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Showing posts with label Evolutionary Biology. Show all posts
Showing posts with label Evolutionary Biology. Show all posts

Thursday, November 21, 2024

Biological evolution is dead in the water (not!)

You will be surprised to hear that biological evolution is dead in the water according to the authors of a paper published in Progress in Biophysics and Molecular Biology.

The authors are Olen Brown, an Emeritus Professor of Biomedical Sciences at the University of Missouri and David Hullender, a Professor in the Department of Mechanical and Aerospace Engineering at the University of Texas at Arlington. These are the same two authors who published two ridiculous papers in the same journal in 2022 and 2023. Up until last December (2023), Denis Noble was one of the editors of the journal [Editorial Board] but he is not longer listed on the journal's website. We can assume that Noble is responsible, in part, for allowing these papers to be published since he has defended the publication of creationist papers in the past. [How the Krebs cycle disproves Darwinism (not!)]

Brown, O.R. and Hullender, D.A. (2024) Biological evolution is dead in the water of Darwin’s warm little pond. Progress in Biophysics and Molecular Biology. 193: 1-6. [doi: 10.1016/j.pbiomolbio.2024.08.003]

Abstract

The origin of life and its evolution are generally taught as occurring by abiogenesis and gene-centric neo-Darwinism. Significant biological evolutionary changes are preserved and given direction (descent with modification) by Darwin's (Spencer's) natural selection by survival of the fittest. Only survival of the fittest (adapted/broadened) is available to provide a ‘naturalistic’ direction to prefer one outcome/reaction over another for abiogenesis. Thus, assembly of first life must reach some threshold (the first minimal cell) before ‘survival of the fittest’ (the only naturalistic explanation available) can function as Darwin proposed for biological change. We propose the novel concept that the requirement for co-origination of vitamins with enzymes is a fundamental, but overlooked, problem that survival of the fittest (even broadly redefined beyond Darwin) cannot reasonably overcome. We support this conclusion with probability calculations. We focus on the stage of evolution involving the transition from non-life to the first, minimal living cell. We show that co-origination of required biochemical processes makes the origin of life probabilistically absurdly improbable even when all assumptions are chosen to unreasonably favor evolutionary theories.

There's something seriously wrong with peer review if a paper like this can be published in a (formerly) reputable journal.

For more information, watch this video of Brown and Hullender explaining their views. The video is sponsored by "Video Lessons to Raise Up Confident Christians."


Saturday, November 16, 2024

Darwin Mythology

How can you possibly be against a book devoted to refuting misinformation about Charles Darwin and his views on evolution? This is an anthology edited by Kostas Kampourakis whose main interest is "the public understanding of evolution and genetics." He currently teaches at the University of Geneva (Geneva, Switzerland).

Kampourakis has assembled a bunch of authors who present their 24 most important myths about Darwin in 24 chapters. It appears that this book was motivated, in part, by Kampoourakis' view that Charles Darwin needs to knocked down a peg or two because it corrupts the general public's view of how science really works. He begins his book by quoting Richard Dawkins, Michael Ghiselin and Jerry Coyne as examples of scientists who see Darwin as a scientific hero.

Darwin was without question a brilliant naturalist, observer and experimentalist and scholar. But this kind of hero-worshipping should be avoided because it is misleading—science is not done, and does not advance, by individuals who make big breakthroughs in one go. Science is done by communities, which consist of individuals many of whom have something important to contribute to the overall achievement. Even when some individuals happen to see something that others do not, the validation of a novel perspective or findings by the community is absolutely necessary. Most importantly, coming up with anything novel takes time and effort—it took Darwin twenty years of painstaking work—while one works in a particular context and with particular resources to hand—and Darwin had experiences and resources that most other lacked. This kind of hero-worshiping is also better avoided because it dehumanizes science; in the last chapter of the present book, I explain how the stories in its twenty-four chapters can help us better understand science as a human activity. My aim is to humanize Darwin and to emphasize a number of points about how science is done.

Tuesday, October 29, 2024

Zach Hancock's 10 most influential papers on evolution

Zach Hancock is a postdoc in the Dept. of Ecology and Evolutionary Biology at the University of Michigan. He has a popular YouTube channel where he has recently posted a video describing his top ten evolutionary biology papers of all time. I've added links to all of the papers below.

Zach emphasizes that this is a personal list and others might disagree with his choices. He is much more interested than I am in explaining the history of life with an emphasis on animals. I'm much more interested in molecular evolution so I would choose a slightly different list as I explain below. Please add your own choices in the comments.

  1. Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y. L., and Postlethwait, J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151(4), 1531-1545. [doi: 10.1093/genetics/151.4.1531]
  2. Coyne, J. A., and Orr, H. A. (1989) Patterns of speciation in Drosophila. Evolution, 43(2), 362-381. [doi: 10.1111/j.1558-5646.1989.tb04233.x]
  3. Lande, R., and Arnold, S. J. (1983) The measurement of selection on correlated characters. Evolution, 1210-1226. [doi: 10.2307/2408842]
  4. Lederberg, J., and Lederberg, E. M. (1952) Replica plating and indirect selection of bacterial mutants. Journal of bacteriology, 63(3), 399-406. [PDF]
  5. Gould, S.J. and Lewontin, R.C. (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society of London. Series B. Biological Sciences 205:581-598. [doi: 10.1098/rspb.1979.0086]
  6. Maynard Smith, J. M. (1974) The theory of games and the evolution of animal conflicts. Journal of theoretical biology, 47(1), 209-221. [doi: 10.1016/0022-5193(74)90110-6"]
  7. Fisher, R.A. (1918) The correlation between relatives on the supposition of Mendelian Inheritance. Proceedings of the Royal Society of Edingurgh [PDF]
  8. Hamilton, W. D. (1964) The genetical evolution of social behaviour. II. Journal of theoretical biology, 7(1), 17-52. [doi: 10.1016/0022-5193(64)90039-6]
  9. Kimura, M. (1968) Evolutionary rate at the molecular level. Nature, 217(5129), 624-626. [PDF]
  10. Wright, S. (1931) Evolution in Mendelian populations. Genetics, 16(2), 97. [doi: 10.1093/genetics/16.2.97]

I disagree with Hamilton (1964). I realize that there are many evolutionary biologists who think that kin selection and the evolution of altruistic behavior is extremely important1 but I think it's restricted to a tiny perecentage of characteristics in a tiny percentage of all living things on the planet. I would delete the Hamilton paper and replace it with ...

Margoliash, E. (1963) Primary structure and evolution of cytochrome c. Proceedings of the National Academy of Sciences, 50(4), 672-679. [PDF]

This is the first accessible paper on using the animo acid seqences of proteins to obtain information on evolution. It's the beginning of the field of molecular evolution and the idea of a molecular clock. Surely that deserves to be one of the most important advances in the field of evolution. (Linus Pauling and Emile Zuckerkandl published similar work on globins at about the same time but their original papers were not as accessible as the Margoliash paper. See Emile Zuckerkandl and the 50th anniversary of the birth of molecular evolution.)

I'm not a big fan of John Maynard Smith and game theory. I think it only applies to a small part of the field of evolution. I would delete the Maynard Smith (1974) paper and replace it with ...

Ohta, T. (1973) Slightly deleterious mutant substitutions in evolution. Nature 246:96-98. [doi:10.1038/246096a0]

This is the beginning of the nearly neutral theory. I agree that putting the Kimura paper on the neutral theory at #2 is a good choice but it's the Ohta paper that really drives home the idea that deleterious mutations can also be fixed under some circumstances and made (some) evolutionary biologists understand that natural selection was not the only game in town.

Finally, I'd like to see one of David Raup's papers in the top ten list but I don't know enough about the other papers to pick one to delete. (I'm skeptical of Lande and Arnold (1983) but I know they have fierce defenders.) Here's a candidate Raup paper that includes Sepkoski.

Raup, David M.; Sepkoski, J. John Jr. (1982) Mass extinctions in the marine fossil record. Science. 215 (4539). [doi:10.1126/science.215.4539.1501]

I'm waiting for the list of the top nine books on evolution—we all know what #1 is going to be.


Image credit: The photo is from Zach's personal website.

1. Richard Dawkins thinks Hamilton is "the greatist Darwinina of my lifetime" [quoted in W.D. Hamilton]

Monday, October 21, 2024

Philip Ball strikes back

Philip Ball believes that we are in the middle of a revolution in our way of thinking about how life works. His ideas are complex but part of his case involves molecular biology and how things work at the molecular level. Ball believes that the old view of molecular biology placed far too much emphasis on coding DNA and ignored all the other functional regions of genomes. He also says that most of our genes specify non-coding RNA instead of mRNA and implies to his readers that a very large fraction of our genome is functional (i.e. not junk).1

In order to build the case for revolution, he tries to demonstrate a paradigm shift in our view of molecular biology by showing a huge gap between the understanding of previous generations of molecular biologists and the post-genomic view. I believe he is wrong about this for two reasons: first, he misrepresents the views of older molecular biologists and, second he misrepresents the discoveries of the past twenty years. I tried to explain why he was wrong about these two claims in a previous post where I discussed an article he published in Scientific American in May 2024: Philip Ball says RNA may rule our genome.

Philip Ball responded to my criticism in a comment under that article.

Older molecular biologists were really stupid

I said ...

Ball begins with the same old myth that writers like him have been repeating for many years. He claims that before ENCODE most molecular biologists were really stupid. According to Philip Ball, most of us thought that coding DNA was the only functional part of the genome and most of the rest was junk DNA.

In the comment section of my earlier post, Philip Ball says,

I’m sorry to say that Larry’s commentary here is dismayingly inaccurate.

Let’s get this one out of the way first:

“He claims that before ENCODE most molecular biologists were really stupid.”

I have never made this claim and never would – it is a pure fabrication on Larry’s part. I guess this is what John Horgan meant in his comment to Larry: credible writers don’t just make up stuff.

I admit that Philip Ball never said those exact words. I'll leave it to the readers to decide whether my characterization of his position is accurate.

I stand by the statements I made although I admit to a bit of hyperbole. Ball has said repeatedly that the molecular biologists of my generation were wedded to the idea that coding regions were the only important part of the genome and he often connects that to the Central Dogma of Molecular Biology. He also claims that the experts in molecular biology dismissed all non-coding DNA as junk. Here's how he puts it in another article that he published recently in Aeon: We are not machines.

Only around 1-2 per cent of the entire human genome actually consists of protein-coding genes. The remainder was long thought to be mostly junk: meaningless sequences accumulated over the course of evolution. But at least some of that non-coding genome is now known to be involved in regulating genes: altering, activating or suppressing their transcription in RNA and translation into proteins.

I interpret that to mean that older molecular biologists, like me, didn't know about functional non-coding DNAs such as centromeres, telomeres, origins of replication, non-coding genes, SARs, and regulatory sequences in spite of the fact that thousands of papers on these sequences were published in the 30 years that preceded the publication of the first draft of the human genome sequence. This is not true, we did know about those things. I don't think it's too much of an exaggeration to say that Philip Ball thinks we were really stupid.

Here's what he says in his book, "How Life Works" (p. 85) when he's talking about the beginning of the human genome project.

Even at its outset, it faced the somewhat troubling issue that just 2 percent or so of our genome actually accounts for protein-coding genes. The conventional narrative was that our biology was all about proteins, for each of which the genome held the template. ... But we had all this other DNA too! What was it for? The common view was that it was mostly just junk, like the stuff in our attics: meaningless material accumulated during evolution, which our cells had no motivation to clear out.

Again, his claim is that in 1990 at the beginning of the human genome project the experts in molecular biology thought that non-coding DNA was mostly junk (98% of the genome). I have repeatedly refuted this myth and challenged anyone to come up with a single scientific paper arguing that all non-coding DNA is junk. I challenge Philip Ball to find a single molecular biology textbook written before 1990 that fails to discuss regulation, non-coding genes, and other non-coding functional elements in the human genome.

The truth is that the molecular biology experts concluded in the 1970s that we had about 30,000 genes and that 90% of our genome is junk and 10% is functional. That 10% consisted of about 2% coding DNA (now thought to be only 1%) and 8% functional non-coding DNA. So the "conventional narrative" was that there was a lot more functional non-coding DNA than coding DNA.

The human genome is full of genes for regulatory RNAs.

"Ball is one of the most meticulous, precise science writers out there. He is the antithesis of hypey, "dumb-it-down" reporting. He is MUCH more credible than you are, Laurence."

John Horgan July, 2024
The title of the article I was discussing is "Revolutionary Genetics Research Shows RNA May Rule Our Genome." In that article Ball says that ENCODE was basically right and there are many more non-coding genes than protein-coding genes. I pointed out that Ball mentions some criticism of this idea but only to dismiss it. I said that "[Ball] wants you to believe that almost of all of those transcripts are functional—that's the revolution that he's promoting." Philip Ball objects to this statement ...

This too is sheer fabrication. I don’t say this in my article, nor in my book. Instead, I say pretty much what Larry seems to want me to say, but for some reason he will not admit it – which is that there is controversy about how many of the transcripts are functional."

Ball states that "ENCODE was basically right" when they claimed that 75% of our genome was transcribed and he goes on to say that ...

Dozens of other research groups, scoping out activity along the human genome, also have found that much of our DNA is churning out 'noncoding' RNA.

He says that ENCODE has identified 37,000 noncoding genes but there may be as many as 96,000. After making these definitive statements, he mentions that there are "still doubters" but then discuss why these discoveries are revolutionary. Later on he quotes John Mattick suspecting that there may be more that 500,000 non-coding genes.

Toward the end of the article, after discussing all kinds of functional RNAs, he brings up the Ponting and Haerty review where they say that most lncRNAs are just noise. He also mentions that the low copy number of non-coding RNAs raises questions about whether they are functional but immediately counters with the standard excuses from his allies.

Ball closes the article with ...

Gingeras says he is perplexed by ongoing claims that ncRNAs are merely noise or junk, as evidence is mounting that they do many things. "It is puzzling why there is such an effort to persuade colleagues to move from a sense of interest and curiosity in the ncRNA field to a more dubious and critical one," he says.

Perhaps the arguments are so intense because they undercut the way we think our biology works. Ever since the epochal discovery about DNA's double helix and how it encodes information, the bedrock idea of molecular biology has been that there are precisely encoded instructions that program specific molecules for particular tasks. But ncRNAs seem to point to a fuzzier, more collective, logic to life. It is a logic that is harder to discern and harder to understand. ut if scientists can learn to live with the fuzziness, this view of life may turn out to be more complete.

What's remarkable about the quote from a leading ENCODE worker (Gingeras) is that he is "puzzled" by scientists who are dubious and critical about claims in the ncRNA field. Isn't that what good scientists are supposed to do? Isn't that exactly what we did when we successfully challenged the dubious claims about junk DNA made in 2012?

There is no doubt in my mind that Philip Ball has fallen hook-line-and-sinker for the ENCODE claims that our genome is buzzing with non-coding genes. He only brings up the counter-arguments to dismiss them and pretend that he is being fair. Nobody who was truly skeptical about the function of transcripts would write an article with the title, "Revolutionary Genetics Research Shows RNA May Rule Our Genome."

However, as Ball points out in other comments, he does have a sentence in his book where he mentions that perhaps only 30% of the genome is functional. He says in the comment that what he believes is that the amount of functional DNA lies somewhere between 10% and 30%. That's not something that he mentions in the Scientific American article but, if he's being honest, it does mean that I was unfair when I said he believes that "almost of all of those transcripts are functional" but I only know that from what he now says, not from the published article.

If I were to take Philip Ball at his word—as expressed in the comment—then he must believe that most of the ENCODE transcripts are junk RNA. That's not a belief that you get from reading his published work.2 Furthermore, if I were to take him at his word, then he must believe that there are some reasonable criteria that must be applied to a transcript in order to decide whether it has a biologically relevant function. So, when he says that ENCODE identified 37,600 non-coding genes he must have these criteria in mind but he doesn't express any serious skepticism about that number. We all know that there's no solid evidence that such a large number of transcripts are functional but that doesn't bother Philip Ball. He thinks we are in the middle of an RNA revolution.


1. In commenting to my previous post, Ball says he believes that somewhere between 70% and 90% of our genome is junk but he doesn't say this in the Scientific American article. Instead, he says that scientists were surprised to learn that 75% of the human genome is transcribed implying that there's a lot of function. He goes on the say that "ENCODE was basically right." But what the ENCODE publicity campaign actually said was that junk DNA is dead and there's practically no junk DNA. If Ball really believes that up to 90% of the genome is junk then to me this means that ENCODE was spectacularly wrong not "basically right."

2. Ball says that 75% of the genome is transcribed. If Ball believes that as little as 10% may be functional then he must believe that less than 10% is transcribed to produce functional RNAs since he has to allow for regulatory sequences and other functional DNA elements. Let's say that 8% is a reasonable number. Ball seems to be willing to admit that 67% of the genome might be transcribed to produce junk RNA.

Thursday, October 03, 2024

Intelligent Design Creationists made up a fake march of progress illustration

Everyone is familiar with the typical March of Progress figures that are often used to illustrate evolution. However, most people don't know that evolutionary biologists object to that depiction of evolution because it seriously misrepresents the reality of human evolution.

Stephen Jay Gould has been one of the most vocal opponents of such icons because they imply a sense of direct linear progress from some primitive ancestor to a modern species when, in fact, the actual evolution involves branching trees with multiple lineages, most of which have gone extinct. In one of his most famous essays, Life's Little Joke (Gould, 1987, 1991), Gould explains why the evolution of horses is falsely depicted as a march of progress.

Tuesday, September 24, 2024

On the evolution of the glycolytic pathway (glycolysis)

Jonathan McLatchie has a PhD in Evolutionary Biology from Newcastle University (UK) and he is currently "resident biologist" and a fellow at the Center for Science and Culture at the Discovery Institute. He is an intelligent design creationist who attacks evolution by questioning standard explanations in the fields of biochemistry and molecular biology.

I've debated him frequently over the years since those are my areas of interest as well. The last time we met was at an evolution conference in London (UK) in 2016 (see photo).

I've always found Jonathan to be more honest and more willing to learn than most of his creationist colleagues so that's why I'm addressing his latest post on Evolution News (sic) where he challenges the evolutionary origins of the glycolytic pathway. As you might expect, his argument is largely based on the idea that since the glycolytic pathway is very complicated, there's no way it could have arisen all at once. He then goes on to reject the idea that the pathway could have evolved incrementally, one step at a time.

Wednesday, August 14, 2024

Is the Teacher Institute for Evolutionary Science spreading misinformation?

The Teacher Institute for Evolutonary Science (TIES) is an organization dedicated to helping teachers explain evolution.

A good teacher can teach any subject as long as they have high-quality resources. TIES provides middle school and elementary teachers the tools they need to effectively teach evolution and answer its critics based on new Next Generation Science Standards.

The Teacher Institute for Evolutionary Science began as a program of the Richard Dawkins Foundation for Reason & Science and it's now part of the Center for Inquiry.

TIES recently posted a video with an interesting title on their YouTube channel: "Beyond DNA: How Epigenetics is Transforming our Understanding of Evolution." This is a presentation by Ben Oldroyd who wrote a book titled "Beyond DNA."

Watch the video and decide for yourself whether you think this is what teachers of evolutionary biology should be telling their students. What part of understanding evolution do you think needs to be transformed by epigenetics?


Thursday, March 21, 2024

Science misinformation is being spread in the lecture halls of top universities

Should universities remove online courses that contain incorrect or misleading information?

There are lots of scientific controversies where different scientists have conflicting views. Eventually these controversies will be solved by normal scientific means involving evidence and logic but for the time being there isn't enough data to settle a genuine scientific controversy. Many of us are interested in these controversies and some of us have chosen to invest time and effort into defending one side or the other.

But there's a dark side of science that infects these debates—false or misleading information used to support one side of a legitimate controversy. To give just one example, I'm frustrated at the constant reference to junk DNA being defined as non-coding DNA. Many scientists believe that this was the way junk DNA was defined by its earliest proponents and then they go on to say that the recent discovery of functional non-coding DNA refutes junk.

I don't know where this idea came from because there's nothing in the scientific literature from 50 years ago to support such a ridiculous claim. It must be coming from somewhere since the idea is so widespread.

Where does misinformation come from and how is it spread?

Wednesday, February 07, 2024

Philip Ball's new book: "How Life Works"

Philip Ball has just published a new book "How Life Works." The subtitle is "A User’s Guide to the New Biology" and that should tell you all you need to know. This is going to be a book about how human genomics has changed everything.

Friday, August 11, 2023

What is the Modern Synthesis?

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?].

Tuesday, August 01, 2023

Help fix the Wikipedia article on evolution

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.


Sunday, February 12, 2023

Happy Darwin Day! 2023

Charles Darwin, the greatest scientist who ever lived, was born on this day in 1809 [Darwin still spurs tributes, debates] [Happy Darwin Day!] [Darwin Day 2017]. Darwin is mostly famous for two things: (1) he described and documented the evidence for evolution and common descent and (2) he provided a plausible scientific explanation of evolution—the theory of natural selection. He put all this in a book, The Origin of Species by Means of Natural Selection published in 1859—a book that spurred a revolution in our understanding of the natural world. (You can still buy a first edition copy of the book but it will cost you several hundred thousand dollars.)

Thursday, October 13, 2022

Macroevolution

(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.


Friday, October 29, 2021

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.


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).

Monday, April 06, 2020

The Function Wars Part VII: Function monism vs function pluralism

This post is mostly about a recent paper published in Studies in History and Philosophy of Biol & Biomed Sci where two philosophers present their view of the function wars. They argue that the best definition of function is a weak etiological account (monism) and pluralistic accounts that include causal role (CR) definitions are mostly invalid. Weak etiological monism is the idea that sequence conservation is the best indication of function but that doesn't necessarily imply that the trait arose by natural selection (adaptation); it could have arisen by neutral processes such as constructive neutral evolution.

The paper makes several dubious claims about ENCODE that I want to discuss but first we need a little background.

Background

The ENCODE publicity campaign created a lot of controversy in 2012 because ENCODE researchers claimed that 80% of the human genome is functional. That claim conflicted with all the evidence that had accumulated up to that point in time. Based on their definition of function, the leading ENCODE researchers announced the death of junk DNA and this position was adopted by leading science writers and leading journals such as Nature and Science.

Let's be very clear about one thing. This was a SCIENTIFIC conflict over how to interpret data and evidence. The ENCODE researchers simply ignored a ton of evidence demonstrating that most of our genome is junk. Instead, they focused on the well-known facts that much of the genome is transcribed and that the genome is full of transcription factor binding sites. Neither of these facts were new and both of them had simple explanations: (1) most of the transcripts are spurious transcripts that have nothing to do with function, and (2) random non-functional transcription factor binding sites are expected from our knowledge of DNA binding proteins. The ENCODE researchers ignored these explanations and attributed function to all transcripts and all transcription factor binding sites. That's why they announced that 80% of the genome is functional.

Wednesday, February 12, 2020

Happy Darwin Day! 2020

Charles Darwin, the greatest scientist who ever lived, was born on this day in 1809 [Darwin still spurs tributes, debates] [Happy Darwin Day!] [Darwin Day 2017]. Darwin is mostly famous for two things: (1) he described and documented the evidence for evolution and common descent and (2) he provided a plausible scientific explanation of evolution—the theory of natural selection. He put all this in a book, The Origin of Species by Means of Natural Selection published in 1859—a book that spurred a revolution in our understanding of the natural world. (You can still buy a first edition copy of the book but it will cost you several hundred thousand dollars.)

Friday, February 07, 2020

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.

Tuesday, January 14, 2020

The Three Domain Hypothesis: RIP

The Three Domain Hypothesis died about twenty years ago but most people didn't notice.

The original idea was promoted by Carl Woese and his colleagues in the early 1980s. It was based on the discovery of archaebacteria as a distinct clade that was different from other bacteria (eubacteria). It also became clear that some eukaryotic genes (e.g. ribosomal RNA) were more closely related to archaebacterial genes and the original data indicated that eukaryotes formed another distinct group separate from either the archaebacteria or eubacteria. This gave rise to the Three Domain Hypothesis where each of the groups, bacteria (Eubacteria), archaebacteria (Archaea), and eukaryotes (Eucarya, Eukaryota), formed a separate clade that contained multiple kingdoms. These clades were called Domains.

Sunday, December 15, 2019

The evolution of citrate synthase

Citrate synthase [EC 2.3.3.1] is one of the key enzymes of the citric acid cycle. It catalyzes the joining of acetyl-CoA and oxaloacetate to produce citrate.
acetyl-CoA + H2O + oxaloacetate → citrate + HS-CoA + H+
We usually think of this reaction in terms of energy production since acetyl-CoA is the end product of glycolysis and the citric acid cycle produces substrates that enter the electron transport system leading to production of ATP. However, it's important to keep in mind that the enzyme also catalyzes the reverse reaction.

Monday, October 21, 2019

The evolution of de novo genes

De novo genes are new genes that arise spontaneously from junk DNA [De novo gene birth]. The frequency of de novo gene creation is important for an understanding of evolution. If it's a frequent event, then species with a large amount of junk DNA might have a selective advantage over species with less junk DNA, especially in a changing environment.

Last week I read a short Nature article on de novo genes [Levy, 2019] and I think the subject deserves more attention. Most new genes in a species appear to arise by gene duplication and subsequent divergence but de novo genes are genes that are unrelated to genes in any other clade so we can assume that they are created from junk DNA that accidentally becomes associated with a promoter causing the DNA to be transcribed. A new gene is formed if the RNA acquires a function. If the transcript contains an open reading frame then it may be translated to produce a polypeptide and if the polypeptide performs a new function then the resulting de novo gene is a new protein-coding gene.

The important question is whether the evolution of de novo genes is a common event or a rare event.