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    A Response To Pigliucci’s Response To Coyne’s Response To Dupre
    By Randall Mayes | October 6th 2012 06:03 PM | 25 comments | Print | E-mail | Track Comments
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    Randall Mayes is a policy analyst specializing in biotechnology. His areas of expertise include technology based economic development and public...

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    I must admit, before reading Massimo Pigliucci’s interesting article on Science 2.0, I was unaware of John Dupre’s so-called scholarship. My curiosity first led to Wikipedia which refers to him as a critic of evolutionary biology. With amazing tools such as Google and YouTube, I was able to watch Dupre debate Alex Rosenberg of Duke University, someone whom I had many exchanges with in his first philosophy of genomics class in 2004. After watching the video, in a matter of minutes it was apparent that Dupre is a philosopher, not an expert in evolution.  

    A clearer picture of his profile may help explain the puzzled comments by posters on PigIiucci’s blog. It may also explain Dupre’s two assertions in his title, Evolutionary Theory’s Welcome Crisis. But, is evolution actually a theory and is it in crisis? When one looks at the historical facts in the debate between creationism, a belief system based on vitalism, and evolutionary biology, a knowledge system based on peer review, what does it tell us about which position is a theory and which one is in a crisis?

    For faith based creationists, a struggle for credibility began when the U.S. Supreme Court  overturned the 1925 Scopes Monkey Trial decision based on the Establishment Clause, a provision of the First Amendment of the U.S. Constitution, which prevents the establishment of a state religion. Then, in 1950 Pope Pius XII wrote in Humani generis that the account of biblical creationism in Genesis is not literal; rather it is a metaphorical source of human origins. These setbacks would understandably have placed anti-evolutionists in crisis mode and explain what would eventually occur.

    In response, the Discovery Institute, a religious think tank, orchestrated a series of state to state lawsuits attempting to force public school curriculums to teach intelligent design (ID) as an alternative to evolution. In one of those cases, Edwards v. Aguillard (1987), a judge ruled against a Louisiana law requiring this practice was unconstitutional because it was specifically intended to advance a particular religion. The court discovered that in one anti-evolution publication the author had crossed out creation 150 times and replaced it with intelligent design.

    From Dupre‘s article, it appears that he is the British equivalent of Michael Behe. Behe is an American biochemist who represented the Discovery Institute in their unsuccessful spin campaigns. In paragraph 3 of his article, Dupre defines a so-called crisis in evolutionary biology in the context of heredity. He claims, “For the last 70 years the dominant paradigm in evolutionary science has been the so-called new synthesis.” For a critic of evolution this may be the version of reality that they would like to convey. But for practitioners of evolutionary biology, microevolution, which explains heredity at the individual level, has two competing schools of thought, genetic determinism and those that recognize the importance of developmental biology.

    Furthermore, his statement does not address the second component of evolution dealing with speciation, referred to as macroevolution. Since the present understanding of evolution transcends what Darwin knew, it is false logic to conclude that if exceptions exist to slow random mutations then evolution is wrong. Darwin never heard of DNA, much less of genes and scientifically did very little to advance our understanding of evolution. The more recent advances in macroevolution supplement the understanding of the modern synthesis which explains microevolution.

    Thomas Kuhn developed the basic model that scholars use for understanding revolutions in science. Kuhn was a physicist, so Peter Bowler adapted Kuhn’s model for evolutionary biology. Bowler argues evolutionary biology experienced a series of mini-revolutions including the findings from the fields of paleontology, geology, and taxonomy in the 1700-1800s which laid the foundation for evolution as an alternative to creation.

    First, creationism and vitalism took an intellectual tail-kicking from Galileo (1610) and Pasteur (1859). Then Darwin made evolution a credible alternative to creationism. The actual paradigm shift brought about by Galileo, Pasteur, and Darwin was from the belief system based on vitalism to knowledge systems.

    After losing all of its law suits and in the process leaving hefty bills for tax payers, the ID movement has subsequently developed a campaign to make evolution controversial. One of their tactics is to cast doubts on the believability of evolution due to inconclusive fossil evidence. They allege that if natural selection, through a progressive series of random mutations over time were accurate, the fossil record would present the representative evidence verifying the intermediate steps.

    Evo-devo explains the gaps in the fossil record. Through regulatory DNA, a network of switches determines the dosage for anatomical and physiological features manifesting in the variety of forms seen in nature. Although evo-devo is an advance in science that informs mechanisms of evolution, ironically Dupre claims it is a source for a crisis in the field that it further advances.

    Mysteriously, in paragraph 4 of his article, Dupre stumbles into the truth when he discusses how evolutionary biology is in the process of reorganizing knowledge and correctly states “without undermining the fundamental tenets of evolutionary theory.”

    Comments

    The history of the creation-evolution controversy in this article went awry in the fourth paragraph. It implies the Discovery Institute was active in the 50s which it was not. Edwards v Aguillard was a US Supreme Court Case not a state case that ruled against the teaching of creationism and not intelligent design. The information that follows seems to be from the Dover Intelligent Design case. Errors like these are fodder for the creationist propaganda mill. Please be more careful.

    randallmayes
    Thanks, I will take out state, my source was wrong. Johnson and the Discovery people were active as a group before they formally organized. But, why is this important?

    You are correct creationism was the topic, but the ID movement thought ID sounded better. This is why I mentioned, "The court discovered that in one anti-evolution publication the author had crossed out creation 150 times and replaced it with intelligent design. Consequently, this is why the ID movement lost this case. This supports the thesis of my essay, who's in crisis and who's promoting a theory.  

    Randall Mayes
    Mr. Mayes,
    Very nice. Thank you very much for writing this.

    Gerhard Adam
    Does anyone truly believe that this "debate" between creationism and evolution has anything to do with science?  Moreover does anything truly believe that it makes one bit of difference?
    randallmayes
    Since some polls say as many as 80-90% of people in the US do not believe in evolution, it is appropriate to ask these people about their worldview and why they believe ID deserves equal standing with scientific findings.
    Randall Mayes
    Gerhard Adam
    ...it is appropriate to ask these people about their worldview and why they believe ID deserves equal standing with scientific findings.
    In what way is this relevant to anything?  What possible difference does it make?  Do you really believe it would change anything if creationism were taught?

    Even the majority of biologists could still be competent and successful without ever once dealing with the issue of evolution.  The mere fact that it is recognized as being part of a "debate" lends credence to ID and creationism.  It's time to ignore it and be done with it.
    You are correct, but not in the way you think.

    First off, Intelligent design and 6 day creationism are two different things and you have to know that. I criticize the 6 day creationists just as much as you do and I can do it by pointing out how a 6 day interpretation makes Genesis incoherent. People often like to conflate the two in order to avoid having to answer the quite serious objections people in the ID movement make. Kind of like how some people like to conflate all Muslims as terrorists to avoid having to look at the terrorists motivations.

    Anyway, back to the point. The debate is about the worldview used to interpret the scientific data. Science is agnostic about there being a designer or not. The scientific method was developed to study the physical world and nothing else. Right now the worldview dominating the area of biology is that of methodological naturalism, only causes appealing to natural causes will be accepted. The possibility of life being designed is rejected before the evidence is even looked at. That is not science. That is philosophy masquerading as science. Those in the Intelligent Design movement hold true to the scientific method, that all explanations be considered. The evidence pointing to common descent nicely fits the idea of a common designer, We see the same in Cell phones, cars, TVs and other things we know are designed. The question is, "Can natural selection acting on random mutation achieve the same thing?" My worldview is compatible with either answer, is yours?

    No other field of science is held in a straight jacket of methodological naturalism like biology. Imagine if Forensics science functioned like biology. Police find a body in the woods that had been shot 6 times in the chest and then set on fire. Would the police try to explain the event by saying that 6 hunters shot at different deer, missed, the bullets continuing downrange to strike the person in the chest. Then, the body was set on fire by a lightning strike. Anyone who even brought that up as anything other than a joke would be sent in for psychiatric evaluation, yet that is the view people like Dawkins, who concedes in his books that life appears designed, take when it comes to explaining the appearance of design in life.

    I work in telecommunications for a living and part of my job is to setup, repair, and program computers. I see lots of "mutations" in the code caused by any number of reasons. There are only 3 outcomes you get. A computer that functions normally (The mutation is somewhere that doesn't cause harm), a computer that is degraded and no longer able to perform its task in the overall system, or a computer that stops working altogether. The more "mutations" you get, the higher the odds that the system will stop working altogether. I have never seen a computer that had a "mutation" in the code that resulted in the code working better than it did before.

    DNA is digital computer code, just that instead of each character having two possibilities, DNA has four. The computers I use at work can be used for all sorts of things just by changing how certain functions are expressed in the code, just like how the same basic design for a dogs paw can be used for a human hand or a bats wing just by changing how certain functions are expressed in the code.

    Just like DNA code, all these functions are interdependent. If I tell the function that resets the outbound phone line to not accept an off-hook command for a minimum of 5 seconds after going on-hook, to allow a particularly slow central office to reset the line, I have to also tell the function that links the inbound and outbound line to send an off-hook command to the outbound line once per second, instead of just once, for whatever I want the timeout period to be. If I don't, a no-dial tone error message will result and the line will be registered by the system as out of service for a period of time, quickly bringing the entire system to a halt if traffic is high enough as more and more lines are listed as out of service. In bioengineering we find similar interdependency. Breed for one particular trait and several undesirable traits can often follow.

    Darwinism was proposed back when life was thought of as little more than electrified jell-o. Under that view, the mechanism is quite plausible. Today we know that life is not simple, it's DNA computer code is more complex and robust that the most advanced operating systems intelligent programers have created.

    I know that if I take a hard drive with Windows 95 on it and program the computer to copy the OS to a second hard drive, reboot from the copied drive, copy that drive back to the original, and repeat, copying errors will quickly result in a dead computer. I know that such a method, no matter how much time you throw at it, will not result in a copy of Windows 7 or something like it. Likewise, variations within a species and loss-of-function mutations, like antibiotic resistance (The pathway that the antibiotic used to get inside the bacteria broke and stopped working), do not explain the diversity of live, as you don't get new functional information, only variations of the same information or broken information that happen to do something useful at the time, like how a broken network driver makes a computer immune to an internet worm.

    The problem with Noe-Darwanisim I have can be summed up here: I look at DNA and see computer code. If natural selection acting upon random mutation creating increased functional complexity doesn't work on the computer code in the computer in front of me, why should I believe it works in the computer code inside every living being?

    Gerhard Adam
    You're incorrect on several major points, and primarily this is due to some serious misinterpretations. 

    The first is in comparing DNA to computer code and relating it to computers.  Nothing could be further from the truth, so any conclusions you draw from such a comparison are wrong.  Programming errors are not "mutations".  They are simply errors.

    Also, you're seriously misunderstanding the concept of "random" as it applies here.  This isn't a kind of "absolutely anything can happen".  There are constraints, based on the elements available, the interactions, the basic chemistry, etc.  In short, the process is NOT random in the way you're using it.  In this context, "random" simply means unpredictable.

    Your explanation about information isn't even remotely close and it's been addressed too many times to repeat it all here.

    In the end, the fundamental problem with Intelligent Design is that you cannot explain "design" and "intelligence" by simply postulating the existence of a designed, intelligent being.  You're simply engaging in a circular argument, where what you're attempting to prove is being created by an individual that has the same unanswered questions.

    So, it is your position that is decidedly unscientific, since you never feel the need to explain your first cause.  You simply postulate it into existence and then go from there.  Sorry, but that doesn't work.

    You may choose to believe it, but don't imagine for a moment that there's anything scientific about such a belief.
    Science is agnostic about there being a designer or not.
    What is that supposed to mean?  As I already stated, if you're going to postulate a designer, then before you can venture off to explain biology, you need to explain what this designer is and where it came from.  You can't simply make stuff up and then begin explaining other things.

    As I said ... DNA is not a digital code, it bears no resemblance to computers, and any analogy to programming is hopelessly flawed.
    "Mysteriously, in paragraph 4 of his article, Dupre stumbles into the truth when he discusses how evolutionary biology is in the process of reorganizing knowledge and correctly states “without undermining the fundamental tenets of evolutionary theory.”

    Finding it mysterious that you agree with the main conclusion of an article should perhaps be a clue that you have totally misunderstood it. In this case the suggestion that I am a "British equivalent of Michael Behe" makes the level of the misunderstanding even more depressingly clear. Please don't even think of trying to read my 'so-called scholarship'. If, however, you were to look at my more accessible book 'Darwin's Legacy', I think you would be able to confirm that I have not the slightest sympathy for ID.

    John Dupre

    randallmayes
    I will check out your book and I am glad we can agree on ID. You are similar to Behe in that you are planting doubts in people minds.

    This is where we disagree.
    Although evo-devo is an advance in science that informs mechanisms of evolution, ironically Dupre claims it is a source for a crisis in the field that it further advances.

    I take this as the thesis of your article. Am I correct?
    Randall Mayes
    Gerhard Adam
    One can only conclude that you either never read Dupre's article, or that there is an inexplicably monumental misunderstanding in your reading of it.
    Those who believe that a supernatural being created the universe have never posed an intellectual challenge to evolutionary theory.

    But nothing more clearly demonstrates that science and creationism are polar opposites than the latter’s assumption that disagreement signals failure. In fact, disagreement – and the deeper insights that result from it – enables new approaches to scientific understanding. For science, unlike for dogmatic belief systems, disagreement is to be encouraged.

    We should leave the creationists to their hollow convictions and happily embrace the uncertainties inherent in a truly empirical approach to understanding the world.
    http://www.project-syndicate.org/commentary/evolutionary-theory-s-welcome-crisis-by-john-dupre
    These statements from the article, already indicate that you are raising false "alarms" in accusing Dupre of anything in support of ID.

    Perhaps some might be offended by the use of the word "crisis".  So what.  Get over it, since it doesn't mean anything except to those that think ID or creationism represents a viable threat.

    Until scientists, and those that support science get over their paranoia about creationism and their faux concern that every item of dissent in biology feeds the creationists, then this entire discussion is a waste of time and pure politics.

    Creationism and ID are not science.  Who cares what they say, think or do.  And this view that teaching creationism in schools is one of the signs of the apocalypse, I would say ... don't kid yourself.  You'd be lucky if half the kids exposed to either view remember a tiny fraction of what they've learned and for those pursuing a more serious interest, they will learn more details. 

    Even if by some chance an individual became a PhD biologist, while retaining a creationist viewpoint, I can't help but marvel at someone's ability to hold such cognitive dissonance in their minds while they were pursuing their degree.  However, I expect that nothing of the sort would ever occur.

    In short, the entire creationism vs evolution discussion is irrelevant and a waste of time.  In fact, it makes science look like religion because of the appearance that science is also in the business of trying to save souls, by converting them to evolution theory rather than ID.
    Gerhard,

    Your point about cognitive dissonance is right on. However, and I hate to break this news to you, but regarding your comment —

    "Even if by some chance an individual became a PhD biologist, while retaining a creationist viewpoint, I can't help but marvel at someone's ability to hold such cognitive dissonance in their minds while they were pursuing their degree.  However, I expect that nothing of the sort would ever occur."

    — it turns out that "nothing" — or rather, something — of this sort HAS indeed occurred at least several times. Perhaps the most high-profile example is Kurt Wise [http://en.wikipedia.org/wiki/Kurt_Wise], who obtained a Harvard Ph.D. in Geology (with a hefty dose of Evolutionary Biology) — his advisor being Stephen Jay Gould, no less! Wise remains an ardent young-earth creationist and ID proponent. The "cognitive dissonance" implications (which I agree are fascinating) have been addressed by Richard Dawkins [http://www.secularhumanism.org/library/fi/dawkins_21_4.html] and Timothy H. Heaton [http://en.wikipedia.org/wiki/Timothy_H._Heaton], among others.

    The National Center for Science Education (NCSE), in its publications and on-line news reports, has fingered other PhDs in geology and biology, as well as other fields with more peripheral relevance to evolutionary biology.

    Gerhard Adam
    ... and this has had what kind of effect?  The point is that anyone publishing in science must pass peer-review, so simply having a degree is largely irrelevant to the question of evolution or geology, or much of anything else.  So, while Wise may be a young earth creationist, unless he publishes something that represents a real change in geologic theories his view is still irrelevant.

    Again ... so what?  This is a tempest in a teapot, and everyone gets all excited despite the fact that these people have no influence on the science.  Instead it still takes on the religious overtones of trying to save the masses.
    Hank
    I think this sentence, ""The creationists are right about one thing: contrary to the impression given by much popular writing on the subject, the theory of evolution is in crisis", is what hangs people up in your essay. Other philosophers seem to get the bigger meaning while biologists tend to react more to anything that looks like it is helping creationists. I think claims about creationism in America are exaggerated, anyway. A few cranks trying to teach evolution in schools are not a national issue whereas cranks that don't give their kids vaccines or try to halt genetics and medical research are a legitimate crisis. But creationism in the US is more of a political issue in the US than a science one. mostly because the anti-religious militants in the US are louder.
    Want more no-nonsense, independent science? Buy Science Left Behind
    randallmayes
    Perhaps we could leave the politics out of the discussion. Maybe Dupre could restate his thesis for biology types and we could work through the merits and not the misunderstandings.
    Randall Mayes
    Gerhard Adam
    But, is evolution actually a theory and is it in crisis?
    Just caught this comment on re-reading.  What would you call it if not a theory?
    randallmayes
    For microevolution, our understanding and treatment of malaria and sickle cell are great examples. We have several mutations acquired through natural selection and passed on through Mendelian inheritance. For macroevolution, the same genes that code for dog paws code for human hands. The genes are regulated by switches that give different phenotypes. Since scientists have proved the theories behind these mechanisms, you could say they are scientific laws, like Mendel's laws. Darwin was unable to establish laws, but paved the way.
    Randall Mayes
    Gerhard Adam
    Sorry, but that just isn't so.  Evolution doesn't, in and of itself, represent much of a theory, without Darwin's qualifying "natural selection" aspect of it.  However, there is nothing within the mechanisms of natural selection that remotely resemble laws in any scientific sense.

    Even your example of genes is true at some levels and not at others.  The mechanisms by which traits are expressed and ultimately selected is hardly settled science.  The fact that natural selection occurs is true regardless of whether all the mechanisms by which it operates are known.  In essence I find the consideration of "theory" to be irrelevant to anything in science.  This is simply a layperson's issue of interpretation and typically misunderstanding of what a theory is.

    randallmayes
    So I guess in you opinion when a genetic counselor tells two people getting married that both have recessive mutations for sickle cell acquired through natural selection against malaria, that when they have kids based on Mendelian genetics three outcomes may occur at these odds depending on which alleles are passed on, that this is a theory.
    Randall Mayes
    Gerhard Adam
    You're concerned about irrelevancies.  What difference does it make what you call it?  There are much more well established principles in science that are still called theories ... so what? 

    The fact that you get antibiotics for an infection doesn't change the fact that it is based on "germ theory".  Again ... so what?  This is a non-issue.

    Interestingly enough, your example demonstrates how silly the whole thing is, because Mendel's genetics is called a "law", despite evolution being called a "theory".  In fact, your examples don't even require evolution to operate [certainly not with respect to any explanatory power].   So, I suspect that your hypothetical couple would accept such an explanation even if they were hardened creationists.

    In addition, Mendel's laws (Segregation and Independent Assortment) don't even apply to the majority of life forms, only having a role in diploid sexual reproduction.

    This sounds like it's simply responding to the creationist arguments that evolution is only a "theory" and that somehow their behavior would change if we suddenly called it a "law".

    More to the point, evolution becomes more problematic in that regard because it is ultimately a historical theory.  It offers little predictive capability regarding the direction natural selection can take beyond some obvious considerations [i.e. exposure to herbicide is likely to produce herbicide resistant plants at some point].  In fact, it is precisely the abuse of such a historical theory that has given rise to much of the silliness we call evolutionary psychology, where every behavior or trait is somehow presumed to have been selected for, regardless of whether we possess the knowledge to know that something is an adaptation or adaptive.
    randallmayes
    I do not blame you for not directly answering the question.

    Kuhn thinks the scientific method is important; theory, hypothesis, and accepted new science.
    My father, an award winning theoretical and experimental physicist, with NASA for 30 years, my mentors at Duke, and I think it is important.  I guess we are all concerned about irrelevancies.

    It is good to have competing theories, some fail and some we use. I refer to Kuhn in my writings and I noticed Dupre did as well. Why do we not refer to your theory that theory as as concept is not important?

    Lets say the same two people getting married have a genetic counselor that checks their blood for gemmules, because he or she believes that pangenisis explains sickle cell. Darwin's theory was based on vitalism, but shortly after Mendel nailed it. Textbooks refer to Mendel's laws. Would the counselor lose their license?

    This is why we reference Kuhn instead of you and this is why genetic counselors, who use routine procedures, do not check for gemmules.

    Randall Mayes
    Gerhard Adam
    It appears that you've switched positions.  Your point was that theory was inadequate and should be referred to as "laws", while my claim was that it didn't make any difference in the application.

    However, you then shift gears by moving into a policy area [i.e. licensing of a practitioner] as if that has anything to do with any of these concepts.  Even asking whether the counselor should lose their license, is not a scientific issue, but rather a political/legal one.

    Similarly, why erect a straw man by mentioning the scientific method.  When did that come into dispute?  The problem was a simple semantic one which you are obscuring with irrelevancies.  My point is simple.  There is nothing gained by referring to a scientific finding as a theory versus a law. 

    For some reason, it is you that is evading the issue in failing to demonstrate that there is a material difference in referring to evolution as a theory versus a law.
    Kuhn thinks the scientific method is important; theory, hypothesis, and accepted new science.
    Where is this in dispute?  When was this even mentioned [except by you]?  Tell me how Kuhn relates to your claiming something should be a law rather than a theory?
    This is why we reference Kuhn instead of you and this is why genetic counselors, who use routine procedures, do not check for gemmules.
    What kind of logical fallacy are you invoking here?  One doesn't have to be a geologist to reject a flat earth.  Do you think genetic counselors don't check for gemmules because of Kuhn?  Do you think it's because we call Mendel's principles "laws" instead of "theory"?  Do you believe that this is some sort of protection that no one will come along and claim gemmules as being a legitimate source of investigation?

    Of course not, because anyone that proposed that would have to demonstrate evidence for why it should be considered and in the absence of such evidence be relegated to the realm of crackpots.  However, what we call the accepted ideas has nothing to do with anything.  In short, nothing would be lost if we dropped the terms "theory" or "law" and just called them "good ideas".

    Mendel's "good idea" would convey the same information as anything else you care to examine.
    I do not blame you for not directly answering the question.
    I did answer the question.  I specifically indicated that what the genetics counselor told people wouldn't change one bit based on whether the principles were called a "theory" or a "law".  It is only in your view that you're assigning some significance to the designation.  Evolution is not diminished by calling it a theory, any more than presuming that it becomes more significant by calling it a law.  Those are simply word games, and while they may be relevant in arguments with creationists, they are irrelevant to the science itself.
    Gerhard Adam
    Since scientists have proved the theories behind these mechanisms, you could say they are scientific laws, like Mendel's laws.
    What theories have been proven?  That genes code for proteins?  That such proteins create structures?  How does a protein produce a trait?  What regulates the role of the proteins?  How do you establish whether a trait is adaptive or an adaptation?

    Does the genome code for a completed immune system?  How about in brain development?

    The truth is that we're only just beginning to understand many of these things, so they are hardly "proven" in any sense of the word.

    You may elect to dispute these claims, so I would ask one question.  What theory do you feel is "proven"? 
    I don't think I can make it any clearer than in the original piece. But here's an even shorter summary: No one worth debating with doubts that evolution happened, but the details of the process are still only very partially understood. Recent advances, including in my view (obviously subject to debate), evo-devo, lateral gene transfer, epigenetic regulation and more (see Massimo Pigliucci's post), have opened up new possibilities and suggested that the new synthesis consensus (Dawkins, Coyne, etc.) is highly questionable. In crisis, even, to make the point perhaps over dramatically. The most important point: we shouldn't try to pretend that everything is totally understood and finished just because if we don't the creationists will get excited. The fact that our ideas are subject to criticism, major development and significant rethinking is just what should distinguish science from mere dogma. Ok?

    John Dupre

    randallmayes
    "the new synthesis consensus (Dawkins, Coyne, etc.) is highly questionable" 
    Epigentics, evodevo, lateral gene transfer, and also micro RNAS work in conjunction with the synthesis, they do not make the synthesis less valid. As Ernst Mayr said there are two major problems, understanding the mechanisms of heredity and development.

    "The most important point: we shouldn't try to pretend that everything is totally understood and finished."
    Researchers will be sorting out whats in the human genome for decades. The ENCODE project just released some new findings. Who is pretending?  People who understand genomics realize how much we do not know. In some cases such as protein folding, we don't even know what we don't know.
    _
    Randall Mayes