‘Junk DNA’

One wonders: Before anyone realized this, would those multiple copies be considered “junk”? From New Scientist: When they studied samples of elephant blood, they found that African elephants have at least 20 copies of the p53 gene from each parent. P53 is an ancient gene found in all multicellular animals. It detects stress or damage in the cell, and stops the cell from dividing until the stress has passed or the DNA is repaired. Humans inherit one copy from each parent, and it has a crucial role in protecting us from cancer. People who have a defective version – a condition called Li-Fraumeni syndrome – usually get cancer in childhood, and their lifetime risk is close to 100 per cent. Read More ›

From obit: Inherent in the idea of gene regulatory networks was the concept that genome sequences that provided information about how genes should be expressed would be as important as the genome sequences that coded for the proteins themselves. Although non-protein-coding DNA was long considered to be “junk,” Davidson recognized that the key regulatory code resided in this genetic material. In 2006, Davidson co-led a group of 240 researchers from more than 70 institutions that sequenced the purple sea urchin’s genome. In 2008, a consortium of institutions led by Davidson’s lab characterized the 23,000 genes of that genome. In parallel, the Davidson group systematically created a comprehensive functional testing strategy to detect all of the control connections between the genes Read More ›

From Quanta Magazine: Emerging data suggests the seemingly impossible — that mysterious new genes arise from “junk” DNA. Genes, like people, have families — lineages that stretch back through time, all the way to a founding member. That ancestor multiplied and spread, morphing a bit with each new iteration. For most of the last 40 years, scientists thought that this was the primary way new genes were born — they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions. Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They’re the Read More ›

Ken Miller is a feted Catholic scientist, friend of Darwinism, and foe of design in nature: From his 1994 textbook: Hundreds of pseudogenes have been discovered in the 1 or 2% of human DNA that has been explored to date, and more are added every month. In fact, the human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. Read More ›

Over at the ID The Future podcast, Casey Luskin has been doing a series on “the top 10 problems with biological and chemical evolution.” Some of the problems he discusses will no doubt be of more interest to certain listeners than to others. However, the segment on junk DNA is particularly worth hearing (about 13 minutes). For those who have been following the debate closely there may not be much new in the segment, but it provides a relatively up-to-date review of some of the recent research, with multiple citations that are useful when talking with a friend or colleague who may still be stuck in the naive and outdated idea that the genome is awash in junk.  Better yet, Read More ›

Which happens purely as a result of natural selection acting on random mutation (Darwinian evolution) building up huge quantities of complex, specified information, of course. Over at Evolution News & Views, Casey Luskin talks about that new book, Junk DNA: A journey through the dark matter of the genome (Nessa Carey), on the newfound functions of junk DNA: A new book from Columbia University Press, Junk DNA: A Journey Through the Dark Matter of the Genome, by virologist Nessa Carey provides a detailed review of the vast evidence being uncovered showing function for “junk DNA.” She explains that junk DNA was initially “dismissed” by biologists because it was thought that if it didn’t code for proteins, it didn’t do anything: Read More ›

Life forms always make sense. Some theories do not. From Phys.org: By sequencing multiple Trichodesmium genomes—and using a wide variety of samples to ensure that there was no error—researchers found that only about 63 percent of the bacteria’s genome is expressed as protein. That’s an incredibly low amount for a bacterium and unheard of for a free-living oligotroph. (lives under very poor conditions, in this case it thrives massively in barren stretches of the ocean) “The unique evolutionary path reflected in this genome contradicts nearly all accounts of free-living microbial genome architectures to date,” said lead author Nathan Walworth, a Ph.D. candidate at USC. “Different evolutionary paths are foundational to all arenas of biology, including biotechnology, so it is important Read More ›

In response to Science writer boilerplate Jonathan Wells writes to say, Based on my reading of thousands of Peer-Reviewed Articles in the professional literature, I’ve distilled a template for writing scientific articles that deal with evolution: 1. Darwinian evolution is a fact. 2. We used [technique(s)] to study [feature(s)] in [name of species], and we unexpectedly found [results inconsistent with Darwinian evolution]. 3. We propose [clever speculations], which might explain why the results appear to conflict with evolutionary theory. 4. We conclude that Darwinian evolution is a fact. Yes, it’s a fact, all right. About the mindset of the people who do that. Wells is the author of The Myth of Junk DNA, which is not short of examples on Read More ›

Not much “junk DNA.” From him: Dan Graur has snarled at the authors of a paper defending ENCODE. How could I then resist? I read the offending paper, and I have to say something that will weaken my own reputation as a snarling attack dog myself: it does make a few good points. But it’s mostly using some valid criticisms to defend an indefensible position. The world yawns and marches on. Friends point out that we do not know anywhere near enough to know what is or is not junk in the geonme, but that under those circumstances, it is wise to assume that any given component is doing something useful. One friend kindly writes to say that the term Read More ›

Further to Junk DNA hires a PR firm (by the time you can’t tell the difference between Darwin’s elite followers and his trolls, you know something is happening): Rob Sheldon writes to say, There may be some very good reasons for onions to have large genomes. Let’s start with an analogy. My son says the computer game “Starcraft” will play on just about any old piece of computer hardware in the house. However, he tells me, when you go to download the game from the website, it takes up 15 GBytes of space. Evidently, in order to be compatible with older hardware, it has to use less CPU power–since the older machines were not as powerful. Much if not most Read More ›

Fights back. Well, that seems to be what’s happening. Further to: New York Times science writer defends junk DNA (Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism), one of the conundrums on which the junk DNA folk rely heavily is the “onion test” (why does the onion have such a large genome?). Without waiting to answer the question, the junk DNA folk assume that that’s because most of it is junk. But let’s face it, when even Francis Collins, the original Christian Nobelist for Darwin, is abandoning ship, they really need to double down on that junk. From Evolution News & Views: What’s so striking about Zimmer’s Read More ›

Worries Carl Zimmer, a “No junk DNA” scenario could help creationists: It’s no coincidence, researchers like Gregory argue, that bona fide creationists have used recent changes in the thinking about junk DNA to try to turn back the clock to the days before Darwin. Zimmer is responding to the recent realization that there is very little junk DNA, and is apparently refurbishing and remarketing the concept, invoking of course the Sacred Name of Darwin: The human genome contains around 20,000 genes, that is, the stretches of DNA that encode proteins. But these genes account for only about 1.2 percent of the total genome. The other 98.8 percent is known as noncoding DNA. Gregory believes that while some noncoding DNA is Read More ›