Archive for February, 2013

More on Margulis

February 26, 2013

In my previous post (An Interview with Lynn Margulis), I discussed the unconventional and fascinating ideas of Lynn Margulis, one of the world’s foremost biologists before her passing in November 2011. I pointed out that Margulis was an evolutionist. I wrote in the second paragraph of the post that

Margulis held an unusual position on biological evolution. A fierce critic of the Neo-Darwinian paradigm, she nonetheless subscribed to an evolutionary picture regarding the emergence of the myriad life-forms on Earth today.

Later in the post I mentioned again that Margulis is an evolutionist. I also provided the link to the interview with Margulis, in which she states that she is an evolutionist – “… all life comes from a common ancestry…”.

Nonetheless, a fuming reader wrote in indignation that… Lynn Margulis believed in evolution. No, really?!

I suggest the following exercise. Read the original post and Matt’s comment on it, and then come back. Here is what the post was about.

In contemporary evolutionary biology, speciation (the process by which one species allegedly becomes two) is absolutely crucial. Yet there is not a single reliable, documented instance of speciation. Margulis rejected Neo-Darwinism partly because of this. Besides her comments on Darwin’s Finches which I featured in the previous post, Margulis makes the following point in the interview:

…neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change – led to new species. I believed it until I looked for evidence.

Margulis makes two arguments about speciation. Firstly, there is not a single unequivocal, documented instance of speciation – Darwin’s Finches don’t cut it. Secondly, Neo-Darwinism requires that biological organisms be infinitely-plastic – just pile mutation upon mutation and you’ll eventually get a new species. Margulis explains why this is unrealistic:

This is the issue I have with neo-Darwinists: they teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.

All laboratory studies of mutation and all instances of selective breeding end in the same way. When you go beyond the enhancement of minor traits – slightly larger crests in pigeons, slightly larger milk production in dairy cows – you get defective creatures (or a spontaneous reversal to the original genome of the organism). This is hardly a promising path for the evolution of more fit organisms, and constitutes a devastating critique of Neo-Darwinism.

Beyond speciation, which was the focus of my previous post, Margulis makes two points which are relevant to Genesis and Genes.

Discover: Why do you have a reputation as a heretic?
Margulis: Anyone who is overtly critical of the foundations of his science is persona non grata. I am critical of evolutionary biology that is based on population genetics…

This is something that I discussed at length in Genesis and Genes. Scientists, like all people, resist the envelope being pushed. They are comfortable making modest progress working within a paradigm, but not when the paradigm itself is challenged. The history of science furnishes us with numerous examples of creative scientists who were ridiculed and professionally-isolated when they opposed the reigning paradigm. Whether it’s Lynn Margulis, Robin Warren, Daniel Schechtman, Ignaz Semmelweis, Alfred Wegener or countless others, radical ideas are often rejected for no better reason than dogma. The lesson for informed consumers of science is that when critics of evolutionary biology are ferociously set-upon by members of the establishment – with charges like “creationist” flying about, you needn’t get upset. To be charged with “quote-mining” is merely an indication that your interlocutor has little up his sleeve beyond Law 101 – when you don’t have a case, impugn your opponent.

Here is a final important point to emerge from the Margulis interview and which was covered in Genesis and Genes – how mathematics can sometimes hamper scientific progress, by providing the reassuring gloss of numbers and equations to otherwise vacuous endeavours. In Genesis and Genes, we saw how mathematics was used in the latter part of the 19th century to obscure the fatal weaknesses of various methods of dating the Earth. I used the term mathemagic – coined by David Klinghoffer of Discovery Institute – to describe this phenomenon. Here is Margulis on the subject.

Discover: You have attacked population genetics – the foundation of much current evolutionary research – as “numerology”. What do you mean by that term?
Margulis: When evolutionary biologists use computer modeling to find out how many mutations you need to get from one species to another, it’s not mathematics – it’s numerology. They are limiting the field of study to something that’s manageable and ignoring what’s most important. They tend to know nothing about atmospheric chemistry and the influence it has on the organisms… They know nothing about biological systems like physiology, ecology, and biochemistry… Evolutionary biology has been taken over by population geneticists. They are reductionists ad absurdum.

In other words, mathematics in population genetics is like the proverbial lamppost. It’s convenient to search under its light, even though you lost your coin elsewhere.

***

Readers are welcome to read the entire interview with Margulis (it’s only a few pages long and is non-technical) and see for themselves whether I misrepresented her views by quote-mining or anything else. The interview can be read here: http://discover.coverleaf.com/discovermagazine/201104?pg=68#pg70

When evolutionary biologists present evidence for the veracity of their claims, they do not present all their evidence all at once. The claim that focussing on one element of the debate is somehow unfair is ludicrous. Speciation is a pillar in the edifice of contemporary evolutionary biology, and it is perfectly legitimate to examine it in isolation from other claims. Even in a book-length treatment of the subject – Genesis and Genes – I explained that it was impossible to look at all the evidence:

A complete review of the evidence used by evolutionary biologists would fill up several volumes. Nonetheless, one can form an impression of the level of evidence from a few examples.

What we have seen about speciation is extremely important in this context. Yes, evolutionary biologists claim that there are many avenues of evidence which prove their point. But speciation is such an important part of the story, and the evidence for it so flimsy, that, as an informed consumer of science, the correct posture to adopt about evolution is extreme scepticism.

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An Interview with Lynn Margulis

February 25, 2013

In Genesis and Genes, I mentioned Lynn Margulis a number of times. A world-famous biologist, she was elected to the United States National Academy of Sciences in 1983 and inducted into the World Academy of Art and Science, the Russian Academy of Natural Sciences, and the American Academy of Arts and Sciences between 1995 and 1998. She was the recipient of the William Procter Prize for Scientific Achievement (1999) and was awarded the National Medal of Science by President Bill Clinton in that same year. Margulis passed away in November 2011.

Margulis held an unusual position on biological evolution. A fierce critic of the Neo-Darwinian paradigm, she nonetheless subscribed to an evolutionary picture regarding the emergence of the myriad life-forms on Earth today. In April 2011, Margulis was interviewed by Discover Magazine.[1] The entire interview is interesting, but in this post I will focus on a few points that are relevant to material treated in Genesis and Genes and this website.

***

Readers of Genesis and Genes are aware that Darwin’s Finches are often misleadingly portrayed as paragons of speciation – the process by which one species becomes two. Documenting speciation is vital for evolutionary biology. As I wrote in Genesis and Genes,

Before Darwin, the consensus was that species can vary only within certain limits. Centuries of artificial selection had seemingly demonstrated such limits experimentally. “Darwin had to show that the limits could be broken,” wrote [Evolutionary biologist Keith Stewart] Thomson, “[and] so do we.”[2]

In the interview with Discover Magazine, Margulis is characteristically forthright about Darwin’s Finches.

Discover: What about the famous “beak of the finch” evolutionary studies of the 1970s? Didn’t they vindicate Darwin?
Margulis: Peter and Rosemary Grant, two married evolutionary biologists, said, “To hell with all this theory; we want to get there and look at speciation happening.”…
Discover: Did the Grants document the emergence of a new species?
Margulis: They saw this big shift: the large-beaked birds going extinct, the small-beaked ones spreading all over the island and being selected for the kinds of seeds they eat. They saw lots of variation within a species, changes over time. But they never found any new species – ever. They would say that if they waited long enough they’d find a new species.

In other words, the Grants did not document an instance of speciation; at best, they predicted that it would occur. To this day, there is not a single unequivocal, documented instance of speciation.

This is an exceptionally important point in the context of becoming an informed consumer of science. In the case of speciation, members of the public who express doubt about this process will inevitably be directed to Wikipedia, where numerous instances of speciation are supposedly documented. The Wikipedia sources are arcane and most people will not be able to check the validity of the speciation claim. But ask yourself: if many dozens of iron-clad examples of speciation exist, would a biologist of Margulis’ calibre express scepticism because of Darwin’s Finches? Would Discover Magazine bother to prod Margulis on finch speciation if the issue were settled?

I pointed out in Genesis and Genes that the Grants themselves never claimed to have witnessed speciation. Regarding a particular finch designated 5110 and whose progeny are believed to be the best candidates for demonstrating speciation, a November 2009 report in the journal Nature stated that “the Grants aren’t yet ready to call 5110’s lineage a new species.” Indeed, “the Grants think there is only a small chance that 5110’s descendants will remain isolated long enough to speciate.”[3]

Elsewhere, Margulis made it clear that speciation has not been documented:

Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity change shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.[4]

Take-home points:

1. Speciation, a sine qua non for evolutionary biology, has not been observed.
2. Wikipedia is a partisan institution, not to be trusted on questions relating to biological evolution.

***

I did not discuss the fossil record in Genesis and Genes. Margulis considers it a prime reason to reject Neo-Darwinism.

Discover: What kind of evidence turned you against neo-Darwinism?
Margulis: What you’d like to see is a good case for gradual change from one species to another in the field, in the laboratory, or in the fossil record – and preferably in all three. Darwin’s big mystery was why there was no record at all before a specific point [currently referred to as the Cambrian Explosion – YB] and then all of a sudden in the fossil record you get nearly all the major types of animals. The palaeontologists Niles Eldredge and Stephen Jay Gould studied lakes in East Africa and on Caribbean islands looking for Darwin’s gradual change from one species of trilobite or snail to another. What they found was lots of back-and-forth variation in the population and then – whoop – a whole new species. There is no gradualism in the fossil record.

Quite true. What is fascinating is that Margulis points out a powerful critique of Neo-Darwinism that is entirely unoriginal – opponents of evolutionary biology have pointed out for yonks that the fossil record is incompatible with Neo-Darwinism. The difference is that Margulis subscribes to an evolutionary worldview. That makes her sufficiently palatable to be granted an interview by Discover Magazine. If you happen to be a critic of evolution with a different worldview, expect nothing but mockery, regardless of the excellence of your work.

References:

[1] The interview can be read online:
http://discover.coverleaf.com/discovermagazine/201104?pg=68#pg70
Retrieved 25th February 2013.

[2] Keith Stewart Thomson, “Natural Selection and Evolution’s Smoking Gun,” American Scientist 85 (1997): 516-518.

[3] Daniel Cressey, “Darwin’s finches tracked to reveal evolution in action” Nature, November 16, 2009. The report can be read online:
http://www.nature.com/news/2009/091116/full/news.2009.1089.html
Retrieved 25th February 2013.

[4] Lynn Margulis, Acquiring Genomes: The Theory of the Origins of the Species, Basic Books, 2003, page 29.

Adam and Eve – A Parable?

February 21, 2013

I am toying with the idea of writing a review of Rabbi Jonathan Sacks’ The Great Partnership. In the meantime, I have been watching a debate between Lord Sacks and Richard Dawkins. The debate took place on 12th September 2012 and was organised by the BBC. It can be watched in its entirety on YouTube.[1]

At one point, Dawkins challenges Lord Sacks regarding his belief in the literal meaning of certain Biblical events. For example, he asks whether the Splitting of the Sea is to be understood literally, to which Lord Sacks answers in the affirmative. Dawkins then asks about Adam and Eve. At this point (at about 18 minutes), Lord Sacks says, “Well, Adam and Eve is clearly a parable, because there was no first human… obviously, the Bible is telling us about the first dawn of civilisation.”

That’s a curious statement. Lord Sacks is an observant Jew; as such, he is bound by certain axiomatic beliefs and allegiances to certain texts and methodologies. Many classical authorities, like Rambam/Maimonides and Sa’adiah Gaon, clearly delineated the circumstances under which we can read Biblical passages as parables and abandon their literal meaning. Though there are disagreements among the classical authorities as to the precise parameters for allegorisation, everyone agreed that one cannot willy-nilly appeal to parable or allegory and neglect the literal meaning of Biblical passages.

Here is one example of a classical commentator delineating his approach to parables. Radak (1160-1235) writes in his introduction to his Bible commentary that,

One of the thirty-two hermeneutical mechanisms [described by Chazal] is parable… this does not apply to passages wherein commandments are specified… Even though we accept the passages literally, they also incorporate allegorical meanings…[2]

So Radak believes that no legal passages may be described as allegorical; one cannot shirk the responsibility of fulfilling commandments by reading them as allegories. Furthermore, Radak seems to argue that an allegorical interpretation of a passage does not mean that one can abandon the literal meaning of the passage; the parable is supplementary to the literal meaning.

Lord Sacks claims that Adam and Eve did not exist as individuals; they are parables for the emergence of civilisation. But Rambam had a radically different understanding. I wrote in Genesis and Genes that,

In the third section of The Guide for the Perplexed Rambam writes:[3]

It is a fundamental belief of Judaism that the world was created ex nihilo and that a specific human being, Adam, was initially created and that from his creation until the time of Moses approximately 2500 years elapsed.

Notice that Rambam characterises this belief as fundamental to Judaism i.e. central and indispensable.

The type of claim made by Lord Sacks about Adam and Eve is not new. Rashba (1235-1310) complained of those who saw the narratives about Abraham and Sarah as a parable for substance and form. He excommunicated them.[4]

Lord Sacks owes his readers and the Jewish public an explanation for his statement in a televised debate. In particular, he must answer the following questions:

1. Are there any rishonim (medieval classical authorities) who believed that Adam and Eve were anything other than flesh and blood human beings?

2. How does he explain the statement of Rambam quoted above?

A little later in the exchange, Dawkins asks Lord Sacks why he believes that the Parting of the Sea is to be understood literally, while Adam and Eve are to be understood symbolically. Rabbi Sacks responds by saying that the rabbis of the tenth century established a rule that if a Biblical narrative is incompatible with established scientific fact, it is not to be understood literally. Of course, in the midst of a debate, he was not going to provide detailed sources, but it is fair to ask him to do so at some later point. The only 10th century rabbi I can think of that Lord Sacks could have had in mind is Rav Sa’adiah Gaon, and to present his viewpoint the way Lord Sacks did is inaccurate and misleading.

References:

[1] http://www.youtube.com/watch?v=roFdPHdhgKQ.
Retrieved 19th February 2013.

[2] והתורה נדרשת בשלושים ושתים מידות ואחת מהן משל… אבל תורה ומצוות לא נאמרו משל… ואף על פי שהדברים כמשמעם, יש בהם גם כן משל, והוא הנסתר.

[3] מורה נבוכים חלק שלישי פרק נ: כאשר היתה פנת התורה שהעולם מחודש ואשר נברא תחלה היה איש אחד ממין האדם והוא אדם הראשון, ולא היה באורך הזמן אשר מאדם עד משה רבינו רק אלפים וחמש מאות שנה בקרוב.

[4] שאלות ותשובות הרשב”א חלק א סימן תיז: … לאמור כי מבראשית עד מתן תורה הכל משל ואברהם ושרה חומר וצורה ושנים עשר בני יעקב שנים עשר מזלות וארבעה מלכים אשר נלחמו את החמשה הם ארבעה יסודות וחמשה הרגשים…

The Tree of Life – Part 2 of 2

February 17, 2013

The world’s foremost atheist (not much of an accomplishment) and most famous writer on evolution is Richard Dawkins. In a recent interview, he was asked,

Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory?[1]

Dawkins replied that it is difficult to pick out the best evidence, since there is so much of it, but he eventually settled on genetic evidence, the sort that we examined in part 1 of this post, in which proteins or genes of different organisms are compared:

There’s an enormous amount of evidence, from all sorts of places, and it’s hard to pick one strand which is more important than any other… I think to me perhaps the most compelling evidence is comparative evidence, from modern animals – particularly biochemical comparative evidence, genetic, molecular evidence.

After briefly explaining the methodology, Dawkins presents his conclusion:

So, you can take any pair of animals you like – kangaroo and lion, horse and cat, human and rat – any pair of animals you like, and count the number of differences in the letters of a particular gene, and you plot it out, and you find that it forms a perfect branching hierarchy. It’s a tree, and what else could that tree be, but a family tree.[2]

Well… baloney. As we’ve seen, evolutionary trees constructed on the basis of genes contradict each other all the time. So it’s time to let Dr. Jekyll speak again. Churakov et al., discussing precisely the example mentioned by Dawkins, found that five genes supported a pattern in which human and armadillo are most closely related; nine genes supported a contradictory history, where human and elephant are most closely related, and eight genes supported a third (hi)story, where elephant and armadillo were closest relatives.[3] And writing in the journal Evolution and Development [4], researchers entitled their paper Conflicting phylogenetic signals at the base of the metazoan tree, and wrote in the summary that “… analyses of… sequences fail to resolve the relationships… We demonstrate that… conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences.”

Genes vs. Bones

The journal Nature weighed in with a review article that spoke about evolution wars.[5] This was not a reference to conflict between biologists and critics of evolution. It was a reference to wars within biology. One problem, as we have seen, is that there is a huge discrepancy between different trees-of-life, depending on which protein or gene you use. But there is also a divergence between tree-of-life models when you contrast those made from anatomical evidence and those made on the basis of genetic evidence. It’s as if you compare two computers. If you look at the hard-drive, the evidence indicates that one computer came from South Korea and the other from Taiwan. But if you look at the motherboard, you conclude that one computer came from Oshkosh and the other from Tierra del Fuego. The widespread disagreement between molecule-based evolutionary trees and anatomy-based evolutionary trees led the Nature writer to comment that “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology [the study of the structure and anatomy of the organism].”

Despite these clear statements in the professional literature, evolutionary biologists persist in overselling their brand. Notwithstanding the research that contradicts their absolutist claims, they often insist, when writing for the broad public, that molecular studies confirm anatomical studies. For example, in his book Galileo’s Finger, Oxford University scientist Peter Atkins boldly states, “The effective prediction is that the details of molecular evolution must be consistent with those of macroscopic evolution.” He then adds, “That is found to be the case: there is not a single instance of the molecular traces of change being inconsistent with our observations of whole organisms.”[6] Yet a variety of reports clearly recognize that these studies frequently conflict with one another. One authoritative review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.”[7] Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.”[8] And despite consistent attempts by apologists to portray developments in this area of biology as something less than a crisis for evolutionary theory, the news is finally making its way into the popular press. In 2009, for example, The Telegraph reported that, “Charles Darwin’s tree of life is ‘wrong and misleading’”.[9]

In July 2010, a Johannesburg educator contacted a distinguished American geneticist and posed a number of questions about evolution to him.[10] The educator has no training in science and little knowledge of biological evolution. He was caught in the cross-fire of the controversy regarding the teaching of evolution in Torah schools and was seeking some enlightenment. In his response, the American biologist played the perfect Mr. Hyde:

There is overwhelming evidence for evolution. The more we learn and the more powerful our technologies become, the greater our insight is into the relationship of all living organisms, past and present.

This statement came with no qualification: nothing about contradictions, difficulties, wars, absurd classifications, incongruities, “burial” or “annihilation” of the tree of life. Just that we have overwhelming evidence for evolution on the basis of advanced research into relationships between organisms. To say that the professor was selling lokshen to the teacher is to insult pasta.

Paradigms

The typical reader, confronted with this material, might think that with so many setbacks, evolutionary biologists would at least countenance a different view of reality. The typical reader, alas, is not familiar with the mechanics of scientific paradigms. Thomas Kuhn was arguably the most influential philosopher of science in the twentieth century. In The Structure of Scientific Revolutions, first published a half-century ago, Kuhn did a marvellous job in describing how the most productive work done by the vast majority of scientists is in solving puzzles within the regnant ideology.[11] Little attention is paid to all the loose ends – those parts of the paradigm which are not explained and, indeed, unexplainable. It is only when the difficulties accumulate to the point where the theoretical structure of the theory collapses that the bulk of the community of scientists acknowledges the problems.

In other words, paradigms are much like flypaper: once stuck, it’s hard to leave. The flood of counter-evidence has not caused biologists to desert the evolutionary paradigm en masse. The lingo changed – where before biologists spoke of the Tree of Life, they now often speak of the web of life or the bush of life [12] or the mosaic of life. Or rather, when they speak to each other they use the new terminology. In pronouncements to the public or in textbooks, it’s the same old story: the tree-of-life is this impossibly gorgeous, perfectly consistent research programme that confirms the Darwinian worldview without a wrinkle.

Paradigms often take at least a generation to overturn. In a trenchant insight into the workings of modern science, the great physicist Max Planck, the father of quantum mechanics, remarked:

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.[13]

Still, there is hope. In the New Scientist article cited above, evolutionary biologist Eric Bapteste writes, “If you don’t have a tree of life, what does it mean for evolutionary biology? At first it’s very scary – but in the past couple of years people have begun to free their minds.” And philosopher of biology John Dupré adds that it is all “part of a revolutionary change in biology. Our standard model of evolution is under enormous pressure.” The belief that all species are related and evolved from common ancestors is sacrosanct among many biologists. No doubt, many will stick to the dogma like a tattoo to a biker. But the Tree of Life has fallen with such a thunderous thud that it is forcing some biologists to consider different possibilities. A paper published in August 2011 by four European evolutionary biologists argues that the Tree of Life is “becoming increasingly implausible.” Although the Tree of Life “has been stretched to fit the data” in various ways, “given our knowledge of the data, it seems that the elastic limit of the original hypothesis has been passed.”[14] Some even go so far as to acknowledge that the whole field has made little progress in the past century: a review article in the journal BioEssays reported that despite a vast increase in the amount of data since Darwin’s time, “our ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years.”[15]

It is quite entertaining to watch researchers swinging from tree to tree, first concluding that they have found The One True Tree, and then, after obtaining contrary results, ditching the first tree and replacing it with a quite different specimen. We could continue to discuss the crises befalling the Tree of Life paradigm, but perhaps it’s best to end by noting that in Stevenson’s novel, the affable Dr. Jekyll is the awful Mr. Hyde. He is so tormented by his inability to stop metamorphosing into his monstrous alter ego that, in desperation, he finally commits suicide.

Concluding Remarks

Those who jump into the evolution debate often drown under the claim that there is overwhelming evidence for evolution. It is a claim that is meant to preclude any possibility of challenging the validity of evolutionary biology. Any instance of counter-evidence is brushed aside, often without careful consideration, because, “Hey, there is overwhelming evidence for evolution.”

My experience has been that those who claim that there is overwhelming evidence for evolution are like the schoolyard bully who always threatens to open up with a machine gun but, when push comes to shove, produces a pea-shooter. The invincible evidence for evolution – when actually chewed rather than swallowed – is far more vulnerable than is made out to be.

Richard Dawkins, widely considered the most influential spokesman for evolutionary biology, stated that genetic analysis constitutes the strongest, most irrefutable evidence for evolutionary biology. The expectation, going back several decades, was that common descent would be smoothly vindicated by genetic data. It would corroborate (or clarify, as the case may be) evidence from anatomy and palaeontology regarding the relationships between all organisms, and would once and for all convince everyone that we are all descendents of bacteria.

This expectation has turned out to be wrong. In a classic case of piling one epicycle atop another, researchers committed to the evolutionary paradigm twist themselves into loops trying to morph trees into bushes, and bushes into webs, and webs into mosaics or whatever the latest metaphor happens to be. The truth is that genetic analysis is a Rorschach test. Evolutionary biologists see relationships because they want to see relationships. The exercise starts within the Darwinian paradigm, and pre-supposes that all organisms are biologically related. But when you allow yourself to look past the evolutionary horizon, you see that the genetic data does not support a picture of common descent. Evolutionary biology is a sartorially-challenged emperor. It’s time to depose him.

References:

[1] http://www.youtube.com/watch?v=5PlqNoCAIgA.

Retrieved 13th February 2011.

[2] See http://www.evolutionnews.org/2011/02/for_darwin_day_false_facts_and043691.html.

Retrieved 12th February 2011.

[3] Mosaic retroposon insertion patterns in placental mammals, Gennady Churakov, Jan Ole Kriegs, Robert Baertsch, Anja Zemann, Jürgen Brosius, and Jürgen Schmitz. Genome Research, Cold Spring Harbor Laboratory Press, March 2009. The article can be viewed here: http://genome.cshlp.org/content/19/5/868.abstract.
Retrieved 13th February 2011.

[4] EVOLUTION & DEVELOPMENT 5:4, 346–359 (2003). See the article here: http://people.vanderbilt.edu/~antonis.rokas/pdfs/2003_Rokas_etal_Choanos_EvolDev.pdf.
Retrieved 13th February 2011.

[5] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).

[6] Peter Atkins, Galileo’s Finger: The Ten Great Ideas of Science, page 16 (Oxford University Press, 2003).

[7] Patterson et al., “Congruence between Molecular and Morphological Phylogenies,” Annual Review of Ecology and Systematics, Vol 24, page 179 (1993).

[8] Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution, Vol. 44, pages S117-S120 (Supplement 1, 1997).

[9] http://www.telegraph.co.uk/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html.
Retrieved 15th July 2012.

[10] See https://torahexplorer.com/2010/07/04/readers-feedback-professor-james-shapiro-rabbi-blue/.

Retrieved 6th August 2012.

[11] Thomas Kuhn, The Structure of Scientific Revolutions, third edition, The University of Chicago Press, 1996.

[12] Here is one example of the genre. An article in Trends in Ecology and Evolution concluded, “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush…” W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7), pages 270-274 (July 7, 1998).

[13] Planck (1949) Scientific Autobiography, pages 33-34.

[14] See http://www.biology-direct.com/content/6/1/41/abstract.
Retrieved 5th September 2011.

[15] Matthew A. Wills, “The tree of life and the rock of ages: are we getting better at estimating phylogeny,” BioEssays, Vol. 24: 203-207 (2002), reporting on the findings of Michael J. Benton, “Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century,” Proceedings of the Royal Society of London B, Vol. 268: 2123-2130 (2001).

The Tree of Life – Part 1 of 2

February 14, 2013

Imagine that you are trying to guess the relationship between Ross, Alan and Peter. When you look at their chins, it seems clear that Ross and Alan are brothers – they share the same chiselled chin, complete with dimple. Peter is left out. Is this enough, though, to conclude that Ross and Alan are brothers, and that Peter is distantly related, if at all? How would we feel if another anatomical feature were compared – the subjects’ eyes, say – and it was discovered that now it is Peter and Alan who have virtually-identical apertures, with Ross the odd man out?

One of the boldest icons of evolutionary biology is the provocatively-titled Tree of Life. It is a core belief of modern evolutionary theory that all life forms – from bacteria to bananas to blue whales to Barry Manilow – are related to one another. This is a corollary of the notion of universal common descent. Evolutionary biologists believe that all life-forms that inhabit Earth today evolved from simpler ancestors. The diagram that depicts the putative relationships between these ancestors and descendants is known as the Tree of Life. Countless students have been shown images of alleged relationships between organisms depicted as points on a tree. At its base is LUCA, the Last Universal Common Ancestor, a one-celled organism from which all of life supposedly evolved. The trunk, branches, boughs and twigs all represent hypothetical relationships between species, with the outermost twigs representing existing species, while extinct species lie lower. So the Tree of Life is no mere diagram; it captures the essence of Neo-Darwinism. It is telling that in Charles Darwin’s On the Origin of Species, there is but one illustration – that of the Tree of Life.

How do biologists decide where to place various organisms on a Tree of Life diagram? One method is to analyse anatomical similarities and differences among various animals. Chimpanzees are anatomically closer to humans than are, say, armadillos. Other methods, adopted since the biochemical revolution in the latter part of the twentieth century, involve the comparison of proteins and DNA. These large biological molecules are made up of numerous components – smaller molecules that join to make up the bigger ones. As a simplified illustration of the procedure used by biologists to determine similarities, let us imagine taking a specific protein from a human, a chimpanzee and an armadillo. When you look at the building blocks of this protein in all three organisms, you might end up with something like this:

Human          A    ^    π    ©    ¤    %    Ω    Я
Chimp            A   ^    B     ©    ¤    %    Ω    Я
Armadillo    A   #    C      *     ≈    ◊     ∫     >

Each entry in the table above designates a building-block of a protein, called an amino acid. The first two strings of letters are very similar; they only differ in the third position (π in humans and B in chimps). So these two proteins have near-identical components. But the third row is very different to the other two; in fact, it is only equal in the first position (A in all three cases). Evolutionary biologists would say that this is evidence that the first two organisms are closely related, but that the third protein comes from a distantly-related creature.

But there’s a catch, and it is related to the thought experiment we conducted at the beginning of this article. Protein or gene comparison is valid, if at all, only if it is consistent regardless of which genes or proteins were used in the comparison. Reverting to our simplified example above, imagine that we compare the three creatures (human, chimp and armadillo) using a different protein. What if the two strings of symbols for chimp and armadillo match perfectly, but the one for humans is different? This exercise would then indicate that the chimp and armadillo are cousins, with humans only distantly-related. Overall, such a clash between the analyses of two proteins would discredit the entire exercise of discovering relationships among organisms based on this methodology. Ellen Prager and Allan Wilson warned in 1976 that:

To test the reliability of the use of proteins for working out phylogenetic relationships, it is essential to determine whether the branching order of the evolutionary tree one obtains depends on the protein studied.[1]

If the analysis gives different trees when applied to different proteins, then something is amiss. A decade later, David Hillis was equally emphatic:

A primary objective of phylogenetic studies is to reconstruct the evolutionary history of a group of organisms. Because the organisms under study have a single history, systematic studies of any set of genetically determined characters should be congruent with other such studies based on different sets of characters in the same organisms. Congruence between studies is strong
evidence that the underlying historical pattern has been discovered; conflict
may indicate theoretical or procedural problems in one or both analyses, or it may indicate that additional data are needed to resolve the phylogenetic relationships in question.[2] [E,phasis added.]

Fast-forward two decades, and the consistent picture that everyone expected – all proteins and genes confirming the same pattern of species relationships – turns out to be illusory. What emerged instead is chaos, as James Degnan and Noah Rosenberg made clear in a paper published in 2009:

Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates.[3]

Translation: the results of protein and DNA studies that purport to shed light on relationships in the living world are desultory to the point of being useless.

The latest research to upset the applecart concerns microRNAs. These are short molecules which regulate gene expression – they help control whether a particular gene will “shout” or “whisper”. MicroRNAs are poorly understood, but it is thought that they may have a major influence on the developmental course of organisms. Consider some statements from a recent Nature article, entitled Rewriting Evolution, about these molecules:

• “Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree.”
• “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree.”
• “What we know at this stage is that we do have a very serious incongruence.”
• “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.”[4]

The article in Nature – perhaps the world’s most prestigious science journal – focused on the work of Kevin Peterson. A molecular paleobiologist at Dartmouth College and a leading researcher in this field, Peterson has “sketched out a radically different diagram for mammals…” The Nature article continues:

When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn’t cooperate… “The microRNAs are totally unambiguous,” he says, “but they give a totally different tree from what everyone else wants.”

For anybody who follows the research about genetic relationships among organisms, nothing quite captures the situation like the famous novel by the Scottish author Robert Louis Stevenson, The Strange Case of Dr. Jekyll and Mr. Hyde. Evolutionary biology suffers from a case of split personality. The dichotomy between announcements to the public on the one hand, and actual research as reported in professional journals on the other hand, is little short of psychotic. As the misanthropic Edward Hyde, evolutionary biologists insist that phylogenetic trees – pictures of relationships drawn on the basis of comparisons of genes or proteins – lead to the inescapable conclusion that all organisms are related and descend from common ancestors. And then they turn into Dr. Jekyll and confess, among themselves, that this is fantasy.

Meet Mr. Hyde. On 21st January 2009, University of Texas evolutionary biologist David Hillis testified before the Texas State Board of Education. He claimed to be one of the “world’s leading experts on the tree of life”. Hillis later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. Hillis was saying that such research has proceeded as smoothly as silk, confirming all predictions made by evolutionary biology, regardless of which organisms and structures were analysed.

Enter Dr. Jekyll. The technical literature is replete with scientific papers that have found contradictions, inconsistencies, and failures of the molecular data to provide a clear picture of universal common descent. In a delicious irony, the issue of New Scientist that was published on the very day that Dr. Hillis testified carried the cover story Darwin Was Wrong. The story was subtitled Cutting down the Tree of Life. (When reading this, one should keep in mind that New Scientist is a bastion of evolution diehards. This cover story was as surprising as reading a denunciation of Stalin in Pravda in 1937 would have been.) The cover story quoted Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France, Michael Rose, an evolutionary biologist at the University of California, Irvine and John Dupré, a philosopher of biology at the University of Exeter, UK.

The article begins with a review of the orthodoxy. “For a long time the holy grail was to build a tree of life,” says Bapteste. “A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded.” “We have no evidence at all that the tree of life is a reality,” he continues. “The problem was that different genes told contradictory evolutionary stories.” “It’s part of a revolutionary change in biology,” says Dupré. “Our standard model of evolution is under enormous pressure.” Rose goes even further. “The tree of life is being politely buried, we all know that,” he says. “What’s less accepted is that our whole fundamental view of biology needs to change.” Biology is vastly more complex than we thought, he says, and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.

The New Scientist article also cited research by Dr. Michael Syvanen, of the University of California at Davis. He compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six organisms. He failed. Once again, different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says. His conclusion: “We’ve just annihilated the tree of life.” [5]

Bapteste, Rose and Dupré by no means represent fringe opinions. One of the leaders in this field, W. Ford Doolittle, explains that “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.” [6] Looking higher up the tree of life, a study published in Science tried to construct an evolutionary history of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” [7] Likewise, Carl Woese, a pioneer in this field, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [read: contradictions in the relationships picture] can be seen everywhere in the universal tree, from its root to the major branching…”[8]

Lynn Margulis was, until she passed away in November 2011, a world-famous biologist. She was elected to the United States National Academy of Sciences in 1983 and inducted into the World Academy of Art and Science, the Russian Academy of Natural Sciences, and the American Academy of Arts and Sciences between 1995 and 1998. She was the recipient of the William Procter Prize for Scientific Achievement (1999) and was awarded the National Medal of Science by President Bill Clinton in that same year. She was also the first wife of the famous late astronomer Carl Sagan. Even though Margulis herself was certainly not religious, she had little patience for practitioners in this field. In an article entitled The Phylogenetic Tree Topples, she explained that “many biologists claim they know for sure that random mutation is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk… pattern!” But she dissented from that view and attacked evolutionary systematists, noting, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.” [9]

Striking admissions of troubles in reconstructing the Tree of Life also came from a paper in the journal PLOS Biology entitled Bushes in the Tree of Life. The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality.” They observe that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” [10] The paper suggests that “certain critical parts of the [Tree of Life] may be difficult to resolve, regardless of the quantity of conventional data available.”

Glug, glug ,glug – swill some magic potion and here’s Mr. Hyde again. Biology textbooks often tout the tree-of-life constructed on the basis of the protein Cytochrome C as confirming the traditional relationships of many animal groups. This is presented as evidence for universal common descent. Over to Dr. Jekyll now. Said textbooks rarely talk about the Cytochrome B tree, which differs strikingly from the classical story. As an article in Trends in Ecology and Evolution stated: “the mitochondrial cytochrome b gene implied… an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates… Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.” [11]

References:

[1] http://www.springerlink.com/content/j7315x8081517q53/. Retrieved 15th July 2012.

[2] http://www.lifesci.utexas.edu/faculty/antisense/papers/Hillis1987ARES.pdf.
Retrieved 15th July 2012.

[3] http://www.stanford.edu/group/rosenberglab/papers/DegnanRosenberg2009-TREE.pdf.
Retrieved 15th July 2012.

[4] The article can be read here: http://www.nature.com/polopoly_fs/1.10885!/menu/main/topColumns/topLeftColumn/pdf/486460a.pdf.
Retrieved 11th July 2012.

[5] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).

[6] W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science, Vol. 284:2124-2128 (June 25, 1999).

[7] Antonis Rokas, Dirk Krueger, Sean B. Carroll, “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” Science, Vol. 310:1933-1938 (Dec. 23, 2005).

[8] Carl Woese “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998).

[9] Lynn Margulis, “The Phylogenetic Tree Topples,” American Scientist, Vol 94 (3) (May-June, 2006).

[10] Antonis Rokas & Sean B. Carroll, “Bushes in the Tree of Life,” PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).

[11] Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14:177-178 (1999).

Replication of Experimental Data

February 10, 2013

In Genesis and Genes, I cited research done by the epidemiologist John Ioannidis:

In a 2005 article in the Journal of the American Medical Association, epidemiologist John Ioannidis showed that among the 45 most highly cited clinical research findings of the past 15 years, 99 percent of molecular research had subsequently been refuted. Epidemiology findings had been contradicted in four-fifths of the cases he looked at, and the usually robust outcomes of clinical trials had a refutation rate of one in four. The revelations struck a chord with the scientific community at large: A recent essay by Ioannidis simply entitled “Why most published research findings are false” has been downloaded more than 100,000 times; the Boston Globe called it “an instant cult classic.”[1]

In 2012 Ioannidis, who is at Stanford, published a paper in Perspectives on Psychological Science.[2] In this post, we will focus on one aspect of that paper viz., the replication of experimental results. Ioannidis points out that contemporary science produces an avalanche of data, with the result that scientists find it difficult to assimilate even a small fraction of the research that is relevant to their area of research. He writes that,

Currently, there are petabytes of scientific information produced on a daily basis and millions of papers are being published annually. [One petabyte is equivalent to one million gigabytes – YB.]

I mentioned this problem in Genesis and Genes:

A paper published in the Proceedings of the National Academy of Scientists in 2006 noted that “More than 5 million biomedical research and review articles have been published in the last 10 years.” That’s an average of 1370 papers per day.[3] And this is just biomedical research.[4]

But the problem is not just volume. Ioannidis points out that raw data is disappearing at gargantuan rates, making it impossible to replicate research, even if one has the inclination and resources to do so:

In most scientific fields, the vast majority of the collected data, protocols, and analyses are not available and/or disappear soon after or even before publication. If one tries to identify the raw data and protocols of papers published only 20 years ago, it is likely that very little is currently available. Even for papers published this week, readily available raw data, protocols, and analysis codes would be the exception rather than the rule. The large majority of currently published papers are mostly synoptic advertisements of the actual research. One cannot even try to reproduce the results based on what is available in the published word.

Ioannidis is not speculating. He is relying on studies that attempt to gauge the repeatability and reproducibility of experiments:

Empirical evidence from diverse fields suggests that when efforts are made to repeat or reproduce published research, the repeatability and reproducibility is dismal (Begley & Ellis, 2012; Donoho, Maleki, Rahman, Shahram, & Stodden, 2009; Hothorn & Leisch, 2011; Ioannidis et al., 2009; Prinz, Schlange, & Asadullah, 2011). Not surprisingly, even hedge funds don’t put much trust on published scientific results (Osherovich, 2011).

This point will be familiar to readers of Genesis and Genes. Recall what I wrote about cancer research:

During a decade as head of global cancer research at Amgen, [Glenn] Begley identified 53 “landmark” publications – papers in top journals, from reputable labs – for his team to reproduce. Begley sought to double-check the findings before trying to build on them for drug development. Result: 47 of the 53 studies (89%) could not be replicated. He described his findings in a commentary piece published in the journal Nature in March 2012. In a Reuters report, Begley said “It was shocking. These are the studies the pharmaceutical industry relies on to identify new targets for drug development… As we tried to reproduce these papers we became convinced you can’t take anything at face value.”[5] Begley’s experience echoes a report from scientists at Bayer AG. In a 2011 paper titled Believe it or not, they analyzed in-house projects that built on “exciting published data” from basic science studies. “Often, key data could not be reproduced,” wrote Khusru Asadullah, vice president and head of target discovery at Bayer HealthCare in Berlin, and colleagues. Of 47 cancer projects at Bayer during 2011, less than one-quarter could reproduce previously reported findings, despite the efforts of three or four scientists working full time for up to a year. Bayer dropped the projects.
Bayer and Amgen found that the prestige of a journal was no guarantee a paper would be solid. “The scientific community assumes that the claims in a preclinical study can be taken at face value,” Begley and Lee Ellis of MD Anderson Cancer Center wrote in Nature. They and others fear the phenomenon is the product of a skewed system of incentives that has academics cutting corners to further their careers. Part way through his project to reproduce promising studies, Begley met for breakfast at a cancer conference with the lead scientist of one of the problematic studies. “We went through the paper line by line, figure by figure,” said Begley. “I explained that we re-did their experiment 50 times and never got their result. He said they’d done it six times and got this result once, but put it in the paper because it made the best story. It’s very disillusioning.”

A specific example of the above can be found in the context of a subject that I wrote about at length in Genesis and Genes, viz. the Tree of Life, which allegedly demonstrates the relationships between all forms of life on Earth. A new paper in Nature informs us that,

As part of the Open Tree of Life project…, we surveyed publications covering all domains of life and found that most phylogenetic trees and nucleotide alignments from the past two decades have been irrevocably lost.

Bryan T. Drew, working in conjunction with the Open Tree of Life Project, decided to check the data supporting the construction of Darwin’s tree. He writes that,

Of 6,193 papers we surveyed in more than 100 peer-reviewed journals, only 17% present accessible trees and alignments. Contacting lead authors to procure data sets was only 19% successful… We estimate that more than 64% of existing alignments or trees are permanently lost.[6]

The Open Tree of Life website adds more reason for concern.[7] An article entitled “The Glass Is Still Pretty Empty” warns:

Sometimes you wonder whether the glass is half full or half empty. But when it is only filled for four percent – the other 96 percent is just air – there is only one conclusion: it is time for more.

Despite Drew’s estimate in Nature that more than 64% of relationships data are lost, the actual number could be much higher. This article says that only a tiny portion of published trees can be checked against the data:

At least that is what some scientists in the phylogenetic community argue, because only about four percent of all published phylogenies are stored in places such as TreeBASE or Dryad… Several journals in the evolutionary biology field recently adopted policies that encourage or require contributors to make their data publicly available online. Yet, this only leads to the storage of a very small percentage of ten-thousands of phylogenies that have been constructed in the past few decades.

Where replication has actually been tried, it has often failed:

A group of scientists from the Netherlands, United Kingdom, and United States recently published an article about current practices for storing datasets with tree estimates. They concluded that “most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data.” As a result, “[m]ost attempts at data re-use seem to end in disappointment.”

As I explained in Genesis and Genes, the public harbours a massively-distorted picture of how contemporary science is done (and in this case, the term public includes science undergraduates). The establishment would have you believe that science is a perfect self-correcting mechanism: experimental results are checked and rechecked; independent teams of researchers verify these results; raw data is available for anyone to examine. Allow me to characterise this vision with a Yiddish term: babkes. Contemporary scientists are swamped by data; they read a minuscule fraction of what is published; virtually nobody has the resources or any incentive to verify others’ research; raw data – the kind that is needed to replicate other laboratories’ results – is lost before anyone else can access it. When replication attempts are made, the rate of success is dismal.

References:

[1] The original research by Ioannidis can be read here: http://jama.ama-assn.org/content/294/2/218.full.pdf+html. Retrieved 5th June 2011.

[2] The entire paper can be read here: http://pps.sagepub.com/content/7/6/645.full.pdf.
Retrieved 10th February 2013.

[3] See http://www.pnas.org/content/103/13/4940.full.pdf+html. Retrieved 23rd July 2011.

[4] Another study estimated that in 2006, 1.35 million scientific articles were published in 23 750 journals [See http://informationr.net/ir/14-1/paper391.html. Retrieved 15th September 2011.] For an introduction to the appalling consequences of such a flood of results, see the excellent article by the distinguished British pharmacologist David Colquhoun, entitled Publish-or-perish: Peer review and the corruption of science. The article was published in The Guardian on Monday, 5th September 2011 and is available online at http://www.guardian.co.uk/science/2011/sep/05/publish-perish-peer-review-science [Retrieved 15th September 2011]. The author laments that “Pressure on scientists to publish has led to a situation where any paper, however bad, can now be printed in a journal that claims to be peer-reviewed.” Colquhoun explains that

The blame for this sad situation lies with the people who have imposed a publish-or-perish culture, namely research funders and senior people in universities. To have “written” 800 papers is regarded as something to boast about rather than being rather shameful. University PR departments encourage exaggerated claims, and hard-pressed authors go along with them.

The author proceeds to list a few examples of the failure of the peer-review system to ensure robust and accurate journal content. He argues that part of the reason for the lapse in academic publication standards is the pressure on academics to publish many papers. He concludes that frequent publication of results should call into question, rather than enhance, one’s credibility as a diligent and focused researcher.

[5] See http://www.newsdaily.com/stories/bre82r12p-us-cancer/. Retrieved 31st March 2012.

[6] See http://www.nature.com/nature/journal/v493/n7432/full/493305f.html.
Retrieved 10th February 2013.

[7] See http://opentreeoflife.org/2012/11/13/small-portion-of-phylogenetic-data-is-stored-publicly/. Retrieved 10th February 2013.

A Further Response to Matt

February 5, 2013

[This exchange began with the post Radical Revision. Matt wrote an email, to which I responded in the post A Response to Matt. Matt has written another email, which is reproduced below with my comments interspersed between his words.]

***

Matt:

First off, thank you for the thoughtful response. I really appreciate your taking the time to answer my questions.
“The standard teaching that I was referring to is that the tetrapods (or close relatives) made the transition from sea to land.”

I would argue that this statement still holds true, regardless of the spinal orientation. The spinal orientation is difficult to know, because it seems that this part of the specimen is embedded in rock. But, there are many equally essential anatomical features which are clearly visible: the structure of the limbs, the shape of the skull (for which there are several specimens), the teeth, the jaw bone. I would argue that the standard teaching, as you have articulated it, is “robust”, even if one particular part of the anatomy were uncertain… especially since there are many other transitional fossils in this series.

My Response:

Here are the bare bones:

1. A claim is made for a fantastically-intricate transformation from sea-life to terrestrial life through an unguided, non-teleological process. This is a change that would require tens of thousands of changes, many of which would have to occur simultaneously and in a coordinated fashion. Nobody has the faintest clue as to what sequence of genetic mutations could lead, in a step-wise fashion, from a sea-dwelling creature to a land-dwelling creature, so the hypothesis depends on the belief that this is, in fact, possible.

2. The only physical basis to the claim rests on the minuscule amount of information about biological organisms that can be gleaned from skeletal remains (even when the remains are complete and perfectly preserved). We know from history (the case of the Coelacanth) that such claims have been made before, and have turned out to be spectacularly wrong.

3. The fossilised skeletal remains in this case turn out to have been deeply misunderstood. The fact that there are also bits of jaw and teeth is immaterial. If you can’t tell the back of the creature from the front, you probably know very little about these organisms.

If this is what you wish to call a robust scientific claim, I am happy to rest my case here and now.

Matt:

“It is significantly weakened by the discovery that basic anatomical features of these creatures were completely misunderstood for the past 150 years.”

Here is where I think you may be taking license. Phrases like “significantly weakened” and “completely misunderstood” are subjective statements. As a “consumer of science”, I prefer more precise and objective terminology. Having read the Nature article and the BBC article, I get the impression that this is a more subtle anatomical distinction than you would like it to be. The researchers who do this work are passionate and I very much appreciate their excitement in proclaiming that “textbooks will have to be rewritten”. However, I think that they are talking about *graduate level* textbooks. I don’t think that they mean to suggest that this overthrows the big picture of where that creature fits into the record.

My Response: In my post, I quoted (not paraphrased) the report in Nature and BBC. Here are some of the relevant phrases from those sources:

1. This study fundamentally revises our current understanding of vertebral column evolution.
2. Researchers have found that our understanding of the anatomy of the first four-legged animals is wrong.
3. New 3D models of fossil remains show that previous renderings of the position of the beasts’ backbones were actually back-to-front.
4. Their vertebrae are actually structurally completely different from what everyone for the last 150 or so years has pictured. The textbook examples turn out to be wrong.

In contrast, Matt writes, “The researchers who do this work are passionate and I very much appreciate their excitement in proclaiming that ‘textbooks will have to be rewritten’.”

Matt’s sentiment is offered without any substantiation and is based on his “impression”.

I leave it to readers to decide whose comments can more accurately be characterised as objective.

Matt:

You claim that this finding “significantly” weakens the notion that Ichthyostega represents a transitional form from fish to amphibian. Allow me to quote the BBC article: “Prof Hutchinson said the findings provided more clues about how the early animals physically moved out of the water and on to land.” This seems to suggest the opposite of your conclusion.

My Response:

I never doubted that Professor Hutchinson would feel upbeat about the results of his research. The discovery that palaeontologists had completely misunderstood a key piece of tetrapod anatomy for 150 years is certainly a positive step – 150 years is a long time to be wrong. Whether the findings really provide more clues about how early animals moved out of the water remains to be seen. The one incontrovertible fact in this episode is that Professor Hutchinson’s own research indicates that a key piece of anatomy was “structurally completely different from what everyone for the last 150 or so years has pictured. The textbook examples turn out to be wrong.” Everything else is, at best, a prediction (more accurately classified as wishful thinking).

The type of sentence quoted by Matt from the BBC report was called – by the great chemist and ardent opponent of evolution Philip Skell – narrative gloss. Narrative gloss comes in two varieties. The first kind occurs when biologists write articles that have nothing to do with evolution, but whose concluding paragraph contains a passionate affirmation of the authors’ loyalty to the Darwinian paradigm. The second kind occurs when biologists write about research that actually undermines the prevailing paradigm, but whose concluding paragraph contains a passionate affirmation of the authors’ loyalty to the Darwinian paradigm. It’s par for the course for the BBC and Hutchinson to declare that a finding by palaeontologists will advance the Darwinian agenda; no alternative is conceivable.

Matt:

In the end, as someone who would like to think of himself as “an informed consumer of science” I musty humbly admit that, not being a paleontologist or zoologist, I don’t feel confident making any serious judgement. Is it safe to say that you too are not an expert on this subject matter?

My Response:

I explain in Genesis and Genes that contemporary scientists are typically people who know a great deal about a very narrow, specialised, technical field, and very little about Science, especially about its history and philosophy. As I wrote,

Many members of the public are unaware that as scientific training progresses, depth is purchased at the cost of breadth. It is at the undergraduate level where the maximum number of courses is taken. The curriculum at this level is designed to give students exposure to a broad range of topics, the better to choose a suitable specialty once they graduate. When pursuing a Master’s degree, the focus narrows, and it shrinks even further when pursuing a PhD., by which time the researcher is engrossed almost exclusively in the specific research interest which will form his doctoral thesis.

The vast majority of science undergraduates do not take a single course in the history/philosophy of science. They do not have the skills that would make them informed consumers of science. And the situation does not improve as their career progresses. Members of the public may feel awed when confronted by general statements made by a professor whose name is followed by an alphabet soup of titles, but the awe is misplaced. Those who have studied the history and philosophy of science are better qualified to assess the general credibility of scientific findings than most scientists. By way of analogy, it is not an artist that you would approach to determine whether a newly-discovered painting is really a Rembrandt. You would approach a museum curator with extensive training in art history.

Matt:

Might I suggest that we contact the researchers themselves and see what they say? Would you post their response?

My Response:

You are, of course, at liberty to contact the writers of the Nature article. My policy is to post any communication which is non-vitriolic, adequately well-written and of some substance.

Having said this, I have to ask, What exactly do you expect Hutchinson to say? I am under no illusion as to where his sympathies lie.

A bit of background. Thomas Kuhn was one of the most influential philosophers of science in the 20th century. One of his key insights, propounded in his seminal work The Structure of Scientific Revolutions, is that the vast majority of scientists work on ordinary problems within a framework called a paradigm. The problems that undermine the framework itself are seldom discussed, or even noticed. It is only once the problems become too difficult and numerous to sustain the framework that the structure comes tumbling down and a new paradigm emerges.

A related insight into how science works comes from two distinguished philosophers of science:

Or, if the flaws appeared within the proper jurisdiction of the old theory… to abandon it as soon as a new, better one can be contrived. Note the last phrase: a defective theory will be abandoned “as soon as a new, better one can be contrived.” Scientists sometimes prefer an inadequate theory to none at all. [Physics, The Human Adventure, Holton and Brush, Rutgers University Press, 2005, Page 38.]

These words apply primarily to theories in physics, which carry relatively little ideological baggage. With evolution, which represents, for many biologists, an indispensable ideological commitment, the fact that a key point is refuted is usually of no consequence. They will continue to adhere to the paradigm.

I gave detailed examples of this phenomenon in chapter 3 of Genesis and Genes. Lord Kelvin and John Joly continued to insist that their calculations of the age of the Earth would not be affected by the discovery of radioactivity, despite all the evidence to the contrary. They died unregenerate, and it was a new generation of scientists who ditched the old paradigm in favour of viewing radioactivity as the ultimate geological timekeeper.

A Response to Matt

February 3, 2013

My last post, Radical Revision, elicited a thoughtful response from Matt. Here is his email to me, and my response.

Matt: Hi, I have a few questions for you:

Could I ask you to clarify your point in why you included the anecdote about tetrapod anatomy in your article? Is it because you claim it to be a finding that “upsets the standard teaching”?

If so, could you please clarify what you think the “standard teaching” is and how you think that this finding “upsets it”? Could you also clarify the big picture for me? What is the importance of Ichthyostega? Why do researchers care about it’s anatomy?

Also, you ended your article, “As we move further away from repeatable, observable and limited phenomena, the claim of scientific knowledge becomes weaker and weaker.” I agree with the pshat of this statement, but I feel like there is implied subtext in your article. Are you referring to anything in particular?

My Response:

As I wrote in the post, the tetrapods (or their close relatives) are the creatures that are believed – by evolutionary biologists – to have made the transition from life in the sea to terrestrial life. This is one of the most crucial episodes in the history of life, as portrayed by evolutionary biologists. All terrestrial life – from bees to beavers to Benny – is supposedly descended from the tetrapods. So they are an exceptionally important element in the history of life. The fact that the textbooks have been wrong about the basic anatomy of tetrapods for the past 150 years is therefore extremely significant.

If you follow the link to the BBC report that I provided in the post, you will see a reconstruction of one of the tetrapods. Many members of the public, when confronted with such reconstructions, entertain exaggerated notions about the reliability and accuracy of this and similar reconstructions. In fact, these reconstructions are based on paltry information contained in fragments of fossilised bones. The report which I discussed in the post underscores this point. For 150 years, the picture which researchers had of the anatomy of these creatures was, literally, back-to-front. How much confidence, then, should one have in the claim that these creatures are sufficiently well understood to convince us that they or their relatives were capable of moving from the sea to land?

Moreover, this is not the first time in history that this sort of thing has happened. In a previous iteration, it was the rhipidistians, and their relative the coelacanth, that were touted as the first fish to make it on land. Based on numerous fossils of the coelacanth, biologists were convinced that this fish had various adaptations that made it possible for it to achieve locomotion on land. In the late 1930s, a living coelacanth was discovered off the coast of South Africa (since then, many coelacanths have been caught and studied). It was now possible to examine the soft tissues of the fish, and to compare what had been predicted from the fossils to the reality. As Peter Forey wrote,

“… [Before the modern discovery of the coelacanth] many fossil coelacanths were described and, on the basis of osteological features, their systematic position as near relatives of the extinct rhipidistians… had become part of “evolutionary fact”, perpetuated today in textbooks. Great things were therefore expected from the study of the soft anatomy and physiology of [the coelacanth]…” [Peter Forey (1980), Latimeria: A Paradoxical Fish, Proceedings of the Royal Society of London, B208: 369-84]

The result of studying living coelacanths: coelacanths had no pre-adaptation at all to life on land. They were fish, pure and simple. You could make gefilte fish with coelacanth. As Barbara Stahl, an expert on this subject, put it,

“… The modern coelacanth shows no evidence of having internal organs pre-adapted for use in a terrestrial environment… The heart is characteristically fish-like… and the gut… is of a type common to all fishes…” [B. J. Stahl (1974) Vertebrate History: Problems in Evolution, McGraw-Hill page 146].

All of this should give informed consumers of science pause when confronted by claims about life emerging from the sea and adapting to land. Life in the sea and life on land are fundamentally different propositions, and tens of thousands of adaptations would have to occur for that transition to happen. (Think of turning a submarine into a tractor, and try to count the number of changes that have to be made). Furthermore, many thousands of these adaptations would have to occur simultaneously. The evidence presented for this fantastical hypothesis turns out to hinge, to a significant extent, on some shards of bone, which have been badly misinterpreted for the past 150 years.

In summary:

1. The standard teaching that I was referring to is that the tetrapods (or close relatives) made the transition from sea to land. It is significantly weakened by the discovery that basic anatomical features of these creatures were completely misunderstood for the past 150 years.

2. Researchers care about tetrapods because they form such an important element in the evolutionary scenario. These are not mere creatures that appear, live and become extinct, like the vast majority of organisms that populate the fossil record. Without some plausible explanation as to how fish become pre-adapted to life on land, the evolutionary scenario becomes another just-so story.

3. My concluding statement was general. Informed consumers of science know how to discriminate between various scientific claims. They can assign appropriate levels of credibility to various scientific claims. As I explain at length in Genesis and Genes, we have greater confidence in scientific results that concern repeatable, observable and limited phenomena. Claims about the alleged transition of fish from life in the sea to life on earth should be treated with extreme scepticism.