The "wisdom" of the Discovery Institute

John G. West is Vice President of the Discovery Institute and one of the founding members of the Center for Science and Culture. He is a leading proponent of Intelligent Design Creationism.

West has reviewed the latest book by Francis Collins; the review was published in The Federalist. [Francis Collins’ Latest Book Doubles Down On His Massive Abuses Of Power]

Popular science books aren't fact-checked

Michael Marshall is a science journalist. He published a short essay in New Scientist where he laments the fact that popular science books may contain lots of errors. The title of the original article was Getting the facts right but the online version is Readers deserve beter from popular science books. The blurb is the same for both versions.

"There is a dirty secret in publishing: most popular science books aren't fact-checked. This needs to change, says Michael Marshall."

Most of you won't be able to read the article because it's behind a paywall but here's a few paragraphs that should stimulate discussion.

No, the problem is much simpler, and it is a dirty secret of non-fiction publishing: most books aren’t fact-checked. If an author makes a mistake or misinterprets a study, nobody stops them.

In journalism, fact-checking practices vary widely. New Scientist has two layers of editors, who each ensure readability and accuracy. Others are even stricter: fact-checkers at The New Yorker re-report entire stories. Non-fiction publishing is far more relaxed. Often, there is no fact-checking at all: editors offer guidance on readability, but take factual claims on trust. The UK publishers of my book The Genesis Quest did this (though my US publishers, a university press, recruited anonymous peer reviewers).

It is easy to see why this has happened. Nuance is difficult to sell. If your book has a counterintuitive thesis, or simply promotes a moral panic, it is easier to market. Non-fiction authors who are rigorous and careful can’t compete. That’s why shops are flooded with books about one neat trick for a better life or how everything you know is wrong. But without fact-checking, these books might as well be scrawled in crayon. Publishers must do better.

For the record, my book was sent out to reviewers and I got back some very helpful comments that caused me to make some serious changes. I also sent it to some of my colleagues and they corrected quite a few errors.

The last part of Marshall's essay is something that I've been worried about for many years, "Non-fiction authors who are rigorous and careful can’t compete."

Note: I inserted an image of Philip Ball's latest book because it's a recently published popular science book. I have no idea whether it was fact-checked or not. (But I have my suspicions.)

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Monday's Molecule #246

Today's molecule is complicated and you may not recognize it right away from the 3D structure. It was discovered in the middle of the last century and has proven to be very useful.

You can use whatever tricks you want to identify today's molecule. Regular readers will know that it's related to at least one Nobel Prize Laureate who will be revealed on Wednesday. I don't think that's going to help you very much.

Email your answer to me at: Monday's Molecule #246. 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).

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.)

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

Comments are closed for at least 24 hours.

UPDATE:The molecule is doxycline, a tetracycline class of broad-spectrum antibiotic. The winner is Chris Dicus. I don't know where Chris is located but I'm pretty sure it's not near me so I'll have to wait unitil he visits Toronto to collect his double-double and chocolage dip donut.

-->

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
#243, Oct. 14, 2024: Mikkel Rasmussen
#244, Oct. 21, 2024: Santi Garcia-Vallve
#245, Nov. 12, 2024: no winner
#246, Nov. 18, 2024: Chris Dicus

---

The figure is from the ACS website: Doxyxycline.

Thiotimoline

There's been a lot of talk recently about scieintific misinformaton on the internet. I started reminiscing about what things were like when I was growing up. I remember when I learned about DNA and when I first heard about black holes.

Then I remembered how excited I was when I first heard about the properties of thiotimoline from a well-known biochemist (Asimov, 1948). I can't say for sure that this tilted me toward choosing a career in biochemistry but it certainly played a role.

Some of you may not be familiar with thiotimoline. Here's the most important characteristic of this amazing molecule as reported in the original paper.

Darwin Mythology

How can you possibly be against a book devoted to refuting misinformation about Charles Darwin and his views on evolution? This is an anthology edited by Kostas Kampourakis whose main interest is "the public understanding of evolution and genetics." He currently teaches at the University of Geneva (Geneva, Switzerland).

Kampourakis has assembled a bunch of authors who present their 24 most important myths about Darwin in 24 chapters. It appears that this book was motivated, in part, by Kampoourakis' view that Charles Darwin needs to knocked down a peg or two because it corrupts the general public's view of how science really works. He begins his book by quoting Richard Dawkins, Michael Ghiselin and Jerry Coyne as examples of scientists who see Darwin as a scientific hero.

Darwin was without question a brilliant naturalist, observer and experimentalist and scholar. But this kind of hero-worshipping should be avoided because it is misleading—science is not done, and does not advance, by individuals who make big breakthroughs in one go. Science is done by communities, which consist of individuals many of whom have something important to contribute to the overall achievement. Even when some individuals happen to see something that others do not, the validation of a novel perspective or findings by the community is absolutely necessary. Most importantly, coming up with anything novel takes time and effort—it took Darwin twenty years of painstaking work—while one works in a particular context and with particular resources to hand—and Darwin had experiences and resources that most other lacked. This kind of hero-worshiping is also better avoided because it dehumanizes science; in the last chapter of the present book, I explain how the stories in its twenty-four chapters can help us better understand science as a human activity. My aim is to humanize Darwin and to emphasize a number of points about how science is done.

Science journal tries to understand misinformation

The November 1, 2024 issue of Science contains three articles on misinformation in science. The articles tend to concentrate on the standard examples such as vaccine misinformation but there's another kind of misinformation that's just as important. I'm talking about scientific misinformation that's spread by journals like Science and Nature.

Do any of you remember the arsenic affair? That's when science accepted a paper by Felisa Wolfe-Simon and her collaborators claiming that they isolated a bacterium that substituted arsenic for phosphorus in its DNA. The paper was published online and was severely criticized after a ridiculous NASA press conference. It was eventually refuted when Rosie Redfield and others looked closely at the bacterial DNA and showed that it did not contain arsenic. The paper has still not been retracted. [See Reviewing the "Arseniclife" Paper.]

And let's not forget the massive misinformation campaign associated with the publication of ENCODE results in 2012.

The success of protein structure prediction software depended on the solved structures deposited in the Protein Data Bank (PDB)

The development of protein structure prediction programs began fifty years ago and culminated in the remarkable success of AlphaFold, developed by Google DeepMind. Demis Hassabis and John Jumper of Google DeepMind received the Nobel Prize in Chemistry (2024) for their work on AlphaFold.

AlphaFold and its predecessors were trained on a database of known protein structures called the Protein Data Bank (PDB). PDB began in 1971 as a collaboration between the Cambridge Crystallographic Centre in the UK and Brookhaven National Laboratory in the US. It utilized standardizing software for collecting and storing atomic coordinates and allowing researchers to search the database from remote locations. It soon became a requirement for researchers to deposit their data in PDB when they published.

Nobel Laureates Andrew Fire and Craig Mello

The Nobel Prize in Physiology or Medicine 2006

"for their discovery of RNA interference - gene silencing by double-stranded RNA"

Craig Mello (left) and Andrew Fire (right) won the Nobel Prize in 2005 for discovering RNA interference in Caenorhabditus elegans. The mechanism involves synthesis of a double-stranded RNA molecule where one of the strands is identical to the coding region of a protein-coding gene and the other strand is a complementary antisense RNA. The double-stranded RNA binds to a protein complex called Dicer, which degrades the "coding" strand RNA leaving a small antisense siRNA. This RNA binds to a RISC complex that seeks out the mRNA that's complementary to the antisense RNA and cleaves the mRNA. (RISC = RNA-induced silencing complex.)

The interference mechanism blocks the synthesis of proteins from the target RNA. It is used to block synthesis of viral proteins following infection and to block synthesis of transposon proteins.

Here's part of the Ceremony Speech.

THEME:
Nobel Laureates

Fifteen years ago, we thought we knew enough about the flow of genetic information to use it for practical purposes. But we did not achieve the expected results. Attempts to silence a gene in an experimental animal were sometimes fruitless, and attempts to use gene technology for improving the colours of flowers could even cause the plants to lose colour completely. These results perplexed the scientific community. Was there an unknown regulatory step on the way from DNA to protein?

This enigma was solved by the 2006 Nobel Laureates, Andrew Fire and Craig Mello. They suspected that RNA contained the solution to the problem and decided to test it in a simple model organism, the nematode worm Caenorhabditis elegans.

Fire and Mello injected different types of RNA into the worms – and usually nothing happened. But they also made the ingenious decision to mix two RNA molecules in a test tube before injection. One RNA molecule was an exact copy of a messenger RNA and the other a mirror image of the messenger. In the test tube, the two RNA molecules bound to each other and formed a double strand. Injection of that double-stranded RNA led to the silencing of the gene. Fire and Mello had discovered a new mechanism for controlling the flow of genetic information.

In their brilliant paper from 1998, Andrew Fire and Craig Mello demonstrated that double-stranded RNA activates an enzymatic mechanism that leads to gene silencing, with the genetic code in the RNA molecule determining which gene to silence. Today, we call this mechanism RNA interference.

---

Photo Credit: The figure is from the Nobel Prize press release.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Monday's Molecule #245

It's Tuesday so it must be time for Monday's Molecule! :-)

Today's molecule is the little green ladder-like thing in the figure. You have to name the class of molecule it refers to and give a brief description of its properties. You also have to indicate that you know something about the pink blob.

You can use whatever tricks you want to identify today's molecule. Regular readers will know that it's related to at least one Nobel Prize Laureate who will be revealed on Wednesday. I don't think that's going to help you very much.

Email your answer to me at: Monday's Molecule #245. 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).

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.)

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

Comments are closed for at least 24 hours.

UPDATE: There was no winner this week.

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
#243, Oct. 14, 2024: Mikkel Rasmussen
#244, Oct. 21, 2024: Santi Garcia-Vallve
#245, Nov. 12, 2024: no winner

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The figure is modified from Hung and Slotkin (2021) The initiation of RNA interference (RNAi) in plants. Current Opinion in Plant Biology 61:102014 [doi: 10.1016/j.pbi.2021.102014] -

Lance Corporal Robert Alexander Hood (1895 - 1917)

Robert Alexander Hood¹ was born in 1895 in a small village north-west of Waterloo, Ontario, Canada. He went to France in 1916 when he was only 21 years old. Robert fought with the 73rd Battalion and he was killed in action at Vimy Ridge on April 12, 1917.

Canadians remember the battle of Vimy Ridge as a great Canadian victory. It was part of the larger Battle of Arras, which in turn was a diversionary attack in support of the larger Nivelle Offensive carried out by the French Army. About 3,600 young Canadian men were killed during the four day battle and 7,000 more were wounded. This is just a small fraction of the casualties on both sides during World War I.

We visited the Canadian War memorial at Vimy Ridge with our granddaughter and found Corporal Hood's name engraved at the base.

---

1. He was a cousin of Ms. Sandwalk's grandfather.

---

Bringing down inflation

Managing the national economy is complicated and I don't pretend to understand it. All I know is that practically the entire world suffered from inflation during and after the COVID-19 pandemic. Various governments have struggled to get inflation under control and some have been more successful that others. For example, here's what the inflation rate for the USA looks like over the past five years. The current inflation rate is about 2.4%.

I just heard a couple of Republican pundits claim that one of the priorities of the new Trump administration is to bring down inflation. Does anyone know what their goal is? Are they aiming at a zero inflation rate or just something below 2.4%? Can someone explain, in simple language, what policies the new administration will use to bring down inflation? Does the general public think that the Trump administration will actually lower the cost of goods by creating a negative inflation rate?

We have a similar situation in Canada. Here's the inflation rate over the past ten years. The current inflation rate is 1.6% (September 2024).

The Canadian opposition parties are blaming the current government for inflation and they are promising to do better. Does anyone in Canada know what their inflation rate goals are and how they hope to achieve them?

Let's assume, for the sake of argument, that my questions are merely rhetorical questions and I actually know the answers. Let's assume that the opposition parties in Canada and the United States (and elsewhere) know full well that current governments have been quite successful at combating inflation. Those opposition parties are deliberately misleading the public by claiming that they would have done better and they will bring down inflation if they are elected. Is is possible to create a society where this kind of rhetoric is not acceptable? Is it possible to create a society where the public is so well educated that opposition parties cannot get away with spreading misinformation?

Or are we doomed to be controlled by an electorate that is incapable of distinguishing between truth and reality?

---

Do plants have junk DNA?

Current Opinion in Plant Biology has a special edition devoted to Genome studies and molecular genetics 2024. The only paper (so far) that discusses plant genomes is one devoted to RNAs. Here's the abstract ...

Anyatama, A., Datta, T., Dwivedi, S. and Trivedi, P.K. (2024) Transcriptional junk: Waste or a key regulator in diverse biological processes? Current Opinion in Plant Biology 82:102639. [doi: 10.1016/j.pbi.2024.102639]

Plant genomes, through their evolutionary journey, have developed a complex composition that includes not only protein-coding sequences but also a significant amount of non-coding DNA, repetitive sequences, and transposable elements, traditionally labeled as “junk DNA”. RNA molecules from these regions, labeled as “transcriptional junk,” include non-coding RNAs, alternatively spliced transcripts, untranslated regions (UTRs), and short open reading frames (sORFs). However, recent research shows that this genetic material plays crucial roles in gene regulation, affecting plant growth, development, hormonal balance, and responses to stresses. Additionally, some of these regulatory regions encode small proteins, such as miRNA-encoded peptides (miPEPs) and microProteins (miPs), which interact with DNA or nuclear proteins, leading to chromatin remodeling and modulation of gene expression. This review aims to consolidate our understanding of the diverse roles that these so-called “transcriptional junk” regions play in regulating various physiological processes in plants.

Were you lied to in your genetics class?

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

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

Philip Ball's view of alternative splicing

Genomics is a powerful tool that allows you to collect massive amounts of data that can point the way to new understanding. But it can also be abused when the results are overinterpreted. We saw an extraordinary example of this in 2012 when ENCODE made unsubstantiated claims that were quickly challenged.

I'm reminded of the caution from Sydney Brenner who warned us about genomics (Brenner, 2000) and the warning in Dan Graur's harsh critique of the 2012 ENCODE claims (Graur et al., 2013) where they said ...

The Editor-in-Chief of Science, [Bruce Alberts,] has recently expressed concern about the future of "small science," given that ENCODE-style Big Science grabs the headlines that decision makers so dearly love. Actually the main function of Big Science is to generate massive amounts of easily accessible data. The road from data to wisdom is quite long and convoluted. Insight, understanding, and scientific progress are generally achieved by "small science." ...

Zach Hancock's 10 most influential papers on evolution

Zach Hancock is a postdoc in the Dept. of Ecology and Evolutionary Biology at the University of Michigan. He has a popular YouTube channel where he has recently posted a video describing his top ten evolutionary biology papers of all time. I've added links to all of the papers below.

Zach emphasizes that this is a personal list and others might disagree with his choices. He is much more interested than I am in explaining the history of life with an emphasis on animals. I'm much more interested in molecular evolution so I would choose a slightly different list as I explain below. Please add your own choices in the comments.

1. Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y. L., and Postlethwait, J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151(4), 1531-1545. [doi: 10.1093/genetics/151.4.1531]
2. Coyne, J. A., and Orr, H. A. (1989) Patterns of speciation in Drosophila. Evolution, 43(2), 362-381. [doi: 10.1111/j.1558-5646.1989.tb04233.x]
3. Lande, R., and Arnold, S. J. (1983) The measurement of selection on correlated characters. Evolution, 1210-1226. [doi: 10.2307/2408842]
4. Lederberg, J., and Lederberg, E. M. (1952) Replica plating and indirect selection of bacterial mutants. Journal of bacteriology, 63(3), 399-406. [PDF]
5. Gould, S.J. and Lewontin, R.C. (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society of London. Series B. Biological Sciences 205:581-598. [doi: 10.1098/rspb.1979.0086]
6. Maynard Smith, J. M. (1974) The theory of games and the evolution of animal conflicts. Journal of theoretical biology, 47(1), 209-221. [doi: 10.1016/0022-5193(74)90110-6"]
7. Fisher, R.A. (1918) The correlation between relatives on the supposition of Mendelian Inheritance. Proceedings of the Royal Society of Edingurgh [PDF]
8. Hamilton, W. D. (1964) The genetical evolution of social behaviour. II. Journal of theoretical biology, 7(1), 17-52. [doi: 10.1016/0022-5193(64)90039-6]
9. Kimura, M. (1968) Evolutionary rate at the molecular level. Nature, 217(5129), 624-626. [PDF]
10. Wright, S. (1931) Evolution in Mendelian populations. Genetics, 16(2), 97. [doi: 10.1093/genetics/16.2.97]

I disagree with Hamilton (1964). I realize that there are many evolutionary biologists who think that kin selection and the evolution of altruistic behavior is extremely important¹ but I think it's restricted to a tiny perecentage of characteristics in a tiny percentage of all living things on the planet. I would delete the Hamilton paper and replace it with ...

Margoliash, E. (1963) Primary structure and evolution of cytochrome c. Proceedings of the National Academy of Sciences, 50(4), 672-679. [PDF]

This is the first accessible paper on using the animo acid seqences of proteins to obtain information on evolution. It's the beginning of the field of molecular evolution and the idea of a molecular clock. Surely that deserves to be one of the most important advances in the field of evolution. (Linus Pauling and Emile Zuckerkandl published similar work on globins at about the same time but their original papers were not as accessible as the Margoliash paper. See Emile Zuckerkandl and the 50th anniversary of the birth of molecular evolution.)

I'm not a big fan of John Maynard Smith and game theory. I think it only applies to a small part of the field of evolution. I would delete the Maynard Smith (1974) paper and replace it with ...

Ohta, T. (1973) Slightly deleterious mutant substitutions in evolution. Nature 246:96-98. [doi:10.1038/246096a0]

This is the beginning of the nearly neutral theory. I agree that putting the Kimura paper on the neutral theory at #2 is a good choice but it's the Ohta paper that really drives home the idea that deleterious mutations can also be fixed under some circumstances and made (some) evolutionary biologists understand that natural selection was not the only game in town.

Finally, I'd like to see one of David Raup's papers in the top ten list but I don't know enough about the other papers to pick one to delete. (I'm skeptical of Lande and Arnold (1983) but I know they have fierce defenders.) Here's a candidate Raup paper that includes Sepkoski.

Raup, David M.; Sepkoski, J. John Jr. (1982) Mass extinctions in the marine fossil record. Science. 215 (4539). [doi:10.1126/science.215.4539.1501]

I'm waiting for the list of the top nine books on evolution—we all know what #1 is going to be.

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Image credit: The photo is from Zach's personal website.

1. Richard Dawkins thinks Hamilton is "the greatist Darwinina of my lifetime" [quoted in W.D. Hamilton]