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Wednesday, June 12, 2013

The Trouble with Darwin

As a biologist, I find Darwin's theory hugely disappointing. It's better than the alternative (which is to believe in magic, basically), but not by much, sadly.
Charles Darwin died before Mendel
proved the existence of genes
.

As scientific theories go, the theory of evolution is easily the weakest of all major scientific theories. It's a commendable piece of work in its ability to stir discussion, but terrible in most other ways.

To be useful, a scientific theory has to do a minimum of two things: explain what can be observed, and provide testable predictions. Darwin's theory is weak on the first count and useless on the second.

Evolutionary theory explains practically nothing, because every explanation of the theory is rooted in "survival of the fittest," which is a circular notion, utterly content-free. "Fittest" means most able to survive. Survival of the fittest means survival of those who survive.

Ironically, Darwin's landmark work was called On the Origin of Species. Yet it doesn't actually explain speciation, except in the most vacuous and speculative of terms. Of course, we can't set too high an expectation for Darwin, since he didn't live to see the publication of Mendel's work (the word "genetics" wouldn't exist until more than 20 years after Darwin's death), but still. Speciation is portrayed by Darwin as the outcome of the accumulation of small, gradual changes. That's all the explanation he offers.

But the explanation is wrong. Or at least it doesn't accord well with the facts. It doesn't explain the Cambrian Explosion, for example, or the sudden appearance of intelligence in hominids, or the rapid recovery (and net expansion!) of the biosphere in the wake of at least five super-massive extinction events in the most recent 15% of Earth's existence.

One of the most frustrating aspects of evolutionary theory (this is no fault of the theory's, though) is that it is so hard to test in the laboratory. The fact is, no one has ever seen speciation happen in the laboratory, under repeatable conditions, and until that happens we're at a distinct disadvantage for understanding speciation. (Incidentally, I don't count plant hybridization or breeding anomalies in fruit flies whose sexuality is under the control of microbial endosymbionts as examples of speciation.)

When I was in school, we were taught that mutations in DNA were the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (they reduce, not increase, survival). Most mutations lead to loss of function (this is easily demonstrated in the lab), not gain of function. Evolutionary theory is great at explaining things like the loss of eyesight by cave-dwelling creatures (e.g., bats). It's terrible at explaining gain of function.

Even if mutations were capable of driving evolution, they simply don't happen fast enough to account for observed rates of speciation. In bacteria, the measured rate of 16S rRNA divergence due to point mutations is only 1% per 50 million years. And yet, there were no flowering plants on earth as recently as 150 million years ago! Does it take a biologist to see the disconnect?

I bring all this up because I've spent some time recently doing genomics research aimed at exploring mechanisms for new-protein creation/differentiation (mechanisms not relying wholly nor even mainly on point mutations), and I wanted to set the stage for discussing that research here. Over the next week or so, I'll be presenting some new ideas and findings. Hopefully, we can put some much-needed flesh on Darwin by exploring testable notions of how new protein motifs can arise quickly (without reliance on magic).

12 comments:

  1. Darwin feels similar to Copernicus in relation to Newton. He has the basic ideas right and presents a passable description of reality as it is observed, but not an explanation. I hope that we are in the phase now that Kepler was in, collecting vast amounts of data that will enable us to actually understand and map out the foundation of a theory that actually explains some of the things that you mention.

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  2. Your painting of fitness measures as circular is wrong. It would be like citing dying as the leading cause of death. You need to unpack a fitness _function_ to understand what makes for reproductive success.

    As for speciation, first, define your terms as it is a complex area, especially for plants. Then having broadened your definition look at Wolbachia research, for example.

    As for prediction, just for a kick off, how about the idea that populations tend to increase their fitness in the absence of other complicating factors. Or that selection produces heritable change.

    You're just showboating dude.

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  3. And for the record, the vast majority of novelty arises from recombination, not mutation.

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  4. Also, give the Big Guy a break because he had no idea of the mechanism (in fact iirc he was a Lamarckian, but then full-on phenotypic inheritance must have been the most likely contender for anyone in the area back then...).

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  5. http://www.futurity.org/science-technology/the-fastest-evolving-fish-on-the-planet/

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  6. The caption on your photo is completely untrue. Gregor Mendel published "Experiments on the hybridization of plants" in 1866. Darwin died in 1882.

    Also, Evolution certainly does explain the Cambrian explosion and speciation. Remember a species isn't anything special it just means the two organisms have evolved separately to a point where they can no longer mate.

    "The overwhelming majority of non-neutral mutations are deleterious" Yes, they are and the offspring with deleterious mutations don't go on to reproduce. Those that don't have deleterious mutations do.

    Deleterious mutations aren't generally passed on so don't accumulate.

    "Even if mutations were capable of driving evolution, they simply don't happen fast enough to account for observed rates of speciation"

    Yes they do. 1% can make a huge difference and flowers are nothing more than adapted leaves.

    Also remember increased complexity in the phenotype doesn't have to mean the same amount of increased complexity in the genotype. 1 Duplication with a small amount of mutation can allow for huge differences in phenotype.

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    Replies
    1. When Mendel's paper was published in 1866 in Verhandlungen des naturforschenden Vereins Brünn, it was seen by very few people (Darwin not among them) and was considered an esoteric horticultural essay on hybridization rather than a study of inheritance per se. It had almost zero impact (it was cited less than five times over the next 30 years). It wasn't until after the turn of the (20th) century that Mendel's work was rediscovered and brought to public prominence.

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  7. Anonymous10:47 AM

    Speciation is a human concept. We decide if two organisms are separate species based on, for example, whether or not they produce viable offspring with each other or if they even choose to breed with each other. This is assuming that they reproduce sexually, at all. Therefore, whether or not anyone has ‘observed’ speciation occurring is a matter of opinion, not fact. However, observed changes in phenotypes and genotypes over long and short periods of time are too numerous to count, and quite obviously lead to speciation by almost any definition of ‘species’.

    Using terms like “Cambrian Explosion”, “sudden appearance of intelligence”, or “rapid recovery of the biosphere” to imply that there has not been enough time for genetic change to produce new types of organisms is sensationalism; as is comparing the rate of one point mutation on bacterial RNA to the rate of evolution of flowering plants. Some mutations occur frequently, and if they were to provide any statistical advantage, would be joined with other ‘positive’ mutations during recombination, resulting in a relatively rapid compounding of genetic change.

    @OCD_Frog

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  8. You are a biologist? I would be very critical of your work…you have degrees in biology and microbiology, yet you do not have the basic ideas of Darwin’s theory of evolution? So you fail to understand the guiding principle in the area you received your degrees in? What exactly did you do? What exactly did you study? It would benefit you to read a few things in the history and philosophy of science.

    You think evolution cannot provide testable predictions? You also think the observation of it is weak? Like I said, what exactly did you do in school? Are you familiar with Lenski’s on-going experiment? I think you need to do some reading…I could provide you with a book…or 20…
    You do know that the phrase “survival of the fittest” was not coined by Darwin, right?

    What you miss about Darwin’s theory is that even though genes were yet to be discovered, and genetics was not yet known, genetics SUPPORTED Darwin’s theory in great detail. It strengthened his theory…

    The Cambrian explosion? It does explain it, actually. “Suddenly” you know the “Cambrian Explosion” happened over the course of about 15 million years, right? You have an odd definition of sudden…

    You are wrong is nearly everything you have said…It might do you some good to do some reading. I could give you the email of Alan Love, one of my professors…
    Ph.D. - History and Philosophy of Science, University of Pittsburgh - 2005
    M.A. - Biology (Ecology, Evolution, and Behavior Program), Indiana University, Bloomington - 2004
    M.A. - Philosophy, University of Pittsburgh - 2002
    B.S. - Biology (Minor: Philosophy), M.I.T. - 1995

    He would strongly disagree with you and I think he is a little more qualified on the topic. Scientists have asked me what the point of history and philosophy is in science. You are the example of why it is needed. I would be impressed if you have actually read more than a few lines of The Origin of Species…

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  9. Anonymous12:24 PM

    I think that it was Konrad Lorenz who once said, "Toss out your favourite hypothesis every morning and think of a better one." So, I agree that it's always good to look at an idea or theory with fresh eyes, and in this is the principal achievement of this post. But I don't see a new idea emerge. And I had the reverse experience: I was a Darwinist long before even reading Darwin's original work, and sometimes fretted about its (perceived) weaknesses; however, reading "The Origin of Species," really refined my perception of Darwin's work. His naturalist experience and insight contributed greatly to his theory—he saw complexity and change and used it to synthesise a concept that was new at the time but in the offing because the notion that life evolves had become so compelling (Darwin beat Alfred Russel Wallace by only a few months).

    And contrary to your assertion, Darwin didn't make a strong case for small, gradual changes being the fundamental driving force of speciation. His observations on pigeons and other domesticated animals highlighted his appreciation of the speed with which evolution (and speciation) occurs. In other words, although gradual, such changes can be quick and lasting providing the basis for additional changes and for increased diversity. Plus the size of a population matters: it provides the playground allowing accumulation of changes and the pool from which any of these changes can be selected, and Darwin appreciated that. His conclusions were neither "vacuous" nor "speculative"—they were firmly grounded in his observations and his thorough analysis of them.

    As for Darwin's theory providing only an imperfect model to explain the Cambrian explosion, I believe it was Steven Jay Gould who made this argument (viewing evolution punctuated by inexplicable leaps and bounds in between times of stasis) and not many scholar have bought into it. The chief argument against this line of thought is that the Cambrian explosion may have been a lot more gradual than what has been assumed. Geological records are not always reliable when it comes to assigning firm time lines, and a lot its interpretation as being a hallmark for the "sudden" appearance of a multitude of life forms has been overplayed.

    So I'll need to see a lot more evidence to even consider your argument that "the theory of evolution is easily the weakest of all major scientific theories." Evolution (as originally described by Darwin and since refined by many other researchers and scholars—off the cuff, I recommend reading E.O. Wilson's "Consilience" and "Sociobiology" and David Sloan Wilson's "Evolution for Everyone") is easily the strongest, most compelling, scientific theory there is.

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  10. To Anonymous above: Using pigeons and other domesticated animals to support evolution and speciation is somewhat deceptive as what you're referring to is artificial selection, not natural selection. In other words, in those cases, intelligence asserts the changes over time in those domesticated animals, even if the selected traits actually make the life form LESS fit. I know humans are the selective pressure and not pure, natural SOTF, so it makes sense, but that's kind of my point.

    I believe in the theory of evolution, just not exactly as it stands. I think there is an inherent intelligence in the universe, in matter itself, and this intelligence ultimately corrals evolution, not randomness and chaos. This intelligence can be glimpsed in the behavior of self-arranging molecules. It can also be seen in the, anything but random, way super-posed particles collapse when observed. It is also the reason for universal laws. Just my two cents.

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