I'm giving a talk next Wednesday (October 1st) to the members of the Senior College (retired faculty). It's at the University of Toronto Faculty Club at 10am. I'll talk for 50 mins then there's a coffee break followed by 50 mins of questions and discussion.
Guests are welcome but you'll have to pay $10 to cover the cost of coffee and cookies. You can also register to watch my talk on Zoom. You can also stay for lunch at the Faculty CLub but you'll have to let me know so I can put you down as a guest.
Here's the link to register: What's in Your Genome?
Wednesday Talk: Wednesday, October 1, 2025, 10am-12pm.
In-person at the Faculty Club and on Zoom
Larry Moran, Biochemistry, University of Toronto
Title: “What’s in Your Genome?”
Abstract: Scientists have been studying the human genome for more than 70 years but today there is considerable controversy about what’s in our genome. The publication of the complete sequence of the human genome in 2001 did nothing to resolve the controversy. For many scientists, the data confirmed their predictions that we have about 30,000 genes and most of our genome is useless junk DNA. Other scientists were shocked to learn that we have so few genes so they began the search for other explanations. Today, the majority of molecular biologists and biochemists believe that most of our genome is functional and there may be as many as 100,000 extra genes that weren’t identified in 2001. The majority of experts in molecular evolution disagree —they believe that 90% of our genome is junk DNA. I will summarize the data from both sides of the controversy and discuss the role that science journalism has played in misrepresenting scientific discoveries about the human genome.
13 comments :
The majority of experts in molecular evolution disagree —they believe that 90% of our genome is junk DNA.
Make that "Almost all". Among people who are aware of the processses that put junk into the genome, namely almost everybody studying molecular evolution, the figure is well over 90%. No, not 90% of the genome, considerably more than 90% of people who study molecular evolution.
But there are organisms which have far less junk and even some with almost none. What do people who are aware of the processes that put junk into the genome make of these organisms?
I would argue the majority of molecular biologists/biochemists who argue for general functionality are those who only think about and study the human genome.
Here is a good place to start:
The bioenergetic costs of a gene
Michael Lynch and Georgi K. Marinov (2015)
https://www.pnas.org/doi/10.1073/pnas.1514974112
I have a question:
According to CHAT GTP outside the pancreas INS transcription (insulin) is minimal, usually only in experimental or pathological contexts.
This means that in roughly 99,9% of the cells the INS gene serves no purpose (besides hypothetical alternative splicings not found so far).
In what category of junk DNA do these INS genes outside the pancreas fall?
That would be the meaningless category of junk. If a gene is junk unless it's expressed in every cell in the body, and presumably at all stages of development, then almost all genes are junk.
Well? How did it go?
@John Harshman I enjoyed it quite a lot. You'd have to ask the people in the audience if they liked it. It seems to me that many did judging from the questions.
is it available on youtube?
This article on spider species reducing their genome size on the Canary islands is fascinating.
https://phys.org/news/2025-10-island-spider-genome-defying-evolutionary.html
“Probably the strongest evidence for the theory is the remarkable uniformity for each protein molecule in the rate of mutant substitutions in the course of evolution.” Kimura M, Ohta T (1971) Nature 229: 467-479.
This so-called strongest evidence, the strict molecular clock, has been empirically disproven and replaced by the relaxed clock that allow for rate variations across species. Consequently, the neutral theory, which relies on it as its central pillar, has been thoroughly debunked. Yet many researchers, particularly in molecular anthropology and evolutionary biology, continue to cling to it with the tenacity of faith rather than the rigor of science.
Gojobori, Kimura et al, 1990 PNAS : “Actually, the concept of "molecular clock" is very important for the neutral theory: from the standpoint of the neutral theory, it is expected that a universally valid and exact molecular evolutionary clock would exist if, for a given molecule, the mutation rate for neutral alleles per year were exactly equal among all organisms at all times.” https://pnas.org/doi/pdf/10.1073/pnas.87.24.10015
Prof. of Univ. Mich. Jianzhi Zhang, Evidence for the neutral theory. “Over the years, the neutral theory has been supported by a number of lines of evidence. First, Zuckerkandl and Pauling 1965 proposes the concept of “molecular clock” based on the authors’ observation that the amino¬acid substitution rate per year for a protein is more or less constant across different evolutionary lineages. Because the rate of neutral substitution equals the rate of neutral mutation, neutral theory can explain the molecular¬clock phenomenon if the neutral mutation rate is constant per year.”
But the genetic equidistance phenomenon (GEP) holds even when mutation rates differ across lineages, i.e., when the strict molecular clock fails. The GEP across species with differing mutation rates is best explained by the Maximum Genetic Diversity (MGD) theory, which posits that genetic distances can reach an upper limit. In contrast, the strict molecular clock applies only to closely related species with similar mutation rates and where genetic distances have not yet approached this upper bound.
Prof. Jianzhi Zhang of the University of Michigan is a leading expert on molecular evolution. In a recent review, Neutral Theory, he summarized what he considers evidence supporting the neutral theory. (https://www.oxfordbibliographies.com/display/document/obo-9780199941728/obo-9780199941728-0081.xml?rskey=TlTBKz&result=77&print). Here, I outline these points and explain why none of them constitutes solid evidence:
1， The strict molecular clock (SMC) is listed as the first line of evidence. However, the SMC has been empirically disproven and replaced by the relaxed molecular clock, which allows for rate variation across lineages.
2，Higher mutation rates in less constrained genes are interpreted as evidence for neutrality. Yet DNA that appears unconstrained could still serve adaptive functions, requiring rapid turnover of alleles.
3， Certain patterns of genetic diversity are said to match neutral theory predictions. In reality, many patterns—most notably Lewontin’s paradox—directly contradict the theory. A theory that only explains a fraction of relevant phenomena is incomplete at best.
4， Synonymous sites evolving faster are assumed to be neutral. This logic is flawed: rapid changes at synonymous sites can also be adaptive, and numerous examples demonstrate functional roles for synonymous mutations.
5，Pseudogenes evolving quickly are interpreted as neutral. But the same reasoning in point 4 applies: high mutation rates do not automatically imply neutrality.
In short, none of the commonly cited “evidence” for the neutral theory withstands closer scrutiny.
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