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Monday, October 17, 2022

University press releases are a major source of science misinformation

Here's an example of a press release that distorts science by promoting incorrect information that is not found in the actual publication.

The problems with press releases are well-known but nobody is doing anything about it. I really like the discussion in Stuart Ritchie's recent (2020) book where he begins with the famous "arsenic affair" in 2010. Sandwalk readers will recall that this started with a press conference by NASA announcing that arsenic replaces phosphorus in the DNA of some bacteria. The announcement was treated with contempt by the blogosphere and eventually the claim was discproved by Rosie Redfield who showed that the experiment was flawed [The Arsenic Affair: No Arsenic in DNA!].

This was a case where the science was wrong and NASA should have known before it called a press conference. Ritchie goes on to document many cases where press releases have distorted the science in the actual publication. He doesn't mention the most egregious example, the ENCODE publicity campaign that successfully convinced most scientists that junk DNA was dead [The 10th anniversary of the ENCODE publicity campaign fiasco].

I like what he says about "churnalism" ...

In an age of 'churnalism', where time-pressed journalists often simply repeat the content of press releases in their articles (science news reports are often worded vitrually identically to a press release), scientists have a great deal of power—and a great deal of responsibility. The constraints of peer review, lax as they might be, aren't present at all when engaging with the media, and scientists' biases about the importance of their results can emerge unchecked. Frustratingly, once the hype bubble has been inflated by a press release, it's difficult to burst.

Press releases of all sorts are failing us but university press releases are the most disappointing because we expect universities to be credible sources of information. It's obvious that scientists have to accept the blame for deliberately distorting their findings but surely the information offices at universities are also at fault? I once suggested that every press release has to include a statement, signed by the scientists, saying that the press release accurately reports the results and conclusions that are in the published article and does not contain any additional information or speculation that has not passed peer review.

Let's look at a recent example where the scientists would not have been able to truthfully sign such a statement.

A group of scientists based largely at The University of Sheffield in Sheffield (UK) recently published a paper in Nature on DNA damage in the human genome. They noted that such damage occurs preferentially at promoters and enhancers and is associated with demethylation and transcription activation. They presented evidence that the genome can be partially protected by a protein called "NuMA." I'll show you the abstract below but for now that's all you need to know.

The University of Sheffield decided to promote itself by issuing a press release: Breaks in ‘junk’ DNA give scientists new insight into neurological disorders. This title is a bit of a surprise since the paper only talks about breaks in enhancers and promoters and the word "junk" doesn't appear anywhere in the published report in Nature.

The first paragraph of the press release isn' very helpful.

‘Junk’ DNA could unlock new treatments for neurological disorders as scientists discover how its breaks and repairs affect our protection against neurological disease.

What could this mean? Surely they don't mean to imply that enhancers and promoters are "junk DNA"? That would be really, really, stupid. The rest of the press release should explain what they mean.

The groundbreaking research from the University of Sheffield’s Neuroscience Institute and Healthy Lifespan Institute gives important new insights into so-called junk DNA—or DNA previously thought to be non-essential to the coding of our genome—and how it impacts on neurological disorders such as Motor Neurone Disease (MND) and Alzheimer’s.

Until now, the body’s repair of junk DNA, which can make up 98 per cent of DNA, has been largely overlooked by scientists, but the new study published in Nature found it is much more vulnerable to breaks from oxidative genomic damage than previously thought. This has vital implications on the development of neurological disorders.

Oops! Apparently, they really are that stupid. The scientists who did this work seem to think that 98% of our genome is junk and that includes all the regulatory sequences. It seems like they are completely unaware of decades of work on discovering the function of these regulatory sequences. According The University of Sheffield, these regulatory sequences have been "largely overlooked by scientists." That will come as a big surprise to many of my colleagues who worked on gene regulation in the 1980s and in all the decades since then. It will probably also be a surprise to biochemistry and molecular biology undergraduates at Sheffield—at least I hope it will be a surprise.

Professor Sherif El-Khamisy, Chair in Molecular Medicine at the University of Sheffield, Co-founder and Deputy Director of the Healthy Lifespan Institute, said: “Until now the repair of what people thought is junk DNA has been mostly overlooked, but our study has shown it may have vital implications on the onset and progression of neurological disease."

I wonder if Professor Sherif El-Khamisy can name a single credible scientist who thinks that regulatory sequences are junk DNA?

There's no excuse for propagating this kind of misinformation about junk DNA. It's completely unnecessary and serves only to discredit the university and its scientists.

Ray, S., Abugable, A.A., Parker, J., Liversidge, K., Palminha, N.M., Liao, C., Acosta-Martin, A.E., Souza, C.D.S., Jurga, M., Sudbery, I. and El-Khamisy, S.F. (2022) A mechanism for oxidative damage repair at gene regulatory elements. Nature, 609:1038-1047. doi:[doi: 10.1038/s41586-022-05217-8]

Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate–early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.

Thursday, October 13, 2022


(This is a copy of an essay that I published in 2006. I made some minor revisions to remove outdated context.)

Overheard at breakfast on the final day of a recent scientific meeting: "Do you believe in macroevolution?" Came the rely: "Well, it depends on how you define it."
                                                                         Roger Lewin (1980)

There is no difference between micro- and macroevolution except that genes between species usually diverge, while genes within species usually combine. The same processes that cause within-species evolution are responsible for above-species evolution.
                                                                         John Wilkins

The minimalist definition of evolution is a change in the hereditary characteristics of a population over the course of many generations. This is a definition that helps us distinguish between changes that are not evolution and changes that meet the minimum criteria. The definition comes from the field of population genetics developed in the early part of the last century. The modern theory of evolution owes much to population genetics and our understanding of how genes work. But is that all there is to evolution?

The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the positions of some of the people at the meeting, the answer can be given as a clear, No.
               Roger Lewin (1980)

No. There's also common descent—the idea that all life has evolved from primitive species over billions of years. Common descent is about the history of life. In this essay I'll describe the main features of how life evolved but keep in mind that this history is a unique event that is accidental, contingent, quirky, and unpredictable. I'll try and point out the most important controversies about common descent.

The complete modern theory of evolution encompasses much more than changes in the genetics of a population. It includes ideas about the causes of speciation, long-term trends, and mass extinctions. This is the domain of macroevolution—loosely defined as evolution above the species level. The kind of evolution that focuses on genes in a population is usually called microevolution.

As a biochemist and a molecular biologist, I tend to view evolution from a molecular perspective. My main interest is molecular evolution and the analysis of sequences of proteins and nucleic acids. One of the goals in writing this essay is to explain this aspect of evolution to the best of my limited ability. However, another important goal is to show how molecular evolution integrates into the bigger picture of evolution as described by all other evolutionary biologists, including paleontologists. When dealing with macroevolution this is very much a learning experience for me since I'm not an expert. Please bear with me while we explore these ideas.

It's difficult to define macroevolution because it's a field of study and not a process. Mark Ridley has one of the best definitions I've seen ...

Macroevolution means evolution on the grand scale, and it is mainly studied in the fossil record. It is contrasted with microevolution, the study of evolution over short time periods., such as that of a human lifetime or less. Microevolution therefore refers to changes in gene frequency within a population .... Macroevolutionary events are more likely to take millions, probably tens of millions of years. Macroevolution refers to things like the trends in horse evolution described by Simpson, and occurring over tens of millions of years, or the origin of major groups, or mass extinctions, or the Cambrian explosion described by Conway Morris. Speciation is the traditional dividing line between micro- and macroevolution.
                                                                         Mark Ridley (1997) p. 227

When we talk about macroevolution we're talking about studies of the history of life on Earth. This takes in all the events that affect the actual historical lineages leading up to today's species. Jeffrey S. Levinton makes this point in his description of the field of macroevolution and it's worth quoting what he says in his book Genetics, Paleontology, and Macroevolution.

Macroevolution must be a field that embraces the ecological theater, including the range of time scales of the ecologist, to the sweeping historical changes available only to paleontological study. It must include the peculiarities of history, which must have had singular effects on the directions that the composition of the world's biota took (e.g., the splitting of continents, the establishment of land and oceanic isthmuses). It must take the entire network of phylogenetic relationships and impose a framework of genetic relationships and appearances of character changes. Then the nature of evolutionary directions and the qualitative transformation of ancestor to descendant over major taxonomic distances must be explained.
                                                                     Jeffrey S. Levinton (2001) p.6

Levinton then goes on to draw a parallel between microevolution and macroevolution on the one hand, and physics and astronomy on the other. He points out that the structure and history of the known universe has to be consistent with modern physics, but that's not sufficient. He gives the big bang as an example of a cosmological hypothesis that doesn't derive directly from fundamental physics. I think this analogy is insightful. Astronomers study the life and death of stars and the interactions of galaxies. Some of them are interested in the formation of planetary systems, especially the unique origin of our own solar system. Explanations of these "macro" phenomena depend on the correctness of the underlying "micro" physics phenomena (e.g., gravity, relativity) but there's more to the field of astronomy than that.

Levinton continues ....

Does the evolutionary biologist differ very much from this scheme of inference? A set of organisms exists today in a partially measurable state of spatial, morphological, and chemical relationships. We have a set of physical and biological laws that might be used to construct predictions about the outcome of the evolutionary process. But, as we all know, we are not very successful, except at solving problems at small scales. We have plausible explanations for the reason why moths living in industrialized areas are rich in dark pigment, but we don't know whether or why life arose more than once or why some groups became extinct (e.g., the dinosaurs) whereas others managed to survive (e.g., horseshoe crabs). Either our laws are inadequate and we have not described the available evidence properly or no such laws can be devised to predict uniquely what should have happened in the history of life. For better or worse, macroevolutionary biology is as much historical as is astronomy, perhaps with looser laws and more diverse objectives....

Indeed, the most profound problem in the study of evolution is to understand how poorly repeatable historical events (e.g., the trapping of an endemic radiation in a lake that dries up) can be distinguished from lawlike repeatable processes. A law that states 'an endemic radiation will become extinct if its structural habitat disappears' has no force because it maps to the singularity of a historical event.
                                                                 Jeffrey S. Levinton (2001) p.6-7

In conclusion, then, macroevolutionary processes are underlain by microevolutionary phenomena and are compatible with microevolutionary theories, but macroevolutionary studies require the formulation of autonomous hypotheses and models (which must be tested using macroevolutionary evidence). In this (epistemologically) very important sense, macroevolution is decoupled from microevolution: macroevolution is an autonomous field of evolutionary study.
     Francisco J. Ayala (1983)

I think it's important to appreciate what macroevolutionary biologists are saying. Most of these scientists are paleontologists and they think of their area of study as an interdisciplinary field that combines geology and biology. According to them, there's an important difference between evolutionary theory and the real history of life. The actual history has to be consistent with modern evolutionary theory (it is) but the unique sequence of historical events doesn't follow directly from application of evolutionary theory. Biological mechanisms such as natural selection and random genetic drift are part of a much larger picture that includes moving continents, asteroid impacts, ice ages, contingency, etc. The field of macroevolution addresses these big picture issues.

Clearly, there are some evolutionary biologists who are only interested in macroevolution. They don't care about microevolution. This is perfectly understandable since they are usually looking at events that take place on a scale of millions of years. They want to understand why some species survive while others perish and why there are some long-term trends in the history of life. (Examples of such trends are the loss of toes during the evolution of horses, the development of elaborate flowers during the evolution of vascular plants, and the tendency of diverse species, such as the marsupial Tasmanian wolf and the common placental wolf, to converge on a similar body plan.)

Nobody denies that macroevolutionary processes involve the fundamental mechanisms of natural selection and random genetic drift, but these microevolutionary processes are not sufficient, by themselves, to explain the history of life. That's why, in the domain of macroevolution, we encounter theories about species sorting and tracking, species selection, and punctuated equilibria.

Micro- and macroevolution are thus different levels of analysis of the same phenomenon: evolution. Macroevolution cannot solely be reduced to microevolution because it encompasses so many other phenomena: adaptive radiation, for example, cannot be reduced only to natural selection, though natural selection helps bring it about.
     Eugenie C. Scott (2004)

As I mentioned earlier, most of macroevolutionary theory is intimately connected with the observed fossil record and, in this sense, it is much more historical than population genetics and evolution within a species. Macroevolution, as a field of study, is the turf of paleontologists and much of the debate about a higher level of evolution (above species and populations) is motivated by the desire of paleontologists to be accepted at the high table of evolutionary theory. It's worth recalling that during the last part of the twentieth century evolutionary theorizing was dominated by population geneticists. Their perspective was described by John Maynard Smith, "... the attitude of population geneticists to any paleontologist rash enough to offer a contribution to evolutionary theory has been to tell him to go away and find another fossil, and not to bother the grownups." (Maynard Smith, 1984)

The distinction between microevolution and macroevolution is often exaggerated, especially by the anti-science crowd. Creationists have gleefully exploited the distinction in order to legitimate their position in the light of clear and obvious examples of evolution that they can't ignore. They claim they can accept microevolution, but they reject macroevolution.

In the real world—the one inhabited by rational human beings—the difference between macroevolution and microevolution is basically a difference in emphasis and level. Some evolutionary biologists are interested in species, trends, and the big picture of evolution, while others are more interested in the mechanics of the underlying mechanisms.

Speciation is critical to conserving the results of both natural selection and genetic drift. Speciation is obviously central to the fate of genetic variation, and a major shaper of patterns of evolutionary change through evolutionary time. It is as if Darwinians—neo- and ulra- most certainly included—care only for the process generating change, and not about its ultimate fate in geological time.
     Niles Eldredge (1995)

The Creationists would have us believe there is some magical barrier separating selection and drift within a species from the evolution of new species and new characteristics. Not only is this imagined barrier invisible to most scientists but, in addition, there is abundant evidence that no such barrier exists. We have numerous examples that show how diverse species are connected by a long series of genetic changes. This is why many scientists claim that macroevoluton is just lots of microevolution over a long period of time.

But wait a minute. I just said that many scientists think of macroevolution as simply a scaled-up version of microevolution, but a few paragraphs ago I said there's more to the theory of evolution than just changes in the frequency of alleles within a population. Don't these statements conflict? Yes, they do ... and therein lies a problem.

When the principle tenets of the Modern Synthesis were being worked out in the 1940's, one of the fundamental conclusions was that macroevolution could be explained by changes in the frequency of alleles within a population due, mostly, to natural selection. This gave rise to the commonly accepted notion that macroevolution is just a lot of microevolution. Let's refer to this as the sufficiency of microevolution argument.

At the time of the synthesis, there were several other explanations that attempted to decouple macroevolution from microevolution. One of these was saltation, or the idea that macroevolution was driven by large-scale mutations (macromutations) leading to the formation of new species. This is the famous "hopeful monster" theory of Goldschmidt. Another decoupling hypothesis was called orthogenesis, or the idea that there is some intrinsic driving force that directs evolution along certain pathways. Some macroevolutionary trends, such as the increase in the size of horses, were thought to be the result of this intrinsic force.

Both of these ideas about macroevolutionary change (saltation and orthogensis) had support from a number of evolutionary biologists. Both were strongly opposed by the group of scientists that produced the Modern Synthesis. One of the key players was the paleontologist George Gaylord Simpson whose books Tempo and Mode in Evolution (1944) and The Major Features of Evolution (1953) attempted to combine paleontology and population genetics. "Tempo" is often praised by evolutionary biologists and many of our classic examples of evolution, such as the bushiness of the horse tree, come from that book. It's influence on paleontologists was profound because it upset the traditional view that macroevolution and the newfangled genetics had nothing in common.

Just as mutation and drift introduce a strong random component into the process of adaptation, mass extinctions introduce chance into the process of diversification. This is because mass extinctions are a sampling process analogous to genetic drift. Instead of sampling allele frequencies, mass extinctions samples species and lineages. ... The punchline? Chance plays a large role in the processes responsible for adaptation and diversity.
        Freeman and Herron (1998)

We see, in context, that the blurring of the distinction between macroevolution and microevolution was part of a counter-attack on the now discredited ideas of saltation and orthogenesis. As usual, when pressing the attack against objectionable ideas, there's a tendency to overrun the objective and inflict collateral damage. In this case, the attack on orthogenesis and the old version of saltation was justified since neither of these ideas offer viable alternatives to natural selection and drift as mechanisms of evolution. Unfortunately, Simpson's attack was so successful that a generation of scientists grew up thinking that macroevolution could be entirely explained by microevolutionary processes. That's why we still see this position being advocated today and that's why many biology textbooks promote the sufficiency of microevolution argument. Gould argues—successfully, in my opinion—that the sufficiency of microevolution became dogma during the hardening of the synthesis in the 1950-'s and 1960's. It was part of an emphasis on the individual as the only real unit of selection.

However, from the beginning of the Modern Synthesis there were other evolutionary biologists who wanted to decouple macroevolution and microevolution—not because they believed in the false doctrines of saltation and orthogenesis, but because they knew of higher level processes that went beyond microevolution. One of these was Ernst Mayr. In his essay "Does Microevolution Explain Macroevolution," Mayr says ...

Among all the claims made during the evolutionary synthesis, perhaps the one that found least acceptance was the assertion that all phenomena of macroevolution can be ‘reduced to,' that is, explained by, microevolutionary genetic processes. Not surprisingly, this claim was usually supported by geneticists but was widely rejected by the very biologists who dealt with macroevolution, the morphologists and paleontologists. Many of them insisted that there is more or less complete discontinuity between the processes at the two levels—that what happens at the species level is entirely different from what happens at the level of the higher categories. Now, 50 years later the controversy remains undecided.
                                                                         Ernst Mayr (1988) p.402

Mayr goes on to make several points about the difference between macroevolution and microevolution. In particular, he emphasizes that macroevolution is concerned with phenotypes and not genotypes, "In this respect, indeed, macroevolution as a field of study is completely decoupled from microevolution." (ibid p. 403). This statement reiterates an important point, namely that macroevolution is a "field of study" and, as such, its focus differs from that of other fields of study such as molecular evolution.

If you think of macroevolution as a field of study rather than a process, then it doesn't make much sense to say that macroevolution can be explained by the process of changing alleles within a population. This would be like saying the entire field of paleontology can be explained by microevolution. This is the point about the meaning of the term "macroevolution" that is so often missed by those who dismiss it as just a bunch of microevolution.

The orthodox believers in the hardened synthesis feel threatened by macroevolution since it implies a kind of evolution that goes beyond the natural selection of individuals within a population. The extreme version of this view is called adaptationism and the believers are called Ultra-Darwinians by their critics. This isn't the place to debate adaptationism: for now, let's just assume that the sufficiency of microevolution argument is related to the pluralist-adaptationist controversy and see how our concept of macroevolution as a field of study relates to the issue. Niles Eldredge describes it like this ...

The very term macroevolution is enough to make an ultra-Darwinian snarl. Macroevolution is counterpoised with microevolution—generation by generation selection- mediated change in gene frequencies within populations. The debate is over the question, Are conventional Darwinian microevolutionary processes sufficient to explain the entire history of life? To ultra-Darwinians, the very term macroevolution suggests that the answer is automatically no. To them, macroevolution implies the action of processes—even genetic processes—that are as yet unknown but must be imagined to yield a satisfactory explanation of the history of life.

But macroevolution need not carry such heavy conceptual baggage. In its most basic usage, it simply means evolution on a large-scale. In particular, to some biologists, it suggests the origin of major groups - such as the origin and radiation of mammals, or the derivation of whales and bats from terrestrial mammalian ancestors. Such sorts of events may or may not demand additional theory for their explanation. Traditional Darwinian explanation, of course, insists not.
                                                              Niles Eldredge (1995) p. 126-127

Eldredge sees macroevolution as a field of study that's mostly concerned with evolution on a large scale. Since he's a paleontologist, it's likely that, for him, macroevolution is the study of evolution based on the fossil record. Eldredge is quite comfortable with the idea that one of the underlying causes of evolution can be natural selection—this includes many changes seen over the course of millions of years. In other words, there is no conflict between microevolution and macroevolution in the sense that microevolution stops and is replaced by macroevolution above the level of species. But there is a conflict in the sense that Eldredge, and many other evolutionary biologists, do not buy the sufficiency of microevolution argument. They believe there are additional theories, and mechanisms, needed to explain macroevolution. Gould says it best ....

We do not advance some special theory for long times and large transitions, fundamentally opposed to the processes of microevolution. Rather, we maintain that nature is organized hierarchically and that no smooth continuum leads across levels. We may attain a unified theory of process, but the processes work differently at different levels and we cannot extrapolate from one level to encompass all events at the next. I believe, in fact, that ... speciation by splitting guarantees that macroevolution must be studied at its own level. ... [S]election among species—not an extrapolation of changes in gene frequencies within populations—may be the motor of macroevolutionary trends. If macroevolution is, as I believe, mainly a story of the differential success of certain kinds of species and, if most species change little in the phyletic mode during the course of their existence, then microevolutionary change within populations is not the stuff (by extrapolation) of major transformations.
                                                         Stephen Jay Gould (1980b) p. 170

Naturalists such as Ernst Mayr and paleontologists such as Gould and Eldredge have all argued convincingly that speciation is an important part of evolution. Since speciation is not a direct consequence of changes in the frequencies of alleles in a population, it follows that microevolution is not sufficient to explain all of evolution. Gould and Eldredge (and others) go even further to argue that there are processes such as species sorting that can only take place above the species level. This means there are evolutionary theories that only apply in the domain of macroevolution.

The idea that there's much more to evolution than genes and population genetics was a favorite theme of Stephen Jay Gould. He advocated a pluralist, hierarchical approach to evolution and his last book The Structure of Evolutionary Theory emphasized macroevolutionary theory—although he often avoided using this term. The Structure of Evolutionary Theory is a huge book that has become required reading for anyone interested in evolution. Remarkably, there's hardly anything in the book about population genetics, molecular evolution, and microevolution as popularly defined. What better way of illustrating that macroevolution must be taken seriously!

Macroevolutionary theory tries to identify patterns and trends that help us understand the big picture. In some cases, the macroevolution biologists have recognized generalities (theories & hypotheses) that only apply to higher level processes. Punctuated equilibria and species sorting are examples of such higher level phenomena. The possible repeatedness of mass extinctions might be another.

Remember that macroevolution should not be contrasted with microevolution because macroevolution deals with history. Microevolution and macroevolution are not competing explanations of the history of life any more than astronomy and physics compete for the correct explanation of the history of the known universe. Both types of explanation are required.

I think species sorting is the easiest higher level phenomena to describe. It illustrates a mechanism that is clearly distinct from changes in the frequencies of alleles within a population. In this sense, it will help explain why microevolution isn't a sufficient explanation for the evolution of life. Of course, one needs to emphasize that macroevolution must be consistent with microevolution.

I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
        Stephen Jay Gould (2002)

If we could track a single lineage through time, say from a single-cell protist to Homo sapiens, then we would see a long series of mutations and fixations as each ancestral population evolved. It might look as though the entire history could be accounted for by microevolutionary processes. This is an illusion because the track of the single lineage ignores all of the branching and all of the other species that lived and died along the way. That track would not explain why Neanderthals became extinct and Cro-Magnon survived. It would not explain why modern humans arose in Africa. It would not tell us why placental mammals became more successful than the dinosaurs. It would not explain why humans don't have wings and can't breathe underwater. It doesn't tell us whether replaying the tape of life will automatically lead to humans. All of those things are part of the domain of macroevolution and microevolution isn't sufficient to help us understand them.

Tuesday, October 11, 2022

On reasoning with creationists

I've been trying to reason with creationists for more than 30 years, beginning with debates on back in the early 1990s. Sometimes we make a little progress but most of the time it's very frustrating.

Over the years, we've encountered a few outstanding examples of creationists whose "reasoning" abilities defy explanation. One of he most famous is Otangelo Grasso - his ability to misunderstand and misconstrue science is legendary. He is one of only a small number of people who are banned from Sandwalk.

Here's an example of his unique unreasoning abiltiies.

Trying to educate a creationist (Otangelo Grasso)

I bring this up because he recently posted an artilce on the Uncommon Descent blog and you just have to read it if you want a good laugh. It shows you that 30 years of attempting to teach science to creationists isn't nearly long enough.

Otangelo Grasso on the difficulties of reasoning with atheists

Monday, October 03, 2022

Evolution by chance

Can natural selection occur by chance or accident? No, with qualifications. Can evolution occur by chance or accident? Yes, definitely.

While tidying up my office I came across an anthology of articles by Richard Dawkins. It included a 2009 review of Jerry Coyne's book Why Evolution Is True (2009) and one of Richard's comments caught my eye because it illustrates the difference between the Dawkins' view of evolution and the current mainstream view that was described by Jerry in his book.

I can illustrate this difference by first quoting from Jerry Coyne's book.

This brings up the most widespread misunderstanding about Darwinism: the idea that, in evolution, "everything happens by chance" (also stated as "everything happens by accident"). This common claim is flatly wrong. No evolutionist—and certainly not Darwin—ever argued that natural selection is based on chance ....

True, the raw materials for evolution—the variations between individuals—are indeed produced by chance mutations. These mutations occur willy-nilly, regardless of whether they are good or bad for the individual. But it is the filitering of that variation by natural selection that produces natural selection, and natural selection is manifestly not random. (p. 119)

It's extremely important to notice that Coyne is referring to NATURAL SELECTION (or Dawinism) in this passage. Natural selection is not random or accidental, according to Coyne. This passage is followed just a few pages later by a section titled "Evolution Without Selection."

Let's take a brief digression here, because it's important to appreciate that natural selection isn't the only process of evolutionary change. Most biologists define evolution as a change in the proportion of alleles (different forms of a gene) in the population.

[Coyne then describes an example of random genetic drift and continues ...] Both drift and selection produce the genetic change that we recognize as evolution. But there's an important difference. Drift is a random process, while selection is the antithesis of randomness. Genetic drift can change the frequencies of alleles regardless of how useful they are to their carrier. Selection, on the other hand, always gets rid of harmful alleles and raises the frequencies of beneficial ones. (pp. 122-123)

Now let's look at Richard Dawkins' review of Coyne's book as published in the Times Literary Supplement in 2009 and reprinted in Books Do Furnish a Life (2021). I picked out an interesting passage from that review in order to illustrate a point.

Coyne is right to identify the most widespread misunderstanding about Darwinism as 'the idea that, in evolution, 'everything happens by chance' ... This common claim is flatly wrong.' Not only is it flatly wrong, it is obviously wrong, transparently wrong, even to the meanest intelligence (a phrase that has me actively restraining myself). If evolution worked by chance, it obviously couldn't work at all. (p. 427)

That last sentence is jarring to many scientists, including me. I think that the Dawkins' statement is 'obviously wrong' and 'transparently wrong' because, as Coyne pointed out, evolution by random genetic drift can occur by chance. [Let's not quibble about the meanings of 'random' and 'chance." That's a red herring in this context.] Clearly, evolution can work by chance so why does Dawkins say it can't?

It's not because Dawkins is unaware of random genetic drift and Neutral Theory. The explanation (I think) is that Dawkins restricts his definition of evolution to evolution by natural selection. From his perspective, the fixation of alleles by random genetic drift doesn't count as real evolution because it doesn't produce adaptations. That's the view that he described in The Extended Phenotype back in 1982 and the view that he has implicitly supported over the past few decades [Richard Dawkins' View of Random Genetic Drift].

This is one of the reasons why we refer to Dawkins as an adaptationist and it's one of the reasons why so many of today's evolutionary biologists—especially those who study evolution at the molecular level—reject the Dawkins' view of evolution in favor of a more pluralistic approach.

Note: I wrote an earlier version of this post in 2009 [Dawkins on Chance] and I wrote a long essay on Evolution by Accident where I describe many other examples of evolution by chance.