Friday, August 19, 2011

Physicists and Biologists

I've just finished reading evolution: a view from the 21st century by James A. Shapiro. I'll write up a full review later on but right now I just want to quote a passage from near the end of the book. He begins the paragraph with a description of those physicists who entered biology in the 1940s and 50s (e.g. Max Delbrück).
Currently another wave of physical scientists is entering the life sciences. They bring with them a much-needed and fruitful sophistication in observation at the micro level, in mathematical formulation of results, and in computational methods of data analysis. Physicists-turned-biologists have an additional advantage of lacking a formal education in the life sciences; consequently, they have not been taught to exclude from their thinking notions previously concluded to be "impossible." We can only hope that their less prejudiced backgrounds will make it easier for them to develop novel conceptual frameworks to complement the analytical and experimental techniques they are introducing.
This insightful observation has great potential beyond solving the major problems in the biological sciences and I wonder if Shapiro fully appreciates the implications.

I have no formal training in physics. I haven't the foggiest idea what quantum chromodynamics (QCD) is all about, beyond what I can read on Wikipedia. I don't have a firm grasp of general relativity and my math skills are very weak.

However, I understand that physics is grappling with unified field theory and that string theory is going nowhere. I've heard rumors that physicists can't find the Higgs boson, although I can't imagine where they might have put it. I have plenty of experience helping Ms. Sandwalk find her car keys and credit card so I've come up with a brilliant idea.

Why don't I move to physics and solve their problems? I've got all the proper qualifications, "lacking a formal education," "less prejudicial background," and I haven't been taught to exclude impossible things. I bet I could convince half a dozen of my biologist colleagues to abandon the difficult problems of biology in order to help the physicists. It shouldn't take more than a few years.

We need a name for this discovery, let's call it The Shapiro Conjecture.1

Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism, and ecology. That's just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.

AFTERTHOUGHT: Biologists have been using computers to analyze complex data sets for over fifty years and we're pretty sophisticated at making observations at the micro level. Why do we need physicists to show us these techniques?


1. See The Salem Conjecture.

53 comments:

  1. The problem in biology is that the traditional training is simply not adequate to provide scientists with the relevant skills in all aspects of the field: a formal background in empirical biology (read: wet-lab skills) does not adequately equip students to become computational biologists. Until such time as we have first year computational biology students who spend their early student days translating genes in the computer lab instead of peering at cells through a microscope, computational biology will continue to be invaded by non-biologists with computational skills.

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  2. "Physicists-turned-biologists have an additional advantage of lacking a formal education in the life sciences"

    Stupidest thing, I've heard today.

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  3. Well, the standard argument is that physicists are inherently smarter. And when you are smarter, your analytical skills and ability to autodidact trump formal education.

    The real life data support the "smart" part: physics majors have consistently highest SAT/ACT/IQ test scores.

    That said, historical role of physicists in biology is widely overblown. E.g., it should be remembered that it was biologist Timofeev-Ressovsky who taught Delbruck some biology when they both were in Berlin. And Gamow's role was more like that of an organizer and a cheerleader. And claiming Pasteur to be physicist is like calling Newton an alchemist (i.e., true but irrelevant). And for Crick there is Watson. Not to mention that 99% of seminal discoveries in biology were made by biologists.

    As for physicists coming into biology today, I predict that their success will be very limited and that most of them will be very disappointed finding out just how hard and poorly tractable biology usually is. The arrogance displayed by some of them is truly astonishing. A friend of mine, a respected physics professor and a very smart guy, once came up with what was basically a Lotka–Volterra model. He was shocked (shocked!) to discover that it is something very well known in biology for well over half a century. In another example, I know a guy who 10 years ago was claiming that "in 20 years we will have a complete working model of a cell and in 30 years bench biology won't exist because we will be able to model an effect of any mutation on an organismal level using computers".

    Every time I see physicist thinking biology hasn't advanced enough because there are too many dolts working in it, I suggest that he should go go and solve a problem of protein folding :-)

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  4. Most optimal approach: cross-training in both biology and computation/
    physics (or whatever you want to call it). Yeah, it's much more work, but it's more about ways of thinking than factual knowledge (actually, it's factual knowledge + ways of thinking).

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  5. One place the physicists have taken over is molecular structure and dynamics. I wish I understood molecular dynamics simulations. They can tell you what is really going on in allostery, and allostery is how it all works. You can run molecular dynamics on the web now, but you really need to understand what's going on, and for that you need physics and math. Lots of it.

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    Replies
    1. MD simulations are a model. They have a lots of drawbacks. You cannot fully trust them. So your "really" maybe not very really.

      Delete
  6. One place the physicists have taken over is molecular structure and dynamics.

    Warning: thou shalt take MD simulations with 2.5 kg of salt. Their real life predictive power is minimal (so far).

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  7. The real life data support the "smart" part: physics majors have consistently highest SAT/ACT/IQ test scores.

    [short rant] Got nothing to do with "smart" in any objective sense. Go read http://cscs.umich.edu/~crshalizi/weblog/523.html . [/short rant]

    Shapiro's thesis was perhaps better articulated by the 13th century Czech theologian Nicholas of Cusa, who maintained that enlightenment was truly attainable only through ignorance.

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  8. "....computational biology will continue to be invaded by non-biologists with computational skills."

    Well many in the field of genomics don't seem to care that a lot of computational biology is done by programmers with very little or no training in biology and thus no way to do the necessary functional assays to verify their data.
    It's not inherently a bad thing but journals in my opinion are too willing to publish these experimentally weak papers.

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  9. Also, thanks for this post Larry; it made my morning.

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  10. One place the physicists have taken over is molecular structure and dynamics. I wish I understood molecular dynamics simulations.

    Molecular structure draws people of many backgrounds: biology, chemistry, physics, and even mathematics. It's been that way for quite a while.

    The important bit about understanding molecular dynamics simulations is in the last word. It's a simulation. Without real data, you can't know if your simulations are accurate; and with real data, you don't need to simulate.

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  11. I've heard rumors that physicists can't find the Higgs boson, although I can't imagine where they might have put it. I have plenty of experience helping Ms. Sandwalk find her car keys and credit card so I've come up with a brilliant idea.

    Check under the sofa cushions.

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  12. ... apparently the Stats/Math/CompSci types have a similar feeling towards Physicists...

    http://xkcd.com/793/

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  13. Hey Dr. Moran, I don't know if you remember me, but you sat next to me at an evolution conference at king's college. I am a grad student studying quantum optics, but at the time I was a physics undergrad who was spending my summer doing research for Rob Beiko in bioinformatics because I found genomics interesting. It saddens me to see you contributing to this pointless rivalry between physicists and biologists, when we're essentially on the same team. With the accelerating pace of technological and theoretical resources available to scientists, I think it is extremely useful for physicists to jump into biology and vice versa, because how will we know what the best practices of our field are if we have never seen our field from the outside. For all we know we could merely be sitting on local maxima, while others have seen the global maximum?

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    Replies
    1. Thanks for this comment.
      I just don't understand why people like so much to divide science into fields instead of uniting.
      It's Science, the totality of human knowledge. We are all in the same boat.

      Delete
  14. The best ones don't do this, but it is fairly common for mathematicians and physicists to waltz into biology convinced that their powerful mathematical techniques will be unknown there, and that they can revolutionize computational biology, to universal applause.

    Generally they achieve no such thing, as they find that starting a long time ago computationally- or mathematically-inclined biologists ransacked the mathematics and physics literature to adapt their methods to computational biology. We picked most of that good stuff up -- and were grateful for it -- decades ago.

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  15. @Joe,

    Some of you have even taught the mathematicians and statisticians a thing or two!

    I agree with you that there are exceptions to every rule. We all know of people from outside biology who have made major contributions to our understanding of evolution. Think of Bill Dembski and David Berlinski.

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  16. In the work on numerical methods for inferring phylogenies, there was a tendency early on for most of the people putting forth methods to be population geneticists or biochemists -- the taxonomists (systematists) made much less of a contribution, probably because so many innumerate people had gone into that field.

    So the phenomenon can be seen even within biology.

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  17. I'm reminded of Neil deGrasse Tyson's oft-repeated quip about a biologist dismissing the "evidence" of life in a martian rock because the tubules formed were too tiny to be produced by terrestrial bacteria. Tyson was flabbergasted with the biologist's response and chided ALL biologists for having a data set of one (life on Earth). For more info, read Death by Black Hole. His hero, Carl Sagan, also had a lot to say about biology and even debated Ernst Mayr on exobiology.

    BTW, there's also the case of the famed mathematical savant Stephen Wolfram and his "revolutionary" take on biology and evolution. He didn't need a background in biology to rethink the nature of biological systems and how biological complexity arises (not by natural selection!). I'm sure all biologists are thankful for his innovative insights. ;-)

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  18. The problem is that few biologists like advanced math or stats. My biologist friends would be the first to admit this. As a result, most biologists have deep misconceptions about some parts of their own fields. Even highly mathematical fields like population genetics and ecology have institutionalized some serious mathematical misconceptions about some of their fundamental quantities.

    For example, the standard method for partitioning ecological or genetic diversity into within- and between-group components is mathematically incorrect, when the Simpson index or heterozygosity are the diversity measures being partitioned. The correct formulas are well known in physics. This institutionalized error leads to big problems for some of the main concerns of these disciplines.

    Ecologists and geneticists have used this incorrect between-group component, divided by total diversity, to measure compositional differentiation between groups. In population genetics this is called Gst, the main measure of genetic differentiation. These measures behave so badly that they can approach zero (indicating no differentiation) even when the groups are maximally differentiated (contain no species or alleles in common)!

    However, this case also illustrates the point that biologists often find the correct solution independently of physicists. Joe Felsenstein, who commented above, is an example. In his online book on population genetics, he analyzed some problems using what turns out to be the correct partitioning function. Unfortunately, geneticists in general still misunderstand this key aspects of their subject. This leads to even deeper problems, including incorrect ideas about the factors controlling genetic drift.

    In an ideal world, physicists and biologists would work together and fill each other's weak spots.

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  19. Re Larry Moran

    Of course, pompous windbag David Berlinski is a philosophy PhD so don't blame the mathematicians or the physicists for him.

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  20. Larry, since genetic drift is one of your (and my) favorite subjects, let's see how well the standard theory works, and see if it couldn't have used some input from physicists or (especially) mathematicians.

    Here's my test. Using the simplest genetic model, Wright's neutral finite island model with infinite alleles, tell me what kinds of model parameters lead to high differentiation, and what would lead to low differentiation, at equilibrium?

    My guess is you will say Nm<<1 means high differentiation and Nm >>1 means low differentiation. (N is the size of each subpopulation, m is the migration rate, so Nm is the number of migrants entering each subpopulation in each generation.) That is the standard textbook theory, for the last sixty or seventy years.

    Would that be your answer?

    Lou

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  21. @SLC,

    But Berlinski thinks he's a mathematician and a physicist! Doesn't that count?

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  22. http://en.wikipedia.org/wiki/David_Berlinski
    "Berlinski was a postdoctoral fellow in mathematics and molecular biology at Columbia University, and was a research fellow at the International Institute for Applied Systems Analysis (IIASA) in Austria and the Institut des Hautes Études Scientifiques (IHES) in France."

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  23. Here is another example of screwed up fundamental concepts, this time in ecology. The most popular diversity measure in ecology is the Shannon entropy (they often call it the Shannon-Weiner index). A zillion papers use it. So let's see how well it works in a simple conservation problem. Suppose we have two equally-large, equally-diverse islands, with no overlapping species. Let's say the diversity (Shannon entropy) of the beetle community on each island is 5.0 (using natural logarithms). So suppose an oil company proposes to destroy one of the islands. If one of the two islands is completely destroyed and the other is preserved, what proportion of the total diversity of the island pair is lost? What proportion is preserved?

    Though it is not needed in this problem, you can assume the beetle species-abundance distributions are the same on the two islands, while the species themselves are different on each island.

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  24. Re Larry Moran

    The late Martin Gardner once posed the question as to how many legs a bactrian camel has if you call a hump a leg. The answer is 4; calling a hump a leg doesn't make it one.

    Re anonymous

    Mr. Berlinski has a PhD in philosophy from Princeton, Un. He has no publications in peer reviewed mathematics journals. Therefore, in no way, shape, form, or regard is he a mathematician.

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  25. Left out of this discussions is chemistry which is important for an understanding of modern biology. Most physicists who made important contributions to molecular biology (Crick, Gilbert, Ramakrishnan etc.) learnt enough chemistry to make a difference. Both Watson and Crick had to learn chemistry to nail down the structure of DNA.

    I think the point is not so much about physicists per se as it's about people with quantitative data analysis skills. It just happens to be physicists who are usually more comfortable with those kinds of skills, although this was more of a case before than now.

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  26. Wavefunction is exactly right--it is not physics per se but strong quantitative reasoning skills that make important contributions to biology, precisely because such skills are rare among biologists. And it isn't really getting better. My undergrad university biology dept even recently wanted to cut the calculus requirement. Most biologists whom I have asked don't even know what a logarithm is. Very few have taken real stats courses either---hence the widespread misuse of null hypothesis testing and p-values in almost any issue of an ecology or genetics journal.

    No reader has tried to answer my two earlier questions (not even Larry). Hope someone will try.

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  27. Lou -

    I would agree that Nm<<1 results in high differentiation and Nm>>1 results in low differentiation of subpopulations.

    I don't think I can answer the question about Shannon diversity without knowing the exact species abundance distribution and calculating it. Obviously, species richness would drop by half. Are you saying that the Shannon index value for island 1 is 5.0 and the Shannon index value for island 2 is 5.0, or that the collective Shannon index value for the diversity of both islands pooled is 5.0?

    If the latter, and the islands have the same species abundance distribution and one island's biota is wiped out, I would venture a guess that the remaining biota's Shannon value is still 5.0.

    I'm very interested to see where I go wrong here.

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  28. Actually, on second thought, whether a large value of Nm results in less differentiation of subpopulations probably depends on whether Nm is large because N is large or m is large.

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  29. Thanks Jaxkayaker for thinking about this. I said that the Shannon index for each individual island is 5.0. You said you would need to know the exact species abundance distributions for each island, in order to calculate the pooled diversity of the two islands, but that is not true. All you need is the information I gave you. The diversity of the pooled islands is necessarily 5.69. This can be proven mathematically, but you can also verify it empirically by choosing any two species-abundance distribution whose entropies are 5.0, and pooling them.
    With 5.69 as the pooled diversity, you can now calculate the proportion of total diversity that is lost by destroying one of the two islands is 5/5.69 = 88%. The proportion saved is also 88%! So here we have two equally diverse, equally large islands with no overlapping species, and the project that destroys one of the islands not only destroys 88% of the total diversity but also preserves 88% of it!!! There is a logical inconsistency in equating Shannon entropy with diversity, if diversity is something that can be conserved.

    More about the migration thing tomorrow...hope someone else will try that one, because Nm is not the controlling factor.

    Thanks for playing!!!

    Lou

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  30. Nice post! It's definitely true, of course, that many biologists are a little weak on their math skills, and it would be a good idea to give biology undergrads more training in that area, I think (much as they would love you for it). But I very much agree with Wavefunction. Biology is basically applied chemistry, and you have to know chemistry to make sense of biology. Claiming that physicists can figure everything out for us because they don't know chemistry or biology and therefore have some kind of "special insight" is just ridiculous -- and I love the Higgs boson analogy, that's absolutely hilarious.

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  31. A Pox upon Thee - biology is a lot more than just applied chemistry.

    Lou - thanks for the partial explanation. Your website and papers have been on my list of things to read (unfortunately, it's a long list).

    I meant that I (as opposed to you or others) would need to know the species abundance distribution to calculate the Shannon index value change. I don't "think math", if you understand what I mean. Thus, I can't conceptualize the behavior of the Shannon index, even though I know how to calculate it.

    I do know that a logarithm is an exponent, however.

    What about the second scenario I described, where the pooled Shannon index value for the two islands is 5.0, and one of the islands' biotas is destroyed, where both islands have the same species abundance distribution and no overlap in species?

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  32. Jaxkayaker, if the pooled diversity is 5, and the two islands are equally large, equally diverse, and with no overlap in species, then each island has to have a Shannon entropy of 5-0.69 = 4.31. (The 0.69 is the natural log of 2 and in this kind of problem it comes out of the fact that all species relative abundances are divided by 2 when you pool the islands.) So now, destroying one of the two islands destroys 4.31/5 = 86% of the total diversity, and the same calculation also gives that 86% is preserved. You will always get this paradoxical result, using Shannon entropy. So if you are an oil company apologist, you could argue that their plan to destroy an island still preserves 86% of the diversity, so why worry? Ecologists could equally well argue that this plan destroys 86%.

    There are hundreds of papers in ecology using Shannon entropy to judge changes in diversity.

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  33. The concept of diversity in genetics is even worse. Geneticists equate gene diversity with heterozygosity. So suppose we have two equally large populations of an endangered species, and suppose that at a particular locus there are 20 equally-common alleles in each population. (This could be a locus connected with the immune system, for example.) Suppose there are no shared alleles between populations.

    Each population therefore has a diversity (heterozygosity) of 0.95. The pooled populations have a diversity of 0.975. So we might wonder, can we let one of these populations go extinct without affecting the species' genetic diversity too much? Well, yes: if we let one population go extinct, the other population would still have 0.95/0.975 = 97% of the original genetic diversity. This makes no sense. Especially when we ask the same question differently: how much genetic diversity would be lost if we let one of the two populations go extinct? The answer is again 97%.

    Now this strangely behaving "diversity" is the basis for the main measure of genetic differentiation in population genetics, Gst. Gst is 1- (mean within-group heterozygosity)/(total heterozygosity). This measure ranges from 0 (no differentiation) to 1 (complete differentiation). Let's apply this to our two populations and see just how nonsensical it is. Our populations share no alleles, so a sensible measure of relative differentiation would give 1.00 (maximal differentiation). But Gst = 1-0.97 = 0.03, near zero, supposedly indicating virtually no differentiation! There are also examples in which almost all populations are genetically identical, yet Gst =1.00, supposedly indicating complete differentiation.

    While Gst does have some legitimate interpretations, it is wildly wrong as a measure of differentiation. Yet there are thousands of papers making this misinterpretation.

    I think this shows that there is a grain of truth to Shapiro's absurd-sounding claim. Both ecology and genetics have often gotten stuck in a sort of "group-think", often for idiosyncratic historical reasons, and it really does help to have a completely naive approach and start from first principles and mathematical results which are well-known in other sciences but not in genetics.

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  34. Lou Jost
    I think this shows that there is a grain of truth to Shapiro's absurd-sounding claim."

    So are you saying that since there is truth in what he is saying, that his ideas are not absurd? They just sound absurd to people who are not educated in the evidence his research has provided?

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  35. Now to the factors controlling drift-mutation-migration equilibrium. I expect just about everybody would say Nm is what controls genetic divergence at neutral loci under the finite island model. Thousands of papers are based on this idea. But the role of Nm is usually derived from the expression for Gst at equilibrium. Nm <<1 makes Gst high, and Nm>>1 makes Gst low. However, as we saw above, Gst has nothing to do with genetic divergence of the populations. It can be close to zero even when the populations have diverged completely (no shared alleles) and can be unity even when most populations are genetically identical. So this criterion in terms of Nm is irrelevant to genetic divergence.

    This is one of the central questions of evolution--what controls genetic divergence of populations when selection is weak or absent? The answer to that forms the backdrop for the action of divergent or normalizing natural selection. Yet because of institutionalized mathematical misconceptions about how to partition heterozygosity, genetics has been stuck on the wrong answer for more than half a century.

    Real measures of divergence exist, and can be connected to the parameters of the finite island model. So the real answer is out there. Interestingly, Nei, who proposed Gst, also proposed a form of the correct answer when he derived his measure of genetic distance. And as I mentioned earlier, Felsenstein (and others) also used a form of the correct answer. But these were eclipsed by silly Gst.

    My colleague Anne Chao and I have done simulations that prove that Nm does not control differentiation. I posted some of these in the comments in the Molecular Ecologist blog:

    http://www.molecularecologist.com/2011/03/should-i-use-fst-gst-or-d-2/#more-662

    My point in these posts is to show that there is an insularity and lack of mathematical rigor in biology that has caused serious errors, invalidating large parts of its literature. Interdisciplinary cross-fertilization would be very helpful. The same could probably be said of all sciences.

    And of all the sciences that could contribute rigorous, relevant math to biology, I suspect economics might be even more promising than physics. Their mathematical sophistication regarding diversity and related subjects far exceeds anything in biology.

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  36. Anonymous, I haven't read his book, so I don't know what evidence he presents. I also disagree with his apparent claim that complete ignorance about a subject is useful. But there is some truth to the milder claim that starting over with a truly open mind can indeed be very useful. I don't think anyone would argue with that. And it is surprisingly hard to attain an open mind when immersed in an environment where everyone believes something wrong, where even the vocabulary of the field presupposes the mistakes.

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  37. At the risk of repeating myself, but at greater length:

    Biology is both applied chemistry and applied information science. But the standard approach to teaching it is purely as applied chemistry - it simply is not taught as an information science. There is a glaring void where we are supposed to have people who can do biology-as-information-science, and this gets filled from both sides because biologists (who ought to have a huge advantage over non-biologists) are not being given the required mathematical skills (Lou's point) and so don't have any clear advantage in this field. Joe Felsenstein is prominent precisely because there are so very few biologists who manage to pick up these skills.

    Instead of waiting for biologists of Joe's calibre to come along by chance, the discipline should get its act together and teach biology-as-information-science. This should be done by biologists, for biology students. If you think the issue can be patched by sending students off to do a semester course in CompSci, think again - the (excellent in other respects) CompSci text book I have been teaching from was written by people who think one finds genes by scanning for "start codons" - and the awareness of biology displayed by this is way above average for computer scientists. Computational biology students should be given a solid background in maths and computing (by specialists in those areas) but most importantly, their biology should be taught (by biologists) as an information science.

    The only alternative is to sit and watch physicists, computer scientists and mathematicians come along to reinvent the wheel.

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  38. Konrad posted:
    "The only alternative is to sit and watch physicists, computer scientists and mathematicians come along to reinvent the wheel".

    Would it not be more correct to say
    "correct the wheel"?

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  39. I think good stats courses are also critical. I have never met a biologist who had taken a good mathematical stats course. The typical result of applied stats courses is a senseless emphasis on null hypotheses and p-values which pervades all of biology. This reliance on p-values tends to absolve biologists from thinking about the meaning of the actual values of their measures. The right model for most problems in life sciences is not null-hypothesis-testing but estimation (and interpretation) of a meaningful measure of the magnitude of the effect of interest, with confidence intervals expressing the statistical uncertainty.

    Jaxkayaker, thanks for having my papers on your to-do list!!! I'd enjoy sending you any of my papers on these subjects, if there are some you can't easily get a hold of.

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  40. @Lou: Totally agreed on the stats - there is a disturbing tendency to teach biologists statistical recipes instead of statistical thinking, which is about as good as not teaching it at all. Almost every stats course for applied disciplines seems to go the recipe-driven route. Strangely, most biologists seem to think one can do good biology by applying statistical recipes without understanding what underlying biological assumptions are implied by their use.

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  41. @konrad-- yes!
    They also seem to learn nothing but null-hypothesis-testing, and they come away thinking that this is the only game in town.
    For a discussion of the inappropriateness of null-hypothesis testing and p-values, check out this blog post by an excellent mathematician/biologist, Tom Leinster, and the comments that follow it:
    http://golem.ph.utexas.edu/category/2010/09/fetishizing_pvalues.html

    Regarding the factors that control the expected value of differentiation at drift-mutation-migration equilibrium at a given locus, the answer is the ratio of mutation rate to pairwise migration rate:
    u(n-1)/m.

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  42. @Lou: yes, that's a frequently-made point (sadly: it needs to be frequently made because it continues to be frequently disregarded; also because it needs to get made separately in separate application areas) and I completely agree, particularly with your central point that in many problems the null hypothesis is known to be false a priori and therefore pointless to test.

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  43. @konrad: Yes, you are right,my point about p-values is not at all novel, but it needs to be repeated over and over. Even today most journal editors and referees do not understand the point. In nature the null hypothesis of "no differences" is virtually always false, if only in the tenth decimal point of some population characteristic. So no matter what a study measures, it will obtain significant results, at whatever significance level the investigator desires, as long as sample size if large enough. This makes science into an empty game which can always be won if you have enough resources.

    By the way, based on Larry's quote, I had imagined Shapiro was a physicist. I see he is actually an accomplished geneticist.

    I look forward to reading Larry's review of Shapiro's book. From what I have gleaned off the internet, the book looks interesting and provocative, if also perhaps somewhat over-stated.

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  44. If anybody wants a preview of Shapiro's views on evolution, while you are waiting for Larry's review, here is a link to an article Shapiro wrote on the subject:

    http://web.mac.com/redifiori/Russell_Di_Fiori/Modern_Synthesis_files/Shapiro.2005.Gene.pdf

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  45. Facile put downs and tongue in cheek satire are far too often the go-to response when anyone dares assail the foundations of Darwinism. You have written true to form. The obvious next thing is to accuse him of being an IDiot, even though he steadfastly maintains that he rejects that point of view as non-scientific. Oh, I forgot; you have already done that. Really, is that all you have?

    Why not, instead of reducing his words to absurdities (how scientific of you!) , respond to his ACTUAL implication in the paragraph you cite; that so many biology professors (apparently, like you) and departments have become so wedded to the idea of Darwinism, specifically slight modifications over time ,as being the only possible (acceptable?) cause of evolution that it is actually beneficial to have people less conditioned by classroom tenets joining the field and making discoveries?

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    1. I AM responding to his ACTUAL implications. I'm pointing out that physics is also dominated by silly ideas and theories so biologists should help them out by showing where they went wrong.

      I also think it's probably a good idea for lawyers to move into medicine and for prominent business leaders to offer their wise advice on university education. It's almost certainly true that in every single field the so-called experts are actually so stupid that just about anyone can learn the required material and do better.

      At least thtat's what people like you and Shapiro think, right?

      BTW, what field are you in?

      Delete
    2. Re Larry Moran

      I'm pointing out that physics is also dominated by silly ideas and theories

      Such as? Actually, I could name a few (e.g SU(6)) but they didn't hang around for long.

      Delete
    3. I was being sarcastic.

      I actually don't think that the average biologist can be of much help to the physicists on their most difficult problems.

      I also don't think that physicists can be of much help to biologists unless they take a few decades to learn about biology.

      Delete
  46. again, you are not responding but just switching back to your original position. Is it not possible that a certain field could become so territorial and turf-protective that it loses sight of its original mission and shuts out ideas that could revitalize and modernize it? Do you accept or reject that possibility? Because it is that, specifically, that Shapiro is suggesting contemporary evolutionary scholarship is caught up in. Please simply explain why you feel that is not the case. That is the allegation that calls for a response, not facile satire.
    I am an artist and writer who is very interested in this subject and am educating myself by studying up on both Shapiro and his detractors. I was first seduced into this field by the smugness and superior tone of Richard Dawkins, as a full disclosure. The more I have read, the more I have come to believe that his smugness is actually pretty much all he has going for him, and he is working it as hard as he can.

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    Replies
    1. It is definitely possible, in theory, that a whole field of science, composed of tens of thousands of experts, could be entirely mistaken about the most fundamental concepts in their discipline.

      That is exactly what Shapiro is saying about evolutionary biologists. He is not an evolutionary biologist.

      On the other hand, it is definitely possible, in theory, that a small number of kooks could completely misunderstand the fundamental concepts in a discipline and think they have some radical new idea that the experts in the field never thought of.

      We've got plenty of example of the latter and none of the former.

      I know where I'm placing MY bet.

      You can read my review of Shapiro's book at: Evolution: A View from the 21st Century.

      Delete
  47. Thank your for thoughtfully providing me with your review. It is informative and provides me with some needed perspective. I would like to point out an error, however. You write "why don’t scientists routinely
    invoke goal-oriented processes? It’s because they have a philosophical bias against religion,
    according to Shapiro.", but then the following paragraph you cite does not support your allegation.
    Shapiro writes, "My
    personal opinion is that the opposition is deeply philosophical in nature and dates
    back to late 19th Century disputes over evolution and also to the early 20th Century
    “mechanism-vitalism” debate ... . " Here, he is not specifically referring to a disagreement over religion. He then goes on to write, "...goal-oriented processes have
    to be relegated to the realms of unscientific fancy and religion."
    This is hardly the same thing as what you are alleging. He is saying that BECAUSE Darwinism flat out rejects the notion of a seeming awareness in the cells (not necessarily a religious proposition) the concept is, in his words 'relegated' to unscientific fancy and religion. In other words, they accept something that Darwinism rejects. The 'bias' that you see him alleging against Darwinism is not in the paragraph you cite, at all. I think it is perhaps in your own way of looking at things.

    What he IS saying is that because Darwinism insists upon only blind, mechanical processes accounting for the entire history of biology following the emergence of the first self-replicating cell, it has a prejudice against ANY other alternative concept/theory, and that INCLUDES religion.

    ReplyDelete