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The Critic's Resource on AntiEvolution

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For Your Consideration as We Await the Announcement of "Censor of the Year": Jamie Farren of Freethought Oasis

Don't discount the dark horse. David Klinghoffer
Categories: Anti-Science News

The War on Humans Has Its Seattle-Area Debut; Online Premiere and E-book by Wesley J. Smith Coming Later This Month

We had a young man in the audience dressed with furry ears on top of his head and a foxtail, but he chose not to ask a question. Foxes rarely do. Evolution News & Views
Categories: Anti-Science News

RNA Shows Design, Too

DNA is the poster child of coded information, but RNA is gaining respect in its own right. Evolution News & Views
Categories: Anti-Science News

Stephen Meyer on Tomorrow's Ham-Nye Debate

"It's a plus because it generates interest in the topic. It's a minus because it inhibits an understanding of the complexity of the issue." David Klinghoffer
Categories: Anti-Science News

What's Wrong with the Miller & Levine Biology Textbook?

After a contentious review process that attracted nationwide media attention, Kenneth Miller and Joseph Levine's new edition of their textbook has been adopted for use in Texas. Casey Luskin
Categories: Anti-Science News

Is There a Good Reason to Believe That Life's Origin Must Be a Fully Natural Event?

Life is an experience that everyone has and thinks they can recognize. A quality we think is very important. Yet no one can define it. Denyse O'Leary
Categories: Anti-Science News

Two Reasons Darwinism Survives

As scientific research continues to reveal the astonishing dimensions of the complexity of life, how does such a dumb theory persist? Granville Sewell
Categories: Anti-Science News

Evolution and Monkeys on Rafts

Darwinism is less a science than a cognitive impediment. Michael Egnor
Categories: Anti-Science News

Tripped Up by Snafu on Starling Murmurations, University of Chicago Evolutionary Biologist Jerry Coyne Tell Us to "Stuff It!"

If it weren't for his activities trying to cast fear on career-vulnerable scientists who are open to intelligent design, there might be something almost endearingly oafish about Dr. Coyne. David Klinghoffer
Categories: Anti-Science News

Approved for Use in Texas Schools, Ken Miller's Textbook Uses Galápagos Finches to Overstate the Case for Evolution

As I have shown in this series, Texas students, and others across the country, deserve better. Casey Luskin
Categories: Anti-Science News

Regulatory codes hidden within exons

ARN ID Update - Tue, 2014-02-04 21:43

Redundancy in the genetic code has long been recognised. Most amino acids can be specified in multiple ways (2-6 synonymous codons). More recently, it has also become known that synonymous codons are non-random, stimulating thought as to why this should be (see here). Since codon usage biases characterise both prokaryotic and eukaryotic genomes, is it possible that they are accidents of evolutionary history? This seems to be ruled out by pervasive evidences of conservation. Since the biases are not removed by mutations, it is inferred that "observed codon preferences in mammalian genomes [. . .] appear to be under selection" (p.1367.) Such a conclusion is reached by deduction from evolutionary theory. If specific (synonymous) codons do not matter when manufacturing proteins, is it possible they are relevant to the regulation of genetic processes? Since there is a presumption favouring simplicity in the minds of most geneticists, this research question has only recently been taken up. There are many synonymous codons when coding for proteins, but are they synonymous if they are also coding regulatory instructions?

"Genomes also contain a parallel regulatory code specifying recognition sequences for transcription factors (TFs), and the genetic and regulatory codes have been assumed to operate independently of one another and to be segregated physically into the coding and noncoding genomic compartments. However, the potential for some coding exons to accommodate transcriptional enhancers or splicing signals has long been recognized." (p.1367)

The challenge of the Human Genome Project has given way to searching for an understanding of multiple overlapping genetic codes. (source here)

With the availability of large amounts of genome data, it is possible to test many hypotheses relevant to the functionality of DNA sequences. The data set used is impressive:

"To define intersections between the regulatory and genetic codes, we generated nucleotideresolution maps of TF occupancy in 81 diverse human cell types using genomic deoxyribonuclease I (DNaseI) footprinting. Collectively, we defined 11,598,043 distinct 6- to 40-base pair (bp) footprints genome-wide (~1,018,514 per cell type), 216,304 of which localized completely within protein-coding exons (~24,842 per cell type). Approximately 14% of all human coding bases contact a TF in at least one cell type (average 1.1% per cell type), and 86.9% of genes contained coding TF footprints (average 33% per cell type)." (p.1367)

A summary of the main findings of the research team is provided in a Perspectives essay by Weatheritt and Babu. The hypothesis of two co-existing codes is fully justified by the evidence. According to the press release: "scientists were stunned to discover that genomes use the genetic code to write two separate languages."

"How widespread is the phenomenon of "regulatory" codes that overlap the genetic code, and how do they constrain the evolution of protein sequences? Stergachis et al. address these questions for the transcription factor-binding regulatory code. They use deoxyribonuclease I (DNase I) footprinting to map transcription factor occupancy (a protein bound to DNA can protect that region from enzymatic cleavage) at nucleotide resolution across the human genome in 81 diverse cell types. The authors determined that ~14% of the codons within 86.9% of human genes are occupied by transcription factors. Such regions, called "duons", therefore encode two types of information: one that is interpreted by the genetic code to make proteins and the other, by the transcription factor-binding regulatory code to influence gene expression. This requirement for transcription factors to bind within protein-coding regions of the genome has led to a considerable bias in codon usage and choice of amino acids, in a manner that is constrained by the binding motif of each transcription factor." (p.1325)

Weatheritt and Babu go further. They suggest a general principle: that redundancy in the genetic code opens the door for, not one, but many regulatory codes that can operate within protein-coding regions of the genome. One research question of the future is: how many overlapping codes can be tolerated by the genetic code?

"This "binding" code joins other "regulatory" codes that govern chromatin organization, enhancers, mRNA structure, mRNA splicing, microRNA target sites, translational efficiency, and cotranslational folding, all of which have been proposed to constrain codon choice, and thus protein evolution." (p.1325)

It should be noted that these research findings do not tell us what binding a transcription factor actually achieves. The field of gene regulation is in its infancy. The research team notes that TF binding "may serve multiple functional roles" but that their analysis is "agnostic" to this functionality. Weatheritt and Babu conclude:

"The investigation of overlapping codes opens new vistas on the functional interpretation of variation in coding regions and makes it clear that the story of the genetic code has not yet run its course." (p.1326)

This discussion of genetic codes is only meaningful if it is recognised that the genome is a carrier of complex specified information. The essence of life is not to be found in chemistry, but in the information carried within the cell. Chemicals are used to carry biological information, but the chemicals are not themselves information. The research team recognises this when they say:

"Our results indicate that simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes. The information architecture of the received genetic code is optimized for superimposition of additional information and this intrinsic flexibility has been extensively exploited by natural selection." (p.1371-2)

There is a problem with the last few words of the above quotation. The flexible information architecture is said to be exploited "by natural selection", yet this claim has not emerged from a study of evidences. Rather, the theoretical framework of neo-Darwinism provides the context for interpreting the evidences, so that all signs of complexity and functionality are automatically associated with the operation of natural selection. Yet, we have no evidence to show that natural selection can either produce or refine complex specified biological information.

There is a perfectly viable alternative hypothesis to consider: that biological information is evidence for intelligent agency. The evidence we have already about the genetic code is sufficient to make the point, but new evidences of overlapping codes add weight to the hypothesis. The genetic code with redundancy overlaps with other regulatory codes in ways that test the ability of molecular biologists (intelligent agents) to understand what's happening, let alone write overlapping codes of their own as a biomimetic exercise. From time to time, leading biologists get the message, but seem at a loss to drive it forward.

"Any living being possesses an enormous amount of "intelligence", very much more than is necessary to build the most magnificent of cathedrals. Today, this "intelligence" is called "information", but it is still the same thing. It is not programmed as in a computer, but rather it is condensed on a molecular scale in the chromosomal DNA or in that of any other organelle in each cell. This "intelligence" is the sine qua non of life. If absent, no living being is imaginable. Where does it come from? This is a problem which concerns both biologists and philosophers and, at present, science seems incapable of solving it." Pierre Grasse, Evolution of Living Organisms: Evidence for a New Theory of Transformation, (New York: Academic Press, 1977, 2).

The decision to endorse a naturalistic explanation rather than advance agnosticism about the origins of hidden overlapping codes is a pointer to hidden ideologies in origins-science. It seems that as long as materialism/naturalism is presumed, then a great number of unwarranted assertions (usually linked to Darwinism or abiogenesis) go unchallenged in academic papers. As soon as it is pointed out that only intelligent agents write codes, there is an outcry that science is being subverted by religious fundamentalists. However, the converse is true: intelligent design theory is based on the evidence of complex specified information. The evidences for naturalistic alternatives all evaporate under close scrutiny.

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Andrew B. Stergachis, Eric Haugen, Anthony Shafer, Wenqing Fu, Benjamin Vernot, Alex Reynolds, Anthony Raubitschek, Steven Ziegler, Emily M. LeProust, Joshua M. Akey and John A. Stamatoyannopoulos.
Science, 13 December 2013, 342, 1367-1372 | DOI:10.1126/science.1243490 [pdf here]

Abstract: Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.

See also:

Weatheritt, R.J. and Babu, M, M. The Hidden Codes That Shape Protein Evolution,
Science, 13 December 2013, 342, 1325-1326 | DOI: 10.1126/science.1248425

Klinghoffer, D. Genome Uses Two Languages Simultaneously; Try That Yourself Sometime, Why Don't You, Evolution News & Views (December 13, 2013)

Luskin, C. Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection, Evolution News & Views (December 20, 2013)

Categories: Anti-Science News

Continuing concern in South Dakota

"A South Dakota lawmaker wants public school teachers to be free to teach intelligent design in their classrooms even though courts have ruled intelligent design is inherently religious — and therefore unconstitutional in school," according to a report from KMEG 14, headquartered in Sioux City, Iowa, just across the Missouri river from South Dakota.

Categories: Pro-Science News

The CSC Seminar on Intelligent Design in the Natural Sciences

ARN ID Update - Tue, 2014-02-04 03:20

This Discovery Institute seminar will prepare students to make research contributions advancing the growing science of intelligent design (ID). The seminar will explore cutting-edge ID work in fields such as molecular biology, biochemistry, embryology, developmental biology, paleontology, computational biology, ID-theoretic mathematics, cosmology, physics, and the history and philosophy of science. This seminar is open to students who intend to pursue graduate studies in the natural sciences or the philosophy of science. Applicants must be college juniors or seniors or already in graduate school.

More information...

Categories: Anti-Science News

Mixed news from Virginia

Virginia's House Bill 207, which would deprive administrators of the ability to prevent teachers from miseducating students about "scientific controversies," is in search of a home.

Categories: Pro-Science News

"Intelligent design" bill deemed "odd"

South Dakota's Senate Bill 112 was deemed the "odd bill of the week" by the Rapid City Journal (February 2, 2014).

Categories: Pro-Science News

Are Republicans Naturally Disposed to be "Anti-Science"?

ID the Future - Fri, 2014-01-31 09:43
Listen Now. On this episode of ID the Future, David Boze discusses Chris Mooney's recent article in The Huffington Post entitled Why Republicans Deny Science: The Quest for a Scientific Explanation. Mooney suggests that Conservatives who reject alarmism on...
Categories: Anti-Science News

Dr. Michael Egnor on Debating Intelligent Design

ID the Future - Fri, 2014-01-31 09:43
Listen Now. On this episode of ID the Future, brain surgeon and ID blogger Michael Egnor talks with CSC Research Coordinator Casey Luskin about his internet debates with Jerry Coyne and the trends and dynamics he sees in the...
Categories: Anti-Science News

David Berlinski: The Nature of Numbers, pt. 2

ID the Future - Fri, 2014-01-31 09:43
Listen Now. On this episode of ID the Future, Dr. David Berlinski continues to discuss the origin and nature of mathematics with CSC Research Coordinator Casey Luskin. Is math something waiting to be discovered, or is it a construct...
Categories: Anti-Science News

At Why Evolution Is True, Jerry Coyne Promotes an Intelligent Design Documentary

Well, good for him. Unwittingly, he shares with his readers a clip that is among the many spectacular sequences in Flight: The Genius of Birds. David Klinghoffer
Categories: Anti-Science News

Two Cheers for the Washington Post, Which Accurately Reports on Virginia's Academic Freedom Bill

We bet these reporters get savaged for it. Evolution News & Views
Categories: Anti-Science News
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