Coyne quickly corrected that omission with a post the next day: The Neutral Theory: a genuinely important supplement to evolution’s “Modern Synthesis”.
Comfort made many mistakes but one of them was praising Philip Ball's book How Life Works. This prompted Ball to respond to my blog post by giving us a link to his own review on the Scientific American website: The Selfish Gene, revisited.
Richard Dawkins published The Selfish Gene in 1976 and in 2017 the Royal Society conducted a popular poll that voted it the most inspiring science book of all time.
I don't think that book is a good representation of modern evolutionary thinking and I've expressed that opinion many times on this blog [The selfish gene vs the lucky allele] ["The Selfish Gene" turns 40] [The "selfish gene" is not a good metaphor to describe evolution] [Die, selfish gene, die!].
The issues are complicated—here's how Dawkins described his book in the 1989 edition.
The selfish gene theory is Darwin's theory, expressed in a way that Darwin did not choose but whose aptness, I should like to think, he would instantly have recognized and delighted in. It is in fact a logical outgrowth of orthodox neo-Darwinism, but expressed as a novel image. Rather than focus on the individual organism, it takes a gene's-eye view of nature. It is a different way of seeing, not a different theory.
My objections are that the book is far too adaptationist and too "Darwinian." It fails to convey the complications of evolution to the general public, including the dominance of chance, accident, and contingency. It misrepresents some views of evolution, especially punctuated equilibria. It focuses too much on genes (alleles) as the unit of selection (evolution?) at the expense of individuals, groups, and species. (Species sorting may not be important but it deserved more than passing dismissal.) It focuses too much on the evolution of animals, especially animal behavior and that feeds into the biases of the general public who know very little about the vast majority of species outside of the animal kingdom.
In this sense, the proper practice of philosophy has to involve science—and by that I mean evidence— if the results are going to produce knowledge. There's lots to debate on this topic, including discussions about the meaning of "knowledge" [Is science the only way of knowing?].
But that's not what I want to talk about today. Today's topic is about the contribution that philosophers can make to science. I'll focus on philosophers of biology and on scientific topics that I'm knowledgeable about and I'll assume that most philosophers agree with Elisabeth Lloyd when she says, "As a philosopher of science, I have always been oriented towards addressing problems that scientists have, not so much problems that philosophers have. That is how to do good philosophy of science."1
Now, let me be clear about the issue. It is blindingly obvious that philosophers could use their deep understanding of logic and argumentation to make significant contributions to biology, especially in cases where scientists are misusing logic. The question is not whether philosophy is incapable of ever contributing to biology but whether it is actually fulfilling that potential.
One of my Facebook friends posted a link to an article on genetic drift on the Stanford Encyclopedia of Philosophy website [Genetic Drift]. The author is Roberta Millstein and the article is a recent update to an older version that I questioned ten years ago [A philosopher's view of random genetic drift]. I noted on Facebook that this was "Another example of philosophers who don’t understand modern science." By this I meant that the article seemed to ignore the abundant molecular evidence of drift.
That prompted a response from defenders of philosophy and Roberta Millstein joined in. Here's the essence of her defense of philosophy.
The Stanford Encyclopedia of Philosophy is, as the name suggests, about philosophy. Thus, the entry surveys views about drift in philosophy -- starting with the history of drift because some philosophical views about drift, such as my own, take that as their starting point -- which include debates about what drift is and other philosophical topics.
Perhaps if biologists had been crystal clear and consistent about what drift is, there would have been less to write about, but there is good evidence for the claim I make in the entry and elsewhere, that in fact scientists use the term in different ways, some of which I think are unproductive (e.g., describing drift in terms of outcome rather than as causal process).
I'll post a separate article about her views on genetic drift but here I want to address the point that biologists aren't always "crystal clear." It turns out that Millstein doesn't agree with my definition of evolution or my definition of allele so when I try to make the case that fixation of neutral alleles is a clear example of random genetic drift this is challenged by evidence that not all biologists accept my definitions so genetic drift isn't as solidly established as I might think.
Part of his argument relies on refuting adaptationism, or the idea that much of the history of life is due to adaptation (natural selection). He describes three different kinds of adaptationism in his book (p. 39) and I think it's useful to know them.
The mutation rate is approximately 100 new mutations per generation. Most of these will be neutral mutations that have no effect on the survival of the individual and almost all of them will be lost within a few generations. A small number of these neutral mutations will become fixed in the population and it's these fixed mutations that produce most of the changes in the genome of evolving populations. According to the neutral theory of population genetics, the number of fixed neutral mutations corresponds to the mutation rate. Thus, in every evolving population there will be 100 new fixed mutations per generation.
Ågren starts out by reminding us that Richard Dawkins' book The Selfish Gene was voted the most influential science book of all time in a 2017 Royal Society poll. He goes on to say,
Regardless of one's views on the poll results—or the book's argument—the far reaching sway of The Selfish Gene means that anyone interested in the history and future of evolutionary theory has no choice but to grapple with its ideas. Chief among these is the so-called gene's-eye view of evolution. This is the approach to biology originally introduced by George Williams in Adaptation and Natural Selection and elaborated and popularized by Dawkins, that it is the genes, and not organisms as Darwin originally envisaged, that deserve the status as the unit of selection in evolution. Emerging in the decades succeeding the Modern Synthesis, the gene's-eye view of evolution has become an emblem of orthodoxy in biology.
It's interesting that the blurbs for the two version also differ ...
Natural selection of random genetic mutation isn't the only way to adapt, argues evolutionary biologist Kevin Lala.
(print version)
Natural selection isn't just something that happens to organisms, their activities also play a role, giving some species – including humans – a supercharged ability to evolve. (online version)
Kevin Lala is a proponent of the "Extended Evolutionary Synthesis" (EES). His particular schtick is niche construction meaning that evolution is promoted by organisms that help create their own environment. This behaviorial characteristic of animals is supposed to call into question the fundamentals of modern evolutionary theory based on population genetics.
Recall that evolution is defined as a change in the frequency of alleles in a population and the main mechanisms of change are natural selection and random genetic drift. Variation (creation of alleles) is caused by mutation.
Genomics is a powerful tool that allows you to collect massive amounts of data that can point the way to new understanding. But it can also be abused when the results are overinterpreted. We saw an extraordinary example of this in 2012 when ENCODE made unsubstantiated claims that were quickly challenged.
I'm reminded of the caution from Sydney Brenner who warned us about genomics (Brenner, 2000) and the warning in Dan Graur's harsh critique of the 2012 ENCODE claims (Graur et al., 2013) where they said ...
The Editor-in-Chief of Science, [Bruce Alberts,] has recently expressed concern about the future of "small science," given that ENCODE-style Big Science grabs the headlines that decision makers so dearly love. Actually the main function of Big Science is to generate massive amounts of easily accessible data. The road from data to wisdom is quite long and convoluted. Insight, understanding, and scientific progress are generally achieved by "small science." ...
The neutral theory was first proposed by Mootoo Kimura in 1968 (Kimura, 1968). The following year, a similar idea was published in a seminal paper by Jack King and Thomas Jukes (King and Jukes, 1969). King and Jukes emphasized the importance of non-Darwinian mechanisms of evolution in order to explain protein based phylogenetic trees and the molecular clock. They made it clear that neutral alleles fixed by random genetic drift play an important part in evolution.
There appears to be considerable latitude at the molecular level for random genetic changes that have no effect upon the fitness of the organism. Selectively neutral mutations, if they occur, become passively fixed as evolutionary changes through the action of random genetic drift.
The idea of selectively neutral changes at the molecular level has not been readily accepted by many classical evolutionists, perhaps because of the pervasiveness of Darwinian thought (King and Jukes, 1969).
I'm discussing a recent paper published by Nils Walter (Walter, 2024). He is arguing against junk DNA by claiming that the human genome contains large numbers of non-coding genes.
This is the fifth post in the series. The first one outlines the issues that led to the current paper and the second one describes Walter's view of a paradigm shift/shaft. The third post describes the differing views on how to define key terms such as 'gene' and 'function.' In the fourth post I discuss his claim that differing opinions on junk DNA are mainly due to philosophical disagreements.
Most of the genes in eukaryotes contain introns that are removed by splicing during processing of the primary transcript. In some cases the gene produces two different functional RNAs due to differential splicing of the introns. If the product is mRNA then two different versions of the protein can be made as shown in the figure from my book What's in Your Genome? This mechanism is known as alternative splicing.
True alternative splicing is rare—less than 5% of all genes are alternatively spliced.1 However, when you analyze all of the transcripts in a tissue you will invariably detect many transcripts from junk DNA and many low abundance splice variants. Those transcripts and splice variants are due to transcription errors and splicing errors. Splicing errors arise from the presence of weak splice sites that are occasionally recognized by the normal spliceosome or by the splice factors responsible for true alternative splicing.
This is a video of a debate that took place in Kraków, Poland on June 2, 2023. The topic was "Intelligent design in nature—illusion or reality?" (Spoiler alert! - the answer is "illusion.") The participants were Michael Behe and Richard v. Sternberg for the creationists and Michael Ruse and Malgorzata Moczydlowska-Vidal for the science/philosophy side. The video is almost three hours long and I don't recommend watching the whole thing.
Ruse, as usual, is incoherant and more focused on religion and telling Christians how they should behave. The Polish paleontologist didn't do a very good job of addressing the claims of the creationists.1 Michael Behe gave his standard pitch about irreducible complexity and the bacterial flagellum.
The interesting part was Sternberg's defense of intelligent design. I hadn't seen him before although I've been familiar with his writings over the past twenty years. His opening presentation begins at 17:50 and it's worth watching to see how important the junk DNA debate is to the ID crowd.
Sternberg begins by noting that he was skeptical of the arguments put forward by Richard Dawkins in "The Selfish Gene" where Dawkins says that 98% of our DNA is noncoding junk. (Dawkins never said any such thing!) Sternberg says that when he started looking for function in this part of the genome he found that it was replete with function. Then he brings up the ENCODE results and claims that they challenged the concept of a gene (not true). Sternberg says that the new definition of a gene is that it is polyfunctional and "constantly changing in real time." He says,
... how can you have a theory based on an entity that you cannot define and how can you discuss the evolution of something that is kind of this amorphous notion ...
Sternberg seems to think that redefining the gene shows that evolutionary biology is out of touch with reality. He claims that the discovery of the epigenome is futher evidence that there are multiple layers of information that take us far beyond the theory of neo-Darwinism that was crafted in the nineteen teens and the 1920s.
Sternberg reflects the views of many Intelligent Design Creationists who tout the "debunking" of junk DNA as one of their greatest intellectual achievements because they predicted all along that there couldn't be large amounts of junk DNA in our genome because that's incompatible with intelligent design. What's different in the case of Richard Sternberg is that the discovery of function in most of our genome is what led him to the position that design is the best explanation.
I find it strange that Intelligent Design Creationists are relying so heavily on the so-called debunking of junk DNA, especially since in Sternberg's case he is well aware of the fact that some prominent scientists have criticized ENCODE. It's a risky strategy to put so much emphasis on a result that may turn out to be wrong. If our genome is mostly junk DNA (it is!) then the major part of their argument for design falls apart.
From reading the ID literature, it seems that they are supremely confident that most of our genome will turn out to be full of function. It will be interesting to see how they respond when the scientific community concludes that 90% of our genome is junk. From my perspective, they are digging themselves into a deep hole that will be very difficult to climb out of. Maybe it's time to stop digging?
Sternberg made one quip that's worth highlighting. At about 1:46:20 he talks about a saying that he learned in the air force; you don't receive flak unless you're over a significant target. That's cute. He uses it to explain why intelligent design is coming under such heavy attack. He is, of course, correct. When you drop bombs on people you can expect them to get upset. When you attack some of the most important concepts in science you can expect some pushback. That doesn't mean your bombing is justified. If it were justified then scientists would embrace your criticisms instead of shooting them down.
Sternberg scores big at 2:51:11 when he asks, "Can there be Darwinian evolution ... or any evolution in general, without natural selection?" The correct answer is yes. Malgorzata Moczydlowska-Vidal says no and so does Michael Ruse. Ruse then goes on to explain why he dismisses random genetic drift. Sternberg then explains neutral evolution and Michael Lynch's drift-barrier hypothesis and why some biologists use them to explain some of the ID challenges. Sternberg (and Behe) appear to know more about evolution than their opponents.
1. She concentrated on presenting evidence for the history of life but both Behe and Sternberg accept common descent and the correct age of the Earth.
You know you're in for a treat when papers published in a (previously) reputable journal make frequent references to Dennis Noble and James Shapiro.
The purpose of this post is to demonstrate that you shouldn't let creationist amateurs publish anti-evolution rants in scientific journals.
I want to discuss two papers that were recently published in the journal Progress in Biophysics and Molecular Biology. This used to be a very reputable journal but its reputation suffered a big blow in 2018 when it published a paper on panspermia. The current editor-in-chief at the time, Denis Noble, defended that article on the grounds that the origin of life is an unsolved problem and all points of view deserve to be covered in a scientific journal. Denis Noble is still on the editorial board along with Tom L. Blundell and Delphine Dean (see editorial board) and they now have to answer for publishing two creationist papers by Olen R. Brown and David A. Hullender.
Serious criticisms of evolutionary theory have been floating around for half a century. The main focus is over the Modern Synthesis and whether it's the best explanation of evolution. That requires a throrough understanding of what the Modern Synthesis actually means and how it's understood by most evolutionary biologists.
One view is that the Modern Synthesis is almost exclusively about natural selection. If that's true, then Stephen Jay Gould makes a good case when he argues that the Modern Synthesis is effectively dead—it was killed off by the neutral theory and the recognition that random genetic drift is a major player in evolution [Is the Modern Synthesis effectively dead?].
The Wikipedia article on evolution [Evolution] is a "Featured article," which means two things: (1) it is one of the best articles Wikipedia has to offer, and (2) it was voted a featured article by Wikipedia editors and that means they will resist any changes.
You will be shocked to learn that the article isn't perfect. It could use some serious updating and revision but my first attempt was reverted by an editor named Efbrazil who has vowed to revert any edits I make unless I can get his approval. So I thought I'd give it a try and you can see the result on the Talk:Evolution pages. My intitial objective is to edit the introductory paragraphs in the lead to eliminate the reference to expression of genes and to introduce the term "allele," which is covered in the main part of the article. Here's the current opening paragraphs of the lead,
In biology, evolution is the change in heritable characteristics of biological populations over successive generations.[1][2] These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Genetic variation tends to exist within any given population as a result of genetic mutation and recombination.[3] Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more or less common within a population over successive generations.[4] It is this process of evolution that has given rise to biodiversity at every level of biological organisation.[5][6]
The theory of evolution by natural selection was conceived independently by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin's book On the Origin of Species.[7] Evolution by natural selection is established by observable facts about living organisms: (1) more offspring are often produced than can possibly survive; (2) traits vary among individuals with respect to their morphology, physiology, and behaviour; (3) different traits confer different rates of survival and reproduction (differential fitness); and (4) traits can be passed from generation to generation (heritability of fitness).[8] In successive generations, members of a population are therefore more likely to be replaced by the offspring of parents with favourable characteristics for that environment. In the early 20th century, other competing ideas of evolution were refuted as the modern synthesis concluded Darwinian evolution acts on Mendelian genetic variation.[9]
I'm also thinking that we should modify the following sentences that don't seem to be appropriate in a "Featured article,"
According to the now largely abandoned neutral theory of molecular evolution most evolutionary changes are the result of the fixation of neutral mutations by genetic drift.[101] In this model, most genetic changes in a population are thus the result of constant mutation pressure and genetic drift.[102] This form of the neutral theory is now largely abandoned since it does not seem to fit the genetic variation seen in nature.[103][104]
Editor Efbrazil seems to be he only editor willing to discuss these problems and he is hard to convince. If anyone else is interested in improving this Wikipedia article, I invite you to participate in the discussion on the Talk pages.
Gert Korthof thinks that the current view of evolution is incomplete and he's looking for a better explanation. He just finished reading my book so he wrote a review on his blog.
Scientists say: 90% of your genome is junk. Have a nice day! Biochemist Laurence Moran defends junk DNA theory
The good news is that I've succeeded in making Gert Korthof think more seriously about junk DNA and random genetic drift. The bad news is that I seem to have given him the impression that natural selection is not an important part of evolution. Furthermore, he insists that "evolution needs both mutation and natural selection" because he doesn't like the idea that random genetic drift may be the most common mechanism of evolution. He thinks that statement only applies at the molecular level. But "evolution" doesn't just refer to adaptation at the level of organisms. It's just not true that all examples of evolution must involve natural selection.
I think I've failed to explain the null hypothesis correctly because Korthof writes,
It's clear this is a polemical book. It is a very forceful criticism of ENCODE and everyone who uncritically accepts and spreads their views including Nature and Science. I agree that this criticism is necessary. However, there is a downside. Moran writes that the ENCODE research goals of documenting all transcripts in the human genome was a waste of money. Only a relatively small group of transcripts have a proven biological function ("only 1000 lncRNAs out of 60,000 were conserved in mammals"; "the number with a proven function is less than 500 in humans"; "The correct null hypothesis is that these long noncoding RNAs are examples of noisy transcription", or junk RNA"). Furthermore, Moran also thinks it is a waste of time and money to identify the functions of the thousands of transcripts that have been found because he knows its all junk. I disagree. The null hypothesis is an hypothesis, not a fact. One cannot assume it is true. That would be the 'null dogma'.
That's a pretty serious misunderstanding of what I meant to say. I think it was a worthwhile effort to document the number of transcripts in various cell types and all the potential regulatory sequences. What I objected to was the assumption by ENCODE researchers that these transcripts and sites were functional simply because they exist. The null hypothesis is no function and scientists must provide evidence of function in order to refute the null hypothesis.
I think it would be a very good idea to stop further genomic surveys and start identifying which transcripts and putative regulatory elements are actually functional. I'd love to know the answer to that very important question. However, I recognize that it will be expensive and time consuming to investigate every transcript and every putative regulatory element. I don't think any lab is going to assign random transcripts and random transcription factor binding sites to graduate students and postdocs because I suspect that most of those sequences aren't going to have a function. If I were giving out grant money I give it to some other lab. In that sense, I believe that it would be a waste of time and money to search for the function of tens of thousands of transcripts and over one million transcription factor binding sites.
That not dogmatic. It's common sense. Most of those transcripts and binding sites are not conserved and not under purifying election. That's pretty good evidence that they aren't functional, especially if you believe in the importance of natural selection.
There's lot more to his review including some interesting appendices. I recommend that you read it carefully to see a different perspective than the one I adocate in my book.
The initial measurement of the difference between the human and chimp genomes was based on aligning 2.4 billion base pairs in the two genomes. This gave a difference of 1.23% by counting base pair substitutions and small deletions and insertions (indels). However, if you look at larger indels, including genes, you can come up with bigger values because you can count the total number of base pairs in each indel; for example, a deletion of 1,000 bp will be equivalent to 1,000 SNPs.
Here are a few questions for ChatGPT and its answers. The AI program takes the most common information on the web and spews it back at you. It cannot tell which information is correct or which information is more accurate.
It's easy to recognize that these answers were written by something that's not very good at critical thinking. I agree with other professors that they mimic typical undergraduate answers but I disagree that these answers would get them a passing grade.
ChatGPT shares one very important feature that's common in undergraduate answers to essay questions: it gives you lots of unecessary information that's not directly relevant to the question.
It's important to note that (lol) these ChatGPT answers share another important feature with many of the answers on my exams: they look very much like BS!
Some evolutionary biologists think—incorrectly, in my opinion—that molecular biology has made no contributions to our understanding of evolution.
PNAS published a series of articles on Gregor Mendel and one of them caught my eye. Here's what Nicholas Barton wrote in his article The "New Synthesis".
During the 1960s and 1970s, there were further conceptual developments—largely independent of the birth of molecular biology during the previous two decades (15). First, there was an understanding that adaptations cannot be explained simply as being “for the good of the species” (16, 17). One must explain how the genetic system (including sexual reproduction, recombination, and a fair meiosis, with each copy of a gene propagating with the same probability) is maintained through selection on individual genes, and remains stable despite mutations that would disrupt the system (17, 19, 20). Second, and related to this, there was an increased awareness of genetic conflicts that arise through sexual reproduction; selfish elements may spread through biased inheritance, even if they reduce individual fitness (19, 21, 22). In the decade following the discovery that DNA carries genetic information, all the fundamental principles of molecular biology were established: the flow of information from sequences of DNA through RNA to protein, the regulation of genes by binding to specific sequences in promoters, and the importance of allostery in allowing arbitrary regulatory networks (23, 24). Yet, the extraordinary achievements of molecular biology had little effect on the conceptual development of evolutionary biology. Conversely, although evolutionary arguments were crucial in the founding of molecular biology, they have had rather little influence in the half-century since (e.g., ref. 25). Of course, molecular biology has revealed an astonishing range of adaptations that demand explanation—for example, the diversity of biochemical pathways, that allow exploitation of almost any conceivable resource, or the efficiency of molecular machines such as the ribosome, which translates the genetic code. Technical advances have brought an accelerating flood of data, most recently, giving us complete genome sequences and expression patterns from any species. Yet, arguably, no fundamentally new principles have been established in molecular biology, and, in evolutionary biology, despite sophisticated theoretical advances and abundant data, we still grapple with the same questions as a century or more ago.
This does not seem fair to me. I think that neutral theory, nearly neutral theory, and the importance of random genetic drift relied heavily on work done by molecular biologists. Similarly, the development of dating techniques using DNA and protein sequences is largely the work of molecular biologists. It wasn't the adaptationists or the paleontologists who discovered that humans and chimpanzees shared a common ancestor 5-7 million years ago and it wasn't either of those groups who discovered the origin of mitochondria.
And some of us are grappling with the idea that most of our genome is junk DNA, a question that never would have occurred to evolutionary biologists from a century ago.
Barton knows all about modern population genetics and the importance of neutral theory because later on he says,
If we consider a single allele, then we can see it as “effectively neutral” if its effect on fitness is less than ∼1/2Ne. This idea was used by Ohta (54) in a modification of the neutral theory, to suggest why larger populations might be less diverse than expected (because a smaller fraction of mutations would be effectively neutral), and why rates of substitution might be constant per year rather than per generation (because species with shorter generation times might tend to have large populations, and have a smaller fraction of effectively neutral mutations that contribute to long-term evolution). Lynch (21) has applied this concept to argue that molecular adaptations that are under weak selection cannot be established or maintained in (relatively) smaller populations, imposing a “drift barrier” to adaptation. Along the same lines, Kondrashov (55) has argued that deleterious mutations with Nes ≈ 1 will accumulate, steadily degrading the population. Both ideas seem problematic if we view adaptation as due to optimization of polygenic traits: Organisms can be well adapted even if drift dominates selection on individual alleles, and, under a model of stabilizing selection on very many traits, any change that degrades fitness can be compensated.
Barton may think that the drift-barrier hypothesis is "problematic" but it certainly seems like a significant advance that owes something to molecular biology.
What do you think? Do you agree with Barton that, "... the extraordinary achievements of molecular biology had little effect on the conceptual development of evolutionary biology."
