Jeff Lowder presents one of the strongest rebuttals against theism, and cases for naturalism I have so far seen

Jeff Lowder of The Secular Outpost debated Frank Turek 22nd september in Kansas. From this debate (video is not available yet), Jeff has compiled a narrated presentation of his powerpoint slides used in the debate, which I think now amounts to one of the strongest cases for naturalism and against the type of theism offered by the likes of William Lane Craig, I have seen to date.

It is long but if you are interested in this sort of thing, it is definitely worth a watch:

John Harshman thinks Nilsson Pilger’s fairytale on eye evolution is science?

In an early post John, who wants to be called doctor, urged readers to take a look at a little paper by Dan Nilsson and Suzanne Pilger. He says it is a good conceptual example of how natural selection acting on variation can gradually create a new feature.

Gee, that must be quite a paper.  He says it can’t be beat!  So what does their paper actually show?  The paper is called , “A Pessimistic Estimate of the Time Required for an Eye to Evolve.” Well, that does sound interesting! Continue reading

Axe, EN&W and protein sequence space (again, again, again)

So I wanted to write a post on the whole “density of functional proteins in amino acid sequence space” because, it seems to me, most ID proponents have some completely unwarranted beliefs about it. Recently it seems the main champion of the idea that evolving new protein functions would be so unlikely as to be practically impossible for evolution, even given several billion years, planet-spanning population sizes and natural selection, is Douglas Axe. He produced a paper in an (actual) peer reviewed journal back in 2004, and ID creationists have been spinning it ever since.

In 2007 a review of Axe 2004 appeared on Panda’s Thumb, by Arthur Hunt: Axe (2004) and the evolution of enzyme function. It recaps what Axe actually did and what he concluded from it, and I will add a bit about how it’s been pushed in ID circles since (see for example how it is pushed here: Imagine: 60 Million Proteins in One Cell Working Together.

This paper is interesting because it relates to the work of Douglas Axe that resulted in a paper in the Journal of Molecular Biology in 2004. Axe answered questions about this paper earlier this year, and also mentioned it in his recent book Undeniable (p. 54). In the paper, Axe estimated the prevalence of sequences that could fold into a functional shape by random combinations. It was already known that the functional space was a small fraction of sequence space, but Axe put a number on it based on his experience with random changes to an enzyme. He estimated that one in 10^74 sequences of 150 amino acids could fold and thereby perform some function — any function.

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Is evolution smarter than you are?

Evolutionists are fond of citing Orgel’s Second Rule: “Evolution is smarter than you are.” I have previously expressed skepticism about this rule (see here and here), but I’ve had no success in persuading people with a naturalistic metaphysical outlook. Yesterday, however, I came across a LiveScience article by Tia Glose titled, The Spooky Secret Behind Artificial Intelligence’s Incredible Power (October 9, 2016), which might prove to be a game-changer. We’ll see.

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Over-egging the case for protein design

Recently, I was browsing through the latest posts over at Evolution News and Views, and an anonymous article titled, Imagine: 60 Million Proteins in One Cell Working Together, caught my eye. By now, most readers at TSZ will be aware that I consider it overwhelmingly likely that the first living thing was designed. However, I’m also highly critical of attempts to over-egg the case for intelligent design. The article I read was one such attempt: it contained some unfortunate errors and omissions.

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How to think about science.

The physicist Arthur Zajonc provides us with his view of science that gives me hope for the future

Science can lead us away from reality into abstractions. It is too easy for the model to take over from the reality it is supposed to represent. The lived experience of the phenomenal world often takes a back seat. Zajonc gives us a couple of examples where the model dominates. The genetic code is one, and the neuroscience of the brain as a representative of the mind is another. If we are not careful our models become idols and the living reality is forgotten.

From a radio documentary featuring Arthur Zajonc he gives his views on Goethe’s science:

If you look at the actual practice that he undertakes it is I think faithful to the core principles of science, namely, it is empirically grounded, it proceeds from one methodical experience to the next, and it comes to a kind of insight, a moment of aperçu, of discovery.

He thinks that all good science proceeds in the way Goethe describes. It begins with insight. An example of which is Newton connecting a falling apple with the movement of the moon.
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In Slight Defense of Granville Sewell: A. Lehninger, Larry Moran, L. Boltzmann

The basic biochemistry textbook I study from is Lehninger Prinicples of Biochemistry. It’s a well regarded college textbook. But there’s a minor problem regarding the book’s Granville-Sewell-like description of entropy:

The randomness or disorder of the components of a chemical system is expressed as entropy,

Nelson, David L.; Cox, Michael M.. Lehninger Principles of Biochemistry (Page 23). W.H. Freeman. Kindle Edition.


And from the textbook written by our very own Larry Moran:

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Why I don’t find keiths’s critique of Plantinga’s Free Will Defense convincing

In a recent post, keiths criticizes Alvin Plantinga’s Free Will theodicy, which (very briefly) goes as follows:

…[S]ome of the free creatures God created went wrong in the exercise of their freedom; this is the source of moral evil. The fact that free creatures sometimes go wrong, however, counts neither against God’s omnipotence nor against his goodness: for He could have forestalled the occurrence of moral evil only by removing the possibility of moral good.
(Plantinga, Alvin (1967). God and Other Minds. Ithaca, New York: Cornell University Press. Pages 166-167.)

Keiths responds:

Suppose God creates each person with free will, so that everything he or she does during life is freely chosen. If God is omniscient, he knows what all of those choices will be before the person is even created. If God simply chooses not to create the people who will go on to commit rape (or even experience the desire to commit rape), then he has prevented those things from happening without depriving anyone of their free will.

There are several things wrong with this reply. Continue reading