Alternative splicing and evolution

The important issue is whether alternative splicing is ubiquitous or rare. What are the evolutionary implications?

I believe that almost all of the splice variants that are routinely detected in eukaryotic cells are the product of splicing errors. (I've summarized the data on splicing errors in the Wikipedia article on Intron.) Database annotators have rejected several hundred thousand of these variants so that the typical human gene now lists only a handful of possible splice variants and very few of these have been experimentally confirmed as genuine examples of alternative splicing.

There are excellent examples of biologically relevant alternative splicing but they are confined to a small number of genes (<5%) and in almost all cases there are only a small number of alternatives (usually two) [Alternative splicing: function vs noise].

Do we need a new theory of evolution?

The classic Modern Synthesis is effectively dead. It was replaced by a more modern version that includes Neutral Theory, Nearly-Neutral Theory, and the importance of random genetic drift. Proponents of the "Extended Evolutionary Synthesis" don't have anything significant to add to our current understanding of evolutionary theory.

The latest kerfuffle in evolution is over a recent article published in The Guardian by Stephen Buranyi, Do we need a new theory of evolution?. The subtitle of the article summarizes the issue ...

A new wave of scientists argues that mainstream evolutionary theory needs an urgent overhaul. Their opponents have dismissed them as misguided careerists – and the conflict may determine the future of biology.

I think Stephen Buranyi did a pretty good job of covering the controversy as long as you ignore the first four paragraphs of his article. He talked to all the right people¹ and he got to the gist of the fundamental problem; namely, the over-emphasis on natural selection as the only significant player in evolution. There's no question that this is a serious problem. Here's a quotation from his article.

Two different views of the history of molecular biology

How can different molecular biologists have such opposite views of the history of their field?

I'm posting links to two papers without comment. One of them is from my friend and colleague Alex Palazzo and the other is from James Shapiro who is not my friend or colleague. Both papers have been published in reputable peer-review journals.

Do scientists write books for the "casual reader"?

I just read a review in Science of Douglas Futuyma’s new book How Birds Evolve: What Science Reveals About Their Origin, Lives, and Diversity. [Contextualizing avian origins and evolution]. Many of you will be familiar with Futuyma because he’s the author of one of the best textbooks on evolution.

Right after reading the review, I signed on to Amazon intending to buy the book but when I saw the price ($95 Cdn) I had second thoughts. Much as I’d like to see how Futuyma handles a complex topic like bird evolution, I don’t think I want to spend that much money.

But there are parts of the review that I find intriguing enough to address because they relate to my concern about science writing. Here’s the first thing that caught my eye. The reviewer, Alan Feduccia, writes,

Although casual readers might find the text somewhat advanced and laborious, the chapters are composed in well-written conversational prose, with expositions on multifarious evolutionary phenomena that are infused with scientific explanations.

This highlights an issue that I’ve been writing about recently. "Casual readers" are not going to buy this book and I’m confident that Futuyma is not writing for casual readers. What’s the point of saying that such readers might find the book "advanced and laborious"? What I want to know is whether the actual intended audience would find the book laborious.

The reviewer goes on to describe some of things that are in the book.

Futuyma’s discussion begins with a section that explains Charles Darwin’s transformative ideas—from natural selection and fitness to brood parasitism to gene flow and genetic drift—and thematic chapters elaborate on the relationship between these ideas and bird lineages. The book describes complex evolutionary issues in understandable terms, ...

That sounds like the kind of science writing that I admire. We should aim for explaining complex issues in terms that are understandable to an audience that is prepared to buy the book. This may mean that the casual readers - who will never buy the book - are left out but that’s okay. It may mean that Futuyuma’s book is not going to win a Pulitzer Price for general nonfiction but that’s okay too since good science books are not high on the list of previous award winners.¹ I’m pretty sure that scientific accuracy isn’t a prominent criterion in selecting award winners (in any category).

The reviewer is somewhat critical of the science in the book and takes Futuyma to task for promoting “just-so” stories and for not fully explaining the speculative nature of some of his conclusions. The reviewer notes that “controversy, not consensus, is grist to the mill of good science” and that strikes me as insightful. The problem is that writing about controversy and attempting to explain both sides of an issue are very hard to do and often in conflict with the emphasis on style that is promoted by science writers and editors.

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1. Previous Pulitzer Prize winning books that might be counted as science books are: The Emperor of All Maladies by Siddhartha Mukherjee (2011); Guns, Germs and Steel: The Fates of Human Societies, by Jared Diamond (1998); The Beak Of The Finch: A Story Of Evolution In Our Time, by Jonathan Weiner (1995); The Ants, by Bert Holldobler and Edward O. Wilson (1990); and On Human Nature, by Edward O. Wilson (1979).

Is the Modern Synthesis effectively dead?

The Modern Synthesis is the version of evolutionary theory popularized by Julian Huxley and supported by the leading evolutionary biologists of the 1930s, 40s, and 50s.

The general idea was to merge Dawrin's view of natural selection with the relatively new field of population genetics. Evolution was now defined as a change in allele frequencies in a population and the emphasis was on natural selection as the most important mechanism although, in the original version by Huxley, the fixation of alleles by random genetic drift can occur in small populations. By the early 1960s the most popular vesion of the Modern Synthesis focused almost exclusively on natural selection—an emphasis that's referred to as the hardening of the synthesis. It was this excessively adaptationist view of evolution that led to Gould and Lewontin's paper on "The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme" (Gould and Lewontin, 1979).

More illusions/delusions of James Shapiro and Denis Noble

It was just a few weeks ago that I discussed short articles by Denis Noble and James Shapiro that were published in the journal Biosemiotics [The illusions of Denis Noble] [The illusions of James Shapiro].

Several readers questioned whether Biosemiotics is a real science journal and they were right: it's a kooky journal and that's why it publishes papers by kooks. However, we now have a new paper by Shapiro and Noble that's about to appear in a legitimate scientific journal; albeit, one that has seen better days. This would normally raise red flags concerning peer review but we're long past the time when we can count on peer review to weed out the kooks.

Here's the paper. I'm not going to discuss all the main points because they were covered in my previous posts. I'll just concentrate on the most ridiculous part in order to illustrate the (lack of) quality of this paper.¹

Shapiro, J. and Noble, D. (2021) What prevents mainstream evolutionists teaching the whole truth about how genomes evolve? Progress in Biophysics and Molecular Biology. [doi: 10.1016/j.pbiomolbio.2021.04.004]

The common belief that the neo-Darwinian Modern Synthesis (MS) was buttressed by the discoveries of molecular biology is incorrect. On the contrary those discoveries have undermined the MS. This article discusses the many processes revealed by molecular studies and genome sequencing that contribute to evolution but nonetheless lie beyond the strict confines of the MS formulated in the 1940s. The core assumptions of the MS that molecular studies have discredited include the idea that DNA is intrinsically a faithful self-replicator, the one-way transfer of heritable information from nucleic acids to other cell molecules, the myth of “selfish DNA,” and the existence of an impenetrable Weismann Barrier separating somatic and germ line cells. Processes fundamental to modern evolutionary theory include symbiogenesis, biosphere interactions between distant taxa (including viruses), horizontal DNA transfers, natural genetic engineering, organismal stress responses that activate intrinsic genome change operators, and macroevolution by genome restructuring (distinct from the gradual accumulation of local microevolutionary changes in the MS). These 21st Century concepts treat the evolving genome as a highly formatted and integrated Read-Write (RW) database rather than a Read-Only Memory (ROM) collection of independent gene units that change by random copying errors. Most of the discoverers of these macroevolutionary processes have been ignored in mainstream textbooks and popularizations of evolutionary biology, as we document in some detail. Ironically, we show that the active view of evolution that emerges from genomics and molecular biology is much closer to the 19th century ideas of both Darwin and Lamarck. The capacity of cells to activate evolutionary genome change under stress can account for some of the most negative clinical results in oncology, especially the sudden appearance of treatment-resistant and more aggressive tumors following therapies intended to eradicate all cancer cells. Knowing that extreme stress can be a trigger for punctuated macroevolutionary change suggests that less lethal therapies may result in longer survival times.

The section on "selfish DNA" is the one that seems to have the highest number of misleading and false statements per paragraph.

1.4. The end of “selfish” or “junk” DNA

A major shortcoming of the MS is that it was based on a “gene-centric” view, which assumed that the genome is basically a collection of “genes” that are the protein-coding units of heredity and heritable variation. As we saw in the quotation from Goldschmidt's 1940 book, this view failed to take the evolutionary importance of chromosome structure into account (Goldschmidt, 1940). It also blinded evolutionary biologists to the importance of McClintock's mid- 20th Century discovery of mobile “controlling elements” (McClintock, 1987). Both the ideas of genetic transposition and control of gene expression by these non-coding mobile elements did not fit within the narrow confines of the MS concepts of genome function and variation. A further empirical assault on the limited MS conceptual framework came in the late 1960s when Britten and Kohne discovered that a significant fraction of genomic DNA from complex eukaryotes consists of highly repetitive sequences rather than the unique coding sequences expected to make up the hereditary material (Britten and Kohne, 1968).

• The title is ridiculous since no respectable scientist ever equated selfish DNA with junk DNA [Selfish genes and transposons].

• The Modern Synthesis (MS) was not based on a "gene-centric" view.
• For the past 50 years, no respectable scientist, and no knowledgeable expert in molecular evolution, has restricted the definition of "gene" to just protein-coding genes.
• For the past 50 years, no expert in molecular evolution has ever thought that the genome is just a collection of protein-coding genes.
• For the past 50 years, experts in molecular biology have known about transposons and have considered the view that some of them might be "controlling elements." They have concluded that most transposon-related sequences are just fragments of defective transposons with no biological function.
• Nobody cares whether mobile genetic elements fit within the narrow confines of the Modern Synthesis as described by Huxley and other in the 1940s because no exeprt in molecular evolution has believed in that view of evolution since the late 1960s.
• The Britten and Kohne paper established that the genomes of most multicellular eukaryotes contain large amounts of repetivie DNA. This was an attempt to resolve the C-value paradox. Britten and Kohne didn't like the idea that this could be junk DNA so they offered some speculation about function. However, futher data established that most of this repetitive DNA is, indeed, junk and Britten and Kohn's speculations have been discredited. Britten and Kohn were attempting to interpret their result within the context of the adaptationist views that characterized the the Modern Synthesis back then. The correct interpretation of their results came with the overthrow of the Modern Synthesis and the adoption of a new view of evolutionary theory that focused on Neutral Theory, Nearly-Neural Theory, and the importance of random geneitc drift. Shaprio and Noble missed that revolution so they continue to attack an old-fashioned strawman version of evolutionay theory.

Before continuing, it's important to realize that by the early 1970s selectionist thinking had been abandoned by the experts in genome evolution. By 1978 Gould and Lewontin tried, unsccessfully, to convince all other biologists to abandon the old selectionist way of thinking [The Spandrels of San Marco and the Panglossian Paradigm]. James Shapiro and Denis Noble are among those other biologists who didn't get the message.

In order to apply selectionist thinking to explain the presence of so much non-coding DNA, evolutionary biologists called this unexpected portion of the genome “junk DNA” (Ohno, 1972) or “selfish DNA” (Orgel and Crick, 1980). Richard Dawkins used an extreme view of these “selfish genes” to erect a whole philosophy of strictly passive evolutionary gradualism (Dawkins, 1976). Today we know that the human genome contains at least 30X as much repetitive non-coding DNA as protein-coding sequences (Lander et al., 2001). Repetitive DNA provides formatting signals for transcription, epigenetic modification and chromosome mechanics and also is the most variable component in the evolutionary diversification of complex genomes (Symonová and Howell, 2018; Subirana et al., 2015; Matsubara et al., 2016; CioffiMde et al., 2015; Chalopin et al., 2015; Shao et al., 2019; Böhne et al., 2008; Li et al., 2016; Oliver et al., 2013). A 2013 plot of organismal complexity against protein-coding and non-coding DNA showed that coding DNA peaked at approximately ∼3 × 10⁷ bp, while the non-coding DNA increased linearly with growing complexity up to ∼2–3 x 10¹⁰ bp (Liu et al., 2013). In other words, non-coding DNA tracked organismal complexity better than the protein-coding genes. The “encyclopedia of DNA elements” (ENCODE) project, which largely abandoned the term “gene,” revealed that the large majority of the so-called junk DNA is actively transcribed in a regulated manner, indicating that it is functional (Consortium, 2012; Pennisi, 2012).

• It is completely, totally, ridiculous to say that the idea of junk DNA was due to selectionist thinking. The first statement in this paragraph is powerful evidence that Shaprio and Noble don't know what they are talking about. The concept of junk DNA is a rejection of selectionist thinking.
• The use of "noncoding DNA" is what's called a "tell."
• Again, equating junk DNA with selfish DNA is stupid. If all the excess DNA were selfish then it isn't junk because it has a function.
• Richard Dawkins' view on evolution is closer to the old-fashioned adaptationist view that was abandoned by the experts by the time he wrote The Selfish Gene. Dawkins book is not really about "genes," however, as is clear to anyone who has read it. He's talking about any piece of DNA that confers a fitness advantage. The Dawkins strawman is a favorite target of the Third Way types but it's just a strawman.
• No significant proportion of repetitive DNA has a function in spite of the references quoted above.
• There is no significant correlation between organismal compexity and noncoding DNA. Lots of very similar species, such as onions, have very different genome sizes.

• No knowledgeable scientist since the 1980s thinks there should be a significant correlation between the number of genes and organismal complexity. We know that most of the phenotypic differences between multicellular species are due to changes in the timing and amount of expression of a standard set of genes. This is the main discovery of evolutionary-developmental biology (evo-devo), another revolution that Shapiro and Nobel missed. They should educate themselves by reading Sean B. Carroll's books.
• The ENCODE researchers did lots of silly things but they did NOT abandon the term "gene."
• The idea that most of our genome is functional because of ENCODE is laughable in 2021. The fact that Shapiro and Noble would bring this up is another "tell" and the fact that they would reference Elizabeth Pennisi is even more revealing. These guys are incapable of thinking critically.

Shaprio and Noble then describe a few examples of repetitive DNA sequences that have a known function and they point out that a number of noncoding genes have been indentified. They imply that these functional sequences make up a signifcant fraction of the genome thus calling the concept of junk DNA into question. They close the section with,

Clearly, none of the eminent scientists who wrote about junk or selfish DNA could possibly have imagined the wide range of cellular functionalities that we know today are executed by ncRNA molecules. The idea that a genome was just a collection of protein coding sequences has proved completely inadequate.

• I don't know about you, dear reader, but I'll match those "eminent scientists" against Shapiro and Noble any day. I'd love to see them try to defend their views in a public debate against some of the leading proponents of junk DNA. I know where my money would be.

Let me close by quoting the last chapter of this paper. I don't intend to comment on it except to say that it gives new meaning to the word "irony."

The campaign to sustain the Modern Synthesis causes real harm in a number of different ways. Among doctors treating bacterial infections, ignorance of real-world evolutionary processes has led to a situation in which the available antibiotics have lost their effectiveness against many life-threatening conditions (CDC et al., 2019). Among the general public, the inability to comprehend the potential all living organisms possess for transferring and reorganizing genomic configurations makes them unprepared to form sound judgements about how society should utilize its growing arsenal of biotechnology tools acquired from our microbial neighbors, like CRISPR (Doudna, 2020). Among oncologists, MS thinking prevents the practitioners treating cancer patients from recognizing the dangers of overtreating tolerable tumors in ways that may provoke a macroevolutionary transition to a far more lethal and untreatable disease (Heng, 2019). Finally, in the battle against obscurantism and anti-evolution prejudice, insistence on an outdated set of assertions about how life can change itself leaves the defenders of rigorous scientific inquiry without satisfactory responses to critics. Clearly, the time has come for the mainstream evolution community to recognize and join the scientific reality of the 21st Century.

Finally, one of the most important properties of kooks is that they find each other and they tend to hang out together, either physically or virtually. I'm not sure why this happens since they often espouse mutually exclusive views. I'm guessing that we can explain it in two different ways: (1) they are all outsiders fighting against a common enemy; namely, real science, and (2) they lack critical thinking skills so they don't see the flaws in each other's arguments.

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1. In case you didn't recognize the quality from the title.

How do you explain evolution to non-experts?

I spent a lot of time explaining evolution in my book. The goal is to educate readers to the level where they can understand the drift-barrier hypothesis and why slightly deleterious mutations can accumulate in species with small populations. This requires some knowledge of random genetic drift and some knowledge of Neutral Theory and Nearly-Neutral Theory. The emphasis is on population genetics as the most important way of understanding evolution.

You can't understand genomes and junk DNA unless you have a firm understanding of evolution. In fact, you can't make sense of anything about genes and gene expression without such knowledge ... what the heck, nothing in all of biology makes sense if you don't know about evolution.

My approach hasn't been copied by popular websites. They usually misrepresent evolution by presenting it as adaptation; natural selection is the only game in town. I'll put in a link to Francis Collins describing evolution in truly bizarre narration but my question for Sandwalk readers is whether this is useful or not. Is it better to dumb down evolution on the NIH: National Huamn Genome Website [Evolution] or is this a bad idea?

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The 20th anniversary of the human genome sequence: 5. 90% of our genome is junk

This is the fifth (and last) post in celebration of the 20th anniversary of publishing the draft sequence. The first four posts dealt with: (1) the way Science chose to commemorate the occasion [Access to the data]; (2) finishing the sequence; (3) the number of genes; and (4) the amount of functional DNA in the genome.

Back in 2001, knowledgeable scientists knew that most of the human genome is junk and the sequence confirmed that knowledge. Subsequent work on the human genome over the past 20 years has provided additional evidence of junk DNA so that we can now be confident that something like 90% of our genome is junk DNA. Here's a list of data and arguments that support that claim.

Of mice and Michael

Michael Behe has published a book containing most of his previously published responses to critics. I was anxious to see how he dealt with my criticisms of The Edge of Evolution but I was disappointed to see that, for the most part, he has just copied excerpts from his 2014 blog posts (pp. 335-355).

I think it might be worthwhile to review the main issues so you can see for yourself whether Michael Behe really answered his critics as the title of his most recent book claims. You can check out the dueling blog posts at the end of this summary to see how the discussion evolved in real time more than four years ago.

Many Sandwalk readers participated in the debate back then and some of them are quoted in Behe's book although he usually just identifies them as commentators.

My Summary

Michael Behe has correctly indentified an extremely improbably evolution event; namely, the development of chloroquine resistance in the malaria parasite. This is an event that is close to the edge of evolution, meaning that more complex events of this type are beyond the edge of evolution and cannot occur naturally. However, several of us have pointed out that his explanation of how that event occurred is incorrect. This is important because he relies on his flawed interpretation of chloroquine resistance to postulate that many observed events in evolution could not possibly have occurred by natural means. Therefore, god(s) must have created them.

In his response to this criticism, he completely misses the point and fails to understand that what is being challenged is his misinterpretation of the mechanisms of evolution and his understanding of mutations.

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The main point of The Edge of Evolution is that many of the beneficial features we see could only have evolved by selecting for a number of different mutations where none of the individual mutations confer a benefit by themselves. Behe claims that these mutations had to occur simultaneously or at least close together in time. He argues that this is possible in some cases but in most cases the (relatively) simultaneous occurrence of multiple mutations is beyond the edge of evolution. The only explanation for the creation of these beneficial features is god(s).

On the importance of random genetic drift in modern evolutionary theory

The latest issue of New Scientist has a number of articles on evolution. All of them are focused on extending and improving the current theory of evolution, which is described as Darwin's version of natural selection [New Scientist doesn't understand modern evolutionary theory].

Most of the criticisms come from a group who want to extend the evolutionary synthesis (EES proponents). Their main goal is to advertise mechanisms that are presumed to enhance adaptation but that weren't explicitly included in the Modern Synthesis that was put together in the late 1940s.

One of the articles addresses random genetic drift [see Survival of the ... luckiest]. The emphasis in this short article is on the effects of drift in small populations and it gives examples of reduced genetic diversity in small populations.

New Scientist doesn't understand modern evolutionary theory

New Scientist has devoted much of their September 26th issue to evolution, but not in a good way. Their emphasis is on 13 ways that we must rethink evolution. Readers of this blog are familiar with this theme because New Scientist is talking about the Extended Evolutionary Synthesis (EES)—a series of critiques of the Modern Synthesis in an attempt to overthrow or extend it [The Extended Evolutionary Synthesis - papers from the Royal Society meeting].

My main criticsm of EES is that its proponents demonstrate a remarkable lack of understanding of modern evolutionary theory and they direct most of their attacks against the old adaptationist version of the Modern Synthesis that was popular in the 1950s. For the most part, EES proponents missed the revolution in evolutionary theory that occrred in the late 1960s with the development of Neutral Theory, Nearly-Neutral Theory, and the importance of random genetic drift. EES proponents have shown time and time again that they have not bothered to read a modern textbook on population genetics.

More misconceptions about junk DNA - what are we doing wrong?

I'm actively following the views of most science writers on junk DNA to see if they are keeping up on the latest results. The latest book is DNA Demystified by Alan McHughen, a molecular geneticist at the University California, Riverside. It's published by Oxford University Press, the same publisher that published John Parrington's book the deeper genome. Parrington's book was full of misleading and incorrect statements about the human genome so I was anxious to see if Oxford had upped it's game.¹, ²

You would think that any book with a title like DNA Demystified would contain the latest interpretations of DNA and genomes, especially with a subtitle like "Unraveling the double Helix." Unfortunately, the book falls far short of its objectives. I don't have time to discuss all of its shortcomings so let's just skip right to the few paragraphs that discuss junk DNA (p.46). I want to emphasize that this is not the main focus of the book. I'm selecting it because it's what I'm interested in and because I want to get a feel for how correct and accurate scientific information is, or is not, being accepted by practicing scientists. Are we falling for fake news?

What's in Your Genome? Chapter 2: The Evolution of Sloppy Genomes

I had to completely reorganize chapter 2 in order to move population genetics closer to the beginning of the book and reduce the number of words.

Chapter 2: The Evolution of Sloppy Genomes

• Fugu sashimi
• Variation in genome size
• The Onion Test
• Instantaneous genome doubling
• Modern evolutionary theory
• Random genetic drift
• Neutral Theory
• Nearly-Neutral Theory
• Box 2-1: Are humans are still evolving?
• Population size and the Drift-Barrier Hypothesis
• Bacteria have small genomes
• On the evolution of sloppy genomes

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The Function Wars Part VI: The problem with selected effect function

The term "Function Wars" refers to the debate over the meaning of 'function,' especially in the context of junk DNA.¹ That debate intensified in 2012 after the ENCODE publicity campaign that tried to redefine function to mean anything they want as long as it refutes junk DNA. This is the sixth in a series of posts exploring the debate and why it's important, or not. Links to the other five posts can be found at the bottom or this post.

The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)Much of the discussion seems like quibbling over semantics but I'm reminded of a similar debate over the mode of evolution: is it gradual or punctuated? As Gould pointed out in 1982, there's a serious issue underlying the debate—an issue that shouldn't get lost in bickering over the meaning of 'gradualistic.' The same warning applies here. It's important to determine how much of the human genome is junk and that requires an understanding of what we mean by junk DNA. However, it's easy to get distracted by focusing on the exact meaning of the word 'function' instead of looking at the big picture.

Are pseudogenes really pseudogenes?

There are many junk DNA skeptics who claim that most of our genome is functional. Some of them have even questioned whether pseudogenes are mostly junk. The latest challenge comes from a recent review in Nature Reviews: Genetics where the authors try to place the burden of proof on those who say that pseudogenes are broken, nonfunctional, genes (Cheetam et al., 2019). The authors of the review try to make the case that we should not label a DNA sequence as a pseudogene until we can prove that it is truly nonfunctional junk.

I'm about to refute this ridiculous stance but first we need a little background.

Contingency, selection, and the long-term evolution experiment

I'm a big fan of Richard Lenski's long-term evolution experiment (LTEE) and of Zachary Blount's work in particular. [Strolling around slopes and valleys in the adaptive landscape] [On the unpredictability of evolution and potentiation in Lenski's long-term evolution experiment] [Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source]

The results of the LTEE raise some interesting questions about evolution. The Lenski experiment began with 12 (almost) identical cultures and these have now "evolved" for 31 years and more than 65,000 generations. All of the cultures have diverged to some extent and one of them (and only one) has developed the ability to use citrate as a carbon source. Many of the cultures exhibit identical, or very similar, mutations that have reached significant frequencies, or even fixation, in the cultures.

Several other laboratory evolution experiments have been completed or are underway in various labs around the world. The overall results are relevant to a discussion about the role of contingency and accident in the history of life [see Evolution by Accident]. Is it true that if you replay the tape of life the results will be quite different? [Replaying life's tape].

Evolution by Accident

Evolution by Accident
v1.43 ©2006 Laurence A. Moran
This essay has been transferred here from an old server that has been decommissioned.Modern concepts of evolutionary change are frequently attacked by those who find the notions of randomness, chance, and accident to be highly distasteful. Some of these critics are intelligent design creationists and their objections have been refuted elsewhere. In this essay I'm more concerned about my fellow evolutionists who go to great lengths to eliminate chance and accident from all discussions about the fundamental causes of evolution. This is my attempt to convince them that evolution is not as predictable as they claim. I was originally stimulated to put my ideas down on paper when I read essays by John Wilkins [Evolution and Chance] and Loren Haarsma [Chance from a Theistic Perspective] on the TalkOrigins Archive.

The privilege of living beings is the possession of a structure and of a mechanism which ensures two things: (i) reproduction true to type of the structure itself, and (ii) reproduction equally true to type, of any accident that occurs in the structure. Once you have that, you have evolution, because you have conservation of accidents. Accidents can then be recombined and offered to natural selection to find out if they are of any meaning or not.
Jacques Monod (1974) p.394The main conclusion of this essay is that a large part of ongoing evolution is determined by stochastic events that might as well be called "chance" or "random." Furthermore, a good deal of the past history of life on Earth was the product of chance events, or accidents, that could not have been predicted. When I say "evolution by accident" I'm referring to all these events. This phrase is intended solely to distinguish "accidental" evolution from that which is determined by non-random natural selection. I will argue that evolution is fundamentally a random process, although this should not be interpreted to mean that all of evolution is entirely due to chance or accident. The end result of evolution by accident is modern species that do not look designed.

Reactionary fringe meets mutation-biased adaptation. 5.3. How history is distorted.

This is the ninth in a series of guest posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution. Click on the links in the box (below) to see the other post in the series.

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Reactionary fringe meets mutation-biased adaptation.
5.3. How history is distorted.
by Arlin Stoltzus
In his famous Materials for the Study of Variation, Bateson (1894) refers to natural selection as "obviously" a "true cause" (p. 5). Punnett (1905) explains that mutations are heritable while environmental fluctuations are not, concluding that "Evolution takes place through the action of selection on these mutations" (p. 53). De Vries begins his major 1905 English treatise by writing that ...

"Darwin discovered the great principle which rules the evolution of organisms. It is the principle of natural selection. It is the sifting out of all organisms of minor worth through the struggle for life. It is only a sieve, and not a force of nature" (p. 6)

Morgan (1916), in his closing summary, writes:

"Evolution has taken place by the incorporation into the race of those mutations that are beneficial to the life and reproduction of the organism" (p. 194)

Reactionary fringe meets mutation-biased adaptation. 5.2. The Modern Synthesis of 1959

This is the eighth in a series of guest posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution.

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Reactionary fringe meets mutation-biased adaptation. 5.2. The Modern Synthesis of 1959
by Arlin Stoltfus
As we learned in What makes it new?, the newness of the effect of biases in the introduction process results from a classical assumption that evolution can be understood as a process of shifting the frequencies of existing alleles. How did this position emerge? Was it a technical, mathematical issue?

Reactionary fringe meets mutation-biased adaptation. 5. Beyond the "Synthesis" debate

This is the sixth in a series of guest posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution.

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Reactionary fringe meets mutation-biased adaptation. 5. Beyond the "Synthesis" debate
by Arlin Stoltzfus
The authors of TREE's hatchet piece imply that the theory of Yampolsky and Stoltzfus (2001) is somehow not new, citing ancient work from Dobzhansky and Haldane. In Box 1, they argue that this theory is part of "standard evolutionary theory," showing a 4-step derivation ending in Eqn IV, which is Eqn 2 of Yampolsky and Stoltzfus (2001), and informing the reader that this is based on "classical" results from Fisher, Haldane and Kimura, who are named, while Yampolsky and Stoltzfus are not named.

Yet, Fisher, Haldane, and Kimura did not make the argument in Box 1, did not follow the 4 steps, and did not derive Eqn IV!