Most of the genes in eukaryotes contain introns that are removed by splicing during processing of the primary transcript. In some cases the gene produces two different functional RNAs due to differential splicing of the introns. If the product is mRNA then two different versions of the protein can be made as shown in the figure from my book What's in Your Genome? This mechanism is known as alternative splicing.
True alternative splicing is rare—less than 5% of all genes are alternatively spliced.1 However, when you analyze all of the transcripts in a tissue you will invariably detect many transcripts from junk DNA and many low abundance splice variants. Those transcripts and splice variants are due to transcription errors and splicing errors. Splicing errors arise from the presence of weak splice sites that are occasionally recognized by the normal spliceosome or by the splice factors responsible for true alternative splicing.
The latest summary of the number of genes in the human genome gets the number of protein-coding genes correct but their estimate of the number of known non-coding genes is far too high.
In order to have a meaningful discussion about molecular genes, we have to agree on the definition of a molecular gene. I support the following definition (see What Is a Gene?).
Jonathan McLatchie is an Intelligent Design Creationist who now blogs frequently on the Discovery website Evolution News [sic]. His latest post is How NOT to Argue Against Irreducible Complexity where he defends the claim that the human male reproductive apparatus is irreducibly complex and therefore must be a product of intelligent design.
You can read the post yourself to see how ID proponents argue. I want to make another point.
McLatchie thinks that the irreducible complexity argument is very powerful evidence for intelligent design. He writes,
The argument from irreducible complexity against evolution and for design has always held strong intuitive appeal for me, and it has hence become my argument of choice in discussions about the scientific merits of evolution versus design.
Let's look at the logic of the argument from irreducible complexity. Assume that we have identified a structure that's irreducibly complex. There are three possible ways to deal with its origin.
There is a plausible naturalistic explanation for the evolution of the irreducibly complex structure.
There is currently no detailed naturalistic explanation that accounts for the evolution of the irreducibly complex structure.
It is impossible for there to ever be a naturalistic explanation; therefore, god did it.
We know that there are good naturalistic explanations for the evolution of irreducibly complex structures. In fact, McLatchie mentions some of them that refuted his earlier claims. Behe has also backed off some of his claims in light of evidence that irreducibly complex structures can evolve without the help of god(s). This establishes that the mere existence of an irreducibly complex structure is not evidence for intelligent design.
Here's how Behe explains it on page 40 of Darwin's Black Box.
Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one cannot definitively rule out the possibility of an indirect, circuitous route.
In some cases there is currently no good naturalistic explanation for the evolution of an irreducibly complex structure. This could be due to a real difficulty in coming up with a plausible scenario or it could be due to the fact that no scientist has bothered to do the investigation required because they don't care. In either case, the current lack of an explanation is not, in itself, evidence for an intelligent designer.
The third possibility is the one that counts. If you can prove that a naturalistic explanation is impossible then there must be a non-naturalistic explanation such as aliens, or god(s). McLatchie says the the sperm flagellum is irreducibly complex and that he cannot imagine how it could have evolved naturally. According to creationist logic, it follows that some alien, or some god, must have designed the original sperm flagellum.
McLatchie won't tell us when this happened or why the intelligent designer was so interested in sperm, but that's typical of Intelligent Design Creationsts—they require detailed explanations from scientists but not from their fellow creationists.
Evelyn Fox Keller died a few days ago (Sept. 22, 2023). She was a professor of History and Philosopher of Science at the Massachusetts Institute of Technology (Boston, MA, USA). Most of the obituaries praise her for her promotion of women scientists and her critiques of science as a male-dominated discipline. More recently, she turned her attention to molecular biology and genomics and many philosophers (and others) seem to think that she made notable contributions in that area as well.
In his new book "What’s in Your Genome?", Laurence A. Moran shows that all the research done in the decades since that letter was written has confirmed what Crick, Jukes, and other specialists believed all along: much of our DNA is indeed a kind of “junk.”
This is a video of a debate that took place in Kraków, Poland on June 2, 2023. The topic was "Intelligent design in nature—illusion or reality?" (Spoiler alert! - the answer is "illusion.") The participants were Michael Behe and Richard v. Sternberg for the creationists and Michael Ruse and Malgorzata Moczydlowska-Vidal for the science/philosophy side. The video is almost three hours long and I don't recommend watching the whole thing.
Ruse, as usual, is incoherant and more focused on religion and telling Christians how they should behave. The Polish paleontologist didn't do a very good job of addressing the claims of the creationists.1 Michael Behe gave his standard pitch about irreducible complexity and the bacterial flagellum.
The interesting part was Sternberg's defense of intelligent design. I hadn't seen him before although I've been familiar with his writings over the past twenty years. His opening presentation begins at 17:50 and it's worth watching to see how important the junk DNA debate is to the ID crowd.
Sternberg begins by noting that he was skeptical of the arguments put forward by Richard Dawkins in "The Selfish Gene" where Dawkins says that 98% of our DNA is noncoding junk. (Dawkins never said any such thing!) Sternberg says that when he started looking for function in this part of the genome he found that it was replete with function. Then he brings up the ENCODE results and claims that they challenged the concept of a gene (not true). Sternberg says that the new definition of a gene is that it is polyfunctional and "constantly changing in real time." He says,
... how can you have a theory based on an entity that you cannot define and how can you discuss the evolution of something that is kind of this amorphous notion ...
Sternberg seems to think that redefining the gene shows that evolutionary biology is out of touch with reality. He claims that the discovery of the epigenome is futher evidence that there are multiple layers of information that take us far beyond the theory of neo-Darwinism that was crafted in the nineteen teens and the 1920s.
Sternberg reflects the views of many Intelligent Design Creationists who tout the "debunking" of junk DNA as one of their greatest intellectual achievements because they predicted all along that there couldn't be large amounts of junk DNA in our genome because that's incompatible with intelligent design. What's different in the case of Richard Sternberg is that the discovery of function in most of our genome is what led him to the position that design is the best explanation.
I find it strange that Intelligent Design Creationists are relying so heavily on the so-called debunking of junk DNA, especially since in Sternberg's case he is well aware of the fact that some prominent scientists have criticized ENCODE. It's a risky strategy to put so much emphasis on a result that may turn out to be wrong. If our genome is mostly junk DNA (it is!) then the major part of their argument for design falls apart.
From reading the ID literature, it seems that they are supremely confident that most of our genome will turn out to be full of function. It will be interesting to see how they respond when the scientific community concludes that 90% of our genome is junk. From my perspective, they are digging themselves into a deep hole that will be very difficult to climb out of. Maybe it's time to stop digging?
Sternberg made one quip that's worth highlighting. At about 1:46:20 he talks about a saying that he learned in the air force; you don't receive flak unless you're over a significant target. That's cute. He uses it to explain why intelligent design is coming under such heavy attack. He is, of course, correct. When you drop bombs on people you can expect them to get upset. When you attack some of the most important concepts in science you can expect some pushback. That doesn't mean your bombing is justified. If it were justified then scientists would embrace your criticisms instead of shooting them down.
Sternberg scores big at 2:51:11 when he asks, "Can there be Darwinian evolution ... or any evolution in general, without natural selection?" The correct answer is yes. Malgorzata Moczydlowska-Vidal says no and so does Michael Ruse. Ruse then goes on to explain why he dismisses random genetic drift. Sternberg then explains neutral evolution and Michael Lynch's drift-barrier hypothesis and why some biologists use them to explain some of the ID challenges. Sternberg (and Behe) appear to know more about evolution than their opponents.
1. She concentrated on presenting evidence for the history of life but both Behe and Sternberg accept common descent and the correct age of the Earth.
This is a very slick video from the Discovery Institute. It shows you what we are up against. Anyone who thinks they can easily refute the claims in this video hasn't tried.
Intelligent Design Creationists know exactly what they are doing and they are very good at it. There are so many thing wrong with this video that it would take a book to correct them all and, furthermore, you would have to convince people that their entire worldview has to change in order to really understand biology. I bet there are many scientists who couldn't deal with a video like this and that's a problem.
Real biology is messy and sloppy. Things do not look as neatly designed as Richard Dawkins and the creationists would have you believe. I've tried to present the case for a sloppy worldview in my latest book.
You know you're in for a treat when papers published in a (previously) reputable journal make frequent references to Dennis Noble and James Shapiro.
The purpose of this post is to demonstrate that you shouldn't let creationist amateurs publish anti-evolution rants in scientific journals.
I want to discuss two papers that were recently published in the journal Progress in Biophysics and Molecular Biology. This used to be a very reputable journal but its reputation suffered a big blow in 2018 when it published a paper on panspermia. The current editor-in-chief at the time, Denis Noble, defended that article on the grounds that the origin of life is an unsolved problem and all points of view deserve to be covered in a scientific journal. Denis Noble is still on the editorial board along with Tom L. Blundell and Delphine Dean (see editorial board) and they now have to answer for publishing two creationist papers by Olen R. Brown and David A. Hullender.
John Mattick continues to promote the idea that he is leading a paradigm shift in molecular biology. He believes that he and his colleagues have discovered a vast world of noncoding genes responsible for intricate gene regulation in complex eukaryotes. The latest salvo was fired a few months ago in June 2023.
Mattick, J.S. (2023) A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. BioEssays:2300080. [doi: 10.1002/bies.202300080]
Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information.
This paper is promoted by a video in which he explains why there's a Kuhnian revolution under way. This paper differs from most of his others on the same topic because Mattick now seems to have acquired some more knowledge of the mutation load argument and the neutral theory of evolution. Now he's not only attacking the so-called "protein centric" paradigm but also the Modern Synthesis. Apparently, a slew of "anomalies" are casting doubt on several old paradigms.
This is still a paradigm shaft but it's a bit more complicated than his previous versions (see: John Mattick's paradigm shaft). Now his "anomalies" include not only large numbers of noncoding genes but also the C-value paradox, repetitive DNA, introns, enhancers, gene silencing, the g-value enigma, pervasive transcription, transvection, and epigenetics. Also, he now seems to be aware of many of the arguments for junk DNA but not so aware that he can reference any of his critics.1 His challenges to the Modern Synthesis include paramutation which, along with epigenetics, violate the paradigm of the Moden Synthesis because of non-genetic inheritance.
But the heart of his revolution is still the discovery of massive numbers of noncoding genes that only he and a few of his diehard colleague can see.
The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the majority of the mammalian genome is differentially and dynamically transcribed during development to produce tens if not hundreds of thousands of short and long non-protein-coding RNAs that show highly specific expression patterns and subcellular locations.
The figure is supposed to show that by 2020 junk DNA had been eliminated and almost all of the mammalian genome is devoted to functional DNA—mostly in the form of noncoding genes. There's only one very tiny problem with this picture—it's not supported by any evidence that all those functional noncoding genes exist. This is still a paradigm shaft of the third kind (false paradigm, false overthrow, false data).
1. There are 124 references; Dawkins and ENCODE make the list along with 14 of his own papers. Most of the papers in my list of Required reading for the junk DNA debate are missing. The absence of Palazzo and Gregory (2023) is particularly noteworthy.
John Mattick is famous for arguing that there's a correlation between genome size and complexity; notably in a 2004 Scientific American article (Mattick, 2004) [Genome Size, Complexity, and the C-Value Paradox ]. That's the article that has the famous Dog-Ass Plot (left) with humans representing the epitome of complexity and genome size. He claims that this correlation is evidence that most of the genomes of complex animals must have a function. He repeats this claim in a recent paper (see below).
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long ‘intergenic’ and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed ‘enhancers’, which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
Paradigm shifts are rare but paradigm shafts are common. A paradigm shaft is when a scientist describes a false paradigm that supposedly ruled in the past then shows how their own work overthrows that old (false) paradigm.1 In many cases, the data that presumably revolutionizes the field is somewhat exaggerated.
John Mattick's view of eukaryotic RNAs is a classic example of a paradigm shaft. At various times in the past he has declared that molecular biology used to be dominated by the Central Dogma, which, according to him, supported the concept that the only function of DNA was to produce proteins (Mattick, 2003; Morris and Mattick, 2014). More recently, he has backed off this claim a little bit by conceding that Crick allowed for functional RNAs but that proteins were the only molecules that could be involved in regulation. The essence of Mattick's argument is that past researchers were constrained by adherance to the paradigm that the only important functional molecules were proteins and RNA served only an intermediate role in protein synsthesis.
These are the criteria used to determine the ranking.
As usual, American universities dominate the rankings taking eight of the top ten positions. (Cambridge and Oxford are the other two.) Most of the top schools are quite old so they are more likely to have had alumni who won Nobel Prizes and more likely to have had Nobel Laureates on staff. Many of the American universities are private and wealthy—they are able to attract the best scientists and the most funding for research.
My school, the University of Toronto (Toronto, Canada), comes in at #24 - far behind the top schools on the list.
It's important to note that the rankings have nothing to do with the quality of undergraduate education at these universities.
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?].
I just learned that Don Voet died on April 11th, 2023. Don and Judy Voet were the authors of one of the most successful biochemistry textbooks of all time and for a long time they were the editors of the journal Biochemistry and Molecular Biology Education (BAMBED). I've known Don for over thirty years and we met often at conferences.
He will be greatly missed. Here's an excerpt from the obituary from the American Society for Biochemistry and Molecular Biology written by my old friend Charlotte Pratt who collaboated with me on my textbook and with Don and Judy Voet on theirs [Don Voet (1938-2023)].
Don’s work over the years demonstrated his conviction that biochemical knowledge has limited value unless it is transmitted fully and honestly to the next generation of scientists. His writing style was intentionally aimed at students of all levels, never dumbed down, and straightforward — a way to invite readers to enter a conversation among professional scientists.
Ever collegial, Don insisted on dropping names into the text, referring to the discoveries of specific researchers wherever possible and borrowing figures from the original publications rather than rendering simplified versions. In cases where visual information was lacking, Don created his own molecular graphics, at a time when modeling software was not accessible to amateurs.
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.
