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].

The Scientific Theory of Intelligent Design

Everything that's happening in the world today is very depressing but there's at least one bright spot. The Intelligent Design Creationists have finally come up with a scientific theory of intelligent design. It's described by mathematics professor Ganville Sewell on the Evolution News (sic) website: Introduction to the Scientific Theory of Intelligent Design.

Here's how Sewell desribes this "scientific theory."

Of course, normally if a scientific theory for some observed phenomenon fails, we just look for an alternative “natural” theory. But what has long been obvious to the layman is finally becoming clear to many scientists, that evolution is different. We are not talking now about explaining earthquakes or comets or volcanos, we are talking about explaining hearts and lungs and eyes and ears. How many theories without design can there be for the origin of circulatory systems, nervous systems, and human brains? Design has finally started to be taken seriously by scientists not because there are minor problems with Darwin’s explanation, but because it has become absurdly, blindingly obvious that neither it nor any other theory that ignores design will ever completely explain living things. Contrary to common belief, science really has no reasonable alternative to design to explain either the origin or evolution of life. In fact, we really have no idea how living things are able to pass their current complex structures on to their descendants without significant degradation, generation after generation, much less how they evolve even more complex structures.

That's it? The scientific theory of intelligent design is that evolution has failed and it is now "absurdly, blindingly obvious" that you need design in order to explain the origin of life or the evolution of life.

I'm still depressed. Is this the best they can do after three decades of pushing intelligent design creationism?¹

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1. Yes.

"Cancer Virus Hunters" by Gregory J. Morgan

That seven Nobel Prizes were awarded directly or indirectly for work in tumor virology illustrates the impact of the field on biomedical understanding. (p. 273)

We've entered a new era in the field of molecular biology. Almost all of the emphasis and excitement these days is based on studies of mammals, especially humans. Most of the big bucks are for studying some aspect of medicine so that even if you are interested in basic science you have to slant it toward curing some disease.

"Enlightened" scientist at the University of Colorado busts the myth that all non-coding DNA is junk!

We've known for 60 years that some non-coding DNA has a function but the latest generation of scientists thinks this was only discovered in their lifetime. Writer Kara Mason posts an article on the Department of Biomedical Informatics website at the University of Colorado.

Which first commandment do Louisiana school children have to obey?

The government of the state of Louisiana (USA) has just passed a law that requires ten commandments to be posted in every classroom of every publicly funded elementary, secondary, and postsecondary school [House Bill No. 71]. Here's the first one that's specified in the law.

I AM the LORD thy God. Thou shalt have no other gods before me. Thou shalt not make to thyself any graven images. Thou shalt not take the Name of the Lord thy God in vain.

Fauci claims (incorrectly) that the lab leak conspiracy theory is not a conspiracy theory

Here's Fauci being interviewed on MSNBC as part of his book promotion tour (see below). He's asked about the lab leak conspiracy theory beginning at 10 mins. He points out that there's no evidence that SARS-CoV-2 came from the Wuhan Institute of Virology (WIV) but he's keeping an "open mind" about the possibility that something could be true in the absence of evidence and in the face of considerable evidence for a natural origin.

The most fascinating part of the interview is when he goes out of his way to say that such a possibility doesn't require a conspiracy theory. Really?

David Gorski (Orac) dismantles Alina Chan's lab leak conspiracy theory

This post is just a place-holder for an article that I've already shared on Facebook. I greatly appreciate the fact that Orac referrd to me several times in his article on Respectful Insolence.

The New York Times goes all in on “lab leak”

Earlier this week, the New York Times op-ed page ran an article by Alina Chan, Queen of lab leak conspiracy theories. How is it wrong? Let me count the ways…

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Pentagon ran secret anti-vax campaign to undermine China during pandemic

This is a Reuters report about misinformation spread by the United States military in order to discredit China's Sinovac vaccine. It was directed at the Philippines and other countries who were purchasing the China vaccine.

Reuters suggests that by undermining public trust in government health initiatives the US military might have cost thousands of lives in the Phillippines.

A REUTERS INVESTIGATION: Pentagon ran secret anti-vax campaign to undermine China during pandemic

The U.S. military launched a clandestine program amid the COVID crisis to discredit China’s Sinovac inoculation – payback for Beijing’s efforts to blame Washington for the pandemic. One target: the Filipino public. Health experts say the gambit was indefensible and put innocent lives at risk.

It shouldn't surprise anyone that nations engage in propaganda wars in order to destabilize or demonize their perceived enemies. The world is a complicated multinational environment and meddling in the affairs of other countries is a routine part of modern international relations. It's important to emphasize that it's not only the "bad guys" who do this sort of thing. Your own country and your friends and allies also spread misinformation in order to convince you that you are one of the "good guys" (e.g. defenders of morality, decency, democracy, and freedom).

I emphasize this for two reasons. One, here in Canada there's a lot of pearl-clutchng these days about foreign interference and the main focus is on China and India and how they might have influenced our elections. I think this is pretty minor stuff compared to what else is going on and the foreign influence from other countries, including the United States.

Second, as mentioned above, we all need to be aware of the fact that misinformation is rampant and that doesn't just include misinformation spread by Russia, China, Iran, and Hamas. We also need to be skeptical about information being spread by the governments of Ukraine, Israel, and the United States. Do not assume that everything they say is truthful.

These days, I find that it's almost impossible to hear, read, or watch any "authority" who convinces me that they are critical thinkers without an agenda. Almost all of them seem to be victims of propaganda.

Note: I'm aware of the fact that this report may not be accurate—it may, in fact, be misinformation. I'm mostly using it as a vehicle to point out that you can't trust anyone these days, including your friends. That's very upsetting because I grew up thinking that the mainstream news outlets (TV, radio, newspapers) could be (mostly) trusted.

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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]