The Selfish Gene: a critic and a defender are both wrong!

Richard Dawkins published The Selfish Gene in 1976 and in 2017 the Royal Society conducted a popular poll that voted it the most inspiring science book of all time.

I don't think that book is a good representation of modern evolutionary thinking and I've expressed that opinion many times on this blog [The selfish gene vs the lucky allele] ["The Selfish Gene" turns 40] [The "selfish gene" is not a good metaphor to describe evolution] [Die, selfish gene, die!].

The issues are complicated—here's how Dawkins described his book in the 1989 edition.

The selfish gene theory is Darwin's theory, expressed in a way that Darwin did not choose but whose aptness, I should like to think, he would instantly have recognized and delighted in. It is in fact a logical outgrowth of orthodox neo-Darwinism, but expressed as a novel image. Rather than focus on the individual organism, it takes a gene's-eye view of nature. It is a different way of seeing, not a different theory.

My objections are that the book is far too adaptationist and too "Darwinian." It fails to convey the complications of evolution to the general public, including the dominance of chance, accident, and contingency. It misrepresents some views of evolution, especially punctuated equilibria. It focuses too much on genes (alleles) as the unit of selection (evolution?) at the expense of individuals, groups, and species. (Species sorting may not be important but it deserved more than passing dismissal.) It focuses too much on the evolution of animals, especially animal behavior and that feeds into the biases of the general public who know very little about the vast majority of species outside of the animal kingdom.

"Atheism of the gaps" or how to misrepresent atheism and abuse philosophy

I am an atheist. That means I don't believe in god(s). I also don't believe in Santa Claus, the tooth fairy, Bigfoot, the Loch Ness monster, or leprechauns.

When I say that I don't believe in leprechauns it means that I don't devote any time at all to the idea that leprechauns might exist and I don't alter my life in any way to allow for that possibility. If you ask me in casual conversation, I might say that leprechauns don't exist.

But I will give you a different answer if you are a philosopher or someone steeped in philosophical musings. In that case I will be careful not to say that lepechauns don't exist because I'm well aware of the fact that you can't prove a negative.

Can DNA fingerprints distinguish between identical twins?

The other day we were watching one of our favorite British crime shows where science and forensics plays a prominent role in catching the criminal.

This one involved a complicated story line with three identical triplets who impersonated each other.¹ DNA was present at one of the crime scenes and it matched the DNA of the triplets but the investigators weren't able to distinguish between the three triplets. I knew that monozygotic twins and triplets had identical DNA fingerprints but I also knew that it was possible to tell them apart if you had more DNA sequences.

A typical DNA fingerprint consists of amplifying selected regions of the genome using PCR. These regions contain short tandem repeats (STRs) consisting of multiple stretches of identical sequences such as AGGCCT or CGCGAT. Individuals differ in the number of these repeats and hence the length of DNA that contains them and this length can be easily detected. The best DNA fingerprint techniques look at about 30 different STR regions and the chance that all 30 will be identical in size in unrelated individuals is extremely low.

Dark matter and junk DNA

It's been almost three years since I created a blog post on What is the "dark matter of the genome"?. I noted that the term was popularized by the philosopher Evelyn Fox Keller who was opposed to the concept of junk DNA. She preferred to think that most of the genome was full of functional sequences that hadn't yet been discovered. The term "dark matter" was her way of emphasizing that most of the genome was a mystery but it wasn't junk.

Since then, the term "dark matter" has been increasingly used by scientists, especially those in the field of genomics. I think it's for the same reasons that Evelyn Fox Keller described. These scientists spend a lot of time and effort analyzing entire genomes for biochemical activity of various sorts and they don't want to admit that they are mostly looking at junk DNA. That's why I summarized my position like this ...

What is "alternate RNA decoding"?

I recently came across a paper in Nature on alternate RNA decoding. It looked interesting so I read the abstract. That didn't help. I was still confused about what the authors were assaying and whether it was anything other than translation or splicing errors. So I read the introduction to try and get a better understanding of alternate RNA decoding.

That didn't help. The rest of the paper wasn't any more helpful.

I'm going to reproduce the abstract and the relevant part of the introduction so you can judge for yourself whether I'm just being stupid or whether the authors should have been more clear about what they are doing. I think I'm reasonably well-informed about basic biochemistry and molecular biology principles and concepts but maybe I'm falling behind in my old age.

Nature is a prestigious journal and in the past (25 years ago) you could assume that any paper published in Nature was probably important. Today, I'm not so sure about that but maybe I'm being too critical.

"Eclipsed Horizons: Unveiling the Dark Genome" challenges the model of junk DNA

Eclipsed Horizons: Unveiling the Darfk Genome is a book by Sudhakaran Prabakaran that promotes the idea of a dark genome and challenges the concept of a genome that's mostly junk DNA. It was published by World Scientific in March 2026. The book costs about $90 (USD) so I'm not going to buy it even though the subject is of great interest to me. I just don't think it's going to be very good after reading the promotional blurb.

Eclipsed Horizons: Unveiling the Dark Genome presents a revolutionary perspective on the human genome, building upon years of research challenging the conventional notion that non-coding DNA is merely "junk." Through rigorous scientific analysis, this book advances a groundbreaking new theory: that these vast non-coding regions — comprising 98% of our genome — function as a sophisticated adaptive reservoir with latent potential that activates in response to environmental challenges.

Dr Prabakaran develops a compelling information-theoretic framework to understand how this "dark genome" operates as nature's supreme adaptive system. Beginning with a speculative scenario of space-adapted humans called Homo minimus, he traces the cosmic origins of life's elements, explores DNA's remarkable information architecture, and examines evolutionary transitions where non-coding regions played crucial roles in developing biological complexity. While incorporating speculative elements to engage readers, this text maintains academic rigor throughout, making it suitable as a textbook on the dark genome. Each chapter builds on empirical research while proposing testable hypotheses about stress-responsive elements of genomic function, regulatory networks, and the dark proteome that activate during environmental crises.

The culminating chapters explore potential implications for humanity's cosmic future, suggesting that the dark genome may harbor adaptations relevant to space environments. This hybrid approach — balancing academic precision with accessible narrative and thoughtful speculation — makes the book valuable for both specialized academic audiences and interested general readers seeking a deeper understanding of genomic complexity beyond conventional paradigms.

Has anybody read this book? Please let me know if Prabakaran is making any good arguments that haven't already been refuted years ago. Does he reference my book?

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Tofino Airport: 1942 and 2026

We visited Tofino on the west coast of Vancouver Island (British Columbia, Canada). We took a seaplane from Vanvouver harbor to the harbor in the town of Tofino. On the return trip we passed over the Tofino-Long Beach Airport (YAZ) located a few kilometers south of Tofino and we got a good photo of it from the air.

The airfield was constructed in 1942, shortly after Canada declared war on Japan. [RCAF Station Tofino]. It's purpose was to protect the west coast from Japanese submarines that were harassing merchant ships in the Eastern Pacific.

My father was Laurence Victor "Vic" Kirsch.¹ He got his wings in April 1942 and joined RCAF 132 Squadron. They were first stationed at Sea Island (now Vancouver International Airport (YVR)) then transferred to Patricia Bay (Pat Bay, now Victoria International Airport (YYJ)). On Oct. 15th the squadron landed at Tofino.

Intelligent Design Creationists are still spreading lies about junk DNA

Intelligent Design Creationists have convinced themselves that there's no junk DNA in the human genome. They predicted this more than 30 years ago based on the idea that their god(s) would never have designed humans with a genome full of junk DNA. They firmly believe that modern science has shown them to have been correct.

The ID creationists are in the midst of congratulating themselves on their successes while celebrating the 30th anniversary of the publication of Darwin's Black Box. Most of the posts on the Science & Culture Today website are laughable and I stopped responding to them several years ago. However, I think it's worthwhile to highlight one of Casey Luskin's posts to show you just how ignorant they are about real science. [Thirty Years of Intelligent Design Predicting the Unexpected Genome]

The evolution of metabolic enzymes in LUCA, Bacteria, and Archaea

The best scenario for the origin of life is that it first arose in hydrothermal vents deep in the ocean. The first catalysts of metabolic reactions were metals and later on simple organic molecules bound to metals. The substrates for all reactions were inorganic compounds such as H₂, CO₂, NH₃, H₂S and phosphate/phosphite.

Over time, the inorganic catalysts were gradually replaced by protein and RNA catalysts that often incorporated the metal ions into their active sites or used cofactors containing metal ions. There are about 400 basic metabolic reactions that are fundamental to life. Some enzyme catalysts are very ancient but others seem to be more recent.

Do scientists at Amgen understand the human genome?

Amgen Inc. is a major pharmaceutical company based in Thousand Oaks, California (USA). [Wikipedia: Amgen] It was founded in 1980 to exploit developments in biotechnology, especially recombinant DNA technology. (Amgen is short for Applied Molecular Genetics.)

Like most pharmaceutical companies, Amgen produces promotional videos that are supposed to show how close they are to cutting edge science. Here's one that celebrates DNA Day and answers the question "What Is the Dark Genome? 98% of DNA explained." Are you impressed?

What Is the Dark Genome?

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Anaerobic carbon fixation in ancient prokaryotes

Most of us were taught that plants are the main source of fixing carbon from carbon dioxide. Some of us even had to memorize the enzymes and reactions of the Calvin Cycle including the complicated reaction catalyzed by rubisco, the main CO₂ fixing enzyme. [Fixing Carbon: the Rubisco Reaction].

We were led to believe that plants were the main source of sugars and other organic molecules but that's because undergraduate biochemistry education emphasizes human biochemistry. Photosynthesis and plants are only important because they are food. We were also taught, incorrectly, that photosynthesis is defined as a carbon-fixation process. [What is photosynthesis?]

It turns out that the Calvin Cycle isn't restricted to plants and it doesn't even require oxygen. Anaerobic bacteria also have a version of the Calvin Cycle and they are perfectly capable of fixing carbon without a major energy source like photosynthesis. [Carbon Dioxide Fixation in the Dark Ocean]

This makes sense since the earliest forms of life had to be able to turn inorganic molecules (e.g. CO₂) into organic molecules so they had to be able to fix carbon. Current models of the origin of life are referred to as Metabolism First models because they postulate that life began with simple metabolic reactions that made organic molecules from inorganic molecules. One of the most important of these early reactions is the fixation of two molecules of CO₂ into a two carbon compound (acetate).

The functions of human protein-coding genes

There are about 20,000 protein-coding genes in the human genome. We'd like to know what all these genes are doing but the only way to find out is to rely on experiments that explore the function of an individual protein.

This functional data has been collected and assembled in a large database called the Gene Ontology Resource (GO). Unfortunately, it only covers about one third of all human proteins.

Feuermann et al. (2025) developed a program to extend the coverage provided by direct annotation of human genes by making use of annotation records in related genes from other species. They constructed phylogenetic trees for 6,333 gene families representing a total of 17,079 human genes. This allowed them to deduce the functions of many more genes by taking advantage of GO annotations in homologous genes.

The "Venn diagram" (their words) illustrates the advantage of combining phylogenetic data with GO annotation. The yellow part represent the fraction of human proteins that have been directly annotated in the GO database while the brown and blue sections show how function can be inferred from a much larger set of proteins by looking at annotations in other species.

The results are not surprising. Most of the proteins are involved in basic metabolism such as cellular processes: (deep blue), cellular metabolism: (blue), and cell structure (cell structure: dark blue). Most of the genes families involved in these functions are derived from single genes that are also found in bacteria. The important point here is that the increase in number of genes in complex eukaryotes is mostly due to gene duplication and subspecialization.

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Feuermann, M., Mi, H., Gaudet, P., Muruganujan, A., Lewis, S.E., Ebert, D., Mushayahama, T., Consortium, G.O. and Thomas, P.D. (2025) A compendium of human gene functions derived from evolutionary modelling. Nature 640:146-154. [doi: 10.1038/s41586-025-08592-0]

Why do scientists at "elite" universities dominate scientific discourse?

We all know that scientists at elite universities publish a lot more papers than scientists at other universities. Why is that? Is it because those universities have better labs and equipment? Is it because the scientists at elite universities are smarter than other scientists? Is it because of the reputation of the universities that makes it easier to get papers accepted in the best journals?

A group of scientists at the University of Colorado (Boulder, Colorado, USA) decided to examine the question and they came up with another answer—one that I have long suspected.

Pervasive transcription = genes + noise

Most of the DNA in the human genome is transcribed at some point in development or in some cell type. This fact has been known since the late 1960s.

There are basically two types of transcripts. Functional transcripts mostly come from genes although there might be a few exceptions (e.g. enhancer RNAs). Non-functional transcripts can be produced by pseudogenes or from virus and transposon fossils. They can also due to transcriptional noise caused by spurious transcription.

Philosophers talk about junk DNA

There is considerable debate in the scientific literature over the amount of junk DNA in the human genome. The standard model was developed 50 years ago; it postulated that only 10% of the genome is functional and 90% is junk. Most of the evidence since then has supported that model but there are many scientists who reject it.

This would seem to be fertile ground for philosophers of biology and, indeed, there are some philosophers who have made a significant contribution, mostly in sorting out how to define function (Brunet et al., 2021; Linquist et al., 2020). Also, many philosophers are interested in the history of biology and some (e.g. Morange, 2020) have done a good job of describing the history of the junk DNA concept.