Predictions, predictions: ID predicts overlapping codes, Darwinism predicts “junk DNA”

_{Denyse O'Leary

January 8, 2020

'Junk DNA', Genetics, Information, Intelligent Design}

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Overlapping genes, or “nested coding,” was anticipated by microbiologist Siegfried Scherer, as Meyer points out. Why? Because human coders layer codes on top of codes, for various reasons including improved storage. Therefore a designing agent, operating behind the veil of biology, would likely do so as well. And so it is.
David Klinghoffer, “Meyer on “Nested Coding”: Another Successful Design Prediction” at Evolution News and Science Today

And, as Klinghoffer reminds us, the Darwinists predicted lots of “junk DNA,” mindless and meaningless evolution’s scrap heap.

Hat tip: Philip Cunningham

Comments

Thanks Larry- Pretty much what we would expect from genetic entropy starting from very good source populations. And pretty much the extent of what blind and mindless processes are capable of.ET_{January 8, 2020
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For anyone who's interested in reading a discussion of pseudogenes from someone who's a little better qualified there's this piece from Larry Moran's blog "Sandwalk". As a taster:
There are many junk DNA skeptics who claim that most of our genome is functional. Some of them have even questioned whether pseudogenes are mostly junk. The latest challenge comes from a recent review in Nature Reviews: Genetics where the authors try to place the burden of proof on those who say that pseudogenes are broken, nonfunctional, genes (Cheetam et al., 2019). The authors of the review try to make the case that we should not label a DNA sequence as a pseudogene until we can prove that it is truly nonfunctional junk. I'm about to refute this ridiculous stance but first we need a little background. What is a pseudogene? The traditional definition of a pseudogene is a DNA sequence that resembles a known gene except that it carries mutations making it nonfunctional [Different kinds of pseudogenes - are they really pseudogenes?]. There are four types of pseudogenes but the two main classes are processed pseudogenes that arise from cDNA copies of functional RNA and duplicated pseudogenes that arise from a gene duplication event followed by inactivation of one of the copies. The formation of a pseudogene from a duplication event is part of the well-studied birth & death evolution of genes where death by inactivation or deletion is the most common fate [On the evolution of duplicated genes: subfunctionalization vs neofunctionalization] [Birth and death of genes in a hybrid frog genome]. The idea that most duplicated genes will become pseudogenes is consistent with a ton of data and fits well with our understanding of mutation rates and genome evolution. This is an important point. We don't arbitrarily assign the word "pseudogene" to any old DNA sequence. The designation is based on the fact that the duplicated region is no longer transcribed, or it is no longer correctly spliced, or that it carries mutations rendering the product nonfunctional. (In the case of protein-coding genes it could be that the reading frame is disrupted.) It's also important to understand that the frequency these inactivating mutations and the rate of fixation of the resulting allele is perfectly consistent with everything we know about molecular evolution.
He also discusses functionality:
Are most pseudogenes functional? All of these functions have caused some workers to question the very existence of pseudogenes and there are many papers in the literature implying that most pseudogenes aren't pseudogenes at all. One of the common characteristics of these papers is a lack of critical thinking and skepticism. Very few of them even mention the possibility that they could be looking at spurious transcripts and/or interactions that are not biologically significant. Here are some examples … Balakirev, E.S., and Ayala, F.J. (2003) Pseudogenes: are they “junk” or functional DNA? Annual review of genetics, 37:123-151. [doi: 10.1146/annurev.genet.37.040103.103949] Milligan, M.J., and Lipovich, L. (2015) Pseudogene-derived lncRNAs: emerging regulators of gene expression. Frontiers in genetics, 5:476. [doi: 10.3389/fgene.2014.00476] Xu, J., and Zhang, J. (2015) Are human translated pseudogenes functional? Molecular Biology and Evolution, 33:755-760 [doi: 10.1093/molbev/msv268] Wen, Y.-Z., Zheng, L.-L., Qu, L.-H., Ayala, F. J., and Lun, Z.-R. (2012) Pseudogenes are not pseudo any more. RNA biology, 9:27-32. [doi: 10.4161/rna.9.1.18277] Johnsson, P., Morris, K.V., and Grandér, D. (2014) Chapter 14: Pseudogenes: a novel source of trans-acting antisense RNAs Pseudogenes (pp. 213-226): Springer. Pink, R.C., Wicks, K., Caley, D.P., Punch, E.K., Jacobs, L., and Carter, D.R.F. (2011) Pseudogenes: pseudo-functional or key regulators in health and disease? Rna, 17:792-798. [doi: 10.1261/rna.2658311] The question is not whether some DNA regions that look like pseudogenes have a function. This is a fact. The real question is whether these regions are exceptions to the general rule that a pseudogene is a pseudogene or whether most pseudogenes have been mislabeled. To me, it seems almost irrational to assume that most pseudogenes are actually functional DNA segments because the direct and circumstantial evidence for junk is very strong.
Seversky_{January 8, 2020
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PaV Interesting item. "Darwin did it" is the real science stopper. Also, Bob O'H questioned you on post #36 on this thread: https://uncommondescent.com/intelligent-design/at-the-scientist-junk-rna-is-top-science-news-in-2019/Silver Asiatic_{January 8, 2020
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Ed:
In fact, many “Darwinists” predict that junk DNA would be weeded out.
That doesn't follow from any of their claims. It's only that which causes the organism or population to be less fit that gets weeded out. So what Darwinists predicted that, Ed? Any references?ET_{January 8, 2020
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SA: Along the lines of your quote, over at Evolution and New. Org, they have an article on "pseudogenes." Psuedogenes are what make the Darwinist trope seemingly work: i.e., genes are duplicated and mutate, thus forming 'pseudogenes.' These, then, are 'recruited'--perhaps the word Darwinists will use is 'exapted,' (Darwinists would be lost without a compendium of words enshrining their thinking--but not necessarily reality). And new genes are formed---eventually. However, if pseudogenes--which in mammals are somewhat abundant, have a function, then what? You'll probably be interested in reading the whole post over at EN. Here's one small part:
[T]he term pseudogene itself asserts a paradigm of non-functionality through its taxonomic construction. Pseudogenes are defined as defective and not genes. This point is highlighted because impartial language in science is known to inherently restrict the neutral investigation between conflicting paradigms. In the case of pseudogenes, the term itself is constructed to support the dominant paradigm and therefore limit, consciously or unconsciously, scientific objectivity in their investigation.
Ten years ago, or so, I argued that eventually science would get things right, but that in the meantime Darwinist ideology would interfere in this needed process of discovery, and that its tenets only served to slow down the whole process. How ironic: the article at EvolutionNews.Org tells us that the needed "motivation" to search for 'function' in these putative "pseudogenes" was LOST because of the simplistic Darwinian classification of so much of the genome. ID is criticized by Darwinists in this way: "Oh, God did it! End of story. So, ID is nothing more than a 'science stopper.'" Well, guess what? We're learning that it is Darwnism that is the real 'science stopper,' and its been at it for over 150 years. [Gone Gofling for the Day!!]PaV_{January 8, 2020
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And, as Klinghoffer reminds us, the Darwinists predicted lots of “junk DNA,” mindless and meaningless evolution’s scrap heap.
In fact, many "Darwinists" predict that junk DNA would be weeded out.Ed George_{January 8, 2020
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PaV - thanks, that is helpful. Bob O'H engaged in some hair-splitting by trying to say, basically, that no evolutionists thought that Junk DNA had "no function". I cited Ohno's paper (and his comments) and Bob's response was that he Ohno thought NC DNA had "some function". Bob never accepted (or it seemed) that the evolutionary consensus for at least a couple of decades was that there was virtually no function and it was Junk. The Scientific American article you quoted offers this also:
Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression.
See that, Bob? Is that a pro-ID bias in Scientific American? I don't think so. Notice, the term "repelled" research and study. Evolutionary theory could have killed off progress. It wasn't until the 1990s that the view "began to change".
But here at UD, we have a long memory.
That is greatly appreciated because Bob O'H decided to try some historical revisionism and pretend that nobody actually considered Non-coding DNA to be non-functional (genomic garbage). I hope Bob is reading this.Silver Asiatic_{January 8, 2020
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SilverAsiatic: This is from 12 years ago. So, for example:
In humans, for example, only about 2 percent of DNA actually codes for proteins. For decades, scientists were puzzled by this phenomenon. With no obvious function, the noncoding portion of a genome was declared useless or sometimes called "selfish DNA," existing only for itself without contributing to an organism's fitness. In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.
As science progressed, and non-coding DNA was more and more seen as 'functional,' the tune that the Darwinists sung began to change. But here at UD, we have a long memory.PaV_{January 8, 2020
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the Darwinists predicted lots of “junk DNA,” mindless and meaningless evolution’s scrap heap
Bob O'H claims that's not the case and that the prediction was that Junk DNA was functional, so there's no problem here at all - supposedly. But then why the term "Junk"? That was intended to signify that non-coding regions had "important functions"?Silver Asiatic_{January 8, 2020
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