Dec 22 2010

Scientific Heresy

If ever there were an oxymoron it is this phrase: “scientific heresy.” I understand it may be used at times as a bit of poetic license,  a metaphor for a new and seemingly outrageous (but scientific) idea, but I despise it none-the-less. The phrase is more often used as a direct or implied criticism of science and scientists, and generates deliberate confusion.

The notion of heresy is – well, Wikipedia actually has a good summary:

Heresy is a controversial or novel change to a system of beliefs, especially a religion, that conflicts with established dogma. It is distinct from apostasy, which is the formal denunciation of one’s religion, principles or cause, and blasphemy, which is irreverence toward religion. The founder or leader of a heretical movement is called a heresiarch, while individuals who espouse heresy or commit heresy, are known as heretics.

Heresiology is the study of heresy.

Now, I’m no heresiologist, but it seems to me that the core of the notion of “heresy” is inexorably tied to the notion of dogma – a fixed set of beliefs promoted and sustained through authority. Dogma and heresy are anathema to science.

Science is not a set of beliefs (and therefore there can be no dogma), it is a set of methods for investigating the natural world, for understanding how it works, what has happened in the past, what is happening in the present, and what is likely to happen in the future. Science is based upon methodological naturalism – essentially that effects in nature must be explained with causes in nature. Magic is not allowed, for no other reason than the fact that magic is not amenable to scientific methodology.

This has been the accepted definition of science for a couple of centuries. Philosophers of science have hashed this out and picked over all the arguments pretty thoroughly. Most practicing scientists understand this.

Institutions of science certainly understand this. In fact, science is institutionalized change. Research is all about changing what we think we know about the universe. Static beliefs that are not amenable to change are of not much use to researchers.

What I often see, however, is people who are not scientists and do no regularly talk to scientists naively characterizing them based upon a negative cardboard stereotype  – perhaps based upon media cliche or the criticisms of anti-scientists.

If you have ever been in a room when a completely disruptive bit of new evidence is being presented, you will have seen scientists light up with excitement about the possibilities. Smashing our previously held conclusions makes scientists giggle like school girls. Sure, there will be appropriate skepticism too. And if the new evidence is crap, you may see only skepticism. But if its compelling, scientists start to drool over the research implications.

So it always amazes me when non-scientists assume that scientists get upset about new evidence. They need to stop thinking that movie scientists are real, and start reading, watching, or talking to real scientists.

Here is a comment from a recent Science Magazine article on the arsenic-based life hubbub:

I think all this criticism is very unfair, but it comes with the territory when you challenge held beliefs. Scientists can be so childish when you upset their status quo, it’s almost as if she committed heresy.

Well, all the criticism was not unfair. Much of it was very well-founded and highly technical. It remains to be seen if the new evidence for bacteria using arsenic in their DNA will stand up to further investigation. Criticism is the way in which we will find out – picking apart the results, replicating the research, and pursuing further implications and angles.

Scientists do not get upset when the status quo is upset – they hate the status quo. The status quo does not garner research grants, high-impact publications, and academic recognition. Disrupting the status quo does that.

Just expect to meet an appropriate level of skepticism when you try to break the so-called status quo. Most such attempts fail – because they are flawed and their conclusions wrong. How do we separate the few nuggets of real new information from the pile of crap – through harsh (but scientific) criticism.

The commenter is confusing being fair with being nice. The self-critical aspect of science is not nice. It’s brutal – necessarily so. But it is still fair and professional, just not politically correct.

This is one critical aspect of science that I feel the public needs to better appreciate. This is also a fun and dramatic aspect of science – real world mud fights where scientists go at each-other’s throats. The mass media needs to appreciate this real drama more so that they will rely on their hackneyed Hollywood cartoon of science less.

Real science is more interesting than this fiction of heresy vs dogma.

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164 responses so far

164 Responses to “Scientific Heresy”

  1. cwfongon 22 Dec 2010 at 12:00 pm

    Scientists, however, can often be dogmatic in their skepticism.

  2. ccbowerson 22 Dec 2010 at 12:00 pm

    Very good post on an important concept. One sentence stood out: “Most practicing scientists understand this.” I’m not sure that this is the case. You can be a very accomplished scientist without really understanding philosophy of science, and I think that this is often the case.

  3. ccbowerson 22 Dec 2010 at 12:06 pm

    “dogmatic in their skepticism.”

    A bit of equivocation there, as the use of “dogmatic” in this case is different than what “dogma” meant in this post.

  4. TimMillson 22 Dec 2010 at 12:09 pm

    Great post, Steve. Thanks!

  5. cwfongon 22 Dec 2010 at 1:20 pm

    cc didn’t get it that dogmatic is the flip side of heretical.

  6. banyanon 22 Dec 2010 at 1:47 pm

    Would it be scientific heresy to say that science should accommodate supernatural hypotheses? What if a “scientist” were to say of some phenomenon that naturalistic explanations have been unsuccessful and so a popular supernatural explanation should be provisionally accepted?

    I would say “that’s not science,” and for good reason, but does experimental naturalism count as dogma?

  7. Michael Meadonon 22 Dec 2010 at 2:02 pm

    “Scientists do not get upset when the status quo is upset – they hate the status quo.” <—- Well said. Well said indeed.

  8. petrucioon 22 Dec 2010 at 3:32 pm

    @banyan
    That would be a ‘hypothesis of the gap’ thinking, filled up with an argument ad populi. The scientific method if needed precisely to filter out such all too human misinterpretations.

    String theory is not experimental, but that doesn’t mean it’s scientific heresy. It does mean we have no current way of validating it.

  9. SARAon 22 Dec 2010 at 3:39 pm

    While I agree generally, its important to remember that Scientists are in fact human. And as humans often have an unconscious bias in a particular theory. They are also just as likely to pursue fame, acceptance and glory as the next human. That does not mean they will ignore all other data or that the process doesn’t work as a result. It means the reality of science and scientists is messy. And painting them into an pretty picture of idyllic science is all about process and they always thrill at the sound of accepted theories shattering like glass – is going to create an even greater problem with the media.
    Because when a scientist randomly acts human the media will paint them all as villains.

    We definitely need to educate the public and the media about the process, its necessity and its credibility. But we should not do so by praising it into some extraordinary pure and chaste process. We need to teach the public that life and science can be messy and often neither is quite as clear as they would prefer.

  10. Darrickon 22 Dec 2010 at 11:42 pm

    cwfong,

    cc is right. Your use of ‘dogmatic’ in your comment “Scientists, however, can often be dogmatic in their skepticism” isn’t the sort of ‘dogmatic’ Steven’s referring to in his article. In fact, Steven’s point was that words like ‘dogma’ and ‘heresy’ get bandied about in reference to science when – unless they’re being used metaphorically – they have absolutely nothing to do with science.

    Unless we have misread you, I’m pretty sure you don’t mean to say that scientists are often dogmatic in their skepticism in exactly the same way that priests are often dogmatic in their faith. Because that would be making the fallacy of equivocation, as cc pointed out.

  11. sonicon 23 Dec 2010 at 3:23 am

    This article articulates an ideal well. It seems that there is a further argument that the current actual practice of science conforms exactly to that ideal.
    But current practice diverges from the ideal.

    I would trust a scientist to operate from a ‘dogma free’ attitude. I would trust a priest with a child. In either case I could expect to be disappointed sometimes.

    Famous scientists claim that some who question their theory are ‘evil’. “The science is settled,” we are told. When I go to the science lane at the local bookstore, the word God appears in many titles.

    Is it possible to scream DOGMA any louder than that?

    Unfortunately these are the communications most received by the general public today.

  12. BillyJoe7on 23 Dec 2010 at 3:58 am

    cwfong,

    “Scientists, however, can often be dogmatic in their skepticism.”

    Scepticism means demanding evidence in support of any proposition before treating that proposition seriously. So, if you are saying that scientist are often dogmatic about requiring evidence, then the only criticism I can see is that scientist should always be dogmatic in demanding evidence.
    Of course, as ccbowers and Derrick have said, you’re probably just unintentionally (or, indeed, unintentionally) equivocating. Nothing new there. ;)

    “cc didn’t get it that dogmatic is the flip side of heretical.”

    Oh, yes, you are too clever for him by far. :)

  13. BillyJoe7on 23 Dec 2010 at 4:12 am

    banyan,

    “Would it be scientific heresy to say that science should accommodate supernatural hypotheses?”

    It’s not scientific heresy, it’s just not science.
    The method of science, as Steven Novella says, is finding natural causes for natural effects.

    “What if a scientist were to say of some phenomenon that naturalistic explanations have been unsuccessful and so a popular supernatural explanation should be provisionally accepted?”

    Then he is not using the scientific method – finding natural casues for natural effects. And scientists do not give up looking just because the search has been unsuccessful so far. The precession of the perihelion of mercury could not be explained till Einstein came along.

    “…so a popular supernatural explanation should be provisionally accepted?”

    Science does not have default positions and certainly not supernatural default positions. Science goes where the evidence leads.

  14. BillyJoe7on 23 Dec 2010 at 4:17 am

    sonic,

    “Famous scientists claim that some who question their theory are ‘evil’. “The science is settled,” we are told.”

    Can you give an example of a famous scientist claiming that some who question their theory are ‘evil’ and that “the science is settled”?

  15. Steven Novellaon 23 Dec 2010 at 7:27 am

    Of course some scientists fall short of the ideal. Scientists are human. And many of the things that pass for popular science are terrible examples of science – that’s partly why they are popular, they are sensational.

    But it is useful and even necessary to define the ideal. There is non-science, and there is bad science, but there is no such thing as “scientific heresy.”

  16. ccbowerson 23 Dec 2010 at 10:14 am

    “But it is useful and even necessary to define the ideal”

    Sometimes you talk about the ideal as if it the same as the reality, and this may be problematic. For those of us who understand the process- this is fine, but for those who don’t understand the process of science (or are already “skeptical” of science) this can be counterproductive. They will see that you are painting a picture that is different than what they see and they will tune you out.

  17. sonicon 23 Dec 2010 at 2:07 pm

    BillyJoe7-
    ‘evil’ should be ‘wicked’. (Richard Dawkins)
    My error–

  18. BillyJoe7on 23 Dec 2010 at 2:21 pm

    ccbowers,

    “Sometimes you talk about the ideal as if it the same as the reality, and this may be problematic.”

    The problem is that sometimes the reality is the ideal but doesn’t look that way to the general public.

    For example, the following quote form Steven Novella’s article would look, to the general public, like an illustration of how scientists outright reject challenges to their “settled” theories:

    “Just expect to meet an appropriate level of skepticism when you try to break the so-called status quo. Most such attempts fail – because they are flawed and their conclusions wrong. How do we separate the few nuggets of real new information from the pile of crap – through harsh (but scientific) criticism…The self-critical aspect of science is not nice. It’s brutal – necessarily so. But it is still fair and professional, just not politically correct.”

    Yet it is just good science.
    You can’t win over the general public by pretending it is otherwise. It is hard to change the “status quo” and rightly so. There has to be a baptism of fire in order to separate the wheat from the chaff.

  19. BillyJoe7on 23 Dec 2010 at 2:28 pm

    sonic,

    “Richard Dawkins”

    I would still like to see the context in which Richard Dawkins claimed that some who question the theory are ‘evil’ and that “the science is settled”.
    Depending on the context, his response could be justifiable.

  20. cwfongon 23 Dec 2010 at 3:42 pm

    dogmatic
    adjective
    your being so dogmatic does not attract me to your religious philosophy: opinionated, peremptory, assertive, insistent, emphatic, adamant, doctrinaire, authoritarian, imperious, dictatorial, uncompromising, unyielding, inflexible, rigid.

    You can call anything equivocal if the meaning depends on the context, but that only goes to show the extent to which you are literal minded (i.e., simplistic).

    It’s equivocation to argue otherwise. Or to contend that I’m required to use the term dogmatic in the same context as someone used it previously.

    And dogmatic IS the flip side of heretical.

    And yes, I do mean to say that scientists are often dogmatic in their skepticism in the same way that priests are often dogmatic in their faith. But not, as someone wants to have me say, exactly, as dogma in the context of science takes on the pretense of the rational, and in the context of faith it takes on the pretense of revelation.
    I’m sure that’s a bit too subtle for the bobbly twins.

    At least sonic knows the difference, but then of course he’s actually a scientist.

  21. cwfongon 23 Dec 2010 at 5:48 pm

    http://www.philvaz.com/apologetics/p88.htm
    Dawkins: “It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).”

    And yet Dawkins still believes that the inheritance of acquired characteristics is impossible, even if those characteristics are behaviors.
    Which, if it turns out he is wrong, means he maintains a faith in evolution that may be no longer based on reason.

  22. daedalus2uon 23 Dec 2010 at 8:14 pm

    I think that saying that magic is “not allowed” is a little bit too strong (a very little bit).

    It isn’t that it is “not allowed”, but rather that it would be extraordinary and so requires extraordinary evidence. Evidence more compelling than the sum total of all human scientific knowledge. Countless millions of scientist-years worth of research. So far there is not a single datum (note singular) that is compatible only with a magical explanation, and there are enormously vast quantities of data that are completely explainable in the complete absence of magic.

    It would be non-scientific to conclude that an otherwise unexplained effect was due to magic, but that is true of every other scientific conclusion as well. There is always room for things we don’t know about in every explanation, even in explanations that fit the data exceedingly well.

    There are always many explanations that fit much of the data. Usually the custom is to go with the explanation that fits more data than any other explanation fits. Often this is problematic because individual scientists can’t personally examine enough of the data, and contemplate it simultaneously, and so appreciate which explanations fit more of it than others. This is especially true in explanations that cross-specialty boundaries and fit the data in many specialties simultaneously (the way some nitric oxide physiology does ;) .

    The term “magic” is probably not well enough defined for us to determine if it can be studied using scientific principles. What ever it is, if it shows any kind of consistency, then it can be studied using the scientific method. If it is so inconsistent that it can’t be studied using the scientific method, then there is no way to study it.

    If there is such a thing as a “scientific heresy”, it would be the idea that there are things that science is incapable of studying. There may be things that science will not give interesting answers to, but I don’t think there is anything that cannot be studied scientifically. I don’t subscribe to the Non-overlapping magisteria (NOMA) of SJG. My response to Dawkin’s criticism that not all grammatically correct questions are legitimate is to take it meta, and instead ask why a nonsensical grammatically correct question is thought worthy of being asked.

    Cwfong, I presume that by “acquired characteristics” you are meaning epigenetic programming of gametes that changes characteristics of offspring. The idea that this is “inheritance of acquired characteristics” is mistaken.

    Epigenetic programming of gametes requires physiology to specifically methylate specific DNA sequences to specifically alter their expression in the next generation to produce specific phenotype changes. The physiology that does that specific methylation is already in the genome. It is not “inheritance of acquired characteristics”, it is “programming of offspring phenotype” via gamete methylation.

    There is nothing about evolution that suggests that if programming of offspring phenotype by methylation of parent gametes could provide improved survival and reproduction of those offspring that physiology to do such things could not evolve.

  23. cwfongon 23 Dec 2010 at 8:34 pm

    daedalus2u, did you ever ask yourself how “The physiology that does that specific methylation is already in the genome?” Was it never at some point in time acquired? And if so, can you be all that sure it wasn’t connected to experience? Otherwise, are all behavioral and their accompanying physiological characteristics that life forms will evolve already in the theoretical genome of life just waiting for the signal to come out? Because it seems you may already believe in the scientific necessity for magic as a functional prerequisite.

  24. ccbowerson 23 Dec 2010 at 10:23 pm

    cwfong-
    “You can call anything equivocal if the meaning depends on the context, but that only goes to show the extent to which you are literal minded (i.e., simplistic).”

    Well, that’s what equivocation means. If in an argument you use 2 different meanings of the word, even the meanings are related… thats equivocation. Sorry for being “too literal minded” (i.e. precise and not sloppy)

  25. BillyJoe7on 23 Dec 2010 at 10:28 pm

    cwfong,

    Methylation contibutes to plasticity.
    Plasticity has a survival advantage.
    Therefore no magic required.
    (And no purposeful directing of evolution towards desired ends)

  26. daedalus2uon 23 Dec 2010 at 10:33 pm

    That physiology presumably was acquired the way that all physiology is acquired, by mutations, duplications, deletions, etc. followed by selection and yet more mutations, duplications, deletions, etc. Repeat over evolutionary time and a great many very complex traits can result. Vastly more traits than we currently understand. A trait that allowed for the programming of offspring phenotype might be a very good survival/reproductive trait, a trait that enhanced the survival and reproduction of individuals who had it, and who passed it on to their descendants.

    Affecting the phenotype of offspring requires the differential expression of different specific genes. Differential expression of different specific genes requires differential regulation of specific genes. Methylation of specific DNA strands requires that there be a specific DNA methyltransferase (and associated control proteins and stuff) that adds methyl groups to those specific DNA strands and not to other DNA strands. Then there also needs to be specific proteins that regulate the readout of the methylated DNA (or not). For example MeCP2 (deletion of which causes Rett Syndrome).

    In no way does the acquisition of the trait of parental imprinting of genes to regulate the phenotype of their offspring require any kind of “inheritance” of “behaviors” other than conventionally through DNA.

    Are you suggesting that some how “behaviors” produce DNA methyltransferase enzymes of specific activity that specifically and differentially methylate specific genes associated with those behaviors? By what mechanism?

    There is no known mechanism by which organism “behaviors” can change the DNA coding of their gametes, the composition or specificity of DNA methyltransferase enzymes, unless there is physiology that couples to the DNA methylation. There are probably effects of diet, where bad diet can increase breaks. There are probably effects of age, where more mutations accumulate over time. There are probably effects of stress where high stress can cause more mutations too. The epigenetic programming of gametes by these things is not well understood.

    If you have some data that shows that behaviors change the genome in characteristic ways such that those behaviors are expressed to a greater extent, I would like to see it. Lysenkoism is clearly wrong. It is not heretical to say that Lysenkoism is wrong, the data and understanding of how DNA is replicated and transmitted clearly says it is wrong. Some people who don’t understand the data, want to rehabilitate the idea that behaviors can be inherited. Usually such people have an agenda that has nothing to do with science.

  27. ccbowerson 23 Dec 2010 at 10:34 pm

    “The problem is that sometimes the reality is the ideal but doesn’t look that way to the general public.”

    Listen, there is no doubt that science “works.” Its the most successful of human endeavours when it comes to acquiring knowledge. All I mean to say is that we don’t need to sugar coat any of it… lets admit the slips and falls along the way (as occurs with any human endevour).

    The real reason why science is successful is not because mistakes aren’t made, but because science itself is not vested in any particular outcome, and (probably most importantly) it is a self-correcting process. Looking at the mistakes made is really how you can see why science works… for every mistake and fraud that get through there are dozens, hundreds, or thousands of scientists to point it out- loudly.

  28. ccbowerson 23 Dec 2010 at 10:37 pm

    I’m also not saying that what I said above isn’t already understood by anyone here, but the general public doesn’t. So when these points are not emphasized, it looks to a layperson that scientists have something to hide by not acknowledging some flaws, as superficial as they often are.

  29. cwfongon 23 Dec 2010 at 10:39 pm

    Bowers: The point that you still don’t get is you can call it that, but it won’t be equivocal unless it’s out of context. You don’t seem to know that with ambiguity, it’s context that determines meaning rather than meaning being the determinant of context.

    So what you are is precisely wrong, the flip side of sloppy.

    So lets see now, so far we see that you don’t do logic, you don’t do science, and now you don’t do language. But you do the banal superbly.

  30. ccbowerson 23 Dec 2010 at 10:48 pm

    cwfong-
    Your insults are lame. Not quite as lame as your perspective on evolution. Do you really think the physiology of methylation developed as a result of an organism wanting it? Why do you love magical thinking so much?

  31. daedalus2uon 23 Dec 2010 at 10:50 pm

    Cc, it isn’t science that slips and falls, it is human beings trying to do science that slip and fall.

    When I make a mistake in arithmetic, I don’t blame mathematics for not being precise, I blame myself for not doing mathematics precisely. When humans make mistakes doing science, we shouldn’t blame science, we should recognize the error came from the imperfect application of science by humans.

    Of course humans try to cover up their errors. At least in science the truth will eventually come out. In everything else? Not so much.

  32. cwfongon 23 Dec 2010 at 11:04 pm

    Daedulus2u, it’s been pointed out before that your use of Lysenkoism as the alternate to neo-Darwinism is simply a red herring.

    And your opening paragraph is the giveaway that you don’t really know how evolution or selection works:
    “That physiology presumably was acquired the way that all physiology is acquired, by mutations, duplications, deletions, etc. followed by selection and yet more mutations, duplications, deletions, etc.”

    What’s driving the deletions and selections for example other than the lessons from the errors of experience? You don’t know, but you “presume” because that’s the prevailing “presumption,” i.e., “an idea that is taken to be true, and often used as the basis for other ideas, although it is not known for certain : underlying presumptions about human nature.”
    In any case there’s a bevy of evolutionary scientists out there now that accept that life’s evolution will turn out to be a self-engineeering process. So I’ll presume to throw my lot in with them and you can wave your magic wand of immaculate selection to your heart’s content.

  33. cwfongon 23 Dec 2010 at 11:22 pm

    Bowers,
    Again you show your ignorance of science, and (to keep it simple for you) the difference between need and want.
    The physiology of methylation developed as a result of an organism wanting it? No, it developed incrementally as a solution to a series of developmental problems. All connected to the organisms experience – or not, if you prefer to think experience is a magical process and the big sieve in the sky is not.
    Stop pretending to be a scientist. Go read up on what the real ones are doing now in this field. You won’t understand it, but at least you’ll know they’re doing exploratory science and not worried about the cries of heresy from the luddites.

  34. ccbowerson 24 Dec 2010 at 12:51 am

    “Cc, it isn’t science that slips and falls, it is human beings trying to do science that slip and fall.”

    Of course. That is what I was saying (thats why I added human endeavour to the second part of the sentence). But your clarification is an important one…. science doesn’t really “do” anything. Humans are the “do-ers” in science.

    cwfong continues with insults to make up for his inadequacies. Pathetic really. Why do you even read this blog, or any of the skeptical blogs? Is it because you know there is something wrong with your thinking, and you go here to “challenge” yourself? That way you can feel justified in your magical thinking?

    Please… come up with a coherent thought and we can have a reasonable discussion. You are still referencing that “big sieve in the sky” phrase… why is this sieve in the sky? I’m not even sure what you are implying here. There is nothing magical needed to understand evolution: Maybe thats why you do not appear to understand it.

  35. cwfongon 24 Dec 2010 at 2:07 am

    cc, you started by your unmerited attack on my syntax and you’re only motive was to provoke me. I have no interest in anything you otherwise might have to say, but I don’t suffer fools as lightly as I might. You’re not a scientist and will never be one – you don’t have the type or level of curiosity that a scientist needs, and that lack of curiosity signifies a concomitant lack of the appropriate intelligence.
    Why do I read this blog? Because the owner is an intelligent man who is usually right, and in fact is basically right on this occasion. But nobody is completely right about anything, and commentary that points that out is how we learn. Or how I learn in any case.

    I can learn from Dr. N, even if he learns nothing back from me. You can be sure I don’t read it to learn anything from you however, nor to try to teach you anything as well. You don’t know about the sieve analogy? Of course you don’t. More evidence of that curiosity gap. You think you understand evolution? Clearly if you don’t know that biological experience plays a role, you haven’t a clue.

    “Science doesn’t really do anything. Humans are the do-ers in science.” What are you, the Polonius of this blog? The windbag of folk wisdom? Reminder of the obvious lest we forget?
    And actually science as an artifact of culture does do do some things that humans don’t. But i’ll leave it to you to someday figure that out. Or ask somebody if you can figure how phrase the question.

  36. sonicon 24 Dec 2010 at 2:17 am

    daedalus2u-
    I’m interested in your take on this idea of magic. I agree that it is too ill defined to be very useful in determining a future study. “Random chance” seems about as magical a concept as one would want to consider, yet science has continued on rather well dispute having embraced it. When our astrophysicists tell us that the universe might be 96% made of something nobody has encountered, it seems a bit early to start throwing-out possible explanations, it seems.

    If something is not very consistent, and is not (yet) controllable, it is difficult to study scientifically– but these difficulties have been overcome before. One just needs to run a large enough test to get enough data to get statistically relevant information. Clearly the larger the test the more problematic the experimental design and application become, but it seems that if someone were consistent and persistent enough, a very rare and uncontrollable occurrence might be discerned.
    Suppose, for example (and I’m being very hypothetical here), that a person actually receives messages by telepathy an average of one time per year. It seems this would be impossible to find the signal through the noise in such a case, impossible in practice perhaps, but not in theory.
    Otherwise the only way to study such a phenomena would be personal.

    The scientific explanation for what happened last time I listened to ‘Four Seasons,” is of interest, but I fear it would be unrevealing at the point of my main interest.

    If science is like the number system, then does Godel’s theorem apply?

  37. daedalus2uon 24 Dec 2010 at 8:51 am

    cwfong, my presumption when faced with something I don’t know the precise details of is to presume it occurs via processes that are known or are knowable. That is a default presumption.

    I am not sure what your default presumption is, assume something for which there is no evidence?

    Nothing is driving the deletions, mutations, duplications. They are occurring because DNA replication does not have perfect fidelity. Many things affect the fidelity of DNA replication, ionizing radiation, oxidative stress, metabolic stress, xenobiotic mutagens. When those mutations occur in germ cells, they affect the next generation. When they occur in somatic cells, they don’t.

    Can behaviors modify the germ line? Yes, exposing one’s reproductive tissues to ionizing radiation will increase the number of DNA breaks in those cells. If those cells become gametes and become an offspring, those DNA breaks may affect future generations. But for radiation exposure to be used to do something specific, such as produce specific behaviors in offspring it has to be aimed really really well, aimed at the precise sequence of DNA to achieve the precise change needed in the precise cell that will form the precise gamete that forms the offspring. This is a level of specificity that is not achievable by known means. Radiation scatters, and the direction a particular photon scatters depends on unknowable details about the positions of photons and scattering atoms.

    There was an excellent comment on ERV’s blog by titmouse

    “A conclusion based upon available evidence isn’t the same thing as “bias.” New evidence will lead to revisions of previous conclusions. No big whoop.”

    “In science you don’t get gold stars for being “right all along” like in the movies. You only get points for weighing the *available* evidence appropriately.”

    “If you bet against the available evidence and it turns out you’re right, that’s just dumb luck. It’s not impressive.”

    http://scienceblogs.com/erv/2010/12/xmrv_erv.php#comment-3033939

    So far there is no mechanism, no data, and no evidence to support the idea that evolution is “self-directing” (what ever that means). You may throw your lot in with people who believe that, but you and they are not doing science when you do that. Why humans have beliefs that cannot be supported with science is not about science, it is about humans, and is one of the things that makes science difficult for humans until they have learned to not do that. That is something that most people can’t do at all, and that few people can do regularly. There may not be anyone who can do it all the time.

    Usually different people have different “blind spots” where they are unable to apply science rigorously. That is why science as a cooperative activity works better (usually) than a single scientist working alone. Sometimes, whole groups of humans trying to be scientists develop “blind spots” by looking at the data a particular way for too long. They lose the ability to see other patterns. That is why humans trying to be scientists have developed heuristics to help with that, statistics, mathematical techniques, peer review, publication of methods, and replication of experiments are techniques to try and get around the “blind spots” that humans trying to be scientist have.

    This is the essence of the dogma that religious groups have. Those caught up in their dogma are unable to fit any experiences or data into a different schema. Humans trying to be scientists try to overcome that bias, humans uninterested in examining their own bias are not trying to be scientists.

  38. ccbowerson 24 Dec 2010 at 9:18 am

    “cc, you started by your unmerited attack on my syntax and you’re only motive was to provoke me”

    For someone willing to throw out baseless insults, you sure are a sensitive one. I am not motivated to provoke anyone. There is nothing personal going on here. Just ideas. Why do you perceive disagreement as a personal attack?

    “You’re not a scientist and will never be one – you don’t have the type or level of curiosity that a scientist needs, and that lack of curiosity signifies a concomitant lack of the appropriate intelligence.”

    Again, baseless nonsense. I am almost curious to a fault. Its my only excuse for engaging your gibberish. Just because I don’t “believe in magic” doesn’t make me close-minded. You are very fond of assumptions and jumping to conclusions. As far as insisting that I am not a scientist… I agree because I decided late in my education to not pursue research (I am narrowing the term scientist to someone active in research). I only participated in research during my education, and didn’t like the day to day grind of research. Not that it matters, but I have a B.S., a doctorate level professional degree, and work in a hospital. I am not being specific here, because I think it is irrelevant.

  39. ccbowerson 24 Dec 2010 at 9:19 am

    “Clearly if you don’t know that biological experience plays a role, you haven’t a clue.”

    I never said that it doesn’t, but you take it an order of magnitude too far

  40. cwfongon 24 Dec 2010 at 12:29 pm

    daedalus2u writes,
    “So far there is no mechanism, no data, and no evidence to support the idea that evolution is “self-directing” (what ever that means).”

    I didn’t write “self-directing,” I wrote that “life’s evolution will turn out to be a self-engineering process.”

    The fact that you don’t know that there’s a difference is telling. So of course you don’t know that there is a mountain of evidence to support both concepts.

    Google and find this, for example: http://escholarship.org/uc/item/1x26754f

  41. daedalus2uon 24 Dec 2010 at 12:55 pm

    Godel’s theorem should apply to science, however because our universe appears to be finite, everything in our universe can be described by a finite description. The proof of Godel’s theorem requires the use of mathematical abstractions which may not be physically realizable in our universe (there may not be enough matter/energy to produce the bits necessary to instantiate the mathematical abstractions needed to carry out the proof).

    In other words, pi is a mathematical abstraction, the ratio of the circumference to the diameter of a circle in Euclidean space. That abstraction is based on mathematical continuity, that is that space and length are infinitely divisible and that distances can be measured in real numbers and not in integral numbers of Planck lengths.

    Pi is a “real” number, but most (virtually all) “real” numbers are not expressible, that is there is not a finite way to express the number. Pi can be expressed in language, or as the sum of an infinite series, but most real numbers don’t have a finite representation.

    In the context of Godel’s theorem, “proof” and “true” are also mathematical abstractions that are (probably) not realizable in physical reality by science. Science can’t prove any hypothesis is true, it can only refute hypotheses that don’t match reality. There will always be multiple explanations that exactly fit any finite set of data but which make different predictions for not yet realized instances.

    This reminds me of a saying my high school physics teacher used to have, which he called the one truth in science, that “this too will change”.

  42. daedalus2uon 24 Dec 2010 at 1:23 pm

    To me, the terms “self-directing” and “self-engineering” in the context of evolution are essentially synonymous.

    The paper you linked to is not about inherited behavioral characteristics, it is about emergent behaviors derived from inherited characteristics which are express under different environmental conditions.

    They are using the term “engineering” as a metaphor to anthropomorphize the behaviors that bacteria exhibit under different environmental conditions. There is no evolution going on here, self-directed or otherwise. These bacteria remain clonal and identical from a genetic standpoint.

    You did say:

    “life’s evolution will turn out to be a self-engineeering process.”

    Could you explain how your statement has a different meaning than

    “life’s evolution will turn out to be a self-[directed] process.”

    I don’t perceive any nuance that distinguishes between these two statements. They are slightly different, if anything the “engineering” one is more problematic. Engineering (in the usual sense) means willful construction for a purpose, implying that “life” is willful (i.e. conscious) and that it constructs the elements of heredity (DNA) for purposes which it willfully has.

    If you want to use idiosyncratic definitions of common terms such as “engineering”, it would be helpful if you gave us the idiosyncratic definitions you are using.

  43. sonicon 24 Dec 2010 at 2:09 pm

    daedalus2u-
    Good point re: Godel’s theorem. I’m guessing you would have similar problems with the use of fractals (good to a point?) Your application of this to pi is cool.
    Now I’m curious about your views re: quantum mechanics-
    If you go with the math, you end up with the ‘many-worlds’ (or something like it), if you go with what we experience you end up with the ‘collapse of the wave-function’ (and the problems of discontinuity, the famous leap)
    Have you considered this situation?

  44. ccbowerson 24 Dec 2010 at 2:10 pm

    I’m enjoying the daedalus2u/ cwfong discussion

  45. cwfongon 24 Dec 2010 at 2:40 pm

    daedalus2u,
    Well for one thing, directed is not the same as engineered, as something else such as your mother nature’s big sieve in the sky could still be summoned up to do the engineering work. And if it’s the biological self doing the engineering, the term is hardly idiosyncratic (unless, as it appears, you have a problem with the inferential aspects of logic).
    Shapiro, for one among many, uses the term thusly:
    “In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by natural genetic engineering.”
    http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html
    And yes, it is willful construction for a biological purpose.
    And all biological forms are aware of their immediate surroundings and the need for an assessment of their purposes. They are in that sense conscious, IOW not asleep. But chances are they don’t need what we call sleep, so consciousness, as a dichotomous conception, would not apply.
    But until you decide to read the literature on the subject there’s little point in discussing these matters further. Or as I suspect, you’ve read it and dismissed it – all the more reason for me to let you be.

  46. ccbowerson 24 Dec 2010 at 3:20 pm

    “Big sieve in the sky” appears to be an meaningless and empty phrase intended to be dismissive. It reminds me of the political platitudes that have become popular lately (not that this is anything new). You still haven’t explained why this “sieve” is in the “sky.” It appears that there is an attempt to draw a parallel to religion, but that seems absurd.

  47. cwfongon 24 Dec 2010 at 4:43 pm

    Read about it in: Conceptual issues in evolutionary biology By Elliott Sober
    Or in: River Out Of Eden, by Dawkins
    Or see his take on sieves here:
    http://en.wikiquote.org/wiki/Richard_Dawkins

    And yes, it does seem to be Dawkins’, et al, unwitting parallel to religion, replacing God with Mother Nature as creator, both with very similar magical powers.

  48. ccbowerson 24 Dec 2010 at 6:14 pm

    I am just not convinced that there is any implication of “magical” with the sieve analogy. It is just a metaphor, therefore has its limits.

  49. cwfongon 24 Dec 2010 at 6:52 pm

    “Just a metaphor” is meaningless as either an excuse or justification for what would otherwise be magical. A platitude in other words to satisfy the average curiosity.

    metaphor
    noun
    • a figure of speech in which a word or phrase is applied to an object or action to which it is not literally applicable
    • a thing regarded as representative or symbolic of something else, esp. something abstract

    So the proposed selective sieve as a “limited metaphor” is by your reckoning either not literally applicable or a misrepresented abstraction.
    Yet Dawkins and Sober among others have argued for its accuracy.
    Jerry Fodor on the other hand (a foe of neo-Darwinists) takes your position that it is in fact an inapt metaphor for a selective process that does other than sort for size or color. IOW, it can’t sort for the complex strategic functions that are needed to drive the forms.

    But I digress, as it’s not my intention to make someone else’s argument for them here. If you’re not convinced by my references, you won’t be convinced by my rhetoric.

  50. sonicon 24 Dec 2010 at 7:39 pm

    cwfong-
    You paid me a complement earlier that I missed- thank-you.
    However, I am not a scientist. I will admit that some of my scientist friends laugh when I proclaim such, but I’m much too sloppy to be a good experimentalist, and I fall for the ‘why’ question too much to be a good theorist.
    To get specific with what you are talking about here-
    doesn’t our experience with pneumonia indicate something other than ‘undirected mutation’?

  51. cwfongon 24 Dec 2010 at 8:28 pm

    sonic, well at least you have an appreciation of science’s complexity and the appropriate level of curiosity.
    I’m not sure how to answer your question about pneumonia. Has our immune system evolved itself to better deal with it, or has it had recourse to a pre-adaptive strategy? I’m not sure if anyone knows, but it’s a good question. Although in either case there would have been an experiential basis somewhere down the line for either process. In short, my understanding is that we select our strategies and they direct the engineering process. With humans, where genome changes seem to take forever, it’s likely that we’re looking at the pre-adaptive function. But it’s also just as likely that I could be wrong, as some parts of our functional apparatuses evolve separately and more quickly than the others.
    In any case I doubt that undirected mutation is the proximate cause of anything, since the essential accomplishment of life has been to take intelligent advantage of the accidents of nature.

  52. cwfongon 24 Dec 2010 at 9:45 pm

    sonic, for what it’s worth:

    Genetic Susceptibility to Pneumonia
    Grant W. Waterer, MBBS, PhD, FRACPa, Richard G. Wunderink, MD, FCCPb
    The persistent mortality from community-acquired pneumonia may be explained by genetic predisposition. Specific mutations or polymorphisms in host response genes that are associated with adverse outcomes from infection can be grouped into four categories: antigen recognition, proinflammatory responses, anti-inflammatory responses, and effector mechanisms. Mannose-binding lectin polymorphisms have a more dominant role in pneumonia when compared with other pattern recognition molecules such as the toll-like receptors. The roles of TNF and lymphotoxin alpha polymorphisms remain unclear despite extensive study. IL-10 and IL-1 receptor antagonist polymorphisms have an important role in the anti-inflammatory response. Specific organ dysfunction, such as ARDS or DIC, may be related to polymorphisms in specific effector genes.

  53. BillyJoe7on 25 Dec 2010 at 1:07 am

    cwfong said:

    “I doubt that undirected mutation is the proximate cause of anything, since the essential accomplishment of life has been to take intelligent advantage of the accidents of nature”.

    There seems to be a conflict in this sentence between the phrases “undirected mutation” and “accidents of nature”. If you are referring to the same thing here, then there seems to be a contradiction. If you are referring to different things, then I would like to know what they are.
    In any case, before intelligent life evolved, mutation must have been “undirected” so it would have had to have been the proximate cause of something.

  54. BillyJoe7on 25 Dec 2010 at 1:24 am

    cwfong,

    “And yes, it does seem to be Dawkins’…unwitting parallel to religion, replacing God with Mother Nature as creator, both with very similar magical powers”.

    What are these “magical powers” that you attribute to “Mother Nature”?
    All I see is the very down to earth process in which every generation supplies the next generation with far too many individuals for the available natural resources for which they must therefore compete, as a result of which only those most adapted to the evironment in which they find themselves survive.

  55. BillyJoe7on 25 Dec 2010 at 1:36 am

    cwfong said:

    “http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html

    And yes, it is willful construction for a biological purpose.
    And all biological forms are aware of their immediate surroundings and the need for an assessment of their purposes.”

    The words “willful”, “purpose”, and “aware” surely must be intended as metaphors or anthropomorphisms. Unless Shapiro is saying that bacteria are literally willful, purposeful, aware organisms. What viruses and prions as well? What about molecules, atoms and subatomic particles? Where does the literal become metaphorical for Shapiro? For you?

  56. cwfongon 25 Dec 2010 at 1:52 am

    TWIMC: Since nothing that we know of “mutates” except a biological function, all of which require a minimum of calculative ability, the ever present accidents of nature had nothing else out there to offer their advantage to. Except for lifelike forms elsewhere in the universe of course.
    Or I suppose you could argue that the word mutate could be used in another context, such as lightning strikes “mutating” a rock. A bit of a stretch, but not necessarily an equivocation in that context. There’s some doubt as to the rock’s advantage in that scenario, but what the hell, this isn’t rocket science.

  57. cwfongon 25 Dec 2010 at 1:58 am

    I see some other inferentially challenged person has added further babble in the interim. No part of which is worthy of a response.

  58. BillyJoe7on 25 Dec 2010 at 2:07 am

    cwfong,

    http://escholarship.org/uc/item/1x26754f

    If you read this article with the assumption that the verbs describing the actions of the bacteria are simply metaphors or anthropomorhisms (that serve the purpose of word economy), you cannot seriously have any objection. If you read these verbs literally, you seriously need more evidence than is presented in this article.

  59. BillyJoe7on 25 Dec 2010 at 2:26 am

    cwfong,

    “Since nothing that we know of “mutates” except a biological function, all of which require a minimum of calculative ability, the ever present accidents of nature had nothing else out there to offer their advantage to. ”

    What I am asking is: how do the “accidents of nature” result in “directed mutations” as opposed to random mutations?

  60. BillyJoe7on 25 Dec 2010 at 2:28 am

    ALIHOM:

    “I see some other inferentially challenged person has added further babble in the interim. No part of which is worthy of a response.”

    I am going to assume that you have no idea how to respond. ;)

  61. sonicon 25 Dec 2010 at 2:31 am

    cwfong-
    I should have said tuberculosis.
    It seems in this case the mutation rate and the development of resistant strains is not what the ‘random’ or ‘unguided’ postulate would predict.
    Sorry for the error- that’s two recently, I think I’ve made my quota fro the year.
    Merry Christmas- Happy New Year!

  62. cwfongon 25 Dec 2010 at 3:04 am

    sonic, without some guidance from the organism, the solving of such complicated problems by pure accident would be like the proverbial monkey typing Hamlet. It would take virtually forever.

  63. BillyJoe7on 25 Dec 2010 at 3:04 am

    sonic,

    “It seems in this case the mutation rate and the development of resistant strains is not what the ‘random’ or ‘unguided’ postulate would predict.”

    Random mutation and natural selection result (amongst other things) in plasticity – because plasticity is advantageous for survival in an environment that is at least partly unpredictable. Nobody is saying that plasticity is random, just that the mutations that result in plasticity are random.

    The genome is a recipe rather than a blueprint. As a recipe, it is plastic and the characteristics of the resulting phenotype will depend also on the features of environment in which the phenotype develops.

  64. BillyJoe7on 25 Dec 2010 at 3:10 am

    cwfong,

    “without some guidance from the organism, the solving of such complicated problems by pure accident would be like the proverbial monkey typing Hamlet. It would take virtually forever.”

    What is the difference between “plasticity” and “guidance from the organism” (if you don’t interpret that phrase literally of course)?

  65. ccbowerson 26 Dec 2010 at 1:05 am

    cwfongon 25 Dec 2010 at 1:58 am
    “I see some other inferentially challenged person has added further babble in the interim. No part of which is worthy of a response.”
    – How about the question about the “magic” in the sieve metaphor. How does this metaphor introduce anything magical? Where does the sieve cause a problem for you?

    “cwfongon 25 Dec 2010 at 3:04 am
    sonic, without some guidance from the organism, the solving of such complicated problems by pure accident would be like the proverbial monkey typing Hamlet.”
    – Not true. Many of the mechanisms for resistance already exist in the organisms for other reasons (perhaps at very low levels). Over time and through mutations bacteria are constantly developing ways to deal with the various chemicals they encounter in their environments. The antibiotics they encounter are just one of those chemicals, and they just amplify the selective pressure for the relevant genes. The bacteria that are better able to handle the chemical are the ones who survive disproportionately. If many mutations are required for resistance, then resistance does take a long time. This partially explains why some antibiotics are used for decades before resistance becomes a problem, and others have resistance problems much sooner.

    I don’t mean to say that mutations are the only mechanism for the development of resistance (yes, the example above is simplistic), but it is not necessary for monkeys to type Hamlet for mutations to be a major mechanism.

  66. cwfongon 26 Dec 2010 at 2:12 am

    Bowers,
    As I already noted, the hypothetical sieve can’t sort for the complex strategic functions that are needed to drive the forms. (Unless you know of some intelligent mechanism, like a God, that exists outside of the organism – maybe some universal cultural artifacts – some Platonic magical formulations – some Hindu turtles?

    And mutations are a mechanism only because the organism either causes them or takes advantage of their accidental nature. In fact some argue that the organism, having learned to use them to advantage, learned in addition how to cause them.

    But you didn’t get any of that because your curiosity is satisfied by being told what happens, and the whys are not seen as a problem.

    Which is a bit surprising because the nurse practitioners I’ve known would know better. They know that even the most basic organisms can learn. And why they need to.

  67. ccbowerson 26 Dec 2010 at 7:18 am

    cwfong-

    “the hypothetical sieve can’t sort for the complex strategic functions that are needed to drive the forms”

    You have implied this, but have provided no evidence for this opinion. Your perspective sounds like an “argument from person incredulity.”

    I failed to mention horizontal gene transfer in the above as an important way to ‘speed up’ the acquisition of resistance in certain situations. I thought you would have mentioned that since I assume that you find this way of transferring genetic material more appealing.

  68. ccbowerson 26 Dec 2010 at 7:29 am

    Perhaps “no evidence” is a little strong, but your argument does not seem to be about evidence, but an appeal to the “complexity” and the assertion that this sieve analogy is insufficient.

    Also, you seem to be very organism -centric in your view. What about at the gene-level or population-level?

  69. daedalus2uon 26 Dec 2010 at 12:52 pm

    cwfong, your only argument is one from incredulity, and you are positing an ability of organisms to understand their genome, understand their environment, and then modify their genome such that it works better in their environment.

    There is no evidence that organisms understand their genome, understand their environment, or are able to manipulate their genome to improve functionality.

    You are making a post hoc argument, that because there is a mutation in an organism’s genome, and because that mutation is advantageous, that the organism recognized it would be good if it happened, wanted it to happen, and then caused it to happen. There is no evidence that this has ever happened, there is certainly no support for the idea that this is common and a driving force for evolution.

    If your idea is correct, then why is evolution of new traits so slow, as in this research?

    http://www.ncbi.nlm.nih.gov/pubmed/18524956

    If E coli could “engineer” itself, why did it take tens of thousands of generations to do so?

  70. cwfongon 26 Dec 2010 at 2:20 pm

    Horizontal gene transfer speeds up things, but that begs the question of where those genetic strategies came from to begin with. And again, why they came. They are, after all, choice oriented algorithms.

    Cells don’t do their engineering based on having gone to a school for the learning of abstractions. And Daedalus would have it that bacteria would have to want to do what they have engineered before they did it. But those scientists I’ve referenced who’ve observed the little buggers in action conclude they do these things because they have to. Incrementally, I might add.
    Of course it can take what seems to us a long time for a new trait to become “genome wide.” Bacteria don’t seek to adapt themselves in unison any more than we do. Hence the beauty of the pre-adaption process. A real time saver from our point of view – a practical necessity from theirs.

    And if my arguments (which aren’t just mine) appear to be from incredulity, it may well be that yours are from the credulous.

  71. daedalus2uon 26 Dec 2010 at 2:44 pm

    So your “argument” is from authority, that because “some scientists” say so, you accept their say so.

    It seems their only “argument” is “because they have to”. Again, an argument from incredulity.

    But in the case of the E coli experiments I referenced, what did they “have to” evolve to be able to do? They didn’t “have to” evolve use citrate, most of them did not. 99.999999%+ of them did not evolve to use citrate.

    What part of that experiment is incompatible with the conventional mutation-selection idea of evolution and so requires a “pre-adaption process” (what ever that is, you have not attempted to describe it).

  72. BillyJoe7on 26 Dec 2010 at 4:18 pm

    a “pre-adaption process” (what ever that is, you have not attempted to describe it).

    I’m not sure what cwfong means by a “pre-adaption process”, but a pre-adaptation process is one in which a function evolves into something other than that for which it evolved in this first place. For example the evolution of sweat glands into mammary glands, or scales into feathers. The more familar term is the one coined by Stephen Gould: “exaptation”. It removes the implication that this is done intentionally.

    Other than that implication of intentionality, there is nothing contrary to the mainstream view of evolutionary theory in the use of the term “pre-adaptation” or “exaptation”. In fact it is an essential part of it.

    The intention, of course, is just an illusion and, if you read all of cwfong/bindle/artfulD’s references, it is clear that most do not intend that interpretation and that their use of certain verbs to describe what bacteria do are just anthropomorphisms. The few that do intend that interpretation are just wildly speculating beyond the evidence.

    a “pre-adaption process” (what ever that is, you have not attempted to describe it).

    As for cwfong, and bindle and artfulD before him, explaining clearly what they mean…..:D
    My impression is that he does not clearly understand the actual fringe hypothesis that he is falsely promoting as progressive mainstream. I refuse to believe that it is possible to clearly understand something and not be able to clearly explain it to the intelligent layman (okay I’ve set myself up for a riposte) in terms he can understand. Certainly, Stephen Gould, Richard Dawkins, and Daniel Dennett seem to have no problem doing so.

  73. cwfongon 26 Dec 2010 at 4:25 pm

    d:
    In case you weren’t aware, all E coli, even from the identical strain, are not individually identical. Some have to do what others don’t. If they didn’t, their evolution (not to mention all evolution) would, by my reckoning, be soon dead in its tracks. And if you don’t get that, I’m not going to explain it.

    As to an argument from authority, all science is to some extent an argument based on the priority of authority. I choose to take those I’ve cited over yours.

    You’re not aware of pre-adaption? It’s quite similar if not identical to preadaptation. http://en.wikipedia.org/wiki/Preadaptation

  74. cwfongon 26 Dec 2010 at 4:46 pm

    By the way, the intensional definition of a choice oriented algorithm is a processor of intentions (Dennett).

  75. daedalus2uon 26 Dec 2010 at 5:01 pm

    So you do mean preadaptation in the sense of telology?

    http://en.wikipedia.org/wiki/Teleology

  76. cwfongon 26 Dec 2010 at 5:24 pm

    No, I don’t. I’ve not stopped beating my wife as well.

  77. cwfongon 26 Dec 2010 at 5:38 pm

    Preadaptation is an anticipatory system. See this article on Biological Function and Anticipatory Systems at http://www.panmere.com/?p=76

  78. daedalus2uon 26 Dec 2010 at 6:54 pm

    There is nothing in that link inconsistent with conventional understanding of evolution, other than the woo-woo BS magic about biology not being consistent with Newtonian physics.

    Selecting for bacteria that trigger low oxygen utilizing enzymes after exposure to lower temperatures, or after exposure to higher temperatures doesn’t show that bacteria are engineering their evolution. It doesn’t show that bacteria are anticipating the conditions they will find themselves in. It certainly does not show that bacteria have the ability to act in non-causal ways and predict the future so that they can respond to the future before it happens the way the author is suggesting represents an incompatibility with physics and chemistry.

    Many systems exhibit these types of behavior. Pavlov’s dogs exhibited salivation before being fed. Were they reading the future? No, they were observing Dr Pavlov bringing them food, and had learned that when Dr Pavlov brought them food, they would get fed, so they started salivating.

    With all due respect to the researchers who selected bacteria, it is not at all the first instance of bacteria anticipating future conditions. When bacteria divide, they are always anticipating that the conditions will be sufficiently favorable that both daughter cells will be able to survive. Bacteria in a closed system will divide until they consume all available nutrients. Why are they are unable to anticipate that they will use up the nutrients and die? For the simple reason that they are unable to anticipate anything. The “observation” of anticipation by bacteria is a false positive. The bacteria are not “anticipating” anything. That particular strain has been selected to exhibit certain properties and so they do exhibit those properties. Some individuals want to ascribe magical woo-woo powers to bacteria, the woo-woo magic of “intention”, and so those individuals misinterpret their observations as evidence for intention.

    It is a false positive due to hyperactive agency detection by a human.

  79. cwfongon 26 Dec 2010 at 7:40 pm

    d.
    Hyperactive agency detection apples more to the intentions of your mother nature woo-woo than to bacteria.

    All life forms have expectations that ATTEMPT to predict the future.
    If you don’t understand that basic concept, further discussion of the effects of experience on behavior with you will be useless.

    And what did that article have to do with Newtonian physics? (Although if you’re alluding somehow to quantum indeterminacy as a necessity for choice, I’ll agree that it wouldn’t hurt.)

    As to argumentative evidence for intentionality in biological systems, I’ll elaborate on what I alluded to earlier as Dennett’s position:

    “Full fledged intensional semantics of the familiar sort emerges, according to Dennett, only when we step up to the more abstract level at which we seek to capture informational patterns that describe systematic relations amongst a system’s goals, representations, and environment. We do this for the sake not of explaining the internal micro-causes of the system’s behavior, but for the sake of understanding the systems’s global capacities and dispositions in terms of recurrent patterns in its responses to environmentally posed problems that are characteristic of wider classes on intelligent systems of which the system in question seems to be a member. Here is the level of informational categorization at which we ascribe the kinds of content supported by cultural evolution. Dennett (1981) calls this ‘intentional system (IS) theory.’” From Daniel Dennett, by Andrew Book, Don Ross, page 150.
    If cultural evolution is integral to all strategic evolution, and I would argue that it is, this would apply to bacteria as much as to us, the recipients of that bacteria’s beneficial input. IOW, bacteria have an evolving culture by necessity. Ask Bonnie Bassler.

  80. daedalus2uon 26 Dec 2010 at 9:08 pm

    Didn’t you read the block quote in your link?

    “Robert Rosen remarked on this situation [2, p. 133-134]:”

    He talks about biological systems unexplainable by physics because of causes before actions.

    He then goes on to say that this isn’t really non-physical, it is physical, but that Physics (as done by physicists) hasn’t caught up with explaining this acausal aspect of physical reality yet.

    No, this is BS nonsense. The bacteria that expressed low O2 enzymes when exposed to certain temperatures before being subjected to low O2 were not reading the future, noting that they would be placed in low O2, and then activating low O2 enzyme expression so as to be ready for the low O2 they were predicting by reading the future.

    Rosen and the blog author are confusing cause and effect, and imputing mystical magical woo-woo abilities to read the future to bacteria. They don’t call those abilities mystical magical woo-woo, they call them “functional entailment” and “anticipation”. I call them nonsense.

    Is that what you mean by “anticipation”? Reading the future and doing things to respond to that future before it happens?

  81. cwfongon 26 Dec 2010 at 10:53 pm

    d,
    I specifically referred to the article on Biological Function and Anticipatory Systems, which Rosen had found here:
    http://news.sciencemag.org/sciencenow/2008/05/09-02.html

    I’m not here to defend the whole damned blog, even though Rosen, who has since died, was a brilliant thinker.

    What I mean by anticipation is the sense of combining biological predictions with expectations. If you truly believe that bacteria don’t act with expectations, you have no conception of the motivational aspects that distinguish a life form’s strategies from its chemical reactions.

    If we have no common ground there, there’s nothing left for us to discuss. In my view there is no evolution that doesn’t have a strategic basis. Your view seems to be there is no evolution that does. Game over.

  82. daedalus2uon 26 Dec 2010 at 11:46 pm

    Is this what you mean by strategy?

    http://en.wikipedia.org/wiki/Strategy

    “a plan of action designed to achieve a particular goal.”?

  83. cwfongon 27 Dec 2010 at 12:28 am

    strategy |ˈstratəjē|
    noun ( pl. -gies)
    a plan of action or policy designed to achieve a major or overall aim

    An aim in the biological sense is not that of a specific goal – it’s a purpose or intention; a desired outcome. Of which there would be many, depending on the survival problems presented to the particular organism or species.

    But why don’t you just admit you don’t believe in strategies and purposes as applied to biological life, and enough with your simplistic gaming ploys. You’re not that good at it. And you know why.

  84. cwfongon 27 Dec 2010 at 1:16 am

    Biological Organisms as Semiosic Systems: the importance of strong and weak anticipation, Edwina Taborsky, https://s.p5.hostingprod.com/@www.biosemiotics.org/ssl/ISBS_OPR_Taborsky.pdf

    Excerpt:
    “The development of a complex and evolving capacity for anticipation and the concomitant capacity of the system to itself make decisions about its future morphological state is a primary characteristic of the development of the biological realm from the physico-chemical realm. The reality of two types of anticipation suggests that the two step evolutionary framework of neodarwinism (Fisher 1930, Mayr 1942) – a framework that rejects anticipation and is instead based around a primary random or uninformed mutation of a single model supported by a post hoc ‘natural selection’ of that model – is an inadequate analysis. The semiosic biological system is not a random or mechanical process but an informed, reasoned and self-controlled process.”

  85. sonicon 27 Dec 2010 at 2:33 am

    From

    http://www.pnas.org/content/97/12/6646.short

    “The SOS response regulates adaptive mutation”

    “Adaptive mutation may reflect an inducible mechanism that generates genetic variability in times of stress.”…
    “Here we show that adaptive mutation is regulated by the SOS response, a complex, graded response to DNA damage that includes induction of gene products blocking cell division and promoting mutation, recombination, and DNA repair.”

    If the life form has its survival threatened, it responds in a way that increases its chances for survival.

    If strategy and intention are emergent properties of matter, then the life form described above is exhibiting them.

  86. cwfongon 27 Dec 2010 at 3:56 am

    sonic,
    Yes, to you and me that’s obvious. Beyond that, however, is the question of long term heritability. It’s not so obvious that this is the mechanism for that, but it does reflect that self mutation can be achieved. Although in this case, our friends here will argue that these are revertants. Even though they claim an unfamiliarity with pre-adaptation.

  87. BillyJoe7on 27 Dec 2010 at 8:28 am

    “Game over”

    Bla bla, bla
    Link.
    Quote.
    Bla, bla, bla
    Link.
    Quote.
    Bla, bla, bla.
    Blankity blink.
    Quility quote
    Bla, bla, bla, bla, bla.

    Here we go round the mulberry bush.

    But…
    You c wfong,
    you r wrong
    It’s not chess you’re playing.
    It’s only
    …solitaire.

  88. daedalus2uon 27 Dec 2010 at 9:09 am

    Billyjoe, cwfong is not “wrong”, he/she is “not even wrong”.

    http://en.wikipedia.org/wiki/Not_even_wrong

    The “intentionality” idea of evolution is not specified well enough to be falsifiable. It doesn’t make any claims that can be tested.

  89. cwfongon 27 Dec 2010 at 1:15 pm

    d,
    You luddites should tell that to Dennett. Of course he’s only a respected philosopher of science that some plastic dummy cited earlier and pretended to have understood. He (Dennett) doesn’t actually do the mechanics, so ignore him. He’s evidently not privy to “a set of methods for investigating the natural world, for understanding how it works, what has happened in the past, what is happening in the present, and what is likely to happen in the future.”
    The citations I’ve given (as has sonic) are all about the testing process.
    Talk about a pair of navel gazing mental midgets. I’d say this proves my point about the persistence of some scientific dogma, except you latter are neither scientists nor philosophers.
    You have to at least think like a scientist to hope to effectively dispute their research. You have to have some ability to draw scientific inference at that level – otherwise you’re simply doing the mechanics. Or not even that.

  90. sonicon 27 Dec 2010 at 2:04 pm

    cwfong-
    We know what we can see. We see that life forms mutate in a number of ways not all of which are well described as ‘random’. The notion that in all of the history of life that all functional change has been caused by ‘random’ mutation is a dogma that violates that observation. The point seems to be to disallow any questioning of the theory.
    Check-out the first review and response here–
    http://www.biology-direct.com/content/2/1/21

    (BTW- I have been called a ‘heretic’ by my scientist friends before)

  91. cwfongon 27 Dec 2010 at 2:36 pm

    sonic, thanks for that citation. Note that at least the reviewer you referenced was somewhat intelligent. Also the author seems to have ducked any discussion of the effects of biological experience. Still a bit cowed by the specter of the prospective naysayers no doubt.

  92. daedalus2uon 27 Dec 2010 at 6:07 pm

    Quoting from your linked to Taborsky paper:

    “Importantly, the mediation is an act of reason. We must insist on this; mediation is not a mechanical act nor is it an act of communication. It is an analytic act. As Peirce noted, “Thought is not necessarily connected with a brain. It appears in the work of bees, of crystals, and throughout the purely physical world; and one can no more deny that it is really there, than that the colors, the shapes, etc., of objects are really there…”

    Do you agree with this? That crystals exhibit thought?

    Later Taborsky says

    “Following Dubois, anticipation is a property not merely of the biological realm, as Rosen (1985) affirmed, but of all systems, physical, biological and social. “As anticipatory properties exist in fundamental physical systems…anticipation must be a key property for any non-living and living systems which are more complex, like physical, chemical, biochemical, ecological, economical, social systems” (Dubois 2000a:28).”

    So you agree that crystals anticipate? Is this the sense by which you are using the term “anticipate” in the context of bacteria? That bacteria “anticipate” the same way that crystals “anticipate”?

    Later

    “The reality of two types of anticipation suggests that the two step evolutionary framework of neodarwinism (Fisher 1930, Mayr 1942) – a framework that rejects anticipation and is instead based around a primary random or uninformed mutation of a single model supported by a post hoc ‘natural selection’ of that model – is an inadequate analysis. The semiosic biological system is not a random or mechanical process but an informed, reasoned and self-controlled process.”

    Later, the remarkable statement is made:

    “The relation provides robust, i.e., immediately functional evolutionary and adaptive capacities. Kauffman claims that “selection is not the sole source of order in organisms” (1993:xiv), and there are “critical limits to the power of selection” (1993:xv). As a network, it provides a wide range of prospective solutions for the system to, in interaction with its informational environment, select as the ‘best solution’. This rejects the Darwinian axiom that a model itself, as a final program, emerges randomly and survives by a reproductive struggle of its individual representatives. Initially, the solution resulting from a 3-2 exploratory search is theoretically, randomly generated. This randomness, however, is reduced as the relation gathers and ‘fine-tunes’ future-oriented hypothetical solutions by constantly comparing them with the state of its current informational identity and the state of its current environment. This means that it is an informed and analytic, rather than random and ignorant, search. The ‘best solution’, again, is a result of an informational process which first develops a co-domain of hypothetical propositions, and then, negotiates between these prospective solutions and the environment, to select the ‘best solution’. “A strong anticipatory system is one in which the anticipated future state is ‘generated by the system itself” (Dubois 2000a:4). Any randomness is internal and reduced to zero by the time a ‘best solution’ is chosen by the system. The emergent model is immediately functional and there is no testing by struggle as required in the thesis of Natural Selection.”

    Which would be fine, except that it contradicts what is observed in reality. When E coli were grown with citrate, it took some 30,000 generations and many years for the E coli to evolve to use citrate. To the extent that the word-salad makes a “prediction”, that prediction is that E coli would evolve to use citrate not as a “a random or mechanical process but an informed, reasoned and self-controlled process.”

    “Any randomness is internal and reduced to zero by the time a ‘best solution’ is chosen by the system. The emergent model is immediately functional and there is no testing by struggle as required in the thesis of Natural Selection.”

    No “testing by struggle”? Then what was E coli doing for those many years and tens of thousands of generations? Maybe it was just playing a joke on those scientists, delaying its expression of citrate utilizing phenotype to throw the scientists off the track. Proof that not only does E coli have a sense of intention, it also has a sense of humor! What a joke it played on those Darwinists. That E coli must be lol.

  93. cwfongon 27 Dec 2010 at 7:28 pm

    d,
    The very fact that you have to ask these juvenile questions tells me that you haven’t the capacity to understand the answers.

    And you don’t need to agree with everyone’s conception of the anticipatory elements of nature to understand they are central to the nature of biological functions.

    I do know what she means however when she talks of anticipation as a natural strategy. Our concept of natural law requires us to presume that natural forces have strategic bases. Do you understand the strategic nature of fractals for example? They are structured in anticipation of destructive forces. They are in that sense, intensional. (Not the same as intentional as has already been pointed out by Dennett, et al.) Yes, the terms are metaphorical – as are in fact the bulk of scientific terminology.

    And as to struggle, it should be clear that she’s suggesting that selection is a process that occurs within the organism and not based on random offerings by mother nature that the organism is forced to blindly test and live or die by the otherwise unpredictable results.
    But why look to me for answers when you’ve teamed up with that other intellectual lilliputian?

  94. daedalus2uon 27 Dec 2010 at 8:05 pm

    If you are unwilling to explain the meaning of the terms you are using, you can’t expect anyone to understand what they mean. I am trying to understand, but there doesn’t seem to be much overlap between what you are saying and what I understand about reality. I am willing to admit the possibility that it could be that I am incapable of understanding it, if so, then I would like to expand my understanding of such things in terms that I am able to understand.

    A fractal is a mathematical construct, a mathematical abstraction.

    Do other mathematical abstractions have “strategic natures”? What is the strategic nature of Gödel’s first incompleteness theorem as opposed to the strategic nature of Gödel’s second incompleteness theorem?

    http://en.wikipedia.org/wiki/G%C3%B6del%27s_incompleteness_theorems

    The second one can be stated:

    “For any formal effectively generated theory T including basic arithmetical truths and also certain truths about formal provability, T includes a statement of its own consistency if and only if T is inconsistent.”

    As I understand what semiosis is (and I am not sure that I am capable of understanding it, that is I don’t think my brain can instantiate what it seems to mean), it applies to everything, and so everything has an intention and a strategic nature and is capable of thought, as in the crystal example.

    Then along the lines of Gödel’s theorems, one could make a statement “the strategic nature of this statement is to not have a strategic nature”. What is the strategic nature of such a statement?

    Is strategic nature analogous to consistency in the sense that Gödel was using it?

  95. cwfongon 27 Dec 2010 at 9:24 pm

    You can’t adequately describe intensional (note the spelling with an ‘s’) concepts in terms of mathematical logic. The element of purpose, as in “the purpose served,” is not a measurable part of the abstraction. People will of course disagree with me on this, but those same people will be found to also leave purpose out of their equations.

    A strategic nature is dependent on the consistency of a universal logic, but not to consistency per se. There is more to the makeup of that logic than mathematical measurement or consistency. Mathematical truths are tautological – there may be no such thing as universal truths. None that we’ll understand as incontrovertibly true in any case.
    Let’s just look briefly at one of your questions in this light: Do “crystals exhibit thought?”

    They exhibit the effects of a strategic formulation essential to maintain the integrity of their forms, which are (and not coincidentally) diverse. Something equivalent to what we call ‘thought’ has gone into this construction and something equivalent to memory is maintained by that
    evidence of integrity. And memory is arguably a form of thought. (And has the potential for awareness, a necessary element of anticipation in a strategic sense, as well as in a biological one.)
    But do they ‘think’ in terms of making choices? Not (to my knowledge) in the biological sense of having more than one choice of options. They do need to react however in a way consistent with their predetermined strategies. The big mystery is how nature has found and used it’s informational makeup – with no discernible calculative mechanism or what we conceive of as sensory apparatus – to evolve itself in such a universally consistent pattern.

    But enough with answering your questions.
    You’ve joined up with that true simpleton, and that’s a deal breaker.

  96. sonicon 28 Dec 2010 at 2:39 am

    cwfong-
    I’m trying to read Taborsky–
    A few statements (Am I getting it?) and one question….
    Systems analysis is a reasonable approach to a cell and multi-cellular entities– that leads to networks and so forth.
    Biological systems exist as quantum mechanical entities, therefore it is reasonable to attempt a description that includes all that entails.
    Some creatures anticipate the future. It is reasonable to imagine that this quality (the ability to anticipate) would have analogs in any life form and in non-life forms as well. To imagine that only a life form could have such an ability could violate the notion that there is nothing ‘magic’ about life.
    But what physics allows the parts to have this quality?
    You don’t have to answer that Q, but you must run into it.
    Am I getting it?

  97. cwfongon 28 Dec 2010 at 3:56 am

    sonic, in my view, what creatures anticipate is not so much the future as some form of repetition of the past – the memories of which are found in their species’ cumulative experience. The universe of course maintains a history of its past in every aspect of its present. Arguably what we see as universal laws have been fashioned by some form of universal experience. Laws are nothing if not anticipatory of the need for their enforcement. So all known physical forces, electromagnetic to gravitational, are in that sense law enforcing, and the energy/particles involved are law abiding in “anticipation” of whatever means of enforcement might apply.
    How’s that for mixing up a mess of metaphors?

  98. BillyJoe7on 28 Dec 2010 at 6:23 am

    I’ll just repeat:

    Anyone who cannot explain an idea in terms that can be clearly understood by the intelligent layman either does not understand that idea or is trying to explain an idea that actually makes no sense in the first place.

    Anyone who cannot explain an idea without a resort of jargon peculiar to the proponents of that idea and the continual use of quotes containing that jargon is speaking bullshit until proven otherwise.

    Everyone who has ever challenged cwrong/bungle/artlessDodge to explain what he means has received the same treatment. His failure to explain the idea is misdirected as a failure of the challenger to understand because of mental deficiency. It doesn’t wash.

    Even poor sonic, who really does want to believe this nonsense, is struggling. And oh so politely.
    (Sonic, if you’re going to respond that indeed you do understand the response given to your question, good on you for lying. I think it’s time to give up the pretense and call him on his clear and present failure to respond meaningfully to legitimate questions.)

    To be entirely clear to anyone else still following this thread, the idea cwfong espouses is just an unimportant piece of fringe science, and barely that. And the quantum connection which he has only alluded to here, is pure unmitigated bullshit.

  99. daedalus2uon 28 Dec 2010 at 7:46 am

    I don’t think it is even fringe science. It makes no predictions that can be tested. It is not even wrong.

  100. sonicon 28 Dec 2010 at 2:52 pm

    Guys-
    And what shall we call ‘string theory’ then?
    What loks like fringe BS may be nothing more than fringe BS. On the other hand, here we find people attempting to model life as informational systems and apply a fairly robust mathematics to that.
    I don’t know how well that will work.
    After all, it could turn out that life is just a random accident and not much more can be said– evolution as random walk (SJG)- or one of my favorites “Evolution is like water on glass- it goes wherever it can.”
    The ‘law of nature’ ‘stuff happens’ isn’t completely satisfying to everyone.
    Shall we make fun of that hypothesis for a while? (That is entirely rhetorical).

  101. cwfongon 28 Dec 2010 at 3:10 pm

    Sonic,
    “Theirs not to reason why, theirs but to do and die.”

  102. BillyJoe7on 29 Dec 2010 at 6:32 am

    Oh, and I forgot….

    If you think Daniel Dennett is on your side of the argument let me just blow wind and tell you you’re smelling roses.

    :D

    Anyway, enough of this.

  103. cwfongon 29 Dec 2010 at 12:18 pm

    Dennett (1981) calls this ‘intentional system (IS) theory’:
    “Full fledged intensional semantics of the familiar sort emerges, according to Dennett, only when we step up to the more abstract level at which we seek to capture informational patterns that describe systematic relations amongst a system’s goals, representations, and environment. We do this for the sake not of explaining the internal micro-causes of the system’s behavior, but for the sake of understanding the systems’s global capacities and dispositions in terms of recurrent patterns in its responses to environmentally posed problems that are characteristic of wider classes on intelligent systems of which the system in question seems to be a member.”

    Of course one has to be able to step up to that more abstract level. (Which is the context where we find intension as the mother of intention.)

  104. BillyJoe7on 29 Dec 2010 at 11:54 pm

    You quote some unknown person interpreting what Dennett said nearly thirty years ago and that is your argument that Dennett supports your nonsense?

    Don’t make me laugh.

    Coincidentally, I just read an article about the Voynich Manuscript. It consists of text that no one can decipher and images of plants that no one can identify. The best guess is that it is just made up gibberish done for the sole purpose of creating mystery.

    Interesting.

    Maybe I’ll coin a phrase to describe the gibberish we’ve been subject to here by cWrong/bungle/artlessDodge:
    The Voynich Illusion.

  105. cwfongon 30 Dec 2010 at 12:58 am

    TWIMC: One would think that for someone to claim to have read and understood Dennett, they’d realize they’d have to have actually read Dennett.

  106. BillyJoe7on 30 Dec 2010 at 6:18 pm

    I would think that someone who had actually read and understood Dennett would actually quote him directly rather than quote someone else’s interpretation of what they think Dennett said ;)

  107. cwfongon 30 Dec 2010 at 6:48 pm

    For those who’ve clearly (and admittedly) neither read nor understood him, here are things Dennett said I tend to be in agreement with (and the negatoid confirmatoids here don’t).
    Excerpted from: Consciousness Explained by Daniel Dennett (Chapter Summaries) Chapter 7, The Evolution of Consciousness 1. Inside The Black Box of Consciousness

    Dennett looks at the evolutionary survival value for a new “trick”. That is “producing” or more simply, predicting or anticipating (no matter how primitively), the future. There are many ways to survive- an organism can armor itself liked a tree or a clam and “hope for the best” or it can develop methods for getting out of harms way. If you perform this latter strategy, you are an animal, and the question on your mind is always: Now what do I do?
    To do this, you need a nervous system, to control your activities through time and space. For navigating through the sea for a suitable home the sea squirt has a rudimentary nervous system. But once rooted, it eats its brain since it is not needed anymore. Brains are anticipation machines. Even the armored clam cannot always stay closed- it snaps shut as a crude but effective harm-anticipator/avoider.

    These early nervous system depended on avoiding noxious contacts and seeking out nutritious bits (and mating opportunities once sex had appeared, of course), but this could still be improved upon by short range anticipation processes.

    (And boy will they hate this part!)

    Evolution in Brains and The Baldwin Effect
    Now a completely new “trick” that Dennett discusses next is the idea that some phenotypic (observable genetically produced variation in an individual) innovations in the brain are not entirely hard-wired, but are a more flexible and “programmable” type of brain processes. In addition to the hard-wired “duck when something is loomingoverhead” response we also have cyclical responses like grow more hair when cold and the waking/sleeping cycles. But sometimes an organism needs to respond to more unpredictable and unknown problems, and so an organism that can re-design it’s “software” wiring is at an advantage. We might call such design changes “development” or just “learning.”
    How can brains learn? One way, that does not require us to invoke miracles, is something related to a process of evolutionary natural selection but occurring within the individual (phenotype). For many years, the most popular explanation was B.F. Skinner’s “behaviorism” involving “operant conditioning”, but today the emphasis is on various theories that move evolution inside the brain. To avoid a major discussion of these various theories (by the way, that could and are being tested in huge computer simulations) let’s just say for our purposes that the brain is capable of reorganizing itself by selecting various brain “structures” or “connections” that control or influence behaviors, and the selection itself is accomplished by a mechanical “weeding-out” process that is genetically part of the nervous system. Not only is this an advantage over organisms that cannot “re-wire” themselves, it also speeds up the process of evolution through a phenomenon known as the “Baldwin” effect.
    Think of the Baldwin effect in this way: let’s say a group of individuals in a species have some considerable variation in the way that they are hard-wired up. One possible way that some of them could (in principle) be wired up has a strong competitive advantage. But a slight difference in the wiring from this particular advantageous state means an individual has no competitive advantage. However thanks to some limited ability to re- wire themselves, some of the individuals can “stumble” upon the particular hard-wiring that has the competitive advantage. Those animals that start out genetically closer (in terms of mathematical connection possibilities) to the hard-wired “good trick” have a competitive advantage without waiting for evolution to randomly re-hard-wire their brains. The next generation will have even more individuals with hard-wiring closer (and therefore easier to learn) to the “Good Trick.”

  108. ccbowerson 31 Dec 2010 at 12:46 am

    Its not that cwfong is promoting a nonsensical, nonfalsifiable, fluff-filled idea about evolution that offers no additional explanatory power, but is based on an argument from incredulity…

    It is just that people who are more intelligent aren’t smart enough to understand him. Duh…

  109. cwfongon 31 Dec 2010 at 1:38 am

    Thank you Nurse Bowers for filling out the usual threesome of doofuses. I cited scientific research and support for everything I proposed, and you naysayers presented nothing but the evidence of your ignorance. The incredulity shown here is in the faith you have in your simplistic dogma, as my “faith” is in the uncertainty of belief and dogma.

    Look at what Dennett had to say above and tell him it’s nonsensical and nonfalsifiable. You three could triple your intelligence and still not understand him. Or understand Taborsky, a truly remarkable intellect at work.

    By the way, how’s that intelligent sieve theory working out for you as a prescription processor? And are you still asking “What is the difference between “plasticity” and “guidance from the organism”?

  110. BillyJoe7on 31 Dec 2010 at 10:33 pm

    cwFong,

    I am at a bit of a disadvantage here because I am on holidays with only limited access to the internet and no access to my copy of Daniel Dennett’s book “Consciousness Explained”.

    Nevertheless…

    Firstly, you still have not quoted Dennett directly. And I have to wonder why? Quote me where Dennett explicitly says that organisms predict and anticipate the future. Dennett does not deny modern evolutionary theory. In fact, he is an exponent of it. Dennett does not promote magic. If he has used these specific words, he has used them anthropomorphically.
    Other than that, I cannot find anything to disagree with in the first part of your post (before the bit about the Baldwin effect).

    The Baldwin Effect:

    There are versions of what is known as the “Baldwin Effect” that are controversial and versions that are not. Dennett’s use of the term is not controversial. Essentially it is to do with the role of brain plasticity in responses to a changes in the environment. Non-controversially, plasticity arises as a result of ordinary evolutionary mechanisms: random mutation and non random selection. Plasticity is selected for because organisms who have well developed brain plasticity have improved survival potential in a changing environment compared to organisms that have less well developed brain plasticity. Nothing magical here.

    As for the phrase, “organisms rewire their brains”. If you mean that literally you are promoting a non-evidence based magical view of evolution. And, if that is a direct quote from Dennett, I can assure you that he meant it to be read metaphorically. Genes are more like a recipe than a blueprint. The phenotype is the result, not of the genotype alone (“blueprint” view of the genotype) but of the genotype interacting with the environment (“recipe” view of the genotype). The plastic brain continues to change (establish new connections and break old connections) throughout life in response to changes in the environmental.

    Note that I said in response to the environmental change Not in anticipation of environmental change.

    Organisms may SEEM to anticipate environmental change as a result of plasticity, but it’s all just random mutation and non-random selection producing a characteristic that improves survival potential by givin the brain a capacity to change in response to environmental changes.

  111. cwfongon 01 Jan 2011 at 12:15 am

    http://www.scribd.com/doc/9787203/Dennett-Consciousness-Explained
    Evolution of Consciousness, Page 171.

    The book is here for anyone to read or download. And to agree or disagree with. Or to misunderstand or misinterpret on a first hand basis.

  112. ccbowerson 01 Jan 2011 at 1:31 am

    cwfong deserves nothing here but to be ignored or ridicule. “nurse bowers?”… “processing prescriptions?”… nice try diverting from argument, but I am not a nurse nor do I process prescriptions, not that there is anything wrong with those things.

    Back to cwfong… he changes his name in order to have people forget how much of a waste of time it is to engage him. It was not the “ArtfulD” or “bindle” names that were the problem… it is still the same person who likes some magic in his reality, and won’t let go. Still probably pissed about the Santa Claus reality. Anyone who points out the gaping holes in his arguments get his “anyone who doesn’t understand my gibberish is too stupid to understand it” nonsense. He IS the room of monkeys with typewriters but he is not typing hamlet…. it is Madlibs.

  113. cwfongon 01 Jan 2011 at 3:50 am

    Ms. Bowers, you are an admitted nurse practitioner, so what’s to be ashamed of? The point is you’re not a scientist and neither are your luddite pals. What have you ever cited that backs up your objections to the discoveries of the nationally recognized scientists that I’ve brought to the attention of the other readers here? Absolutely nothing.
    You don’t have the capacity to examine their conclusions and make objections at their level, so, just as your cohort has done with the Dennett material, you lash out deceitfully at those who’ve gone to the trouble of introducing us to them and summarizing their ideas.

    And Ms. Bowers, you make these lame comments here that I’ve been charitable to call banal. They are simply dumb, but you have no way of knowing that, just as your pals have no way of seeing past their own particular impairments.
    You and the others claim I’m hiding something from you. But if what I’m saying is gibberish, why are you so concerned that there’s something there behind it that you need to know? Is it because it’s not simply me you don’t understand but those I’ve cited, and some sort of envy has got the better of you?
    But I must admit you make good foils that allow me to elaborate on various points of commentary. Why, look ma. I’ve got three stooges!

  114. BillyJoe7on 01 Jan 2011 at 7:17 am

    cwfong,

    And yet still no direct quotes from Dennett.

    Still just unattributed quotes from others interpreting what he said and, belatedly, some interpretations of your own which you seem unable to defend with direct quotes or even a response to my defence of Dennett’s science-based philosophical worldview.

    I have read enough of Dennett to know he is not a magical mystery man. Which makes me wonder about the others you have mentioned who, according to you, like a bit of magic mixed in with their science.

  115. cwfongon 01 Jan 2011 at 1:19 pm

    Yeah, he got me. That thing online above that’s purported to be Dennett’s book that one could get their ‘quotes’ from directly and ‘prove’ he was misquoted – well I rewrote it and changed the parts that didn’t fit with what the others that I quoted quoted, and then I went back in time and published it on Scribd without anyone and especially Dennett being the wiser.
    Because I confess that all those scientists and reviewers that I’ve cited earlier are all in a conspiracy with and orchestrated by me to fool not just these stooges but everyone in the wide wide world.

  116. cwfongon 01 Jan 2011 at 6:54 pm

    And here’s a direct quote from Dennett that I will have allegedly made up about the Baldwin Effect:
    “It is not that the Baldwin effect accounts for otherwise inexplicable differences in tempo in evolution, but that it accounts, as Maynard Smith so crisply shows, for the evolution, in sexually reproducing species, of traits that theory would otherwise declare to be all but unevolvable- those needles in a haystack that would otherwise be invisible to natural selection.”

    I will also have imagined Dennett giving this example of how learned experience (allegedly) drives adaptation:
    “The learned human Good Trick of animal husbandry. Dogs that could more readily learn to herd had a huge selective advantage, but only because of their interactions with their foresighted, looking-ahead “masters.” In this case, it was the “mind directed” activities of another species that created the gradients up which first unconscious and later, artificial, selection could drive the genomes of those wolf-kins.”

  117. BillyJoe7on 01 Jan 2011 at 11:19 pm

    Dennett:

    It is not that the Baldwin effect accounts for otherwise inexplicable differences in tempo in evolution, but that it accounts, as Maynard Smith so crisply shows, for the evolution, in sexually reproducing species, of traits that theory would otherwise declare to be all but unevolvable- those needles in a haystack that would otherwise be invisible to natural selection.

    I haven’t read the context but my guess is that he is talking here about plasticity – that characteristic that evolved through random chance and non-random selection! – and which, in turn, increased the efficiency and speed of evolutionary change.
    Nothing magical here.
    Now, do you have a quote which states his belief in actual magic or are we done here?

    The learned human Good Trick of animal husbandry. Dogs that could more readily learn to herd had a huge selective advantage, but only because of their interactions with their foresighted, looking-ahead “masters.” In this case, it was the “mind directed” activities of another species that created the gradients up which first unconscious and later, artificial, selection could drive the genomes of those wolf-kins.

    Yes, the human brain evolved to overcome the tyranny of the genes. We can use contraceptives to prevent our genes moving into the next generation if we so desire. We can breed animals that suit our needs. In selected instances we can even manipulate the genome removing genes we don’t want or adding those we do. In the future genomes may come fully tailor made.
    Thanks for your information and education. ;)

    Now…what was that about bacteria?

  118. Eric Thomsonon 02 Jan 2011 at 12:27 am

    cwfong, the baldwin effect is just good old fashioned natural selection, not inheritance of acquired characteristics (the latter can happen, incidentally, such as in bacterial induction of genetic material).

    (I guess technically passing on a mutation to an offspring is inheritance of aquired characteristics, if we wanted to really stretch the meaning of the term by extending it to any changes in the germ line rather than phenotypically meaningful genetic changes acquired as organisms adapt to their environments.

    cwfong, do you thnk final causes should be reintegrated into biology? With all respect, while you do sometimes cite science, you seem to be motivated by extrascientific considerations. I’m wondering what you think of purpose in biology, if that is the extrascientific angle that concerns you.

  119. cwfongon 02 Jan 2011 at 1:06 am

    Someone point out to this simpleton that Dennett’s talking about the heritability of acquired traits.
    Plasticity is not the mechanism, it’s the internal environment where the experience of the organism is assessed and adaptive behaviors are learned. The Baldwin effect refers to the mechanism by with these behaviors take on the status of heritable traits. Traits that the natural selection theory “would otherwise declare to be all but unevolvable.” I.e., “that would otherwise be invisible to natural selection.”

    The point of his whole exposition, and the use of the Baldwin phraseology is that he is NOT talking about evolution through random chance, he’s talking about evolution based on the experience of the organism.
    Proof positive that Moe, Larry and Curley can’t understand what they have read, especially if it’s something they don’t want to know.
    Applicable to bacteria, dogs, humans, and arguably space aliens with anticipatory capabilities.

  120. cwfongon 02 Jan 2011 at 1:10 am

    Eric writes:
    “I guess technically passing on a mutation to an offspring is inheritance of aquired characteristics, if we wanted to really stretch the meaning of the term by extending it to any changes in the germ line rather than phenotypically meaningful genetic changes acquired as organisms adapt to their environments.”
    I guess you could because that’s what Dennett did.

  121. cwfongon 02 Jan 2011 at 1:17 am

    Eric, there was no final cause, unless you can explain how something will have come from nothing. As to purpose in biology, it’s the acquired basis of anticipation.

  122. cwfongon 02 Jan 2011 at 1:49 am

    As an afterthought, it has to be pointed out again that Dennett went further that Eric seems willing to because for one thing, his use of the term Baldwin Effect would signify (in a semiotic sense of course) that he was concerned with that particular hypothetical, and not with some facetious play on words.

  123. cwfongon 02 Jan 2011 at 2:13 am

    And Eric, didn’t you like this paper either?

    https://s.p5.hostingprod.com/@www.biosemiotics.org/ssl/ISBS_OPR_Taborsky.pdf

    Because I’d have to say, it lit up my confirmation bias apparatus like the proverbial lantern in the dark.

  124. cwfongon 02 Jan 2011 at 2:25 am

    By the simpleton I was addressing wasn’t Eric whose comment I hadn’t yet seen. But he’s welcome to join in on the fun. We need a Shemp.

  125. cwfongon 02 Jan 2011 at 3:35 am

    Foundations Of Biology: On The Problem Of “Purpose” In Biology In Relation To Our Acceptance Of The Darwinian Theory OF Natural Selection, Paul S Agutter and Denys Wheatley.
    Hardly viewed by the writers as an extrascientific consideration, in the likely case none of you have read it.

  126. daedalus2uon 02 Jan 2011 at 10:00 am

    cwfong, so what is the mechanism by which experience by an organism changes the DNA in its germ cells to produce a genotype that will produce a phenotype that recapitulates the experience?

  127. cwfongon 02 Jan 2011 at 1:13 pm

    You tell me. I’m pointing out what Dennett wrote, not what he didn’t write. Was he wrong? Then why don’t you tell him why, and how such behavioral traits are actually recapitulated as you put it.
    Because they clearly are, and though you and your kin here find it magical, it is likely nothing more than, as Dennett named it, one hell of a “good trick.”

  128. daedalus2uon 02 Jan 2011 at 1:44 pm

    Can you provide a link to the actual data showing that behaviors change genes? Not an interpretation of data that is not shown, but the data that was used to form that interpretation?

  129. cwfongon 02 Jan 2011 at 3:07 pm

    I’d rather point you to the researchers who have acted on the assumption that experience may well drive evolution, rather than accept the dogma that life could not acquire the required purposes, let alone the skills.

    And I’ve already done that several times here. All you need to do is want (i.e., aspire) to read the material with a mind that’s open to the analytical. These people make mistakes and learn from them. You seem to want only to search for their mistakes and so far have ignored the learning aspects.

  130. cwfongon 02 Jan 2011 at 4:15 pm

    Don’t overlook this one in particular:
    Self-engineering capabilities of bacteria
    Eshel Ben-Jacob1,2,† and Herbert Levine2
    http://star.tau.ac.il/~eshel/papers/Interface.pdf

  131. BillyJoe7on 02 Jan 2011 at 6:01 pm

    cwFong,

    Show me the friggin’ quote already.

    That’s all you need to prove your point that Dennett supports the view that the inheritance of acquired characteristics (“experience driving evolution) is an important evolutionary mechanism.

    As I said, I don’t have the book at hand but I am convinced he would have been talking about something like brain plasticity and its SEEMINGLY magical effects achieved through an ACTUAL naturalistic mechanism

    We’re travelling back home from our holiday today so will have access to my copy of Dennett’s book tonight, therefore a chapter or page number is all I need.

  132. cwfongon 02 Jan 2011 at 7:14 pm

    What, the Scribd online published version cited earlier isn’t good enough? In any case he won’t find what he doesn’t want to find – the discouragement of his convictions.

    But if it were me, I’d look for this part:
    Behaviors have to anticipate the advantage to be taken of both the intentional and accidental. Accident on the other hand has no capacity to take advantage of behavior. It cannot acquire motivation or incentive – it can’t do more than serve our capabilities there. Accidents that do otherwise are misdefined as accidental.

  133. daedalus2uon 02 Jan 2011 at 9:03 pm

    Cwfong, that link doesn’t provide any data about experience causing heritable changes. They specifically say:

    “We note that the example of bursts of sectors also provides additional support to the assumption that the colonial ‘learning’ does not simply reflects a genetic shift or selection of random mutations. Had it been a mutation that can generate a colony better adapted to the antibiotic we would expect to observe the emergence of a sector when the bacteria are first grown in the presence of the antibiotic stress.”

    Colonies change when they are subjected to certain stresses. There is nothing startling about that. There is also no indication that there is any change in genetics that is heritable as a consequence of the stress.

  134. cwfongon 02 Jan 2011 at 10:05 pm

    You picked an example, or thought you did, to suit your purposes. What else is new.
    Ask yourself: How did those colonies continue to replicate themselves and still maintain the lessons learned that formed and supported their adaptive strategies?

    Then reread that quote and see that what it actually conveys is the exact opposite of what you seem to think it’s saying.

    “the colonial ‘learning’ does not simply reflect a genetic shift or selection of random mutations.”
    In other words they’re pointing out that it was not the commonly accepted or expected process of mutation but seemed more akin to one of self-engineering. Simply put, the strategy involved seemed not to require an accident of mutation to persist in succeeding generations.
    You should also have seen that the purpose of the research was to determine more precisely how this engineering process could have worked, and do so with such immediacy.
    And you should also have been looking at the other literature before, as a putative scientist, being satisfied with finding what you thought was one piece of self serving data. That’s what your pals here are doing, but you at least should know better.

    Go read and study the other material and then come back. Otherwise I’m done with this back and forth.

  135. BillyJoe7on 03 Jan 2011 at 3:04 am

    cwfong,

    Are you really leaving? Well, of course you are. Now that we have you firmly by the short and curlies and on the verge of yanking them out along with all the underlying paraphenalia?

    :D

    Is this the chapter in Daniel Dennett’s book “Consciousness Explained” that you are referring to: “Evolution in brains and the Baldwin Effect” pp182 – 187?

    Hey, I think it just might!
    But, if it’s not, it doesn’t matter, because you have read the whole book, right?
    So let’s take a look shall we…

    Whilst reading the chapter, I made notes about the bits that I thought you might have misunderstood. The bits that might just have resulted in you thinking he was saying something which I know is the complete opposite of his actual point of view. As I was writing these points down I had to admit that I could well understand how someone, coming where you are coming from, could have misunderstood what he was saying.

    But, then, all of a sudden, out of the blue, in black and white, with absolutely no possibility of misinterpretation, I came across this bit:

    “This process, the Baldwin Effect, might look at first like the discredited Lamarckian idea, but it is not”

    Oops!

    I mean, how did you miss that sentence, cwrong/bungle? It is in the penultimate paragraph of that chapter. Go on, read it again and confirm what it says. Now, prove what an artless dodge you are and make Dennett mean the opposite of what he quite clearly and unequivocally actually says. Here it is again:

    “THIS PROCESS, THE BALDWIN EFFECT, MIGHT LOOK LIKE THE DISCREDITED LAMARCKIAN IDEA, BUT IT IS NOT”

    Really, cwfong, I suggest you read Dennett again. But first put completely out of your mind the mistaken idea that Dennett supports lamarckian inheritance. See if you can’t see what he is quite clearly and painstakingly trying to tell you: that the clever tricks that random mutation and non-random selection can perform are far, far greater than anything you are willing to credit.

    (Of course this puts all your other links and references into question as well. But, hey, I am on holidays, so I’m going to be generous. I will let you have them all….as long as you leave me Mr. Dennett :) )

    regards,
    BillyJoe

  136. cwfongon 03 Jan 2011 at 4:42 am

    That’s right, the Baldwin effect is based on inheritance of learned behaviors, and Lamarck was based on what he thought was evolution of acquired forms. Lamarck believed in short that behaviors then evolved to fit the forms. But as Baldwin much later proposed, and the Taborsky paper explains, it’s the learned and functional behaviors that are heritable, and physical formations have to follow function.

    So this amateur stooge (Moe?) is confirming that Dennett has said exactly what I wrote he said above. And Lamarck had not been mentioned on this thread until Moe mentioned it.

    Just as poor daedalus misread the Ben_Jacob paper, old Moe here has misread Dennett, because he clearly spelled out the differences in the theories and poor Moe completely missed that part. Like his unfortunate crony, he saw only what he wanted to see, and out of his ignorance of the history and the details of the theories, convinced himself he’d seen it.

    And yet even now he doesn’t seem to realize that he’s just confirmed exactly what he claimed would not be found in Dennett’s book: that organisms can rewire themselves with behavioral traits that will then be heritable. IOW, the heritability of learned behaviors. Bada bing, bada boom

    Watch how he tries to wiggles out of this one. Should be a hoot.

    And by the way, what was it again that Dennett said about anticipation?

  137. BillyJoe7on 03 Jan 2011 at 6:17 am

    cwfong,

    “That’s right, the Baldwin effect is based on inheritance of learned behaviors, and Lamarck was based on what he thought was evolution of acquired forms.”

    You are doubly wrong here.
    The term “Lamarckism”, as used by Dennett, refers to both.
    The mechanism of the Baldwin Effect is entirely different.

    I’ll expand on this:

    ——————————-

    Firstly, the difference in definitions:
    You are restricting Lamarckism to the inheritance of forms only. Dennett, on the other hand, uses the term Lamarckism in the more inclusive sense – what Dawkins has referred to as the extended phenotype

    If you have doubt that this is the case, let me just refer you to another quote from Daniel Dennett’s book:
    (same book, ch 7.6, p 208)

    “The discredited Lamarckian idea of the genetic transmission of individual acquired characteristics was initially attractive to biologists in part because of its presumed capacity to speed new inventions into the genome (For a fine demolition of Lamarckism, see Dawkins’ discussion in “The Extended Phenotype” 1882)”

    I trust I don’t need to remind you what is meant by the “extended phenotype”.
    But just in case:

    http://en.wikipedia.org/wiki/The_Extended_Phenotype

    “The main idea is that phenotype should not be limited to biological processes such as protein biosynthesis or tissue growth, but extended to other aspects such as cognitive activities and more generally to the behavior of the animal in its environment.”

    Okay then, since we are discussing Dennett’s book, let’s just use the term as Dennett uses it shall we. ;)

    ————————————-

    Secondly, not only is behaviour included in Dennett’s (and Dawkins’) reference to Lamarkian inheritance, he explicitely states that inheritance (of both types) cannot be inherited in a Lamarckian fashion.

    “That does not and cannot happen”
    (again same book, ch 7.6, p 208)

    IN other words, Lamarckian type inheritance of phenotypic (form) and extended phenotypic (behaviours) does not and cannot happen.

    The mechanism of the Baldwin Effect, as described by Dennett, is nothing more than random mutation and non-random selection. This Darwinian type inheritance results in brain plasticity (because of the survival advantage of soft-wired brains over and above hard-wired brains). This plasticity, in turn, speeds up evolution and this occurs entirely through the mechanism of natural selection.

    The Baldwin Effect has nothing at all to do with Lamarckian type inheritance – of form or behaviour. If you think Dennett is promoting a type of Lamarckian inheritance for behaviour, please quote where he does so.

  138. BillyJoe7on 03 Jan 2011 at 6:18 am

    ..sorry, I messed up the bolding :(

  139. cwfongon 03 Jan 2011 at 12:19 pm

    Again, as I predicted, this rant above is purely a desperate red herring as Lamarck was never mentioned here before BillyMoe so desperately brought it up. Dennett is not promoting anything from Lamarck and it’s a blatantly dishonest tactic to claim I’m promoting that as either his or my position. Being dumb is one thing but being a lying turd is quite another.

    Dennett is describing how a Baldwin like effect seems to be taking place as part of the evolutionary process, and was careful to point out that this is NOT Lamarckian. BillyMoe has never grasped the difference. Lamarck was about evolution of physical forms. Baldwin is about the evolution of the functional apparatus that both uses and produces forms.

    It is NOT about random mutation, it’s about a clear exception to that dynamic, and that’s why Dennett brought it up – as the mechanism by which learned behaviors(not prewired but learned from experience) take on the status of heritable traits. Traits that the natural selection theory “would otherwise declare to be all but unevolvable.” I.e., “that would otherwise be invisible to natural selection.” OTHERWISE BE INVISIBLE TO NATURAL SELECTION – Dennett’s words, not mine.

    Why do I bother to correct the idiocy that this fool comes out with. Because he’s made himself a spokesperson for this blog and the owner goes along with it – presumably for theatrical effect. But it’s fast becoming a Theatre of the Absurd and the audience needs to know this nut is not in any way a writer or producer, he’s simply a bad actor.

  140. daedalus2uon 03 Jan 2011 at 2:25 pm

    cwfong, how do bacteria produce the physical forms and make them heritable without changing their genome?

  141. cwfongon 03 Jan 2011 at 3:35 pm

    They don’t do this without changing their genomes. That’s the point, and the reason for the research. Go read it, contact the researchers directly, consider the real possibility that they know what they’re looking for and how to know it when they see it.
    Don’t approach them with this kind of question however.
    One that shows your mind is closed to such auxiliary hypotheses.

  142. cwfongon 03 Jan 2011 at 3:44 pm

    For example read this again, but this time with an open mind:
    Rethinking The Genetic Theory Of Inheritance: Heritability May Not Be Limited To DNA
    http://www.sciencedaily.com/releases/2009/01/090118200632.htm

  143. Eric Thomsonon 03 Jan 2011 at 4:24 pm

    cwfong: this theoretically interesting, but still unconfirmed, Baldwin Effect is still just a special case of natural selection.

    Epigenetic influences are important factor to consider in development. If you could describe the data in your own words, and how it supports your position, that would be much more helpful than links (argumental ad a-href-ium was a specialty of bindle).

    You cited:
    “Foundations Of Biology: On The Problem Of “Purpose” In Biology In Relation To Our Acceptance Of The Darwinian Theory OF Natural Selection, Paul S Agutter and Denys Wheatley.
    Hardly viewed by the writers as an extrascientific consideration, in the likely case none of you have read it.”

    You couldn’t have picked a worse example.

    Lines like the following are not even sophomoric, they are pre-school:
    “It is argued that there is and always has been a clear distinction between life sciences and physical sciences, explicit in the use of the word biology. If this distinction is real, it implies that biological phenomena can never be entirely satisfactorily explained in terms of extant physicochemical laws.”
    Seriously? The use of a different word is deep and significant metaphysically? Wow. Mark Twain, meet Samuel Clemens, apparently you didn’t know you were different people.

    The article is a soft philosophy-history piece that reads like a junior high cut and paste. It is precisely coming off as precommitted to final cause or purpose in nature, rather than forced there by the data. It’s exactly doing what I said.

    Just awful. Please don’t suggest crap like that ever again. Just make your arguments, see if they stand on their merits, and bring in data and evidence to make your points, don’t send people off on these silly wild goose chases you are wasting our time unless you can put into your own words what the evidence, data, and theory suggest. Sorry, that’s the blogosphere.

    Also, I was trying to get a sense for where you are coming from, and you respond as if you were hit with a hot poker. If you have extrascientific concerns, that’s not necessarily a bad thing. I have extrascientific concerns…sports, for instance.

  144. Eric Thomsonon 03 Jan 2011 at 4:30 pm

    Also, they don’t even cite the huge literature on function claims in biology from the past forty years (from Wright, Cummins, Millikan, et al). I see why it is published in a POS journal. Just awful.

  145. cwfongon 03 Jan 2011 at 5:13 pm

    Eric, I agree that I responded a bit defensively – and based on your timing and related questions, I’m still not willing to trust your motives here. For example, I don’t agree that the article I cited is crap.

    I have put in my own words what I conceive are the means and necessities for the acquisition of purposes by life, and those such as yourself that don’t believe that this is happening cry out for further proof of concept. When I offer it, they cry out for me to return to my own exposition of the concept.

    I don’t agree that final cause as the creative font of purpose is at the hub of the argument presented by Agutter, etal. I do know however that any hint of evolutionary purpose is anathema to the neoDarwinist agenda.
    But my view is simply this: Evolution is not a “thing” that “has” a purpose. It’s our metaphorical concept of a process that “serves” a purpose – and not just one but a litany of those acquired along its way.
    The cited paper is supportive of that view, even if not the same approach, or from the same direction. If it wastes your time, don’t read it through, because to me it’s a waste of time to hear these same stale objections over and over. Sorry, but that’s also the blogosphere.

  146. BillyJoe7on 03 Jan 2011 at 6:37 pm

    cwfong,

    Dennett is not promoting anything from Lamarck and it’s a blatantly dishonest tactic to claim I’m promoting that as either his or my position.

    Actually, I’m not dishonestly claiming anything about your position. I’m still, after all this time, trying to get a sense of what you actual position is. If you are not talking about Lamarckian inheritance, what on Earth are you talking about? How exactly do your views on evolution differ from, say, Steven Novella’s (since these discussions usually result from you criticising something he says)? How do they differ from what we might call the mainstream view? And how does anything Dennett has written support anything other than the mainstream view?

    Dennett is describing how a Baldwin like effect seems to be taking place as part of the evolutionary process, and was careful to point out that this is NOT Lamarckian. Lamarck was about evolution of physical forms. Baldwin is about the evolution of the functional apparatus that both uses and produces forms.

    Maybe Lamarck was about the evolution of forms but, what is commonly referred to these days as Lamarckism (or neo-Lamarckism), covers both territories. It is certainly what Dennett and Dawkins argue against when they argue against Lamarckism .

    “It is NOT about random mutation”

    Of course it is.

    In Dennett’s example of the Baldwin Effect, he starts with a population of organisms that have different ways in which their brains are hard-wired. That wiring up and those differences between the organisms were the result of random mutation (and natural selection) in the organisms’ ancestors. Figure 7.1 shows the adaptive landscape of these organisms – the “needle in a haystack” situation.

    Next he considers a population of organisms whose brains are both hard-wired and soft-wired. Again, both the soft-wiring and the hard-wiring were the result of random mutation (and natural selection) in the organisms ancestors. It is the soft-wiring that gives plasticity to the brain, meaning that plasticity is the result of random mutation (and natural selection). As a result of this plasticity (which, may I reiterate, is the result of random mutation and natural selection) the wiring up in these organisms brains can change as a result of changes in the environment. Those organisms whose plasticity covers a range of possible changes that includes a configuration that increases their fitness in the changed environment tend to survive. Over time these organisms come to predominate. That is the Baldwin Effect. Figure 7.2 shows the adaptive landscape of these organisms – the “invisible needle in the haystack” gives way to a “visible hill that natural selection can climb”.

    “…it’s about a clear exception to that dynamic, and that’s why Dennett brought it up – as the mechanism by which learned behaviors(not prewired but learned from experience) take on the status of heritable traits.”

    The learned behaviours are only possible because of plasticity. They are what plasticity is all about. And plasticity is the result of random mutation and natural selection. Dennett talks about “a mechanical selector” and a “multitude of candidates for selection” (or “various brain structures that control or influence behaviour”). These are the result of ordinary random mutation and natural selection or, as Dennett says, “genetically installed in the nervous system” .

    ” Traits that the natural selection theory “would otherwise declare to be all but unevolvable.” I.e., “that would otherwise be invisible to natural selection.” OTHERWISE BE INVISIBLE TO NATURAL SELECTION – Dennett’s words, not mine.”

    But you misunderstand what he says.
    When he says thay are “all but unevolvable” and “invisible” to natural selection, he is referring to hard-wired brains. He is saying that, if all there ever was was hard-wired brains, these traits would almost certainly not have evolved because they would be like searching for “a needle in a haystack” in the genetic landscape. But random mutation and natural selection resulted in brains that are also soft-wired resulting in neuronal connections that can change in response to changes in the environment.
    This is completely in tune with the modern view of evolution.

  147. cwfongon 03 Jan 2011 at 6:45 pm

    BillyMoe has now switched from lying to his audience to lying to himself.

    Baldwin would not apply if this wasn’t about the inheritance of learned behaviors by other than the random mutation process. It’s that simple.

  148. BillyJoe7on 03 Jan 2011 at 6:52 pm

    cwfong,

    But my view is simply this: Evolution is not a “thing” that “has” a purpose. It’s our metaphorical concept of a process that “serves” a purpose – and not just one but a litany of those acquired along its way.

    Evolution is our metaphorical concept of a process that “serves” a purpose (or many purposes acquired along the way)?

    So we have both the direct mention of the word metaphor and the use of scare quotes which, I assume, is a signal that you are using that word as a metaphor, in your statement of your view on evolution.
    Is it any wonder that you can’t get your point across?

    Isn’t it possible to state your view clearly and unambiguously?
    Please leave the ivory tower of your self-importance and reveal yourself to us lesser mortals ;)

  149. BillyJoe7on 03 Jan 2011 at 7:08 pm

    cwfong,

    “Baldwin would not apply if this wasn’t about the inheritance of learned behaviors by other than the random mutation process. It’s that simple.”

    Thanks for your explanation. ;)

    In the mean time, here is Dennett on the Baldwin Effect:

    “Cutural evolution and the transmission of its products is the [third medium of evolution], and it depends on phenotypic plasticity [the second medium of evolution], in much the same way as phenotypic plasticity depends on genetic variation [the first medium of evolution].”

    “Amazingly, this capability, itself a product of genetic evolution by natural selection, not only gives the organisms who have it an edge over their hard-wired cousins who cannot redesign themselves, but also reflects back on the process of genetic evolution and speeds it up”

    The last two mediums, phenotypic plasticity and cultural evolution speed up the process of the first medium, genetic change.

  150. cwfongon 03 Jan 2011 at 8:10 pm

    TWIMC: Plasticity, exactly as I said before, is not the mechanism, it’s the internal environment where the experience of the organism is assessed and adaptive behaviors are learned. The Baldwin effect refers to the mechanism by with these behaviors take on the status of heritable traits. Traits that the natural selection theory “would otherwise declare to be all but unevolvable.” I.e., “that would otherwise be invisible to natural selection.”

    To the extent that plasticity itself had evolved, the organisms involved may well have taken earlier advantage of random acts of nature. All organisms do. That’s why Dennett used the term amazingly, because in his own words, the organisms that have it also (and paradoxically) “have an edge over their hard-wired cousins who cannot redesign themselves.”
    I know it’s hard for BillyMoe to draw the inference from “cannot” to “can” but if he could, he’d know this means those cousins with plasticity CAN redesign themselves, and thus effectively pass, via the Baldwin process, those designs on to their progeny. And by reference to Baldwin, he restricts the process to learned behaviors (which however I’m told by others are designed in the “form” of symbolic algorithms – but I digress).
    Note that cultural evolution would NOT apply if there was no plasticity to enable the Baldwin effect to occur. Because I believe it’s Dennett’s position that hard wired cousins cannot evolve behaviors by cultural means alone. But again I have digressed.

  151. cwfongon 03 Jan 2011 at 8:24 pm

    And did he mean to say earlier that evolution is not a metaphor for a process, but is a function with a physical reality – like Mother Nature in the flesh? Yeah, I think he did mean that. He does think at that same creationist level.

    And when is he going to tell us what Dennett really said about anticipation?

  152. Eric Thomsonon 03 Jan 2011 at 9:15 pm

    cwfong: I overreacted too. Just want to understand.

    You said:
    “But my view is simply this: Evolution is not a “thing” that “has” a purpose. It’s our metaphorical concept of a process that “serves” a purpose – and not just one but a litany of those acquired along its way.”

    I don’t really get this. Can we talk about a specific example? For instance, the heart’s function is to pump blood, that’s its main purpose. Now your turn. Is there something you can glean from that to help me understand your position?

  153. BillyJoe7on 03 Jan 2011 at 9:33 pm

    cwfong,

    Plasticity, exactly as I said before, is not the mechanism, it’s the internal environment where the experience of the organism is assessed and adaptive behaviors are learned. The Baldwin effect refers to the mechanism by with these behaviors take on the status of heritable traits. Traits that the natural selection theory “would otherwise declare to be all but unevolvable.” I.e., “that would otherwise be invisible to natural selection.”

    I’m not saying anything different.
    But I’m still waiting for you to clearly state the mechanism of the Baldwin Effect and to explain how it is not part of the modern view of evolution.

    To the extent that plasticity itself had evolved, the organisms involved may well have taken earlier advantage of random acts of nature. All organisms do.

    “may well have taken advantage of random acts of nature”
    How else could plasticity have evolved?
    (just asking the question)

    That’s why Dennett used the term amazingly, because in his own words, the organisms that have it also (and paradoxically) “have an edge over their hard-wired cousins who cannot redesign themselves.”

    Why paradoxically?
    Surely it follows that organisms with soft-wired brains would have a survival advantage over their hard-wired cousins in environments that change over the lifetimes of the organisms.

    I know it’s hard for BillyMoe to draw the inference from “cannot” to “can” but if he could, he’d know this means those cousins with plasticity CAN redesign themselves, and thus effectively pass, via the Baldwin process, those designs on to their progeny.

    The sentence “those cousins with plasticity can redesign themselves” is clearly a metaphor.

    In other words, organisms with brains that exhibit plasticity and that live in an environment that changes unpredictably or chaotically during the their lifetimes, have increased survival potential compared to those organisms who have hard-wired brains. This is because the change in the environment, which acts as an imput into the brains of these organisms, causes a rewiring of neuronal connections within the brains of these organisms which results in that organism’s increased survival potential under those changed environmmental conditions compared with those organisms who have hard-wired brains.
    (I’m trying to be as complete and pedantic as possible here :) )

    Dennett simply uses the metaphor to effect an economy of words.

    And by reference to Baldwin, he restricts the process to learned behaviors. Note that cultural evolution would NOT apply if there was no plasticity to enable the Baldwin effect to occur. Because I believe it’s Dennett’s position that hard wired cousins cannot evolve behaviors by cultural means alone.

    Yes, I’m sure that is what he meant when he said:
    “Cutural evolution…is the [third medium of evolution], and it depends on phenotypic plasticity [the second medium of evolution], in much the same way as phenotypic plasticity depends on genetic variation [the first medium of evolution].”
    ;)

  154. BillyJoe7on 03 Jan 2011 at 9:48 pm

    cwfong,

    And did he mean to say earlier that evolution is not a metaphor for a process, but is a function with a physical reality – like Mother Nature in the flesh? Yeah, I think he did mean that. He does think at that same creationist level.

    Whose is using “a blatantly dishonest tactic to claim I’m promoting that as my position” now? ;)

    And when is he going to tell us what Dennett really said about anticipation?

    When are you going to show us that he is referring to bacteria? :)

    Really, who disagrees that organisms can overcome “the tyranny of the genes”? Who disagrees that, anticipating an unwanted preganancy, we can simply use contraceptives to prevent the genes, that have created us as protective armour, being transmitted into the next generation?

  155. BillyJoe7on 03 Jan 2011 at 9:49 pm

    BTW, is it just me, or does everyone else find everything in this commentary written in italics.

  156. BillyJoe7on 03 Jan 2011 at 9:54 pm

    Eric replying to cwfong,

    You said:
    “But my view is simply this: Evolution is not a “thing” that “has” a purpose. It’s our metaphorical concept of a process that “serves” a purpose – and not just one but a litany of those acquired along its way.”

    I don’t really get this.

    Join the queue. :D

  157. BillyJoe7on 03 Jan 2011 at 9:58 pm

    …sorry, I messed up again:
    Let me try again:

    ————————————–

    Eric replying to cwfong,

    You said:
    “But my view is simply this: Evolution is not a “thing” that “has” a purpose. It’s our metaphorical concept of a process that “serves” a purpose – and not just one but a litany of those acquired along its way.”

    I don’t really get this.

    Join the queue. :D
    (My appeal for clarification is about 9 posts up)

  158. cwfongon 03 Jan 2011 at 10:14 pm

    Wrong again on all counts, but useless at this point to explain why.
    But it gives me the chance to point out a further glitch in the speculative process here:
    The problem we actually have with the hypothetical hard wired only version of the brain is that there likely are no brains, human or non-human, that don’t have the capacity to learn and retain new and improved strategies. So the argument that Dennett has made to explain that there’s an element of the Baldwin effect extant in some but not all related organisms is really, in my view, a compromise with the reality that the Baldwin effect is more likely functional across the board. Look up the literature on the subject and see how it’s supposed to work and why, and some may reach the same conclusion I have.

  159. cwfongon 03 Jan 2011 at 10:46 pm

    Eric, I can’t really answer your question with this mental midget throwing spitballs from the peanut gallery. Which is of course the intent behind the throwing.

    I really thought the meaning would be clear to someone who’s given some prior thought to the problem of purpose. Think about anticipation for example, and the purposes that this function serves. You won’t have the one without some acquisition of the other.

    Read, if only to be critical, the Taborsky paper on the subject. Draw inferences, seek counterfactuals, etc.

    Otherwise, I’ll leave the idiot to his delights.

  160. BillyJoe7on 03 Jan 2011 at 11:25 pm

    In other words, no, you can’t explain your view clearly and unambiguously.

    And I thought perhaps we were getting so close this time.

    …oh well :(

  161. BillyJoe7on 03 Jan 2011 at 11:59 pm

    cwfong,

    Wrong again on all counts, but useless at this point to explain why.

    Yes, certainly, you are no Dennett or Dawkins.
    That, at least, is very clear.

    The problem we actually have with the hypothetical hard wired only version of the brain is that there likely are no brains, human or non-human, that don’t have the capacity to learn and retain new and improved strategies. So the argument that Dennett has made to explain that there’s an element of the Baldwin effect extant in some but not all related organisms is really, in my view, a compromise with the reality that the Baldwin effect is more likely functional across the board.

    Well, is that your view?
    Well, hey, consciousness did not arrive all of a sudden either.
    Like life itself.
    At one point in time, there was clearly no living thing in existence. At some later time, life was definitely present. At least on the that tiny blue dot we call Earth.
    When exactly did the transition occur?
    Who can tell?
    When exactly does a child become an adult?

    And when, oh when, will we be judged fit enough by The Great Master to hear the answer to the question that we’ve been asking for some time now…

    What exactly do you mean, cwrong/bungle/artlessDodge?
    Oh elevated one?
    What exactly do you mean?

    Look up the literature on the subject and see how it’s supposed to work and why, and some may reach the same conclusion I have.

    And in a puff of smoke he disappears.
    But wait….

    ….he will return to play his tricks another day, ever linking, ever quoting, forever hinting…with questions that will never be answered.

    And thus will it ever be so.

  162. BillyJoe7on 04 Jan 2011 at 12:02 am

    “Man of passion rise again, we won’t cross you out.
    For we do love you like a son, of that there’s no doubt.
    Tell us: is it you who are here for our good cheer?
    Or are we here for the glory, for the story, for the gory satisfaction
    of telling you how absolutely awful you really are? ”

    (“A Passion Play”, Ian Anderson)

  163. cwfongon 08 Jan 2011 at 11:00 pm

    Alexander Badyaev, an evolutionary biologist at the University of Arizona, has been studying little songbirds called house finches, which were native to deserts in the American Southwest and Mexico before they began spreading throughout the United States in the 1940s through the pet trade and natural dispersal.
    Badyaev tracked the birds through 19 generations over a span of 15 years at a study site in Montana, and found that the population was developing unique beak morphologies as adaptations to the new environment at a surprisingly rapid rate. According to the Modern Synthesis, beak shape should change as random mutations create a pool of phenotypes, which eventually get whittled down to those that are most advantageous. But the new habitats were so different from their original habitats, the only way for finches to survive would be if their beak shape had changed rapidly—too rapidly to have resulted from just random mutations. If that were the only way for them to evolve, the original desert-dwelling house finch populations would have been wiped out by the pressures present in their new habitats, Badyaev reasons. Instead, they’re thriving.
    How was this possible? To answer the question, Badyaev looked into the developmental patterns that give rise to the beak’s structure in house finches. He found a complex interplay of processes, such as the migration of five islands of neural crest cells that constitute skeletal beak components in the embryo. Interacting embryonic processes result in an initial level of phenotypic variation greater than what would be predicted from underlying genotypic variation alone.
    Because the drivers of this baseline phenotypic variation acted during development in the egg, Badyaev says, selection was essentially blind to the creation of this initial pool of phenotypic variation. It was only later, when young birds began feeding on the foods available in their new habitat, that selection could determine which beaks were more or less suited to the environment. “Selection does not see the developmental process by which this beak was produced,” he notes. “But it’s exactly there that resides the opportunity for diversification.” ‘

  164. cwfongon 08 Jan 2011 at 11:05 pm

    http://www.u.arizona.edu/~abadyaev/pubs/115.pdf

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