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.

Were you lied to in your genetics class?

There's a disturbing trend in popular science these days. The goal is to convince the general public that much of what we thought we knew is wrong. I think it's related to the general mistrust of science.

A recently posted YouTube video tries to make the case that you were lied to about genetics. I'll get to than in a little while but first let me summarize what I was taught in a university genetics class in 1965.

Scite Assistant (AI) answers the question "How much of the human genome consist of junk DNA?"

Scite Assistant is billed as "your AI research partner" and as "ChatGPT for researchers." It's supposed to draw on peer-reviewed published scientific papers for its information and it will give you an answer with genuine citations.

That sounds like a good idea until you realize that the scientific literature is full of misinformation and conflicting information. What we need is an AI assistant that can help us sort throught the misinformation and give us a genuine well-informed answer on controversial issues.

Let's pick the question of junk DNA as a completley random (!) example of such an issue. The scientific literature is full of false information about the origin of the term "junk DNA" and what it was originally intended to describe. It's also full of false information about recent results and how they pertain to junk DNA.

Is the Teacher Institute for Evolutionary Science spreading misinformation?

The Teacher Institute for Evolutonary Science (TIES) is an organization dedicated to helping teachers explain evolution.

A good teacher can teach any subject as long as they have high-quality resources. TIES provides middle school and elementary teachers the tools they need to effectively teach evolution and answer its critics based on new Next Generation Science Standards.

The Teacher Institute for Evolutionary Science began as a program of the Richard Dawkins Foundation for Reason & Science and it's now part of the Center for Inquiry.

TIES recently posted a video with an interesting title on their YouTube channel: "Beyond DNA: How Epigenetics is Transforming our Understanding of Evolution." This is a presentation by Ben Oldroyd who wrote a book titled "Beyond DNA."

Watch the video and decide for yourself whether you think this is what teachers of evolutionary biology should be telling their students. What part of understanding evolution do you think needs to be transformed by epigenetics?

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Anti-science New York Times doubles down on the lab leak conspiracy theory

On June 3, 2024,the New York Times published an opinion piece by Alina Chan in which she promoted the lab leak conspiracy theory about the origin of COVID-19. Her views are not shared by the scientific community and the newspaper was criticized by many who pointed out the many flaws in Chan's arguments and her lack of objectivity.¹

I suspect that some people at the NYT might have been somewhat embarrassed by the response to their reckless behavior so they prepared a response. It was written by David Leonhardt who identifies himself as "a senior writer at the New York Times who runs "The Morning", our flagship daily newsletter." He published his article on the website that he runs and the title sounds like it might be an objective appraisal of the evidence in favor of a natural origin of COVID-19 originating in the Wuhan market: Two Covid Theories.

Don't be fooled by the title. Leonhardt makes no attempt to summarize the massive amount of evidence in favor of a natural origin. Instead, he treats the scientific view and the lab leak conspiracy theory as equally probable.

Do you find both explanations plausible? I do.

As I’ve followed this debate over the past few years, I have gone back and forth about which is more likely. Today, I’m close to 50-50. I have heard similar sentiments from some experts.

“No one has proof,” Julian Barnes, who covers intelligence agencies for The Times, told me. “Everyone is using logic.” Julian’s advice to the rest of us: “Be wary, keep an open mind, rule nothing out.”

Let's be clear about what's necessary in order for the lab leak conspiracy theory to be probable.

1. There has to be evidence that SARS-CoV-2 was present in the Wuhan Institute of Virology (WIV) before the pandemic started. There is none.
2. The graduate students, post-docs, scientists, and research technicians at WIV all deny that they were working with SARS-CoV-2 or any closely-related virus before the pandemic started. In order for the lab leak conspiracy theory to be true they must be lying and engaging in a massive coverup. This is totally inconsistent with their behavior over the past two decades. (The woman in the photo is Shi Zhengli, an internationally renowned scientist who Alina Chan accuses of lying—a claim that David Leonhardt thinks is quite possible.)

The latest opinion piece looks to me like an attempt to defend the NYT against accusations that it is anti-science. You would think that in such a defense, the author would be able to present good scientific evidence for the lab leak conspiracy theory, right? Here's the three arguments advanced by David Leonhardt in support of this massive conspiracy.

1. COVID-19 was first detected near the market in Wuhan and the Wuhan Virolgy Institute is in Wuhan.
2. Leaks happen.
3. China controls the evidence (i.e. conspiracy).

I think we are fully justified in claiming that the NYT is anti-science. I think the newspaper owes the scientific community an apology for ignoring the evidence of a natural origin and disparaging the reputations of reputable scientists who reject the lab leak conspiracy theory in favor of a natural origin.

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1. [The New York Times promotes the lab leak conspiracy theory] [Real scientists destroy the Alina Chan lab leak conspiracy theory] [The New York Times goes all in on “lab leak”] [No, gain of function research did not cause COVID-19]

What really happened between Rosalind Franklin, James Watson, and Francis Crick?

That's part of the title of podcast by Kat Arney who interviews Matthew Cobb [Double helix double crossing? What really happened between Rosalind Franklin, James Watson and Francis Crick?].

Matthew Cobb is one of the world's leading experts on the history of molecular biology.

The way it’s usually told, Franklin was effectively ripped off and belittled by the Cambridge team, especially Watson, and has only recently been restored to her rightful place as one of the key discoverers of the double helix. It’s a dramatic narrative, with heroes, villains and a grand prize. But, as I found out when I sat down for a chat with Matthew Cobb, science author and Professor of Zoology at the University of Manchester, the real story is a lot more nuanced.

Photo 51 did not belong to Rosalind Franklin and it had (almost) nothing to do with solving the structure of DNA. Franklin and Wilkins would never have gotten the structure on their own. Crick and Watson did not "steal" any data. Whether they behaved ethically is debatable.

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ChatGPT gets two-thirds of science textbook questions wrong: time to bring it into the classroom!

The November 16th issue of Nature has an article about ChatGPT: ChatGPT has entered the classroom: how LLMs could transform education. It reports that the latest version (GPT4) can only answer one third of questions correctly in physical chemistry, physics, and calculus. Nevertheless, the article promotes the idea that ChatGPT should be brought into the classroom!

An editorial in the same issue explains Why teachers should explore ChatGPT’s potential — despite the risks.

Many students now use AI chatbots to help with their assignments. Educators need to study how to include these tools in teaching and learning — and minimize pitfalls.

I don't get it. It seems to me that the problems with ChatGPT far outweigh the advantages and the best approach for now is to warn students that using AI tools may be terribly misleading and could lead to them failing a course if they trust the output. That doesn't mean that there's no potential for improvement in the future but this can only happen if the sources of information used by these tools were to become much more reliable. No improvements in the algorithms are going to help with that.

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Two Heidelberg graduate students reject junk DNA

Science in School is a magazine for European science teachers. Two graduate students¹ have just published an article in the November issue: Not junk after all: the importance of non-coding RNAs.

Note: The article has been edited to remove some of the references to junk DNA and the editor has added the following disclaimer to the end of the article: Editor’s note: Some parts of the introduction and conclusion were rephrased to avoid any misunderstanding concerning the nature of ‘junk DNA’, which is not the focus of this article. Here's a link to the revised article: Not junk after all: the importance of non-coding RNAs. More changes are expected.

Not junk after all: the importance of non-coding RNAs

Originally assumed to be useless ‘junk DNA’, sections of the genome that don’t encode proteins have been revealed as a source of many important non-coding RNA structures.

The central dogma of molecular biology is that DNA is used as a template to create messenger RNA (mRNA), which in turn is translated into proteins that build the tissues in our bodies and carry out the main functions of our cells and organs. In other words, DNA → mRNA → proteins. Interestingly, though, only 2% of the DNA in our whole genome codes for proteins! So, what does the other 98% of the human genome do? In the mid-1900s, it was widely believed that a great part of our genome was useless, repetitive ‘junk DNA’. However, this belief goes against the evolution theory, which suggests that useless sequences would be eliminated from the genome since their maintenance requires energy. In the late 20th century and the early 21st century, this junk DNA has been shown to not only contain important regulatory elements for transcription, but also sequences that encode various non-coding RNAs that have functions in many cellular mechanisms.

I just finshed a podcast interview with Kat Arney and one of the questions she asked was what is the most important thing I'd like scientists to know about this topic. I picked evolution—I'd like modern researchers to understand that there's more to evolution than natural selection. You can see the problem in this example where two students who are working toward a Ph.D. at a top lab in Europe think that junk DNA "goes against the evolution theory."

That's sad. It's also sad that these two students think that 98% of our genome might be devoted to regulation and non-coding genes.

We need to focus on educating the next generation of scientists and that starts with educating science teachers. This is not the way to do it.

Here's the contact information for Science in School. I've written the editor at editor@scienceinschool.org. Please send a message if you are as concerned about the spread of scientific misinformation as I am.

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Zuzana Koskova at the European Molecular Biology Laboratory in Heidelberg (Germany) and Miguel Hernandez at the University Hospital, Heidelberg. I tried sending an email message to Zuzana Koskova but got no reply. I was unable to find contact information for Miguel Hernandez.

ChatGPT won't pass my exams!

Here are a few questions for ChatGPT and its answers. The AI program takes the most common information on the web and spews it back at you. It cannot tell which information is correct or which information is more accurate.

It's easy to recognize that these answers were written by something that's not very good at critical thinking. I agree with other professors that they mimic typical undergraduate answers but I disagree that these answers would get them a passing grade.

ChatGPT shares one very important feature that's common in undergraduate answers to essay questions: it gives you lots of unecessary information that's not directly relevant to the question.

It's important to note that (lol) these ChatGPT answers share another important feature with many of the answers on my exams: they look very much like BS!

Jupiter weighs two quettagrams

New names for very large and very small weights and sizes have been adopted.

Last November's meeting of the General Conference on Weights and Measures wasn't covered by the major media outlets so you probably don't know that the mass of an electron is now one rontogram and the diameter of the universe is about one ronnameter [SI units get new prefixes for huge and tiny numbers].¹

The official SI prefixes for very large things are now ronna (10²⁷) and quetta (10³⁰) and the prefixes for very small things are ronto (10^-27) and quecto (10^-30).

This is annoying because we've just gotten used to zetta, yotta, zepto, and yocto (adopted in 1991). I suspect that the change was prompted by the huge storage capacity of your latest smartphone (several yottabytes) and the wealth of the world's richest people (several zeptocents). Or maybe it was the price of houses in Toronto. Or something like that. In any case, we needed to prepare for kilo or mega increases.

The bad news is that the latest additions used up the last two available letters of the alphabet so if things get any bigger or smaller we may have to add a few more letters to the alphabet.

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1. A friendly reader has pointed out that my title should have been "The mass of Jupiter is two quettagrams." My bad.

Publishing a science book - Lesson #1: The publisher is always right about everything

Don't bother trying to reason with a publisher. All of them have different views on proper style and every single one of them is absolutely certain that their style is the only correct one.

I'm in the middle of the copyedit stage of my book. This is the stage where a copyeditor goes through your manuscript and makes any corrections to spelling and grammar. This is a lot of work for any copyeditor having to deal with one of my manuscripts and I greatly appreciate the effort. My book is a lot better now than it was a few weeks ago. (Who knew that there was only one l in canceled?)

It's also the stage where the publisher imposes their particular style on the manusript and that can be a problem. I'll document some of the issues in subsequent posts but to give you an example, consider the titles of books in the reference list. I wrote it like this: The Selfish Gene and Molecular and Genome Evolution. This is not in line with my publisher's handbook of style so the titles were converted to lowercase as in: The selfish gene and Molecular and genome evolution. I objected, pointing to numerous other science books that used the same titles that are on the covers of the books and suggesting that my readers were more familiar with The Selfish Gene than with The selfish gene.

I was overruled by my publisher who noted that they make their style choices for good reasons—it's for "consistency, clarity, and ease of reading." I assume that publishers, such as Oxford, would make the same argument while insisting that the title should be The Selfish Gene.

In case you ever find yourself in this position, you should keep in mind that your contract will almost certainly say that the publisher has complete control of your book and they can make any changes they want as long as it doesn't affect the meaning of what you wrote.

Here's what it says in my contract, "The Publisher shall publish the Author's work in whatever style and format it thinks most suitable ... While the Publisher may, in its sole discretion, consult the Author with respect to said style and format, the Publisher retains the right to make all final decisions on matters of format, design, selling price and marketing."

I was aware of some issues with inappropriate covers and tiles in the past so I had an extra sentence added to the contract that said, "The Publisher and Author will discuss and agree upon the title and cover design." It's a good thing I put that in because the publisher was pressuring me to change the title of the book and I was able to resist.

Authors can't win most fights over style and format. I've been discussing the publishing of science books with a number of other authors over the past few months and several of them told me not to bother trying to argue with a publisher because they will never give in. They have a set style for all books and they won't make an exception for an individual author no matter how good an argument you make.

I didn't listen to those other authors. Silly me.

I'm thinking of trying to write a standard set of guidelines that scientists could put into their contracts to cover the most egregious style restrictions. It might be helpful if all science writers would insist on inserting these guidelines into their contracts.

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Can the AI program ChatGPT pass my exam?

There's a lot of talk about ChatGPT and how it can prepare lectures and get good grades on undergraduate exams. However, ChatGPT is only as good as the information that's popular on the internet and that's not always enough to get a good grade on my exam.

ChatGPT is an artificial intelligence (AI) program that's designed to answer questions using a style and language that's very much like the responses you would get from a real person. It was developed by OpenAI, a tech company in San Francisco. You can create an account and log in to ask any question you want.

Several professors have challenged it with exam questions and they report that ChatGPT would easily pass their exams. I was skeptical, especially when it came to answering questions on controversial topics where there was no clear answer. I also suspected that ChatGPT would get it's answers from the internet and this means that popular, but incorrect, views would likely be part of ChatGPT's response.

Here are my questions and the AI program's answers. It did quite well in some cases but not so well in others. My main concern is that programs like this might be judged to be reliable sources of information despite the fact that the real source is suspect.

What I'm reading these days

So many books ... so little time.

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Science education in an age of misinformation

I just read an annoying article in Boston Review: The Inflated Promise of Science Education. It was written by Catarina Dutilh Novaes, a Professor of Philosophy, and Silvia Ivani, a teaching fellow in philosophy. Their main point was that the old-fashioned way of teaching science has failed because the general public mistrusts scientists. This mistrust stems, in part, from "legacies of scientific or medical racism and the commercialization of biomedical science."

The way to fix this, according to the authors, is for scientists to address these "perceived moral failures" by engaging more with society.

"... science should be done with and for society; research and innovation should be the product of the joint efforts of scientists and citizens and should serve societal interests. To advance this goal, Horizon 2020 encouraged the adoption of dialogical engagement practices: those that establish two-way communication between experts and citizens at various stages of the scientific process (including in the design of scientific projects and planning of research priorities)."

Clearly, scientific education ought to mean the implanting of a rational, sceptical, experimental habit of mind. It ought to mean acquiring a method – a method that can be used on any problem that one meets – and not simply piling up a lot of facts.

George Orwell

This is nonsense. It has nothing to do with science education; instead, the authors are focusing on policy decisions such as convincing people to get vaccinations.

The good news is that the Boston Review article links to a report from Stanford University that's much more intelligent: Science Education in an Age of Misinformation. The philosophers think that this report advocates "... a well-meaning but arguably limited approach to the problem along the lines of the deficit model ...." where "deficit model refers to a mode of science communication where scientists just dispense knowledge to the general public who are supposed to accept it uncritically.

I don't know of very many science educators who think this is the right way to teach. I think the prevailing model is to teach the nature of science (NOS) [The Nature of Science (NOS)]. That requires educating students and the general public about the way science goes about creating knowledge and why evidence-based knowledge is reliable. It's connected to teaching critical thinking, not teaching a bunch scientific facts. The "deficit model" is not the current standard in science education and it hasn't been seriously defended for decades.

"Appreciating the scientific process can be even more important than knowing scientific facts. People often encounter claims that something is scientifically known. If they understand how science generates and assesses evidence bearing on these claims, they possess analytical methods and critical thinking skills that are relevant to a wide variety of facts and concepts and can be used in a wide variety of contexts.”

National Science Foundation, Science and Technology Indicators, 2008

An important part of the modern approach as described in the Stanford report is teaching students (and the general public) how to gather information and determine whether or not it's reliable. That means you have to learn how to evalute the reliabiltiy of your sources and whether you can trust those who claim to be experts. I taught an undergraduate course on this topic for many years and I learned that it's not easy to teach the nature of science and critical thinking.

The Stanford Report is about the nature of science (NOS) model and how to implement it in the age of social media. Specifically, it's about teaching ways to evaluate your sources when you are inundated with misinformation.

The main part of this approach is going to seem controversial to many because it emphasizes the importance of experts and there's a growing reluctance in our society to trust experts. That's what the Boston Globe article was all about. The solutions advocated by the authors of that article are very different than the ones presented in the Sanford report.

The authors of the Standford report recognize that there's a widepread belief that well-educated people can make wise decisions based entirely on their own knowledge and judgement, in other words, that they can be "intellectually independent." They reject that false belief.

The ideal envisioned by the great American educator and philosopher John Dewey—that it is possible to educate students to be fully intellectually independent—is simply a delusion. We are always dependent on the knowledge of others. Moreover, the idea that education can educate independent critical thinkers ignores the fact that to think critically in any domain you need some expertise in that domain. How then, is education to prepare students for a context where they are faced with knowledge claims based on ideas, evidence, and arguments they do not understand?

The goal of science education is to teach students how to figure out which source of information is supported by the real experts and that's not an easy task. It seems pretty obvious that scientists are the experts but not all scientists are experts so how do you tell the difference between science quacks and expert scientists?

The answer requires some knowledge about how science works and how scientists behave. The Stanford reports says that this means acquiring an understanding of "science as a social practice." I think "social practice" is bad choice of terms and I would have preferred that they stick with "nature of science" but that was their choice."

The mechanisms for recognizing the real experts relies on critical thinking but it's not easy. Two of the lead authors¹ of the Stanford Report published a short synopsis in Science last month (October 2022) [https://doi.org/10.1126/science.abq8-93]. Their heuristic is shown on the right.

The idea here is that you can judge the quality of scientific information by questioning the credentials of the authors. This is how "outsiders" can make judgements about the quality of the information without being experts themselves. The rules are pretty good but I wish there had been a bit more on "Unbiased scientific information" as a criterion. I think that you can make a judgement based on whether the "experts" take the time to discuss alternative hypotheses and explain the positions of those who disagree with them but this only applies to genuine scientific controversies and if you don't know that there's a controversy then you have no reason to apply this filter.

For example, if a paper is telling you about the wonderful world of regulatory RNAs and points out that there are 100,000 newly discovered genes for these RNAs, you would have no reason to question that if the scientists have no conflict of interest and come from prestigious universities. You would have to reply on the reviewers of the paper, and the journal, to insist that alternative explanations (e.g. junk RNA) were mentioned. That process doesn't always work.

There's no easy way to fix that problem. Scientists are biased all the time but outsiders (i.e. non-experts) have no way of recognizing bias. I used to think that we could rely on science journalists to alert us to these biases and point out that the topic is controversial and no consensus has been reached. That didn't work either.

At least the heuristic works some of the time so we should make sure we teach it to students of all ages. It would be even nicer if we could teach scientists how to be credible and how to recognize their own biases.

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1. The third author is my former supervisor, Bruce Alberts, who has been interested in science education for more than fifty years. He did a pretty good job of educating me! :-)

University press releases are a major source of science misinformation

Here's an example of a press release that distorts science by promoting incorrect information that is not found in the actual publication.

The problems with press releases are well-known but nobody is doing anything about it. I really like the discussion in Stuart Ritchie's recent (2020) book where he begins with the famous "arsenic affair" in 2010. Sandwalk readers will recall that this started with a press conference by NASA announcing that arsenic replaces phosphorus in the DNA of some bacteria. The announcement was treated with contempt by the blogosphere and eventually the claim was discproved by Rosie Redfield who showed that the experiment was flawed [The Arsenic Affair: No Arsenic in DNA!].

This was a case where the science was wrong and NASA should have known before it called a press conference. Ritchie goes on to document many cases where press releases have distorted the science in the actual publication. He doesn't mention the most egregious example, the ENCODE publicity campaign that successfully convinced most scientists that junk DNA was dead [The 10th anniversary of the ENCODE publicity campaign fiasco].

I like what he says about "churnalism" ...

In an age of 'churnalism', where time-pressed journalists often simply repeat the content of press releases in their articles (science news reports are often worded vitrually identically to a press release), scientists have a great deal of power—and a great deal of responsibility. The constraints of peer review, lax as they might be, aren't present at all when engaging with the media, and scientists' biases about the importance of their results can emerge unchecked. Frustratingly, once the hype bubble has been inflated by a press release, it's difficult to burst.

Press releases of all sorts are failing us but university press releases are the most disappointing because we expect universities to be credible sources of information. It's obvious that scientists have to accept the blame for deliberately distorting their findings but surely the information offices at universities are also at fault? I once suggested that every press release has to include a statement, signed by the scientists, saying that the press release accurately reports the results and conclusions that are in the published article and does not contain any additional information or speculation that has not passed peer review.

Let's look at a recent example where the scientists would not have been able to truthfully sign such a statement.

A group of scientists based largely at The University of Sheffield in Sheffield (UK) recently published a paper in Nature on DNA damage in the human genome. They noted that such damage occurs preferentially at promoters and enhancers and is associated with demethylation and transcription activation. They presented evidence that the genome can be partially protected by a protein called "NuMA." I'll show you the abstract below but for now that's all you need to know.

The University of Sheffield decided to promote itself by issuing a press release: Breaks in ‘junk’ DNA give scientists new insight into neurological disorders. This title is a bit of a surprise since the paper only talks about breaks in enhancers and promoters and the word "junk" doesn't appear anywhere in the published report in Nature.

The first paragraph of the press release isn' very helpful.

‘Junk’ DNA could unlock new treatments for neurological disorders as scientists discover how its breaks and repairs affect our protection against neurological disease.

What could this mean? Surely they don't mean to imply that enhancers and promoters are "junk DNA"? That would be really, really, stupid. The rest of the press release should explain what they mean.

The groundbreaking research from the University of Sheffield’s Neuroscience Institute and Healthy Lifespan Institute gives important new insights into so-called junk DNA—or DNA previously thought to be non-essential to the coding of our genome—and how it impacts on neurological disorders such as Motor Neurone Disease (MND) and Alzheimer’s.

Until now, the body’s repair of junk DNA, which can make up 98 per cent of DNA, has been largely overlooked by scientists, but the new study published in Nature found it is much more vulnerable to breaks from oxidative genomic damage than previously thought. This has vital implications on the development of neurological disorders.

Oops! Apparently, they really are that stupid. The scientists who did this work seem to think that 98% of our genome is junk and that includes all the regulatory sequences. It seems like they are completely unaware of decades of work on discovering the function of these regulatory sequences. According The University of Sheffield, these regulatory sequences have been "largely overlooked by scientists." That will come as a big surprise to many of my colleagues who worked on gene regulation in the 1980s and in all the decades since then. It will probably also be a surprise to biochemistry and molecular biology undergraduates at Sheffield—at least I hope it will be a surprise.

Professor Sherif El-Khamisy, Chair in Molecular Medicine at the University of Sheffield, Co-founder and Deputy Director of the Healthy Lifespan Institute, said: “Until now the repair of what people thought is junk DNA has been mostly overlooked, but our study has shown it may have vital implications on the onset and progression of neurological disease."

I wonder if Professor Sherif El-Khamisy can name a single credible scientist who thinks that regulatory sequences are junk DNA?

There's no excuse for propagating this kind of misinformation about junk DNA. It's completely unnecessary and serves only to discredit the university and its scientists.

Ray, S., Abugable, A.A., Parker, J., Liversidge, K., Palminha, N.M., Liao, C., Acosta-Martin, A.E., Souza, C.D.S., Jurga, M., Sudbery, I. and El-Khamisy, S.F. (2022) A mechanism for oxidative damage repair at gene regulatory elements. Nature, 609:1038-1047. doi:[doi: 10.1038/s41586-022-05217-8]

Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate–early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.

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The trouble with Wikipedia

I used to think that Wikipedia was a pretty good source of information even for scientific subjects. It wasn't perfect, but most of the articles could be fixed.

I was wrong. It took me more than two months to make the article on Non-coding DNA acceptable and my changes met with considerable resistance. Along the way, I learned that the old article on Junk DNA had been deleted ten years ago because the general scientific consensus was that junk DNA doesn't exist. So I started to work on a new "Junk DNA" article only to discover that it was going to be very difficult to get it approved. The powerful cult of experienced Wikipedia editors were clearly going to withhold approval of a new article on that subject.

I tried editing some other articles in order to correct misinformation but I ran into the same kind of resistance [see Allele, Gene, Human genome, Evolution, Alternative splicing, Intron]. Frequently, strange editors pop out the woodwork to restore (revert) my attempts on the grounds that I was refuting well-sourced information. I even had one editor named tgeorgescu tell me that, "Friend, Wikipedians aren’t interested in what you know. They are interested in what you can cite, i.e. reliable sources."

How can you tell which sources are reliable unless you know something about the subject?

Much of this bad behavior is covered in a Wikipedia article on Why Wikipedia is not so great. Here's the part that concerns me the most.

People revert edits without explaining themselves (Example: an edit on Economics) (a proper explanation usually works better on the talk page than in an edit summary). Then, when somebody reverts, also without an explanation, an edit war often results. There's not enough grounding in Wikiquette to explain that reverts without comments are inconsiderate and almost never justified except for spam and simple vandalism, and even in those cases comments need to be made for tracking purposes.

There's a culture of hostility and conflict rather than of good will and cooperation. Even experienced Wikipedians fail to assume good faith in their collaborators. It seems fighting off perceived intruders and making egotistical reversions are a higher priority than incorporating helpful collaborators into Wikipedia's community. Glaring errors and omissions are completely ignored by veteran Wikiholics (many of whom pose as scientists, for example, but have no verifiable credentials) who have nothing to contribute but egotistical reverts.

In another article on Criticism of Wikipedia the contributors raise a number of issues including the bad behavior of the cult of long-time Wikipedia editors. It also points out that anonymous editors who refuse to reveal their identify and areas of expertise leads to a lack of accountability.

This sort of behavior is frustrating and it has an effect. Well-meaning scientists are quickly discouraged from fixing articles because of all the hassle they have to go through.

I now see that the problem can't be easily fixed and Wikipedia science articles are not reliable.

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Science communication in the modern world

Science editors asked young scientists to imagine what kind of course they would have created if they could go back to a time before the pandemic [A pandemic education]. Three of the courses were about science communication.

COM 145: Identification, analysis, and communication of scientific evidence

This course focuses on developing the skills required to translate scientific evidence into accessible information for the general public, especially under circumstances that lead to the intensification of fear and misinformation. Discussions will cover the principles of the scientific method, as well as its theoretical and practical relevance in counteracting the dissemination of pseudoscience, particularly on social media. This course discusses chapters from Carl Sagan’s book The Demon-Haunted World, certain peer-reviewed and retracted papers, and materials related to key science issues, such as the anti-vaccine movement. For the final project, students will comprehensibly communicate a scientific topic to the public.

Camila Fonseca Amorim da Silva University of Sao Paulo, Sao Paulo, Brazil

COM 198: Everyday science communication

As scientific discoveries become increasingly specialized, the lack of understanding by the general public undermines trust in scientists and causes the spread of misinformation. This course will be taught by scientists and communication specialists who will provide students with a toolset to explain scientific concepts, as well as their own research projects, to the general public. Upon completion of this course, students will be able to explain to their grandparents that viruses exist even though they can’t see them, convince their neighbors that vaccines don’t contain tracking devices, and explain the concept of exponential growth to governmental officials.

Anna Uzonyi Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

COM 232: Introduction to talking to regular people

Communicating science is difficult. Many scientists, having immersed themselves in the language of their field, have completely forgotten how to talk to regular people. This course hones introductory science communication skills, such as how to talk about scary things without generating mass panic, how to calmly discourage the hoarding of paper hygiene products, and how to explain why scientific knowledge changes over time. The final project will include cross examination from law school faculty, who are otherwise completely uninvolved with the course and possess minimal scientific training. Recommended for science majors who are unable to discuss impactful scientific findings without citing a P value.

Joseph Michael Cusimano Bernard J. Dunn School of Pharmacy, Shenandoah University, Winchester, VA, USA.

They sound like interesting courses but my own take on science communication is somewhat different. I think it's very difficult for practicing scientists to communicate effectively with the general public so I tend to view science communication at several different levels. My goal is to communicate with an audience of scientists, science journalists, and people who are already familiar with science. The idea is to make sure that this intermediate group understands the scientific facts in my field and to make sure they are familiar with the major controversies.

My hope is that this intermediate group will disseminate this information to their less-informed friends and relatives and, more importantly, stop the spread of misinformation whenever they hear it.

Take junk DNA for example. It's very difficult to convince the average person that 90% of our genome is junk because the idea is so counter-intuitive and contrary to the popular counter-narratives. However, I have a chance of convincing the intermediate group, including science journalists and other scientists, who can follow the scientific arguments. If I succeed, they will at least stop spreading misinformation and false narratives and start presenting alternatives to their sudiences.

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Science writing in the age of denial

Here's an interesting presentation by Sean B. Carroll, the evolutionary biologist and author of several books on evolution. He's also written a fascinating book on Jacques Monod and he gave a talk at the University of Toronto a few years ago on the role of chance in evolution—I have a signed copy of his book (see the photo and my blog post: Biologist Sean Carroll in Toronto).

Sean likes to emphasize the importance of storytelling in science communication and education. By this he sometimes means stories about individual scientists and sometimes stories about the history of a subject. As Vice President for Science Education at the Howard Hughes Medical Institute in Washington DC (USA) he has helped craft some short videos for high school students and the presentation contains an example of one on evolution. I'm not sure I fully agree with his emphasis on storytelling—as least not to the extent that he promotes it—but some version of it can be useful as long as it doesn't get in the way of understanding important concepts.

I leave it to you to decide whether the short HHMI video is the best way to teach high school students about evolution. I personally don't like the undue emphasis on natural selection and natural history.

The reason for drawing your attention to an old 2012 presentation is to remind you about the charactieristics of science denial. Sean explains the six rules of denialism.

1. Doubt the Science
2. Question Scientist's Motives and Integrity
3. Magnify Disagreements among Scientists and Cite Gadflies as Authorities
4. Exaggerate Potential Harm
5. Appeal to Personal Freedom
6. Acceptance Would Repudiate Key Philosophy

His examples are the denial of evolution by creationists and the rejection of vaccinations by chiropractors. Today, we see how the same rules apply to those who reject COVID-19 vaccinations and to the Lab Leak Conspiracy Theory.

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Should we teach genomics and evolution to medical students?

Rama Singh,¹ a biology professor at McMaster Universtiy in Hamilton (Ontario, Canada) has just published an interesting article on The Conversation website. It's about Medical schools need to prepare doctors for revolutionary advances in genetics. You can read the full article yourself but let me highlight the last few paragraphs to start the discussion.

Future physicians will be part of health networks involving medical lab technicians, data analysts, disease specialists and the patients and their family members. The physician would need to be knowledgeable about the basic principles of genetics, genomics and evolution to be able to take part in the chain of communication, information sharing and decision-making process.

This would require a more in-depth knowledge of genomics than generally provided in basic genetics courses.

Much has changed in genetics since the discovery of DNA, but much less has changed how genetics and evolution are taught in medical schools.

In 2013-14 a survey of course curriculums in American and Canadian medical schools showed that while most medical schools taught genetics, most respondents felt the amount of time spent was insufficient preparation for clinical practice as it did not provide them with sufficient knowledge base. The survey showed that only 15 per cent of schools covered evolutionary genetics in their programs.

A simple viable solution may require that all medical applicants entering medical schools have completed rigorous courses in genetics and genomics.

Here's the problem. I've just finished research on a book about modern evolution and genomics so I think I know a little bit about the subject. I'm also on the editorial board of a journal that publishes research on biochemistry and molecular biology education. I've written a biochemistry textbook and I have far too many years of experience trying to teach this material to graduate students and undergraduates at the University of Toronto. I can safely say that we (university teachers) have done a horrible job of teaching evolution and genomics to our students. We have turned out an entire generation of students who don't understand modern molecular evolution and don't understand what's in your genome.

What this means is that there's an extremely small pool of students who have completed "rigorous courses in genetics and genomics." Nobody will be able to apply to medical school. I doubt that we could teach this material to medical students with or without the appropriate background.

But you don't have to take my word for it. Some people have tried to teach this material to health science workers so we can see how it's working at that level. Take a look at the The Genomics Education Programme supported by the NHS in the United Kingdom. They have a series of short videos and longer lessons that are designed to educate health care specialists. Here's the blurb that defines their objective.

Rapid advances in technology and understanding mean that genomics is now more relevant than ever before. As genomics increasingly becomes a part of mainstream NHS care, all healthcare professionals, and not just genomics specialists, need to have a good understanding of its relevance and potential to impact the diagnosis, treatment and management of people in our care.

In 2014, Health Education England (HEE) launched a four-year £20 million Genomics Education Programme (GEP) to ensure that our 1.2 million-strong NHS workforce has the knowledge, skills and experience to keep the UK at the heart of the genomics revolution in healthcare.

Funding for the programme has since been extended to enable us to continue our work in providing co-ordinated national direction of education and training in genomics and developing resources for a wide range of professionals.

They describe genes as 'coding' genes that build proteins. There's no mention of noncoding genes. The define a genome as "both genes (coding) and non-coding DNA." They also say that your genome is all of the DNA in our cells (46 chromosomes, 23 pairs). I don't see anything in their education packages that covers modern molecular evolution. In one of the packages they say,

The term ‘junk DNA’ has been used since the 1970s to describe non-coding regions of the genome, but today it is considered inaccurate and misleading. The term ‘junk’ suggests that 98% of the genome has no use, but in recent years, studies and projects have used advances in technology to shed light on these regions and have come to different conclusions about how much of the genome has a biological function.

Here's a link to a short video called What is a genome?. I recommend that you watch it to see the level that these experts think is suitable for health care professionals in the UK and to see the level of expertise of those who made the video. This is what seven years of work by experts and £20 million will get you.

All of this tells me that teaching genomics and evolution to medical students is going to be a lot more difficult than Rama Singh imagines. Not only would we have to counter several years of misinformation but we would have to rely on teachers who probably don't understand either topic.

Let's start by teaching these things correctly to biology and biochemistry majors. That's going to be hard enough for now.

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1. Full displosure: Rama and I shared an NSERC grant in 1981 on genetic variation in Drosophila.

Why is the Central Dogma so hard to understand?

The Central Dogma of molecular biology states ...

... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958).

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid (F.H.C. Crick, 1970).

This is not difficult to understand since Francis Crick made it very clear in his original 1958 paper and again in his 1970 paper in Nature [see Basic Concepts: The Central Dogma of Molecular Biology]. There's nothing particularly complicated about the Central Dogma. It merely states the obvious fact that sequence information can flow from nucleic acid to protein but not the other way around.

So, why do so many scientists have trouble grasping this simple idea? Why do they continue to misinterpret the Central Dogma while quoting Crick? I seems obvious that they haven't read the paper(s) they are referencing.

I just came across another example of such ignorance and it is so outrageous that I just can't help sharing it with you. Here's a few sentences from a recent review in the 2020 issue of Annual Reviews of Genomics and Human Genetics (Zerbino et al., 2020).

Once the role of DNA was proven, genes became physical components. Protein-coding genes could be characterized by the genetic code, which was determined in 1965, and could thus be defined by the open reading frames (ORFs). However, exceptions to Francis Crick's central dogma of genes as blueprints for protein synthesis (Crick, 1958) were already being uncovered: first tRNA and rRNA and then a broad variety of noncoding RNAs.

I can't imagine what the authors were thinking when they wrote this. If the Central Dogma actually said that the only role for genes was to make proteins then surely the discovery of tRNA and rRNA would have refuted the Central Dogma and relegated it to the dustbin of history. So why bother even mentioning it in 2020?

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Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163. [PDF]

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

Zerbino, D.R., Frankish, A. and Flicek, P. (2020) "Progress, Challenges, and Surprises in Annotating the Human Genome." Annual review of genomics and human genetics 21:55-79. [doi: 10.1146/annurev-genom-121119-083418]