Impractical Naturalism of Dan Graur vs. the NIH

I’ll be making a presentation at AM-NAT 2016, and Dan Graur will be the poster boy of impractical naturalism. Below are some things I collected from his websites, some of which I view as highly anti-science. The aim of my presentation isn’t to settle the question of God or no God or ultimate questions of whether godless naturalism is the best description of reality. The goal is to suggest there are some unspoken naturalistic creeds that often take priority over experiments and observations. In a manner of speaking, there are some interpretations of naturalism that actually go against dispassionate examination of how the natural world actually operates.
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Epigenetic Memory Changes during Embryogenesis

DNA is not just a static read-only memory (ROM) for coding proteins, but hosts dynamic random access memory (RAM) in the form of methylations and histone modifications for regulation of gene expression, cellular differentiation, learning and cognition, and who knows what else. The picture below depicts how rapidly the RAM aspect of DNA is changed during embryogenesis.
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Philosophy and Complexity of Rube Goldberg Machines

Michael Behe is best known for coining the phrase Irreducible Complexity, but I think his likening of biological systems to Rube Goldberg machines is a better way to frame the problem of evolving the black boxes and the other extravagances of the biological world.
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Chargaff Parity Rule 2, Biased/Non-Random Mutations

There is an approximate 8% excess of Adenine and Thymine above random in the DNA of humans. This suggests mutational bias and/or non-random mutation. If 3 billion coins were found to be 58% heads vs. 42% tails, then the chance hypothesis of a random unbiased coin flip would be easily rejected. The odds of such an event happening are astronomical according to the binomial distribution.

But such an imbalance is reflected in the human genome where:
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The Reasonableness of Atheism and Black Swans

As an ID proponent and creationist, the irony is that at the time in my life where I have the greatest level of faith in ID and creation, it is also the time in my life at some level I wish it were not true. I have concluded if the Christian God is the Intelligent Designer then he also makes the world a miserable place by design, that He has cursed this world because of Adam’s sin. See Malicious Intelligent Design.
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ID falsifiable, not science, not positive, not directly testable

There was a time when people believed the moon craters were the product of intelligent design because they were so perfectly round “they must have been made by intelligent creatures living on the moon”. That idea was falsified. If hypothetically someone had said back then, “The Flying Spaghetti Monster (FSM) made the moon craters”, the claim would have been falsifiable, but it really doesn’t make a positive case for the FSM, doesn’t make the FSM directly testable, doesn’t make the FSM science. Substitute the word “ID” instead for “FSM”, and one will see why I think even though ID is falsifiable, I don’t think ID has a positive case, and I don’t think ID is directly testable, and I don’t think ID is science at least for things like biology.

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Absolute Fitness in Theoretical Evolutionary Genetics

Joe Felsenstein, like other population geneticists, holds a special place in the Creation/Evolution controversy because his works are regarded highly by many creationists who are familiar with genetics. This is a thread for all of us (myself included) to try to learn and understand one of the key concepts in his book Theoretical Evolutionary Genetics, namely absolute fitness. He has generously made his book available on his website (a book of this calibre could sell for hundreds of dollars).
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Pastor Hates Jesus after Reading Coyne’s Book

Bruce Gerencser was a pastor for 27 years until he started reading books with non-Christian viewpoints. One of the 5 most influential books in his conversion to atheism was Jerry Coyne’s book, Why Evolution is True. Bruce’s kids are no longer evangelicals and left the faith that he once taught them. He openly says he hates Jesus now.

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Dictionary halting problem makes A=A fallible

It would seem superficially this is correct

A=A, necessarily and infallibly true

but it is false for non-trivial A and where the EQUAL SIGN means equal in essence, not just equal in description. This is a consequence of the dictionary and halting problem that has been well demonstrated by first rate mathematical logicians and computer scientists (like Alonzo Church who was a devout Christian) who actually work with formal languages vs. people clinging to antiquated and non-rigorous theological notions.
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Coyne hoodwinked and duped

Jerry Coyne represents himself as the epitome of science, reason and critical thinking. But “Dr. Reason” or shall we say “Dr. EvolutionIsTrue” often ends up as the butt of jokes and sarcasm in the ID community.

He got hoodwinked recently. He was pranked into believing a particular internet account was real and then started quoting from it to support his arguments. Turned out his evidence was from a faked source. Finally someone intervened to stop Coyne from making anymore a joke of himself. Coyne was forced to make a retraction:
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Repetitive DNA and ENCODE

[Here is something I just sent Casey Luskin and friends regarding the ENCODE 2015 conference. Some editorial changes to protect the guilty…]

One thing the ENCODE consortium drove home is that DNA acts like a Dynamic Random Access memory for methylation marks. That is to say, even though the DNA sequence isn’t changed, like computer RAM which isn’t physically removed, it’s electronic state can be modified. The repetitive DNA acts like physical hardware so even if the repetitive sequences aren’t changed, they can still act as memory storage devices for regulatory information. ENCODE collects huge amounts of data on methylation marks during various stages of the cell. This is like trying to take a few snapshots of a computer memory to figure out how Windows 8 works. The complexity of the task is beyond description.
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The Sugar Code and other -omics

[Thank you to Elizabeth Liddle, the admins and the mods for hosting this discussion.]

I’ve long suspected the 3.1 to 3.5 gigabases of human DNA (which equates to roughly 750 to 875 megabytes) is woefully insufficient to create something as complex as a human being. The problem is there is only limited transgenerational epigenetic inheritance so it’s hard to assert large amounts of information are stored outside the DNA.

Further, the question arises how is this non-DNA information stored since it’s not easy to localize, in fact, if there is a large amount of information outside the DNA, it is in a form that is NOT localizable, but distributed and so deeply redundant that it provides the ability to self-heal and self-correct for injury and error. If so, in a sense, damage and changes to this information bearing system is not very heritable since bad variation in the non-DNA information source can get repaired and reset, otherwise the organism just dies. In that sense the organism is fundamentally immutable as a form, suggestive of a created kind rather than something that can evolve in the macro-evolutionary sense.
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