"Understanding Life" books from Cambridge University Press

Cambridge University Press is publishing a series of inexpensive books on biology topics. The books all have similar titles beginning with the word "Understanding." The "Understanding Life" series is edited by Kostas Kampourakis.

I have three of these books: Understanding Genes (2022) by Kostas Kampourakis, Understanding Evolution (2020) also by Kostas Kampourakis, and Understanding Species (2023) by John Wilkins. Others are:

Kostas Kampourakis cautions us against teaching Mendelian genetics

A few weeks ago I put up a post on Were you lied to in your genetics class?. At the time I thought it was just a fringe view being expressed by a graduate student who didn't understand genetics but now I realize that it's much more important than that.

Kostas Kampourakis is a respected scientist who is being promoted by the National Center for Science Education (NCSE) as an excellent communicator of evolution. Here's a short video (below) where he explains why teachers are making a mistake by saying that Mendel is the father of genetics and that simple Mendelian genetics can explain complex traits.

I'm struggling to understand his point. Here's what I think he means.

Kampourakis uses the example of eye color in Drosophila. He agrees that segregation of the allele responsible for eye color may follow the Mendelian rules¹ but it's wrong to assume that there's a single gene responsible for eye color in fruit flies. He thinks that the goal is to understand the complexities of development and standard Mendelian genetics gives a completely distorted view of that subject, assuming, of course, that teachers can't separate genetics from understanding development.

Part of the problem is that we use the word "trait" differently. Take Mendel's example of pea color as another example. [Identity of the Product of Mendel's Green Cotyledon Gene (Update)] What Mendel was studying was the segregation of alleles in a gene called sgr (stay-green). It codes for an enzyme involved in the degradation of chlorophyll during senescence. When the enzyme is defective, chlorophyll isn't degraded and one of the visible phenotypes is that peas stay green instead of turning yellow.

I believe that the fundamental trait is the lack of an enzyme for degrading chlorophyll and this is what I would teach my students. I would also show them that the phenotype can be easily explained once you understand the biochemistry. It shows you that the connection between the fundamental trait and the visible phenotype can be mysterious so you should be careful about jumping to conclusions.

I think that Kampourakis sees this differently. He thinks that the example of green vs yellow peas is used to teach students that the color of peas is completely determined by a single gene. He thinks that the "trait" is the develpment of seed color in peas.

Kampourakis believes that "people looking for explanations and whatever happens to them in terms of disease and their own features, they find hard to reconcile the simplistic model that they have been taught with the realities of life." I think what he means is that students are being taught that single genes will always determine complex characteristics. He attributes that to the teaching of Mendelian genetics.

If he is correct, then that kind of teaching has to stop but I don't think it's the fault of Mendelian genetics. Mendelian genetics—indeed the entire field of genetics sensu stricto—is about the segregation of alleles. It is not about development even though we have come to learn a lot about development through genetics and the phenotype of mutants. I think that genetics and development are separate topics.

Kampourakis disagrees. He says, "we need, I think, to teach genetics from a developmental perspective. We need to show that genes do not determine traits but they are implicated in development." I believe this perspective comes from a more fundamental bias that distinguishes his worldview from mine. I tend to see genetics as a subject that covers all of biology and that includes all species such as bacteria, viruses, and single-cell eukaryotes. He tends to see things from a human perspective, which is much more complex than dealing with simple organisms. I think we should concentrate on teaching students about simple well-understood model organisms and then move on to explaining how this applies to more complex organisms. Kampourakis seems to be implying that we should jump right into reaching high school students about the most challenging issues in biology.

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1. Actually, the common allele for white eye in Drosophila (see image) is X-linked so it doesn't follow the standard rules for Mendelian segregation!

Kostas Kampourakis says that human races do not exist

Populous, geographically disperse, species are often subdivided into subspecies, races, demes, or geographically differentiated populations. Homo sapiens is no exception; there are many subpopulations whose overall genetic compositions are significantly different—so different, in fact, that we have no trouble identifying members of those subpopulations and the sequence of their genomes can assign them to the different groups.¹

We could use the word "race" to distinguish the largest of these subpopulations if the word wasn't so loaded with non-scientific meaning. I believe that, from a scientific perspective, humans races exist. [Do Human Races Exist?]. Jerry Coyne is much better (braver?) than I at defending the biological and evolutionary reality of human races and attacking the well-meaning, but mistaken, attempt to deny the existence of human races. [Genetic ignorance in the service of ideology] It's part of a larger effort to combat something he calls The Ideological Subversion of Biology. The point he's making is that we are teaching our children a number of misconceptions that conflict with science and this contributes to a mistrust of science.

Biological evolution is dead in the water (not!)

You will be surprised to hear that biological evolution is dead in the water according to the authors of a paper published in Progress in Biophysics and Molecular Biology.

The authors are Olen Brown, an Emeritus Professor of Biomedical Sciences at the University of Missouri and David Hullender, a Professor in the Department of Mechanical and Aerospace Engineering at the University of Texas at Arlington. These are the same two authors who published two ridiculous papers in the same journal in 2022 and 2023. Up until last December (2023), Denis Noble was one of the editors of the journal [Editorial Board] but he is not longer listed on the journal's website. We can assume that Noble is responsible, in part, for allowing these papers to be published since he has defended the publication of creationist papers in the past. [How the Krebs cycle disproves Darwinism (not!)]

Brown, O.R. and Hullender, D.A. (2024) Biological evolution is dead in the water of Darwin’s warm little pond. Progress in Biophysics and Molecular Biology. 193: 1-6. [doi: 10.1016/j.pbiomolbio.2024.08.003]

Abstract

The origin of life and its evolution are generally taught as occurring by abiogenesis and gene-centric neo-Darwinism. Significant biological evolutionary changes are preserved and given direction (descent with modification) by Darwin's (Spencer's) natural selection by survival of the fittest. Only survival of the fittest (adapted/broadened) is available to provide a ‘naturalistic’ direction to prefer one outcome/reaction over another for abiogenesis. Thus, assembly of first life must reach some threshold (the first minimal cell) before ‘survival of the fittest’ (the only naturalistic explanation available) can function as Darwin proposed for biological change. We propose the novel concept that the requirement for co-origination of vitamins with enzymes is a fundamental, but overlooked, problem that survival of the fittest (even broadly redefined beyond Darwin) cannot reasonably overcome. We support this conclusion with probability calculations. We focus on the stage of evolution involving the transition from non-life to the first, minimal living cell. We show that co-origination of required biochemical processes makes the origin of life probabilistically absurdly improbable even when all assumptions are chosen to unreasonably favor evolutionary theories.

There's something seriously wrong with peer review if a paper like this can be published in a (formerly) reputable journal.

For more information, watch this video of Brown and Hullender explaining their views. The video is sponsored by "Video Lessons to Raise Up Confident Christians."

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Nobel Laureate Charles Nicolle

The Nobel Prize in Physiology or Medicine 1928

"for his work on typhus"

Charles Jules Henri Nicolle (1886 - 1936) was a French scientist who studied typhus while he was Director of the Pasteur Institute in Tunis. He realized that patients suffering from typhus were usually contageous but when they entered the hospital they were no longer contageous after a bath and a change of clothes. This led him to conclude that the disease was being spread by something in the clothing and lice were a prime suspect.

He soon confirmed his hypothesis by infecting chimpanzees and showing that the disease could be transferred by lice from one infected chimp to another uninfected animal. Further research showed that the disease was actually being transferred by microbes in lice excrement and through insect bites. In addition to lice, mites and fleas can also transmit various forms of typhus.

Nicolle was not able to develop a vaccine against typhus. Even today there is no effective vaccine available but the disease can be treated by antibiotics, especially doxycycline. [See Monday's Molecule #246]

It's pretty amazing to think that the cause of such a horrible disease was only discovered in the lifetime of our parents or grandparents (or great-grandparents).

Here's part of the Award Ceremony Speech.

THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

In awarding the 1928 Nobel Prize for Medicine to Dr. Charles Nicolle, Director of the Pasteur Institute at Tunis, the Caroline Institute wished to pay tribute to a man who has realized one of the greatest conquests in the field of prophylactic medicine, i.e. the vanquishing of typhus.

... The disease has been known since the beginning of all time. The plague which devastated Attica, especially Athens in the year 430 B.C., and which Thucydides describes in his work on the Peloponnesian War, was most likely an epidemic of typhus. The picture that the great historian draws of the disease agrees in certain respects, down to the smallest details, with the clinical picture we were able to observe during the Great War. Epidemics followed one another without respite during the great wars of the sixteenth and seventeenth centuries. At the end of the Thirty Years’ War, typhus raged over the whole of Central Europe. The Napoleonic Wars caused the disease to flare up again. In the general disorganization which followed the Grand Army’s retreat from Russia, typhus claimed innumerable victims amongst the troops and amongst the civilian population. Further epidemics broke out during the Crimean War and the Russo-Turkish War, affecting both sides.

With the progress of civilization and during the period of peace and prosperity which, in all, lasted from the end of the nineteenth century until 1914, typhus seemed of its own accord to have become restricted to certain remote regions of Europe and to certain extra-European countries where, from time immemorial, the disease had existed endemically.

At the beginning of this North Africa was among these non-European countries where the disease had been a veritable national scourge for several centuries. As soon as he took up his appointment as Director of the Pasteur Institute at Tunis, young Dr. Charles Nicolle was immediately brought into contact with the scientific and practical problems that typhus had created in this country.

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Photo Credit: The figure is from Wikipedia.

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.

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.

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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

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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.

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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.

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

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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?

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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]

Three lungfish species have huge genomes

Lungfish are our closest living fish cousins. All living terrestrial vertebrates (e.g. amphibians, mammals, reptiles) descent from a common ancestor with lungfish. The split occurred about 400 million years ago (4Ma) (Devonian) when there were 70-100 different lungfish species.

This relationship (lungfish-tetrapods) was firmly established recently by comparing the genome of the Australian lungfish (Neoceratodus forsteri) with that of tetrapods (Meyer et al., 2021). The other possibility had been ceolacanth-tetrapods. Coelacanths and lungfish are related—they form the class Sarcopterygii (lobe-finned fish).

Santi Garcia-Vallvé reviews my book

Santi Garcia-Vallvé has reviewed my book in the journal Mètode. It's written in Catalan but Santi was kind enough to send me a translation.

OUR GENOME HAS NOT YET SPOKEN ITS LAST WORD

What's in Your Genome? 90% of Your Genome Is Junk. Laurence A. Moran. Aevo University of Toronto Press (UTP). May 2023. 392 pages.

What's in Your Genome? exposes a variety of topics and concepts in molecular biology, genetics, and evolution that have been misunderstood by scientists and the general public. Many of these concepts are widely accepted, despite ongoing debate about them. Although the author, Larry Moran, has exhaustively discussed most of these issues on his blog "Sandwalk: Strolling with a sceptical biochemist", discussing them in a book allows for a more in-depth investigation.

One of these recurring themes is Francis Crick 's 1957 proposal of the Central Dogma of Molecular Biology. In his book Molecular Biology of the gene, James Watson adapted this concept by summarizing in a figure the flow of genetic information from DNA to RNA and then to proteins. This version was widely adopted, and many scientists now assume that it was the original definition. However, Crick claimed that once the information had been transferred to the proteins, it could not be returned to nucleic acids. Other controversial topics discussed in the book include the number of genes encoded in the human genome, the concept of Junk DNA and the prevalence of alternative splicing in the transcription of the human genome. Larry takes a certain viewpoint on all these problems, as evidenced by the title of the book, but he also presents arguments from all sides. Throughout the book, he argues that scientists must present evidence in support of and against their findings, as well as contextualise their discoveries in light of the knowledge of the subject. Thus, the first chapters of the book describe in depth the basic ideas of genetics, genetics and evolution that are required to understand the arguments that he will present later, showing also when and how they were discovered.

This is a highly recommendable book that pushed us to think about how research findings are explained and the importance of placing them in their proper context. The media frequently looks for stunning headlines and there is growing demand to assess the social impact of a project, article or scientific project. However, if we exaggerate our findings, we risk exacerbating further diminishing the general lack of interest in scientific news. Everyone is responsible that this does not happen.

Santi Garcia-Vallvé is an associate professor in the Department of Biochemistry and Biotechnology at Rovira i Virgili University (URV) in Tarragona, Spain, and a member of the Chemoinformatics and Nutrition research group."

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