Structure of the mitochondrial respirasome (electron transport complexes)

The membranes of bacterial cells and mitochondria contain a series of complexes that catalyze the oxidation of NADH. A lengthy electron transport chain leads eventually to the reduction of oxygen to water. Electrons lose energy as they pass down the chain and this is coupled to the transport of protons (H⁺) from one side of the membrane to the other. This proton gradient is used to drive ATP synthesis by the ATP synthase complex. The mechanism of making ATP is chemiosmosis but the pathway is often called oxidative phosphorylation or respiration.

The discovery of chemiosmosis (Chemiosmotic Theory) is one the few examples of a genuine paradigm shift. It is largely due to the work of Peter Mitchell [Ode to Peter Mitchell].

Tom Cech rejects junk DNA

A few months ago (June, 2024) I commented on an article by Tom Cech in The New York Times. [Tom Cech writes about the "dark matter" of the genome] In that article he expressed the view that 75% of the human genome consists of "dark matter" that is copied into RNAs of unknown function. He believes that many of these mysterious RNAs will turn out to have exciting functions.

I suspected that Cech is opposed to junk DNA and that suspicion is confirmed in his new book The Catalyst.

Michael Shermer supports Matt Ridley and the lab leak conspiracy theory

Back in 2021 Matt Ridley teamed up with Alina Chan to publish a book promoting the lab leak conspiracy theory about the origin of SARS-CoV-2. (See my summary of a review here.)

Yesterday (March 25, 2025) Michael Shermer interviewed Matt Ridley on The Michael Shermer Show podcast. The reason for the interview was to promote Ridley's new book Birds, Sex and Beauty: The Extraordinary Implications of Charles Darwin's Strangest Idea but Shermer started off the interview by asking about Ridley's previous book with Alina Chan. At 2 mins he asks,

Before we get into the new book, do you want to take a victory lap for your previous book. I mean the lab leak hypothesis is looking more and more like you called it years ago.

It's all downhill from there. I have lost all respect for Michael Shermer. It's a shame that this podcast is hosted on the Skeptic magazine website.

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Zeynep Tufekci writes in the New York Times defending the conspiracy part of the COVID-19 lab leak conspiracy theory

Zeynep Tufekci is Henry G. Bryant Professor of Sociology and Public Affairs at Princeton University (Princeton, NJ, USA). She is often praised for her non-academic writings in the popular press.

Ten days ago (March 16, 2025) she published an opinion piece in the New York Times where she discussed the lab leak conspiracy theory concerning the origin of the SARS-CoV-2 virus that caused the COVID-19 pandemic. As most Sandwalk readers know, there is no evidence to support that claim and plenty of evidence that the virus came from animals in the Wuhan market.

Google's "Generative AI" lies about junk DNA

Every now and then I check Google to see if there's any news about junk DNA. I use "junk DNA" as my search query.

The first thing I see at the top of the results page is a summary of the topic created by Google's Generative AI, which it claims is experimental. The AI summary is different every time you start a new search but all of the responses are similar in that they criticize the idea of junk DNA. Here's an example from today,

The misinformation spread by ENCODE in 2012 is gradually being recognized

I want to draw your attention to an excellent online book on bacterial genomes: Bacterial Genomes:Trees and Networks. The author is Aswin Sai Narain Seshasayee of the National Centre for Biological Sciences at the Tata Institute of Fundamental Research in Bangalore, India. Here's a link to Chapter 3: The genome: how much DNA? where he explains why bacterial genomes don't have very much junk DNA.

The chapter contains an excellent summary of the history of genome sizes in bacteria and eukaryotes and a detailed description of both the c-value paradox and the mutation load arguments. The relationship between junk DNA and population size is described.

I was especially pleased to see that the author didn't pull any punches in describing the ENCODE publicity campaign and their false statements about junk DNA.

In 2012, a post-human-genome project called ENCODE, which aims to experimentally identify regions of the human genome that undergo transcription—or are bound by a set of DNA-binding proteins, or undergo chemical changes called epigenetic modifications—came to a stunning conclusion that at least 80% of the human genome is functional and that it was time to sing a requiem for the concept of junk DNA! However, this conclusion, which has been severely criticised since its publication, ignores decades of well-supported arguments from evolutionary biology arising from the c-value paradox, some of which we have described here or will do so shortly; it does not quite explain why this conclusion—if broadly applied to the genomes of other multicellular eukaryotes—would not imply that a fish needs 100 times as much functional DNA as a human; and plays “fast and loose” with the definition of the term ‘function’. While the ENCODE project, a great success in many ways, has provided an invaluable resource for the study of human molecular biology, we can safely ignore its ill-fated conclusion on what fraction of the human genome is functional.

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Happy St. Patrick's Day! 2025

Happy St. Patrick's Day! These are my great-grandparents Thomas Keys Foster, born in County Tyrone on September 5, 1852 and Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. Thomas came to Canada in 1876 to join his older brother, George, on his farm near London, Ontario, Canada. Eliza came the following year and worked on the same farm. Thomas and Eliza decided to move out west where they got married in 1882 in Winnipeg, Manitoba, Canada.

The couple obtained a land grant near Salcoats, Saskatchewan, a few miles south of Yorkton, where they build a sod house and later on a wood frame house that they named "Fairview" after a hill in Ireland overlooking the house where Eliza was born. That's where my grandmother, Ella, was born.

Steven Pinker talks at Richard Dawkins

This is a lengthy conversation between Richard Dawkins and Steven Pinker. It took place in Boston at the Chevalier Theatre in September 2024. The video appeared on YouTube last month.

In my opinion, the important point is how deeply Pinker buys into the adaptationist perspective of Dawkins. He asks no challenging questions and he seems to be of the opinion that the Dawkins' view of evolution is the dominant view of evolutionary biologists. I'm an admirer of Richard Dawkins but I have not drunk the Kool-Aid.

Pinker has drunk the Kool-Aid and most of the video is him pontificating about his incorrect views of evolution.

Junk DNA is gradually making its way into mainstream textbooks

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.

The gene's-eye view of evolution

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.

Why Trust Science?

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.

What is photosynthesis?

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.

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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.)

Guess what happens when Nature asks EES proponents to write reviews of books by other EES proponents?

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.

Intelligent Design Creationists launch a new attack on junk DNA (are they getting worried?)

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).

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New Scientist promotes misinformation about evolution

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.