Monday's Molecule #242

It's been a while since the last Monday's Molecule on May 19, 2014 but I think it's time to revive that tradition. I'll show you a molecule and you have to guess what it is without searching the internet. In other words, you have to recognize it immediately or it doesn't count. Email your answer to me at: Monday's Molecule #242. The first one with the correct answer wins. I will only post the names of winners to avoid embarrassment. The winner will be treated to a free coffee and donut at Tim Hortons if you are ever in Toronto or Mississauga (Ontario, Canada).¹

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

Today's molecule (right) looks very complicated but I'm not going to ask you to give me a complete chemical name. The simple common name will do but you have to briefly explain it's biological significance and why it's always discussed in biochemistry textbooks.

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

Comments are closed for at least 24 hours.

UPDATE: The winner is Elie Huvier who pointed out that the molecule is a thymine dimer with a cyclobutane ring. Thymine dimers are mutations caused by ultraviolet light, which causes photodimerization of adjacent stacked pyrimidines in DNA. Elie Huvier was the first one to identify the molecule and describe its significance.

Winners

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

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

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

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

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

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

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

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

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

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

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1. I still owe some previous winners. If you are one of them, then you should email me to set up a time and place.

Intelligent Design Creationists made up a fake march of progress illustration

Everyone is familiar with the typical March of Progress figures that are often used to illustrate evolution. However, most people don't know that evolutionary biologists object to that depiction of evolution because it seriously misrepresents the reality of human evolution.

Stephen Jay Gould has been one of the most vocal opponents of such icons because they imply a sense of direct linear progress from some primitive ancestor to a modern species when, in fact, the actual evolution involves branching trees with multiple lineages, most of which have gone extinct. In one of his most famous essays, Life's Little Joke (Gould, 1987, 1991), Gould explains why the evolution of horses is falsely depicted as a march of progress.

Jonathan Wells (1942 - 2024)

Johnathan Wells died recently. He was a well-known Intelligent Design Creationist and that's why Evolution News (sic) is eulogizing him by posting multiple tributes and excerpts from his books and essays.

I think it's only fair to post links to my efforts to demonstrate the serious flaws in his arguments. I'm particularly proud of the series of articles I wrote when he published his book The Myth of Junk DNA. I went through every chapter and analyzed his arguments against junk DNA. It won't surprise anyone to learn that I found those arguments lacking in substance and in some cases I discovered that Wells had misrepresented the science.

Here are my posts.

• Jonathan, Moonies, and Junk DNA
• Junk & Jonathan: Part I—Getting the History Correct
• Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?
• Junk & Jonathan: Part 3—The Preface
• Junk & Jonathan: Part 4—Chapter 1
• Junk & Jonathan: Part 5—Chapter 2
• Junk & Jonathan: Part 6—Chapter 3
• Junk & Jonathan: Part 7—Chapter 4
• Junk & Jonathan: Part 8—Chapter 5
• Junk & Jonathan: Part 9—Chapter 6
• Junk & Jonathan: Part 10—Chapter 7
• Junk & Jonathan: Part 11—Chapter 8
• Junk & Jonathan: Part 12—Chapter 9
• Junk & Jonathan: Part 13—Chapter 10

Jonathan Wells never responded directly to my criticism but he did respond to a comment that Paul McBride made on one of his blog posts. Paul asked him why he didn't respond to my post and here's what Wells said,

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

This is typical of the attitude of most Intelligent Design Creationists. They are happy to publish lengthy books denegrating science and scientists but couldn't be bothered responding to criticism.

Here's are some other post of mine where I demonstrate the flawed thinking of Jonathan Wells.

• Jonathan Wells talks about junk DNA
• Jonathan Wells illustrates zombie science by revisiting junk DNA
• Brace yourselves, a new "Icons" is coming
• Jonathan Wells proves that life must have been created by gods
• Answering ten questions from the IDiots
• John Mattick vs. Jonathan Wells
• Some Questions for IDiots
• American Loons: #409 Jonathan Wells and #411 John West
• A Dishonest Intelligent Design Proponent?
• We Called Out IDiot Jonathan Wells, and He Folded
• Jonathan Wells Sends His Regrets
• Watch Jonathan Wells Screw Up
• Jonathan Wells Talks About Sequence Conservation
• Ohmygod! These photographs are faked!
• Fossil Horses and Directed Evolution
• Peppered Moths and the Confused IDiots
• Jonathan Wells reviews the Christiane Nüsslein-Volhard and Wieschaus Experiment

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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].

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]

Telomere length in humans

Telomeres are repetitive DNA sequences at the ends of chromosomes. In humans, the repeat sequence is TTAGGG. The purpose of telomeres is to protect the ends of the chromosomes from shortening after DNA replication [Telomeres].

Telomeres are just one of many functional DNA elements in the human genome. The average length of human telomeres was long thought to be about 10 kb and since there are 24 distinct chromosomes in the human genome this amounts to about 480 kb of telomere sequence or about 0.015% of the human genome. With the advent of new sequencng technology it is now possible to generate long reads of DNA sequence and this has led to a somewhat shorter estimate of telomere length (Karimian et al., 2024). The figure from thier paper shows that the average length of telomeres gets shorter with age but the starting length in newborns (cord DNA) is about 8 kb instead of 10 kb. The authors explain why their sequencing technique is likely to give more accurate results than the earlier estimates.

This doesn't make much difference to the previous estimate but I thought I'd post an update since I overestimated the contribution of telomeres in my book and I made a calculation error in a previous post [Telomeres].

If we use 8 kb as the average length, then that means a total of 8 × 2 × 24 = 384 kb or 0.012% of the standard human genome, which includes 22 autosomes and both sex chromsomes.

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Image Credit: The image shows human chromosomes (blue) labelled with a telomere probe (yellow), from Christopher Counter at Duke University.

Karimian, K., Groot, A., Huso, V., Kahidi, R., Tan, K.-T., Sholes, S., Keener, R., McDyer, J.F., Alder, J.K., Li, H., Rechtsteiner, A. and Greider, C. (2024) Human telomere length is chromosome end–specific and conserved across individuals. Science 384:533-539. [doi: 10.1126/science.ado0431]

University of Toronto President explains why the Occupy for Palestine demands are unreasonable and unacceptable

The Occupy for Palestine protestors have occupied part of the campus of the University of Toronto. The protestors are making two demands on the university.

• “terminate all partnerships with Israeli academic institutions that operate in the Occupied Palestinian Territories, or sustain the apartheid policies, occupation and illegal settlement of these territories.”
• “divest its endowment, pension fund, and other financial holdings from all companies that provide Israel with military goods or services which sustain the Israeli apartheid, occupation and illegal settlement of the Palestinian Territories, as well as the ongoing attacks on Gaza.”

The President of the University of Toronto, Meric Gertler, has responded to these demands with a letter sent to the members of Occupy for Palestine [President Meric Gertler’s response to members of Occupy for Palestine].

With respect to the first demand, President Gertler points out that the university has a history of opposition to academic boycotts.

Such demands are antithetical to the University’s firm conviction that the best way to protect human rights is by staunchly defending and promoting academic freedom, freedom of expression, and the unfettered circulation of ideas within the global scholarly community. We have consistently emphasized that it is both inappropriate and, ultimately, counterproductive to single out academics working or studying in a particular country, and to hold them accountable for the actions or policies of their country’s government. Faculty and students are often among the most trenchant critics of their own government’s policies or actions. Events over the past year confirm that Israeli academics – as well as university leaders – have been amongst the most vociferous critics of the current government and its policies.

For this reason, the university rejects the Occupy for Palestine's first demand.

The second demand is unreasonable because the University does not directly control the pension fund; those investments are controlled by a Board of Trustees, some of whom are appointed by staff and faculty because a large percentage of the pension fund is their money. Also, the pension fund is a joint fund with the University of Guelph and Queen's University. Similarly, with respect to the endowment fund, the University does not directly control direct investments in companies so it cannot comply with the demand even if it wished to.

However, notwithstanding those practicalities, there are fundamental principles at stake that need to be addressed.

... the University’s Policy on Social and Political Issues with Respect to University Divestment notes in its opening Preamble that “As a general matter, the University does not take positions on social or political issues apart from those directly pertinent to higher education and academic research.” Accordingly, “the University will not consider proposals for restrictions on its investments that require the institution to take sides in matters that are properly the subject of ongoing academic inquiry and debate.” It further notes, as a corollary, that the University’s response to any requests for divestment “must be governed by the fundamental place of diversity of opinion within its community. Except in those situations in which the University must settle on an answer to controversial questions about how best to achieve its academic mission, the University risks abandoning its core values if it takes sides in ongoing debates and is perceived to be advancing a specific political or social position.”

This is consistent with the Chicago Principles on free expression and the Kalven Report on the University's role in political and social action. Meric Gertler does not specifically mention the Kalven Report from the University of Chicago but it's clear that it forms the basis of the University of Toronto's position. For that reason, and because that position is not widely understood, I quote from the report.

A university has a great and unique role to play in fostering the development of social and political values in a society. The role is defined by the distinctive mission of the university and defined too by the distinctive characteristics of the university as a community. It is a role for the long term.

The mission of the university is the discovery, improvement, and dissemination of knowledge. Its domain of inquiry and scrutiny includes all aspects and all values of society. A university faithful to its mission will provide enduring challenges to social values, policies, practices, and institutions. By design and by effect, it is the institution which creates discontent with the existing social arrangements and proposes new ones. In brief, a good university, like Socrates, will be upsetting.

The instrument of dissent and criticism is the individual faculty member or the individual student. The university is the home and sponsor of critics; it is not itself the critic. It is, to go back once again to the classic phrase, a community of scholars. To perform its mission in the society, a university must sustain an extraordinary environment of freedom of inquiry and maintain an independence from political fashions, passions, and pressures. A university, if it is to be true to its faith in intellectual inquiry, must embrace, be hospitable to, and encourage the widest diversity of views within its own community. It is a community but only for the limited, albeit great, purposes of teaching and research. It is not a club, it is not a trade association, it is not a lobby.

Since the university is a community only for these limited and distinctive purposes, it is a community which cannot take collective action on the issues of the day without endangering the conditions for its existence and effectiveness. There is no mechanism by which it can reach a collective position without inhibiting that full freedom of dissent on which it thrives. It cannot insist that all of its members favor a given view of social policy; if it takes collective action, therefore, it does so at the price of censuring any minority who do not agree with the view adopted. In brief, it is a community which cannot resort to majority vote to reach positions on public issues.

I am a University of Toronto retired professor and I fully support the position of the University President. The university cannot and should not take a position on social issues. I fully support the rights of students and faculty to express their personal views on such issues. For example, we may protest the behavior of the Israel government, of Hamas, the governments of Russia or Ukraine, and even, especially, our own government. Those are all legitimate targets of protest. The university is not a legitimate target. The university is not our enemy.

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Junk DNA debate: Casey Luskin vs Dan Stern Cardinale

Here's a link to the junk DNA debate between Dan Stern Cardinale and Casey Luskin. The debate took place on May 2, 2024.

I mentioned in a previous post that Luskin should have been called out on his repeated attempts to equate junk DNA with non-coding DNA. This allowed him to portray all non-coding functions as evidence against junk DNA. [Casey Luskin posts misleading quotes about junk DNA].

There are several other things that I would have done differently. I would have made it clear that 10% of the genome is functional and we don't know the function of some of that fraction. Thus, all newly discovered functional regions could still fit into the 10% and 90% of the genome is still junk. Every time Casey mentions a new function he should have been challenged to specify exactly what percentage of the genome he is referring to. (Dan tried to do this but he was too nice, and let Casey off the hook.)

The idea here is to make it clear to viewers that recent discoveries of functional regions do not affect the idea that most of our genome is junk.

I would also attempt to get Casey to admit that there's a scientific controversy over junk DNA so there are many papers defending junk DNA and criticizing the arguments of junk DNA opponents. For every quotation from a scientist who opposes junk, there's an equally significant quotation from one who supports junk. Why does Casey only quote scientists who agree with him? Is this cherry-picking? Is selectively rattling off quotations and references from people who agree with you a reasonable way to have a serious scientific debate?

I think the arguments over transcripts should begin with presenting all the scientific evidence that spurious transcripts exist - for example, random DNA sequences inserted into a cell nucleus are transcribed and spurious transcription is easily documented in well-studied organisms such as bacteria and yeast. The characteristics of spurious transcription are that the transcripts are present in very small amounts, that they are rapidly degraded, that they come from regions of the genome that are not under purifying selection, and they are cell/tissue specific. So what is the most reasonable explanation when you look at such transcripts?

Casey Luskin's attempt to avoid the best explanation (spurius transcription) is a classic example ad hoc rescue and it might have been useful to point this out to viewers.

Regulation is not new. There was serious discussion and debate over the amount of the genome devoted to regulation back in the late 1960s when the concept of junk DNA was first proposed. Casey should have been challenged to state what percentage of the genome is devoted to regulation and if he comes up with an unreasonable number he should have to give examples of many well-studied genes that have been shown to have that level of regulation. (Hint: There aren't any.) All of the detailed work on the regulation of dozens of specific human genes has shown that you don't need more than a few transcription factor binding sites to control expression. Is there any reason to suppose that the other genes require ten or a hundred times more regulatory sequences to control expression?

What is the trend line? Ever since the ENCODE publicity disaster of 2012 there has been a flood of papers defending junk DNA and the data supporting junk DNA is now stronger that it has ever been because we now know from hundreds of thousands of human genome sequences that only about 10% is under purifying selection. There have also been a lot of papers fleshing out the 10% of the genome that's functional. There have only been a handful of papers published in the past ten years that seriously attempt to present evidence that most of our genome is functional. I would have challenged Casey to come up with a single scientific publication in the past ten years claiming, with supporting data, that most of the genome is functional.

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Casey Luskin posts misleading quotes about junk DNA

On Thursday May 2, 2024, Casey Luskin and Dan Stern Cardinale debated junk DNA on the YouTube channel "The NonSequitor Show." David Klinghoffer thinks that this debate went very well for the ID side [Debate: Casey Luskin Versus Rutgers Biologist Dan Cardinale, Thursday, May 2]. I agree with Klinghoffer; Luskin did an excellent job of promoting his case because many of his statements and claims were not challenged effectively.

I'll be putting up a separate post on the debate but for now I'd like to address an article by Casey Luskin that he posted before the debate as preparation for what he was going to say. The article consists of a bunch of quotes from prominent scientists about junk DNA [“Junk DNA” from Three Perspectives: Some Key Quotes]. Here are the three perspectives, according to Luskin.

Category 1: Quotes from evolutionists claiming (or repeating the widespread belief) that non-coding DNA is “junk” and has no function.

Some of the quotes represent the actual position of junk DNA proponents but Luskin has also picked out stupid quotes from scientists who think, incorrectly, that all non-coding DNA is junk. This is deliberate as we will see below.

Category 2: Early quotes from intelligent design theorists predicting function for non-coding “junk” DNA.

Luskin builds the case for function in non-coding DNA by quoting religious scientists who "predict" that there will be functional DNA in non-coding regions of the genome. This is disingenuous at best because Luskin knows full well that from the very beginning of the scientific debate we knew about functional non-coding DNA. It was never the case that all non-coding DNA was assumed to be junk.

Category 3: Quotes from mainstream scientific sources saying that we’ve experienced a shift in our thinking that junk DNA actually has function.

Many of these quotes are from scientists announcing that some non-coding DNA has a function. They support Luskin's false claim that all non-coding DNA was thought to be junk and the discovery of functional regions of non-coding DNA has resulted in a "paradigm shift" in our view of the human genome.

Casey Luskin should not have been allowed to get away with equating junk DNA and non-coding DNA in the debate. He should have been challenged to retract that false claim at the very beginning of the debate and called out whenever he used the term "non-coding DNA" during the debate.

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Why do Intelligent Design Creationists still lie about junk DNA?

Intelligent Design Creationists are heavily invested in refuting junk DNA because it casts doubt on their model of an intelligently designed human. Over the years they have advanced all kinds of arguments against junk DNA and some ID supporters actually address the real scientific issues (e.g. Jonathan Wells). However, most Intelligent Design Creationists are as ignorant about the scientific dispute over junk DNA as they are about evolution and lots of other science issues that conflict with their underlying religious beliefs.

A few days ago (March 26, 2024), the Discovery Institute's Center for Science and Culture published a short video on "The MYTH of Junk DNA" where they ignored most of the science and appealed to the majority of creationists who don't care about the truth. We have enough data to conclude that the Discovery Institute isn't just ignorant of the real science but is actually lying in this video. We know this because there are prominent Senior Fellows of the Center for Science and Culture who know that the material in this video is wrong and/or mispleading.

Thesis defense: 50th anniversary

Today is the 50th anniversary of my Ph.D. oral defense. The event took place in the Department of Biochemical Sciences at Princeton University back in 1974. It began with a departmental seminar. When the seminar was over I retired with my committee to a small classroom for the oral exam.

I don't remember everyone who was on my committee. My Ph.D. supervisor (Bruce Alberts) was there, as was my second reader, Abe Worcel. I know Uli Laemmli was there and so was Arnie Levine. I'm pretty sure the external member of the committee was Nancy Nossal from NIH in Bethesda, MD (USA). It's a bit of a blur after all these years.

I remember being fairly confident about the exam. After five and a half years I was pretty sure that everyone on my committee wanted to get rid of me and the easiest way to do that was to let me pass. Bruce stood to gain $3000 per year of research money and Uli was going to get back the basement of his house where I had been living for the past month after getting kicked out of the married graduate students housing project for taking too long to complete my thesis.

The toughest questions were from Uli Laemmli, which should not come as a surprise to anyone who knows him. He has this annoying habit of expecting people to understand the basic physics and chemistry behind the biochemical sciences. Fortunately, my inability to answer most of his questions didn't deter him from voting to pass me.