‘Junk DNA’

Our physics color commentator Rob Sheldon offers some thoughts on junk DNA, the claim that most of the human genome does nothing (often an argument for explicitly Darwinian evolution): a) Chance is the truly unfalsifiable hypothesis, because all it gives you is a number. 1:10, 1:10^500 are all the same as far as the Darwinist is concerned. Even Dembski’s “1:10^150” possibility bound is not a limit to them. So everything I say about designers has to be seen against that light. Of course, in the Darwinist’s defense, they don’t really get probability and logarithms. b) A designer is recognized by a pattern. Writing experts can isolate a piece of scribal work to within 50 years by looking at the style. Read More ›

Graur’s latest claim that 75% of the human genome is non-functional has attracted a lot of digital ink. Pop science loves that sort of thing. From Kerry Grens at the Scientist: Up to 25 percent of the human genome is critical, while the rest has no function, according to a study published July 11 in Genome Biology and Evolution. The estimate, generated by looking at fertility rates and the expected frequency of deleterious mutations, contradicts a 2012 claim from a large international group called ENCODE, which estimated that 80 percent of the genome is functional. “For 80% of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but Read More ›

I was in the server room with my system administrator the other day, discussing how we could cut costs in the server room.
Read More ›

These are a pair of videos from the AM-Nat Biology conference. I have had lots of other things going on so I’ve been slow getting these up, but Salvador’s talks became more relevant as Dan Graur doubles down to try to prove that the genome is mostly junk. You can get the rest of the talks from the AM-Nat Biology conference (that have been uploaded so far) from here.

A paper at Nature from Karen Adelman & Emily Egan (Nature 543, 183–185 (09 March 2017) doi:10.1038/543183a) It emerges that nascent non-coding RNAs transcribed from regulatory DNA sequences called enhancers bind to the enzyme CBP to promote its activity locally. In turn, the activities of CBP stimulate further enhancer transcription. (paywall) More. See also: Cod gene puzzle: At least no one is claiming it is “junk RNA” Follow UD News at Twitter!

From ScienceDaily: Researchers at the University of Oslo (UiO) keep discovering surprises in the Atlantic cod genome. The most recent study has revealed an unusual amount of short and identical DNA sequences, which might give cod an evolutionary advantage. Or else it is something the cod could live with or else it makes no difference at present. If we don’t have any very definite information, why talk about “evolutionary advantage” at all? Interesting: “We have already found a fish species that has even more tandem repeats than cod, namely the related haddock. Both cod (Latin name: Gadus morhua) and haddock (Melanogrammus aeglefinus) are members of the cod family (Gadidae). This may indicate that the whole group has an increased proportion Read More ›

By limiting what cells can become. From Joshua A. Krisch at The Scientist: The results suggest that a particular class of noncoding RNA works in concert with the latent viral elements of the genome work to limit stem cell potential, and that removing a key miRNA can lift this limitation—at least in vitro. “At first we were a bit dubious about our findings,” said coauthor Lin He, an associate professor of developmental biology at the University of California, Berkeley. “In this experiment, we definitively show that the progeny [of embryonic stem cells] can go to both embryonic and extra-embryonic lineages. That was a pretty incredible moment for us, because we actually convinced ourselves that this finding was real.” More. See Read More ›

From ScienceDaily: They have determined that several thousands of the retroviruses that have established themselves in our genome may serve as “docking platforms” for a protein called TRIM28. This protein has the ability to “switch off” not only viruses but also the standard genes adjacent to them in the DNA helix, allowing the presence of ERV to affect gene expression. This switching-off mechanism may behave differently in different people, since retroviruses are a type of genetic material that may end up in different places in the genome. This makes it a possible tool for evolution, and even a possible underlying cause of neurological diseases. In fact, there are studies that indicate a deviating regulation of ERV in several neurological diseases Read More ›

From ScienceDaily: Although it is widely viewed as a vestigial organ with little known function, recent research suggests that the appendix may serve an important purpose. In particular, it may serve as a reservoir for beneficial gut bacteria. Several other mammal species also have an appendix, and studying how it evolved and functions in these species may shed light on this mysterious organ in humans. Heather F. Smith, Ph.D., Associate Professor, Midwestern University Arizona College of Osteopathic Medicine, is currently studying the evolution of the appendix across mammals. Dr. Smith’s international research team gathered data on the presence or absence of the appendix and other gastrointestinal and environmental traits for 533 mammal species. They mapped the data onto a phylogeny Read More ›

From ScienceDaily: A study from Massachusetts General Hospital (MGH) investigators has found a surprising role for what had been considered a nonfunctional “junk” RNA molecule: controlling the cellular response to stress. In their report in the Dec. 15 issue of Cell, the researchers describe finding that a highly specific interaction between two elements previously known to repress gene transcription — B2 RNA and EZH2, an enzyme previously known only to silence genes — actually induces the expression of stress-response genes in mouse cells. … Less than 2 percent of the genome in mammals actually codes for proteins, and for many years it was thought that noncoding DNA was a useless artifact. While some is translated into RNA molecules required for Read More ›

In the midst of a fairly heavy fog, if not blackout, in the pop science media, Mazur has done more than anyone to let the public know that evolutionary biology is being forced to rethink a commitment to Darwinism (or neo-Darwinism or a lightly stretched synthesis, or whatever your PR person wants to call it now). For one thing, the genome maps just don’t support the underlying genetic fundamentalism. And perhaps she was one of the few who even could do it. She has written mainly for popular media and her books are a valuable introduction for the layperson as to why Darwinism is failing as an explanation. They are especially helpful for those who do not have any religious Read More ›

From ScienceDaily: The stretches of DNA between genes, littered with repeating sequences, were once considered the “junk of the genome,” but scientists are learning that some of this junk is far from harmless clutter. Researchers at the University of North Carolina Lineberger Comprehensive Cancer Center report in the journal Cell Reports that certain short, repetitive sequences of DNA, or “junk,” play an important role in the development of Ewing sarcoma, a rare bone and soft tissue cancer that occurs most commonly in children and adolescents. “Some people may still think of these non-coding sequences as junk; that they don’t really do anything but act as hangers-on to the more famous parts of the genome,” said the study’s senior author Ian Read More ›

From Prieto-Godino LL, Rytz R, Bargeton B, Abuin L, Arguello JR, Peraro MD, Benton R, at Nature: Olfactory receptor pseudo-pseudogenes,² Nature 2016 Oct 24 doi:10.1038/nature19824. PMID:27776356 Abstract: Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. Here we report the characterization of a pseudogene in the chemosensory variant ionotropic glutamate receptor repertoire of Drosophila sechellia, an insect endemic to the Seychelles that feeds almost exclusively on the Read More ›

From Carrie Arnold at Nova: One of the few survivors of the asteroid impact 65 million years ago was a small, furry, shrew-like creature that lived in underground burrows and only ventured out at night, when predators weren’t active. The critter—already the product of some 100 million years of evolution—looked like a modern mammal, with body hair and mammary glands, except for one tiny detail: according to a recent genetic study, it didn’t have a placenta. And its kind might never have evolved one if not for a chance encounter with a retrovirus. Unlike most viruses, which infect, replicate, and then leave their host, retroviruses elbow their way into their host’s genome where they are copied and passed on to Read More ›