amount of inevitable blind luck) progress has been made under that paradigm and no other.

    @BJ:

    I started writing my bit before noticing you had written yours. Yes, that is a more succinct way of putting it. Science would be the first to accomodate evidence to the contrary of materialism.

    However, where would that leave us? Good evidence for supernaturalism would be a complete lack of consistency in physical laws and outcomes of experiments. We would be stymied.

    Or what if we assumed supernaturalism to be a valid construct alongside of or even in place of materialism? How would we define the limit of inquiry or the validity of a response? If we accept that a supernatural explanation is a legitimate one, then at any point I could write an article on a really poorly done study, claim a supernatural explanation for my findings (spurious or not) and then reasonably demand that my results be accepted by the world at large. The very premise of supernaturalism means that my results could be different from yours and still be equally as valid. So how would we ever settle any disagreement in answers to questions?

    So yes, as I said above, it is not only a consistently and unequivocally validated philosophy of science, but also an absolutely necessary tenet that literally everyone accepts except when it suits their argument. I would love to see what Lewontin would envision science to be if “[allowed] a Divine Foot in the door..”

  21. Mlemaon 11 Dec 2012 at 10:29 pm

    sonic, I think I understand what you’re saying, but for once (and I can hardly believe I’m saying this) I agree with BJ (although it really would be nice if he could learn to comment in a respectful way as nybgrus does). I agree with what Richard Lewontin is saying, but I don’t think it’s something that would fit into a science class.

    I see it as: there’s no point in considering the divine in science, except in a personal way if an individual wishes. We know that there are basic questions of existence that science can’t answer. Science is just one branch of human knowledge. It’s just not useful to consider God, a god, gods, as we try to understand our existence as a material one.

    I do think that good scientists, and good teachers, adopt an agnostic attitude about any theory. So I would envision elements of evolution being introduced as: “this is what scientists believe based on current evidence…” I think that those who insist on phrasing things as “this is the way it is” aren’t really being scientific. When we study the history of science, what we learn first is that we’re always learning, and still learning. There may be major breakthroughs in areas of science that will recast certain aspects of evolutionary theory (as genetics did) and who knows? (dare I say) perhaps find a new theory altogether that will do better at answering questions which are now unanswered. But i predict it will never be “helpful” to science to look for the divine in the universe. (and it might not be helpful to the divine either) :)

  22. ccbowerson 11 Dec 2012 at 11:41 pm

    “Additionally, I would posit that one of the best ways to ensure, make easy, and make more available the sort of higher learning we both would certainly like is to ensure that a reasonable minimum is already met.”

    Absolutely, but I viewed the struggles in meeting the minimum standards only partly an education issue as we are discussing here. There are larger societal issues such as poverty, cultural attitudes, politics, etc that come into play that are beyond the scope of this conversation. If only the issues in education didn’t carry so much baggage and people driven by ideology (on various sides)- we could actually look at the evidence for what works, then apply those strategies that have the best supporting evidence for each goal or problem identified. Another problem is that education is very fragmented in the US, since each state sets its own standards. Anyways, this is a topic that can go off on many tangents, and I don’t want to drag this on too much

  23. BillyJoe7on 12 Dec 2012 at 6:20 am

    for once (and I can hardly believe I’m saying this) I agree with BJ
    That is because, for once in your life, you are correct.

    (although it really would be nice if he could learn to comment in a respectful way as nybgrus does)
    The difference is that sonic doesn’t read my posts and therefore I do not feel as restrained as nybgrus does (actually, come to think of it, he said he would no longer respond to my posts. So, oops, sorry sonic for upsetting you with my disrespectful tone.)

    there’s no point in considering the divine in science
    But there IS a point. And the point is that there is no evidence for gods and that, therefore, gods are failed hypotheses that should be discarded and gods are unnecessary hypotheses that should be razored.

    except in a personal way if an individual wishes.
    That’s where there is no point. What is the point in believing in something based on what you wish to be true, rather than what the evidence shows you to be true?

    We know that there are basic questions of existence that science can’t answer.
    Perhaps, but then neither can anything outside of science. Otherwise name one thing that has been verified as true by something outside of science.

    Science is just one branch of human knowledge.
    Correct. There is the holly trinity of science, mathematics and logic.

    It’s just not useful to consider God, a god, gods, as we try to understand our existence as a material one.
    It is not useful, period.

    I do think that good scientists, and good teachers, adopt an agnostic attitude about any theory.
    Agnostic means “lack of knowledge, unknown, or unknowable”. I think you meant sceptical.

    So I would envision elements of evolution being introduced as: “this is what scientists believe based on current evidence…”
    It should be much stronger than that: “this is what scientists believe to be factual based on the overwhelming amount of evidence from many diverse fields of study”

    I think that those who insist on phrasing things as “this is the way it is” aren’t really being scientific.
    Agreed, but this is largely a strawman.

    There may be major breakthroughs in areas of science that will recast certain aspects of evolutionary theory (as genetics did) and who knows? (dare I say) perhaps find a new theory altogether that will do better at answering questions which are now unanswered.
    Perhaps, but at present there is not even a hint that a new theory is even needed.

    But i predict it will never be “helpful” to science to look for the divine in the universe.
    But, if it is there, science should be able to find it. As it is, the evidence that should be there if gods existed and that isn’t there, is evidence against the existence of gods.

    (and it might not be helpful to the divine either)
    Well, the faeries at the bottom of my garden don’t like it much either.

  24. SteveAon 12 Dec 2012 at 7:28 am

    BJ7: “he [Sonic] said he would no longer respond to my posts.”

    You’re kidding? That was his comeback?

    Sonic, you’ve got a lot of unfinished business in the ‘Seeing with touch’ thread. A lot.

    Why don’t you deal with that before you start posting elsewhere.

  25. sonicon 12 Dec 2012 at 11:54 am

    ccbowers-
    Here is a message from Robert Jastrow – I’m wondering what your take is-
    http://www.leaderu.com/truth/1truth18b.html
    If a teacher wanted to use that article as a means of handling questions about god and science, I would think it would be an excellent one.
    BTW- Note I’m saying as a way of dealing with student questions. I think that in order to get the student onto the subjects of interest, sometimes it is best to answer any questions in such a way that the student can put his attention back to the subject at hand.
    I’m quite curious- would you have a specific objection to that article?

    Mlema-
    I’m not suggesting that a teacher would have to say those things, I’m saying that it wouldn’t bother me if one did.
    So when a student asked, “Isn’t the Big Bang basically in agreement with theology?” Or, “Doesn’t science show there is no god?” I would think these types of things would be appropriate.
    In the ‘science’ section at my local bookstore there are a number of books with the word ‘God’ in the title. Keeping god out of the science classroom doesn’t seem realistic in all cases.
    What do you think of the approach taken by Jastrow in the article I linked to above?
    Other than that I agree with what you say about teaching science in general.

    nybrus-
    I think our disagreements on this subject would begin with the Lewonitin statement.
    To me he is talking about himself and the numerous top evolutionary scientists that he worked with over his stellar career.
    As he actually is talking about himself and people that he worked with and knew I’m wondering in what sense you think he is mistaken.
    Is he wrong about himself? Is he wrong about one of the people he worked with?
    Which one and why do you think so?

    I’m sure we can agree that all logic starts with a premise, so for me the Lewontinin statement is critical in understanding why the data is interpreted the way it is.

  26. sonicon 12 Dec 2012 at 1:08 pm

    SteveA-
    I missed your comment earlier.
    If you have a specific question about something I’ve said, I will be happy to attempt an answer.
    If you are thinking I’m wrong about something– well, what is that? It is entirely possible that I agree– after all, I learn things all the time and I know that some things I thought before were wrong…

    Otherwise I don’t know what your comment is about as I am unaware of any ‘unfinished business’ you refer to.

  27. nybgruson 12 Dec 2012 at 1:34 pm

    @mlema:

    I agree with BJ (although it really would be nice if he could learn to comment in a respectful way as nybgrus does).

    First off, thank you. It is something I am genuinely working on (and have been over the years of commenting on this blog and SBM). However, I do often feel viscerally much like BJ does and am just as much a non-accomodationist as he is. The difference is that my field of work and my goals are different than his and a different tack (i.e. the one I generally take) is much more fruitful than his. However, I do value his bluntness (and that of PZ Myers) since I think many tacks are useful in different contexts and it gives me an opportunity to state that I agree fully with what he says and then expound upon it in my own way. Essentially a “good cop, bad cop” routine though not pre-conceived but rather opportunistic.

    However, I disagree with you (and in the same vein the Jastrow post that sonic linked) when you say:

    We know that there are basic questions of existence that science can’t answer.

    No, we don’t. There may be. We have reason to believe certain questions may be more difficult to answer and perhaps impossible. But everything we know right now leads us to believe that there is no fundamentally unanswerable question.

    The problem is that the answer may not be a persnally satisfying one. “Why are we here on this earth, leading lives of conscioussness and directed purpose?” may well have the answer of “Just because.” I believe this is the answer, as does Dawkins for example, though Lawrence Krauss disagrees and still holds out hope for some deeper intrinsic “meaning.” This does not, however, cloud his scientific judgement nor does he imbue this meaning with some sort of supernaturalistic meaning. Personally, I am quite satisfied with the answer of “just because.” I find it to be the single most empowering realization we can come to as human beings.

    Think about it – we personify deities to provide meaning to life, order to the universe, and a purpose for being. There is no evidence deities exist and plenty that they don’t. If they don’t exist, these personifications become us. We become the creators, the crafters of our own destiny and purpose, and thus become liberated to follow our own creative and productive desires rather than try and mold ourselves into someone we think something else wishes us to be. Rather than find it perplexing and generating a feeling of being lost at sea, it gives me this awesome freedom and power to swim in any direction I want and do whatever makes me and the most people possible happy, more fulfilled, and (in my case vis-a-vis my chosen profession) healthier and longer lived.

    So I would envision elements of evolution being introduced as: “this is what scientists believe based on current evidence…” I think that those who insist on phrasing things as “this is the way it is” aren’t really being scientific.

    I do agree with you here in principle, but in practice I think such statements inevitably do a great disservice to the state of evolutionary theory. There is literally no other theoretical framework in all of the sciences – I would argue in all of human knowledge – that is more well supported. We are more likely to discover that all those galaxies we think we see are nothing more than artifacts generated by as of yet unkown quantum abberations than we are to discover that there is some deep intrinsic flaw with the core aspects of evolutionary theory.

    Discussing finer details, being truly scientific and skeptical and being able to truly understand why no scientist can ever say “I am 100% sure of” anything is not something children and young people can grasp. It is a very abstract concept (much like “infinity” or even “billions of years”); one that is not viscerally immediate to our extremely limited ability to perceive and process the world around us. The average adolescent can’t fundamentally grasp just how far the other side of the planet is, let alone the nearest star or galaxy. So offering equivocating statement – as fair as they may be from a scientific standpoint – only serves to muddy the waters and engender unreasonable concern over the validity of the statements of fact by the science teacher.

    Imagine if we started each science lesson with a discourse on the merits (or lack thereof) of solipsism and how that may alter the interpretation of evidence? No, we need our children to be educated in the facts of the matter first, and then if they grasp the fundamentals move on deeper and deeper into such discussions. The kind of discussion we tend to have here would be unfathomable for all except the most advanced of high school students. In fact, I have become sort of a mentor to a very, very bright 16 year old because he was part of a medical interest program that I helped teach and he discovered I am an atheist and secular humanist and recahed out to me. He comes from a very Catholic family, has no non-religious friends, and was yearning for more rigorous scientific discourse. The level he is at is truly impressive for a 16 year old. Yet he still cannot adequately process the finer and deeper points of such discussions. Which is why they should not reasonably be part of the standard educational curriculum for high schoolers.

  28. nybgruson 12 Dec 2012 at 1:36 pm

    @ccbowers:

    I think we are very much on the same page here. I agree with you fully. I too am happy to let the conversation go since you are correct that it is a deep and protracted one where we will just continue to talk about different facets of it in agreement with each other. Best wishes for your bright and skeptical 6 year old!

  29. nybgruson 12 Dec 2012 at 2:09 pm

    @sonic:

    This is a response that requires much more time than I can devote at the moment. However, at least part of it is answered in my response to mlema.

    In regards to the Lewontin statement – I do not care for whom he is speaking. The basic premise he puts forth is flawed. At least in the snippet I read (I sadly do not have time to read him more deeply) he seems to be arguing that the reason why science does not allow for supernatural explanations is pure dogma and ideology, to such an extent that it won’t even allow “the foot of the Divine in the door.” This is simply false. There is no dogma associated with the materialistic foundations of science any more than there is dogma associated with the chemistry foundations that atoms with extra electrons in the outer orbital shell donate electrons to those with deficient outer orbitals to create a stable full orbital system. A student trying to argue a missed chemistry test question by asserting it is “dogma” that the rules of valence theory dictate a different answer than the student provided would be ridiculous. We know those rules because of consistent, verifiable, and unchanging results. If the student can provide an alternate explanation with sufficient evidence to demonstrate an exception to the rule… then that student would win a Nobel prize.

    But to merely pine for a supernatural explanation and complain that the “dogma” of science doesn’t allow it to enter misses the boat in exactly the same way as our chemistry student did. As I said, humans are capable of cognitive dissonance and it is in our nature to want to see what we want to see. This is part of the human condition, and in the case of Lewontin in the snippet you provided that is what is happening there.

    As for the Jastrow piece, this is also an example of exactly the same. Note the copious amounts of assumptions he makes and the false dichotomy he posits as well as the specific word choice he brings into account, even shifting from “creation” to “Creation” towards the end. Yes he says that he is agnostic and not a believer at the end, but that simply doesn’t jibe with the rest of what he writes. It belies his deeper wish that there were “something more” which is also not an uncommon thing to encounter – a scientist who must be atheistic and materialistic due to evidence, but still wishes to find something else.

    From Jastrow:

    It was literally the moment of Creation.

    Why must it be the moment of “Creation” and not merely the moment of creation? Or just the moment at which the arrow of time was fixed and the four fundamentals forces began to separate from unity?

    From a philosophical point of view, this finding has traumatic implications for science. Scientists have always felt more comfortable with the idea of a Universe that has existed forever, because their thinking is permeated with the idea of Cause and Effect; they believe that every event that takes place in the world can be explained in a rational way as the consequence of some previous event.

    Why must it be traumatic? Science, by definition, adapts to new informations and incorporates it. And why does the Big Bang absolutely require that the universe was not eternal? The necessary assumption here is that the condensate of the singularity itself did not exist eternally prior to the change in conditions required for inflationary cosmology to begin. Furthermore, he neglects to consider the fact that causality as an assumption is being challenged itself and that science can and is accomodating this. Rather than being “traumatic” to science, it merely means we need to amend and improve our understanding. We know, for example, that the arrow of time and causality break down in the conditions of the earliest universe. Thus, speaking in terms of causality simply makes no sense, unless you wish to demand science stick to that vernacular in order to demonstrate how science falls apart and thus position your false dichotomy of Creation. However, science can and has amended its language based on this knowledge to accomodate various notions on causality. Recently in fact, it has been theoretically demonstrated that at a quantum level events can be both cause and effect to themselves. How this happens, what it actually means, and the implications thereof are as of yet unknown. But to assume that such problems are necessarily a death knell for science’s ability to answer the questions Jastrow finds daunting is nothing more than a sophisticated argument from incredulity.

    Einstein once said, “The scientist is possessed of a sense of infinite causation.” If there is a religion in science, this statement can be regarded as its principal article of faith.

    A sophisticated argument from authority. Einstein has been wrong on other topics, no need for him to be right here. And also notice the word choice of calling it a religion in science. Once again it is no more a religion than the valence electron model of chemistry is a religion, but using such verbiage allows for the further positioning of the false dichotomy he is setting up.

    An important event occurred-the origin of the world-for which there is no known cause or explanation within the realm of science. The Universe flashed into being, and we cannot find out what caused that to happen.

    Argument from incredulity again. No explanation currently within the realm of science. And then he states that “we cannot find out what caused that to happen” as if by fiat. Why can’t we?

    He continues on with a few more sentences merely re-iterating the same unjustified claim.

    Why is that? The answer has to do with the conditions that prevailed in the first moments of the Universe’s existence. At that time it must have been compressed to an enormous-perhaps infinite-density, temperature and pressure. The shock of that moment must have destroyed every relic of an earlier, pre-creation Universe that could have yielded a clue to the cause of the great explosion. To find that cause, the scientist must reconstruct the chain of events that took place prior to the seeming moment of creation, and led to the appearance of our Universe as their end product. But just this, he cannot do. For all the evidence he might have examined to that end has been melted down and destroyed in the intense heat and pressure of the first moment. No clue remains to the nature of the forces-natural or supernatural that conspired to bring about the event we call the Big Bang.

    Finally he tries to answer. And essentially boils down to another argument from incredulity. We have been able to explore and exptrapolate the state of the universe down to 10^-30 or so second since the initial inflation event. We are working on simulating Planck length scales of the universe. We are learning ever more and gaining ever more computing power to model it accurately. Why would we possibly assume we can never answer these questions? Absolutely they are tough, and certainly if there are questions unanswered it may be this. But assuming it to simply be the case based on the limited knowledge he had at the time is, IMHO, unjustifiable.

    And if that wasn’t bad enough this is the jump off point for his false dichotomy. Even if he is right and we genuinely can never find the answers to these questions, it does not in any way provide evidence for any sort of supernaturalism or divine causality. It merely means that we are incapable of answering a question. To use this assumption is one thing (false, as I believe and have tried to explain). But to then further posit on the assumption that the assumption is correct that there must be some creedence to a divine causation is patently wrong.

    Creationists think this way. If they disprove evolution that means creation is correct. No. It only means that evolution is incorrect. So even if Jastrow were to prove that we cannot answer the questions (something he cannot, by definition do anyways, but lets grant the assumption here) that doesn not mean that divine or supernatural intervention must be correct. You need actual evidence of this to assert the claim, not merely an absence of evidence on a different claim.

    Now, can you imagine having this sort of conversation with a high school student? Most adults wouldn’t be able to keep up. Also, just because books in the science section in Barnes and Noble have the word “god” in them, doesn’t mean it must necessarily or even reasonably be part of a high school curriculum.

  30. sonicon 12 Dec 2012 at 5:16 pm

    nybrus-
    If you want to take the time for a fuller answer, please take these notes into consideration-

    Is Lewontin wrong about himself or one of the people he worked with over his long and stellar career?
    You hint he is wrong (accusing him of cognitive dissonance) without giving any evidence for his error.
    If he is wrong about himself, can you tell me why you think so.
    If he is wrong about someone else, please be specific who he is wrong about and please tell me why you think he is wrong about that specific person.
    Your generalities and false analogies don’t answer the questions that you raise when you deny what the man says about himself and the people he worked with.

    Regarding Jastrow’s article-
    Again, Jastrow is talking about actual people (the scientists he knew and worked with as well as those he read…) and their reactions to the discovery the universe had a beginning. He gives Einstein as a specific.
    Your claims that it ‘need not be that way..’ are true, but it is that way. Actual people had actual reactions.

    Jastrow probably knows the history– the materialist philosophy stated that the universe was eternal and had no beginning. Theists suggested that the universe had a beginning. That’s the historical hypothesis. And the theists were right!
    And that’s the point– science hasn’t disproved god– any agnostic could see that. And he discusses his own reaction and how it has given him pause as an agnostic.

    Yes, I can imagine having a discussion like this with a high school student or even a fourth grader. Actually, I don’t have to imagine- the kids I deal with often have ideas about god and creation and they tell me these things and they have all sorts of questions.
    I don’t have any answers for them on that subject. Perhaps that’s why the conversations can go like they do.

  31. Mlemaon 12 Dec 2012 at 7:28 pm

    sonic – I don’t think I really read your first comment very carefully the first time I read it. And, yeah, i have to admit that God is going to come up in science class. Hey, look how often it comes up here where everybody’s an atheist or agnostic? Even if God only exists as a human construct, there are going to be questions. And I’m wondering if there are those who are not content to stay within what is known and would like to actually control the way kids think. Or maybe there are just people who are angry or unhappy when they meet with fundamental disagreements or can’t really feel sure in their sureness. Regarding Jastrow – I agree that ideology affects how we draw conslusions, because in the end all we can know is a subjective reality, which we believe to be shared and consistent and knowable somehow in a way beyond subjectivity. But it’s my opinion that realists understand: we don’t really know. So, in the end, it’s all belief and a personal choice about what do you trust as reality?

    nybgrus, thank you for your thorough expounding of your thoughts. Please don’t think that this short reply is any reflection of dismissal. I read what you said very carefully. I guess I’m too tired right now to form any intelligible reply. i think these things might come down to theories about how we know things, what we can know, (that kind of thing). Personally, I think anytime somebody accepts a conclusion about causation of any kind before there’s evidence, they’re probably operating on an ideology. I see this happen in both atheists and theists. I think it’s just very hard to suspend judgement. As you say, people want causation, whether it’s: God did it, or some materialistic thing that happened before caused it (even if we don’t know that there was a materialistic thing that could have happened) True agnosticism is a hard line to walk. I think we have to teach evolution as theory no matter what we believe to be fact, because that’s the state of the science. Some think thats unfortunate, others accept it as an invitation to continue to study. Honestly, I think people here know I’m no expert. But I was taught evolution as fact, and it didn’t really help me understand much about how science works. Just like learning the catechism didn’t really teach me much about God.

    When reading your comments on your feelings of controlling your own fate, I kept thinking of something I’d read in a book I picked up in a bookstore somewhere a long time ago: “we are gods that shit”. I’ve tried to find where that came from. I’m thinkng it must have been the book: The Denial of Death
    http://en.wikipedia.org/wiki/The_Denial_of_Death
    which I’m guessing based on this coming up:
    http://michaelhindes.com/rohr-gods-who-shit/
    but that’s unrelated and I’m rambling

  32. Mlemaon 12 Dec 2012 at 7:33 pm

    oh! almost forgot! BillyJoe, thanks for emphasizing my opinions so! I’m a little embarrassed by the attention :)
    (just teasing you my friend – I know you don’t think so, but: I DO respect your opinions)
    M

  33. nybgruson 12 Dec 2012 at 8:24 pm

    @mlema:

    not sure if it was an inadvertent gaff or not but when you say:

    I think we have to teach evolution as theory no matter what we believe to be fact, because that’s the state of the science.

    That’s not quite right. A theory is a robust explantory model that incorporates a lot of facts and explains them all. A theory is “higher” than a mere fact in this sense.

    So being taught that evolution is a fact is not incorrect, merely incomplete. And in school, kids should be taught the various facts of evolution. As they get more advanced they can then move on to understanding the theory more deeply.

    In any event they should be educated in the method and critical analysis and practical application of all these concepts. That is the goal, and the facts of science – like evolution – are the tool used to illustrate the grander concepts. But the facts are also important, at least to superficially understand and appreciate.

  34. Mlemaon 12 Dec 2012 at 9:03 pm

    sorry, it’s probably ’cause I’m tired, but I thought that the facts were what were most important in science. And the theory is what we use to explain why we think the facts are what they are. The more we can test the theory and finds that it’s explanatory and workable, the more confidence we have in the theory. Finally, we may accept the theory as “proven” and useable until something comes along that doesn’t fit. Then we re-work it, expand it, or throw it out?
    If we take a theory as “fact”, aren’t we going to have to make everything fit into it, even in some nonsensical way if we have to? or are you saying it’s a fact but facts can change?

    “In any event they should be educated in the method and critical analysis and practical application of all these concepts.”

    this I can readily agree with.

    Is this a definition problem?

  35. nybgruson 12 Dec 2012 at 9:24 pm

    No, evolution is a fact and a theory because it is so well supported that it would be perverse not to call it a fact. Other theories – like string theory say – would not also be considered a fact in the same sense since it is yet to be well supported. As CERN and future endeavors fill in the facts they may support string theory (or another theory) well enough that it may finally be called “fact” as well.

    So yes, it would take an inordinate amount of evidence to overturn the core fundamentals of evolutionary theory since it is so well established. That is why certain types think it is a dogma. But it is no more a dogma than 2 + 2 = 4.

    Or to perhaps be a little more clear – the theory of evolution is a large and adaptable theory. The fact of evolution is the reality of universal (or at least near universal) common ancestry with random mutation and natural selection driving speciation. Other facets like drift, fixation, neutral mutations, fitness landscapes etc are other facts of evolution. Those facts of evolution are then used to predict and explain new findings as the theory becomes refined.

  36. Mlemaon 12 Dec 2012 at 9:42 pm

    After I posted my comment I read the definition of “scientific theory” and I understand that the theory of evolution is fact because it’s been proven that the plants and creatures of the earth have evolved. But I personally still think it’s proper to introduce children to the “theory” of evolution, in the same way we might introduce them to the “theory” of general relativity. These are accepted facts, but properly called scientific theory, and properly held in a place to be continually investigated, testing the predictive power any currently associated concepts.

  37. ccbowerson 12 Dec 2012 at 10:30 pm

    “But I personally still think it’s proper to introduce children to the “theory” of evolution, in the same way we might introduce them to the “theory” of general relativity. ”

    I would avoid comparing “theory” and “facts” because it reinforces the misconception that these are terms that are the same spectrum (i.e. that theories “graduate” to fact status). I would avoid using the term “fact” in this context to learners (children or otherwise), unless you are intending to address the misconception. The concept of “theory” is important to explain, because many people either learned it incorrectly in school (I certainly remember being taught the misconception at some point in school), or they get confused by the common usage of the term.

  38. ccbowerson 12 Dec 2012 at 10:33 pm

    nybgrus-

    Thanks for the kind words as well. I see you have been commenting on this blog more lately… were you gone for a while or is it my imagination?

  39. Mlemaon 12 Dec 2012 at 10:34 pm

    I guess I mean teenagers.

  40. Mlemaon 12 Dec 2012 at 10:50 pm

    ccbowers, forgive my confusion, but are you saying that evolution should NOT be introduced as fact, but as theory? That is my thought – with a careful explanation of what we mean by scientific theory.
    That is, if we should avoid comparing facts and theories, do you think we should say that evolution is a fact or a scientific theory? Or do we separate them such as, fact: there are many fossils showing that the plants and animals on earth used to be different… the theory is: they’ve evolved. (vast oversimplification)

  41. sonicon 12 Dec 2012 at 11:09 pm

    Mlema-
    Here’s my thinking–
    With science you have facts- results of experiments and observations.
    Then you have conclusions and statements about those facts that are induced from the facts.
    This induction is a logical operation.
    All logic starts with a premise.

    In order to understand the conclusions one must grasp the logic. In order to follow the logic one must know the premises.

    I believe Lewontin’s statement is important in understanding the premises and therefore the logical operations that follow. He claims it “… is the key to an understanding of the real struggle between science and the supernatural.”

    I haven’t read anything that makes me question that yet.
    Have you?

  42. ccbowerson 13 Dec 2012 at 12:42 am

    “ccbowers, forgive my confusion, but are you saying that evolution should NOT be introduced as fact, but as theory?”

    I would like to avoiding adding confusion to the common misconception about these terms, and even the wording of your question would add to the confusion. Much of the confusion seems to arise from the distinction between the common uses of the terms “fact” and “theory”, and their precise meaning in this context. Evolution should be discussed as a theory (more precisely, theories), because it is a scientific explanation for what is observed… Just as we talk about the “germ theory” of infectious disease or “cell theory.”

    Fact has multiple meanings (Sonic’s usage is an example of one), but commonly the term fact is used to mean that something is “true.” The common misconception is that if something is a theory, it hasn’t risen to the level of fact, but obviously that is not what we mean by theory at all. I don’t think the term fact is needed other than to clarify the common misconception.

  43. BillyJoe7on 13 Dec 2012 at 6:10 am

    sonic: “SteveA-I am unaware of any ‘unfinished business’ you refer to.”

    1) What is your definition of ‘random’ in the context of evolution?
    2) What is the difference between “non-random mutation” and “directed mutation”?
    3) What is the proposed mechanism for “non-random mutation”?

  44. sonicon 13 Dec 2012 at 9:51 am

    Something about this has been gnawing on me and now it’s kind of funny –

    Apparently a teacher should not be allowed to tell her student what the person who made the discovery that confirmed the Big Bang theory, Arno Penzias, thought about the theory.
    I get the impression that it should be forbidden for a teacher to tell her students what Hawking had to say about the universe having a beginning.
    Perhaps a teacher should get fired for allowing a student to read what the Founder/Director of NASA’s Goddard Institute had to say about the finding that the universe had a beginning.

    I can’t imagine what could justify this level of censorship.

    If I’m forced to guess, I think something like what Lewontin is talking about must be in play– closing the door on the divine foot??

    That seems very odd to me, but it is my guess.
    Am I right?

  45. nybgruson 13 Dec 2012 at 10:31 am

    @sonic:

    This is very basic and you are way over thinking it.

    Why shouldn’t a teacher include what Arno Penzias thought about the theory? Because that isn’t science. His thoughts on the topic – unless they are specifically about the science of the theory – are immaterial to the theory itself. Existential concerns and pontifications about the implications of the theory to the human condition as Penzias sees it is not science. It is not relevant to learning the facts of the theory and the theory itself.

    By the exact same token, Hawking’s thoughts on the implications of the beginning of the universe and his conclusions that the evidence demonstrates no God or gods should also not be included in physics classes since they are also not science.

    There is no censorship here sonic. Discussions of Jean-Paul Sartre also do not belong in a chemistry or physics class. Discussions about conscioussness as Rene Descartes thought about it do not belong in an algebra class. It is not censorship it is called “sticking to the subject matter.”

    Of course, there is a gray zone and inevitably some judgement calls and difficulty completely eschewing the non-relevant parts. In a world of perfect intellectual honesty these wouldn’t be a problem. But we have many educators and people in power who want nothing more than any door in which to stick their particular ideology. So referring to Lewontin’s complaint that “a divine foot cannot get in the door” (besides having no place in a high school physics class because it is irrelevant to the material these students need to know and understand) is more than likely going to be used as a “foot in the door” for ideology in science class.

    If a student asks “Is there scientific evidence for the existence of god?” then I think the best answer is “that is not the topic of discussion in class today” and the second best answer is “not to the extent that I know, but that is not a topic of discussion.” If a student asks “what are the implications of the big bang theory” then the only appropriate answer is a scientific one discussing the growth of the field of inflationary cosmology and how it relates to background microwave radiation, etc. Not something to do with a discussion of teolological, theological, or human condition implications. If you want to have those discussions there are appropriate classes and your own free time for that.

    Yes, I’d like to tell these students that there probably is no god and that there certainly is zero scientific evidence to support a god hypothesis, the prior probability is extremely low, and that there is ample evidence against any specific gods to rule them out as possibilities. But that also only has a very tenuous place in science class and would inevitably lead to a shouting match of culture wars and be a complete waste of time. Stick to the facts, the science, and nothing else is a much more reasonable solution. One that literally everyone is totally fine with, except for those few facts that directly contradict what some theists are teaching their children at home (which is why evolution is always the hot button issue – you never see people up in arms about Euclidean geometry or teaching the Pauli exclusion principle). The beef is that the fair, plain, simple, and factual teaching of science sides against them. Unfortunately that is, as the kids says these days, tough beans. Since the only talking points oppositionists have are theological ones – since there is absolutely no scientific opposition to evolutionary theory, especially at a high school level – that is what they try and insert into science class. Which is wrong and should be stopped. That is not censorship, sonic. Trying to insert the same talking points using quotes from scientists – cherry picked or not – is just as disingenuous and obvious to anyone applying intellectual honesty.

    If I’m forced to guess, I think something like what Lewontin is talking about must be in play– closing the door on the divine foot??

    There is no evidence the foot exists in the first place, which is why it doesn’t belong in the science classroom, and why there is no door that can be closed on it.

    That seems very odd to me, but it is my guess.
    Am I right?

    So no, you are not right.

  46. nybgruson 13 Dec 2012 at 10:46 am

    As for the whole Theory vs Fact thing….

    I can see ccbowers point in that it can be confusing. But it is only so because of the concerted effort on the part of ideologues coupled with the generall lazy and uninformed thinking of the general populace that engenders this confusion. Well, that and the fact that colloquial use differs from scientific use, which is exploited by said ideologues.

    The reality is you can and should teach evolution as a fact and a theory and a set of facts. The whole point of science class is to… well… learn science! Which includes understanding what a theory is, what a fact is, how they work together, how they overlap, and what it all actually means. Evolution is an excellent example to use in teaching this.

    The fact of evolution is that it is not only the sole explanatation for the diversity of life on the planet (NB not the explanation for the origin of llife on this planet) but also so well supported that it would be difficult to conceive of a scenario in which it would be overturned wholesale.

    The facts of evolution are things like random mutation and gene duplication leading to opportunities for selective pressure to act, allelic frequency changes and equilibria such as the Hardy-Weinberg equation, genetic drift, founder effect, neutral/silent mutations, sympatric and allopatric speciation, morphological changes through the fossil record, etc etc.

    The theory of evolution is the overarching framework that explains all the facts in tandem, that predicts new discoveries, and that is verified empirically from numerous separate lines of evidence to then validate that fact that evolution is the best and true explanation for the diversity of life.

    Bringing in existential concerns about what that may mean to your particular theology or what that means to the human condition is absolutely irrelevant. At no point in your scientific studies and career does that ever become relevant. There are other courses where that can be relevant and indeed a very interesting discussion. But not in science class. That is why it is not censorship to ban such discussion – unless you can come up with a convincing argument as to why the merits of veganism should be vigorously discussed in a science class in the context of evolutionary theory. And that is also why it is perfectly reasonable and correct to teach the theory, facts, and fact of evolution.

    Oh yeah, and I almost forgot @ccbowers:

    Thanks for the kind words as well. I see you have been commenting on this blog more lately… were you gone for a while or is it my imagination?

    You are welcome. And yes, I was “gone” as I just recently finished my 3rd year of school and am in my final year now. I was on holiday with my fiancee’s family and then my own for a couple of weeks and then had guests come visit at my home afterwards so now I am finally getting the time to be able to post more. I still really don’t have time and should be doing more productive work, but a year of very hard work has left me enjoying my holiday time. That coupled with the fact that I now have my beautiful Cannondale full carbon road bike back means I spend my days doing this and going for very long bike rides and have even more trouble being particularly productive. As my good friend (currently doing a yearlong NIH research fellowship at UPitt in regenerative ophthalmology) told me: “Take advantage of being in a position to put off work occassionally. Even at the highest levels of academia we still do it and you will have less opportunity in the future.” So here I am, posting away. LOL.

  47. ccbowerson 13 Dec 2012 at 2:13 pm

    “The reality is you can and should teach evolution as a fact and a theory and a set of facts. The whole point of science class is to… well… learn science!”

    I agree with your comments on this, I was objecting to the framing used in Mlema’s question. I would not compare and contrast these terms while speaking of evolution without being prepared to provide a full explanation of what these terms mean, and how they both apply.

    “And yes, I was “gone” as I just recently finished my 3rd year of school”

    If you are willing to disclose, I am curious: what program are you in?

  48. nybgruson 13 Dec 2012 at 2:35 pm

    @ccbowers:

    Fair enough. There’s that intellectual honesty kicking in again, requiring us to caveat, hedge, and preempt things we normally wouldn’t think twice about. To borrow from what Lennon once said, can you imagine a world where someone can say “I think grape soda is better than cherry coke” and I respond “Yeah, well that’s just your theory” and nobody has to quibble over my colloquial and innacurate use of the word and try and ply that into a wedge to teach creationism?

    As for what program I am in…. I don’t make it a point to hide specifics about myself but I am also a little cautious about making a point to actively advertise those specifics at the same time. Not because of you specifically, but you know, teh internets.

    I’ll tell you what though – my throwaway junk email which I never check but only use to sign up for garbage to have spam sent that way is my user name at yahoo. Send me an email there and I’ll check it at some point today and say hello, if you are keen. Also, I fully intend on attending TAM next year and will obviously spend some time at the SBM and SGU areas so if you are around there we could also share a libation of choice.

  49. ccbowerson 13 Dec 2012 at 3:16 pm

    nybgrus-

    I understand. I am pretty careful what I’ve disclosed about myself as well. I’ve even seen some questionable behavior about obtaining personal information from previous commenters of this blog. I’ve never been to TAM, but went to NECCS last year and really enjoyed it. Unfortunately I’ll be in Japan during NECSS so I won’t be going this year. I have a friend who live on the Upper East side of manhattan so NECCS was more convenient for me, and I enjoy that its large enough, but not too large. Perhaps its for the best- she is in her last year of her ED residency so I don’t want to intrude 2 years in a row

  50. BillyJoe7on 13 Dec 2012 at 4:15 pm

    “Trying to insert the same talking points using quotes from scientists – cherry picked or not – is just as disingenuous and obvious to anyone applying intellectual honesty.”

    I was going to use both those words – ‘disingenuous’ and ‘dishonest’ – in my last post, but decided to apply a bit of self-censorship. I regret that now. What other conclusion can we come to other than that sonic is being disingenuous and dishonest in his postings on this topic.

    If he is not a creationists then he will need to explain why he references creationists and the sort of people creationists reference and misquote. If he is a creationists, why does he hide that fact. He pretends he is just “asking questions”, but who can believe that he doesn’t have a point of view. I felt I was getting close to getting into his head in that thread “Seeing with Touch”, by asking some specific questions about non-random mutation. But he won’t even say whether or not he believes in non-random mutation. He claims merely to reference and quote authors that do just to provide “food for thought” for those who accept the modern theory of evolution. How disingenuous and dishonest is that.

    His tactic with me until recently, was to just stop the conversation and simply disappear from the thread. In his last post to me he stated that, unless he gets the right response from me, he will stop responding to my posts altogether. That is what has happened. He will no longer respond to my posts. And now, in this thread, he even pretends not to understand the “unfinished business” Steve referred to above.

    And in this thread, where you have given a series of excellent explanations about how science works, using evolution as an example, his lack of response sticks out like, sorry, dogs balls. He has simply ignored all that (like he has done before when I have tried to have a discussion with him about how science works and what is meant by facts in science) and continued to go on and on about the pitiful lack of gods foot in the door and the scientists who seem to support that view. I really think it’s time we called him to account. Accommodationism be damned.

    What is he on about? What is his point of view? Why does he keep referencing creationists and those creationists reference? Why won’t he answer those questions about non-random mutation? Is it acceptable to simply ignore confronting questions?

  51. Mlemaon 13 Dec 2012 at 6:10 pm

    sonic,

    “I believe Lewontin’s statement is important in understanding the premises and therefore the logical operations that follow. He claims it “… is the key to an understanding of the real struggle between science and the supernatural.”

    I haven’t read anything that makes me question that yet.
    Have you?”

    I don’t know sonic. I’m not really tuned into that struggle so much I guess. But I do understand what you and he are saying about ideologies affecting the formation of premises and therefore the logical operations that follow.

  52. Mlemaon 13 Dec 2012 at 6:32 pm

    ccbowers,
    somehow I don’t think a teacher could really get through a course in evolution without talking about facts and theory. I think learning what these terms mean, that is, what “scientific theory” is, and what we mean when we say “facts” in science, would be a very important part of the coursework. Staying away from certain terms for fear of confusing people is a bit condescending I think.

    I thought your comment “… There are larger societal issues such as poverty, cultural attitudes, politics, etc that come into play.” was really insightful. So when you re-entered the conversation with a reply to my recent comment, I was eager to know what your thoughts were on how to frame the theory of evolution to young people. I’m sorry I framed my own question objectionably. If you don’t want to answer, that’s ok of course.
    thanks

  53. nybgruson 13 Dec 2012 at 7:15 pm

    @BJ:

    I’m unfamiliar with the “Seeing with Touch” unfinished business… is it something worth my time to catch up on? I’m guessing not, but it sure seems to be coming up a bit.

    What other conclusion can we come to other than that sonic is being disingenuous and dishonest in his postings on this topic.

    I would be forced to agree, except I reserve just a little bit of open mindedness on the topic. Certainly my conversations with him (I am assuming the male pronoun, please correct me if I am wrong) on evolution have been an odd mix of back and forth and certainly smacks of creationist tactics from time to time. However, I genuinely can’t discern wether it is a creationist tactic at play or just someone with creationist leanings for whatever reason who truly just can’t quite assimilate the entirety of what I have been saying on the topic. Certainly there have been others that were so obvious I was able to pick them out instantly, in particular one commenter whose handle escapes me at the moment but was a fierce William Lane Craig acolyte and led to a 500+ comment spree right here at neurologica. But I just don’t get quite the same vibe from sonic. To me it could just as easily be someone trying to cling onto some vestiges of what he once thought and still hopes to be true, amongst other possibilities.

    Is it acceptable to simply ignore confronting questions?

    Sure. Nobody here is under any onus to answer any questions. If you don’t, of course, then it is reasonable to make assumptions if you wish, but this is the internet after all. I don’t have to respond to every question posed at me and I certainly don’t.

    I would, however, also be curious at the answers to BJ’s questions if you would be so kind sonic. I will be the first to say that the answer doesn’t really matter. It will merely allow us to streamline conversation a bit. If you are a creationist seeking to hone your tactics, that’s fine. If you admit it we can engage more readily like that. I assure you that your rhetorical tactics would be finely honed trying to argue with the likes of those here. And from my end you would either learn the error of your ways, or at the very least hone my own rhetorical tactics. If, however, you are genuinely lost on the topics and “just asking questions” in a naive sort of way, then there is nothing wrong with that either. In any event, coming clean and clear with your intentions and desires, whatever they may be, can only serve to benefit everyone involved. If not… c’est la vie and we continue the status quo.

  54. ccbowerson 13 Dec 2012 at 8:45 pm

    “somehow I don’t think a teacher could really get through a course in evolution without talking about facts and theory. I think learning what these terms mean, that is, what “scientific theory” is, and what we mean when we say “facts” in science, would be a very important part of the coursework”

    I agree, and thats what I said that above. I was just saying that I wouldn’t bring up the confusion if I wasn’t prepared to clarify the confusion… it could simply make it worse. Of course in a class about evolution, this would have to be addressed (and should), but in other settings in which this is not possible I would avoid it altogether.

  55. ccbowerson 13 Dec 2012 at 8:47 pm

    “I agree, and thats what I said that above.”

    Woops, it looks like one of the comments I thought I posted earlier did not get posted. Oh well… I now see why I am being misunderstood.

  56. ccbowerson 13 Dec 2012 at 9:02 pm

    “So when you re-entered the conversation with a reply to my recent comment, I was eager to know what your thoughts were on how to frame the theory of evolution to young people.”

    I did do that, but it was in a comment that was never posted (though I thought it was). I must have closed out the broswer earlier today without clicking submit… oh well, I guess ‘work’ got in the way of ‘play.’ I think nybgrus did a good job in his comments above, although some of the details would depend on the age group we are talking about.

  57. ccbowerson 13 Dec 2012 at 9:07 pm

    “I’ll tell you what though – my throwaway junk email which I never check but only use to sign up for garbage to have spam sent that way is my user name at yahoo.”

    Funny, I use my yahoo account for the very same purpose, although its a different username. I guess for those of us who have had a yahoo account for a while thats what happens to it

  58. sonicon 14 Dec 2012 at 1:55 am

    nybgrus-
    I will answer the questions for you- no problem.

    But first a clarification- I haven’t read much of the bible. What i have read seems like alagory and I don’t get it at all. I am not an atheist. I don’t know if there is a god, but it wouldn’t bother me or surprise me if there is. Well, maybe a little surprise.
    I don’t discount the experiment that ‘life comes from life’. I don’t know any reason to believe otherwise. The implications of that experiment are unclear. I’m not sure that life can come from inanimate matter– if that makes me a creationist, then I am one.
    Of course a demonstration would put that doubt to rest.

    I read stuff and have ideas and questions. Sometimes commentors here have interesting things to say about these things- you certainly often do.
    I’ve said these things before.
    OK?

    Here are best answers I can give now-
    Definition of random–
    The word random is used in a variety of ways by biologists.

    For example–
    http://www.the-scientist.com/?articles.view/articleNo/27910/title/Are-mutations-truly-random-/
    “Do genetic mutations really occur at random spots along the genome, as researchers have long supposed? Maybe not, according to a study published online today (January 13) in Proceedings of the Royal Society B, which proposes a mechanism for how new mutations might preferentially form around existing ones….
    One interesting implication of this mechanism of SNP formation is that “it attracts mutations to where polymorphisms already exists, where it is likely to be tolerated [or even] beneficial,” and vice versa, Amos said. “If you bias the mutations that do occur to where other mutations [already exist], you’re more likely to do good than if mutations occurred randomly.”

    In terms of evolution the term is used this way-
    http://evolution.berkeley.edu/evosite/evo101/IIIC1aRandom.shtml
    “In this respect, mutations are random—whether a particular mutation happens or not is generally unrelated to how useful that mutation would be…
    Researchers have performed many experiments in this area. Though results can be interpreted in several ways, none unambiguously support directed mutation. Nevertheless, scientists are still doing research that provides evidence relevant to this issue.”

    Mutations are often not random in terms of where, when, and how they occur. Some mutations may be at random (a cosmic ray breaks the DNA), but in general mutations are non-random in that they occur in some places much more than others and can be induced by stressors and so forth.

    For the most part mutations have been considered random with regard to ‘fitness’- that is whether or not it aids in the reproductive success of the organism. There is some question about this and some of the experimental evidence for mutations not being random in this sense is linked to below. This is an area that is of interest to me.

    continued below–

  59. sonicon 14 Dec 2012 at 1:56 am

    The term ‘directed’ mutation is a loaded term and one that I would prefer to avoid. The reason for that is that many people relate the idea of a mutation being directed as an act of god.
    And that is likely to bring more emotion than reason.

    So perhaps the better term would be ‘adaptive’ mutation.
    This is a much less charged term and aptly describes one possible phenomena under discussion.

    The phenomena of adaptive mutation would be that organisms can respond to stresses through mutations to certain areas of the genome that will allow for survival; that is they adapt by mutating– adaptive mutation.
    There are a number of experiments and a number of discussions of the results on this topic.

    Here is a list of papers that include a number of experiments indicating mutations can be adaptive.
    http://shapiro.bsd.uchicago.edu/Adaptive_mutation.html

    Here is an article and a list of experiments that bring the notion into question-
    http://www.genetics.org/content/148/4/1453.full

    There is another notion that evolution followed the path it followed not due to chance mutations, but due to laws or design– a preferred path of evolution- much like we have for stars, for example.
    This is very controversial and I’d think the evidence for that hypothesis could only be inferred from study of molecular evolution and how that occurs. If we knew how that occurred, then by looking at how things actually came out, it might be possible to infer a ‘preferred path’ or some such thing. The example of the way insects evolved the same trait using the same genetic mechanisms might be an example of something that if seen often enough in other creatures might lead to the conclusion that it wasn’t an accident that those genes did what they did.
    But that is highly speculative as any such conclusion would depend on understanding molecular evolution well enough to be able to discount other hypothesis regarding how the sequences got that way.

    At this point I don’t think there is a model of molecular evolution that can account for all the major molecular phenomena.
    The point being that any conclusion about preferred paths and such will depend greatly on what the accurate model of molecular evolution looks like and to what extent it is deterministic.
    IMHO.

    As far as mechanisms that might produce such effects as ‘adaptive mutations’ or ‘preferred path’ situations:

    The mechanism for adaptive mutations might be like what the researcher above said. (mutations tending to occur in the same spot)
    or–
    it might be that when we have a good model of molecular evolution it will become clear why things have evolved the way they have. (Again the star analogy)
    or–
    The mechanism might be like QED- perhaps if there is a Feynman in biology one day he too will say-”…while I am describing to you how Nature works, you won’t understand why Nature works that way. But you see, nobody understands that.”

    In a nutshell- when it comes to possible mechanism:
    I have no idea.

    OK?

  60. sonicon 14 Dec 2012 at 2:27 am

    nybgrus-
    Now to something more interesting–

    I don’t think you are going to get far teaching science by sticking to the ‘facts’.

    Let’s take the question, “How old is the Earth?”
    The fact is that nobody knows. The fact is that no experiment could ever determine the age of the Earth. End of class? No–

    There are facts that are used to estimate the age of the Earth – experimental evidence regarding radioactive decay, and the discovery of various rocks in various conditions among other observations. The age of the Earth is then inferred from these other facts.
    But the inference is logical and starts with a premise. A premise is not a fact, but something assumed true– in this case one premise is that radioactive decay rates have been constant over the ages. But there is no way to know that– it is assumed. It is not a fact.
    So if we stick to facts, we can’t induce the age of the Earth by our knowledge about decay rates because we have to make an assumption about the past, and nature in general, to do so. We accept the assumption that decay rates have been constant because it seems OK, we have no reason not to, and it allows for us to do the rest of the calculations.

    I’m not saying the assumptions are wrong or that they are even doubtful. I’m saying they are not facts in the usual sense of the word.

    In the case of biology one can see the trouble of ‘sticking to the facts’ as soon as one asks “How did life begin?”
    The actual experimentally validated fact in this case is that ‘life comes only from life.’
    It is at this point that the text will change from talking about things that are observably true to what ‘scientists believe…’
    That’s an quote from the textbook I saw– “… scientists believe life came from non-life…”
    I’m pretty sure many of them do. And that’s just fine. Is it OK if somebody waits to see the actual demonstration of this fact before accepting it? Just asking. :-)

    Anyway—
    This idea of ‘sticking to the facts’ sounds good, but nobody really wants to do it– especially the poor students who want to learn something other than a long list of seemingly unrelated descriptions of experiments and observations. They would like to know some of the inferences and conclusions as well.

    BTW-
    When I say a teacher could say ‘x’ to a student, I mean exactly that, not as part of a lecture or something to be tested on. I did mention putting the Lewontin quote at the beginning of a biology book– and I stand by that. It would certainly end any discussion of god or the supernatural in the science class.

  61. BillyJoe7on 14 Dec 2012 at 7:12 am

    So you are not a creationist, you are simply someone who provides links and quotations which are accidentally similar to links and quotations used by creationists. It seems, instead, that you are a sort of post-modernists who believes all opinions are equally valid including the opinions of those, shall we say, residing in the borderlands of science if not in the fringe. But ideas can be weighed on the basis of merit.

    For example, there is no reason to believe that life cannot arise naturally from non-life and every reason to believe that it did. If life did not arise naturally from non-life then it must have been through a supernatural creative act. If you believe that then, yes, you are a creationist. At the interface there is essentially no difference between life and non-life. Are prions and viruses examples of life or non-life? It’s hard to tell isn’t it? So there’s essentially no difference between life and non-life and therefore every reason to believe life could have arisen from non-life. And there’s no reason to believe in supernatural creation. Evidence and all that. Put that on your scales.

    As for “adaptive mutation”, what you fail to realise is that adative mutation, itself, is the product of random mutation and natural selection. And, despite what the borderland and fringe dwellers of science would have you believe, adaptive mutation is a random mechanism. You have previously linked to articles that seem to, or claim to, demonstrate non-random mutation, and when I have shown you why this is not the case, the silence has been deafening. Instead of just taking in all you read in a non-descriminating way, if you actually weigh the evidence, the case for “adaptive mutation” by means of non-random mutation is simply a non starter.

    You don’t have a mechanism because no one has a mechanism. Except for that creationist you linked to who posits God as the supernatural creator of non-random mutations as a means to direct evolution towards desired ends like human life. You gave three possible mechanisms. The first – mutations tending to occur in the same spot – is not a mechanism. The mechanism must explain the “tending” part. By what possible mechanism could mutations tend to occur in the same spot? The second – positing finding a future possible mechanism for something yet to be demonstrated to exist – is pseudoscience. The third – extrapolating Feynman’s observations about quantum theory to evolution – would make Feynman roll in his grave.

    You say you are not an atheist but you also say that you don’t know that there are gods. But it also sounds like you do not hold a belief in gods, therefore you are an atheist. Welcome to the club. In fact, there is no evidence that gods exists and the absence of evidence you would expect to find if gods did exist. There is no reason to believe faeries exist and no reason to believe gods exist. Use your weighing machine and make a decision. It’s not that hard.

    Anyway, I’m talking to a brick wall.

  62. locutusbrgon 14 Dec 2012 at 5:35 pm

    @ sonic
    As usual your description of what makes something a “fact” is as fluid and as facile as the rest of your arguments. Is it a fact that you a concerned skeptic and atheist? Multiple lines of evidence from from comments across many posts show you disregard evidence, and post opinion as science. You minimize overwhelming evidence, and present minimal fringe evidence as equal. You point at holes in the scientific evidence and say that they are glaring. You write well and extensively but you fail to acknowledge even your most minimal errors. Yes all evidence points to you as an ideologue but it is not a “fact”.

  63. nybgruson 14 Dec 2012 at 6:10 pm

    @locutus:

    Well and succinctly said. I was planning a much more in depth, detailed, and point by point response which is why I am only now sitting down to it. I think it will be a bit more abbreviated in light of your and BJ’s posts. Mine will be forthcoming, since it will contain many links and be held up in moderation. In any event I wouldn’t likely be looking at this before tomorrow morning anyways. I’ve actually started enjoying my vacation!

  64. ccbowerson 14 Dec 2012 at 6:57 pm

    locutusbrg –

    That was well done, without expending too much energy typing like BJ7. No offense to him, but he spends a lot of energy with his foot on the gas going nowhere sometimes. Once arguments start repeating themselves without progress, its just no longer worth the effort

    nybgrus-

    I eventually sent that email

  65. nybgruson 14 Dec 2012 at 7:05 pm

    @sonic:

    I’m not sure that life can come from inanimate matter– if that makes me a creationist, then I am one.

    There is significant evidence, both direct and indirect, for abiogenesis (part 1 of 5 of a Niel de Grasse Tyson special on the topic. I’ve watched it all and enjoyed it. You should as well). Yes, life can come from non life. And unless you posit a deity for which no evidence exists or that life has always been just as the universe has always been, then it is an inescapable conclusion.

    Of course a demonstration would put that doubt to rest.

    As locutus said… there is plenty of evidence to make me believe that isn’t the case. Watch the videos and take some time to learn about it. If you do actually change your mind, I’ll be impressed and proven wrong.

    Sometimes commentors here have interesting things to say about these things- you certainly often do.

    Thank you. I mean that sincerely. But a better way to compliment me and the others here would be to actually take to heart what we say, learn from it, and then apply it rather than continuing the same loops of rhetoric over and over again. The reality is, sonic, that despite being mostly agreeable to have discourse with every time I do I feel like it is our first conversation. In the years we have been commenting back and forth and I have taken the time to detail explanations of evolutionary theory to you, it seems like almost none of it has stuck.

    Mutations are often not random in terms of where, when, and how they occur. Some mutations may be at random (a cosmic ray breaks the DNA), but in general mutations are non-random in that they occur in some places much more than others and can be induced by stressors and so forth.

    I believe this is your own statement here. There is more to random mutation than just cosmic rays. The intrinsic instability and decay of DNA and RNA is a random mutation process. That is how we determined that the half life of DNA is 521 years under optimal conditions. The spontaneous decay with imperfect repair and maintainence leads to random mutations.

    There are such things as non-random mutations which you start getting into. But, just like Shapiro whom you link in your posts, you focus entirely too much and quite wrongly on the topic. I’ve already demonstrated the fallacies in Shapiro’s work here before. And I’ll note rather proudly of myself that I did so completely independently of Jerry Coyne, whose further demolishments of Shapiro’s work were right around the time I wrote my own and he has written even more since then. I strongly suggest you read through Coyne’s writings on the topic to understand why your inclusion of Shapiro is completely immaterial to the conversation.

    For the most part mutations have been considered random with regard to ‘fitness’- that is whether or not it aids in the reproductive success of the organism

    No. This is fundamentally incorrect. They are random in the truest sense of being random. Fitness comes in later in terms of selection and the proliferation or fixation of mutated alleles. Shapiro does not save you here. Please read what Jerry Coyne has written on the topic, linked above, since you profess an interest in this topic.

    So perhaps the better term would be ‘adaptive’ mutation.

    Not really. It is a substitute word and does not define the basic core of evolutionary theory. “Directed” or “adapted” mutation does occur – there are specific sites that are hypermutable and processes that preferentially mutate areas that are already mutated. Nobody is disputing that. But the processes that generate this “adaptive” mutation were the random mutations in the first place. Even more so, the adapative mutation is random as well!. Let that sink in a moment. Yes, it is focused in a specific area, but within that area the mutations are random! It is a mechanism by which to increase the likelihood of any mutations happening so that a lucky beneficial one has a higher chance of occuring. So no matter how you slice it the mutations are random!

    There is another notion that evolution followed the path it followed not due to chance mutations, but due to laws or design– a preferred path of evolution- much like we have for stars, for example.

    Of course evolution followed a path dictated by physical laws. Everything does. That does not equate to a “preferred path” for evolution. That is like saying you randomly threw a ball and the ball “preferred” to land somewhere within a 25 meter radius and not in Anarctica. No… just like every other process evolution works randomly with the materials at hand and within the confines of the physical laws of the universe. That is a limitation of reality, not a preferred path.

    This is very controversial and I’d think the evidence for that hypothesis could only be inferred from study of molecular evolution and how that occurs.

    Which has been done and demonstrates quite clearly your assertion is false.

    If we knew how that occurred, then by looking at how things actually came out, it might be possible to infer a ‘preferred path’ or some such thing.

    Interestingly enough, we have data to demonstrate this. But once again, it is not a “preferred path” as in a foreward thinking process. It is merely following a fitness landscape and making the most likely changes based on physical laws.

    Don’t forget that “random” doesn’t mean “all possibilities are equal.” Think about this:

    If I give you a bowl full of red, blue, green, and white marbles and ask you to pick one at random, what are the odds you will get a red ball? You can’t answer the question, can you? You might want to say 25%. But that is only true if there are equal numbers of balls and they were equally likely to be picked.

    What if we had equal numbers of balls but all the red ones were on top and you couldn’t reach more than 2cm down?

    What if there were 10,000 red balls and only 500 of each of the other colors?

    What if there were equal numbers, but the red balls were very slippery and hard to pick up?

    What if there were twice as many red balls and the blue balls had spikes on them that made them painful to pick up?

    Do any of these scenarios mean you can’t pick a ball at random? Of course not. It just changes the odds of what the random outcome will be! And that is the concept behind these adapative mutations and predicting molecular level changes – once we understand how many balls there are and how hard or easy it is to pick them up, we can predict with greater accuracy what the outcome will be… but they will still be random.

    So when you say:

    The example of the way insects evolved the same trait using the same genetic mechanisms might be an example of something that if seen often enough in other creatures might lead to the conclusion that it wasn’t an accident that those genes did what they did.

    No, that is not the correct inference any more than my example of throwing a ball randomly. If I stand in one spot and throw a ball randomly and you observe where it lands, would you then assume that because it always lands within 25m of me it can’t be an accident where it landed? Of course not. You can only conclude that my physical limitations mean I can’t throw the ball more than 25m and that is all. Specifically where it lands is still an accident.

    So when a whole bunch of insects evolve the same trait using the same genetic mechanisms, that doesn’t mean they didn’t evolve them by accident. It just means that when faced with the same (or similar) selective pressures they used the physical limitations of reality to come to the same evolutionary answer. The reason that “answer” was reached in the first place was because it was the easiest answer to come to. Which means that subsequent insects would be more likely to come to that same answer. It is like stacking the bowl full of marbles to have a lot of red marbles and being surprised that randomly red marbles come up a lot.

    But that is highly speculative as any such conclusion would depend on understanding molecular evolution well enough to be able to discount other hypothesis regarding how the sequences got that way.

    We understand enough about molecular evolution and the evidence we see to conclude that is how the sequences got that way. First off, we have the red marble fish bowl analogy. Next, we have the fact that in all homologies we see the sequences are essentially never absolutely identical. There is always a little variation because much variation is neutral. We would expect this to occur if the mutations leading to the evolutionary answer were random and merely happened upon the most likely “answer.” And lastly, we see an example of a completely different “answer” to the same problem in almost every case. Sex is a way of increasing gene recombination and mutability to increase evolutionary fitness. And we see every single crazy way of having “sex” you can imagine – from bacterial pili, to the “standard” mammalian model, to insects using similar methods to us, to insects literally breaking through the carapace of the female since there is no equivalent “vaginal tract” in that species, to using sperm as a trigger to spawn without actually incorporating the sperm’s genetic material, to parthenogenesis, and on and on and on.

    At this point I don’t think there is a model of molecular evolution that can account for all the major molecular phenomena.

    Of course not! If we had a model that encompassed everything we’d be done with science, wouldn’t we? But the model we have explains a heck of a lot, continues to work, and there is no better alternative. Certainly not Shapiro’s and definitely not Casey Luskin’s.

    In a nutshell- when it comes to possible mechanism:
    I have no idea.

    But we do. And I have been trying to educate you specifically on this a number of times. Continuing to say “I have no idea” and then just repeating the same tired talking points doesn’t help you answer your questions. Of course, the answers are probably not what you would like them to be, but that is no reason to ignore them and say you don’t know. Because you do. And so do we. Everything you have written in this vein is in some way a nirvana fallacy. Because we don’t know everything we can’t say we know anything. That is a load of bollocks and a common creationist tactic.

    I don’t think you are going to get far teaching science by sticking to the ‘facts’.

    O Rly?

    Let’s take the question, “How old is the Earth?”
    The fact is that nobody knows. The fact is that no experiment could ever determine the age of the Earth. End of class?

    Woah, woah there buddy. Yes, we do know. It is 4.54 +/- 0.05 billion years old. You are correct no single experiment can determine the age of the earth. And we may never know the age of the earth down to the minute or hour or even day. But once again, this is a nirvana fallacy. We know the age of the earth for all practical and scientific purposes and there is no way to dispute that.

    There are facts that are used to estimate the age of the Earth – experimental evidence regarding radioactive decay, and the discovery of various rocks in various conditions among other observations. The age of the Earth is then inferred from these other facts.
    But the inference is logical and starts with a premise. A premise is not a fact, but something assumed true– in this case one premise is that radioactive decay rates have been constant over the ages. But there is no way to know that– it is assumed. It is not a fact.
    So if we stick to facts, we can’t induce the age of the Earth by our knowledge about decay rates because we have to make an assumption about the past, and nature in general, to do so. We accept the assumption that decay rates have been constant because it seems OK, we have no reason not to, and it allows for us to do the rest of the calculations.

    By this definition, as locutus pointed out, we can’t say that atoms exist, that radioactive decay even happens, that air is material and not magical, that cells use proteins as ion channels.. essentially we can’t say anything. This is solipsism at its finest.

    The reason that the age of the earth is a fact is not because we hinge everything on a premise, but because a vast multitude of lines of evidence, consistently and independently verified, all agree on the age of the earth. Each of these lines of evidence is further supported by other lines of evidence. All of this is empirically verifiable.

    We don’t just assume that radioactive decay is constant. We test it. We still have experiments running today from the beginning of the radioactive era to confirm this. We put radioactive samples through vaccuums, intense pressures, heat, outer space, any condition we can possibly imagine and then test to see if there is a change. When there isn’t a change out to many decimal places we can be pretty darned sure of our “facts.”

    So no, sonic, none of these things are built on assumptions. The only assumption involved is one that solipsism is a non-starter, which is a pretty damned reasonable one to make. Everything else is built on empirical data independently verified over and over and over again. If we can’t teach those things as facts, then we can’t teach anything.

    I’m not saying the assumptions are wrong or that they are even doubtful. I’m saying they are not facts in the usual sense of the word.

    Yes, they are facts in every single sense of the word. Because if they aren’t nothing is.

    n the case of biology one can see the trouble of ‘sticking to the facts’ as soon as one asks “How did life begin?”
    The actual experimentally validated fact in this case is that ‘life comes only from life.’
    It is at this point that the text will change from talking about things that are observably true to what ‘scientists believe…’

    Once again incorrect. See the videos I linked above.

    That’s an quote from the textbook I saw– “… scientists believe life came from non-life…”

    And that is why I hate colloquial uses of terms sometimes. Yes, I believe life came from non-life… because I have evidence to lead me to that belief. This is not on par with saying “Some people believe chanting a magical incantation over a cracker literally turns it into the flesh of a dead god.” This is the exact same argument as the “well evolution is just a theory after all.”

    Please sonic, try and have some intellectual honesty here!

    Anyways, this has gotten long enough and probably illustrates my points reasonably well. And you have a lot of reading and watching to do Sonic! After all, you are interested in these questions as you say. Perhaps you could also be interested in the answers?

  66. nybgruson 14 Dec 2012 at 7:08 pm

    lol, so now my comment is in moderation. And it turned out much longer than I had originally hoped. I did link some pretty cool (IMO) stuff in there though. And I figure that even if it doesn’t get through to sonic perhaps some others reading here would find it interesting and/or useful. And I managed to not screw up the HTML tags until the very end!

    In any event, thanks for letting me know ccbowers. I probably wouldn’t have checked for ages if you hadn’t.

  67. nybgruson 14 Dec 2012 at 7:22 pm

    Oh yeah, and I sent you one back ccbowers.

  68. Mlemaon 14 Dec 2012 at 9:13 pm

    I think I’m learning that not everyone who calls himself a skeptic necessarily practices skepticism. or even logic for that matter.

  69. ccbowerson 14 Dec 2012 at 9:44 pm

    “I think I’m learning that not everyone who calls himself a skeptic necessarily practices skepticism. or even logic for that matter.”

    Yeah, that is a problem, especially when you combine it with intellectual overconfidence that is common in skeptical circles. But…its a bit like the problem of Democracy, that it “is the worst form of government except all the others that have been tried.” Skeptics aren’t all perfect in their application of skepticism, but they are trying which is more than I can say for other groups

  70. BillyJoe7on 14 Dec 2012 at 11:56 pm

    ccbowers,

    That was a little unfair. I use both succinct and expanded commentary depending on circumstances and inclination. And how can you avoid repetition when you are responding to someone who consistently fails to address the arguments you have raised against their position but then keeps repeating their discredited nonsense anyway. Besides, there may be new readers here who are unfamiliar with the arguments.
    I appreciated locutus succinct summary as well but I didn’t think it made mine superfluous.

  71. BillyJoe7on 15 Dec 2012 at 12:00 am

    Mlema,

    Succinct reply to a succinct post: I’m glad you’ve seen the light ;)

  72. ccbowerson 15 Dec 2012 at 12:21 am

    “That was a little unfair. I use both succinct and expanded commentary depending on circumstances and inclination.”

    Sorry. I appreciate your efforts and what you contribute, and perhaps you misunderstand what I mean. My point was not that your comments are not often well thought out or too wordy, and I do not blame you for repetition, but in your “conversation” with certain others, there seems to be no progress. But… I’m not blaming you for this necessarily. Your point about new readers is a good point, but reading the same conversations over and over is a bit tiring. I guess if I’m not willing to fight some of these battles, I guess I shouldn’t complain when someone else does. I just wonder if these types of conversations are not food for trolls or pseudotrolls.

    For me, I find the most interesting arguments with people I respect intellectually, like the quote “Truth springs from argument amongst friends.”

  73. sonicon 15 Dec 2012 at 12:40 am

    locutusbrg-
    I try to use the word ‘fact’ the way it is defined in the dictionary. If you have a specific usage that is problematic, please point it out so that I could correct it.

    I’m sure there is a great deal I don’t know. I’m sure I’ve said things that were wrong.
    Have I repeatedly made the same error? You make it sound as if I’ve been banging my head against some wall and not realizing it. :-) I might be doing just that.

    If you would tell me what that is I will take it under consideration anew.
    Thanks

    nybgrus-
    I await any information you have that would be helpful.

    ccbowers, mlema, et. al.,
    Am I being an idiot and missing something basic and obvious? I know that is a possibility. Apparently something in this last bit was too much. I wonder what that was.
    I know I say some wild things, I don’t think I’ve ever tried to deny that, but apparently something here is too much.
    Is it a straw that broke the camels back, or is it more like I just dropped the big one?
    I’m curious.

  74. ccbowerson 15 Dec 2012 at 1:18 am

    “Am I being an idiot and missing something basic and obvious?”

    Sonic, you occasionally make good points, but most often what locutusbrg says applies. I think you get a kick out of pushing BJ7′s buttons, and while this can be mildly entertaining, often it is just retreads of tired arguments. Perhaps the pushing of buttons thing is just coincidence due to a conflict of personalities between you two, I don’t know. Sorry if this offends you, but I am trying to be as matter of fact about it as possible. Although this conversation did go to a strange place, I don’t think you ‘dropped a big one’. Its just pretty typical conversation I guess, but it might feel strange because usually not everyone chimes in like this. lets move on

  75. BillyJoe7on 15 Dec 2012 at 5:43 am

    I never thought of sonic as a troll. Interesting thought though. He does keep coming back for another whack. And here he is on a science blog pulling out a dictionary to get the definition of ‘fact’. God help us. I mean how many times does it have to be explained to him what a ‘fact’ is in science. I can think of at least three occasions myself. And nybgrus tried to educate him only a couple of days ago in that long post that he mostly ignored.

  76. nybgruson 15 Dec 2012 at 7:56 am

    nybgrus-
    I await any information you have that would be helpful.

    my rather long comment with a lot of links is still in moderation. though as BJ pointed out, you didn’t exactly take to heart my other long comment.

    I’ll also add that it is nothing big you have done just now sonic. It is just that you keep re-iterating the same talking points over and over. It appears to us, to me specifically, that you don’t actually assimilate, learn from, and use what we write. For all the years we have been chatting about evolution, your stance doesn’t seem to have… evolved (sorry I couldn’t resist).

    For example, instead of taking all the information I have written and accepted that there is absolutely no challenge to the core paradigm of evolutionary theory that random (yes RANDOM) mutation and selection are the primary, principle, and original driving forces of evolution you continue to try and throw Shapiro at me. Someone I demonstrated to be false on this very blog earlier this year – a conversation you were a part of!

    All of this is in my longer post as well. Read through it when it comes out of moderation.

  77. nybgruson 15 Dec 2012 at 7:57 am

    oh, I will add quickly that the way you are using “fact” inevitably leads to solipsism which is something else I pointed out in my long post, which is why locutus said what he did and why he was so accurate.

  78. ccbowerson 15 Dec 2012 at 9:26 am

    “I never thought of sonic as a troll.”

    Hmm. I didn’t mean to say that, exactly. I shouldn’t comment when I’m sleep deprived, but if I stuck to that rule this would be the last one. I guess I wasn’t really writing about Sonic only, but speaking more generally (about previous others like cfwong). I understand that I mixed those more general comments with specific comments about Sonic, so I understand why Sonic thinks he’s being targeted.

    No progress plus dubious references does not necessarily mean troll. It could just mean he finds certain ideas compelling, and can’t let go of them (or he doesn’t buy the counter-arguments). We all like to make provocative statements from time to time, and only at the extremes of that do the trolls live

  79. sonicon 15 Dec 2012 at 1:36 pm

    ccbowers-
    I agree with what you say, pretty much.
    I do tend to repeat things unnecessarily. I don’t like ‘pushing buttons’ or whatever, but I probably do that because I tend to say things that go against the norm.
    It is an everyday thing for me, so no offense.
    I learn new things regularly and I hope I have acknowledged when I have made an error- in fact I know I have from time to time.
    I realize I can be very stubborn, but I don’t think I’m incorrigible.
    If there is a particular thing or time when I have failed to acknowledge an error, if you want to bring it up I’ll see what it looks like to me now.
    Otherwise–
    Thank- you for the comment and let’s move on…

    nygbrus-
    I want to wait to see what you have put together before replying-
    I have learned much from you and our conversations and look forward to more.
    If you divide up the comment so that two or fewer links are in a comment, it won’t have to wait moderation–
    Just a thought.

  80. Mlemaon 15 Dec 2012 at 3:59 pm

    sonic, I wasn’t talking about you. BillyJoe is missing his former sparring partner cwfong, so he’s trying to make you into a creationist. It’s ridiculous. He’s tried picking at me for a while now, but I’m not smart enough to satisfy his desire for a good fight. He’s dragged everybody into the row, just like he used to do with cwfong. This is his site and he patrols it for anyone whose comments have the least little bit of dissension (as he sees it) – then he hurls insults and tired critiques that have long ago lost their foundation for any new reader.

    Sadly, my dear friend BillyJoe, I must bid you adieu. As much as I’ve truly enjoyed our conversations in the past, you’re just not able to make me feel welcome anymore. I can’t seem to change the way I think just to avoid your condemnation. I have a feeling it’s not what you meant, or even wanted. But sometimes things just happen randomly. :)

    cheers

  81. BillyJoe7on 15 Dec 2012 at 4:34 pm

    ccbowers,

    It is interesting that you bring up cwfong. He was a troll in the sense that, as soon as his arguments were defeated, he would disappear and then reappear under a different moniker using exactly the same discredited arguments. In fact, cwfong was his third incarnation. And Jeremiah was his last. I can’t remember the first two. When I altered his name to cwrong, he bizzarely accused me of racism and disappeared in a huff. When he returned as Jeremiah, he tried to uncover my identity and issued veiled threats of personal harm.

    When sonic first appeared I thought he was yet another incarnation of cwrong because his arguments were the same tired old discredited ones supporting “adaptive mutation”. Jeremiah is the only poster I have ever come across who I have had absolutely no respect for and perhaps some of this loathing has washed off onto sonic who espouses the same views. But sonic is actually an innocent lamb compared with these others. I mean, after everyone whacking him for days, he comes back with that cute little post of his: “I agree with what you say….thank you for your comment…I have learned so much from you…”

    Sonic, if you are reading this, I wish you would learn something, but you can’t do that by ignoring every counter argument presented to you. I suspect you hold the views you do because you don’t understand how science works, so you have no idea how to weigh evidence. You don’t know how to recognise quacks, cranks, and fringe-dwellers. But we will see how you go with nybgrus’ post (if it ever comes out of moderation). Perhaps you will surprise us.

  82. BillyJoe7on 15 Dec 2012 at 5:16 pm

    Mlema,

    I didn’t see your post when I wrote mine.

    But I think we all recognised who you were talking about and that it was not sonic. ;)
    Unfortunately you suffer the same problem as sonic. You never address the actual argument presented against your view. One-liners and off-hand dismissals do not make an counter-argument. I have paid you more respect than you deserve. How many times have I responded to your posts with a considered and detailed reply only to be met with one of those one-liners or off-hand dismissals? I’ve accepted that without complaint, because it merely demonstrates to everyone that you cannot defend your position.

    Your takedown of me is totally unjustified and completely lacking in substance.

    I have no problem with dissention, but surely dissention has to be justified. There must be a reasonable point to be made. And it must be able to stand against criticism. I do not believe in accommodationism because I feel it just allows posters to get away with espousing nonsense based on emotion. I don’t respect beliefs based on emotion. I respect beliefs based on evidence. So kill the messenger if that is all you have left to offer.

    The adaptive mutationists we have seen in this blog have, apart from sonic, come in with all guns blazing, usually delivering a broadside to Steven Novella for something he has innocently said in one of his posts, sometimes only tangentially related to evolution. So I did not pick the fight, as you characterise it. For a while I was only one willing to accept the challenge. I actually felt inadequate for the task, but there was no one else either able or willing to do so. Others have since been drawn in but it is bizarre to say that I have drawn them in. If they didn’t think it was worthwhile they wouldn’t bother now would they?

    Anyway, Mlema, my friend (yes, I feel the same way), I thank you for your last paragraph and I will remember you for that.

  83. nybgruson 15 Dec 2012 at 9:27 pm

    I will try and paste it in a few posts below. I am copying the source html to try and preserve the tags and links so we’ll see what happens:

    ============================================
    ============================================
    @sonic:

    I’m not sure that life can come from inanimate matter– if that makes me a creationist, then I am one.

    There is significant evidence, both direct and indirect, for abiogenesis (part 1 of 5 of a Niel de Grasse Tyson special on the topic. I’ve watched it all and enjoyed it. You should as well). Yes, life can come from non life. And unless you posit a deity for which no evidence exists or that life has always been just as the universe has always been, then it is an inescapable conclusion.

    Of course a demonstration would put that doubt to rest.

    As locutus said… there is plenty of evidence to make me believe that isn’t the case. Watch the videos and take some time to learn about it. If you do actually change your mind, I’ll be impressed and proven wrong.

    Sometimes commentors here have interesting things to say about these things- you certainly often do.

    Thank you. I mean that sincerely. But a better way to compliment me and the others here would be to actually take to heart what we say, learn from it, and then apply it rather than continuing the same loops of rhetoric over and over again. The reality is, sonic, that despite being mostly agreeable to have discourse with every time I do I feel like it is our first conversation. In the years we have been commenting back and forth and I have taken the time to detail explanations of evolutionary theory to you, it seems like almost none of it has stuck.

    Mutations are often not random in terms of where, when, and how they occur. Some mutations may be at random (a cosmic ray breaks the DNA), but in general mutations are non-random in that they occur in some places much more than others and can be induced by stressors and so forth.

    I believe this is your own statement here. There is more to random mutation than just cosmic rays. The intrinsic instability and decay of DNA and RNA is a random mutation process. That is how we determined that the half life of DNA is 521 years under optimal conditions. The spontaneous decay with imperfect repair and maintainence leads to random mutations.

  84. nybgruson 15 Dec 2012 at 9:28 pm

    There are such things as non-random mutations which you start getting into. But, just like Shapiro whom you link in your posts, you focus entirely too much and quite wrongly on the topic. I’ve already demonstrated the fallacies in Shapiro’s work here before. And I’ll note rather proudly of myself that I did so completely independently of Jerry Coyne, whose further demolishments of Shapiro’s work

  85. nybgruson 15 Dec 2012 at 9:33 pm

    were right around the time I wrote my own and he has written even more since then. I strongly suggest you read through Coyne’s writings on the topic to understand why your inclusion of Shapiro is completely immaterial to the conversation.

    For the most part mutations have been considered random with regard to ‘fitness’- that is whether or not it aids in the reproductive success of the organism

    No. This is fundamentally incorrect. They are random in the truest sense of being random. Fitness comes in later in terms of selection and the proliferation or fixation of mutated alleles. Shapiro does not save you here. Please read what Jerry Coyne has written on the topic, linked above, since you profess an interest in this topic.

    So perhaps the better term would be ‘adaptive’ mutation.

    Not really. It is a substitute word and does not define the basic core of evolutionary theory. “Directed” or “adapted” mutation does occur – there are specific sites that are hypermutable and processes that preferentially mutate areas that are already mutated. Nobody is disputing that. But the processes that generate this “adaptive” mutation were the random mutations in the first place. Even more so, the adapative mutation is random as well!. Let that sink in a moment. Yes, it is focused in a specific area, but within that area the mutations are random! It is a mechanism by which to increase the likelihood of any mutations happening so that a lucky beneficial one has a higher chance of occuring. So no matter how you slice it the mutations are random!

    There is another notion that evolution followed the path it followed not due to chance mutations, but due to laws or design– a preferred path of evolution- much like we have for stars, for example.

    Of course evolution followed a path dictated by physical laws. Everything does. That does not equate to a “preferred path” for evolution. That is like saying you randomly threw a ball and the ball “preferred” to land somewhere within a 25 meter radius and not in Anarctica. No… just like every other process evolution works randomly with the materials at hand and within the confines of the physical laws of the universe. That is a limitation of reality, not a preferred path.

    This is very controversial and I’d think the evidence for that hypothesis could only be inferred from study of molecular evolution and how that occurs.

    Which has been done and demonstrates quite clearly your assertion is false.

    If we knew how that occurred, then by looking at how things actually came out, it might be possible to infer a ‘preferred path’ or some such thing.

    Interestingly enough, we have data to demonstrate this. But once again, it is not a “preferred path” as in a foreward thinking process. It is merely following a fitness landscape and making the most likely changes based on physical laws.
    Don’t forget that “random” doesn’t mean “all possibilities are equal.” Think about this:
    If I give you a bowl full of red, blue, green, and white marbles and ask you to pick one at random, what are the odds you will get a red ball? You can’t answer the question, can you? You might want to say 25%. But that is only true if there are equal numbers of balls and they were equally likely to be picked.
    What if we had equal numbers of balls but all the red ones were on top and you couldn’t reach more than 2cm down?
    What if there were 10,000 red balls and only 500 of each of the other colors?
    What if there were equal numbers, but the red balls were very slippery and hard to pick up?
    What if there were twice as many red balls and the blue balls had spikes on them that made them painful to pick up?
    Do any of these scenarios mean you can’t pick a ball at random? Of course not. It just changes the odds of what the random outcome will be! And that is the concept behind these adapative mutations and predicting molecular level changes – once we understand how many balls there are and how hard or easy it is to pick them up, we can predict with greater accuracy what the outcome will be… but they will still be random.
    So when you say:

    The example of the way insects evolved the same trait using the same genetic mechanisms might be an example of something that if seen often enough in other creatures might lead to the conclusion that it wasn’t an accident that those genes did what they did.

    No, that is not the correct inference any more than my example of throwing a ball randomly. If I stand in one spot and throw a ball randomly and you observe where it lands, would you then assume that because it always lands within 25m of me it can’t be an accident where it landed? Of course not. You can only conclude that my physical limitations mean I can’t throw the ball more than 25m and that is all. Specifically where it lands is still an accident.
    So when a whole bunch of insects evolve the same trait using the same genetic mechanisms, that doesn’t mean they didn’t evolve them by accident. It just means that when faced with the same (or similar) selective pressures they used the physical limitations of reality to come to the same evolutionary answer. The reason that “answer” was reached in the first place was because it was the easiest answer to come to. Which means that subsequent insects would be more likely to come to that same answer. It is like stacking the bowl full of marbles to have a lot of red marbles and being surprised that randomly red marbles come up a lot.

    But that is highly speculative as any such conclusion would depend on understanding molecular evolution well enough to be able to discount other hypothesis regarding how the sequences got that way.

    We understand enough about molecular evolution and the evidence we see to conclude that is how the sequences got that way. First off, we have the red marble fish bowl analogy. Next, we have the fact that in all homologies we see the sequences are essentially never absolutely identical. There is always a little variation because much variation is neutral. We would expect this to occur if the mutations leading to the evolutionary answer were random and merely happened upon the most likely “answer.” And lastly, we see an example of a completely different “answer” to the same problem in almost every case. Sex is a way of increasing gene recombination and mutability to increase evolutionary fitness. And we see every single crazy way of having “sex” you can imagine – from bacterial pili, to the “standard” mammalian model, to insects using similar methods to us, to insects literally breaking through the carapace of the female since there is no equivalent “vaginal tract” in that species, to using sperm as a trigger to spawn without actually incorporating the sperm’s genetic material, to parthenogenesis, and on and on and on.

    At this point I don’t think there is a model of molecular evolution that can account for all the major molecular phenomena.

    Of course not! If we had a model that encompassed everything we’d be done with science, wouldn’t we? But the model we have explains a heck of a lot, continues to work, and there is no better alternative. Certainly not Shapiro’s and definitely not Casey Luskin’s.

    In a nutshell- when it comes to possible mechanism:
    I have no idea.

  86. nybgruson 15 Dec 2012 at 9:36 pm

    But we do. And I have been trying to educate you specifically on this a number of times. Continuing to say “I have no idea” and then just repeating the same tired talking points doesn’t help you answer your questions. Of course, the answers are probably not what you would like them to be, but that is no reason to ignore them and say you don’t know. Because you do. And so do we. Everything you have written in this vein is in some way a nirvana fallacy. Because we don’t know everything we can’t say we know anything. That is a load of bollocks and a common creationist tactic.

    I don’t think you are going to get far teaching science by sticking to the ‘facts’.

    O Rly?

    Let’s take the question, “How old is the Earth?”
    The fact is that nobody knows. The fact is that no experiment could ever determine the age of the Earth. End of class?

    Woah, woah there buddy. Yes, we do know. It is 4.54 +/- 0.05 billion years old. You are correct no single experiment can determine the age of the earth. And we may never know the age of the earth down to the minute or hour or even day. But once again, this is a nirvana fallacy. We know the age of the earth for all practical and scientific purposes and there is no way to dispute that.

    There are facts that are used to estimate the age of the Earth – experimental evidence regarding radioactive decay, and the discovery of various rocks in various conditions among other observations. The age of the Earth is then inferred from these other facts.
    But the inference is logical and starts with a premise. A premise is not a fact, but something assumed true– in this case one premise is that radioactive decay rates have been constant over the ages. But there is no way to know that– it is assumed. It is not a fact.
    So if we stick to facts, we can’t induce the age of the Earth by our knowledge about decay rates because we have to make an assumption about the past, and nature in general, to do so. We accept the assumption that decay rates have been constant because it seems OK, we have no reason not to, and it allows for us to do the rest of the calculations.

    By this definition, as locutus pointed out, we can’t say that atoms exist, that radioactive decay even happens, that air is material and not magical, that cells use proteins as ion channels.. essentially we can’t say anything. This is solipsism at its finest.
    The reason that the age of the earth is a fact is not because we hinge everything on a premise, but because a vast multitude of lines of evidence, consistently and independently verified, all agree on the age of the earth. Each of these lines of evidence is further supported by other lines of evidence. All of this is empirically verifiable.
    We don’t just assume that radioactive decay is constant. We test it. We still have experiments running today from the beginning of the radioactive era to confirm this. We put radioactive samples through vaccuums, intense pressures, heat, outer space, any condition we can possibly imagine and then test to see if there is a change. When there isn’t a change out to many decimal places we can be pretty darned sure of our “facts.”
    So no, sonic, none of these things are built on assumptions. The only assumption involved is one that solipsism is a non-starter, which is a pretty damned reasonable one to make. Everything else is built on empirical data independently verified over and over and over again. If we can’t teach those things as facts, then we can’t teach anything.

    I’m not saying the assumptions are wrong or that they are even doubtful. I’m saying they are not facts in the usual sense of the word.

    Yes, they are facts in every single sense of the word. Because if they aren’t nothing is.

    n the case of biology one can see the trouble of ‘sticking to the facts’ as soon as one asks “How did life begin?”
    The actual experimentally validated fact in this case is that ‘life comes only from life.’
    It is at this point that the text will change from talking about things that are observably true to what ‘scientists believe…’

    Once again incorrect. See the videos I linked above.

    That’s an quote from the textbook I saw– “… scientists believe life came from non-life…”

    And that is why I hate colloquial uses of terms sometimes. Yes, I believe life came from non-life… because I have evidence to lead me to that belief. This is not on par with saying “Some people believe chanting a magical incantation over a cracker literally turns it into the flesh of a dead god.” This is the exact same argument as the “well evolution is just a theory after all.”
    Please sonic, try and have some intellectual honesty here!
    Anyways, this has gotten long enough and probably illustrates my points reasonably well. And you have a lot of reading and watching to do Sonic! After all, you are interested in these questions as you say. Perhaps you could also be interested in the answers?

    </blockquote

  87. ccbowerson 16 Dec 2012 at 11:04 am

    nybrgus
    “were right around the time I wrote my own and he has written even more since then. I strongly suggest you read through Coyne’s writings on the topic to understand why your inclusion of Shapiro is completely immaterial to the conversation.”

    I believe that this was a topic on this week’s SGU. I was busy making dinner while I was listening so I couldn’t really concentrate during that part, but I’m pretty sure they discussed this.

    BJ7
    “It is interesting that you bring up cwfong”

    CWfong was previously artfulD, and maybe Paisley (maybe not), but Sonic has been around since before CWfong and is a very different in his posts.

  88. ccbowerson 16 Dec 2012 at 11:24 am

    nybgrus,
    I’m glad that you brought up the nirvana fallacy, (~perfect solution fallacy) because its used in nearly every unwarranted criticism of science, and is often used in politics as well when one side finds the proposed solution to a problem politically inconvenient. Alternative medicine lives off this fallacy (along with many others), when they point to problems with particular medications in the past and the FDA.

  89. nybgruson 16 Dec 2012 at 1:50 pm

    @ccbowers:

    I have finally caught up on SGU. I only started listening about 6 months ago and decided to catch up on all of them for the year. I haven’t heard the latest though, so I would be keen to hear the crews’ take on it, though based on my reading I doubt their conclusion will be much different to mine.

    As for the nirvana fallacy… it is rampant all over. In the wake of the school shooting numerous people I know have immediately lept up to pre-emptively comment on gun control. One of the biggest common tropes? That drugs are illegal and you can still get them, that if guns were illegal criminals would still have them and that there would still be gun crime. That is a Nirvana fallacy in that if the banning of guns doesn’t completely remove all gun crime then it isn’t worth it and we shouldn’t regulate them at all (so Nirvana followed by false dichotomy). Such discussions tend to be emotional and vitriolic, but I managed to shut them up by pointing out the Nirvana fallacy and then saying one little thing: If I could sign a piece of paper that said I would never be allowed to own or even hold a gun for the rest of my life, but doing so would save just one life it would be worth it.

  90. sonicon 16 Dec 2012 at 2:53 pm

    First let me thank nybgrus for the comments. I have to assimilate- I’ll get to that in a bit.
    But I have a question that I need to have answered to facilitate future communications-

    I’m wondering- is my description of the relationship between fact, induction, and assumption wrong in some way?
    The actual dating of the earth involves more observations, inductions and assumptions than I listed, but I wasn’t really trying to be exhaustive. I was trying to distinguish between different operations that occur in coming to a conclusion.
    And what I said about which part is which– am I misusing the words? Because I really do try to be accurate in the usage, but I’m not seeing the error.

    I know I can be blind as a bat when it comes to my own stuff sometimes- I never try to proofread my own thing– so it wouldn’t surprise me too much if I’m missing something obvious.
    Any specifics would be helpful.

  91. BillyJoe7on 16 Dec 2012 at 3:53 pm

    ccbowers,

    Oh, yes, artlessDodge. But I don’t think the other one was Paisley. It was a short monosyllable name that’s on the tip of my tongue but I just can’t remember. When cwfong first came on the scene, he engaged me in a friendly discussion about illusions, although it was clear he had no idea what an illusion was. He only returned to the nastiness later on. That’s why, initially, I thought sonic may have been a reincarnation. If he was on the scene before artfulD, I must have missed his posts. Perhaps he on a hiatus when I first arrived here.
    Anyway, this is all by the by.

  92. nybgruson 16 Dec 2012 at 4:05 pm

    You are welcome Sonic. Hopefully you find it useful.

    As for your thoughts and descriptions of fact, induction, and assumption… yes you are wrong in some way, but not a blatantly obvious way (well, not to most people anyways).

    You are correct that there is very sophisticated discussion in the philosophy of science as to the precise definitions, utilizations, and applications of “fact,” “theory,” and “hypothesis.” You are also correct that there is actually a base assumption we must make in order for the scientific method to work: that the universe exists as something separate from our consciousness independently of our consciousness. The corollary to that is that we can actually observe this universe.

    In other words, a “universe” in which we are a disembodied consciousness, completely alone but generating all other perceived consciousnesses and the rest of the universe is indistinguishable from a reality in which the universe and all other consciousnesses are actually separate and independent from our own. It is the “brain in a vat” notion. Solipsism counters and says that the only thing we can actually be certain of is our own consciousness and nothing else. Obviously we cannot necessary prove solipsism to be wrong, but if we accept it as a valid premise then we are essentially done. It literally adds nothing to the conversation.

    Lets say I accept solipsism as a valid idea. I am then faced with two choices – do absolutely nothing and assume my conscioussness is the only one in the universe and is generating the universe I perceive, or accept that this may be the case but continue to do science to test my universe anyways. So we are either paralyzed and unable to assert anything as factual or true, or we do what we are doing anyways. The outcome is the same whether we accept the premises of solipsism or not.

    So now that we have accepted that the universe is independent of our conscioussness we then need to define what a fact, hypothesis, and theory are. Facts are defined as those things consistently observable by many observers and through many repetitions. Pretty much every serious philosopher of science agrees on that basic premise. It is at this point that we diverge.

    Most would agree that if we combine facts to produce independently and repeatably verifiable outcomes those complex constructs would also become “facts.” Using your age of the earth example, that means that the fact that radioactive decay happens, coupled with the fact that it is immutable under all tested conditions, coupled with the fact that many different types of radioactive decay converge on the same time frame for the age of the earth, then makes the age of the earth a “fact.”

    Some, however, disagree and posit that a “hypothesis” cannot “become” a “fact” despite this high level of empirically and independently verified data to support it. It is a purist construct in that we use “facts” to test “hypotheses” and that “theories” explain and predict the facts and hypotheses. Thus the age of the earth remains a hypothesis and the theory of solar system genesis explains the facts and hypothesis revolving around the age and composition of the earth.

    However, these are nomenclatural concerns which are esoteric enough that even the likes of me are unaffected by the discussion. This is the sort of thing that Karl Popper and Massimo Piggluicci are concerned with as a way of further refining what we are doing and how we do it not as a way of radically restructuring it or changing our understanding of the universe thus far. Whether the philosophers of science ultimately decide on the commonly agreed upon notions of “fact” or the more purist nomenclature of say Bock and Fitzhugh will not change how scientists on the ground actually do things or how valid our conclusions thus far are. It could change the language we use to describe what we already do, but will not change the fundamental meaning of what we have done.

    So if it makes you feel better, I can rewrite my statement before as saying:

    We should stick to teaching the facts, hypotheses, and theories of science as accepted by robust data and scientific consensus since that is unequivocally the best possible knowledge we have

    and it would not change anything else I have written nor would it open the door for teaching things like divine feet in doors or existential ramifications of said facts, hypotheses, and theories.

    So where you really make your mistake (and it is a common creationist trope to do so as well, so hopefully you can forgive our confusion on the matter) is that your posts on the topic tend to address the semantics of the discussion rather than the actual implications of what it all means and also tend to go down the road to hard solipsism along the way.

    It is equivalent to a teacher telling a 1st grader that 2+2 = 4 and you insist that is nonsensical to teach because what is “two” and are we certain that additive properties of mathematics are stable across all equations and what about base 2 and base 6 number systems and what about the case where 2 + 2 = 5 for large values of 2 and so on. Yes, each individual point is not entirely invalid, but the application serves no purpose except to derail conversation and obfuscate primary school level education with the cutting edge of the philosophy of science and ignoring everything in between.

    In short, you are picking nits and missing the forest for the trees every time you engage in this sort of discussion. Most people wouldn’t pick up on it or if they did know how to respond or what it even means. But the folks around here aren’t “most people.” Oh you also tend to throw down a whole bunch of info at once, some of it very off base, some totally right, and most right in the middle in what becomes the equivalent of a Gish Gallop which also lends to the feeling we get that you are just parroting creatonist talking points.

    The Wiki article offers some useful points to read as well.

    NB: I am not a philosopher of science and it is certainly not my forte. But I find it interesting and read about it, so hopefully I am not too far off base on my comments here. As usual and of course, I welcome genuine critics and corrections as warranted.

  93. ccbowerson 16 Dec 2012 at 6:05 pm

    BJ7
    I believe you are thinking of bindle

  94. BillyJoe7on 16 Dec 2012 at 10:43 pm

    Ah, yes, bindle.
    (Hey, either you have a good memory, or mine is failing)

  95. sonicon 17 Dec 2012 at 12:23 pm

    nybgrus-
    Wow!

    I’ve gotten into the written stuff a bit and things are going better- but this video was a rough start–
    Just so you know- I’m sure the next comment will include much more agreements.
    This comment includes things that are pretty harsh, like I say- I know the next will be less so– OK?

    I watched some of the video. It seems like a pretty slick version of stuff I’ve read.
    But–
    A good friend of mine did work in this field at the university. I’ve talked to him about it more than once. I’m not an origin of life expert like he is , but I’m aware of some of the leading hypothesis and the reasons they might be plausible and the problems with them. He has no doubt that there is a chemical formula for life. His last project on the subject was an attempt to explain the ‘handedness’ of life as a result of certain consequences of the behavior of the weak-force, but the funding stopped and so- what ya gonna do, man? :-(

    I understand that the chiralmetry of life might be explained by the consequences of the nature of the fundemental forces and the desire to reduce the phenomena that way, but I don’t really have a clue if his idea was any good.

    I tend to study only when I’m intensely interested. I learn quickly, but my interst has a stochastic quality that allows for holes in the learning. I am aware of this.
    My interests might be stochastic, but they are not random walk. :-)
    Well, not completely random walk… I don’t think, so… :-)

    Anyway-
    I read most of the book “Signature in the Cell,” which is excellent in that is it gives good and clear explainations of what the pluses and minuses of the various hypothesis are (Thomas Nagel didn’t give it book of the year for nothing).
    But it gets a bit into ‘intelligent design’ and while I can appriciate some of the efforts, they haven’t really got a unit of either intelligence or design. I have considered notions like ‘specified information’ when I was studying probability, but the problem I had with the things I was thinking about is the same as the problem I have with the way it is discussed in the book– there is something missing– a test, a unit of measure… hard to put finger on exactly, but something not right…
    It would be cool if they could come up with that, but until they do, I think their arguments will lack a certain power.
    I have wondered what a unit of design would be, but I can’t think of what it would be.

    Anyway–
    This recent article calls for a new approach.
    http://www.livescience.com/25453-life-origin-reframed.html

    I actually think he is correct in that a new approach is needed and what is being discussed here might be a better approach. We’ll see if it gains any traction.

    Perhaps if you have a specific hypothesis that you think is correct we could discuss that. The seven major contenders are linked to in the article I linked to. I don’t know much, like I say- but I might be able to find good references or links to the experimental results or whatever.

    I’ve grown tired of the promise the evidence is coming. I’ve read a number of times how a researcher was just days away from abiogenesis. Oh yes, the evidence is just around the corner. And I haven’t figured out how to falsify the position.

    Can you tell me how you would falsify your current position on this subject?

    BTW—
    I don’t think I’m going to do well learning from a video like that.
    One of the problems for me is that i am overly aware of the emotive music in the background. This is very distracting to me and I don’t listen to music while I’m trying to learn things for that reason. I love music- but not while I’m learning about something else. I’ve play musical instruments my whole life– I know what they are shooting for… I like it but not when I’m trying to learn. Clouds judgement to have the emotional manipulations going on…
    That’s what I experience, so you can see why it’s a difficulty— I’m really good at reading.
    But video with background music– not so good…

    Other problems-
    The video never did state the actual experimental evidence regarding the origin of life (life comes from life). Instead it begins with question begging assertions that involve claims that have not been demonstrated.
    And all the while the emotive music is doing what– I’m sorry, I’m hypersensitive– I know…

    I did see a part where the guy said this– “Life really is chemistry, there’s no question about that. In fact, it’s a chemistry that when you get the recipe right, it goes and it goes fairly quickly.”

    Man, if he would just demonstrate instead of assert.

    And the music is doing what? Never mind–
    Perhaps I have some condition of hypersensitivity. Probably has a name. I wouldn’t know.

    But I prefer to read.

    And I have been and will have more pleasant things to say soon.
    Wow!

  96. sonicon 17 Dec 2012 at 12:37 pm

    I’m thinking the bit I wrote about facts and assumptions is basically a mediocre description of the relationship between premises, logic, data and conclusions.
    I used the words assumptions, induction, fact and estimations or conclusions.
    Perhaps if I had used those other words the description wouldn’t be so mediocre.
    Well, I’m probably being nice to say it’s mediocre, but the ideas are in there…

    I do think it is important to note that these distinctions are meaningful. For example, I find that when I get confused and fail to differentiate between my assumptions and facts, I most easily harbor delusion. — Don’t ask me how I know that. :-)
    That’s one form of delusion– forgetting to differentiate between assumption and fact- right?

    Are you suggesting that understanding this relationship is ‘missing the forest for the trees’? I find that disconcerting.

    I have questions and stuff, but I’m not trying to denigrate science or what has been discovered. In fact, when you realize to what degree the premises have been checked over and the data searched and the logical operations honed– in physics the logical operations consist of mathematics. Amazing… The most amazing thing. The logical operations rest on certain assumptions that when listed seem reasonable. The logical operations are mathematical. The data is collected by instruments that are made to the highest possible tolerance by experts with billions of dollars to spend.
    This ain’t no ordinary microscope, dude!
    Amazing.

    It appears my questioning is incorrigable, inveterate and congenital however.
    Bad case. You wouldn’t be the first to point that out.

    Oh– important notice– I don’t know what you mean when you say ‘creationist’. I have seen the term used as an adjective and noun with the apparent meaning of ‘evil, stupid, wrong, foolish, horrible, hateful…’ or something like that.
    It seems to be used as a curse word sometimes. I get the impression that I’m not supposed to like it.
    But when I think of a creationist I think of a lady who took care of my brothers and me for a while. One of her favorite phrases was ‘all over creation’.
    I love her very much. :-)
    I have some idea why the term is used in a derogatory manner like it is, but I really don’t know what it means and I don’t have the same negative connotations that people here seem to have.

    So if you could define the term or use a different one, I’d be much obliged.

    Still assimilating the other stuff- give it a few more hours…

  97. BillyJoe7on 17 Dec 2012 at 3:03 pm

    Well, I’m just going to be polite: (:

  98. nybgruson 17 Dec 2012 at 3:17 pm

    His last project on the subject was an attempt to explain the ‘handedness’ of life as a result of certain consequences of the behavior of the weak-force, but the funding stopped and so- what ya gonna do, man?

    What to do indeed. It is an interesting question. The current state of evidence leads us to believe it was random – there was a 50/50 shot at the preference for chirality and once that was locked in everything else fell into suit since that was the random selection at the beginning, thus lowering the barrier for that chirality and not the other. However, deeper analysis could lead us to determine there is a particular reason why dextra chirality was preferred – i.e. it was the lower energy state or something like that leading it to be a more attainable peak on the fitness landscape.

    However, that does not directly have to do with abiogenesis.

    My interests might be stochastic, but they are not random walk.
    Well, not completely random walk… I don’t think, so…

    I haven’t read it (yet) but The Drunkards Walk by Leonard Mlodinow might interest you as well.

    I read most of the book “Signature in the Cell,” which is excellent in that is it gives good and clear explainations of what the pluses and minuses of the various hypothesis are

    Except that it can’t be an excellent review of explanations since the author is Meyer and his ID notions are fundamentally bankrupt. There is a reason why ID is pseudoscientific garbage and nearly anything, but essentially all “conclusions,” coming from supporters of it aren’t worth the paper they are printed on.

    Thomas Nagel didn’t give it book of the year for nothing

    And the Templeton Foundation doesn’t give away awards for nothing either. That doesn’t mean it becomes worthwhile.

    Nagel is an interesting guy and I liked his discussions about the idea of “being a bat” and how a bat’s acoustic perception of the world is simply an untranslateable experience for visually perceptive species like ourselves. However, his thoughts on “reductionism” and the “neo-Darwinian synthesis” are, well, wrong.

    But it gets a bit into ‘intelligent design’ and while I can appriciate some of the efforts, they haven’t really got a unit of either intelligence or design.

    A bit? That is the entire purpose of the book and Meyer’s entire raison d’être. In fact, there was the case of him coming out and saying something outside the party line of ID/creationism and he was censured by the theologians in his midst and then renegged and changed his tune. (Sorry link isn’t handy and I am writing quickly since I should actually do some real work today. There is a chance I may be confusing that with Dembski though, but in any event they are essentially equivalent DI minions).

    And of course – that is the problem. You complain about “waiting for the evidence to come” in abiogenesis which has vastly more evidence than anything out of the ID camp and yet you are content to read and use ID talking points as valid critiques of evolutionary theory. That makes no sense Sonic.

    The entirety of Meyer and Dembski’s arguments hinge on this “measured complexity” and units of “design” and “intelligence” but 15 years later there is literally nothing to how for it. Nada. Zip. Zero. Zilch.

    hard to put finger on exactly, but something not right…

    Almost there Sonic. Not “not quite right” but “entirely wrong” is what you should be thinking.

    It would be cool if they could come up with that, but until they do, I think their arguments will lack a certain power.

    Once again, no. Not a certain power. Any power. Do you see the hypocrisy of your thinking here where missing literally every single scientific basis of validity means they are “interesting but lack a certain power” whereas in abiogenesis the evidence is quite strong though not yet definitive and somehow that is not interesting or worth your consideration until some arbitrary threshold you define is met?

    I actually think he is correct in that a new approach is needed and what is being discussed here might be a better approach. We’ll see if it gains any traction.

    Not quite. Expanding our approach is useful. And certainly the ideas mentioned in that article are not unreasonable. But in no way is that a legitimate premise for replacing what we are already doing. Also, the use of “top-down” is problematic in that there is no evidence at all to make us think of life or evolution having any sort of “top-down” mechanisms, nor even what those mechanisms would be. That is more along the lines of Shapiro and I hope I’ve amply demonstrated why he doesn’t know what he is talking about.

    Perhaps if you have a specific hypothesis that you think is correct we could discuss that. The seven major contenders are linked to in the article I linked to. I don’t know much, like I say- but I might be able to find good references or links to the experimental results or whatever.

    The 7 hypotheses (not theories, by technical definition) are not mutually exclusive and could all have contributed to varying degrees. The point is that we have evidence – both empirical and historical – that complex organic molecules can form spontaneously from simple inorganic precursors and even gain replicative capacity. The fact that we haven’t been able to empirically demonstrate that they can go further than this doesn’t mean much. It took a billion years the first time around, why would you expect it to happen in your lifetime right now?

    ’ve grown tired of the promise the evidence is coming. I’ve read a number of times how a researcher was just days away from abiogenesis. Oh yes, the evidence is just around the corner. And I haven’t figured out how to falsify the position.

    The evidence is here Sonic. You just don’t seem to like it for some reason. Have we taken a jar of inorganic chemicals and turned it into a prosimian? Of course not. But the evidence that this could happen and likely did happen is there. What there isn’t evidence for and what keeps promising that “it is just around the corner” is every single other proposed theory about the origin of life and its diversity. Especially ID/creationism.

    How would one falsify the hypothesis? Specifically what would falsify it for me? Clear evidence that simple inorganic molecules can’t organize into more complex organic ones and that complex organic molecules can’t preferentialy self replicate. The thing is if even one example exists – even if it isn’t under “precisely” the conditions of an early earth, that is enough. Once you demonstrate it could happen, combined with the evidence that it did happen until a better hypothesis comes to light we provisionally accept it. And we have that.

    What would demonstrate to you that it is a valid position? What would falsify it for you?

    I don’t think I’m going to do well learning from a video like that.

    I’ll address this simply: it is a popular science documentary. If you’d rather focus on the ancillary things about it and complain that the music is making you skeptical of the message or that there isn’t enough hard hitting data and empirical experiments for you, then fine. But you don’t seem to have the time, desire, capacity, or some combination thereof to actually trudge through the dry stuff. Which is why I figured that a popular documentary version of it by Neil de Grasse friggin’ Tyson would be sufficient. You know, a really legitimate and extremely well respected scientist with expertise in the topic. But c’est la vie.

    This ties in, by the way to our general critiques of your approach. You credulously accept garbage “science” and discredited claims by fringe scientists as valid critiques of abiogenesis and the modern evolutionary synthesis, but then you nit pick about music choice muddying your objective assimilation of data from actual legitimate and well regarded scientists explaining the mainstream consensus and current understanding for the average person.

    Man, if he would just demonstrate instead of assert.

    Really sonic? Really? You bring up references by Meyer and Shapiro and then complain that Tyson is just asserting and not demonstrating? Do you really not see the double standard at play here?

    That’s one form of delusion– forgetting to differentiate between assumption and fact- right?

    Are you suggesting that understanding this relationship is ‘missing the forest for the trees’? I find that disconcerting.

    No. That’s not what I said. I don’t have the time or patience to reiterate it all, so just re-read what I wrote.

    I don’t know what you mean when you say ‘creationist’. I have seen the term used as an adjective and noun with the apparent meaning of ‘evil, stupid, wrong, foolish, horrible, hateful…’ or something like that.

    We’ve tried to explain. It doesn’t seem to make sense to you.

    Firstly, you espouse creationist ideas and reference creationist authors and fringe scientists whose wrongheaded ideas are loved by creationists (yes, ID and creationism are the same thing).

    Next you use the same sort of rhetorical tactics and repeat them ad nauseum (like the Shapiro thing for example) without ever modifying or improving your stance. I get that you think you are, but if you are then your writing and discourse sure doesn’t reflect that.

    Lastly, horrible, evil, and hateful are certainly not part of the description of “creationist.” It can be, but not necessarily so. Wrong and foolish, yes. Brainwashed, usually. Stupid, sometimes.

    I get the impression that I’m not supposed to like it.

    That you definitely shouldn’t. The ideas of creationism, the tactics and methods of creationists, are wrong and fundamentally bankrupt.

    But when I think of a creationist I think of a lady who took care of my brothers and me for a while. One of her favorite phrases was ‘all over creation’.
    I love her very much

    We aren’t talking about individual creationists but the idea of creatonism. And this is yet another creationist tactic. How could you possible think that we genuinely meant the sweet little old religious lady is a hateful, evil person because she holds creationist ideas? Oh my FSM. The ideas are bankrupt and the popular and well known creationists are known for specific tactics and tired defeated talking points.

  99. sonicon 17 Dec 2012 at 4:22 pm

    nybrus-
    the article you linked to about DNA half-life discusses what happens to DNA after cell death.
    While that is interesting, I think we were discussing evolution and the data from that article is non sequitur.

    Regarding Shapiro-
    You will note that the article I linked to about this includes an explanation of what he is talking about that is different than his. I’m not endorsing his work, I brought it up as an area of interest and I gave a link to papers both pro and con.
    I have read Coyne about Shapiro. I don’t know that Shapiro is attacking ‘Neo-Darwinism’ as Coyne seems to be very worried about, but if he is I can understand why a Darwinist would object.

    I have to say this (a bit like the video problem)– I will quote from Coyne here–
    “I hate to give attention to my Chicago colleague James Shapiro’s bizarre ideas about evolution, which he publishes weekly on HuffPo rather than in peer-reviewed journals. His Big Idea is that natural selection has not only been overemphasized in evolution, but appears to play very little role at all.  Even though he’s spreading nonsense in a widely-read place, I don’t go after him very often, for he just uses my criticisms as the basis of yet another abstruse and incoherent post. Like the creationists whose ideas he appropriates, he resembles those toy rubber clowns that are impossible to knock down.  But once again, and for the last time, I wade into the fray. . .”

    I count too many illogics to take this as an introduction to a reasoned evaluation of the man’s work. I feel emotionally charged reading it- that is my rationality has been decreased by the consistent use of charged words and ad hominem.

    I prefer the kind of analysis of the data that appears in the link I provided here-
    http://www.genetics.org/content/148/4/1453.full
    While this brings into question much of what Shapiro says, it does so without mention of him and it does so by discussing the actual evidence.

    Anyway,
    Here is some of what occurred the last “last time” Coyne commented on Shapiro’s work–

    Shapiro- “There is no way we can reasonably apply the term “random mutation” to a DNA transfer process that utilizes dedicated surface structures for bringing two cells together, assembles a multi-protein DNA transport pore connecting the cells, and initiates DNA transfer replication at a specific site on plasmid DNA.” [JAC: yes we can; for the transfer is a genomic change that occurs randomly!]

    Apparently the assertion of randomness in this case is too obvious to be explained rather than just asserted. I admit- I’m missing it…
    You also assert the mutations are random even if they are focused on a specific area. Random with respect to what?
    Not location, not timing (they occur more frequently under stress) and the exchanges tend to be of genes- whole cloth, not random sequences of DNA.

    I think the claim is they are random with respect to reproductive success- that’s the link to the Berkeley site I gave. It explains this pretty well I think.

    Perhaps we could discuss the various ways the word ‘random’ has been used in the various branches of biology and this would be a good lesson to both of us on making sure we are using the words correctly.

    Anyway–
    Later Coyne says something that I find revealing–
    “So no, there isn’t an insuperable problem here for “neo-Darwinism.” We just have to expand our idea of “mutation.”

    This I agree with completely. “Mutation plus selection” is always going to be true as a means of evolving. Any theory of evolution is going to fit that model. (variations that reproduce continue- those that don’t reproduce don’t continue would be a loose way of saying it).
    The discussion then is about what types of mutations are occurring and what is being selected for. (if we confuse the act of reproduction with ‘what is being selected for’, I think it becomes rather circular in that ‘what reproduces is what reproduces.’ I have links to the work of Kingsolver who I believe is the expert in this field if you would like to see some of the observational data regarding what is being selected for.)

    My point is this-
    The real question regarding mutation is how to describe it– and I’ve noticed it is the molecular biologists (the ones who actually study the way mutations occur and so forth) are the one’s saying ‘random’ isn’t the best description.

    My attempt to discuss this includes links to his work and the list of experiments he is basing his thought on and a paper that basically looks at the evidence from a different perspective.
    Can you understand why I find it odd that someone would accuse me of being an ideologue?

    Some events in the universe seem destined to be best described as ‘random’. Where a cannonball lands after firing the cannon is not one of them. As there is currently no model of molecular evolution that deals with all the known factors- just how ‘random’ mutation will end up being in that sense is unknown as well.

    I’m fairly certain that as far as ‘evolution’ is concerned the actual claim is that mutations are random with respect to ‘reproductive success’. You can find that at the link I provided to the Berkeley website about evolution.
    If you want to question that statement, please refer to that site and tell me what is wrong with what they are saying–

    Your link to the story about insect evolution is better than the one I had before to the same observations (I think I have science daily version). Thank- you for that.

    BTW- I studied probability and statistics at the university. I’m sorry if my comments make you think I’m ignorant about the subject– you might want to consider that I’m not. Thanks

    You claim “We understand enough about molecular evolution and the evidence we see to conclude that is how the sequences got that way…”
    And that’s the assertion that is being questioned by those who are looking at the actual sequences for the first time. (note it is molecular biologists that seem to be having the most problems– doesn’t Coyne have a post about that?)

    Regarding mechanisms to explain the various activities involved in the ‘adaptive’ mutation process- I an aware that such mechanisms have been studied and delineated. If you look at the paper I linked to about the subject (not the Shapiro one, the other) I believe you will find links to these studies.
    My comment about mechanism was regarding the possibility of ‘preferred pathway’ type ideas– I don’t know how much the ultimate model of molecular evolution depends on things for which no mechanisms are known (coherence and such) and that is what I mean when I say “I don’t know,”
    If you would look at the links I provided I think you will see that I have included the papers that detail the mechanisms and proposed mechanisms under discussion regarding ‘adaptive’ mutation.
    Sorry for the confusion.

    More later–

  100. sonicon 17 Dec 2012 at 4:37 pm

    nybgrus-
    I just skimmed and saw this-

    You say-
    “…it can’t be an excellent review of explanations since the author is Meyer…”

    Can you name the logical fallacy here?

    Seriously- I have read numerous reviews of the book including at Panda’s Thumb and so forth and the complaints are about the style (first person narrative isn’t my favorite either) and the introduction of ‘Intelligent design’ into the discussion- a complaint I also made.
    I have yet to find any discussion that doesn’t say his outline of the theories and hypothesis isn’t good. Or says nothing about that part at all.
    Obviously he is slanted in his analysis, but that doesn’t mean his summery of the hypothesis and the evidences and so forth isn’t good.

    Can you find anyone who has read the book that takes him to task for his detailing of the various current hypothesis regarding the OOL?

    I’d be interested.

    And I asked for a definition of ‘creationist’. You don’t give me one. Fine, what is the definition of ‘creationism’ that you are using?
    Do creationists believe in creationism? What is the relationship.

    It comes across as vague hate filled language and I would really prefer to get it narrowed down what you mean. I realize there is a lot of baggage that goes with the term, so if you could define it in a sentence or two– “Creationism is …” “Creationists are people who…” I can fill in the baggage part.
    Perhaps there is a website I can go to that will explain it.
    Thank-you.

  101. nybgruson 17 Dec 2012 at 5:31 pm

    the article you linked to about DNA half-life discusses what happens to DNA after cell death.
    While that is interesting, I think we were discussing evolution and the data from that article is non sequitur.

    Not even close to a non-sequiter. Do you think that the processes that degrade DNA simply don’t exist in a living cell? That the environmental and chemical forces at play magically appear only after the cell dies? No. They are always ongoing but are being constantly repaired and constrained by the processes of a living cell. It is directly pertinent and absolutely relevant.

    I count too many illogics to take this as an introduction to a reasoned evaluation of the man’s work. I feel emotionally charged reading it- that is my rationality has been decreased by the consistent use of charged words and ad hominem.

    Ad hominem and emotion do not invalidate an argument. They are only fallacies if they are the only argument. Coyne and others have emotionlessly critiqued Shapiro’s work. After a while, emotion creeps in. Just because it is there – just like how just because there is music in NdGT’s documentary – doesn’t mean the message is invalid.

    Apparently the assertion of randomness in this case is too obvious to be explained rather than just asserted. I admit- I’m missing it…

    Yes, it is obvious and elementary. Because which DNA sequence or gene is transmitted is random. Yes, whole genes are transferred but that is actually quite rare. Most of the times in these sorts of transfers part of the gene is truncated and/or excess DNA is included. In other words the fact that the transfer is hapenning isn’t random, but what gets transferred is random. This is why transfection rates in trying to introduce new genes into bacteria have such extremely low success rates. The advantage we have is that we can use billions of bacteria to ensure that even at such low rates – due to the random nature of DNA transfer and uptake – some of them will have a useful gene product and we can select for it.

    A molecular biologist should know this. Shapiro clearly ignores it.

    You also assert the mutations are random even if they are focused on a specific area. Random with respect to what?

    Random with respect to what nucleotide sequence actually emerges. Random with respect to fitness is also a reasonable statement.

    Not location, not timing (they occur more frequently under stress) and the exchanges tend to be of genes- whole cloth, not random sequences of DNA.

    Some types of mutations happen more frequently under stress and more often in a specific location. Not all and not even most. And the mechanisms which create this increased frequency in certain times and places arose by random mutations creating the cellular machinery to promote this. And, as I pointed out above, exchanges of genes are not whole cloth and they are actually random sequences of DNA which only sometimes yield the entire useful gene being transferred.

    “Mutation plus selection” is always going to be true as a means of evolving.

    Good. Now add “random” as the basis of all mutation and you are there.

    The real question regarding mutation is how to describe it– and I’ve noticed it is the molecular biologists (the ones who actually study the way mutations occur and so forth) are the one’s saying ‘random’ isn’t the best description.

    No, only some mol bio guys do. And that is because they get so narrowly focused they lose site of the larger picture and then think they know better than evolutionary biologists. Doesn’t work that way.

    My attempt to discuss this includes links to his work and the list of experiments he is basing his thought on and a paper that basically looks at the evidence from a different perspective.
    Can you understand why I find it odd that someone would accuse me of being an ideologue?

    No, because the papers you link to and the quotes you cherry pick make you look like an ideologue. You think that the ICR or the DI don’t link to papers and quote references?

    As there is currently no model of molecular evolution that deals with all the known factors- just how ‘random’ mutation will end up being in that sense is unknown as well.

    Not correct. We can actually test randomness to determine the likelihood that an outcome is random. We don’t need a model complete down to the tiniest detail to know this. You claim to have studied probability and statistics, so don’t forget that random does not mean equally probable.

    You say-
    “…it can’t be an excellent review of explanations since the author is Meyer…”

    Can you name the logical fallacy here?

    Once again, it is only a logical fallacy if that is my only argument. It is already established that anything coming out of the DI, ICR, Meyer, Dembski, or Luskin is almost certainly going to be garbage. That isn’t an ad homimen fallacy, it is a fact.

    Seriously- I have read numerous reviews of the book including at Panda’s Thumb and so forth and the complaints are about the style (first person narrative isn’t my favorite either) and the introduction of ‘Intelligent design’ into the discussion- a complaint I also made.
    I have yet to find any discussion that doesn’t say his outline of the theories and hypothesis isn’t good.

    Really? Because my 5 second google search shows otherwise.

    And I asked for a definition of ‘creationist’. You don’t give me one. Fine, what is the definition of ‘creationism’ that you are using?
    Do creationists believe in creationism? What is the relationship.

    Creationist (noun): A person who uses cherry picked studies, quote mining, Gish Gallops, arguments from incredulity and authority, pseudoscientific studies, straw men, other misrepresentations of science, to further their ideology which is almost always an attack on evolution rather than a presentation of evidence for creation.

    Creationist tactics can be used in toto or in part, intentionally or not.

    Or this handy but not all inclusive list.

    As we have said, you aren’t clearly engaging in 100% de facto creationist tactics, but enough to make us wonder. Myself included.

  102. ccbowerson 17 Dec 2012 at 8:43 pm

    “Do you see the hypocrisy of your thinking here where missing literally every single scientific basis of validity means they are “interesting but lack a certain power” whereas in abiogenesis the evidence is quite strong though not yet definitive and somehow that is not interesting or worth your consideration until some arbitrary threshold you define is met?”

    This is the crux of the problem with Sonic’s arguments/stance on these topics. He not only has a double-standard, but the two standards are not even in the same ballpark. He is hyperskeptical of a certain scientific theory or ideas (in this case abiogenesis) to the point of creating an unreasonable threshold for evidence, and this is a way of using the ‘perfect solution fallacy’ to imply false equivalence to some fringe scientific theory or nonscientific theory (in this case creationism) for which he requires little to no evidence. In fact, often the rationale for the fringe theory is that the accepted scientific theories aren’t perfect. This is motivation reasoning in action

  103. sonicon 18 Dec 2012 at 3:20 am

    nybgrus-
    yes, DNA degrades in the cell while the cell is alive. And it decays after the cell dies.
    No doubt.

    You insult me no end with your statement that I haven’t taken an interest in or considered the evidence for abiogenesis.
    Why do you think I’ve read books about it? How many articles from the science magazines do you think I’ve read? How many times have I conversed with my friend on this subject? The guy was claiming he would produce life from non-life in just a few days. It was years ago, but I’m still waiting. No interest or consideration?

    You insult your own intelligence when you make such a statement- especially after you suggest the answer to the situation lies in a video that begins by begging the question! You understand to beg the question is to refuse to examine the evidence- right?

    See, I can get emotional– I haven’t considered the evidence– and you come with a video that begs the question, written for grammar school children. Wow!

    Have a moment–
    Now for something more constructive–

    As far as what is meant when the word ‘random’ is used to modify the word ‘mutation’-
    From the Berkeley site linked to above-
    “In this respect, mutations are random — whether a particular mutation happens or not is unrelated to how useful that mutation would be.”

    from “The Blind Watchmaker” by Dawkins-
    “We can now see that the question of whether mutation is really random is not a trivial question. Its answer depends on what we understand random to mean. If you take ‘random mutation’ to mean that mutations are not influenced by external events, then X-rays disprove the contention that mutation is random. If you think ‘random mutation’ implies that all genes are equally likely to mutate, then hot spots show that mutation is not random. If you think ‘random mutation’ implies that at all chromosomal loci the mutation pressure is zero, then once again mutation is not random. It is only if you define ‘random’ as meaning ‘no general bias towards bodily improvement’ that mutation is truly random.”

    I’m not sure that what you are saying about the mutations being ‘random’ during the process that Shapiro is talking about is completely in agreement with the experimental evidence anyway–

    http://www.ncbi.nlm.nih.gov/pubmed/22038780
    http://www.ncbi.nlm.nih.gov/pubmed/15101972

    Please note- these are interesting results. They don’t prove anything nor am I insinuating they do. I do think they are of interest in answering the question-

    Random with respect to what?
    We have to answer that before moving on.

  104. sonicon 18 Dec 2012 at 3:28 am

    ccbowers-
    I have read quite a bit about this ‘origin of life’ stuff. I have tried to imagine the various scenarios that are currently in vogue, but I just don’t see that they can work.
    The RNA guys have the most interesting experiments to me, if I had to bet on one of the existing ‘which came first’, I’d go with that– but it is hard to ignore that the ‘metabolism first’ people have me fairly convinced that the RNA guys are wrong. Ouch!

    I’m pretty certain that every objection I have to a currently hypothosized solution to the origin of life comes from scientific articles.

    So for me to say I don’t find the ‘RNA world’ scenario convincing isn’t really controversial, I don’t think. And for me to say I don’t find the ‘metabolism first’ convincing isn’t really controversial either. And for me to say I don’t find the idea that life came from outer space convincing isn’t really controversial either- is it?

    This business about the clay substrates sounds a bit too much like ‘man came from mud’– I’m admitting I have a difficult time being rational with that one. :-)

    Which scenario do you think correct- metabolism first or RNA world or something else?

    I don’t understand why I have to believe the actual experimental evidence has to be wrong given the situation. I mean ‘life comes from life’ is one of the most useful, experimentally validated datums in all of science.
    Throw it out because of the claim that life came from space? I don’t know why I would do that. Honestly- I don’t know why I would throw out a well tested, exteremly useful experimental result on the undemonstrated claim that life came from outer space. (Sorry for the reductio ad absurdum– but it is funny, no?)

    Of course my reasoning is motivated. Are you thinking someone’s isn’t?

    So which one you buying? RNA or metabolism or something else?

  105. nybgruson 18 Dec 2012 at 10:40 am

    Very well sonic, my apologies for insulting your intelligence. It was not my intent, but I will stick with the fact that at a minimum your writing does not serve well to illustrate your more reasoned and researched thoughts on these topics.

    yes, DNA degrades in the cell while the cell is alive. And it decays after the cell dies.
    No doubt.

    So then why would you simply toss out my reference and call it a non-sequiter? That is one of the sources of completely random (in every respect) mutation in the genome of a living organism.

    especially after you suggest the answer to the situation lies in a video that begins by begging the question! You understand to beg the question is to refuse to examine the evidence- right?

    You understand that the video was not a live action version of a peer reviewed paper, right? That it was a documentary on the state of evidence, by an eminent scientist. It “begs the question” because the purpose was to demonstrate the state of evidence supporting the notion of abiogenesis.

    And you may have read extensively on it, but you seem to be missing a fundamental facet of understanding here: life exists on earth. At one point no life existed. Unless you posit a magical deity then at some point, somehow, abiogenesis must have occurred. There is no question to beg. It must have happened else I wouldn’t be here writing about it. Precisely how that happened is what is currently up for debate. The hypotheses that you mention are potential solutions to the question you say is begged – each of which has some evidence to support it and many of which are non-exclusive. Panspermia only changes the idea to saying that the abiogenesis didn’t occur on earth. But if it occurred elsewhere it would have had to follow some sort of process which would likely be described by the other hypothesis posited.

    And that is the point – your question was not about a specific mechanism for precisely how it occurred. For that we do not yet have a definitive answer, only a number of leads. But for the concept of abiogenesis there really is little question that it must have happened. Not only is there no other plausible explanation, but the evidence for how it happened demonstrates that it could happen and since it obviously did happen, then we are done – no questions to be begged merely mechanisms to be answered.

    from “The Blind Watchmaker” by Dawkins-

    None of that addresses any of my points. You also conveniently excluded the following sentence:

    “All three kinds of real non-randomness we have considered are powerless to move evolution in the direction of adaptive improvement as opposed to any other (functionally) ‘random’ direction.”

    In other words, completely in line with my last reply which was:

    Random with respect to what nucleotide sequence actually emerges. Random with respect to fitness is also a reasonable statement.

    Dawkins then goes on to condemn the caricature of random in exactly the same way I have been. Random does not mean every conceivable possibility in every conceivable location at every conceivable time with equal probability.

    And he, in this section of the book, does not address the random mutations that occur by DNA degeneration and poor repair, which is random in respect to everything and the initial and prime mover of mutation. All those other things he talks about came after to help constrain the DNA which is why we get more and less conserved areas.

    But note that my definition of random fits in perfectly with his and there is no conflict with his.

    Random with respect to what?
    We have to answer that before moving on.

    Asked and answered at least twice now. Do remember that “random” does not mean every conceivable outcome is equally likely. It only means that the specific base pair sequence that arises is not pre-determined and that overall it is irrespective of the fitness of the organism.

    Your links are nothing but more of the same, which I have discussed, shown where they belong in evolutionary theory, and do not at all conflict with anything I have been saying.

    So for me to say I don’t find the ‘RNA world’ scenario convincing isn’t really controversial, I don’t think. And for me to say I don’t find the ‘metabolism first’ convincing isn’t really controversial either. And for me to say I don’t find the idea that life came from outer space convincing isn’t really controversial either- is it?

    No, it isn’t. But you are now having two arguments – one about abiogenesis having happened at all and the other about specifically how it happened. The latter is what you address in this quote and I agree with you. The former is what you are calling “begging the question” and I hope I have demonstrated why it is not, in fact, begging the question.

    This business about the clay substrates sounds a bit too much like ‘man came from mud’– I’m admitting I have a difficult time being rational with that one.

    I know that was tongue in cheek, but yes it is a very viable hypothesis (once again not mutually exclusive of the others) because we have demonstrated the formation of protobionts using clay substrates as an organizing medium.

    I don’t understand why I have to believe the actual experimental evidence has to be wrong given the situation. I mean ‘life comes from life’ is one of the most useful, experimentally validated datums in all of science.

    And now you are having two separate arguments again. Abiogenesis does not invalidate “life comes from life.” They are two separate topics. It is trivially obvious that once life emerges that the easiest way for life to continue is from life, rather than coming up de novo again. And certainly no other manner would allow for the development of complex life. But to say that the first incidence of life came from inorganic material only describes that – the first life.

    Do you see how now twice you have been having two separate arguments, seamlessly switching from one talking point to the other to try and validate your stance? Your argument against abiogenesis has become that it invalidates “life coming from life.” Now that is what we call a non-sequiter or in this case perhaps a strawman (or both).

    Throw it out because of the claim that life came from space? I don’t know why I would do that. Honestly- I don’t know why I would throw out a well tested, exteremly useful experimental result on the undemonstrated claim that life came from outer space. (Sorry for the reductio ad absurdum– but it is funny, no?)

    Reductio ad absurdum is useful as a rhetorical tactic if the outcomes of my argument logically led to your absurd conclusion. They do not. Nobody in their right mind is even contemplating throwing out the “life comes from life” theory. So yeah, I also don’t know why anyone would throw it out.

    It is the same as when creationists conflate the evolution of life with the origin of life… which you haven’t overtly done but it does seem interesting that somehow our conversation got onto that topic. Evolution does not speak about the origins of life (though in my opinion and that of Dawkins, eventually it will). And “life comes from life” does not address the origin(s) of life.

  106. ccbowerson 18 Dec 2012 at 11:34 am

    “I have read quite a bit about this ‘origin of life’ stuff. I have tried to imagine the various scenarios that are currently in vogue, but I just don’t see that they can work.”

    Well, I guess it depends on what you mean: the concept of abiogenesis itself (in the broadest sense), or specific theories about how it occurred. You are talking about skepticism of the latter, but I was commenting on your broader criticism of the concept itself. You seem to conflate the two, and they are very different. If you want to use limitations in the current theories regarding abiogenesis to bring doubt to the idea itself, what is the alternative? A biogenesis seems to me to be a logical conclusion to the idea that life did not always exist (but does now). I see no alternative but creationism, which is a nonscientific idea, unless you have another explanation. Your main argument against this seems to be incredulity

  107. sonicon 18 Dec 2012 at 11:36 am

    Guys-
    Re abiogenesis–
    Here is a better link to the last paper I’ve read on this subject.
    http://arxiv.org/pdf/1207.4803v2.pdf

    I haven’t assimilated completely, but I have enough to say this paper covers much of what I would say about this (and much more!)

    In particular I recognize the difficulties with the current approach he does, I agree with the need for new thinking here, and I find his approach very interesting.
    I have not assimilated to the point I would endorse it, but the approach suggested and the proposed means of defining life are very interesting.

    Read it and see what you think.

  108. ccbowerson 18 Dec 2012 at 12:00 pm

    I didn’t read nybgrus’s comment before mine, and it appears that he already made the point I was trying to make. Doubting the idea of abiogenesis since you don’t like the current theories describing the mechanisms is like doubting the existence of the moon due to your dissatisfaction with current theories of how it was formed

  109. nybgruson 18 Dec 2012 at 12:47 pm

    Sonic:

    The paper is indeed interesting. It essentially supports exactly what I have been saying and furthe refines the discussion to make it more rigorous. Except for a couple of parts that jumped out at me as bordering on potentially false and something a creationist might latch onto, it is overall a very good and interesting discussion.

    To start with the purpose of this paper is not to refute abiogenesis. In fact, in much the same way that the video I linked you to “begs the question” so does this paper. The inherent assumption the authors make is that abiogenesis has occurred – for exactly the same reasons I posited above. The purpose of this paper is to rigorously define “life” such that the events of abiogenesis can be better elucidated and teased apart from simpler replicative systems like crystals, which we tend to agree is “non-life.” It also seeks to broaden but not replace the definition of life.

    First off, they make the same point I have:

    While we have stressed that Darwinian evolution lacks a capacity to elucidate the physical mechanisms underlying the transition from non-life to life or to distinguish nonliving from living, evolution of some sort must still drive this transition (even if it does not define it).

    Recall how many times I have said that evolution and abiogenesis are not the same thing, and the former does not attempt to describe the latter. I have also recently said it is my belief that eventually evolution will describe abiogenesis as well, and here the author further confirms that while not the defining facet of the transition from non-life to life, evolution of some sort must still drive this transition. In other words, completely in concordance with what I have been saying.

    Also recall how I have said that the various hypotheses describing the mechanisms of the origin of life are not mutually exclusive. That RNA-world and metabolic world are not “either-or” considerations. The authors say the same themselves:

    Purely analog life-forms could have existed in the past but are not likely to survive over geological timescales without acquiring explicitly digitized informational protocols. Therefore life-forms that “go digital” may be the only systems that survive in the long-run and are thus the only remaining product
    of the processes that led to life. As such, the onset of Darwinian evolution in a chemical system was likely not the critical step in the emergence of life.

    In other words, in the milieu of early earth over a couple billion years, we can easily envision analog type metabolic processes degrading rapidly over and over again until some event – either intrinsic or a chance interaction with a separately arising trivial digital replicative process – allows for retention of fidelity of the analog system and thus the progression towards more complex life. Once again, this is in concordance with what I have been saying.

    The crux of their thesis is:

    In so doing, it forces new thinking in how life might have arisen on a lifeless planet, by shifting emphasis to the origins of information control, rather than – for example – the onset of Darwinian evolution or the appearance of autocatalytic sets

    Which seems eminently reasonable to me. Note that they are not saying a new paradigm other than abiogenesis is called for, merely that the definition of life can be amended in order to broaden it, and thus capture a more meaningful solution to abiogenesis. In this quote they are taking it a step further back by saying that the onset of Darwinian evolution as a marker for “life begins here” is too late and that a simpler and more generic definition of life is called for. They also differentiate it from the trivially replicating systems like crystal structures. All of this is reasonable and still in concordance with everything I have been saying.

    Where I disagree with them comes only in two passages. The first I think could be explained by them not rigorously defining a specific word choice:

    It makes sense to try to explain life’s origin only if it resulted from processes of moderately highly probability, so that we can reasonably expect to explain it in terms of known science. It then follows from simple statistics that there will have been a large ensemble of systems proceeding down the pathway toward life, and no obvious reason why only one member successfully completed the journey.

    To a creationist this would be an “in” to saying that what we know is not of “moderately high probability” and thus goddidit. To me it should be taken in context. In our every day lives people tend to think of “moderately high probability” as being in at least the double digits of likelihood if not higher than that. Probabilities of 1% or less seem “highly improbable.” But in the context of abiogenesis and evolution over billions of years, probability vastly less than 1% are still reasonably considered “moderately high probability.” I won’t belabor the point since you have asserted your knowledge of statistics and probability, so the law of large numbers should be trivially obvious in this case.

    The second statement is further reinforcement of what I have been saying as well. Many self replicating systems arose by random chance alone and for some reason a particular system progressed further and thus quickly came to dominate the living landscape of the earth. In all likelihood it was the system that stumbled upon the lowest peak on the fitness landscape closest to it, but it is also possible that it stumbled on a much higher peak that was less likely but still possible. This is an important note – in our experiments, we may find a fitness peak lower than what was chanced upon in the origin and subsequent evolution of life on earth. This may yield a different mechanism and/or a different form of life than what we currently see to exist. That would not invalidate abiogenesis, since we expect there to be more than one pathway to OOL, some more likely than others, all very improbable, but also likely inevitable thanks to the law of large numbers. Of course, we don’t have a numerator as to how many times life has originated in the universe so we can’t actually compute a probability. We know at least 1 time, but we don’t know how many more times – if at all – it actually happened.

    The other part I disagree with is where I think they went a little off the rails:

    DNA does not contain a blueprint for building the entire cell, but instead contains only small
    parts of a much larger biological algorithm, that may be roughly described as the epigenetic components
    of an organism. The algorithm for building an organism is therefore not only stored in a linear digital
    sequence (tape), but also in the current state of the entire system (e.g. epigenetic factors such as the
    level of gene expression, post-translational modifications of proteins, methylation patterns, chromatin
    architecture, nucleosome distribution, cellular phenotype, and environmental context). The algorithm
    itself is therefore highly delocalized, distributed inextricably throughout the very physical system whose
    dynamics it encodes

    While it is correct that DNA does not contain a blueprint for the entire cell, it is the “recipe” for the cell. Think of it like baking a cake versus building a house. The house is a blueprint that tells you exactly where everything is supposed to go, how it goes there, and why. A recipe is a guideline for how to put things together to come up with a cake. Depending on how much of each ingredient and how long and at what heat you bake it, the cake will come out differently. You can also add extra stuff to change the flavor of the cake. So the outcomes can be different, but at the end of the day it is still a cake.

    However, without the DNA none of the other machinery would exist, the “top-down” control wouldn’t exist, the methylation patterns wouldn’t exist, and nothing would happen. So while the control and development is decentralized, the origin of it all is still 100% encoded in the DNA itself. This short paragraph is bordering on Shapiro’s incorrect thoughts and would be something the likes of Behe would support as well since it implies that there is something other than DNA at the heart of cellular regulation and replication and the system is irreducibly complex. The former is simply not true – the DNA is still the unequivocal source of all the regulation and thus still fully describes the ultimate functioning of the cell. The fact that there are higher order of control which develop as a result of this merely allows for more degrees of freedom in the actual phenotype and action of the cell, which makes sense since that allows for greater adaptive ability and thus more room for evolution to work. The latter is true – the systems are irreducibly complex, but that doesn’t mean they can’t have arisen from simpler processes over time. The arch of a bridge is irreducibly complex – every single stone (especially the capstone) needs to be in place for it to work, removing any part destroys the function of the whole, and you cannot build it up sequentially by merely adding bricks. But if you put in a wooden support, build the arch, and then remove the support you have your irreducibly complex structure. And that is how it works with irreducibly complex biological systems.

    All in all a good article – one which fully supports the notion of abiogenesis and is almost 100% in concordance with everything I have been saying about it.

  110. sonicon 18 Dec 2012 at 1:43 pm

    nybgrus-
    Glad you liked the article and I agree that the points you bring up are questionable aspects of what is being said.

    With this comes other possible good news–

    We are getting somewhere with this ‘random’ business!
    Here is an article that covers the subject well IMHO.
    http://quod.lib.umich.edu/p/ptb/6959004.0002.003?rgn=main;view=fulltext

    Parts three and four in particular attempt to identify the consensus view of “the biologists of the Modern Synthesis” about the chance character of all genetic mutations and the factors involved.
    Is this reference agreeable as a means to discuss the definition of random as used by evolutionists? And is it good for a discussion of the ramifications of that definition?
    Can we agree on this reference?

    I find the discussion of Jablonka and Lamb’s work instructive in that it is clear this is an area of some confusion even with these researchers. I’m not completely familiar with their work, but the issues covered in this article are great!

    BTW- I think the experimental evidence is the ultimate decider in this case. I note the number of experiments and the ability to see what is really going on has increased since the days of Cairns, Foster and the experiment that has been analyzed to death.
    I link to three experiments that seem to me to be relevant- more of those types of findings are available if you are interested.
    I note that most of what I consider challenges to the Modern Synthesis come from the people doing those experiments- that is I agree with Coyne on that.

    I hope you can excuse me for allowing that some of the findings might possibly have some slight implications to our understanding of life has actually evolved on Earth. And that I’m wondering how, not if, evolution has occurred.
    Good distinction– no?

    Anyway, if we could agree that this paper is a good reference…

  111. sonicon 18 Dec 2012 at 3:38 pm

    regarding abiogenesis and experiment and motivated reasoning–

    The experimental evidence regarding how life begins is this– life comes from life.
    The experiment started over 100 years ago- an experiment that began by assembling all the so called ‘building blocks’ of life- and continues today.
    No life in the jar unless life itself is introduced. That’s the claim and the claim is so demonstrated.

    The experimental evidence doesn’t say life came from chemistry- it says life from life. This result seems to imply that something about life is irreducible– that is you don’t get it from something else; that is abiogenesis is not possible.
    I realize there is evidence to the contrary regarding life- that is it is reducible to ‘building blocks’ and there is not absolute dividing line between life and non-life, and so forth, but I have a hard time ignoring the fundamental experiment in this regard.

    Excuse me for being so stubborn. BTW- I’m not suggesting you join me in this view- only that you understand it is based on experimental evidence- is ultimately falsifiable and that is what I’m asking for- a falsification of the experimental evidence by means of actual experimental demonstration. I don’t think that is an arbitrary thing to want. I’d demand the same of ‘cold fusion’. Wouldn’t you?
    So while I may be wildly off base in requesting that a well known experiment be rejected by actual demonstration rather than argument, It doesn’t seem that odd to me.
    OK?

    I’ll give you three possibilities-
    1- there is a chemical formula for life and we haven’t found it yet
    2- there isn’t a chemical formula for life per se- but there is a solution to the apparent paradox that is outside the current thinking (like Einstein’s relativity or QM was to physics)
    3- life is irreducible and a creation from a currently unrecognized force in science

    How many of those possibilities are you willing to entertain?

    When it comes to reasoning, isn’t the degree of motivation proportional to the number of options allowable?
    Isn’t the problem of creationism that they demand the answer be some version of #3?
    And isn’t this decision before the fact what motivates the reasoning?

    I’m not suggesting that you personally open your mind to any of the three possibilities– you may all ready have decided which it is. And that is fine with me.

    But, I would hope that you would recognize to the degree you have certainty about your choice you have motivated your reasoning so as to maintain that certainty.

    Have I done that too?
    You bet.

    Personally I think option #2 is most interesting. I mean Einstein figured out how it could be that the speed of light would measure the same regardless if you were moving towards the source or away from it. Solution? Space-time is malleable. When I walk past someone on the street, time passes at a different rate for me than it does for the person I’m passing. How can I not like that sort of result? I love it.

    I’m not sure anyone saw that explanation coming and now that we have it, I’m still not so sure anyone really understands how things could be that way– they just are.
    So if the solution was as wild as relativity or QM– that option is my favorite–

    Option #1 has a certain appeal in that it contains a certain finality to it. From my perspective this result would be a relief- and I note that many who come to accept #1 as fact express the relief and freedom they experience when they do come to that conclusion.

    Option #3 is interesting in a number of ways as well. If there is an unrecognized force– what is it like and where does it come from and… wonderful a new thing to learn about.
    But it is also the scariest in that it means there is a possibility that the source of life is outside the physical somehow and that might mean I will have to take ultimate responsibility for what I have done. I am motivated to reject the notion on that basis alone– :-)

    Hope this clears things up as far as where I’m coming from in all this.

  112. nybgruson 18 Dec 2012 at 3:57 pm

    sorry sonic but it doesn’t clear it up. I am still reading through the link you provided… well, I was actually reading that exact same article before you provided it, but either way I am still reading through it, so I will address your second post:

    You are still writing as if the “experiment” that life comes from life would be falsified if life came from non-life. It won’t be. That experiment is settled and has very little, if anything, to do with abiogenesis. Your implicit assumption is that the “experiment” that “life comes from life” means that only life can come from life. That is not what the “experiment” tells us at all – it only tells us that is one way (and indeed the most common way) for life to arise. It does not inform us at all about other ways life can arise.

    So yes, you are being unreasonably stubborn in holding on to that point since it is your only talking point and it has essentially no bearing on the discussion of abiogenesis.

    I have no motivated reasoning to maintain my stance that abiogenesis happened. As I have repeated endlessly and ccbowers pointed out, it must have happened at some point. If there is a “force” required that we have yet to elucidate, that is possible though it is highly unlikely and would still fall into the realm of scientific discourse and would not in any way contradict anything I have said. As such, 1 and 2 of your choices are not mutually exclusive and either being true would still fit into what I have been arguing. #3 is either indistinguishable from #2 or it is magical thinking and does not belong in the realm of science or reality.

    In any event, the rest of what you say in not unreasonable or it reiterates the same points yet again.

    The crux of our disagreement here is that you continue to confabulate the mechanisms of abiogenesis with the concept of abiogenesis as a whole. Furthermore, you seem to restrict yourself to only acknowledging evidence that culminates in the generation of life as you recognize it. In other words, if the experiment doesn’t yield at least a bacterium, then it contributes nothing to the conversation of abiogenesis. Bollocks. We have numerous empirical data to support that mechanisms for the spontaneous generation of complex organic and self replicating molecules from completely inorganic molecules coupled with the fact that abiogenesis must have occured. That alone is enough to reasonably confirm the theory of abiogenesis. The precise mechanisms have yet to be elucidated, but as we have discussed here and at SBM endlessly, you don’t need a mechanism to demonstrate an effect (in this case abiogenesis). Unless other empirical evidence demonstrates that something other than abiogenesis is what actually happened or was more likely to have happened there is simply no alternative.

    It is like the Higgs boson. It was hypothesized though not discovered. The only way to disprove the existence of the Higgs would be to validate a physical model that did not include the Higgs. But if all the other elements of the standard model were in place and we just couldn’t verify the Higgs itself, we would be almost as confident of its existence because everything else supported it. The same for abiogenesis: there is no alternative model, there exists evidence pointing in the direction of abiogenesis and allowing for the plausibility, and we know life is here and once was not. So until a better model, with at least equivalent empirical support comes about, we are left with abiogenesis as the only option and likely to be correct.

    Once again, do not confabulate the mechanisms of abiogenesis with the theory of it.

  113. ccbowerson 18 Dec 2012 at 9:46 pm

    “The experimental evidence doesn’t say life came from chemistry- it says life from life. This result seems to imply that something about life is irreducible– that is you don’t get it from something else; that is abiogenesis is not possible….
    …I’ll give you three possibilities…”

    Again with the obfuscation. Saying that experiments can show that abiogenesis is not possible is like saying that bumblebees can’t fly because we have failed to explain how they can fly. Of course this argument fails because it is incongruent with reality. Experiments may shed some light about the possible mechanisms for abiogenesis, but the idea of abiogenesis is a logical conclusion derived from 2 facts:

    1. Currently, there is life in the Universe
    2. Fact #1 was not always so (i.e. there was a point in time in which there was no life in the universe)

    To say that life only comes from life does not get you anywhere unless you are arguing that life has existed since the begining of the universe, which is riduculous unless you are appealing to a creator. If you are appealing to a supernatural creator then all bets are off… the discussion will end because the evidence becomes meaningless. Why are you making this more complicated than it needs to be?

  114. BillyJoe7on 18 Dec 2012 at 10:55 pm

    sonic,

    I’m leaving abiogenesis and evolution to nybgrus, because you have enough on your plate there already.
    But now you demonstrate how you also misunderstand relativity and I can’t remain silent:

    ” Einstein figured out how it could be that the speed of light would measure the same regardless if you were moving towards the source or away from it. Solution? Space-time is malleable. ”

    Spacetime is not malleable. That was the whole point of Einstein’s exercise – to find something that was constant. And he found it. And he called it spacetime. Everything and everyone travels through spacetime at the same rate in all reference frames. Let that sink in, sonic. And, with that understanding comes the revelation that the constancy of the speed of light is not really special at all.
    I’ll explain it for you if you like.

    “When I walk past someone on the street, time passes at a different rate for me than it does for the person I’m passing. How can I not like that sort of result? I love it.”

    No, that is not correct. Time passes for you at the same rate as it passes for the person you are passing. But….but…if you were both able to observe each other’s watch, you would both observe that the other’s watch was slowed down relative to your own.
    You are talking about relativity and you don’t even to bring that concept of relativity into your story.

  115. sonicon 19 Dec 2012 at 2:25 am

    nybgrus-
    Question re ‘random’

    All three kinds of real non-randomness we have considered are powerless to move evolution in the direction of adaptive improvement as opposed to any other (functionally) ‘random’ direction.”
    is not the same as
    Random with respect to what nucleotide sequence actually emerges.
    It is the same as–
    Random with respect to fitness is also a reasonable statement.

    “the direction of adaptive improvement” is a paraphrase of ‘improved fitness’ (which is a paraphrase of increased reproduction).

    I don’t see how that would imply what you are saying about nucleotide sequence.

    Take the example of the entire genetic code doubling. We know this occurs. In what way is that random to the sequence that emerges?

    BTW- your link to the book review was exactly what I said you would find. Even the people who hate the book, the man, the whole creationist thing have nothing bad to say about the way the origin of life stuff is handled.
    The review you linked to didn’t mention it at all.
    Now go read what Nagle wrote about it. I’m advocating a rounding of the education here :-)

    I’m learning some interesting things–

  116. sonicon 19 Dec 2012 at 3:30 am

    ccbowers-
    I think you have a bit of a false dilemma. It is possible for life to exist as an irreducible without there being a creator in the usual sense of the word.
    The two ideas are often linked, but they are not the same idea.

    Let’s see if we can simplify–
    I can imagine that the experiment that shows ‘all life comes from life’ is meaningful and that the only way we know that life can begin is in fact the only way- and the implication that there is something irreducible about life is true. I know- I have a wild imagination, right?
    And I put that possibility as one of three on a list that I think might end up being correct.

    I noted that it wasn’t necessarily my favorite choice, all though clearly I have not ruled this out as a possibility.
    Apparently that makes me a creationist. But I’ve come to this conclusion before over this issue.
    Yeah, I said I wouldn’t close the door- scientists aren’t really that way- oh, wait… Yea, that’s why I think the quote that started this whole mess is more accurate than anyone was willing to admit.
    There you go… :-)

    I’m not exactly sure here– is it that you can’t imagine that there is something irreducible about life, is it that you refuse to, you’ve all ready concluded strongly there isn’t and it is now impossible to imagine–
    I’m wondering what your relationship to this idea is.
    Seriously- I’d like to know.

  117. BillyJoe7on 19 Dec 2012 at 6:01 am

    Just a suggestion to those responding to sonic…

    As informative as they have been, I think it is time to stop posting long comments. It just gives sonic too much wiggle room. I think you need to ask him specific and pointed questions and not let him waffle on and on so as to avoid answering those questions. And ignore any further comments that he makes unless and until he answers those questions. Otherwise this thread is going to descend into gibberish (if it hasn’t already, judging by his last two comments). Oh, and refuse to let him answer with yet another link or quotation. We want to know what he thinks, not what the thinks someone else thinks.

    …anyway, just a suggestion.

    (It seems to me that sonic spends his whole time giving everything an airing without actually agreeing with anything. That way he doesn’t have to defend anything he brings up. And that way he can force everyone else to defend their position. In return, he can simply throw up a counterview by someone who he thinks is worth listening to simply because he has that counterview.)

  118. ccbowerson 19 Dec 2012 at 9:24 am

    “I think you have a bit of a false dilemma.”

    No, its a true dilemma, and you haven’t demonstrated that it isn’t. My previous comment still stands unexamined by you. Your supposed 3 options still boil down to abiogenesis or creator, but you have created subcategories that do not add anything to this discussion. If life did not always exist, it either came from nonlife or a creator. Where again is the 3rd option?

    “I’m not exactly sure here– is it that you can’t imagine that there is something irreducible about life, is it that you refuse to, you’ve all ready concluded strongly there isn’t and it is now impossible to imagine. I’m wondering what your relationship to this idea is.”

    Yeah, yeah. The implication here is that I am not open minded enough to understand. I am just following the logic of the situation, and you keep wanting to cloud the discussion with irrelevant details. It is not that complicated, but you keep adding complication in order to wedge-in ideas that you are attached to.

    “It just gives sonic too much wiggle room. I think you need to ask him specific and pointed questions and not let him waffle on and on so as to avoid answering those questions.”

    I think that is what I have been doing.

  119. nybgruson 19 Dec 2012 at 11:42 am

    fair point re: wiggle room BJ.

    Sonic, everything ccbowers has been saying is spot on.

    For my brief points:

    All three kinds of real non-randomness we have considered are powerless to move evolution in the direction of adaptive improvement as opposed to any other (functionally) ‘random’ direction.”
    is not the same as
    Random with respect to what nucleotide sequence actually emerges.
    It is the same as–
    Random with respect to fitness is also a reasonable statement.

    Random with respect to nucleotide sequence and random with respect to fitness are nested concepts. If the mutation is not random with respect to fitness it cannot be random with respect to nucleotide sequence. The converse is not necessarily true. A non-random nucleotide sequence can be random with respect to fitness, but it most likely wouldn’t be.

    Think about it – if the sequence arising is non-random, then it will be consistently neutral, negative, or positive since the sequence is the same in all cases. Thus it will no longer be random with respect to fitness. The only escape from this is if you posit that the sequence is non-random but the placement in the genome is random. Only then would it be random with respect to fitness still.

    But, we have evidence that this is not the case. The nucleotide sequence that emerges from all mutation events – whether directed at hot spots or induced in hypermutable regions or horizontal gene transfer by transduction or transfection – are random.

    You still haven’t addressed the fact that horizontal gene transfer is random, and not a consistent transfer of gene products wholesale. Until you do, I will not continue the conversation.

    Take the example of the entire genetic code doubling. We know this occurs. In what way is that random to the sequence that emerges?

    Irrelevant example. It has nothing to do with the conversation at hand. Duplication of genes is a way to take selective pressure off of a gene and allow one copy to mutate randomly and thus evolve new functionality.

  120. nybgruson 19 Dec 2012 at 11:56 am

    I’ll add that the characterization that sonic never actually posits his own views and merely keeps tossing up whatever contrarian viewpoint he can find in a link is true. Note that he argued that horizontal gene transfer is absolutely not random:

    Not location, not timing (they occur more frequently under stress) and the exchanges tend to be of genes- whole cloth, not random sequences of DNA.

    -12/17/12 @15:22

    Yes, they are random. That point just suddenly got dropped without any further discussion on your part sonic. It is a significant point that directly undermines your position.

    Next we have the decay of DNA issue where sonic initially called my reference a non-sequiter and then was forced to admit:

    yes, DNA degrades in the cell while the cell is alive. And it decays after the cell dies.
    No doubt.

    -12/18/12 @ 02:20

    And that is it. Yet another point that directly undermines your position, but no further discussion, just falls off the radar and continue on with the same commentary as if those two points were never made.

    These points specifically demonstrate how random mutation – in every sense of the word – is always present in all genomes. Even non-random mutations like conjugation, transduction, transfection, somatic hypermutability, and “hot spots” are still not only higher order processes originating from random mutations leading to the development of the necessary proteins and signal cascades, but in actuality are still random themselves!.

    So fine, sonic, you aren’t a creationist. You are just someone who doesn’t seem to understand or care to understand important points which undermine your position, which seems to be specifically a serious bugaboo about “random.”

  121. sonicon 19 Dec 2012 at 4:51 pm

    ccbowers-
    What I have suggested as a third option is the idea that the problem isn’t even being asked the right way or seen in the proper way–
    Example-
    Is light a wave or a particle?– seems like a dilemma given the evidence.
    Turns out we just weren’t asking the question the right way. Who would have guessed?

    I’m not sure the same isn’t true here. That’s all. Not complicated.

    So I give 3 options-
    1. abiogenesis
    2. we haven’t even seen the question in the right way yet.
    3. life is irreducible (note this doesn’t mean there is ‘god the creator’) and is the result of a force not currently recognized in science (again-not necessarily god).

    So I could try to leave god out of option three- there could be a ‘life force’ or some such thing that hasn’t been seen as of yet– but option 3 does include god and creation in my mind. I’m not trying to hide that.

    These options come about as I attempt to accommodate the possibility that what we know from experiment about how every known life that has come into being is in fact how every life has ever come into being.
    That is possible- right?

    Here is a link to the speech given by Huxley (the person who coined the term ‘abiogenesis’) where he discusses ‘biogenesis’ and the evidences for it.
    http://aleph0.clarku.edu/huxley/CE8/B-Ab.html

    “Thus the evidence, direct and indirect, in favour of Biogenesis for all known forms of life must, I think, be admitted to be of great weight…
    But though I cannot express this conviction of mine too strongly, I must carefully guard myself against the supposition that I intend to suggest that no such thing as Abiogenesis ever has taken [256] place in the past, or ever will take place in the future…
    but I beg you once more to recollect that I have no right to call my opinion anything but an act of philosophical faith…”

    I link so you can read the part I cut out. It goes over the reasons for his faith and why he doesn’t think this experimental evidence is the last word. I agree with everything he says about that– I cut it to save space. (It is a form of ‘cherry-picking’ and I would prefer if you read the whole thing. That’s why the link).

    Anyway–
    I have absolutely no problem with this. I am aware that much evidence has accumulated since then as well. I have looked into the various attempts and theories regarding the ‘evolution of living protoplasm from not living matter’. I understand why someone would think it possible for this to occur.

    With that said– I haven’t seen the evidence that takes my lack of faith to the place his faith took him immediately.

    OK?

  122. sonicon 19 Dec 2012 at 4:57 pm

    nybgrus-
    regarding gene transfer–
    you are correct, I made a mistake–

    What I should have said is: Genetic material can pass between cells in times of stress and that this sometimes leads to an acquisition of genetic material that adds in the survival of the organisms involved in the transfers.
    (Horizontal gene transfer is really horizontal genetic material transfer– I know– I really did make a mistake here).

    Thank-you for bringing it to my attention.

    Your point about DNA decay is given to you. If you want I can state this – random mutations most definately occur. There is no question about that and I am sorry if you thought I was trying to assert that no mutation at any time is random.
    That is obviously wrong.
    RANDOM MUTATIONS DO IN FACT OCCUR.
    OK?

    The question is- are all mutations random as defined by evolutionary theory which states “random mutations”?

    In order to have a reasonable discussion about that, we need to determine what the word ‘random’ is referring to in this case.
    We had agreed to consider the same reference- one I think does an excellent job of delineating the history and usages of the term.
    From the reference I get that ‘random’ means ‘random with respect to fitness’ is the consensus view as to what the word refers to in the context of evolution.
    Am I mistaken about the reference? Is there one you would prefer to use that suggests otherwise?

    Anyway- if you want to go with the definition that random in the case of evolutionary biology refers to ‘random with respect to fitness’ then we can carry on with that.

    otherwise-
    The question I asked is– when the entire genome doubles– not just a single gene double, but the entire genome doubles– how is that mutation random in respect to the sequence that emerges?
    A reasonable question given that you claim all mutations are random with respect to what nucleotide sequence actually emerges.
    I believe a clear explanation of that particular case would clarify considerably.

    Please feel free to point out if I make an error like the one above. I really don’t want to say things that are wrong– I don’t mind controversial and I realize that these things (controversial and wrong) overlap.
    So if you will point to an error and give the reference I believe I can correct as I have done here.

  123. nybgruson 19 Dec 2012 at 5:31 pm

    RANDOM MUTATIONS DO IN FACT OCCUR.

    Good. Then our discussion is essentially done.

    Note that the modern evolutionay synthesis does not state:

    “Only random mutations in every respect coupled with selection drive evolution.”

    The modern synthesis takes into account non-random (with respect to something specific) mutations and not only incorporates but explains them handily. Furthermore, the mutations even though non-random in certain respects (i.e. temporality or locality) are still random in the specific nucleotide sequences that arise from each mutagenic episode (obviously within the constraints of reality – you won’t get any completely novel nucleotides beyond the standard AGTCU).

    Using the frame of reference that all mutations are random with respect to fitness. Is, in my opinion, a valid and reasonably complete statement.

    when the entire genome doubles– not just a single gene double, but the entire genome doubles– how is that mutation random in respect to the sequence that emerges?

    The context here is crucial. In the case of normal cellular division it is neither random nor part of the evolutionary process, so the question becomes a non-sequiter.

    If you mean doubling of whole genomes as in the case of plants where this occurs, then the random aspect is both when it occurs as well as how much of the genome is actually duplicated. In most cases there is a lost of fidelity and/or incomplete doubling. There is also a degree of randomness as to whether that doubling is actually passed on to offspring or not. So at heart, despite the notion that the whole genome is being copied (and thus your insinuation that this is not random since every copy can be predicted), there is a significant amount of random variation in when, how much, with what fidelity, and whether it is passed on or not.

    A reasonable question given that you claim all mutations are random with respect to what nucleotide sequence actually emerges.

    But the doubling event itself is not a mutation. It is a doubling event. It is events after the doubling (or in the lack of fidelity during the doubling which is random) that are the actual mutation. Thus, my stance that all mutations are random with respect to the specific nucleotide sequence that emerges is still valid. In no literature I have seen does an extra copy of DNA = mutation. Mutation is always defined as “a change in the nucleotide sequence” so by definition just a doubling event is not a mutation (though, as I said, mutations do occur during doubling events).

  124. nybgruson 19 Dec 2012 at 5:52 pm

    So I give 3 options-
    1. abiogenesis
    2. we haven’t even seen the question in the right way yet.
    3. life is irreducible (note this doesn’t mean there is ‘god the creator’) and is the result of a force not currently recognized in science (again-not necessarily god).

    Number 1 is what we have the most evidence and prior plausibility for.

    Number 2 is possible indeed, but is more or less pointless to discuss unless you actually have some way of framing the question that alters our outlook on #1 (which you haven’t presented yet nor have I heard – not that I am an expert in abiogenesis).

    Number 3 doesn’t merit consideration in the conversation. Whether or not life is irreducible does not prohibit #1 or #2 (or any other theory). Irreducibility in and of itself is not a defining quality that can dictate a theorem (as evidence by how abysmally poorly Behe et al have been doing). Furthermore, we know enough about the forces that exist in nature to have a reasonably solid stance that no completely novel force is suddenly going to be discovered that is the lynchpin for the discussion of life. In other words, for that hypothesis to have merit, we would have to imagine two absolutely identical systems where one has this “force” and the other not and one is alive and the other isn’t. This is vitalism couched in sciencey words and has very little merit.

    These options come about as I attempt to accommodate the possibility that what we know from experiment about how every known life that has come into being is in fact how every life has ever come into being.

    This is another way of saying “life begets life” which we know to be true, but not exclusively true.

    Here is a link to the speech given by Huxley

    Interesting that you cite him saying exactly what I have been trying to say – that life begets life but that this does not mean abiogenesis didn’t or won’t happen. All it really means, coupled with what we know, is that complex life won’t arise from abiogenesis; in other words a cat won’t spontaneously assemble from dirt.

    The point is that is was, almost certainly, a slow progression from simpler molecules to more complex interactions. There are multiple plausible mechanisms, some with more plausibility than others, and that is about all we have.

    Anything else, particularly “other” ideas, are pure speculation and nothing more.

  125. sonicon 20 Dec 2012 at 12:46 am

    ccbowers, et. al—
    Let me apologize for being slow here.
    I just got it myself– it’s been sometime coming. Thank-you for helping me get here.

    The question being begged by abiogenesis is “Can life come from inanimate matter?”
    The options–

    1) Yes, it can, or
    2) No, Life is a gift from god, or
    3) No life is life– spirit whatever you want to call it, not matter.

    Well, those are the main options that people I know consider and I’m personally willing for any of the above to be true, so

    One looks to the experimental evidence to help determine the answer.
    “Life comes from life,” is the result of the experiment that most closely tests the hypothesis.
    This seems to indicate either 2 or 3 is likely. Certainly if 3 is true, then the experiment would turn out that way, and the experiment might turn out that way if 2 were true and 1 predicts something else pretty much.

    But this doesn’t disprove 1. No, many people who have studied the issue have decided that life does come from inanimate matter. They have good reasons for this determination too.
    Yet, when asked to demonstrate the claim, they only promise that it will be forth coming.
    The claim remains unsubstantiated.

    This does not disprove 1. In fact, I’m not sure anything could.

    If you tell me 2 and/or 3 is out of bounds, I’ll understand.
    And I hope you’ll understand what I mean by begging the question.
    Sorry it took so long to get here…

  126. sonicon 20 Dec 2012 at 12:53 am

    nybrus-
    Yes, I’ve always agreed that random mutations occur.
    And I’m quite sure that you can find an aspect of any mutation that at least appears random if you will decide what it is random with respect to in an ad hoc manner.

    But I don’t think that’s the way the theory works.

    I think the theory claims the mutations are random with respect to fitness.
    I have supplied three references that I think back up my statement about the way the word is used in evolutionary science. You have not supplied me with a single reference that supports your claim about the nucleotide sequence despite my request to get a reference we can agree on to the meaning of the word.

    As ‘what is it random in regards to’ is a critical question when one claims randomness, I really do think it would be best to clear that up.
    Reference please?

    I believe a gene doubling is called an ‘amplification’ mutation.
    And I think ‘amplification mutations’ include any duplication of a region of DNA that includes a gene– all the way up to and including the entire chromosome.
    Just to pick a nit or two.

    Yes, Huxley is saying some of what you are saying, there is largely agreement, but there is at least one big difference.
    He understands his thinking abiogenesis is true is a matter of ‘philosophic faith’.
    You claim there is no alternative.

    I think Huxley is right on this one, my friend.
    What can I say?

  127. BillyJoe7on 20 Dec 2012 at 5:12 am

    sonic,

    “The question being begged by abiogenesis is “Can life come from inanimate matter?”
    The options–

    1) Yes, it can, or
    2) No, Life is a gift from the gods, or
    3) No life is life– spirit whatever you want to call it, not matter.”

    The question being begged by #2 is “Do gods exist?”
    The question being begged by #3 is “Do spirits exist?”

    “One looks to the experimental evidence to help determine the answer.”

    There is no evidence in support of the existence of gods.
    There is no evidence in support of the existence of spirits.

    “many people who have studied the issue have decided that life does come from inanimate matter. They have good reasons for this determination too.
    Yet, when asked to demonstrate the claim, they only promise that it will be forth coming.”

    I will give YOU three options, sonic:

    1) You are disingenuous.
    2) You are a liar.
    3) You are an idiot.

  128. BillyJoe7on 20 Dec 2012 at 5:33 am

    sonic,

    “I’m quite sure that you can find an aspect of any mutation that at least appears random”
    I am quite sure that you can find an aspect of any mutation that at least appears non-random.

    “if you will decide what it is random with respect to in an ad hoc manner.”
    if you decide on the definition of random in an ad hoc manner.

    “But I don’t think that’s the way the theory works.”
    But that’s not the way the theory works.

    “I believe a gene doubling is called an ‘amplification’ mutation.”
    I believe gene doubling is called gene amplification.

    “I think the theory claims the mutations are random with respect to fitness (ie nucleotide sequence).”
    Correct.

    “abiogenesis…there is no alternative.”
    Correct.

  129. ccbowerson 20 Dec 2012 at 10:39 am

    “The question being begged by abiogenesis is “Can life come from inanimate matter?”
    The options–
    1) Yes, it can, or
    2) No, Life is a gift from god, or
    3) No life is life– spirit whatever you want to call it, not matter.”

    You are reframing the question in a way that does not make sense. We already have life (this is why we are looking to mechanisms), so to wonder if life can come from nonlife is only a question for people who have an ideological committment to a creator. Fine if you want that, but it is not a scientific idea.

    As I said before: “If life did not always exist, it either came from nonlife or a creator. Where again is the 3rd option?” Your option #3 does not even address the question, and is really an alternate version of #2 because it still requires a creator of some kind. The end.

    There is no progress here because of your obfuscation. Your only “out” is an appeal to new science, for which there is no reason to believe is necessary. This can always be done for any quesion, but there is no compelling reason to do so, no evidence for, and as a result should be cut out with Occam’s razor.

  130. ccbowerson 20 Dec 2012 at 10:44 am

    …actually an appeal to new science still would be abiogenesis, but would just point to a different mechanism. So you are still down to 2 options. Sonic, if you had a legit point it should not be so hard to communicate it. I have listened for several days. I guess you don’t.

  131. nybgruson 20 Dec 2012 at 11:48 am

    Sonic:

    I believe a gene doubling is called an ‘amplification’ mutation.
    And I think ‘amplification mutations’ include any duplication of a region of DNA that includes a gene– all the way up to and including the entire chromosome.

    We conclude that amplification and mutation are independent outcomes of adaptive genetic change.
    -PLoS Biology

    In other words it is a short hand way of referring to the package of amplification and mutation. The amplification itself is not technically a mutation. A simple high fidelity gene or genome duplication is not considered a mutation event. If the doubling is deleterious or lethal (like say an autosomal trisomy in humans which isn’t 13, 18, or 21) then the organism dies and the process which led to the random duplication event is selected against. If it is neutral or beneficial, then one copy of the gene becomes free from selection pressure and can then have random mutations act on it for a chance at novel function.

    Since independent mutation events are very unlikely to hit the exact same nucleotide site, each observed mutation should be found in only a single mutant strain. By contrast, if different strains share common ancestry subsequent to the MRCA (i.e. are not independent), by definition they will share some fraction of their mutations. Thus, detection of the exact same mutations in two or more strains constitutes a signature of non-independence.
    -PloS One

    I’ll make a separate post with 3 more references for you to read on about mutation and how it works.

    The nucleotide sequence of a mutation is always random. Now obviously, if you are talking about a point mutation of a single nucleotide (SNP) then you have in essence a 25% chance that the random mutation will be the same in two independent mutagenic events because there are only 4 nucleotides to choose from. That is a first approximation of course, since tautomers of nucleotides can be substituted and uracil can be erroneously inserted instead of thymine, but you get the idea.

    He understands his thinking abiogenesis is true is a matter of ‘philosophic faith’.
    You claim there is no alternative.

    I think Huxley is right on this one, my friend.
    What can I say?

    Do you really think Huxley would say the same with what we now know (you know, considering he died 117 years ago, before molecular science even existed)? Do you think his religious beliefs may have played a role in this? And lastly, don’t you think it funny that you have to go all the way back to Huxley to try and grasp at a straw in the abiogenesis conversation? Can’t you find someone more recent, preferably not a devout theist?

    I mean really, “I think [a man who died 117 years ago] is right on [the topic of molecular interactions that didn't exist as a thought in his time]?”

    Well, those are the main options that people I know consider and I’m personally willing for any of the above to be true, so

    One looks to the experimental evidence to help determine the answer.
    “Life comes from life,” is the result of the experiment that most closely tests the hypothesis.
    This seems to indicate either 2 or 3 is likely.

    No, it does not! That is NOT the way science works, sonic. The evidence demonstrates that life begets life and nothing else. It does not speak on abiogenesis at all. Seriously, it doesn’t. This is why we are having such a hard time with the conversation.

    You are making the argument that because all the swans you have ever seen are white, that all swans must be white and only white. You are not even considering what a single black swan would actually do to your argument.

    Just because life begets life doesn’t mean only life begets life, it is just the most common way. One single instance of abiogenesis in all of the universe in 13 billion years completely shatters your thesis. Never mind the evidence and a priori plausibilities we have in place to demonstrate validity to the thought of abiogenesis.

    But this doesn’t disprove 1. No, many people who have studied the issue have decided that life does come from inanimate matter. They have good reasons for this determination too.
    Yet, when asked to demonstrate the claim, they only promise that it will be forth coming.
    The claim remains unsubstantiated.

    Just look at the wikipedia article on the topic. It lists all the experiments and thoughts on it. I’ve said it before, and I’ll say it again: we do not have conclusive empirical proof of a specific pathway leading to “life” but we do have numerous experiments demonstrating that all the complex organic components of life can and do form spontaneously from simpler inorganic molecules in an open thermodynamic system. We have proof that these can also spontaneously assemble and replicate. We have no evidence that any physical laws or fundamental forces we have discovered would preclude this. We have evidence that there was ample time for this to happen gradually. And of course, we have evidence that there is life here and at one time there wasn’t. While this doesn’t “prove” abiogenesis happened, it demonstrated so many pathways and so much plausibility that it would be perverse to think something else happened. Sometimes perverse ideas pan out (like microbes living in the lining of your stomach causing ulcers) but most of the time they don’t. And until you (or someone) comes up with a perverse idea that explains things better than abiogenesis and doesn’t include magic (godidit) any reasonable person should provisionally accept abiogenesis as the best hypothesis with the vast preponderance of evidence supporting it. In other words, no need to wait for more evidence – we have plenty enough to accept the hypothesis as reasonable scientists and pursue specific mechanisms in our research. In other words, we aren’t doing research to prove abiogenesis, we are doing research to determine the possible and most likely ways in which it did happen on the reasonable assumption that it has.

  132. nybgruson 20 Dec 2012 at 11:49 am

    The molecular basis of mutation:

    http://www.ncbi.nlm.nih.gov/books/NBK21322/

    Chapter 14: Mutation, repair and recombination:

    http://www.ncbi.nlm.nih.gov/books/NBK21114/

  133. nybgruson 20 Dec 2012 at 11:50 am

    Gene mutation, Eastern Washington University:

    http://www.biology.ewu.edu/aHerr/Genetics/Bio310/Pages/ch13pges/ch13note.html

    Wikipedia abiogenesis:

    http://en.wikipedia.org/wiki/Abiogenesis#Current_models

  134. sonicon 20 Dec 2012 at 2:49 pm

    nybrgus-
    Until I see your next postings– oh, I see them now- thanks–

    First off–
    AHA– yes, you can claim that mutations are independent- and that is something I can completely understand and I think it is at the heart of the earlier statements I was having trouble understanding– right? (Oh, this is good!!)
    If you want to apply the mathematics that is usually applied (statistics and probability aka Fisher et al) then this is an important assumption that will allow for the math to be valid.
    The determination of this is difficult in reality and I believe this is part of the debate about how to interpret the results of certain experiments.
    But I understand what you are saying with this and I believe this takes care of an earlier misunderstanding. Yippee!

    You say an amplification is not a mutation and your reference is an article that distinguishes between ‘point mutation’ and ‘amplification’,”

    I say that amplification is a form of mutation and my reference is the ‘biology direct’ dictionary that defines the term –
    “Mutation
    Definition (genetics)
    (1) A permanent, heritable change in the nucleotide sequence in a gene or a chromosome; the process in which such a change occurs in a gene or in a chromosome.

    Further we have this (from the biology online dictionary)-
    Duplication mutation
    Definition
    A type of mutation in which a portion of a genetic material or a chromosome is duplicated or replicated, resulting in multiple copies of that region.
    Supplement-
    Duplication results from an unequal crossing-over between misaligned homologous chromosomes during meiosis. It may involve a replication of a portion of DNA, or of an entire chromosome.”

    Note- in the synonyms section ‘gene amplification’ is listed specifically as a synonym for ‘duplication mutation’

    I really do believe if we can get the words right the disagreements are about very specific things and there is actually a great deal of agreement. (I was in the math department– terms are defined exactly, I realize that isn’t always possible, but I’m seriously thinking f we clear up the words the disagreements and agreement will become obvious and the agreements will be big and the disagreements clarified. That’s what I’m shooting for with all the ‘word play’.
    Understanding. OK?

    No, I don’t have to go anywhere on abiogenesis.
    I can point to the actual experimental evidence.
    It is you that denies the evidence by ‘logical’ argument.

    And I do know what a black swan would do to ‘my position’– falsify it.
    And what would falsify yours, I wonder?
    Please stop hassling me because ‘my position’ is falsifiable and yours isn’t.
    It makes you look a bit foolish when you think about it.
    In fact, stop calling the actual experimental evidence ‘my position’. It isn’t my position- it is the experimental evidence for crying out loud.

    Oh, and I’m going to quote the experiment that shows how life arises and you are going to say it has nothing to do with how life arises.
    Enough.
    Imagine if the tables were turned and the results showed that life comes from chemistry.
    If I then said– but that doesn’t show that the first one wasn’t from god– your experiment is inconclusive and in fact irrelevant to the question– well you would know what was behind that, wouldn’t you?
    In the same way I know what is behind your claim that the experimental evidence that shows how life arises is irrelevant to the question as to how life arises.
    OK?

    And Huxley aka Darwin’s Bulldog, invented the term ‘agnostic’ for his religious position. And had this to say about his position as well-
    “Nevertheless I know that I am, in spite of myself, exactly what the Christian would call, and, so far as I can see, is justified in calling, atheist and infidel…”
    http://en.wikipedia.org/wiki/Thomas_Henry_Huxley_and_agnosticism#Thomas_Henry_Huxley

    I have seen it done a few times– the dismissal of a position based on the person who is making the statements religious beliefs.
    I’m trying to understand how this works–

    Do you reject ‘classical physics’ on the same grounds- Newton’s beliefs?
    If not, why not?
    Do you reject the efficacy of vaccine based on the beliefs of Jenner and Pasteur?
    If not, why not?
    Do you reject ‘Planck’s constant’ due to Planck’s religious views?
    How about Maxwell and electrodynamics?

    How do you determine when the ad hominem applies? is the question. It seems arbitrary.
    Probably like it looks arbitrary to some that i would ask for a demonstration of a claim.
    You know– such an arbitrary thing to do… :-)

  135. BillyJoe7on 20 Dec 2012 at 4:08 pm

    Ah we’ll, I tried to warn you, nybgrus.
    With his content-less posts he has probed your content-full posts and has found a piece of string with which he is now attempting to hang you.
    So funny and so sad. And so sonic.

  136. nybgruson 20 Dec 2012 at 5:38 pm

    We all leave strings behind, BJ. Nobody is perfect except god and we know it doesn’t exist….

    Thankfully my strings are pretty short and thin, so I doubt I’ll endure much neck trauma as a result.

    I say that amplification is a form of mutation and my reference is the ‘biology direct’ dictionary that defines the term –

    Very well, you have used semantics to find the single exception to the “all mutations result in random nucleotide sequences.” Or did you?

    The duplication event itself is random, that much is established.

    How about what is duplicated? Well lets see:

    Duplication results from an unequal crossing-over between misaligned homologous chromosomes during meiosis. It may involve a replication of a portion of DNA, or of an entire chromosome

    Hmm… seems to me that the overall sequence of a duplication event would still be random. You can say “the sequence will be almost entirely like a portion of the genome from 1 base pair to the entirety of the genome” and that is about as specific as you can get. Precisely which part of the genome is duplicated is random. Whether it is 1% or 100% of the genome is random. Where the 1% starts and ends is random. Even the fidelity of 100% duplication is not perfect, which means the duplicated nucleotide sequence cannot be the same as the original which means… the resulting nucleotide sequence is random.

    Lets do this as a simple test of the premise. Lets say I give you the entire Drosophila genome.

    Now, first step – predict when a duplication event will occur. Oh right, that’s random.

    Next step: let’s say a duplication event has occurred. Predict how much of the genome is duplicated. Oh, that’s random too.

    OK, next step: A duplication event has occurred, it comprises 10% of the fly genome. Predict if it is heritable or not. Oh right, that’s random too.

    Ok fine, next step: Duplication event has occurred, it comprises 10% of the genome, and it is heritable. That means that the fly offspring will get 110% of the DNA it normally would. Predict which 10% was duplicated. Oh, random too.

    OK… duplication has occured, 10% of genome, heritable, and it is on the the R arm of chromosome 2. Predict which specific 10% was duplicated? Oh.. random again.

    OK… duplication has occurred, but this time 100% of the genome, it is heritable. Predict the exact nucleotide sequence of all 279megabases. Oh, right, you can’t even do that because there is still random error in duplication due to less than 100% fidelity in transcription processes.

    What I am getting at, sonic, is that all DNA copying or creation of any kind generates a random nucleotide sequence. You cannot predict the precise nucleotide sequence, or even what errors will be inserted where.

    So no matter how you slice it, it is still random and the nucleotide sequence generated at the end of any mutation event, no matter how broad you decide to define that is still at heart, and usually on multiple levels random.

    And what would falsify yours, I wonder?
    Please stop hassling me because ‘my position’ is falsifiable and yours isn’t.

    My position is falsifiable – evidence of any other mechanism for the instantiation of life that isn’t abiogenesis would falsify it.

    I am hassling you because the “other” hypothesis you have been positing make no sense at a fundamental level. Either you are reiterating abiogenesis in different words or you are invoking some magical force or some non-magical force we have no reason to believe exists. In other words, you haven’t been able to formulate any cogent thought beyond “what about something other than abiogenesis?” without invoking magic or really, really far fetched ideas. And you complain that I am hassling you for such poor hypothesis generation?

    Oh, and I’m going to quote the experiment that shows how life arises and you are going to say it has nothing to do with how life arises.
    Enough.

    Now I’ve had enough. That is such a ridiculously gross misrepresentation of my position that I am seriously just about to be done with you for now… and probably will because I leave town to have holidays with my family in less than two days anyways.

    I never said that it has nothing to do with life. In fact, I clearly stated:

    The evidence demonstrates that life begets life and nothing else. It does not speak on abiogenesis at all…Just because life begets life doesn’t mean only life begets life, it is just the most common way.

    See there? I even said it is the most common way. But the experimental data you are so desperately clining to doesn’t explain the origin of life. It only explains how life continues and propagates and becomes more complex. That is why your only talking point is irrelevant because it doesn’t address the concept of abiogenesis or the origin of life.

    How do you determine when the ad hominem applies? is the question. It seems arbitrary

    Nothing arbitrary at all. It applies when it is material to the discussion. I never tried to discredit Huxley based on his theological beliefs. I was positing that his beliefs and the time period in which he lived would make his word choice in terms of “philosophical faith” different in context. Furthermore, claiming that his contemporary Christians would call him an atheist doesn’t mean anything. Ken Ham thinks Pat Robertson isn’t a True Christian (™) and that his denies the true word of god. Is Pat Robertson an atheist?

    In any event it was all a tangential side point. You still haven’t addressed how the only leeway you can seem to get is by citing someone who agreed abiogenesis was likely and possible, though not proven, and died 117 years ago!. How about a legitimate scientist today?

    Don’t forget – we aren’t debating the specific mechanisms of abiogenesis. We are debating the concept as a whole. I’ve already said numerous times there is no clearcut evidence which mechanism(s) actually happened, but we have enough evidence that it did and multiple lines of evidence pointing to the plausibility of gradual chemical evolution to life.

    You have absolutely nothing except a lack of evidence on which to try and build a theory of your own, which you can’t even articulate properly, and involves invoking undiscovered and unpredicted “forces.” So really, who has the weaker stance on this one?

    With that, I bid you (and all) adieu and very happy holidays. I will probably be much more quite on these fora until the New Year.

  137. sonicon 20 Dec 2012 at 10:45 pm

    nybgrus-
    If you read this on your return I hope we can move forward this way–

    How is the word ‘random’ used in evolutionary theory?

    If we can determine what the claim of ‘random’ is in evolutionary theory, then we can look and see if any of Shapiro’s experiments bring that into question.
    That is what I would like to determine.

    At this point it seems they do in a number of ways- but it all depends on what is meant exactly by the term ‘random’ in the phrase ‘random mutations’. Let’s get what is meant by ‘random’ and then see if Shapiro’s claims hold any water by comparing the experiments to the claim.
    OK?

  138. nybgruson 20 Dec 2012 at 11:54 pm

    Oh lord we’re back to this?

    There are non-random mutations. Never non-random in nucleotide sequence – at least not to my knowledge, not that I know anyone else knows, and certainly not in any of the major evolutionary pathways we know – but certainly quite non-random in other respects.

    Nobody is disputing this

    But at heart those mechanisms for selective non-random mutagenesis evolved from random mutation and selection, random mutation and selection is still a primary driver of evolution in large part via genetic drift, the nucleotide sequences that arise in non-random mutagenic events (like horizontal gene transfer, somatic hypermutability, “hot spots,” stress induced hypermutagenesis) are still random and then selected for in some way or another (this is how the immune system works), and while they do exert non-local controls, they still arise 100% of the genome and cannot exist without it.

    So nobody is questioning that these semi-non-random events occur. Shapiro’s mistake is that he thinks this deals a blow to the modern evolutionary synthesis. It does not. The modern synthesis easily takes into account these novel mutagenic pathways, they do not violate any principles of the synthesis, and they do not replace or otherwise undermine the modern synthesis.

    That’s it. Nothing more than that. He is doing good science – he is correct in his observations. He is not correct about the implications of his observations.

  139. BillyJoe7on 21 Dec 2012 at 6:07 am

    Mary, Mary, quite contrary,
    How does your garden grow?
    With sea shells, and cockle shells,
    And pretty maids all in a row.

    I think it’s high time we saw Shapiro’s pretty maids in action…

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