Feb 12 2010

A Darwin Day Celebration

Today is Darwin Day – the anniversary of the birthday of Charles Darwin on February 12, 1809. The Darwin Day Foundation is promoting Darwin Day as an international holiday, celebrating science and humanity. It is more than just a celebration of one great scientist – it is a recognition of the power of science as a human institution. It is also about defending science from anti-scientific goons who would seek to undermine or destroy it in order to protect their world view.

I decided to do my part by picking a random anti-evolution post and dissecting it – always a good time. As usual, the DiscoTute’s propaganda blog presents an embarrassment of riches for any hungry skeptic.

At the top of page is a post by Casey Luskin, who seems intent on refighting the Dover vs Kitzmiller trial in which intelligent design (ID) theory was soundly trounced and properly tagged as a religious belief, not science. Luskin, it seems, just cannot accept this defeat and so obsessively goes over it again and again, rehashing arguments that have been discredited years ago.

His current post is no different. Now he is picking on testimony about how the genome can acquire new information, writing:

Virtually all of those “publications” mentioned by Judge Jones came from one single paper Miller discussed at trial, a review article, co-authored by Manyuan Long of the University of Chicago. The article does not even contain the word “information,” much less the phrase “new genetic information.”

Luskin is an exemplar of denialism – showcasing the many ways in which denialists seek to create doubt and confusion, rather than engage in sincere scientific inquiry or discourse. Here he is picking on the fact that the judge in the case mostly quoted from one publication in defending his conclusion that the defenders of evolution in the trial, and specifically Kenneth Miller, presented evidence to support the conclusion that evolutionary processes can result in increased information. But the one article was a review article, which means it brought together and summarized the research of many studies. This is not the same as citing one study.

Then he tries to make hay of the fact that the paper does not contain the word “information.” The paper concerns how new genes with new functions evolve. Since genes contain genetic information, new genes means new information. But Luskin does not appear to be interested in being fair or in honestly explaining the issue – just throwing doubt on whatever evolutionary biologists say.

ID proponents have a history of abusing the very concept of “information” and change the operational definition as needed. Luskin tries to turn this around on the biologists. This is a classic denialist strategy – arbitrarily shift your definitions around, and then accuse scientists of not using your definition in their criticisms. He writes:

A closer look shows that the NCSE is equivocating over the meanings of the words “information” and “new,” and that the NCSE’s citations are largely bluffs, revealing little about how new genetic functional information could originate via unguided evolutionary mechanisms. This bluff was accepted at face value by Judge Jones, who incorporated it in his highly misguided legal ruling.

While complaining about the NCSE “equivocating” over the meaning of “information”, Luskin then shifts slyly over to the phrase “functional information”. This is now an old ID trick. Claim that information theory argues against evolution, which requires increasing information (at least in some lines) over evolutionary time. But when mathematicians who actually understand information theory show how evolution can increase information, they shift over to “specified” information or “functional” information – without operationally defining it. And then they have the gall to claim that scientists are being squirrely.

He also throws in “unguided evolution” – another ID canard. Evolution is not unguided, at least not in the sense relevant to information theory. Mutations may be random, but natural selection is the process of cumulative non-random survival.

Let’s get to the specifics of the papers presented by Miller at the trial. They demonstrate, for example, that genes, parts of genes, groups of genes, and even entire chromosomes can be duplicated from parent to offspring. Where there was one gene there are now two.

ID proponents claim that the second gene is merely a duplication and does not represent new information, but they are being willfully ignorant. The duplication itself is only part of the process. Now that there are two genes for the same protein, one is redundant. This means that if one gene randomly mutates so that it makes a different protein, the organism will likely not suffer because the original copy of the gene, and therefore its protein product, remains. The duplicate copy is therefore free to mutate and evolve in random directions. It is therefore ripe for being coopted for another use.

Fastforward a bit through evolutionary history, and eventually we have two related but distinct genes coding for related but distinct proteins – two genes where previously there was one. This is new genetic information.

ID proponents just ignore the second part of that process. This is similar to their strategy of arguing that mutations are random and therefore cannot provide direction in evolution. Correct but irrelevant – natural selection provides the direction. They also argue that natural selection can only remove information, not create it. Correct but irrelevant – mutations provide new information. Evolution happens when mutations and selection happen together, it is a straw man to argue that either alone does not produce evolutionary change.

Getting back to genes – the evidence presented at trial was a sample of the scientific evidence that gene duplication and other changes to the genome have in fact happened throughout evolutionary history, and produce a pattern consistent with common descent.

Richard Dawkins also addresses this issue in a somewhat longer post that is worth reading. He goes over some basics of information and complexity, and applies it to evolution. He discusses, for example, the hemoglobin protein:

The dozen or so different globins inside you are descended from an ancient globin gene which, in a remote ancestor who lived about half a billion years ago, duplicated, after which both copies stayed in the genome. There were then two copies of it, in different parts of the genome of all descendant animals. One copy was destined to give rise to the alpha cluster (on what would eventually become Chromosome 11 in our genome), the other to the beta cluster (on Chromosome 16). As the aeons passed, there were further duplications (and doubtless some deletions as well). Around 400 million years ago the ancestral alpha gene duplicated again, but this time the two copies remained near neighbours of each other, in a cluster on the same chromosome.

He then goes on to point out that the branching pattern of descent among copies of ancestral genes conforms to the branching patterns of descent of the organisms that have those genes – a nice confirmation of common descent.

Regarding the entire issue of information and ID nonsense he writes:

The “information challenge” turns out to be none other than our old friend: “How could something as complex as an eye evolve?” It is just dressed up in fancy mathematical language — perhaps in an attempt to bamboozle. Or perhaps those who ask it have already bamboozled themselves, and don’t realise that it is the same old — and thoroughly answered — question.

This mirrors what I wrote about – their “bamboozle” over information theory, and specifically gene duplication, is the same old tune about mutations and natural selection, just with new jargon.

Luskin, of course, attempted to respond to Dawkins but in typical fashion butchered what Dawkins was saying:

The difference between the Darwinist and ID definitions of information is equivalent to the difference between getting 10 consecutive losing hands in a poker game versus getting 10 consecutive royal flushes. One implicates design, while the other does not.

You see how he is assuming in his straw man of the evolutionary position only the random duplication or mutations, and not the whole bit about natural selection? To correct his terrible analogy – what scientists are saying is that evolution is like dealing out a hand and having an unlimited ability to discard and draw new cards. I bet I could get a royal flush every single time with this evolutionary method. The cards I draw are random – but evolution allows me to draw new cards and only keep the ones that work.

But even this better analogy contains a misconception – because there is no predetermined hand in evolution. Rather, evolution is like drawing cards at random but getting to keep the ones you like and redraw as much as you like in order to make a winning hand. But that winning hand does not have to be a royal flush – it can be anything that works.

And with evolution, you don’t have to discard if you don’t want to. You can keep cards you don’t use, just in case they become useful in the future. Of course, your hand will become littered with cards you don’t use, but that’s OK. You are allowed to use just the cards you want.

Luskin is a useful idiot in that he reminds us why we celebrate Darwin Day – to remind ourselves not just that evolution is a legitimate and powerful science while creationism/ID is not science, but also the underlying reasons for this distinction. Science is a process of honest discovery. Creationism/ID is ideological propaganda, and its proponents are promoting doubt and confusion, not understanding.

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75 responses so far

75 Responses to “A Darwin Day Celebration”

  1. superdaveon 12 Feb 2010 at 10:05 am

    I’m glad that you are out there to counter this guy’s argument because I would have grown tired of him long ago. He won’t ever quit so we need people who won’t quit either.

  2. superdaveon 12 Feb 2010 at 10:15 am

    If Luskin can use coincidences as proof of intelligent design can we use the same tactic? How about the fact that Darwin knew nothing about DNA and genetics yet their discovery totally fit the requirements for the kind of information storage mechanism that Evolution needs in order to work.

  3. CWon 12 Feb 2010 at 12:02 pm

    Happy Birthday Charles Darwin, and Happy Darwin Day everyone. Ever since I started listening to SGU and reading blogs/books about evolution, I’ve become obsessed with the subject. I never grow tired of re-reading some of the same talking points, because I’ve noticed that I can discuss the subject with more authority and confidence – which I attribute to reading the material constantly.

    I’m still trying to get my head around the details regarding the argument about information. I guess it seems rather straightforward and obvious, but I must be not understanding this argument that comes from Creationists. The distinction of different information types. The Dawkins link was good for me to reference, and thanks again for taking the time to explain it.

  4. theshortearedowlon 12 Feb 2010 at 12:12 pm

    I think there should be a clause in new NSF grants that the recipient be required to respond to, say, 3 creationist arguments each year. That would prevent all the burden falling on the few noble individuals who have not yet been reduced to gibbering by the whole business.

  5. theshortearedowlon 12 Feb 2010 at 12:16 pm

    In fact, it could be divided up by discipline – astronomers and astophysicists could answer UFOlogists and astrologers; physicists could debunk perpetual motion machines; doctors and medical researchers can explain why acupuncture is suspect and homeopathy is impossible.

  6. theshortearedowlon 12 Feb 2010 at 12:17 pm

    Oh, and everyone with a relevant background gets at least one anti-vaxxer. That one needs all the help it can get.

  7. Daneel Olivawon 12 Feb 2010 at 12:24 pm

    Hahahaha. I loved your last paragraph. “Luskin is a useful idiot” would make a sweet t-shift.

  8. artfulDon 13 Feb 2010 at 3:58 pm

    Dawkins wrote in the article cited,
    “if natural selection feeds information into gene pools, what is the information about? It is about how to survive. Strictly it is about how to survive and reproduce, in the conditions that prevailed when previous generations were alive.”
    So far, so good, but what he doesn’t get into, and as far as I can tell never has, is the clear inference here that it’s life that is metaphorically asking the “how” questions (if not the five “w” ones at some point as well).
    And if so, it’s life that selects from experience the information that, as Dawkins surmises, is then fed into its gene pools.

    And if we evolve because life asks its own questions, then life must be intelligently providing its own answers appropriate to their purpose. Quite a bit different from picking appropriate cards drawn at random from nature’s dealer. And certainly no less effective, as far as the increase of useful information is concerned.
    And in fact Darwin understood this intuitively as a mechanism for natural selection, even if followers such as Dawkins don’t seem to.

  9. dubarnikon 13 Feb 2010 at 8:11 pm

    artfulD writes ” …it’s life that selects from experience the information that, as Dawkins surmises, is then fed into its gene pools. And if we evolve because life asks its own questions, then life must be intelligently providing its own answers appropriate to their purpose.”

    Oh, I get it. Life = God and we have intelligent design.

    No thank you. I gave at the office.

  10. Michael Hutzleron 13 Feb 2010 at 11:22 pm

    A metaphorical question does not imply intelligence. Natural selection is based one very simple question: “Did you reproduce?” If the answer is yes, you contributed to the gene pool for the next generation. The catch is that no one asks and no one answers. Life reproduces (or more often fails) without stopping to ask.

    Confusing the metaphorical question with an actual question is the fallacy of reification.

  11. artfulDon 14 Feb 2010 at 12:33 am

    The fact that all organisms need and have at least a rudimentary form of intelligence to function, and the purpose of that function is to solve problems, and make choices as part of the process, leads to a recognition that all such choices involve the question of their predictable effects. But since each organism can have a different way of assessing and ranking consequences, we can’t assume their questioning process resembles ours in any particular way. So we need to use the word in a metaphorical sense precisely to avoid confusing their questioning process with ours.
    Which is beside the point of whether or not such intelligence plays a part in evolution, since most biologists agree that it does. They earnestly, gravely, soberly, somberly, and seriously disagree as to the “how” mechanism.
    As to natural selection simply being based on the question,”did you reproduce,” who or what do you propose will be asking that question? Neither the IDiots or the Neo-Darwinists have an answer for that.

  12. Michael Hutzleron 14 Feb 2010 at 10:30 am

    Bacteria do not make choices or rank consequences. Ascribing choice to simple responses is the anthropomorphic fallacy. There is no intelligence or choice if the same stimulus always elicits the same response.

    Biologists do not agree that intelligence plays a role. If a bacterium has features which resulted in it arriving in a nutrient rich environment, it will have many progeny with those features, yet despite this, most lines it produces will reach a dead end.

    Humans ask metaphorical questions. Nature operates independently of those questions. As for the metaphorical question, “Did you reproduce?”, the population of the subsequent generation is the metaphorical answerer.

  13. artfulDon 14 Feb 2010 at 12:06 pm

    https://www.researchgate.net/publication/5794057_Bacteria_are_small_but_not_stupid_cognition_natural_genetic_engineering_and_socio-bacteriology

  14. Lenoxuson 14 Feb 2010 at 12:30 pm

    Whoa, Dawkins is totally off his rocker. First, as Ben Stein showed us all, Dawkins was absolutely convinced that panspermia must be true. Now, he thinks that our bodies contain “a dozen or so different goblins“, descended from “ancient goblins“. Am I somehow misrepresenting him here? Of course not.

  15. Heinleineron 14 Feb 2010 at 12:31 pm

    artfulD, the point is that nothing asks the question. If you ask what does 2 + 2 equal, the answer is 4. 2 + 2 = 4 even if nobody asks that question. Similarly, if something is capable of replicating itself, you will tend to see more of it. If something is capable of replicating itself faster or better than something else, it will overtake said something else. Nothing needs to ask any questions; the universe simply works, and we can ascribe all the meaning we want to that, whether or not it exists.

    If you want to say that bacteria have sentience or cognition, you might as well say that Fickian diffusion is the result of solute molecules willfully moving toward areas of lower concentration. You might say that objects intelligently desire to lower their gravitational potential energy, so they fall to the earth! You might say that electrons in excited atomic energy levels step down a notch in order to impress us with fluorescence.

    Okay, so you probably wont say that. You’ll probably agree that the processes mentioned above are merely physical and chemical processes. So are bacteria, although they’re a combination of many simultaneous chemical processes.

    You seek only to misdirect, and your use of the term “Neo-Darwinists” reflects that, because no such group as Neo-Darwinists exists. The term you’re looking for is “all biologists alive today.”

  16. artfulDon 14 Feb 2010 at 3:25 pm

    Another excellent exposition concerning the choice making functions of all living organisms:

    http://www.questia.com/PM.qst;jsessionid=L3jVx0nvfC1WlQMl7XPMn1DGvhQxnyckPL1plbj29YNfmbTpWy5T!743789914!-1358995715?a=o&d=114698351

  17. artfulDon 14 Feb 2010 at 5:48 pm

    To mention some aspects of choice or its lack that may not be found in the cited material, there are likely no occasions in nature where “the same stimulus always elicits the same response,” even in a deterministic universe. Causation just doesn’t work in that simplistic way, even in a lab situation where isolating stimuli nevertheless requires the further causation of intentional manipulation.
    That aside, life makes reactive choices between conflicting stimuli, even if limited to the simplest set of options, such as to avoid or not avoid, resist or not resist. But life is not only reactive but proactive, meaning it can create or control a situation by causing something to happen rather than simply responding to it during or after it has happened – and perhaps most importantly it is proactive in identifying and preventing potential problems.

  18. Michael Hutzleron 14 Feb 2010 at 6:14 pm

    The first article refutes your claim that most biologists agree with you. The first paragraph of the actual talk specifies that he is taking a minority viewpoint. All the reference shows is that one biologist agrees with you. Your claim of “most” fails.

    With the second, incorrectly linked reference, you have made it to two people. There is a lot of circular logic in the form of redefinition of terms to suit the premise, but no actual evidence.

  19. artfulDon 14 Feb 2010 at 7:14 pm

    Most biologists do agree that intelligence plays a role. The minority position that Shapiro takes is about how, and how much, that intelligent role is determinative in their evolution.
    Your position was that “there is no intelligence or choice if the same stimulus always elicits the same response.” That either means you don’t see intelligence in your bacteria at all, or that if you do, it’s not there to make choices. Either way, all the citations in the world that are confirmative with those already offered won’t change your mind.

    However, the real questions are whether you can argue with any conviction that Shapiro and other prominent biologists of the same persuasion are wrong first about bacterial intelligence and then about its purposes.

  20. artfulDon 14 Feb 2010 at 8:25 pm

    By the way, the full Shapiro paper can be obtained here.
    http://shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdf

    Show me where it says what you claim he said in the “actual talk” about taking a minority viewpoint, and what part of his views he was referring to. And how that article then refutes any actual claim that I made based on its contents..
    Otherwise it seems you argumentation here is more than fallacious, it’s dishonest.

  21. artfulDon 14 Feb 2010 at 8:46 pm

    Relevant excerpt from:
    NYR Books
    Volume 44, Number 10 · June 12, 1997
    Darwinian Fundamentalism
    By Stephen Jay Gould
    http://www.nybooks.com/articles/1151

    “Darwin clearly loved his distinctive theory of natural selection—the powerful idea that he often identified in letters as his dear
    “child.” But, like any good parent, he understood limits and imposed discipline. He knew that the complex and comprehensive
    phenomena of evolution could not be fully rendered by any single cause, even one so ubiquitous and powerful as his own
    brainchild.
    In this light, especially given history’s tendency to recycle great issues, I am amused by an irony that has recently ensnared
    evolutionary theory. A movement of strict constructionism, a self-styled form of Darwinian fundamentalism, has risen to some
    prominence in a variety of fields, from the English biological heartland of John Maynard Smith to the uncompromising
    ideology (albeit in graceful prose) of his compatriot Richard Dawkins, to the equally narrow and more ponderous writing of
    the American philosopher Daniel Dennett (who entitled his latest book Darwin’s Dangerous Idea).”

  22. Michael Hutzleron 14 Feb 2010 at 9:23 pm

    As I said, in the first paragraph he places his views in the minority: “The conventional wisdom is an extension of the mechanistic views that came to dominate biological thought…”.
    You claimed that “most biologists” accepted the idea, but right there, your source states the opposite. This was the work of someone trying to change minds. If the views had reversed, he would claim rather than anticipate victory: “My own view is that we are witnessing a major paradigm shift in the life sciences…”.

  23. artfulDon 14 Feb 2010 at 10:00 pm

    No, you said: “The first paragraph of the actual talk specifies that he is taking a minority viewpoint.”

    But in fact he’s talking about mechanistic views that “came to dominate biological thought.” Note the past tense, and that mechanistic views nevertheless do not posit that life forms are an unintelligent mechanism, nor do they rule out the necessity for making either reactive or proactive choices.

    What I wrote also was: “Which is beside the point of whether or not such intelligence plays a part in evolution, since most biologists agree that it does.” You sneakily left out what I then wrote: “They earnestly, gravely, soberly, somberly, and seriously disagree as to the “how” mechanism.”
    That last part is where the paradigm shift comes in.
    About which you have had nothing to say as to its relevance to your claims of early life’s lack of intelligence or absence of any need and ability for making predictive choices.

  24. Michael Hutzleron 14 Feb 2010 at 11:28 pm

    Well, then, let’s wait for that paradigm shift to occur. Newton produced a paradigm shift. Experiments confirmed it. The Cavendish Experiment came over 100 years after Principia, but it came. Where it broke down at extremes, Einstein proposed relativity which became a new paradigm when experiments confirmed its predictions. Darwin and Wallace produced an actual paradigm shift in biology. Their hypothesis anticipated real discoveries and experiments which confirmed their predictions. The impact of survival on populations is solidly grounded in evidence.

    Shapiro is claiming a pardigm shift in the works, but doesn’t have any experimental support. No one has demonstrated any sign of an anticipatory process in bacteria. Shapiro’s modeling of Pseudomonas swarming was based on kinetics, not “intelligence” or “choice”. He is relying upon anthropomorphization and metaphor, but it will take data, not thought experiments to realize his supposed paradigm. He can invoke McClinock and Margulis all he wants, but their ideas were supported by the data prior to acceptance. To date, his metaphor remains nothing but a metaphor.

  25. artfulDon 14 Feb 2010 at 11:49 pm

    Glad you mentioned Margulis, and that her ideas are supported by data, which would include her demonstrated belief that organisms are makers of intelligent choices.

    And it’s simply not true, and you have to be extremely ignorant not to know it’s untrue, that Shapiro offers no supporting data.

    http://shapiro.bsd.uchicago.edu/index3.html?content=cv.html

    Read ‘em and weep.

  26. Michael Hutzleron 15 Feb 2010 at 12:46 am

    Wrong. That is argument from authority. What Margulis believes about intelligent choices is as meaningless as Newton’s belief in alchemy. Margulis’s development of endosymbiosis, by virtue of evidence, was science.

    Shapiro’s CV is also argument from authority.

    Thank you for supporting Dr. Novella’s excellent post by resorting to a card metaphor. I’m afraid that the evidence beats your pair of fallacies.

  27. artfulDon 15 Feb 2010 at 1:44 am

    The link was supposed to go to Shapiro’s publications as well:
    http://shapiro.bsd.uchicago.edu/publications.html
    Still pretending there weren’t any?

    And Margulis has a book, What Is Life, that goes into what to you will be excruciating detail about evidence of cell intelligence.

    And you’re confirming then that intelligent choice in bacteria and the like doesn’t exist? Even Dr. Novella has conceded in the past that early life forms contributed to their survival and evolution by calculative use of learning by trial and error choices. And his concept of natural selection, Neo-Darwinist that it is, is still much more sophisticated then yours.

    And the card metaphor was his, not mine. But then you seem to get everything bassackwards. You should hope you’re not using your real name and that these opinions don’t come back to bite you there.

  28. Michael Hutzleron 15 Feb 2010 at 2:04 am

    You are in a feeble spot to argue ad hominem after you posted a CV.

    Another reality check for you: “Read ‘em and weep.” is a card metaphor.

    Cut your losses.

  29. artfulDon 15 Feb 2010 at 2:41 am

    “Read ‘em and weep” is an idiom, not a metaphor.

    “Evolution is like drawing cards at random” was the metaphor.

    Ad hominum refers to the fallacy of attacking an opponent’s motives or character rather than the policy or position they maintain.
    Although not a fallacy when their motives and character are suspect.
    Like asking, “What are you, some high school kid being home schooled by Wikipedia?”

  30. SteveAon 15 Feb 2010 at 10:26 am

    “Michael Hutzler”

    Michael, artfulID belongs to the ‘I might be a crank, but I posted last, so that means I won the argument!’ school of rhetoric.

    Often the best response is a yawn…

  31. lurchwurmon 15 Feb 2010 at 11:34 am

    Thank goodness for people like artfulD that are willing to ask these types of questions. Even if everything Hutzler is saying about whether these biologists actually pondered these questions (which I believe they did) is true, why are still not in a position to ask these questions?

    The problem at hand is really an antinomy. Human Reason can make viable claims for both cases, and neither contains a self-contradiction, only contradicts each other.

    Heinleiner said that things just happen, because they behave like eternal truths. Unfortunately, he used the example of “2 + 2 = 4,” at which every modern Philospher of Mathematics would have cringed. “2 + 2 = 4″ is only an eternal truth in a logical system, specifically modulus 10 arithmetic. “2 + 2 = 0″ is an eternal truth in modulus 2 arithmetic (considering “2″ as “1 + 1 (which is 0)”).

    In the same vein, paradoxes are eternal truths, even in logical systems that we accept as sufficient for Science. Take probability theory: “All ravens are black; This raven is black and That raven is black; therefore, “All ravens are black” is more confirmed.” That would be the conclusion we want in Science, right? That getting MORE evidence means MORE confirmation? In fact, in probability theory, the conjunction of two pieces of evidence monotonically DECREASES the probability.

    The problem with the argument that Einstein found a paradigm shift of physics solely in response to boundary conditions of Newtonian physics is a canard. There was so much happening at the turn of the 20th century. So much wonderful thought about our own thinking. Einstein was deeply involved in the problems of how Non-Euclidean Geometry is possible. Newtonian Physics was completely determined by Euclidean Geometry, but Mathematicians at the end of the 19th century discovered systems that contradicted the parallel postulate of Euclidean Geometry (a key postulate for many results in the Principia). These systems were shown to be logically consistent. This sparked a major debate as to how we should actually think of the way things in the actual world correspond to Geometry, i.e., which Geometry should be used? Einstein made the genius insight that Euclidean Geometry works within referential frames, but over significant distance, spacetime is curved. If you follow Einstein’s history before coming up General Relativity, you will find copious historical documents to support the claim that the question of Non-Euclidean Geometry really bothered him. It made him question, as evidenced by his interactions with the Vienna Circle, if we could actually establish truth about the natural world.

    Without his genius along with a lot of other philosophical, mathematical, and scientific geniuses at the time confronting the issues regarding truth in the mathematical sciences, we would still be stuck in the model of THINKING in a strictly Euclidean-sense. The turn of the 20th century is a good model to show that philosophical inquiry will always be important, because mathematics no longer holds the place of certainty that it once did. It is just one formal system (albeit not striclty logical, see: Godel) among many.

    If not for people like artfulD thinking about the “larger picture,” we could stay in a state of mental stasis. If not for philosophers diligently working to provide justification for Science, Science would only have Mathematical and Formal Logic arguments to present to IDiots, which are, at base, tautological within their own systems. It takes human reason to determine if those logical systems hold weight, and there is no “higher appeal” for those reasons other than mere cogency :)

  32. lurchwurmon 15 Feb 2010 at 12:23 pm

    I need to make a few minor corrections to my original post:

    1.) My main thesis is “We cannot stop asking philosophical questions because scientific consensus and mathematical models point us in a certain direction.” As a side note, I am a supporter of science, but I also am skeptical of how far it can take us based upon my philosophical inquiry into mathematics and formal systems.

    2.) When I said that Einstein made the genius insight that Euclidean Geometry works in referential frames, I meant to say that Newtonian Mechanics works in referential frames. With Euclidean Geometry, I meant to say that spacetime is curved at large distances, but it acts like standard Euclidean Geometry at small distances. Sorry about that.

    3.) The “All ravens are black” statement is not strictly a paradox in probability theory. Probability Theory will not ambiguously assign two different values to the same argument. The paradox was more with human reasoning using classical probability theory. In science, we would want to say that MORE evidence means MORE confirmation, but classical probability theory (which is counterintuitive) would not support such a claim when the evidence is seen as a conjunction of two pieces of evidence (you would obviously have to have a more sophisticated system to account for the way modern scientists use probability theory).

    The overall point of my statement is that a lot of mathematical and logical systems DO contain paradoxes (such as the infamous, “the set of all sets that do not contain themselves as members” in naive set theory) as eternal truths.

  33. lurchwurmon 15 Feb 2010 at 12:44 pm

    I meant to add to my thesis that “Great scientific thinkers, such as Albert Einstein, were troubled by philosophical findings of their time that directly contradicted the science, yet nevertheless pondered them seriously (rather than discounting them because the current scientific practice does not support them). In Einstein’s case, he ended up presenting a scientific theory that reflected the work done by philosophers and mathematics in collaboration at the time.”

    Wow. If I am going to have any hope of a philosophical career, I am going to need to correct this problem with not completing and connecting my thoughts when I present my arguments. Fortunately, Steve provides a great blog that provokes a lot of deep thought in which I can hone my ability to make philosophical arguments. Thanks Steve for all the great work :)

  34. artfulDon 15 Feb 2010 at 12:59 pm

    Lurchwurm, thanks for the support, even though I’m about to bite the hand that supported me. There is a paradox presented here, but it’s not antinomous. There is no contradiction between two beliefs or conclusions that are in themselves reasonable. The paradox is to believe that biological systems that make their own choices evolved from systems that couldn’t have done so, yet are at the same time biological.
    Begging the question of when that choice making intelligence that one biological form claims it’s now making use of (because it presumably can) kicked in along the evolutionary trail of the biological. Would that be one of those things that just happened?
    Or is it that if there was no intelligence needed for life to be operative, the intelligence that we now claim to be operating with is simply an illusory happening?
    (Cue in the idiots yawning.)

  35. lurchwurmon 15 Feb 2010 at 2:16 pm

    I had an unstated premise in my statement regarding antinomies. The two views that I believe are antinomous are

    1.) An intelligent system is immanently intelligent.

    2.) An intelligent system gains intelligence through mediation.

    I believe those two statements form an antinomy; however, I know that you are making a much more complex argument about the paradox of an intelligent biological system evolving from an unintelligent biological systems.

    I was more interested in the whole concept of being offended by the notion of even bringing up these types of questions. My point was that many great scientific thinkers were deeply troubled by questions that could not be explained “within the current system.” I was following Wittgenstein’s lead from the Philosophical Investigations in which different claims “within” a formal system cannot be used as justification to argue against someone making claims “within” another system. There must be a mediated form of argument in which we try to find where the systems contradict each other and really discover why those contradictions exist rather than “being in this camp” or “being in that camp.”

  36. artfulDon 15 Feb 2010 at 3:06 pm

    The problem being that neither of us was promoting the view that an intelligent system is immanently intelligent. That could have been offered as a reason why some biological systems at least have appeared to be unintelligent, but it wasn’t. Even a bad reason would have been better than none at all. Or that some biological systems just happen not to be systematic.
    Further, those two particular views are not antinomous, as first they’d need to be contradictory. Yet they could both serve as premises to the conclusive inference that the very nature of intelligence is to add to its efficacy intelligently.

  37. Michael Hutzleron 15 Feb 2010 at 4:28 pm

    lurchwurm,

    I’m all for metaphors. I found McClintock’s “genetic intelligence” a useful model for contemplating biology and evade anthropomorpic fallacies by contemplating the appearance of intelligence, directly. Metaphors and even failed hypotheses teach us. The problem lies when we assume the metaphor is reality without testing.

    There was no canard is discussing paradigms that were realized when an idea was tested. I oversimplified greatly and I appreciate your expansion. There was also more to confirming gravitation than the Cavendish experiment. There are non-Euclidian geometries that do not describe the universe. They have their merits, and some have applications beyond the theoretical. I respect the power of ideas, including paradoxes.

    Also, I can hold the simultaneous respect for Shapiro, Margulis, and others to introduce new ideas that provoke thought, and dismiss the ideas as speculation that is missing the needed support. Bold ideas may be rejected, and most will be, but the process of rejecting them is a learning experience, and one failed idea may inspire the one that works.

    To date, I have seen nothing convincing on distinguishing intelligence from the appearance of intelligence. Mostly, the metaphor asks you to look at things differently, but nothing changes. There is no reason the metaphor is to be taken as reality over the model that has served fairly well. Do I think the idea is garbage? No. I actually would love to see it succeed or at least yield some results that put us closer to understanding the nature of thought. There are some fascinating experiments, but none suggest that bacterial behavior can be explained better than by kinetic modeling. (The model of swarming was one of my favorite papers.) What happens if you find bacteria that have intelligence, remove the key genes and they continue to live. Isolated self-replicating molecules make the problem of what constitutes living and intelligent more gray.

    My view is not locked in, but the evidence is ambiguous or missing. This is an idea worthy of contemplation and exploration but it is far from ready for acceptance.

  38. Heinleineron 15 Feb 2010 at 5:04 pm

    Well Lurchworm, thanks for pointing out the inaccuracy with my Math example. I don’t exactly have a background in philosophy, so I suppose I was speaking to the perspective of the lay person with regard to conceptions of mechanistic processes. Hence I gave real-world scientific examples of physical processes that occur quite predictably.

    Do you wish to comment on any of those?

  39. artfulDon 15 Feb 2010 at 5:11 pm

    “Bacteria do not make choices or rank consequences.”

    But that’s not locked in because of course even if they don’t it’s possible that they do, but one is entitled to allege that it doesn’t happen and is not a thing that happens if the happening hasn’t been proven to one’s personal satisfaction.

  40. Heinleineron 15 Feb 2010 at 5:17 pm

    “There are no teacups orbiting the Earth.”

    But that’s not locked in because of course even if we can’t see any it’s possible that there are, but no one is entitled to allege that there aren’t, and that there aren’t multiple kettles of Earl Gray orbiting us if hasn’t been proven to one’s satisfaction.

  41. artfulDon 15 Feb 2010 at 5:43 pm

    And 2 plus 2 equals 4 only if the purpose is to explain the decimal system of measurement. It’s not an axiom in service of a truthful purpose in the quantum universe where, if the theories are correct, there will be no two particles that can by that measure be identical in size, time, characteristics, purpose, and corresponding place to any other two.

  42. artfulDon 15 Feb 2010 at 5:57 pm

    And if there were a purpose to be served by any particular object or series of objects to be in orbit around the earth, some intelligent entity can’t be ruled out as having at least acceded to that purpose.

    Or if there were no intelligent entities, there likely wouldn’t be any teapots at all other than in their platonic model in some Olympian dining room.

  43. lurchwurmon 15 Feb 2010 at 7:26 pm

    @Michael Hutzler:

    First off, as artfulD pointed out, I didn’t accurately address the actual biological argument being made. I was trying to interject my own experience in philosophy with dealing with logical/mathematical theories.

    The problem with rejecting bold ideas is the problem I was trying to get at, which Non-Euclidean Geometry was a prime example of. For centuries, Euclidean Geometry stood as a towering giant which was not even questioned as to its validity to explain all of physical reality.

    The problem was that the parallel postulate was seen as indubitable, but yet, amongst major mathematicians, there was a suspicion that it was actually independent of the other axioms, i.e., it wasn’t needed to prove Euclidean Geometry (in the strictly Logical sense, it couldn’t be proved from the other axioms). Scores of Mathematicians tried to give proofs of the paralell postulate, in vain, for centuries. But the idea was so entrenched in the scientific community at the time, that to doubt it was seen as treason to Science. Gauss himself believed that consistent Non-Euclidean Geometries existed, but he did not write any papers on it, because even he could have been discredited if positive results for NE Geometry didn’t pan out during his lifetime.

    Finally, Riemann and Kline took the bold step of rethinking the way Geometry should be viewed (as spaces defined by how group transformations act on them rather than as collections of infinitely long lines and circles that join to create shapes). At first, this caused a lot of anxiety, and people kept trying to prove the parallel postulate for a few more decades, until a Euclidean Sphere was given as a model for Riemann’s Elliptical NE Geometry. This showed definitively that a Euclidean model could be used in a system that specifically negated the parallel postulate (in the elliptical geometry, its obvious that there are NO parallel lines, because a line on a sphere will intersect with infinitely many lines through at lease two points). As a result, the fact that there is a model of NE elliptical Geometry means that NE elliptical Geometry is consistent; therefore, there now existed two systems that could possibly explain physical reality.

    The main point is that the turn of the 20th century showed that a reliance on mathematical and logical systems can lead to error, and the justification needed for any theory requires a new way of thinking, which philosophers have been trying to iron for the past century (by examining language, logic, truth, meaning, mathematics, science). It just appears to me that there’s too much scientific bravado in this particular discussion in which a heavy reliance on old ways of thinking about science are still pervasive, in which authority is given to mathematical models. It would be good to really read what philosophers are looking into nowadays, because they are really trying to come to grips with how we could really give accurate predictions in a rigorous way when mathematical and logical models themselves are in question.

  44. artfulDon 15 Feb 2010 at 7:26 pm

    For lurchwurm’s intelligence only: The strategic tactic of their scientific questioning that Einstein, et al, had and have in common is to form an understanding of any mechanistic function by looking first for the purpose that the function serves, and then from where and whence that purpose arose. They recognized there is no function that doesn’t serve either its own purpose or that of someone or something else’s. And the problem with this latest devotion to modeling as the preferred method of explaining the nature of mechanistic functioning is that the models are not programmed to consider any but the simplest assumptions of purpose – delineating any such purpose in accordance with the function’s successes instead of by it’s intended and often multiple purposes. The models are not asked or expected to otherwise discover other of the innumerable and varieties of such purposes on their own. They are presumed incapable of forming valid inference from the data. And their operators have come to
    distrust the use of any such inference they are tempted to draw on their own.
    Biological mechanisms differ from virtually all others by the ways that they have come to serve their own purposes. A concept that apparently is a bit too abstract for our antagonists here to grasp.

  45. artfulDon 15 Feb 2010 at 7:35 pm

    Editing of the syntax above is optional.

  46. lurchwurmon 15 Feb 2010 at 8:40 pm

    Regarding why I thought immanent intelligence was part of the debate: I have seen posters on this blog several times in the past state their belief that the process of evolution is immanently intelligent, but after looking back at this specific post, it is true that that viewpoint was not asserted in this post.

    Regarding my statement about reliance on mathematical models, please don’t assume that I don’t think mathematics and logic is important. I am more interested with how modern thinking about mathematics and logic can be reconciled with the attempt to fully explain processes in nature strictly through mathematical models. I’m also interested in where the demarcation is in which we can say that a particular process is not intelligent?

  47. lurchwurmon 15 Feb 2010 at 9:21 pm

    @artfulD:

    I was just thinking about a question similar to this today (in regards to your statement about how biological organisms are expected to make their own inferences of purpose, but mechanistic functions are not). Consider a separate example in the realm of AI, in which an AI agent is rational iff it tries to maximize its performance measure, e.g., picking up x amount of trash in t amount of time. This agent is simply a formal system, and thus, not biological strictly; however, it may be possible for it derive some type of intention.

    Specifically, the possibility arises when one considers what it would take to persuade the agent to make an irrational decision, i.e., one that does not maximize performance measure.

    Let’s say that the agent’s performance measure is its wife level of happiness. Its knowledge base originally consists strictly of four propositions, “Giving your wife 12 roses will be sufficient for one day’s worth of happiness”, “You do not know how many units of work your external body will handle before breaking down”, “It takes 20 units of work to pick 12 roses”, “If your wife is ever sad for an entire day, you will shut down.” Now, at this point, would the agent be able to derive a purpose out of all this? Would the agent determine that it has a higher purpose of staying alive so that it could meet its rationality (namely contuining to make its wife happy), or would it still assume that is merely there to make its wife happy?

    Let us now try to persuade the agent by inserting into its knowledge base the following propositions: “If you exert 60 units of work to take your wife out to eat, she will be happy for an entire week if your dinner was successful”, “Your dinner may be unsuccessful, yet your wife could still be happy for 3 days”, “Your dinner could spark a major argument, and your wife would not be happy for an entire year.” Clearly, there is a gamble in this situation. Before this persuasive statement, the agent had certainty that it would ONLY make its wife happy by its actions. Now, it has information in which it could make its wife happy more efficiently but also at the risk of the agent losing its life. Given that its uncertain how long its going to live anyway, could it determine different purposes on its own? Would it see that the fact that uncertainty in its life expectancy means it should have the purpose of taking the gamble of going out to dinner so that the wife’s happiness is sustained with less effort? Or, would it think that it should take the certain road of picking roses every day, even though, it doesn’t know how long it’s going to live?

  48. artfulDon 15 Feb 2010 at 11:18 pm

    First of all (to pick and choose some responses), the agent has limited options, and none of them were of its own choosing – which is part of the function of biological intelligence, which will have chosen some of its options by its trial and error experience, or all of them over time if you accept that it participates in its own selective processes.
    And it’s doubtful the agent has emotions, having no need for such, and no actual self-awareness that comes from sensory input that feeds into fight or flight responsive systems as one example.
    So it has no fear of death, even if it could conceive of its dying. (Nor do most biological systems, but that’s another story.)

    And it has no sense of happiness that comes with having satisfied the needs of its own choice making successes – having no ability to fulfill some of its own purposes if you will. Probably no empathetic systems as well that would look into and be concerned with a wife’s feelings, especially if, like itself, the wife didn’t have any.

    I don’t doubt that some day we will be able to construct an intelligent choice making system that will be taught how to assess its own risks, but the hard part will be to give it a purpose for doing so that will separate itself from our purposes in constructing and instructing it.
    Begging the question of whether life has ever completely separated itself from some unknown purposes somewhere back in the causative history of the cosmos. Which the ID adherents are convinced hasn’t happened, and thus can’t seem to concede that we have at least gained some freedom to add our own to those that that were almost certainly unintended (and thus not intended) to be involved with our causation.
    And I doubt we will soon construct an agent that will live with such uncertainty of purpose, if at the same time it hasn’t found a way to live without recourse to our help.
    And especially not if it can’t infer from our behaviors that it has any need to look for a separate purpose, or that we might want it to. More especially as we have no idea how to convince it without deceit that it has the potential for separating its purposes from ours.
    I could go on but you get the drift – which is essentially that we can’t yet make a machine that, in the words of our antagonists, can assess and rank the consequences of actions taken by any choices not dependent on its makers purposes.

  49. lurchwurmon 16 Feb 2010 at 12:15 am

    wow, that pretty much narrows down exactly what the problem is in my example under the current state of technology. Barring the restrictions currently in place, this is the type of thing I plan on doing philosophical research into: determining if an agent could in fact be persuaded to go against its criteria of rationality as set forth in its initial set of choices. However, my exact formulation was more along the lines of “Could we persuade an agent to make an initially irrational decision to pursue a goal with an uncertain outcome that, if successful, would result in higher rationality overall?”

    Your previous post has made me realize how many assumptions I am going to have strip away from this agent. I will need to take away any rationality tied to emotion, survival, or any other biological intelligence concerns. Basically, my initial research should only look at the ability to determine more successful purposes in very limiting cases.

  50. artfulDon 16 Feb 2010 at 1:01 am

    Another assumption to drop might be that you would need to persuade the agent to do anything on the assumption that it won’t otherwise want to do it. Because all you really have to do with a machine to change the course of its logical processing is slip it a false premise or two. Because an essential difference between us and them is that we can purposefully lie to them but they can’t intentionally lie to us.

  51. artfulDon 16 Feb 2010 at 1:36 am

    In other words make ‘em an offer they can’t refuse to believe.

  52. lurchwurmon 16 Feb 2010 at 10:10 am

    After looking over yesterday’s transcripts in the comments, I just realized how intellectually sloppy my argumentation was. I was going too much overkill on arguing about mathematics when Michael Hutzler did not even bring that up. I apologize to Hutzler for misrepresenting his position, even though I still agree with artfulD’s take on intelligence in biological sytstems. I guess the only thing I really accurately addressed was Heinleiner’s statement about “2 + 2 = 4″ being an eternal truth. I’ll work next time to stay on target more, and only debate those issues that are currently being addressed!

  53. artfulDon 16 Feb 2010 at 12:54 pm

    @lurchwurm:
    Yes, but my guess is you felt intuitively that Hutzler didn’t bring it up for a reason (assuming he was smart enough to have a reason). The use of mathematical calculations is an active and proactive intelligent process. The bacteria that he used as an example of unintelligent life can clearly do such calculations. He’d have been hard pressed to argue they aren’t doing so for an intelligent purpose. He’d also have to address that in many ways bacteria are smarter than we are. They can survive without our help, yet we can’t survive as we are presently constituted without theirs. They can mutate on command, and we cannot. They know how to do things proactively that we don’t, and need their know-how to do for us.
    So I don’t think there was overkill there on your part at all. In fact you can see that it caused him to respond to you thusly: “I oversimplified greatly and I appreciate your expansion.”

    Causative as well of the more than several concessions to follow.

  54. Heinleineron 16 Feb 2010 at 4:56 pm

    artfulD,

    The quantity of self-congratulatory verbiage you’ve been spewing over the past 13 comments with Lurchworm is really getting out of hand. Your attempts to portray yourself and Lurchworm as some sort of valorous logical heroes, and us as your “antagonists” is extremely grating. Your accusation that somebody in the thread doesn’t understand natural selection like Dr. Novella does is just sad. Natural selection is not hard to understand; it’s the consequences that may be more difficult to intuit, and you’re clearly having trouble if you’re trying to invoke so-called bacterial intelligence. I’m having trouble deciding if this is simply an extremely extended case of Poe’s law, or if you’re just a hardcore contrarian. The topic has been massively, MASSIVELY derailed (Darwin Day Celebration, anyone?), and this will be my last post in it, as I’ve got to study for my MCAT and can’t waste more time boggling over your quite undeserved self-satisfaction. But to address simply your last post.

    “The bacteria that he used as an example of unintelligent life can clearly do such calculations.”

    False premise. I’ve put a population of E. Coli bacteria into a nutrient broth, and analyzed their growth curves (Undergraduate Chemical Engineering lab in biotechnology). They eat all the broth, then they run out of food, and then they slowly start dying, then they experience a short phase of necrotic growth (the eat the dying), then they all die, because they ran out of nutrients. Stupid bacteria! They should’ve instituted population control initiatives.

    Okay, the experiment was real, but I’m joking about that analysis at the end. But the growth curve mentioned is what happens. Bacteria eat food, they eat whatever’s around them, and they grow. Why are you saying that they are doing calculations when they do that? They’re just eating to replicate their genomes. They are survival machines, for their genes.

    “He’d also have to address that in many ways bacteria are smarter than we are. They can survive without our help, yet we can’t survive as we are presently constituted without theirs.”

    Non sequitur. We have an endosymbiotic relationship with bacteria; therefore, they are smarter than us? That doesn’t work. I suppose, then, that Chlamydia trachomatis is a stupid bacterium, since it can’t replicate outside of its host cells? That’s right. They can’t survive without their host! Oh wait, that’s an entire Phylum of bacteria that’s obligate intracellular parasites. Chlamydiae.

    “They can mutate on command, and we cannot.”

    Now, what exactly does that have to do with intelligence? In the first place, this statement isn’t even true in any sense! Bacteria don’t force themselves to mutate! Certainly, there may be portions of the genome which are less strongly conserved than others, but these are completely different things. Bacteria (and Archaea) are capable of amazingly complex metabolism, but their morphology is pretty standard. Of course there is some variance in morphology, but not nearly to the extent as in Eukaryota.

    If, after 10000 (or however many) generations in a glucose and citrate-containing environment, a certain bacterium in a population gains the ability to suddenly metabolize citrate (when such ability was absent before), it will have access to more resources than its peers and replace them proportionally in the population, because its alleles have greater fitness in the environment. There is absolutely no need to assume any intelligence anywhere in this process. You’re introducing assumptions that do not need to be made to a model which is already fully consistent with the mutation and natural selection explanation. It is a common mistake of the amateur Biology students to say something like, “The bacteria want to be able to metabolize citrate, so they evolve that ability.” Mutations occur because of periodic errors in replicating bacterial chromosomes (about 1 error for every 1,000,000,000 bases copied by DNA polymerase, I think), and because of possible damage to the DNA by metabolic processes. A mutation at a codon which codes for amino acids at the active site of a metabolic enzyme may be enough to allow the bacterium to metabolize citrate in a way which enters it into the intermediates already present in its metabolic processes, in effect doubling the resources available for catabolism and anabolism (assuming there was as much citrate as there was glucose).

    Assuming no genetic drift or lateral gene transfer (an isolated population of bacteria in a flask, for instance), the only way new alleles can enter in to the population is through mutation. Bacteria do NOT decide that they want to mutate a certain ability!

    “They know how to do things proactively that we don’t, and need their know-how to do for us.”

    Bacteria, if motile, will move away from poisons in solution, and will move toward food. This is simply chemotaxis. This is not intelligence. Natural selection has favored individuals which move toward greater concentrations of food particles, and away from greater concentrations of particles which damage the cell. Yes, this is reacting and responding to the environment. But where exactly does “intelligence” fit in, here?

    Bacteria will sometimes enter into a spore phase under poor nutrient conditions, where they pause their metabolic processes and wait until nutrient conditions are more amenable to growth before they continue replication. Natural selection favors individuals who cease their metabolic processes and hibernate when nutrient conditions are poor. No intelligence needs to be assumed here.

    If, by your last quote, you meant something else besides chemotaxis or entering a spore state, please PLEASE give me an example of what “things” bacteria do “proactively” that we don’t. You clearly think you’ve proven your point, or at least disproven somebody else’s points here, but you haven’t provided any evidence or examples of bacterial intelligence.

    And don’t just quote another paper at me. You can link it, and I encourage that, but only if you take something from inside the paper, and type it here as a concrete example of bacterial intelligence. And I am NOT talking about quoting abstracts.

    If you’ve reached the end of my post and read and considered everything, congratulations. Like I said, this is my last post, and you may feel free to pick it apart as you like, and perhaps somebody else will take up my defense. I don’t care. But I’d like you to think a little harder about what you’re saying, and to stop denigrating people you think aren’t as smart as you just because they don’t agree with you.

  55. SquirrelEliteon 16 Feb 2010 at 5:16 pm

    Heinleiner,

    Good comment.

    I got bored with their back and forth a long time ago and have mostly ignored this comment thread, but I endorse your reasoning.

    Good luck on the MCAT!

    I hope you grok all the questions.

  56. artfulDon 16 Feb 2010 at 5:41 pm

    Heinleiner, two words, quorum sensing.
    As you should presumably know, quorum sensing is a type of decision-making process used by decentralized groups, including many species of bacteria, to coordinate behavior.

    This and other of their decision-making processes were shown all though your examples of what you’ve personally observed them doing. Because without knowing you’ve done so, you’ve also made assumptions as to their purposes.

  57. artfulDon 16 Feb 2010 at 6:25 pm

    And speaking of Darwin Day celebration, here’s what the person who understood biological purposes better than anyone then or even now had to say about natural selection:
    “But as my conclusions have lately been much misrepresented, and it has been stated that I attribute the modification of species exclusively to natural selection, I may be permitted to remark that in the first edition of this work, and subsequently, I placed in a most conspicuous position—namely, at the close of the Introduction—the following words: ‘I am convinced that natural selection has been the main but not the exclusive means of modification.’ This has been of no avail. Great is the power of steady misrepresentation; but the history of science shows that fortunately this power does not long endure.”

    Although he seems to have been wrong about how long his ideas will continue to be misrepresented.

  58. Heinleineron 16 Feb 2010 at 6:48 pm

    Oh man. As I should “presumably” know… and then you copy the first line of the wikipedia article on quorum sensing. Which does not prove any sort of intelligence. Then you speak of misrepresenting natural selection. Double irony knockout. I’m TKO’d.

  59. Heinleineron 16 Feb 2010 at 6:56 pm

    ‘I am convinced that natural selection has been the main but not the exclusive means of modification.’

    Darwin then went on to say, “One day people will discover that bacteria have intelligence, and will be able to direct their own evolution through intelligent decision making. That’s totally one of the other means of modification I’m advocating. And if somebody in a world-wide electronic communication network thread mentions how natural selection can lead to change in metabolic activities, they OBVIOUSLY believe that natural selection is the ONLY means of modification, because otherwise, why wouldn’t they delineate every single other means of modification currently understood? It’s not like they have better things to do with their time.”

    That’s in the lost 7th edition.

  60. artfulDon 16 Feb 2010 at 7:16 pm

    Heinleiner, I was going to cite this TED talk but you wanted something in writing. But are you now objecting to what Wikipedia says or just to using it at all.
    Because it clearly describes a the decision making process which is a function of intelligence. Or better, it can’t function without intelligence.

    But let’s see how you an explain what’s wrong with this:

    http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html

    By the way, what happened to that “my last post” declaration?

  61. artfulDon 16 Feb 2010 at 7:27 pm

    I was keeping this as a sort of a hole card, but what the hell, might as well play it:
    Wetware: A Computer in Every Living Cell
    ~ Dennis Bray

    Description:
    How does a single-cell creature, such as an amoeba, lead such a sophisticated life? How does it hunt living prey, respond to lights, sounds, and smells, and display complex sequences of movements without the benefit of a nervous system? This book offers a startling and original answer.

    In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence.

  62. artfulDon 16 Feb 2010 at 7:52 pm

    Something else Heinleiner asked for:

    Quorum quenching and proactive host defense
    Lian-Hui Zhang1, 2,

    1 Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
    2 Department of Biological Sciences, The National University of Singapore, Singapore 117543

    Abstract

    Both plants and humans have inducible defense mechanisms. This passive defense strategy leaves the host unprotected for a period of time until resistance is activated. Moreover, many bacterial pathogens have evolved cell–cell communication (quorum-sensing) mechanisms to mount population-density-dependent attacks to overwhelm the host’s defense responses. Several chemicals and enzymes have been investigated for years for their potential to target the key components of bacterial quorum-sensing systems. These quorum-quenching reagents, which block bacterial cell–cell communications, can disintegrate a bacterial population-density-dependent attack. It has now been shown that a quorum-quenching mechanism can be engineered in plants and might be used as a strategy in controlling bacterial pathogens and to build up a proactive defense barrier.

    (Sorry, I don’t have permission to post the entire paper.)

  63. Heinleineron 16 Feb 2010 at 8:45 pm

    I’m periodically coming back on the computer to take quizzes from my textbook, and I have a quick chance to check back here. You keep throwing straw men into my arguments, and it’s really irritating. This is a good exercise in both solidifying my own knowledge of biology and cutting my skeptical teeth.

    Post 1: I was not objecting to Wikipedia use. I was merely commenting on the irony of you having to look up quorum sensing on Wikipedia and telling me I should know what it is, when you had to look it up and copy the description word for word yourself.

    Unless you’re going to explain exactly how quorum sensing implies intelligence, we’re never going to get anywhere here. I’d like you to define, in your own words, a.) what bacterial intelligence is, b.) how it compares/contrasts to human intelligence, and c.) why quorum sensing can or can not be explained by natural selection (because I can’t tell if you think it can or can’t be).

    If you answer a.), b.), and c.), maybe I’ll have a better idea of where you’re coming from, and why you just can’t seem to stop posting here.

    Post 2: What’s your “play” here, exactly? It looks like an argument from authority. I don’t have time to read an entire book, sorry. Yes, metabolism is VERY complex, and it can appear like a computer program. The programmer? Mainly natural (and other) selection, lateral gene transfer, and epigenetics. No “intelligence” required. If you’re interested in how evolution can be related to computer programs, might I suggest reading The Blind Watchmaker or The Extended Phenotype, if you have the time. I have the feeling that intelligence is being used as a metaphor (in the book you mentioned), here, but seeing as it’s an entire book, I can’t read it and tell you. And I can’t be sure what you’re trying to say til you pin down what your ideas about intelligence are, in your own words, please.

    Post 3: What are you trying to prove here? That quorum sensing exists? I don’t really doubt that. I can visualize how it could emerge through natural (and other) types of selection. That bacteria communicate with each other through cell-cell signals is known to me. Some bacterial species will combine to form fruiting bodies as a means of dispersing themselves; that’s right, temporarily multicellular bacteria! That requires extensive cell-cell communication. But that QS exists does nothing to prove your point about intelligence.

    “Moreover, many bacterial pathogens have evolved cell–cell communication (quorum-sensing) mechanisms to mount population-density-dependent attacks to overwhelm the host’s defense responses.”

    Not all bacteria make their living as parasites, but for those that do, you will often see cell-cell signaling mechanisms to mount population-density dependent attacks which overwhelm the host’s defense responses. That is what I am getting from that abstract. For bacteria with a parasitic lifestyle, natural selection favors alleles which allow bacteria to invade their host, reproduce, and spread to new hosts. It happens in many strains, probably (and I’m guessing here) due to convergent evolution, because massive population-spikes are effective host invasion motifs. There’s nothing about this that natural selection fails to explain, and nothing that requires invoking intelligence as an explanatory tool.

    If quorum-sensing is your trump-card argument that bacteria have intelligence, either your idea of intelligence is completely different from mine and you’re right within your own definition, or your argument doesn’t have a leg to stand on. Well, that may be a false dichotomy, contingent upon your response, so I’m open to a reply! So please explain.

  64. artfulDon 16 Feb 2010 at 9:01 pm

    intelligence
    noun
    1 the ability to acquire and apply knowledge and skills

    Which doesn’t even mention the ability to make both reactive and proactive choice, which I personally feel should be part of the definition if it applies to biological life.

    But even by your own observations, which can’t seem to recognize any proactive choice making in your bacteria, the standard definition above would indicate the bacteria have intelligence.

    I’ve already answered as many of your other questions as I choose to, either directly or indirectly with references to Shapiro, Margulis, et al, and if you complain or rejoice that I have failed to educate you because I cannot, then I accept that I have no expectations that I can, and to do further than advise you to read the book would be a waste of both our efforts.

  65. Heinleineron 16 Feb 2010 at 9:21 pm

    So, you think all reactive and proactive choice is intelligence? Then you fail to understand it. I guess we are done here, then!

  66. artfulDon 16 Feb 2010 at 9:44 pm

    I forgot to point out, in my own words, that quorum sensing is a strategy, one which requires intelligence in and for its application.
    And bacteria carry with them a form of culture which is the milieu in which bacteria teach each other certain of the quorum sensing tactics, most of which are otherwise instinctive – somewhat like the more advanced animal cultures where young animals are taught to hunt, how and where to hide, etc.
    Because the cultural learning process, in my view, started with the first formation of living entities into cooperative groups – arising perhaps as soon as activities have to be coordinated for mutual benefit. Perhaps it’s to be seen as an emergent process that represents the particular group dynamic.
    In the case of bacteria, it will involve either (or both) teaching by demonstration, or learning by feedback during the process that is otherwise instinctive., etc. Because it has appeared to me at least that instincts are strategies that were first learned and then passed on by a form of selection directed by the organism itself.
    An aspect of natural selection, as I have interpreted some of Darwin’s writing to mean, that includes these biological forms as a part of that nature that is involved in its own selective processes.

  67. artfulDon 16 Feb 2010 at 9:56 pm

    Heinleiner,
    And I note you are as dishonest as the other guy was here in trying to score points by twisting my words to infer some other meaning. Which is why I didn’t address your initial comments here, and shouldn’t have done so recently, except you seemed to be a good foil to show how the misrepresentation of Darwin’s theories have persisted. A good example of the deliberateness of maintaining a self satisfying and delusional form of ignorance.

  68. Heinleineron 16 Feb 2010 at 9:57 pm

    In one the papers that you have cited, the biologists stated that “many bacterial pathogens have evolved cell–cell communication (quorum-sensing) mechanisms”.

    But now you’re saying “bacteria teach each other certain of the quorum sensing tactics”. “In the case of bacteria, it will involve either (or both) teaching by demonstration, or learning by feedback during the process that is otherwise instinctive., etc.”

    That’s certainly not evolution, it’s intelligence (learning specifically), and it hasn’t been observed in the papers you’ve sighted. Are you sure you understand lateral gene transfer?

    The reason I’m asking you define bacterial intelligence is because what you’re saying is not agreeing with the papers you are citing.

    My hypothesis is that your ideas are nebulous, and can’t be pinned down, which is intentional, because you, as an internet polemicist, can extend the debate ad infinitum if your ideas are never pinned down. Instead you defer to others’ opinions and claim you don’t have to explain them in your own view because you’ve already done so. You’re a not-so artful dodger of questions when you contradict yourself, though. I’ve seen you post in other threads, and you never stop. You’re not interested in the truth, you just want to argue and subtly insult other peoples’ intelligence. And now, truly, I bid you adieu.

  69. lurchwurmon 16 Feb 2010 at 10:40 pm

    Heinleiner said: “the point is that nothing asks the question. If you ask what does 2 + 2 equal, the answer is 4. 2 + 2 = 4 even if nobody asks that question. Similarly, if something is capable of replicating itself, you will tend to see more of it. If something is capable of replicating itself faster or better than something else, it will overtake said something else. Nothing needs to ask any questions; the universe simply works, and we can ascribe all the meaning we want to that, whether or not it exists.”

    I do not have the technical biological knowledge to comment on the recent exchanges between artfulD and Heinleiner. I would just like to comment on the quote above from Heinleiner.

    The quote above presents a real philosophical question for Heinleiner that stems from his example of bacteria merely “eating what’s around.” You said that “if something is capable of replicating itself, you will tend to see more of it.” Now, is that really like “2 + 2 = 4?” You used those two examples to show that the universe “simply works,” however, is “you will tend to see more of it” on the same level as “2 + 2 = 4?” In the “2 + 2″ example, clearly, it does not have a choice in the matter, because I think we’d all agree that “2 + 2 = 4″ is an immutable fact in mod 10 arithmetic, and you are correct, that it’s true whether or not someone asks about it. The problem is that biological organisms that “you will tend to see more of” inherently have a choice just by the very way you make that statement, and you would be incorrect, from a logical standpoint, to say that a biological organism does not have said choice. The organism could clearly allow itself to simply die without giving itself nutrition at all. That is not a logical impossibility like “2 + 2 = 5 in mod 10 arithmetic.” The philosophical problem is that there is a choice being made, regardless how seemingly insignificant. A choice necessitates the need for an intention of some kind and some form of intelligence. Now, the bacteria, as you said, may be stupid in the way we normally think of intelligence as a performance metric. The logical problem is that you would be incorrect to make the statement, “it is impossible for the bacteria to not try to sustain itself.”

  70. artfulDon 16 Feb 2010 at 10:42 pm

    There is no intelligence that doesn’t involve learning. Except maybe yours. The papers I cite are representative of what has become the conventional wisdom.

    And all behavioral instincts have evolved from the organisms historical experience. Some of the writings by Shapiro and Margulis for example will acknowledge this. But when writing for peer review publications, such explanations are not specifically included if not essential to the research presented.
    But I do my own research, and like to show some of the results to see how the ignoramuses like you will attempt to counter any of the newer ideas, whether mine or the others I’ve cited. Because most like you have no ideas of your own and get highly irritated when it seems others can do what you cannot.

  71. artfulDon 16 Feb 2010 at 10:58 pm

    Sorry lurchwurm, I didn’t see your post before I presented mine, which should have had Heinleiner’s moniker prominently displayed as the ignoramus described therein.
    I know you like to present your arguments in a more cordial fashion but this guy has never acknowledged that he has anything to learn from those with that approach. Or from those with any dissenting or non-dogmatic approach for that matter.
    So good luck with trying to match logic with sophistry.

  72. lurchwurmon 16 Feb 2010 at 11:18 pm

    Well, I prefer to be cordial, because I know we are all struggling to deal with this non-sense called life :) As much as I admire your arguments and knowledge and willingness to address any issue, if I didn’t agree with you, I would find you absolutely revolting. Nobody wants to constantly be insulted. However, I can only hope that if I didn’t agree with you, I would try to stay as clear-headed as possible when dealing with you, and for the most part, I think Heinleiner has done a fairly good job of trying to take you seriously. Unfortunately, I think he has let your abrasiveness affect his ability to actually listen to what you are really saying, which is the unfortunate side-product of everyone wanting to be right.

    I prefer to try to find philosophical problems to present, because most of the time, they can really cut to the heart of a problem, and a lot of the time, they can make people think in a different way, even if the problem doesn’t get directly solved in their mind.

  73. artfulDon 17 Feb 2010 at 12:53 am

    But in fact you didn’t at first agree with me, yet I didn’t insult you. Nor did I insult Hutzler until he revealed his devious side. And this latest guy has been devious from the get go. But I make no excuses for my tactics. These guys are found all over the place, devoid of any ideas of their own, irritated by their own lack of understanding anything new, and thus with the need to begin, not by asking questions about mine, but by attacking what they can’t understand from the getgo. They are simply like the proverbial fools, not to be suffered gladly.

    I don’t put you in that class, although when it comes down to it you are pretty damned naive about the efficacy of your philosophy.

  74. lurchwurmon 17 Feb 2010 at 1:06 am

    It’s definitely still a work in progress for me. In fact, I have a LONG way to go. And yes, you didn’t insult me. But I still don’t see how insulting somebody is going to help the matter. That’s my only criticism. Other than that, I think you are very cogent in your argumentation.

  75. artfulDon 17 Feb 2010 at 1:37 am

    It’s actually not insult, it’s ridicule. Works best as a counter to deceptive strategies. The only defense against it is honesty, the application of which the deceptive have no skills for. It requires them to actually know what they’re talking about.

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