John Mattick's seminar at the University of Toronto

I just learned that John Mattick gave a seminar this morning at the Department of Cell & Systems Biology at the University of Toronto. Unfortunately, I was unable to attend.

Most Sandwalk readers will recognize Mattick as one of the few remaining vocal opponents of junk DNA. He is probably best known for his dog-ass plot but this is only one of the ways he misrepresents science.

On the evolution of the glycolytic pathway (glycolysis)

Jonathan McLatchie has a PhD in Evolutionary Biology from Newcastle University (UK) and he is currently "resident biologist" and a fellow at the Center for Science and Culture at the Discovery Institute. He is an intelligent design creationist who attacks evolution by questioning standard explanations in the fields of biochemistry and molecular biology.

I've debated him frequently over the years since those are my areas of interest as well. The last time we met was at an evolution conference in London (UK) in 2016 (see photo).

I've always found Jonathan to be more honest and more willing to learn than most of his creationist colleagues so that's why I'm addressing his latest post on Evolution News (sic) where he challenges the evolutionary origins of the glycolytic pathway. As you might expect, his argument is largely based on the idea that since the glycolytic pathway is very complicated, there's no way it could have arisen all at once. He then goes on to reject the idea that the pathway could have evolved incrementally, one step at a time.

Should Scientific American endorse United States political candidates?

Scientific American has endorsed Kamala Harris, a candidate for president of the United States. I think this is a mistake and so do many other scientists and even journalists [Scientific American Didn’t Need to Endorse Anybody].

I agree with those who say that science should stay out of politics as much as possible. But this is just one of many indications that Scientific American is sliding rapidly downhill and no longer qualifies as a real science magazine.

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The DNA papers

The DNA papers is a series of podcasts on the discovery that DNA is the source of genetic information. Each podcast is a discussion among experts on the history of molecular biology, including some who have been regularly featured on this blog. I draw your attention to episodes 6 and 15 where you can hear Matt Meselson one of the key figures in the 'phage group.

The key take-home lesson is that the importance of DNA was recognized by a small group of scientists who were paying attention to the scientific literature. By the time of Watson and Crick (1953) this small group was already convinced that DNA was the "stuff of life," which is why they realized that solving the structure was extremely important.

This is not unusual. There are many cases where a small group of knowledgeable experts are well in advance of the average scientist who often doesn't even realize that a revolution is under way.

• Episode 1 on Friedrich Miescher and the discovery of nuclein
• Episode 2 on Albrecht Kossel and the discovery of the building blocks of nuclein
• Episode 3 on Walter Sutton and the relation between chromosomes and heredity
• Episode 4 on Fred Griffith and the discovery of bacterial transformation/li>
• Episode 5 on Phoebus Levene, DNA chemistry and the tetranucleotide hypothesis
• Episode 6 on William Astbury, Florence Bell and the first X-ray pictures of DNA
• Episode 7 on Oswald Avery, Colin McLeod, and Maclyn McCarty and the chemical basis of bacterial transformation
• Episode 8 on Maclyn McCarty, Oswald Avery and the enzymatic evidence for DNA as the transforming substance
• Episode 9 on Erwin Chargaff and the evidence for non-uniformity of nucleotide base composition in DNA
• Episode 10 on Harriet Ephrussi-Taylor, Rollin Hotchkiss and the demonstration of bacterial transformation as a general phenomenon
• Episode 11 on Alfred Hershey, Martha Chase, and the conclusive evidence for the function of DNA as the material of heredity
• Episode 12 on Maurice Wilkins, Rosalind Franklin, their collaborators, and the data that supported the double helix model for DNA structure
• Episode 13 on James Watson, Francis Crick, and the DNA Double Helix
• Episode 14 on Matthew Meselson, Franklin Stahl, and semiconservative replication of DNA
• Episode 15 A conversation with Matthew Meselson and Franklin Stahl

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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.

The New York Times questions for Kamala Harris: Foreign Policy

The first two posts of this series cover 11 of the 21 questions that The New York Times wants to ask Kamala Harris. [The New York Times has 21 questions for Kamala Harris (and Trump?)] [The New York Times questions for Kamala Harris: Social Issues].

In this post I'll address the 7 questions on foreign policy using the same format.

The New York Times questions for Kamala Harris: Social Issues

In the first post of this series, I covered the reasons why Republicans want the media to attack Kamala Harris on specific policy issues and why I think the Democrats should resist this pressure. I also pointed out the double standard—nobody is asking Trump to explain in detail how he will achieve his policy objectives. [The New York Times has 21 questions for Kamala Harris (and Trump?)]

The New York Times has 21 questions for Kamala Harris (and Trump?)

I am not an American but I find American politics fascinating. I believe that presidential elections are part of a larger culture war with Democrats and Republicans on the opposite sides of many cultural issues such as gun control, LGBTQ+ rights, abortion, religion, racism, education, sexism, and health care. I think Republicans have been exploiting this culture war very effectively in order to win seats in Congress and, sometimes, the White House. They have succeeded in stacking the Supreme Court of the United States. Republicans appeal to voters who are very uneasy about the kind of rapid cultural change that's happening all around them.

Some transcription factors can be both activators and repressors! Textbooks have been saying this for decades

This is another post about a bad press release based on a lack of knowledge of the history of the field.

Here's the press release from Washington State University as reported in SciTechDaily

Scientists Discover “Spatial Grammar” in DNA: Breakthrough Could Rewrite Genetics Textbooks

“Contrary to what you will find in textbooks, transcription factors that act as true activators or repressors are surprisingly rare,” said WSU assistant professor Sascha Duttke, who led much of the research at WSU’s School of Molecular Biosciences in the College of Veterinary Medicine.

Rather, the scientists found that most activators can also function as repressors.

“If you remove an activator, your hypothesis is you lose activation,” said Bayley McDonald, a WSU graduate student who was part of the research team. “But that was true in only 50% to 60% of the cases, so we knew something was off.”

Looking closer, researchers found the function of many transcription factors was highly position-dependent.

They discovered that the spacing between transcription factors and their position relative to where a gene’s transcription began determined the level of gene activity. For example, transcription factors might activate gene expression when positioned upstream or ahead of where a gene’s transcription begins but inhibit its activity when located downstream, or after a gene’s transcription start site.

... By integrating this newly discovered ‘spatial grammar,’ Christopher Benner, associate professor at UC San Diego, anticipates scientists can gain a deeper understanding of how mutations or genetic variations can affect gene expression and contribute to disease.

”The potential applications are vast,” Benner said. “At the very least, it will change the way scientists study gene expression.”

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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Zach Hancock explains junk DNA

Zach Hancock is a postdoc in ecology & evoluvionary biology at the University of Michigan. He has a YouTube channel with several thousand subscribers. You might recall that he interviewed me last year when my book came out [Zach Hancock interviews me on his YouTube channel].

He has just posted a new video on junk DNA that's well worth watching. He tries to correct all the falsehoods and misinformation on junk DNA, especially those promoted by creationists. It's well worth watching.

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Is Casey Luskin lying about junk DNA or is he just stupid?

I'm going to address a recent article by Casey Luskin on Evolution News (sic) and a podcast on a Current Topics in Science podcast produce by Christ Jesus Ministries. But first, some background.

A recent paper in Nature looked at a region on chromosome 21 where mutations associated with autoimmune and inflammatory disease were clustered. This region did not contain any known genes and is referred to in the paper as a "gene desert." The authors reasoned that it probably contained one or more regulatory sites and, as expected, they were able to identify an enhancer element that helps control expression of a nearby gene called ETS2 (Stankey et al., 2024).

The results were promoted in a BBC article: The 'gene deserts' unravelling the mysteries of disease. The subtitle of the article tells you where this is going, "Mutations in these regions of so-called "junk" DNA are increasingly being linked to a range of diseases, from Crohn's to cancer." The article implies that since only 2% of the human genome codes for proteins the remaining 98% "has no obvious meaning or purpose." The caption to one of the figures says, "Gene deserts are regions of so-called genetic "junk" that do not code for proteins – but they may play an important role in disease." Thus, according to the BBC, the discovery of a regulatory sequence conflicts with the idea of junk DNA.

There's no mention of junk DNA in the original Nature article and none of the comments by the senior author (James Lee) in the BBC article suggest that he is confused about junk DNA.

An article published in Nature Communications looked at expression of human endogenous retrovirus elements (HERV's) in human brain. The authors found that expression of two HERV sequences is associated with risk for schizophrenia but the authors noted that is wasn't clear how this expression played a role in psychiatric disorders (Duarte et al., 2024)

Although the term "junk DNA" was not mentioned in the original article, the press release from King's College, London makes the point that HERVS were assumed to be junk DNA. The implication is that this is one of the first publications to discover a possible function for this junk DNA. (Functional elements derived from HERVs have been known for three decades.)

Casey Luskin wrote about these studies yesterday in an article on the intelligent design website: Disease-Associated “Junk” DNA Is Evidence of Function and talks about it in the podcast that I link to below.

Luskin continues to promote the false claim that all non-coding DNA was assumed to be junk. That allows him to highlight all studies that discover new functional elements in non-coding DNA and claim that it refutes junk DNA. He's been doing this for years in spite of multiple attempts to correct him. Therefore, the answer to the question in the title in obvious, he is a liar—judge for yourselves whether he is also stupid.

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Duarte et al. (2024) Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nature Communications 15: 3803 [doi: 10.1038/s41467-024-48153-z]

Stankey et al. (2024) A disease-associated gene desert directs macrophage inflammation through ETS2. Nature 630: 447–456 [doi: 10.1038/s41586-024-07501-1]

Bastille Day 2024

Today is the Fête Nationale in France known also as "le quatorze juillet" or Bastille Day.

This is the day in 1789 when French citizens stormed and captured the Bastille—a Royalist fortress in Paris. It marks the symbolic beginning of the French revolution although the real beginning is when the Third Estate transformed itself into the National Assembly on June 17, 1789 [Tennis Court Oath].

We visited the site of the Bastille (Place de la Bastille) when we were in Paris a few years ago. There's nothing left of the former castle but the site still resonates with meaning and history.

My wife's 5th great-grandfather is William Playfair (1759-1823), the inventor of pie charts and bar graphs [Bar Graphs, Pie Charts, and Darwin]. His work attracted the attention of the French King so he moved to Paris in 1787 to set up an engineering business. Playfair was present at the storming of the Bastille on July 14, 1789. He is recorded as one of one of about 1000 militia who took part in the action: "William Playfair, ingénieur anglais, petit hôtel de Lamaignon rue Couture Sainte Catherine."

His residence, the Hôtel de Lamaignon, still exists. It was about a kilometer west of the Bastille.

In honor of the French national day I invite you to sing the French national anthem, La Marseillaise. An English translation is provided so you can see that La Marseillaise is truly a revolutionary call to arms. (A much better translation can be found here.)

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Check out Uncertain Principles for another version of La Marseillaise—this is the famous scene in Casablanca.

Reposted and modified from 2017.

My ancestor's house in New Amsterdam (1655)

This is the 400th anniversary of the founding of New Amsterdam by Dutch settlers. The map shows what the city looked like in 1660, a few years before it was taken over by the British and renamed New York. The red oval shows the location of Abraham Rychen's house; he sold it in 1655.

Abraham Rycken was born in 1618 in Nijmegen, Netherlands. He is my 9th great-grandfather. Abraham married Grietje Harmensen, the daughter of settler Harmen Harmensen. Harmen was an armorer for the Dutch army and later retired to a farm on Riker's Island where he made tomahawks for the indigenous people who lived there and on Long Island. Harmen was killed in 1643 by a native using one of his tomahawks.

Jerry Coyne changes his mind about the lab leak conspiracy theory and now rejects it

Jerry Coyne was initially convinced by Alina Chan's arguments in favor of the lab leak conspiracy theory concerning the origin of SARS-CoV-2. His mind was changed by reading Paul Offit's rebuttal [Lab Leak Mania].

Here's how Jerry describes his conversion in an article posted on his website [The lab leak theory for the origin of the Covid virus is once again deep-sixed].