The idea that most of the human genome is junk originated more that 50 years ago. Since then, evidence in support of this concept has steadily accumulated but it has been stongly resisted by most biochemists and molecular biologists. Opposition is even stronger among scientists in other fields and in the general public thanks to a steady stream of anti-junk articles in the popular press.
Much of this opposition to junk DNA stems from a massive publiciy campaign launched by ENCODE researchers and the leading science journals back in 2012.
It's likely that most of the controversy over junk DNA is related to differing views on evolution and the power of natural selection. Most people think that natural selection is very powerful so that modern species must be extremely well-adapted to their present environment. They tend to believe that complexity is simply a reflection of sophisticated fine-tuning and this must apply to the human genome. According to this view, the presence of huge amounts of DNA with an unknown function is just a temporary situation and in the next few years most of this 'dark matter' will turn out to have a function. It has to have a function otherwise natural selection would have eliminated it.
I'm reveiwing some of the contributions to Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory. In this post I want to cover Arvid Ågren's contribution on the gene's-eye view of evolution.
Ågren starts out by reminding us that Richard Dawkins' book The Selfish Gene was voted the most influential science book of all time in a 2017 Royal Society poll. He goes on to say,
Regardless of one's views on the poll results—or the book's argument—the far reaching sway of The Selfish Gene means that anyone interested in the history and future of evolutionary theory has no choice but to grapple with its ideas. Chief among these is the so-called gene's-eye view of evolution. This is the approach to biology originally introduced by George Williams in Adaptation and Natural Selection and elaborated and popularized by Dawkins, that it is the genes, and not organisms as Darwin originally envisaged, that deserve the status as the unit of selection in evolution. Emerging in the decades succeeding the Modern Synthesis, the gene's-eye view of evolution has become an emblem of orthodoxy in biology.
Bruce Alberts,1 Karen Hopkin, and Keith Roberts have published an essay on Why Trust Science.
In this essay, we address the question of why we can trust science—and how we can identify which scientific claims we can trust. We begin by explaining how scientists work together, as part of a larger scientific community, to generate knowledge that is reliable. We describe how the scientific process builds a consensus, and how new evidence can change the ways that scientists—and, ultimately, the rest of us—see the world. Last, but not least, we explain how, as informed citizens, we can all become “competent outsiders” who are equipped to evaluate scientific claims and are able to separate science facts from science fiction.
Most of the essay describes an idealized version of how science works with an emphasis on collaboration and rigorous oversight. They claim that the work of scientists can usually be trusted because it is self-correcting.
A recent commentary in Nature prompts me to revisit an old bugaboo. The commentary discusses some recent work on CO2 fixation in plants [A genetic switch drove photosynthesis in plants1]. It begins with,
Photosynthesis, which uses energy from the Sun and carbon dioxide from the atmosphere to create carbohydrates, might be the most influential set of biochemical reactions on the planet.
Here's the problem. That's not a very good definition of photosynthesis. I discuss a much better definition in a post from seven years ago: Scientists confused about photosynthesis. A better definition is that photosynthesis is the process by which light energy is captured and converted to chemical energy. The direct products of photosynthesis are ATP and reducing equivalents such as NADPH. These cofactors are used to drive all sorts of reactions in the cell including DNA synthesis, protein synthesis, lipid synthesis, and carbohydrate synthesis.
This is very obvious when you examine photosynthetic bacteria but, unfortunately, photosynthesis was initially studied in large plants where much of the chemical energy produced by photosynthesis is used to fix CO2 and make carbohydrates. This led to the widespread belief that photosynthesis is all about making carbohydrates.
1. I'm using the title from the printed version of the journal. The web version has a different title. (I don't know why.)
There are a bunch of people who think that evolutionary theory needs to be extensively revised. They focus their attacks on a particular (incorrect) version of the Modern Synthesis and they promote a new version called the Extended Evolutionary Synthesis (EES).
Most EES proponents have very little in common except that they see themselves as revolutionaries. They each have their own little hobbyhorse that is presumably being suppressed by classical evolutionary biologists. Some of them belong to a cult called The Third Way (of Evolution). They are very good at promoting their point of view through whatever means it takes to get attention. The media loves them.
The Center for Science and Culture (sic) and the Discovery Institute (sic) have published another propaganda video on junk DNA. The emphasis is on their claim that ID predicted a functional genome and that prediction turned out to be correct! The difference between this video an previous attempts to rationalize their failures is that I now get a personal mention and a caricature in this latest video.
I think I understand the problem. The ID creationists are getting worried about junk DNA as they realize that more and more scientists are beginning to understand the real problems with the ENCODE data and previous claims of function. This is why they are attempting to rebut the science behind junk DNA. But the real problem is that they simply don't understand the science as you can see in the video.
Once again, we are faced with a question about whether Intelligent Design Creationists are stupid or lying (or both).
The December 7th issue of New Scientist features a cover promoting an article by Kevin Lala, an evolutionary biologist at the University of St. Andrews in Scotland (formerly Kevin Laland). The title of the article in the journal is DIY evolution but the online version is The extraordinary ways species control their own evolutionary fate.
It's interesting that the blurbs for the two version also differ ...
Natural selection of random genetic mutation isn't the only way to adapt, argues evolutionary biologist Kevin Lala.
(print version)
Natural selection isn't just something that happens to organisms, their activities also play a role, giving some species – including humans – a supercharged ability to evolve. (online version)
Kevin Lala is a proponent of the "Extended Evolutionary Synthesis" (EES). His particular schtick is niche construction meaning that evolution is promoted by organisms that help create their own environment. This behaviorial characteristic of animals is supposed to call into question the fundamentals of modern evolutionary theory based on population genetics.
Recall that evolution is defined as a change in the frequency of alleles in a population and the main mechanisms of change are natural selection and random genetic drift. Variation (creation of alleles) is caused by mutation.
This is a video of a debate/discussion between Alex O'Connor and Francis Collins on the existence of God. I'm not impressed with any of the points made by either side. Here's the YouTube description.
"'Does God Exist?' is perhaps the most important question to human existence because of its far reaching implications. What you believe about the existence of God—and by extension, who or what God might be—has the power to profoundly influence your values, and the course of your life.
To explore this question from opposing perspectives, we’ve brought together two intellectual heavyweights.
Alex O’Connor is an Oxford philosopher and self-proclaimed atheist, who has described himself as 'violently agnostic' about the existence of God. In recent years, he’s gained substantial recognition in the academic world and beyond, with nearly a million YouTube subscribers. His show, Within Reason, has featured intellectual giants like Jordan Peterson, Richard Dawkins, William Lane Craig, and Sam Harris.
On the other side, we have Dr. Francis Collins—one of the most decorated scientists of our time. From 1993 to 2003, he led the Human Genome Project, the monumental effort to map all human genes.
Dr. Collins is perhaps the most notable scientist to transition from atheism to belief in God, famously chronicling his journey in the New York Times bestseller, The Language of God. In it, he presents compelling arguments for the existence of a higher power.
In this episode, we explore the various lines of evidence for and against the existence of God. We begin by defining the concept of 'evidence' itself before delving into topics such as the fine-tuning of the universe, the moral argument, the resurrection of Jesus and the world's holy texts.
We found this to be a deeply stimulating discussion, and we believe it will be for you as well. So, join us as we navigate the complexities, the debates, and the profound mysteries surrounding the existence of God."
Zack Hancock has posted a lengthy (2 hours) video explaining why Denis Noble, James Shapiro, and the rest of The Third Way of Evolution crowd are wrong about evolution. You may not agree with everything Zack says but if you are really interested in following this debate then you should watch the entire video.
If you want to get to the juicy parts first then watch the section on "Chapter VII: Crusade against genetic reductionism" beginning with a short introduction at 1:35. In the last few minutes Zack gets into motive by asking why Denis Noble and James Shaprio seem to be so comfortable with supporters like Intelligent Design Creationists.
William Hasletine is a well-respected molecular biologist with an outstanding track record dating back to the time when he was a graduate student under Jim Watson and Wally Gilbert where he studied the regulation of gene expression in bacteria (Ph.D. in 1973). This is why I was surprised to see his recent article in Forbes where he seems to have fallen hook-line-and-sinker for postgenomics gobbledygook. It looks like Haseltine is losing the ability to think critically as he concentrates more on technology and public policy.
On January 9, 2023 the US House of Representatives created the Select Subcommittee on the Coronavirus Pandemic. It was chaired by Republican representative Brad Wenstrup of Ohio. There were nine Republicans on the subcommittee and seven Democrats.
Cambridge University Press is publishing a series of inexpensive books on biology topics. The books all have similar titles beginning with the word "Understanding." The "Understanding Life" series is edited by Kostas Kampourakis.
A few weeks ago I put up a post on Were you lied to in your genetics class?. At the time I thought it was just a fringe view being expressed by a graduate student who didn't understand genetics but now I realize that it's much more important than that.
Kostas Kampourakis is a respected scientist who is being promoted by the National Center for Science Education (NCSE) as an excellent communicator of evolution. Here's a short video (below) where he explains why teachers are making a mistake by saying that Mendel is the father of genetics and that simple Mendelian genetics can explain complex traits.
I'm struggling to understand his point. Here's what I think he means.
Kampourakis uses the example of eye color in Drosophila. He agrees that segregation of the allele responsible for eye color may follow the Mendelian rules1 but it's wrong to assume that there's a single gene responsible for eye color in fruit flies. He thinks that the goal is to understand the complexities of development and standard Mendelian genetics gives a completely distorted view of that subject, assuming, of course, that teachers can't separate genetics from understanding development.
Part of the problem is that we use the word "trait" differently. Take Mendel's example of pea color as another example. [Identity of the Product of Mendel's Green Cotyledon Gene (Update)] What Mendel was studying was the segregation of alleles in a gene called sgr (stay-green). It codes for an enzyme involved in the degradation of chlorophyll during senescence. When the enzyme is defective, chlorophyll isn't degraded and one of the visible phenotypes is that peas stay green instead of turning yellow.
I believe that the fundamental trait is the lack of an enzyme for degrading chlorophyll and this is what I would teach my students. I would also show them that the phenotype can be easily explained once you understand the biochemistry. It shows you that the connection between the fundamental trait and the visible phenotype can be mysterious so you should be careful about jumping to conclusions.
I think that Kampourakis sees this differently. He thinks that the example of green vs yellow peas is used to teach students that the color of peas is completely determined by a single gene. He thinks that the "trait" is the develpment of seed color in peas.
Kampourakis believes that "people looking for explanations and whatever happens to them in terms of disease and their own features, they find hard to reconcile the simplistic model that they have been taught with the realities of life." I think what he means is that students are being taught that single genes will always determine complex characteristics. He attributes that to the teaching of Mendelian genetics.
If he is correct, then that kind of teaching has to stop but I don't think it's the fault of Mendelian genetics. Mendelian genetics—indeed the entire field of genetics sensu stricto—is about the segregation of alleles. It is not about development even though we have come to learn a lot about development through genetics and the phenotype of mutants. I think that genetics and development are separate topics.
Kampourakis disagrees. He says, "we need, I think, to teach genetics from a developmental perspective. We need to show that genes do not determine traits but they are implicated in development." I believe this perspective comes from a more fundamental bias that distinguishes his worldview from mine. I tend to see genetics as a subject that covers all of biology and that includes all species such as bacteria, viruses, and single-cell eukaryotes. He tends to see things from a human perspective, which is much more complex than dealing with simple organisms. I think we should concentrate on teaching students about simple well-understood model organisms and then move on to explaining how this applies to more complex organisms. Kampourakis seems to be implying that we should jump right into reaching high school students about the most challenging issues in biology.
1. Actually, the common allele for white eye in Drosophila (see image) is X-linked so it doesn't follow the standard rules for Mendelian segregation!
Populous, geographically disperse, species are often subdivided into subspecies, races, demes, or geographically differentiated populations. Homo sapiens is no exception; there are many subpopulations whose overall genetic compositions are significantly different—so different, in fact, that we have no trouble identifying members of those subpopulations and the sequence of their genomes can assign them to the different groups.1
We could use the word "race" to distinguish the largest of these subpopulations if the word wasn't so loaded with non-scientific meaning. I believe that, from a scientific perspective, humans races exist. [Do Human Races Exist?]. Jerry Coyne is much better (braver?) than I at defending the biological and evolutionary reality of human races and attacking the well-meaning, but mistaken, attempt to deny the existence of human races. [Genetic ignorance in the service of ideology] It's part of a larger effort to combat something he calls The Ideological Subversion of Biology. The point he's making is that we are teaching our children a number of misconceptions that conflict with science and this contributes to a mistrust of science.
