Sandwalk: September 2024

Monday, September 09, 2024

The DNA papers

The DNA papers is a series of podcasts on the discovery that DNA is the source of genetic information. Each podcast is a discussion among experts on the history of molecular biology, including some who have been regularly featured on this blog. I draw your attention to episodes 6 and 15 where you can hear Matt Meselson one of the key figures in the 'phage group.

The key take-home lesson is that the importance of DNA was recognized by a small group of scientists who were paying attention to the scientific literature. By the time of Watson and Crick (1953) this small group was already convinced that DNA was the "stuff of life," which is why they realized that solving the structure was extremely important.

This is not unusual. There are many cases where a small group of knowledgeable experts are well in advance of the average scientist who often doesn't even realize that a revolution is under way.

Episode 1 on Friedrich Miescher and the discovery of nuclein
Episode 2 on Albrecht Kossel and the discovery of the building blocks of nuclein
Episode 3 on Walter Sutton and the relation between chromosomes and heredity
Episode 4 on Fred Griffith and the discovery of bacterial transformation/li>
Episode 5 on Phoebus Levene, DNA chemistry and the tetranucleotide hypothesis
Episode 6 on William Astbury, Florence Bell and the first X-ray pictures of DNA
Episode 7 on Oswald Avery, Colin McLeod, and Maclyn McCarty and the chemical basis of bacterial transformation
Episode 8 on Maclyn McCarty, Oswald Avery and the enzymatic evidence for DNA as the transforming substance
Episode 9 on Erwin Chargaff and the evidence for non-uniformity of nucleotide base composition in DNA
Episode 10 on Harriet Ephrussi-Taylor, Rollin Hotchkiss and the demonstration of bacterial transformation as a general phenomenon
Episode 11 on Alfred Hershey, Martha Chase, and the conclusive evidence for the function of DNA as the material of heredity
Episode 12 on Maurice Wilkins, Rosalind Franklin, their collaborators, and the data that supported the double helix model for DNA structure
Episode 13 on James Watson, Francis Crick, and the DNA Double Helix
Episode 14 on Matthew Meselson, Franklin Stahl, and semiconservative replication of DNA
Episode 15 A conversation with Matthew Meselson and Franklin Stahl

Sunday, September 01, 2024

Scite Assistant (AI) answers the question "How much of the human genome consist of junk DNA?"

Scite Assistant is billed as "your AI research partner" and as "ChatGPT for researchers." It's supposed to draw on peer-reviewed published scientific papers for its information and it will give you an answer with genuine citations.

That sounds like a good idea until you realize that the scientific literature is full of misinformation and conflicting information. What we need is an AI assistant that can help us sort throught the misinformation and give us a genuine well-informed answer on controversial issues.

Let's pick the question of junk DNA as a completley random (!) example of such an issue. The scientific literature is full of false information about the origin of the term "junk DNA" and what it was originally intended to describe. It's also full of false information about recent results and how they pertain to junk DNA.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Peter Atkins

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat. Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.

Richard Lewontin

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Monday, September 09, 2024

The DNA papers

Sunday, September 01, 2024

Scite Assistant (AI) answers the question "How much of the human genome consist of junk DNA?"