The Sternberg-Collins Paradox for non-random SINE insertion mutations

One of the most brilliant evolutionary biologists of the present day, Richard Sternberg, PhD PhD was ousted and permanently blacklisted by the National Institutes of Health and the Smithsonian Museum for his ID sympathies.

Sternberg is neither a Creationist nor Darwinist but classifies himself as a Process Structuralist which means he is not much involved in the ultimate questions of how things came to be, he just appreciates the amazing patterns of similarity and diversity in biology.

He was labelled by some of his former supporters as an intellectual terrorist after he used his position as editor of a journal to publish an ID-friendly article by Stephen Meyer in 2004. He paid dearly for that decision, and his subsequent dismissal from the NIH and Smithsonian precipitated special investigations by members of Congress and the White House a decade ago. Unfortunately, nothing of consequence was done for Sternberg and he was destroyed professionally and personally.

Despite his circumstances, he continued to publish excellent essays such as the one that highlights the non-random patterns of SINES (presumed by some to be junkDNA) which are present in mice and rats (link below).
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ID In A Nutshell

ID is like the old locked room mysteries.

Scenario: Mr Body is found in a locked room with two bullet wounds in the back of his head. Lethal weapon found in his hand.

All the people known to profit from his death have airtight alibis. Security cameras show no one entering the room after Mr Body enters.

Only Mr Body’s fingerprints are found on the gun.

1. Suicide?
2. Magic or Divine Intervention?
3. Space Aliens having unknown technology?
4. Something else?

Interestingly, number one has actually been put forward in at least one actual, recent case.
If we substitute biogenesis for Mr Body’s death, ID proponents assume number two or number three.
If we substitute evolution for Mr Body’s Death, then Michael Behe and Mendel’s Accountant proponents assume number two or number three.

What do you guys think? What assumption do you think is most reasonable? I’m not asking what really happened. I’m asking what is the first working hypothesis that comes to mind?

New data on human genomic diversity

The extent of variation present in human populations and the consequences of genetic load seem to be topics of perennial interest here (see, for example, recent comments in the Evolution Visualized thread).  Recent issues of Nature have published a flurry of papers aimed at getting a better handle on just how much genetic diversity is likely to exist among humans.   One notable paper from last August is the following:

Analysis of protein-coding genetic variation in 60,706 humans

In this study, Monkol Lek and many, many colleagues sequenced the exomes–i.e., the portion of DNA sequences that code for proteins along with some accompanying untranslated regions–of more than 60,000 people.  The results were pretty spectacular.  The paper is incredibly dense, but here are some highlights:

  • The authors found more than 7 million reliably identified variants.  Most were single base pair substitutions, but the variants also include more than 300,000 insertions/deletions.
  • On average, 1 out of every 8 nucleotides is variable.  However, the overwhelming majority of variants are rare.  That is they are found in only a single or a few individuals
  • The frequency of different kinds of variants is proportional to both the rate at which they occur as well as the extent to which they are likely to be deleterious.  This is not at all surprising, but it’s neatly demonstrated.  For example,  63.1% of all possible CpG transitions (i.e., a cytosine adjacent to a guanine that mutates to a thymine) were observed, while only 3% of possible transversions were present.  CpG transitions are among the most common type of substitution in mammals, while transversions are less frequent.  Likewise, the proportion of possible synonymous variants that were actually observed was much higher than the proportion of possible nonsynonymous variants that were observed, which is consistent with the generally accepted notion that nonsynonymous mutations are usually subject to stronger purify selection than synonymous mutations.
  • They identified almost 180,000 different protein truncation variants (PTVs), which are protein-coding genes predicted to be shortened due to an introduced stop codon, a frameshift, or removal of a critical splice site.  Amazingly (to me at least), the average genome in their dataset includes 85 PTVs in the heterozygous state and almost 35 PTVs in the homozygous state.
  • They identified more than 100 variants previously thought to contribute to disease phenotypes that are present at anomalously high frequencies in human populations (> 1%).  Based on the fact that the evidence of pathogenicity for most of these variants is actually extremely weak, the authors suggest that these variants are most likely benign.

There is a lot more in the paper that’s worth chewing over, so give it a read.  This is easily the largest dataset of its type ever generated, but it has limitations.  The sampling is heavily biased toward Europeans, and there is likely some variation missing, especially in Central and Middle Eastern Asia.

I imagine that within a few years, we’ll have datasets of similar size consisting of high-coverage, whole genome sequences, which will no doubt show even larger amounts of genomic variation.  It’s an exciting time to be interested in biology!

Scientific Metaphysics & Its Consequences

In a recent comment, Fifthmonarchyman engaged with my accusation that his remarks on what brains can’t do is based on his ignorance of neuroscience. He responded by saying

it’s not about neuroscience it’s about ontology.

Brains don’t comprehend because they are not minds. I would think that someone so enamored with philosophy would have a handle on different categories of existence.

It is precisely as a philosopher that I want to express my complete rejection of the assumptions implicit in this remark.

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Is TSZ one of the Penumbra of Attack Sites?

As most know, our favourite author and commenter of incoherent word salad over at Uncommon Descent, He Who Shall Not Be Named, often makes reference to those nasty attack sites. More recently, he has referred to the penumbra of attack sites

i was was just wondering if people here thought that TSZ is one of these attack sites referred to by GEM.

 

 

Cumulative Selection Explained!

The battle over cumulative selection and Dawkins’ Weasel program has raged on for some months [years?] here at TSZ and across numerous threads. So can it possibly be that we now, finally, have a definitive statement about cumulative selection?

Mung: And whether or not my program demonstrates the power of cumulative selection has not been settled…

To which keiths responded:

keiths: Anyone who understands cumulative selection can see that it doesn’t, because your fitness functions don’t reward proximity to the target — only an exact match. The fitness landscapes are flat except for a spike at the site of the target.

So there you have it. You need a target and a fitness function that rewards proximity to the target.

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What is a decision?

Arcatia has stated that before any thought can occur, first there must be a chemical change in the brain.  So if before any decision is made, we first need a chemical change, then it is not really a decision, now is it?  It is merely a response to that chemical change, for which we have no control over.

 

On several occasions keiths has ducked and dodged away from this problem.  Arcatia now seems to want to run away from it, as has every other materialist here on this forum.  About the best you can hope for is some kind of obfuscated rant about what is meaning, what is will, how do we know we know, what’s the epistemological  nature of the epistemology…and on, and on the deflections to anything that could be considered an answer go.  Generally people here pretend that if you stick the suffix “sian” at the end of any name, you have said something profound.

 

So it deserves it own thread.  Let the bullshit answers speak for themselves.  In the end we will see if anyone actually tries to address it.  Its the toughest question for materialists to wiggle out of in my opinion.