Warning! These men (Crick and Dawkins) are dangerous!

Lock the doors! Hide the children! The boogeymen will get you! Francis Crick and Richard Dawkins have destroyed biology by reducing humans to nothing more than genes! They are destroying humanity by denigrating agency and purpose.

That's the message conveyed by Denis Noble and others in numerous books and articles aimed at the general public. The latest attempt is an article by Denis Noble, his brother Raymond Noble, and their colleague, Reine Bourret: We've got biology wrong, and that's why the Human Genome Project failed. The subtitle is, "Crick and Dawkins' Selfish Gene made a mistake."

Early mammal-like ancestors (mammaliaforms)

The popular view of mammal evolution is that mammals arose about 100 million years ago and diversified rapidly after the asteroid impact about 65 million years ago. This view is somewhat misleading since the current view is that the crown group (Mammalia) arose almost 200 million years ago.

The first mammals were the monotremes, represented today by the platypus and the echidnas. Later on, the remaining lineage split into the marsupials and the placentals around 120 million years ago.

Denisovans

The Denisovans¹ are a distinct group of humans (genus Homo) that shared a common ancestor with Neanderthals about 450,000 years ago. That clade shared a common ancestor with Homo sapiens about 650,000 years ago.

The figure below is from Dediu and Levinson (2018). The dates are controversial, and there's no consensus on whether the Denisovans and Neanderthals are separate species.

Philip Ball's view of life

Philip Ball has written many books but I want to concentrate on what he says in one of his latest books, How Life Works.

I expressed some skepticism about that book before I read it: Philip Ball's new book: "How Life Works". At that time (February 2024), I promised to write a review but that never happened for two reasons. First, there were just too many misrepresentations and misinterpretations to cover and I got bored and frustrated trying to document them. Second, I found it very difficult to come to grips with Ball's main thesis, which seems to have something to do with agency or some higher level of control of human development.

Defining a gene: the selfish Mendelian gene and the molecular gene

I recently commented on an article in Nature by Nathaniel Comfort where he criticized Dawkins' book The Selfish Gene. I also criticized Jerry Coyne's response because he (Coyne) failed to mention the most serious issue with Dawkins' book; namely, his (Dawkins) failure to give adaquate coverage to neutral theory and random genetic drift. [The Selfish Gene: a critic and a defender are both wrong!

Coyne quickly corrected that omission with a post the next day: The Neutral Theory: a genuinely important supplement to evolution’s “Modern Synthesis”.

Comfort made many mistakes but one of them was praising Philip Ball's book How Life Works. This prompted Ball to respond to my blog post by giving us a link to his own review on the Scientific American website: The Selfish Gene, revisited.

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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