Enjoy! (Spot the lies.1)
1. In Luskin's case, we know he is lying. [Is Casey Luskin lying about junk DNA or is he just stupid?]
Strolling with a skeptical biochemist
Enjoy! (Spot the lies.1)
1. In Luskin's case, we know he is lying. [Is Casey Luskin lying about junk DNA or is he just stupid?]
This is a video of a debate/discussion between Alex O'Connor and Francis Collins on the existence of God. I'm not impressed with any of the points made by either side. Here's the YouTube description.
"'Does God Exist?' is perhaps the most important question to human existence because of its far reaching implications. What you believe about the existence of God—and by extension, who or what God might be—has the power to profoundly influence your values, and the course of your life.
To explore this question from opposing perspectives, we’ve brought together two intellectual heavyweights.
Alex O’Connor is an Oxford philosopher and self-proclaimed atheist, who has described himself as 'violently agnostic' about the existence of God. In recent years, he’s gained substantial recognition in the academic world and beyond, with nearly a million YouTube subscribers. His show, Within Reason, has featured intellectual giants like Jordan Peterson, Richard Dawkins, William Lane Craig, and Sam Harris.
On the other side, we have Dr. Francis Collins—one of the most decorated scientists of our time. From 1993 to 2003, he led the Human Genome Project, the monumental effort to map all human genes.
Dr. Collins is perhaps the most notable scientist to transition from atheism to belief in God, famously chronicling his journey in the New York Times bestseller, The Language of God. In it, he presents compelling arguments for the existence of a higher power.
In this episode, we explore the various lines of evidence for and against the existence of God. We begin by defining the concept of 'evidence' itself before delving into topics such as the fine-tuning of the universe, the moral argument, the resurrection of Jesus and the world's holy texts.
We found this to be a deeply stimulating discussion, and we believe it will be for you as well. So, join us as we navigate the complexities, the debates, and the profound mysteries surrounding the existence of God."
If you want to get to the juicy parts first then watch the section on "Chapter VII: Crusade against genetic reductionism" beginning with a short introduction at 1:35. In the last few minutes Zack gets into motive by asking why Denis Noble and James Shaprio seem to be so comfortable with supporters like Intelligent Design Creationists.
A New Dogma Of Molecular Biology: A Paradigm Shift by William A. Haseltine
The mandate of the subcommittee was to investigate the origins of COVID-19, gain-of-function research, coronavirus-related government spending, and mask and vaccine mandates. Its report was released on Dec. 2, 2024: AFTER ACTION REVIEW OF THE COVID-19 PANDEMIC: The Lessons Learned and a Path Forward.
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 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.
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!
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.
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."
"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 LaureatesYour 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.
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.
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]
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.)
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.
-->The figure is from the ACS website: Doxyxycline.
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.
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.