Professor Shapiro – Part 3

This series of posts deals with correspondence between Rabbi Blue (a pseudonym), Professor James Shapiro and me. Rabbi Blue is a Johannesburg educator at a Jewish day school. He contacted me after the school that employs him implemented a change to the biology curriculum. Rabbi Blue forwarded to me correspondence he had had with Professor Shapiro, a world-famous biologist at the University of Chicago ( Here is part 3 of the series. 


 Professor Shapiro’s response to Rabbi Blue’s email:

Dear Rabbi Blue,

You are right. 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. Not surprisingly, however, the most recent molecular evidence tells us that the gradualist process envisioned by Darwin in the mid-19th Century cannot account for major events in evolutionary history. These include the horizontal transfer of large amounts of DNA between distant organisms, cell fusions to generate organelles such as mitochondria and chloroplasts, and whole genome duplications at key evolutionary divergences, such as the origins and radiation of flowering plants (what Darwin called “that abominable mystery”) and the origins of vertebrates. These sudden events affecting many characters at the same time are well-documented in the DNA record, and they require an alternative view of the evolutionary process. 

It is essential to separate out three issues in the evolution-creationism debate: the origin of life, the fact of evolution, the mechanisms of evolution. We do not yet have enough information to discuss the origin of life scientifically. All the evidence we have tells us that evolution by descent with modification has taken place and continues today (think about bacterial antibiotic resistance). Our molecular insights tell us that we need to formulate new theories about the processes behind evolution. Darwin’s natural selection of “numerous, successive, slight variations” is neither accurate nor adequate to account for the dramatic genome changes we can document through DNA sequencing. 


 My comment: It is refreshing (and rare) to see a contemporary biologist acknowledge any weaknesses within the Neo-Darwinian paradigm, much less that important chunks of it are neither accurate nor adequate. Nonetheless, there is much to say. 

In about twenty years of investigating Neo-Darwinism, I have come across the mantra of overwhelming evidence too many times to count. It’s like getting a cheque for a million dollars: mouth-watering when you see it, bitter when it bounces. When you ask evolutionary biologists to present their overwhelming evidence, the only thing that is overwhelming about their response is the sheer paucity of convincing evidence. Of course, in this short correspondence, Professor Shapiro did not set out to demonstrate to Rabbi Blue what evidence led him to his conclusions. But his one reference to evidence for descent with modification is telling. He refers to bacterial antibiotic resistance. This is a well-known phenomenon, and has been studied to bits all over the world. But it is hardly evidence for descent with modification. That putative process requires, inter alia, speciation – the accumulation of a sufficient number of mutations that leads to the divergence of a daughter species from its mother species. If there were a case in which the mutations seen in bacterial colonies led to changes which indicated speciation, it would count as superb evidence for Neo-Darwinism. But there isn’t. No matter how long and how hard these bacterial mutations are studied, the bugs stay bugs. To state that these mutations can accumulate until speciation occurs, as Professor Shapiro believes, is speculation. Maybe they will, and maybe they won’t. We haven’t seen it happen yet. 

Professor Shapiro is a top-notch biologist. But he is not the only top-notch biologist. Here is what another first-rate researcher had to say on this very matter: 

“[No evidence] exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes… But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another… Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution… throughout the whole array of higher multicellular organisms.” [Alan Linton, University of Bristol, Scant Search for the Maker, Times Higher Education Supplement, April 20, 2001, Book section, 29].  

Here is another world-class researcher making much the same point: 

“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.” [Lynn Margulis, Acquiring Genomes: The Theory of the Origins of the Species, Basic Books, 2003, p. 29].  

Here are first-rank biologists who read the evidence regarding mutations quite differently to Professor Shapiro. They do not assume that mutations can be accumulated until a daughter species forms. They take the evidence as it is. Lots of bacterial mutations have been documented. Many are interesting, but certainly do not demonstrate that one species of bacteria can mutate into another species. 

Richard Lenski was elected in 2006 to the USA National Academy of Sciences on the strength of his long experiment (running since 1988) in continuously culturing that ubiquitous laboratory warrior, E. coli. He has nurtured about 50 000 (fifty-thousand) generations of this bacterium. Lenski has recorded the mutations that have been observed over these long years. These changes are overwhelmingly degradative. Here is an analogy to help the uninitiated to understand this term. Imagine that your car alarm goes off at 2 a.m. This is very annoying. Eventually, after futile tinkering under the hood, you snip the electrical wire that supplies power from the car battery to the alarm system. Peace reigns over the neighbourhood again. Now – was the act of cutting the wire productive? Yes and no. If you are talking about the immediate benefit, you could argue that it was. There was an immediate gain in that silence was restored. But could you argue that in the long term, this was a step which would possibly lead to increased complexity within the car’s operating systems? No! The change was degradative. It degraded the functioning of the system, to give you instant gratification. [See Genetic Entropy & the Mystery of the Genome, Dr. J.C. Sanford, Elim Publishing, 2005.] 

The vast majority of mutations that have been observed are downright lethal or at least deleterious to the organism. Of those touted as beneficial by biologists, virtually all are degradative. Here is a specific example of such a mutation. In Lenski’s experiment, one adaptation was an increase in cell size and in many cultures, a more rounded cell shape. However, although this mutation increased fitness under the specific laboratory conditions, it also “increased the bacteria’s sensitivity to osmotic stress and decreased their ability to survive long periods in stationary phase cultures, so the phenotype of this adaptation depends on the environment of the cells.” [Philippe N, Pelosi L, Lenski RE, Schneider D (February 2009). “Evolution of penicillin-binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli”. Journal of Bacteriology 191 (3): 909–21. Another interesting mutation reported by Lenski concerns the ability of E. coli to use citrate. See this response by Dr. Michael Behe:] 

This is the trouble with bacterial mutations. The poor critters indeed mutate, but the overwhelming majority of mutations are deleterious to the organism. Those that are not are usually trivial. The tiny fraction that confer an advantage do so by paying the price of degrading the overall complexity of the organism. There is no indication whatsoever that an accumulation of such mutations can lead to speciation. If all you do is cut wires under the bonnet, don’t expect your alarm system to improve over time, no matter how satisfying your night sleep becomes. 

The same point may be made for insect “resistance” to insecticides like dieldrin. The insects do not gain any resistance by mutations; they lose sensitivity to the drug. The price they pay is a more sluggish nervous response, hardly a promising avenue for the evolution of more advanced organisms. [Dr. Lee Spetner’s Not By Chance! is a comprehensive treatment of this subject.] 

The same is true of millions of fruit flies in laboratories all over the world. Suffering infernal indignities, they have taught biologists a lot. They can mutate in a hundred different ways, sometimes producing grotesque creatures with legs growing where there should have been antennae. But they never become anything other than fruit flies. All you see is a rearrangement of existing genetic material. 

In short, Professor Shapiro’s reference to bacterial antibiotic resistance is about as relevant to descent with modification as is the claim that I can walk to the Moon because I have demonstrated the ability to walk across the room. If there were a case of unambiguous speciation, you can bet your life on the fact that it would be cited constantly by Neo-Darwinists. But Professor Shapiro and his colleagues are reduced to using examples – like bacterial antibiotic resistance – which are at best ambiguous and at worst deceptive. 

It is the same with all examples of what forms the supposedly overwhelming evidence for Neo-Darwinism. Whether it is Kettlewell’s moths, the Miller-Urey experiment or Darwin’s finches, the common denominator is that they are meretricious. Once examined closely, they are exposed as so many layers of emperor garments – naked emperors, that is. 

Rabbi Blue, one of the most enduring lessons in the history of science is that practising scientists are, by-and-large, ignorant of the history of science. Repeatedly, they make predictions about the fact that in their discipline, there are only loose ends to be tied, because the basic picture is so complete that there cannot be much more to do. Here is an egregious example to keep in mind when Professor Shapiro makes reassuring noises about the fact that all that remains to do is to fine-tune the mechanisms of evolution: 

When Max Planck was a twenty-year-old graduate student, he was unsure as to the field he should specialise in. One of his professors, Philip von Jolly, advised him against becoming a physicist. He argued that after the discovery of the two laws of thermodynamics, all that was left to do was to tie up loose ends. [It Must Be Beautiful – Great Equations of Modern Science, Graham Farmelo (editor), Granta Books, 2003, page 6.] This was not merely Jolly’s own opinion. This is how the physics community saw things.  Just in case you don’t know – Planck is one of the giants of modern physics, credited with introducing the concept of quantization, which was instrumental – just a few years later – in the revolution involving quantum mechanics and relativity. 


 Professor Shapiro’s statement that 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 is even more unfortunate. That was the dogma taught to several generations of students. It went (and still goes) under the provocative name of 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. The trunk, branches, boughs and twigs all supposedly represent relationships between species, with the outermost twigs representing existing species, while extinct species lie lower. This image – the tree of life – is the icon of those biological relationships which Professor Shapiro claims are understood with crystal clarity. This picture is essential to Neo-Darwinism. It is telling that in the whole of The Origin of Species, there is but one illustration – that of the Tree of Life. 

Things changed dramatically in the early 1990s, when it became possible to sequence actual bacterial genes rather than just RNA. Everybody in the community of evolutionary biologists expected these DNA sequences to confirm the RNA tree. Fast forward twenty years: on 21st January 2009, New Scientist published a cover story entitled Darwin Was Wrong. The subtitle was Cutting down the Tree of Life. 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. All share Professor Shapiro’s general loyalty to Neo-Darwinism. 

The article begins with a review of the orthodoxy. “For a long time the holy grail was to build a tree of life,” says Eric Bapteste… “A few years ago it looked as though the grail was within reach.” In other words, exactly what Professor Shapiro says – the target of insight into the relationship of all living organisms, past and present was within sight. 

The article continues, “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,” says Bapteste… “The problem was that different genes told contradictory evolutionary stories.” [Emphasis added]. 

A study published in Science tried to construct a picture of animal relationships but concluded that “[D]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” [ 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).] 

Professor Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [read: contradictions in the relationships pictures] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.” [Carl Woese “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998).] 

Of course, none of this led to evolutionary biologists deserting the paradigm en masse. Instead, the lingo changed – now they speak not of the tree of life but of the web of life or the bush of life. Well, this is exactly the problem with paradigms – they’re much like fly paper: once stuck, it’s hard to leave. But some biologists are using more dramatic language. The New Scientist article continues, “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. 

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. 

At any rate, these results and many others tell you something about the murkiness that characterizes current ideas about the relationships between organisms. Professor Shapiro’s assurances that 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 should be paraphrased as follows: The more we learn and the more powerful our technologies become, the clearer it becomes that common descent is entirely unsupported by the genetic data.


One Response to “Professor Shapiro – Part 3”

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