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]

Tom Cech writes about the "dark matter" of the genome

Tom Cech won a Nobel Prize for discovering one example of a catalytic RNA. He recently published an article in the New York Times extolling the virtues of RNA and non-coding genes [The Long-Overlooked Molecule That Will Define a Generation of Science]. There's a fair amount of hype in the article but the main point is quite valid—over the past fifty years we have learned about dozens of important non-coding RNAs that we didn't know about at the beginning of molecular biology [see: Non-coding RNA, Non-coding DNA].

The main issue in this field concerns the number of non-coding genes in the human genome. I cover the available data in my book and conclude that there are fewer than 1000 (p.214). Those scientists who promote the importance of RNA (e.g. Tom Cech) would like you to believe that there are many more non-coding genes; indeed, most of those scientists believe that there are more non-coding genes than coding genes (i.e. > 20,000). They rarely present evidence for such a claim beyond noting that much of our genome is transcribed.

Tom Cech is wise enough to avoid publishing an estimate of the number of non-coding genes but his bias is evident in the following paragraph from near the end of his article.

Although most scientists now agree on RNA's bright promise, we are still only beginning to unlock its potential. Consider, for instance, that some 75 percent of the human genome consists of dark matter that is copied into RNAs of unknown function. While some researchers have dismissed this dark matter as junk or noise, I expect it will be the source of even more exciting breakthroughs.

Let's dissect this to see where the bias lies. The first thing you note is the use of the term "dark matter" to make it sound like there's a lot of mysterious DNA in our genome. This is not true. We know a heck of a lot about our genome, including the fact that it's full of junk DNA. Only 10% of the genome is under purifying selection and assumed to be functional. The rest is full of introns, pseudogenes, and various classes of repetitive sequences made up mostly of degraded transposons and viruses. The entire genome has been sequenced—there's not much mystery there. I don't know why anyone refers to this as "dark matter" unless they have a hidden agenda.

The second thing you notice is the statement that 75% of the genome is transcribed at some time or another and, according to Tom Cech, these transcripts have an unknown function. That's strange since protein-coding genes take up roughly 40% of our genome and we know a great deal about coding DNA, UTRs, and introns. If you add in the known examples of non-coding genes, this accounts for an additional 2-3% of the genome.¹

Almost all the rest of the transcripts come from non-conserved DNA and those transcripts are present at less than one copy per cell. As the ENCODE researchers noted in 2014, they are likely to be junk RNA resulting from spurious transcription. I'd say we know a great deal about the fraction of the genome that's transcribed and there's not much indication that it's hiding a plethora of undiscovered functional RNAs.

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Photo credit: University of Colorado, Boulder.

1. In my book I make a generous estimate of 5,000 non-coding genes in order to avoid quibbling over a smaller number and in order to demonstrate that even with such a obvious over-estimate the genome is still 90% junk.

June 6, 1944: My father on D-Day

This year is the 80th anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy in World War II.¹

For us baby boomers, it has always meant a day of special significance for our parents. In my case, it was my father who took part in the invasions. That's him on the right as he looked in 1944. He was an RAF pilot flying rocket-firing typhoons in close support of the ground troops. His missions were limited to quick strikes and reconnaissance during the first few days of the invasion because Normandy was at the limit of their range from southern England. During the second week of the invasion (June 14th) his squadron landed in Crepon, Normandy and things became very hectic from then on with several close support missions every day [see Hawker Hurricanes and Typhoons in World War II].

The New York Times promotes the lab leak conspiracy theory

Scientists have been actively investigating the origin of SARS-CoV-2 for the past four years. The evidence strongly favors early transmission from infected animals in the Huanan seafood market in Wuhan, China (Worobey et al., 2022; Alwine et al., 2023; Dwyer, 2023; Holmes et al., 2021; Holmes, 2024). The virus probably originated in bats in China or southest asia. [The case for a natural origin of SARS-CoV-2] [Real scientists discuss the lab leak conspiracy theory]

Some people have suggested that the infectious virus, SARS-Cov-2, escaped from a lab in the Wuhan Institute of Virology in spite of the fact that there's not a shred of evidence that the scientists there ever worked with such a strain before the pandemic and all the scientists deny that they had ever seen the pandemic virus before the pandemic began. Such suggestions have all the characteristics of a conspiracy theory (Lewandowsky et al., 2023; Goodrum et al., 2023).¹

The New York Times has just published an opinion piece that promotes the lab leak conspiracy theory. It just happened to coincide with a Republican witch hunt investigation into Dr. Fauci and the origins of SARS-CoV-2. The article is written by Alina Chan who wrote a book on the subject with co-author Matt Ridley [Alina Chan teams up with Matt Ridley to promote the lab leak conspiracy theory].

Here's the link to the NYT article: Why the Pandemic Probably Started in a Lab, in 5 Key Points. As you can see from the title, Alina Chan has five reasons why the scientists at the Wuhan Institute of Virology were working on SARS-Cov-2 before the pandemic began and why they are denying that the virus escaped from their lab. All of these five points have been discredited and/or discounted but that didn't stop the newspaper from promoting them.²

1. The SARS-like virus that caused the pandemic emerged in Wuhan, the city where the world’s foremost research lab for SARS-like viruses is located.

   This is just about the only thing in the lab leak conspiracy theory that is true.

2. The year before the outbreak, the Wuhan institute, working with U.S. partners, had proposed creating viruses with SARS‑CoV‑2’s defining feature.

This is extremely misleading. The researchers at WIV worked in collabortion with scientists in other countries, including the United States, on investigating the features of coronaviruses that could lead to infection of humans. That's exactly what you would expect them to do. They never created a virus that could be infectious.

3. The Wuhan lab pursued this type of work under low biosafety conditions that could not have contained an airborne virus as infectious as SARS‑CoV‑2.

   The labs followed all the standard procedures for work of this type and passed an international inspection.

4. The hypothesis that Covid-19 came from an animal at the Huanan Seafood Market in Wuhan is not supported by strong evidence.

   That's a lie. There is strong evidence that the outbreak began in the market.

5. Key evidence that would be expected if the virus had emerged from the wildlife trade is still missing.

   It's true that the exact infectious animal carrying SARS-CoV-2 has not been identified but the circumstantial evidence is strong—just as strong as the circumstantial evidence that sends some people to jail. It's crazy to say that evidence for animal transmission is missing when ALL the evidence for the presence of SARS-CoV-2 at WIT is also missing.

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1. The researchers at WIV are highly respected international experts on virology, especially coronaviruses. They published in the best international journals. Since they all deny that they were working with SARS-CoV-2 before the pandemic, the lab leak hypothesis absolutely requires that several hundred reseachers are lying and covering up the fact that the virus leaked from their labs. In other words, a conspiracy is an essential part of the lab leak conspiracy theory [see Most scientists dismiss the lab leak conspiracy theory].

2. It's amazing how many media personalities have assumed that there must be some element of truth in this opinion piece just because it was published in the New York TImes. It's even more amazing that these media personalities couldn't find any real scientists to interview.

Alwine, J.C., Casadevall, A., Enquist, L.W., Goodrum, F.D. and Imperiale, M.J. (2023) A critical analysis of the evidence for the SARS-CoV-2 origin hypotheses, Am Soc Microbiol. 97: e00365-00323. [doi: 10.1128/jvi.00365-23]

Dwyer, D.E. (2023) The origins of severe acute respiratory syndrome-coronavirus-2. Seminars in Respiratory and Critical Care Medicine, Thieme Medical Publishers, Inc. [doi: 10.1055/s-0042-1759564]

Goodrum, F., Lowen, A.C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M.J., Atwood, W., Avgousti, D., Baines, J. and Banfield, B. (2023) Virology under the microscope—a call for rational discourse. Journal of virology 97:e00089-00023. [doi: 10.1128/jvi.00089-23]

Holmes, E.C., Goldstein, S.A., Rasmussen, A.L., Robertson, D.L., Crits-Christoph, A., Wertheim, J.O., Anthony, S.J., Barclay, W.S., Boni, M.F., Doherty, P.C., Farrar, J., Geoghegan, J.L., Jiang, X., Leibowitz, J.L., Neil, S.J.D., Skern, T., Weiss, S., R, Worobey, M., Anderson, K.G., Garry, R.F. and Rambaut, A. (2021) The origins of SARS-CoV-2: A critical review. Cell 184:4848-4856. [doi: 10.1016/j.cell.2021.08.017]

Holmes, E.C. (2024) The emergence and evolution of SARS-CoV-2. Annual review of virology 11. [doi: 10.1146/annurev-virology-093022-013037]

Lewandowsky, S., Jacobs, P.H. and Neil, S. (2023) Leak or Leap? Evidence and Cognition Surrounding the Origins of the SARS-CoV-2 Virus. Covid Conspiracy Theories in Global Perspective, ed. Michael Butter and Peter Knight:26-39. [PDF]

Worobey, M., Levy, J.I., Malpica Serrano, L., Crits-Christoph, A., Pekar, J.E., Goldstein, S.A., Rasmussen, A.L., Kraemer, M.U., Newman, C. and Koopmans, M.P. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 377:951-959. [doi: 10.1126/science.abp8715]