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.

BREAKING NEWS: Intelligent Design Creationists claim that this year's Nobel Prize refutes junk DNA and confirms IDC predictions!

This is a Come Let Us Reason Together (sic) podcast moderated by Lenny Esposito with Faxale "Fuz" Rana of Reasons to Believe and Casey Luskin of the Discovery Institute. They discuss this year's Nobel Prize for the discovery of microRNAs and "how it supports intelligent design and weakens the evolutionary paradigm." Casey Luskin devoted a post to the topic on the Discovery Institute propaganda blog: 2024 Nobel Prize Awarded for the Discovery of Function for a Type of “Junk DNA”.

Enjoy! (Spot the lies.¹)

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1. In Luskin's case, we know he is lying. [Is Casey Luskin lying about junk DNA or is he just stupid?]

Francis Collins on the existence of God

This is a video of a debate/discussion between Alex O'Connor and Francis Collins on the existence of God. I'm not impressed with any of the points made by either side. Here's the YouTube description.

"'Does God Exist?' is perhaps the most important question to human existence because of its far reaching implications. What you believe about the existence of God—and by extension, who or what God might be—has the power to profoundly influence your values, and the course of your life.

To explore this question from opposing perspectives, we’ve brought together two intellectual heavyweights.

Alex O’Connor is an Oxford philosopher and self-proclaimed atheist, who has described himself as 'violently agnostic' about the existence of God. In recent years, he’s gained substantial recognition in the academic world and beyond, with nearly a million YouTube subscribers. His show, Within Reason, has featured intellectual giants like Jordan Peterson, Richard Dawkins, William Lane Craig, and Sam Harris.

On the other side, we have Dr. Francis Collins—one of the most decorated scientists of our time. From 1993 to 2003, he led the Human Genome Project, the monumental effort to map all human genes.

Dr. Collins is perhaps the most notable scientist to transition from atheism to belief in God, famously chronicling his journey in the New York Times bestseller, The Language of God. In it, he presents compelling arguments for the existence of a higher power.

In this episode, we explore the various lines of evidence for and against the existence of God. We begin by defining the concept of 'evidence' itself before delving into topics such as the fine-tuning of the universe, the moral argument, the resurrection of Jesus and the world's holy texts.

We found this to be a deeply stimulating discussion, and we believe it will be for you as well. So, join us as we navigate the complexities, the debates, and the profound mysteries surrounding the existence of God."

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Zack Hancock explains why Denis Noble and James Shapiro are wrong about evolution

Zack Hancock has posted a lengthy (2 hours) video explaining why Denis Noble, James Shapiro, and the rest of The Third Way of Evolution crowd are wrong about evolution. You may not agree with everything Zack says but if you are really interested in following this debate then you should watch the entire video.

If you want to get to the juicy parts first then watch the section on "Chapter VII: Crusade against genetic reductionism" beginning with a short introduction at 1:35. In the last few minutes Zack gets into motive by asking why Denis Noble and James Shaprio seem to be so comfortable with supporters like Intelligent Design Creationists.

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William Haseltine misrepresents molecular biology and calls for a paradigm shift

William Hasletine is a well-respected molecular biologist with an outstanding track record dating back to the time when he was a graduate student under Jim Watson and Wally Gilbert where he studied the regulation of gene expression in bacteria (Ph.D. in 1973). This is why I was surprised to see his recent article in Forbes where he seems to have fallen hook-line-and-sinker for postgenomics gobbledygook. It looks like Haseltine is losing the ability to think critically as he concentrates more on technology and public policy.

A New Dogma Of Molecular Biology: A Paradigm Shift by William A. Haseltine

United States House of Representatives supports the lab leak conspiracy theory

On January 9, 2023 the US House of Representatives created the Select Subcommittee on the Coronavirus Pandemic. It was chaired by Republican representative Brad Wenstrup of Ohio. There were nine Republicans on the subcommittee and seven Democrats.

The mandate of the subcommittee was to investigate the origins of COVID-19, gain-of-function research, coronavirus-related government spending, and mask and vaccine mandates. Its report was released on Dec. 2, 2024: AFTER ACTION REVIEW OF THE COVID-19 PANDEMIC: The Lessons Learned and a Path Forward.

"Understanding Life" books from Cambridge University Press

Cambridge University Press is publishing a series of inexpensive books on biology topics. The books all have similar titles beginning with the word "Understanding." The "Understanding Life" series is edited by Kostas Kampourakis.

I have three of these books: Understanding Genes (2022) by Kostas Kampourakis, Understanding Evolution (2020) also by Kostas Kampourakis, and Understanding Species (2023) by John Wilkins. Others are:

Kostas Kampourakis cautions us against teaching Mendelian genetics

A few weeks ago I put up a post on Were you lied to in your genetics class?. At the time I thought it was just a fringe view being expressed by a graduate student who didn't understand genetics but now I realize that it's much more important than that.

Kostas Kampourakis is a respected scientist who is being promoted by the National Center for Science Education (NCSE) as an excellent communicator of evolution. Here's a short video (below) where he explains why teachers are making a mistake by saying that Mendel is the father of genetics and that simple Mendelian genetics can explain complex traits.

I'm struggling to understand his point. Here's what I think he means.

Kampourakis uses the example of eye color in Drosophila. He agrees that segregation of the allele responsible for eye color may follow the Mendelian rules¹ but it's wrong to assume that there's a single gene responsible for eye color in fruit flies. He thinks that the goal is to understand the complexities of development and standard Mendelian genetics gives a completely distorted view of that subject, assuming, of course, that teachers can't separate genetics from understanding development.

Part of the problem is that we use the word "trait" differently. Take Mendel's example of pea color as another example. [Identity of the Product of Mendel's Green Cotyledon Gene (Update)] What Mendel was studying was the segregation of alleles in a gene called sgr (stay-green). It codes for an enzyme involved in the degradation of chlorophyll during senescence. When the enzyme is defective, chlorophyll isn't degraded and one of the visible phenotypes is that peas stay green instead of turning yellow.

I believe that the fundamental trait is the lack of an enzyme for degrading chlorophyll and this is what I would teach my students. I would also show them that the phenotype can be easily explained once you understand the biochemistry. It shows you that the connection between the fundamental trait and the visible phenotype can be mysterious so you should be careful about jumping to conclusions.

I think that Kampourakis sees this differently. He thinks that the example of green vs yellow peas is used to teach students that the color of peas is completely determined by a single gene. He thinks that the "trait" is the develpment of seed color in peas.

Kampourakis believes that "people looking for explanations and whatever happens to them in terms of disease and their own features, they find hard to reconcile the simplistic model that they have been taught with the realities of life." I think what he means is that students are being taught that single genes will always determine complex characteristics. He attributes that to the teaching of Mendelian genetics.

If he is correct, then that kind of teaching has to stop but I don't think it's the fault of Mendelian genetics. Mendelian genetics—indeed the entire field of genetics sensu stricto—is about the segregation of alleles. It is not about development even though we have come to learn a lot about development through genetics and the phenotype of mutants. I think that genetics and development are separate topics.

Kampourakis disagrees. He says, "we need, I think, to teach genetics from a developmental perspective. We need to show that genes do not determine traits but they are implicated in development." I believe this perspective comes from a more fundamental bias that distinguishes his worldview from mine. I tend to see genetics as a subject that covers all of biology and that includes all species such as bacteria, viruses, and single-cell eukaryotes. He tends to see things from a human perspective, which is much more complex than dealing with simple organisms. I think we should concentrate on teaching students about simple well-understood model organisms and then move on to explaining how this applies to more complex organisms. Kampourakis seems to be implying that we should jump right into reaching high school students about the most challenging issues in biology.

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1. Actually, the common allele for white eye in Drosophila (see image) is X-linked so it doesn't follow the standard rules for Mendelian segregation!

Kostas Kampourakis says that human races do not exist

Populous, geographically disperse, species are often subdivided into subspecies, races, demes, or geographically differentiated populations. Homo sapiens is no exception; there are many subpopulations whose overall genetic compositions are significantly different—so different, in fact, that we have no trouble identifying members of those subpopulations and the sequence of their genomes can assign them to the different groups.¹

We could use the word "race" to distinguish the largest of these subpopulations if the word wasn't so loaded with non-scientific meaning. I believe that, from a scientific perspective, humans races exist. [Do Human Races Exist?]. Jerry Coyne is much better (braver?) than I at defending the biological and evolutionary reality of human races and attacking the well-meaning, but mistaken, attempt to deny the existence of human races. [Genetic ignorance in the service of ideology] It's part of a larger effort to combat something he calls The Ideological Subversion of Biology. The point he's making is that we are teaching our children a number of misconceptions that conflict with science and this contributes to a mistrust of science.

Biological evolution is dead in the water (not!)

You will be surprised to hear that biological evolution is dead in the water according to the authors of a paper published in Progress in Biophysics and Molecular Biology.

The authors are Olen Brown, an Emeritus Professor of Biomedical Sciences at the University of Missouri and David Hullender, a Professor in the Department of Mechanical and Aerospace Engineering at the University of Texas at Arlington. These are the same two authors who published two ridiculous papers in the same journal in 2022 and 2023. Up until last December (2023), Denis Noble was one of the editors of the journal [Editorial Board] but he is not longer listed on the journal's website. We can assume that Noble is responsible, in part, for allowing these papers to be published since he has defended the publication of creationist papers in the past. [How the Krebs cycle disproves Darwinism (not!)]

Brown, O.R. and Hullender, D.A. (2024) Biological evolution is dead in the water of Darwin’s warm little pond. Progress in Biophysics and Molecular Biology. 193: 1-6. [doi: 10.1016/j.pbiomolbio.2024.08.003]

Abstract

The origin of life and its evolution are generally taught as occurring by abiogenesis and gene-centric neo-Darwinism. Significant biological evolutionary changes are preserved and given direction (descent with modification) by Darwin's (Spencer's) natural selection by survival of the fittest. Only survival of the fittest (adapted/broadened) is available to provide a ‘naturalistic’ direction to prefer one outcome/reaction over another for abiogenesis. Thus, assembly of first life must reach some threshold (the first minimal cell) before ‘survival of the fittest’ (the only naturalistic explanation available) can function as Darwin proposed for biological change. We propose the novel concept that the requirement for co-origination of vitamins with enzymes is a fundamental, but overlooked, problem that survival of the fittest (even broadly redefined beyond Darwin) cannot reasonably overcome. We support this conclusion with probability calculations. We focus on the stage of evolution involving the transition from non-life to the first, minimal living cell. We show that co-origination of required biochemical processes makes the origin of life probabilistically absurdly improbable even when all assumptions are chosen to unreasonably favor evolutionary theories.

There's something seriously wrong with peer review if a paper like this can be published in a (formerly) reputable journal.

For more information, watch this video of Brown and Hullender explaining their views. The video is sponsored by "Video Lessons to Raise Up Confident Christians."

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Nobel Laureate Charles Nicolle

The Nobel Prize in Physiology or Medicine 1928

"for his work on typhus"

Charles Jules Henri Nicolle (1886 - 1936) was a French scientist who studied typhus while he was Director of the Pasteur Institute in Tunis. He realized that patients suffering from typhus were usually contageous but when they entered the hospital they were no longer contageous after a bath and a change of clothes. This led him to conclude that the disease was being spread by something in the clothing and lice were a prime suspect.

He soon confirmed his hypothesis by infecting chimpanzees and showing that the disease could be transferred by lice from one infected chimp to another uninfected animal. Further research showed that the disease was actually being transferred by microbes in lice excrement and through insect bites. In addition to lice, mites and fleas can also transmit various forms of typhus.

Nicolle was not able to develop a vaccine against typhus. Even today there is no effective vaccine available but the disease can be treated by antibiotics, especially doxycycline. [See Monday's Molecule #246]

It's pretty amazing to think that the cause of such a horrible disease was only discovered in the lifetime of our parents or grandparents (or great-grandparents).

Here's part of the Award Ceremony Speech.

THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

In awarding the 1928 Nobel Prize for Medicine to Dr. Charles Nicolle, Director of the Pasteur Institute at Tunis, the Caroline Institute wished to pay tribute to a man who has realized one of the greatest conquests in the field of prophylactic medicine, i.e. the vanquishing of typhus.

... The disease has been known since the beginning of all time. The plague which devastated Attica, especially Athens in the year 430 B.C., and which Thucydides describes in his work on the Peloponnesian War, was most likely an epidemic of typhus. The picture that the great historian draws of the disease agrees in certain respects, down to the smallest details, with the clinical picture we were able to observe during the Great War. Epidemics followed one another without respite during the great wars of the sixteenth and seventeenth centuries. At the end of the Thirty Years’ War, typhus raged over the whole of Central Europe. The Napoleonic Wars caused the disease to flare up again. In the general disorganization which followed the Grand Army’s retreat from Russia, typhus claimed innumerable victims amongst the troops and amongst the civilian population. Further epidemics broke out during the Crimean War and the Russo-Turkish War, affecting both sides.

With the progress of civilization and during the period of peace and prosperity which, in all, lasted from the end of the nineteenth century until 1914, typhus seemed of its own accord to have become restricted to certain remote regions of Europe and to certain extra-European countries where, from time immemorial, the disease had existed endemically.

At the beginning of this North Africa was among these non-European countries where the disease had been a veritable national scourge for several centuries. As soon as he took up his appointment as Director of the Pasteur Institute at Tunis, young Dr. Charles Nicolle was immediately brought into contact with the scientific and practical problems that typhus had created in this country.

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Photo Credit: The figure is from Wikipedia.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

The "wisdom" of the Discovery Institute

John G. West is Vice President of the Discovery Institute and one of the founding members of the Center for Science and Culture. He is a leading proponent of Intelligent Design Creationism.

West has reviewed the latest book by Francis Collins; the review was published in The Federalist. [Francis Collins’ Latest Book Doubles Down On His Massive Abuses Of Power]

Popular science books aren't fact-checked

Michael Marshall is a science journalist. He published a short essay in New Scientist where he laments the fact that popular science books may contain lots of errors. The title of the original article was Getting the facts right but the online version is Readers deserve beter from popular science books. The blurb is the same for both versions.

"There is a dirty secret in publishing: most popular science books aren't fact-checked. This needs to change, says Michael Marshall."

Most of you won't be able to read the article because it's behind a paywall but here's a few paragraphs that should stimulate discussion.

No, the problem is much simpler, and it is a dirty secret of non-fiction publishing: most books aren’t fact-checked. If an author makes a mistake or misinterprets a study, nobody stops them.

In journalism, fact-checking practices vary widely. New Scientist has two layers of editors, who each ensure readability and accuracy. Others are even stricter: fact-checkers at The New Yorker re-report entire stories. Non-fiction publishing is far more relaxed. Often, there is no fact-checking at all: editors offer guidance on readability, but take factual claims on trust. The UK publishers of my book The Genesis Quest did this (though my US publishers, a university press, recruited anonymous peer reviewers).

It is easy to see why this has happened. Nuance is difficult to sell. If your book has a counterintuitive thesis, or simply promotes a moral panic, it is easier to market. Non-fiction authors who are rigorous and careful can’t compete. That’s why shops are flooded with books about one neat trick for a better life or how everything you know is wrong. But without fact-checking, these books might as well be scrawled in crayon. Publishers must do better.

For the record, my book was sent out to reviewers and I got back some very helpful comments that caused me to make some serious changes. I also sent it to some of my colleagues and they corrected quite a few errors.

The last part of Marshall's essay is something that I've been worried about for many years, "Non-fiction authors who are rigorous and careful can’t compete."

Note: I inserted an image of Philip Ball's latest book because it's a recently published popular science book. I have no idea whether it was fact-checked or not. (But I have my suspicions.)

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Monday's Molecule #246

Today's molecule is complicated and you may not recognize it right away from the 3D structure. It was discovered in the middle of the last century and has proven to be very useful.

You can use whatever tricks you want to identify today's molecule. Regular readers will know that it's related to at least one Nobel Prize Laureate who will be revealed on Wednesday. I don't think that's going to help you very much.

Email your answer to me at: Monday's Molecule #246. The first one with the correct answer wins. I will only post the names of winners to avoid embarrassment. The winner will be treated to a free coffee and donut at Tim Hortons if you are ever in Toronto or Mississauga (Ontario, Canada).

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

In order to win you must give your correct name. Anonymous and pseudoanonymous players can't win.

Comments are closed for at least 24 hours.

UPDATE:The molecule is doxycline, a tetracycline class of broad-spectrum antibiotic. The winner is Chris Dicus. I don't know where Chris is located but I'm pretty sure it's not near me so I'll have to wait unitil he visits Toronto to collect his double-double and chocolage dip donut.

-->

Winners

#145, Oct. 17, 2011: Bill Chaney, Roger Fan
#146, Oct. 24, 2011: DK
#147, Oct. 31, 2011: Joseph C. Somody
#148, Nov. 7, 2011: Jason Oakley
#149, Nov. 15, 2011: Thomas Ferraro, Vipulan Vigneswaran
#150, Nov. 21, 2011: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
#151, Nov. 28, 2011: Philip Rodger

#152, Dec. 5, 2011: 凌嘉誠 (Alex Ling)
#153, Dec. 12, 2011: Bill Chaney
#154, Dec. 19, 2011: Joseph C. Somody
#155, Jan. 9, 2012: Dima Klenchin
#156, Jan. 23, 2012: David Schuller
#157, Jan. 30, 2012: Peter Monaghan
#158, Feb. 7, 2012: Thomas Ferraro, Charles Motraghi
#159, Feb. 13, 2012: Joseph C. Somody
#160, March 5, 2012: Albi Celaj
#161, March 12, 2012: Bill Chaney, Raul A. Félix de Sousa

#162, March 19, 2012: no winner
#163, March 26, 2012: John Runnels, Raul A. Félix de Sousa
#164, April 2, 2012: Sean Ridout
#165, April 9, 2012: no winner
#166, April 16, 2012: Raul A. Félix de Sousa
#167, April 23, 2012: Dima Klenchin, Deena Allan
#168, April 30, 2012: Sean Ridout
#169, May 7, 2012: Matt McFarlane
#170, May 14, 2012: no winner
#171, May 21, 2012: no winner

#172, May 29, 2012: Mike Hamilton, Dmitri Tchigvintsev
#173, June 4, 2012: Bill Chaney, Matt McFarlane
#174, June 18, 2012: Raul A. Félix de Sousa
#175, June 25, 2012: Raul A. Félix de Sousa
#176, July 2, 2012: Raul A. Félix de Sousa
#177, July 16, 2012: Sean Ridout, William Grecia
#178, July 23, 2012: Raul A. Félix de Sousa
#179, July 30, 2012: Bill Chaney and Raul A. Félix de Sousa
#180, Aug. 7, 2012: Raul A. Félix de Sousa
#181, Aug. 13, 2012: Matt McFarlane

#182, Aug. 20, 2012: Stephen Spiro
#183, Aug. 27, 2012: Raul A. Félix de Sousa
#184, Sept. 3, 2012: Matt McFarlane
#185, Sept. 10, 2012: Matt Talarico
#186, Sept. 17, 2012: no winner
#187, Sept. 24, 2012: Mikkel Rasmussen
#188, Oct. 1, 2012: John Runnels
#189, Oct. 8, 2012: Raúl Mancera

#190, Oct. 15, 2012: Raul A. Félix de Sousa
#191, Oct. 22, 2012: Mikkel Rasmussen
#192, Nov. 12, 2012: Seth Kasowitz, Bill Gunn
#193, Nov. 19, 2012: Michael Rasmussen
#194, Dec. 4, 2012: Paul Clapham, Jacob Toth
#195, Dec. 10, 2012: Jacob Toth
#196, Dec. 17, 2012: Bill Chaney, Dima Klenchin, Bill Gunn
#197, Jan. 14, 2013: Evey Salara
#198, Jan. 21, 2013: Piotr Gasiorowski
#199, March 11, 2013: Bill Gunn, River Jiang

#200, March 18, 2013: Bill Gunn
#201, April 8, 2013: Michael Florea
#202, April 15, 2013: no winner
#203, April 29, 2013: Anders Ernberg
#204, May 6, 2013: Alex Ling, Michael Florea
#205, May 13, 2013: Bill Chaney
#206, June 24, 2013: Michael Florea
#207, July 2, 2013: Matt McFarlane
#208, July 8, 2013: no winner
#209, July 15, 2013: Rosie Redfield, Thuc Quyen Huynh
#210, July 22, 2013: Jacob Toth
#211, July 29, 2013: Alex Ling, Matt McFarlane
#212, August 5, 2013: Brian Shewchuk
#213, Sept. 2, 2013: no winner
#214, Sept. 9, 2013: Bill Chaney
#215, Sept. 16, 2013: Zhimeng Yu
#216, Sept. 23, 2013: Mark Sturtevant, Jacob Toth

#217, Sept. 30, 2013: Susan Heaphy
#218, Oct. 7, 2013: Piotr Gasiorowski, Jacob Troth
#219, Oct. 14, 2013: Jean-Marc Neuhaus
#220, Oct. 21, 2013: Jean-Marc Neuhaus
#221, Oct. 28, 2013: Zhimeng Yu
#222, Nov. 10, 2013: Caroline Josefsson, Andrew Wallace
#223, Nov. 18, 2013: Dean Bruce, Ariel Gershon
#224, Nov. 25, 2013: Jon Nuelle, Ariel Gershon

#225, Dec. 2, 2013: Jean-Marc Neuhaus
#226, Dec. 9, 2013: Bill Gunn
#227, Dec. 16, 2013: Piotr Gasiorowski
#228, Jan. 13, 2014: Tom Mueller
#229, Jan. 20, 2014: Tommy Stuleanu
#230, Jan. 27, 2014: Bill Gunn, Ariel Gershon

#231; March 3, 2014: Keith Conover, Nevraj Kejiou
#232, March 10, 2014: Philip Johnson
#233, March 17, 2014: Jean-Marc Neuhaus
#234, March 24, 2014: Frank Schmidt, Raul Félix de Sousa
#235, March 31, 2014: Jon Binkley
#236, April 7, 2014: no winner
#237, April 21, 2014: Dean Bruce
#238, April 28, 2014: Dean Bruce
#239, May 5, 2014: Piotr Gąsiorowski
#240, May 12, 2014: James Wagstaff
#241, May 19, 2014: no winner
#242, Oct. 7, 2024: Elie Huvier
#243, Oct. 14, 2024: Mikkel Rasmussen
#244, Oct. 21, 2024: Santi Garcia-Vallve
#245, Nov. 12, 2024: no winner
#246, Nov. 18, 2024: Chris Dicus

---

The figure is from the ACS website: Doxyxycline.

Thiotimoline

There's been a lot of talk recently about scieintific misinformaton on the internet. I started reminiscing about what things were like when I was growing up. I remember when I learned about DNA and when I first heard about black holes.

Then I remembered how excited I was when I first heard about the properties of thiotimoline from a well-known biochemist (Asimov, 1948). I can't say for sure that this tilted me toward choosing a career in biochemistry but it certainly played a role.

Some of you may not be familiar with thiotimoline. Here's the most important characteristic of this amazing molecule as reported in the original paper.

Darwin Mythology

How can you possibly be against a book devoted to refuting misinformation about Charles Darwin and his views on evolution? This is an anthology edited by Kostas Kampourakis whose main interest is "the public understanding of evolution and genetics." He currently teaches at the University of Geneva (Geneva, Switzerland).

Kampourakis has assembled a bunch of authors who present their 24 most important myths about Darwin in 24 chapters. It appears that this book was motivated, in part, by Kampoourakis' view that Charles Darwin needs to knocked down a peg or two because it corrupts the general public's view of how science really works. He begins his book by quoting Richard Dawkins, Michael Ghiselin and Jerry Coyne as examples of scientists who see Darwin as a scientific hero.

Darwin was without question a brilliant naturalist, observer and experimentalist and scholar. But this kind of hero-worshipping should be avoided because it is misleading—science is not done, and does not advance, by individuals who make big breakthroughs in one go. Science is done by communities, which consist of individuals many of whom have something important to contribute to the overall achievement. Even when some individuals happen to see something that others do not, the validation of a novel perspective or findings by the community is absolutely necessary. Most importantly, coming up with anything novel takes time and effort—it took Darwin twenty years of painstaking work—while one works in a particular context and with particular resources to hand—and Darwin had experiences and resources that most other lacked. This kind of hero-worshiping is also better avoided because it dehumanizes science; in the last chapter of the present book, I explain how the stories in its twenty-four chapters can help us better understand science as a human activity. My aim is to humanize Darwin and to emphasize a number of points about how science is done.

Science journal tries to understand misinformation

The November 1, 2024 issue of Science contains three articles on misinformation in science. The articles tend to concentrate on the standard examples such as vaccine misinformation but there's another kind of misinformation that's just as important. I'm talking about scientific misinformation that's spread by journals like Science and Nature.

Do any of you remember the arsenic affair? That's when science accepted a paper by Felisa Wolfe-Simon and her collaborators claiming that they isolated a bacterium that substituted arsenic for phosphorus in its DNA. The paper was published online and was severely criticized after a ridiculous NASA press conference. It was eventually refuted when Rosie Redfield and others looked closely at the bacterial DNA and showed that it did not contain arsenic. The paper has still not been retracted. [See Reviewing the "Arseniclife" Paper.]

And let's not forget the massive misinformation campaign associated with the publication of ENCODE results in 2012.

The success of protein structure prediction software depended on the solved structures deposited in the Protein Data Bank (PDB)

The development of protein structure prediction programs began fifty years ago and culminated in the remarkable success of AlphaFold, developed by Google DeepMind. Demis Hassabis and John Jumper of Google DeepMind received the Nobel Prize in Chemistry (2024) for their work on AlphaFold.

AlphaFold and its predecessors were trained on a database of known protein structures called the Protein Data Bank (PDB). PDB began in 1971 as a collaboration between the Cambridge Crystallographic Centre in the UK and Brookhaven National Laboratory in the US. It utilized standardizing software for collecting and storing atomic coordinates and allowing researchers to search the database from remote locations. It soon became a requirement for researchers to deposit their data in PDB when they published.