February 9, 2009 | David F. Coppedge

Science Special Issue on Darwin: Is Ignorance Evidence?

It’s fair to confess that scientists cannot be expected to know everything.  Often, though, ignorance is presented as evidence that a paradigm needs to continue.  The idea is that by following the consensus paradigm, scientists can hope to one day fill in the blanks in our knowledge.  How long should this practice continue with a theory as important as Darwinism, whose central claim for 150 years has been that all living organisms have descended from a common ancestor by an unguided process of natural selection?  If ignorance of that process is widespread and deep, is it time to think outside the box?
    Maybe some recent examples can refine thinking on this question.  Science celebrated Darwin’s birthday with some Review articles on issues in speciation.  Each author is convinced of evolution.  None of them were trying to cast doubt on Darwin’s theory.  But how important are the following instances of ignorance they outlined?

  1. Kingdom ignorance:  Five scientists from London and Harvard examined the “Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity.”1  Here’s how they contextualized their challenge:

    The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread.  Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology—including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination—mean that we still do not understand what a bacterial species is.  This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine.  Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion.  The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.
        The species debate in microbiology is not only about a human desire to catalog bacterial diversity in a consistent manner, but is also a fundamental argument because of what it reveals about our ignorance of how evolutionary forces form, shape, and extinguish bacterial genetic lineages, of the mechanisms of differentiation between subpopulations sharing common descent, and of the process of adaptation to new niches and changing environments.

    They discussed several approaches to the problem, but none was unproblematic.  This indicates that for microbes, which comprise the vast majority of organisms on Earth, and have occupied the majority of the evolutionary timeline, scientists do not even know what constitutes a species – let alone how to describe the origin of species.

  2. Selection ignorance:  Elisabeth Pennisi’s essay had a revealing title: “Evolutionary Biology: Agreeing to Disagree.2  Natural selection is the keystone of Darwin’s hypothesis, but on what does it act – the individual, or the group?  or the gene?  Pennisi investigated the ongoing controversy about kin selection, the idea that selection operates on family groups.  This idea has received mixed acceptance by other Darwinians who favor individual selection (see, for instance, the 09/30/2007, 05/31/2004, and 05/07/2002 entries).
        William Hamilton and J.B.S. Haldane expounded the idea of kin selection in the 1960s to explain social behavior in insects.  How could nature select drones that cannot pass on their genes?  It must act at the group level, they argued.  Darwin himself was “flummoxed” by the phenomenon of social insects, Pennisi said, and worried that this “special difficulty” might topple his theory.  For a solution, he had suggested that selection might operate on families.
        After Hamilton’s work in the 1960s, kin selection became the traditional explanation for eusociality in insects.  Edward O. Wilson was an advocate for the idea in the 1970s but now feels it is ineffective.  “The theory that traditionalists use leads them anywhere they want to go,” he complained.  “To make [a theory] really stand [up], you have to show that that’s the only result that can come from your theory, and they haven’t done that.”  Such comments have made kin selectionists very unhappy.  The situation remains at a standoff.  Pennisi described it as a rift between evolutionary biologists, with both sides agreeing to disagree.
  3. Queens and jesters:  How about the pace of evolution?  Do biologists agree about that?  Michael J. Benton described “two ways of viewing evolution” in his essay.3  The “Red Queen” model portrays lots of change occurring under the hood, but little outward sign of progress – like the Alice in Wonderland character who had to keep running just to stay in one place (see 09/07/2006 and 05/16/2004).  The “Court Jester” model says that “evolution, speciation, and extinction rarely happen except in response to unpredictable changes in the physical environment, recalling the capricious behavior of the licensed fool of Medieval times.”  Traditionally, he said, “biologists have tended to think in a Red Queen, Darwinian, intrinsic, biotic factors way, and geologists in a Court Jester, extrinsic, physical factors way.”
        Benton portrayed the relative importance of these models as an unresolved debate that will require further research.  “In the future, the identification of diversification shifts across numerous taxa may provide evidence for the relative importance of the Red Queen and Court Jester worldviews,” he said.  “If the majority of diversification shifts are coordinated, and associated with particular climatic, tectonic, and geographic drivers, then the Court Jester model of macroevolution would prevail…. If, on the other hand, the majority of diversification shifts are unique to particular clades, and not coordinated temporally with others, then the Red Queen worldview might be considered.”  It’s surprising to think that such a basic question remains unresolved; the options seem mutually exclusive.  It is evident there is no clear choice between these “worldviews” after so many decades of evolutionary theorizing and evidence-hunting.  Benton hoped for a compromise: “The realization that the Red Queen and Court Jester models may be scale-dependent, and that evolution may be pluralistic, opens opportunities for dialog.”  It is not clear just how two models based on capricious mechanisms might provide a stronger theory.
        Earlier, Benton had opened with, “A key question about the origin of modern biodiversity is how today’s 10 million species arose from a single ultimate species of microbial life 3500 million years ago (Ma).”  Wasn’t that the very question Charles Darwin had answered?
  4. Maladaptive radiation:  Another suggestive title adorned an essay by Gavrilets and Losos: “Adaptive Radiation: Contrasting Theory with Data.4  Adaptive radiation refers to situations where a founder population invades a new habitat, and the descendents radiate into a plethora of diverse species.  Adaptive radiation is often claimed as the explanation for biodiversity in a region, but how solid is the evolutionary theory behind it?  There are good cases, and there are poor cases, the authors said, but, “In almost all cases, more data are needed.  Future progress in our understanding of adaptive radiation will be most successful if theoretical and empirical approaches are integrated, as has happened in other areas of evolutionary biology.”  Presumably they were not referring to the success of the other three stories (above).
        Gavrilets and Losos listed 10 patterns of adaptive radiation, then offered some general conclusions.  Remarkably, all three conclusions bemoaned the lack of evidence and the need for further study: e.g., “The number of adaptive radiations that have been extensively studied from the many different perspectives relevant to our discussions is surprisingly small.  More detailed studies, integrating across a variety of approaches and disciplines, is needed to build a reservoir of case studies from which generalizations can be drawn.
        They retold the story of Darwin’s surprise at the diversity of Galapagos animals.  Since the voyage of the Beagle, they said, adaptive radiation has astonished scientists and the public alike for 150 years.  “But how exactly radiation occurs, and how it differs among taxa and in different settings, as well as why some lineages radiate and others do not, are still unclear,” they ended.  “Most likely this is because there is no single answer: Lineages vary in manifold ways, various evolutionary factors act simultaneously, similar evolutionary outcomes can be achieved via alternative paths, and the contingencies of place and time play a large role in guiding the evolutionary process.”  And yet contingency and guidance seem poles apart.  What Darwin had tried to do was explain the phenomena of life with reference to “laws of nature,” not contingencies.  150 years later, these authors show, biologists seem to have made little progress.
  5. Speciation challenges:  Another paper in the Science special issue on Speciation dealt with “Evidence for Ecological Speciation and Its Alternative,” by Dolph Schluter.5  His opening paragraph will suffice to show there is lack of certainty in this subject, too:

    Natural selection commonly drives the origin of species, as Darwin initially claimed.  Mechanisms of speciation by selection fall into two broad categories: ecological and mutation-order.  Under ecological speciation, divergence is driven by divergent natural selection between environments, whereas under mutation-order speciation, divergence occurs when different mutations arise and are fixed in separate populations adapting to similar selection pressures.  Tests of parallel evolution of reproductive isolation, trait-based assortative mating, and reproductive isolation by active selection have demonstrated that ecological speciation is a common means by which new species arise.  Evidence for mutation-order speciation by natural selection is more limited and has been best documented by instances of reproductive isolation resulting from intragenomic conflict.  However, we still have not identified all aspects of selection, and identifying the underlying genes for reproductive isolation remains challenging.

    Schluter did not seem to notice that his statements assume evolution to demonstrate evolution.  He used a bandwagon argument for support: “It took evolutionary biologists nearly 150 years, but at last we can agree with Darwin that the origin of species, ‘that mystery of mysteries’, really does occur by means of natural selection.”  If that is true, the next question seems puzzling: “The main question today is how does selection lead to speciation?
        The essay explored progress on the species question since Darwin.  For one thing, the whole concept of species has changed, altering what biologists mean by speciation in the first place.  The nature and role of natural selection has been revised several times.  There are still holes in the theory: “At this point, the most glaring deficiency is our knowledge of the impact of selection on genes.”  That seems a pretty major deficiency.  Again, later, he reiterated this point: “The most obvious shortcoming of our current understanding of speciation is that the threads connecting genes and selection are still few.  We have many cases of ecological selection generating reproductive isolation with little knowledge of the genetic changes that allow it.”  What if, as in the 01/28/2009 entry, natural selection theory itself is being called into question?  What would that end of the thread hold onto?
        Nevertheless, Schluter beamed over the prospect that Darwin, if he were alive today, would be pleased.  He would find the discoveries made in the 150 years since “the greatest book ever written” (not the Bible, obviously) “staggering.”  He continued, “Mostly, I expect that he would be chuffed by mounting evidence for the role of natural selection on phenotypic traits in the origin of species.  This is really what On the Origin of Species was all about.”  Problems?  Gaps?  No worries.  There’s plenty of time.  “But we hardly have time to complain.  So many new model systems for speciation are being developed that the filling of major gaps is imminent,” he crowed.  “By the time we reach the bicentennial of the greatest book ever written, I expect that we will have that much more to celebrate.”  When knowledge is put in future tense, it suggest that ignorance is in the present tense.  Ignorance seems hardly a cause for celebration this year.

  6. Predictable evolution?  Another paper in the special issue put most of the knowledge in the future.  David L. Stern and Virginie Orgogozo asked, “Is Genetic Evolution Predictable?”6  They discussed the idea that mutations cluster around certain “hot-spot genes,” making it somewhat predictable, in theory, which way the genome will go.  That remains to be determined, though, because “further understanding of this predictability requires incorporation of the specific functions and characteristics of genes into evolutionary theory.”  Genes might change, in other words, with no apparent change to the creature or its fitness.
        In the conclusion, they cast some doubt on the thesis.  Seeming patterns may be noise, or due to artificial selection by scientists.  “These emerging patterns in the distribution of mutations causing phenotypic diversity derive, however, from a limited set of data culled from the published literature.  It is possible,” they said further, “that these patterns reflect biases in the way scientists have searched for evolutionarily relevant mutations.”  Resolution of the question will require more research.

The remaining articles and book reviews in the special issue of Science on speciation, in honor of Darwin, also refer to controversies, debates, questions, and calls for further research.  The only exception was Massimo Pigliucci’s review of Jerry Coyne’s Why Evolution Is True (Viking, 2009).  Pigliucci’s title bluffs proudly: “The Overwhelming Evidence.7  Pigliucci’s homage to Darwin was matched by his disdain for creationists and other aspects of “American anti-intellectualism.”  For example, he scoffed, “there is no dearth of obtuse minds when it comes to creationism.”  Scientific evidence, Pigliucci argued, is the domain of evolutionary biologists.  “The problem with the creation-evolution issue, however, is that it is not about the evidence.  The clash is not a scientific debate, it is a social controversy.”  His certainty over evolution, notwithstanding, did have some chinks:

Coyne subscribes to one species concept (based on reproductive isolation) and one chief mode of speciation, allopatry.  He and I disagree on this and on other aspects of current evolutionary theory, but this is not the place to entertain technical arguments at the cutting edge of the field.  Still, readers of Coyne’s book will get a fairly conservative version of evolutionary theory, with occasional hints about the many heated discussions that characterize any live science and that eventually fuel its progress toward a better understanding of the natural world.

Whether science is progressive or not is a big debate among philosophers and historians of science.  Nevertheless, Pigliucci called philosophy into his court when pointing out a criticism of one branch of evolutionary theory he shares with Coyne:

Coyne admits that the issue goes far beyond science, into philosophy and questions of meaning and morality.  Which is why philosophers have been very helpful in this arena during the past several years.  It is a matter of explaining to the public not just the power but the limits of science.  Coyne is critical, for instance, of much evolutionary psychology and the facile just-so stories that have abounded of late to “explain” all sorts of human behaviors, from rape to depression.  I’m with him on this.  The point is not that aspects of human behavior did not evolve by natural selection, but rather that the usually high standards of behavioral genetics are simply not met by most, though not all, the evolutionary psychology literature.

Perhaps the reader can find those high standards in the six papers listed above.

1.  Fraser, Alm, Polz, Spratt and Hanage, “Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity,” Science, 6 February 2009: Vol. 323. no. 5915, pp. 741-746, DOI: 10.1126/science.1159388.
2.  Elisabeth Pennisi, “Evolutionary Biology: Agreeing to Disagree,” Science, 6 February 2009: Vol. 323. no. 5915, pp. 706-708, DOI: 10.1126/science.323.5915.706.
3.  Michael J. Benton, “The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time,” Science, 6 February 2009: Vol. 323. no. 5915, pp. 728-732, DOI: 10.1126/science.1157719.
4.  Sergey Gavrilets and Jonathan B. Losos, “Adaptive Radiation: Contrasting Theory with Data,” Science, 6 February 2009: Vol. 323. no. 5915, pp. 732-737, DOI: 10.1126/science.1157966.
5.  Dolph Schluter, “Evidence for Ecological Speciation and Its Alternative,” Science, 6 February 2009: Vol. 323. no. 5915, pp. 737-741, DOI: 10.1126/science.1160006.
6.  David L. Stern and Virginie Orgogozo, “Is Genetic Evolution Predictable?”, Science, 6 February 2009: Vol. 323. no. 5915, pp. 746-751, DOI: 10.1126/science.1158997.
7.  Massimo Pigliucci, “The Overwhelming Evidence,” Science, 6 February 2009: Vol. 323. no. 5915, pp. 716-717, DOI: 10.1126/science.1168718.

Coyne and Pigliucci tell us (again) that there is such overwhelming evidence for evolution.  OK, put up or shut up.  They don’t know what a species is, they don’t know what the target of selection is, they don’t know if natural selection is a queen or a jester, they don’t know what adaptive radiation is, they don’t know how speciation operates (the main reason for Darwin’s little storybook), and they can’t connect mutations to any actual benefit to an organism.  Other than those little minor matters, evolution is so supported by such mountains of evidence that only a fool with an agenda could dare question it.
    Colin Patterson of the British Natural History Museum once posed a question to his fellow evolutionary biologists: “Can you tell me anything about evolution, any one thing that is true?”  He got a surprised silence.  He told them, “I had been working on this stuff for twenty years, and there was not one thing I knew about it” (see ARN).  Notice he asked if they knew anything – something they knew was true – not what they thought about it, what they guessed about it, what stories they could tell about it.  Would that more evolutionary biologists would ask that question.  All we see in paper after paper is competing guesses, modified models, controversies, debates, changing definitions, and the inevitable, “future research should be able to shed light on this question.”  The articles above show that basic, fundamental tenets of Darwinism are no more nearer solution than they were to Darwin.  What has increased is not their knowledge, but the sophistication of their ignorance.  Then Pigliucci and Coyne pompously blast away about the “overwhelming evidence” for evolution and how stupid the creationists are.  This is not good salesmanship.
    Are you a good shopper?  Of course you are.  You’ve learned to check the specs, not the hype.  When a salesman comes to you shouting, “Acme Widgets are superior to all the other garbage out there, and the testimonials are so globally unanimous, that only a complete idiot would even look at the competitor’s product, which is produced by evil, wicked, stupid ignoramuses who only want to make a buck out of your gullibility.”  You know that you have to blow off the bluff of the chuff (chuff, n.: a boorish, proud, insensitive fellow) and look at what the product can do.  Evolutionists dare not allow you to do that with their product because the competitor will always win hands down.  That’s why they must have a monopoly in marketing.  The special effects in the evolutionary ads require rigging and selective illumination to highlight the glow and keep other things in the dark.  When you ask to see the goods, you get vaporware on back order.
    Evolutionary biology today is a sad case of what happens with protectionism and totalitarianism in the marketplace of ideas.  To get the good stuff you have to go to the black market, which is really the white market when the black light is turned off, the doors are opened and the sun shines in.

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