Happy birthday human genome sequence!

The draft sequences of the human genome were published fifteen years ago. The International Human Genome Project (IGHP) published its draft sequence in Nature on Feb. 15, 2001 (Lander et al., 2001) and Celera Genomics published its draft sequence in Science on Feb. 16, 2001 (Venter et al., 2001).¹

For me the timing was perfect since I was scheduled to give a Journal Club talk on March 16th and you could hardly ask for a better topic.

Justice Scalia's Misunderstanding

Antonin Gregory Scalia (March 11, 1936 – February 13, 2016), justice of the Supreme Court of the United States, died a few days ago. This creates a crisis in American politics because they have a strange set of Constitutional requirements guaranteed to maximize the probability of crises every time they need a new Supreme Court justice.

Scalia's death reminded me of the dissenting opinion in EDWARDS V. AGUILLARD (June 19, 1987). This was the case that invalidated Louisiana's "Balanced Treatment for Creation-Science and Evolution-Science Act." Stephen Jay Gould was puzzled by the dissenting opinion so he wrote a wonderful essay to explain Justice Scalia's Misunderstanding.

It's worth reading the entire essay but here's the conclusion,

Following this theme, Scalia presents his most confused statement in the written dissent:

Creation science, its proponents insist, no more must explain whence life came than evolution must explain whence came the inanimate materials from which it says life evolved. But even if that were not so, to posit a past creator is not to posit the eternal and personal God who is the object of religious veneration.

True indeed; one might be a creationist in some vernacular sense by maintaining a highly abstract and impersonal view of the creator. But Aristotle's unmoved mover is no more part of science than the Lord of Genesis. Science does not deal with questions of ultimate origins. We would object just as strongly if the Aristotelophiles of Delaware forced a law through the state legislature requiring that creation of each species ex nihilo by an unmoved mover be presented every time evolution is discussed in class. The difference is only historical circumstance, not the logic of argument The unmoved mover doesn't pack much political punch; fundamentalism ranks among our most potent irrationalisms.

Consider also, indeed especially, Scalia's false concept of science. He equates creation and evolution because creationists can't explain life's beginning, while evolutionists can't resolve the ultimate origin of the inorganic components that later aggregated to life. But this inability is the very heart of creationist logic and the central reason why their doctrine is not science, while science's inability to specify the ultimate origin of matter is irrelevant because we are not trying to do any such thing. We know that we can't, and we do not even consider such a question as part of science.

We understand Hutton's wisdom. We do not search for unattainable ultimates.

We define evolution, using Darwin's phrase, as "descent with modification" from prior living things. Our documentation of life's evolutionary tree records one of science's greatest triumphs, a profoundly liberating discovery on the oldest maxim that truth can make us free. We have made this discovery by recognizing what can be answered and what must be left alone. If Justice Scalia heeded our definitions and our practices, he would understand why creationism cannot qualify as science. He would also, by the way, sense the excitement of evolution and its evidence; no person of substance could be unmoved by something so interesting. Only Aristotle's creator may be so impassive.

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Happy Valentine's Day!

Who was Saint Valentine? Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer¹ sometime around 1380.

It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?

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1. Geoffrey Chaucer is my distant cousin by marriage [My Connection to Geoffrey Chaucer and Medieval Science ].

Michael Denton discovers non-adaptive evolution ... attributes it to gods

Readers of this blog will know that I'm a fan of Evolution by Accident. I don't think that the history of life can be explained in strict Darwinian terms (i.e. natural selection) and I think that modern evolutionary theory includes Neutral Theory and a major role for random genetic drift.

This is the view of many modern evolutionary biologists. Their work and views have been reported frequently on Sandwalk over the past ten years but you can find it in all the evolutionary biology textbooks. I'm just the messenger here. It's evolutionary biologists who have made the case for non-adaptive evolution beginning long before The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.

This is what a strawman looks like

This is another post about the stupidity of Intelligent Design Creationists. Stop reading if you don't need any more convincing.

Today is Darwin Day. It's the anniversary of the birth of Charles Darwin (Feb. 12, 1809 - April 19, 1882).

This is not a happy day for the Discovery Institute so they've put up a series of posts on Evolution News & Views (sic) to discredit Darwin and "Darwinism."

One of them is by the newly rejuvenated poster boy, Michael Denton: On Darwin Day, Darwinism Is Well Past Its "Sell By" Date. Here's the part I want you to see,

To understand the core weakness of the Darwinian worldview, it is important to understand what Darwinian natural selection requires. The process will work its magic, building up functional structures in organisms, only when two very strict conditions are met: First, the structure must be adaptive—that is, helpful to the organism in flourishing in its environment—and second, there must be a continuum of structures, functional all along the way, leading from an ancestor species to the descendent.

That is, the thing we are trying to explain must in some way help the creature survive, and between the creature and the creature's ancestor there must be a gradual change, each step of which is stable and enhances fitness, or success in reproduction.

Strictly speaking, that's a reasonable explanation of Darwinism as most evolutionary biologists understand it. But here's the problem. There aren't very many evolutionary biologists who are strict Darwinists these days even though there are many who tilt strongly in that direction.

Replaying life's tape

Intelligent Design Creationists are promoting a structuralist view of evolution [What is structuralism?]. The idea is that the history of life as we know it was largely preordained by the initial laws of physics and chemistry. According to this view, once life got under way it was inevitable that it would eventually evolve the way it did resulting in humans or something that closely resembles humans.

Structuralism is based on the idea of intrinsic forms that severely limit evolutionary pathways. These forms are constrained, and defined, by the physics of matter and energy. Some creationists like this idea because they believe that god created the universe and fine-tuned it for life. According to their faith, once the original laws of physics and chemistry were set up it was just a matter of time before humans evolved. These creationists can make their belief in a creator god compatible with evolution as they see it.

(Let's not forget that there are many structuralists who are legitimate scientists and some of them are atheists. Structuralism is not a creationist invention.)

The conflict between structuralists and others is brought into focus by Stephen Jay Gould writing in Wonderful Life.

Junk DNA doesn't exist according to "Conceptual Revolutions in Science"

The blog "Conceptual Revolutions in Science" only publishes "evidence-based, paradigm-shifting scientific news" according to their home page.

The man behind the website is Adam B. Dorfman (@DorfmanAdam). He has an MBA from my university and he currently works at a software company. Here's how he describes himself on the website.

Breaking up with Richard Dawkins

Some of you are aware of recent attacks on Richard Dawkins. This video by Brian Dalton (Mr. Deity)¹ is directed at certain people who have led the attacks. Some of them are my friends but I'm having second thoughts. They should pay close attention.

I disagree with several scientific ideas that Richard Dawkins has promoted and we have discussed these disagreements in person and on the internet. I've always found him to be polite and respectful.

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1. Brian will be at Imagine No Religion 2016.

Intelligent Design Creationism and the fine-tuning argument

Michael Denton and the Discovery Institute are promoting his new book, Evolution: Still a Theory in Crisis. I haven't yet read the book. I ordered from Amazon.ca and I won't get it until March.

Denton tries to explain the connection between the fine-tuning argument and structuralism in a recent post on Evolution News & Views: Natural Life: Cosmological Fine-Tuning as an Argument for Structuralism. I've dealt with structuralism already [What is "structuralism"?] so let's think about fine tuning.

The essence of the fine-tuning argument is that the basic laws of physics and chemistry are so precise that even slight changes would result in a universe where life is impossible. The focus is usually on the fundamental constants such as the speed of light and the charge on an electron. I don't know enough about physics to evaluate the argument that these are fine-tuned so I have to rely on physicists to inform me.

The Fermi Paradox: Are we alone in the universe?

All available evidence suggests that we are quite likely the only advanced life form in the Milky Way galaxy. Maybe our planet harbors the only life in the entire universe.

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Can theology produce true knowledge?

Matthew Cobb wasn't happy with the way Denis Alexander reviewed Jerry Coyne's book. Recall that Denis Alexander is a biochemist at Cambridge University (UK) and we had a little debate a week or so ago [Is there a conflict between science and religion?]. His position is that there's no conflict between science and religion because a person who believes in god can always make their views conform to the discoveries of science. I didn't accept his premise—that gods exist—so we had a discussion about whether there's any evidence to support his belief in god.

If you believe in such a being then that conflicts with science as a way of knowing because you are believing in something without reliable evidence to support your belief. Scientists shouldn't do that and neither should any others who practice the scientific way of knowing. Denis Alexander thinks there are other, equally valid, ways of knowing but he wasn't able to offer any evidence that those other ways produce true knowledge.

Matthew Cob wrote a letter to the editor in which he asked, "I wonder if Dr Alexander, or indeed any reader, could provide an example of knowledge gained through theology, and above all tell us how they know that knowledge is true?" [see Matthew Cobb battles with the faithful over my book].

A DNA quiz

Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.

I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.

Try the quiz yourself before reading any further. There are spoilers below!

What is "structuralism"?

The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.

You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.

The most intellectual creationists explain why there are still Darwinists when Darwinism has been falsified

You are probably wondering why "Darwinism" persists after the creationists have thoroughly demonstrated that it is a failed theory. Lucky for you, the most intelligent and intellectual of all Intelligent Design Creationists, David Berlinski and Michael Denton, have gotten together to explain it in a short (15 mins) podcast.

It's moderated by David Klinghoffer who introduces it like this ... [Michael Denton and David Berlinski Discuss: How Does Darwinism Hang On?]

If the most brilliant Darwin critics, like David Berlinski and Michael Denton, are right, how then does Darwinism hang on? How does a failed theory maintain its grip on our science and on our culture? Why is there a sense of stalemate? On ID the Future, we posed these questions to Dr. Berlinski and Dr. Denton.

If you are interested in the conflict between Intelligent Design and science you owe it to yourself to see/hear the best they've got on their side.

ID the Future: More Berlinski and Denton.

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Berlinski and Denton challenge Darwinism

It's fun to listen to the "ID the Future" podcasts. It shows us the very best of Intelligent Design Creationists. This time we get a twofer— David Berlinski and Michael Denton posing their most challenging questions to Darwinists. Here's how David Klinghoffer introduces the pair ... [Berlinski and Denton: If You Could Pose One Challenge to a Thoughtful Darwinist, What Would It Be?].

You can always dream. While the evolutionist side in the Darwin debate is long on rhetoric and insults, serious debate or dialogue is woefully rare. But imagine you had the opportunity to sit down with a thoughtful, honest, well-informed Darwinist and pose one question or challenge. What would it be?

I had the opportunity to pose that question to two of the most brilliant minds in the intelligent design community -- Michael Denton and David Berlinski. Take a well-spent 15 minutes and listen to their answers -- focusing respectively on the insect body plan and the enigma of whale evolution -- recorded as an episode of ID the Future.

Berlinski wants a detailed mathematical estimate of the number of mutations required to go from a land animal to a whale. Denton wants details on the formation of insect body plans.

It's important to note that these are questions about the history of life. You could easily answer "I don't know" to both questions and it would not affect our understanding of evolution and common descent one iota. The answers have nothing to do with "Darwinism" per se and nothing to do with evolutionary theory (which is not Darwinism).

Listen to the very best minds in the Intelligent Design Creationist community ... and weep for them. This is all they've got.

Id the Future: Berlinski and Denton

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