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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CRISPR goes retro: Bacteria can also take ‘RNA mug shots’ of threatening RNA-viruses.

The emergence of life for the first time on this planet constitutes the classic question of what came first; the chicken or the egg?!  Did a self-replicating DNA system occur before transcription or translation evolved (the DNA World) or did a self-replicating RNA system first emerge (the RNA world) or did self-replicating protein system first emerge (the Protein World)…or … let’s just leave it there for now. Continue reading

Wright, Fisher, and the Weasel

Richard Dawkins’s computer simulation algorithm explores how long it takes a 28-letter-long phrase to evolve to become the phrase “Methinks it is like a weasel”. The Weasel program has a single example of the phrase which produces a number of offspring, with each letter subject to mutation, where there are 27 possible letters, the 26 letters A-Z and a space. The offspring that is closest to that target replaces the single parent. The purpose of the program is to show that creationist orators who argue that evolutionary biology explains adaptations by “chance” are misleading their audiences. Pure random mutation without any selection would lead to a random sequence of 28-letter phrases. There are 27^{28} possible 28-letter phrases, so it should take about 10^{40} different phrases before we found the target. That is without arranging that the phrase that replaces the parent is the one closest to the target. Once that highly nonrandom condition is imposed, the number of generations to success drops dramatically, from 10^{40} to mere thousands.

Although Dawkins’s Weasel algorithm is a dramatic success at making clear the difference between pure “chance” and selection, it differs from standard evolutionary models. It has only one haploid adult in each generation, and since the offspring that is most fit is always chosen, the strength of selection is in effect infinite. How does this compare to the standard Wright-Fisher model of theoretical population genetics? Continue reading

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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Conservation and function of long noncoding RNAs

How about some cool science as we head toward the weekend?

Let’s talk about long noncoding RNAs (lncRNA) – they are (somewhat arbitrarily) defined as stretches of DNA that are at least 200 base pairs in length that are transcribed into mRNA but have little potential to code for proteins. Determining the function (if one exists) of a particular lncRNA can often be difficult.  In part, this may be due to the fact that lncRNA evolve much more quickly than protein-coding genes do and therefore exhibit a much smaller degree of sequence conservation, which can make identifying orthologs in other related organisms more difficult.  Nevertheless, if a particular lncRNA is functionally important, we would usually expect to see copies of it in related organisms, so finding these homologs can be an important indicator of function.

A new paper in Genes and Development by Quinn et al. is a useful demonstration of this.  The authors find evidence of 47 homologs of roX, an lncRNA involved in X chromosome dosage compensation,  across 35 fruit fly species.  The researchers identity roX homologs based on a combination of short regions of sequence conservation (“microhomology”), RNA secondary structure and synteny (i.e., similarity in location along a chromosome)  Here is the abstract (I believe the paper itself is open access): Continue reading

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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Tiny sponge fossil predates the Cambrian explosion

New tools could allow scientists to discover other fossils that significantly predate the start of the Cambrian explosion, according to David Bottjer, a professor at the USC Dornsife College of Letters, Arts and Sciences and co-author of a study announcing the finding of the sponge in the Proceedings of the National Academy of Sciences.

“Fundamental traits in sponges were not suddenly appearing in the Cambrian Period, which is when many think these traits were evolving, but many million years earlier,” Bottjer said. “To reveal these types of findings, you have to use pretty high-tech approaches and work with the best people around the world.”

https://news.usc.edu/83632/tiny-sponge-fossil-predates-the-cambrian-explosion/

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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Lawyers and Scientists

There’s been a skirmish between Larry Moran and Barry Arrington about whether Barry understands the Theory of Evolution, and the latest salvo is a piece at UD, entitled, Can a Lowly Lawyer Make a Useful Contribution? Maybe.

Well, in a sense, Barry makes a useful contribution in that post, as he gives a very nice illustration of a common misunderstanding about the process of hypothesis testing, in this case, basic model-fitting and null hypothesis testing, the workhorse (with all its faults) of scientific research.  Barry writes:

[Philip]Johnson is saying that attorneys are trained to detect baloney.  And that training is very helpful in the evolution debate, because that debate is chock-full of faulty logic (especially circular reasoning), abuse of language (especially equivocations), assumptions masquerading as facts, unexamined premises, etc. etc.

Consider, to take one example of many, cladistics.  It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it.  But I bet if one asked, 9 out of 10 materialist evolutionists, even the trained scientists among them, would tell you that cladistics is powerful evidence for common descent.  As Johnson argues, a lawyer’s training may help him understand when faulty arguments are being made, sometimes even better than those with a far superior grasp of the technical aspects of the field.  This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.

In summary, I am trained to evaluate arguments by stripping them down to examine the meaning of the terms used, exposing the underlying assumptions, and following the logic (or, as is often the case, exposing the lack of logic).  And I think I do a pretty fair job of that, both in my legal practice and here at UD.

Barry has made two common errors here.  First he has confused the assumption of common descent with the conclusion of common descent, and thus detected circular reasoning where there is none.  Secondly he has confused the process of fitting a model with the broader concept of a hypothesised model.

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Alzheimer’s and Evolution

I have to say, while the UD “newsdesk” is terrible source for comment on scientific news, the links themselves are often interesting.  Today, the UD “newsdesk” reports on a pretty interesting study, reported in Nature, here, and a preprint of which seems to be open access here

It’s been apparent for a while from Genome-Wide Association Studies (GWAS) that “risk” alleles for various mental disorders, despite being statistically significant, have extremely small effect sizes.  In other words, while the studies show that many mental disorders are indeed associated with specific alleles (and we already know that many are highly heritable, including schizophrenia, ADHD and Alzheimer’s), there aren’t just a few rogue alleles of large effect (well, there are, but they are far rarer than these disorders), but instead, a whole cocktail of alleles with very slightly raised Odds Ratios for certain disorders (and some are shared between multiple disorders).  This means that the vast majority of people carrying these “risk alleles” are perfectly fine. That would help explain why they have not been weeded out by selection.

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The Twilight of Intelligent Design (Open thread)

Sunset

It just dawned on me that ID is dead.

Dembski is off all radar. He doesn’t even show up in the search box at South Carolina bible college or whatever. The last post on the Design Inference is a year old.

Meyer’s book went up like a firework and came down with the stick.

Most of the static websites are moribund. UD has banned virtually all dissenters. The few brave enough to wander over to TSZ bail out after a couple of rounds. The biologic institute inflates its “selected publications” with publications that have nothing to do with the biologic institute and seems to be doing no more than pretending to produce output.

Bio-Complexity is moribund.

Behe doesn’t seem to have much to say.

The big guys won’t come out to debate. The small ones mostly won’t leave heavily censored sites. Even the UD newsdesk peddles 6 year old stories as “news”.

And all the threads are about religion. Or tossing coins.

I don’t know why I hadn’t seen it before.

It’s dead.

Posted at “After the Bar Closes on Jan. 05 2014,16:37 by Febble (Elizabeth Liddle) Continue reading

The Double-Blind Newcombian Placebo Paradox

Here’s something I slopped together recently. I’m not really familiar with the literature on any of this, so maybe it’s all pretty well known (or well known to be confused).  Anyhow, comments are welcome, and I apologize in advance for my usual pile of typos, grammatical  errors, and other miscellaneous blunders.

W

 

Johnny Woulda, 45, has had chronic tendonitis in both of his elbows since he was about 30.  He’s always been told that there’s no help for it except rest and steroid injections, but the rest hasn’t worked, and he’s afraid the injections will be worse for him than the elbow pain.  He takes a bus to work every day and one day he sees a poster that says “Do you have tendonitis? We are testing a new non-steroidal oral drug, and if you are an otherwise healthy male between the ages of 18 and 48 you could earn $100 by taking part in our clinical trial.”  The drug company, Montrezl, is interested in testing the effectiveness of their experimental product, Elbowftra©.  Based on their tests on chimpanzees, which have no belief one way or the other whether they are being given a real drug, they believe that Elbowftra© drug would have at least a 50% effectiveness rate on humans people—higher if the person is credulous (the sort of person now spending a ton of money on herbal remedies).  The FDA has assured Montrezl that if they can confirm that at least 30% more human volunteers are cured by Elbowftra© than are cured by a sugar pill placebo, as determined by blind reviewers, they should have no problem getting their drug approved.  On the other hand, if there’s not much difference between Ebowftra’s effectiveness and that of a placebo, there isn’t much hope.

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Neuroimaging

I’ve been meaning to write a post in this for a while, but as usual, Barry Arrington has prompted me into action (I’m really very grateful to Barry sometimes :))  (Golly, just checked – it’s already half way down the UD page!  Does Barry really want his posts buried quite so rapidly?  We are going to see fossilisation at this rate!)

Anyhoo….  Neuroimaging is one of the things I do.  Here is one of my favorite images (probably the most reproduced fMRI image of all time), by Fox et al, 2005:

Although it may not have the form that some readers might be more familiar with, as it’s plotted on a “flat[ish] map” of the cortical surface.

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