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New genes come from junk DNA?

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Further to “Linc RNA–once believed useless–plays a role in the genome, here is some interesting research on fruit flies:

From ScienceDaily:

Geneticists have long puzzled about how completely new genes appear. In a well-known model proposed by Nobel laureate Susumu Ohno, new functions appear when existing genes are duplicated and then diverge in function. Begun’s laboratory discovered a few years ago that new genes could also appear from previously non-coding stretches of DNA, and similar effects have since been discovered in other animals and plants.

“This is the first example of totally new genes still spreading through a species,” said Li Zhao, a postdoctoral researcher at UC Davis and first author on the paper.

from The Scientist:

“Until recently, de novo origin of genes was considered to be so unlikely as to be impossible,” comparative genomicist Aoife McLysaght of the Smurfit Institute of Genetics at Trinity College in Dublin, Ireland, who was not involved in the study, told The Scientist in an e-mail. “[T]his population level analysis is important because it gives a new insight into the very early stages of the origin and establishment of genes de novo.”

“To show [the formation of de novo genes] at the population genetics level is really a nice story,” agreed evolutionary biologist Diethard Tautz of the Max Planck Institute for Evolutionary Biology in Plön, Germany, who also did not participate in the research. “It shows the power of generating from nothing, so to speak.”

First, it’s junk. Now it’s “nothing.”

See also:What? Darwin’s followers did not use junk DNA as an argument for their position? Of course they did. It would have been a slam dunk, if their position were correct.

Comments
Lincoln, Are you seriously going to claim that evolutionists have not been saying for years (including many of the leading figures in American culture)that junk DNA is a prediction of Darwinian evolution, and that if the there really is no junk DNA than then this is a big problem for the theory? Let me make sure you want to stand firmly behind that statement, and don't go running off and claim you are not saying that when you are proven wrong.phoodoo
January 24, 2014
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This isn't that new, see On the origin of new genes in Drosophila by Zhou Q et al Genome Res. 2008;18:1446–1455 etc etc ad nauseum. This work has been going on for years. Still quite funny how the claims about "junk DNA" raise their head again. Does anyone use that term other than ID theorists and creationists when discussing genetics ? In the end it isn't very good for ID. The only argument ID have is it can't be done with a random search of all the space. But stored and forwarded copies with changes means that there exists mechanistic (spontaneous i.e. no ID) mechanisms for copying genes and there exists mechanistic (spontaneous i.e. no ID) mechanisms for mutations and there exists a mechanistic (spontaneous i.e. no ID) mechanisms for selection (i.e. natural selection). ID theorists claim that random searches are impossible (and that's a fact which also brutal for a "designer" unless it is outside of our spacetime) but the copy and mutate with natural selection is a biased random walk. Whilst biased random walks have no guarantee of success (and neither does the random search that is so loved by ID theorists when constructing their arguments about how nature doesn't work) the time is vastly reduced from brute force. What people forget is that we're not looking for an EXACT match but a just-good-enough. This is a significant point that dramatically changes the problem landscape. If you are brute forcing a software key then you need an EXACT match but given isoforms exist then clearly an exact match is not a requirement for nature. How good is good-enough ? NO one knows. ID theorists don't know though they seem to be demanding exact matches. A biased random walk must have "islands" of fitness. Why ? Well for a sequence to be naturally selected it must be fitter in some way that other combinations.If the distance between islands of fitness is too great (the worse case is to have only ONE fit solution), then the time complexity of O(c^n) is a brutal barrier to success. In effect the near impossibility of a solution becomes a natural selector in that nature randomly discovers the advantages of dynamic programming.Lincoln Phipps
January 24, 2014
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An aha moment- thanks bornagain77...Joe
January 24, 2014
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Hate to burst you guys bubble, but they have not actually demonstrated that a functional protein/gene can arise from non-coding sequences, they merely hypothesize that the similar sequences they found in non-coding regions,,, "gives a new insight into the very early stages of the origin and establishment of genes de novo.” Personally, I certainly would not put any stock whatsoever into this since they merely believe that the similar sequences they found 'gives insight' into how evolution happene9d because of course, in their Darwinian worldview, IT MUST have evolved. There is no other option for them! In other words, There is no actual empirical evidence that sequences that not currently code for proteins will magically start coding for proteins in the future. In fact, This study is another example of how Darwinian presupposition constantly mislead science down rabbit trails!bornagain77
January 24, 2014
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New genes can arise from non-coding sequences by design. THat is exactly what I was trying to tell wd400 earlier, in another thread. The alleged junk DNA is there for future considerations, sort of like a stock room with parts ready for assembly and use. Also, as Dr Spetner pointed out, there is no reason to say that gene duplications are a Darwinian mechanism. IOW if Darwinism/ neo-darwinism wants to call on point mutations for the source of variation, they are welcome to it. All other genetic changes have to first be demonstrated to be happenstance/ accidents as opposed to just baldly declaring them to be.Joe
January 24, 2014
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#7 "This is exactly what I have always stated here. New genes are intelligently engineered as non coding sequences, and when they are functional they are released as coding sequences." That's what James Shapiro calls "natural genetic engineering." Unfortunately, the present ID is being derailed and mislead by the consciousness-talk and super-naturalism (heavenly interventions overriding natural laws), micro vs macro evolution, natural vs ???, the absurd part-time intelligent agency helping out when the "nature" can't do it... from Discovery Institute and their choir. As result, thanks chiefly to DI, this whole field of cellular intelligence, natural genetic engineering, cellular biochemical networks as self-programming distributed computers which are the intelligence behind the design of evolutionary novelty, etc, has been and will continue to be claimed by neo-Darwinists as what they were always saying, as they gradually phase out the "random mutation" from their story and morph it into whatever the latest findings come out in these fields.nightlight
January 24, 2014
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wd400:
I’m not sure it’s good news for your side that new genes can arise from junk sequences, though…
It is extremely good news for our side. This is exactly what I have always stated here. New genes are intelligently engineered as non coding sequences, and when they are functional they are released as coding sequences. That simply means that NS has no role in engineering new genes (it can simply act in fixing them once they are ready). That simply means that new genes are either generated by a merely random search (which is practically impossible) or that they are designed. That simply means that "our side" is right. :)gpuccio
January 24, 2014
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The vehicle of a friend of mine broke down on a lonely road in Alaska. The hose going to his cabin heater broke, destroying the integrity of his car's cooling system. He left his car, and began walking up the road to pray. There, laying on the side of the road was the correct hose, cut to the correct length, with the needed hose clamps. He, an air conditioning engineer, was able to permanently repair his vehicle. Darwinists say, "accidents happen". He calls it a miracle.Moose Dr
January 23, 2014
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Funny how all these comparative genomic studies, (i.e. seeing faces in the clouds studies :) , which are always done by Darwinists with Darwinian assumptions of course, the studies always seem to support Darwinian evolution, but when push comes to shove in actually demonstrating in the lab that Darwinian evolution is feasible, then their stories always falls completely apart. For instance in fruit flies, the species they considered in their comparative analysis, we find such examples against Darwinism as the following,,,
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://eebweb.arizona.edu/nachman/Suggested%20Papers/Lab%20papers%20fall%202010/Burke_et_al_2010.pdf Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html ...Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells Fruit fly with the wings of beauty - July 2012 Excerpt: But a closer examination of the transparent wings of Goniurellia tridens reveals a piece of evolutionary(?) art. Each wing carries a precisely detailed image of an ant-like insect, complete with six legs, two antennae, a head, thorax and tapered abdomen. http://www.thenational.ae/news/uae-news/science/fruit-fly-with-the-wings-of-beauty 'No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution' – Jonathan Wells 50 million year old Fruit Fly fossil compared to modern Fruit Fly - picture http://en.harunyahya.net/fruit-fly-fossils-creation-museum/ Seeing the Natural World With a Physicist’s Lens - November 2010 Excerpt: Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them;,, the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head;,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. per NY Times Development of a fly embryo in real time - video http://www.youtube.com/watch?v=OQ86d9sTeaQ Criticality in morphogenesis - September 17, 2013 Excerpt: In many regards, a brief time-lapse video can teach more about embryonic development than any amount of reading. It is hard not to be impressed how a repeatable form reliably emerges despite considerable variation in both genes and environment. While it had been hoped that concepts borrowed from statistical mechanics or the ideas of self-organized criticality could help to create some kind of physics-based theory of development, much of what has been done lies only at the level of metaphor. In a paper just released to ArXiv, William Bialek and his colleagues from Princeton University, have taken their search for the signature of criticality in a more specific direction. They looked at a particular set of transcription factors in Drosophila embryos which control spatiotemporal development. By analyzing fluctuations in the expression levels of these so-called gap genes, they found evidence for critical (fine) tuning in this particular network. http://phys.org/news/2013-09-criticality-morphogenesis.html "The brain of a small fruit fly uses energy in the micro-watts for complex flight control and visual information processing to find and fly to food. I don't think a supercomputer could yet simulate what the fruit fly brain does even while using megawatts of energy. The difference of over ten orders of magnitude and the level of energy used is an indication of just how incredible biological systems are. Professor Keiichi Namba, Osaka University http://www.youtube.com/watch?feature=player_detailpage&v=uw0-MHI_248#t=1645s TEDx Video: Flight of the Fruit Fly - October 8, 2013 Excerpt: "Dickinson is a very intense guy himself, and gives a remarkable discussion of what makes the engineering that goes into fruit fly flight so amazing." (4:50 minute mark of video lists several fascinating high tech 'accessories' of the fruit fly, such as a gyroscope) http://www.evolutionnews.org/2013/10/video_flight_of077641.html
bornagain77
January 23, 2014
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Mapou, You should read Ohno, or perhaps read up about neofunctionalization which is the model of gene evolution that Ohno proposed.wd400
January 23, 2014
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Anytime someone told you gene duplication was thought to be the major driver of new gene function they were also implying that the de novo origin of genes from junk DNA was unlikely. I'm not sure it's good news for your side that new genes can arise from junk sequences, though...wd400
January 23, 2014
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ScienceDaily:
In a well-known model proposed by Nobel laureate Susumu Ohno, new functions appear when existing genes are duplicated and then diverge in function.
How does anybody conclude from this that new genes are created? Copying an existing gene and mutating it is not the same as creating a new gene with a novel functionality. Sorry. It's just a variant of an old gene. Besides, how did this gene creation capability evolve? How does an organism know what kind of new gene is needed? This has DESIGN written all over it.Mapou
January 23, 2014
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“Until recently, de novo origin of genes was considered to be so unlikely as to be impossible,” comparative genomicist Aoife McLysaght of the Smurfit Institute of Genetics at Trinity College in Dublin, Ireland, who was not involved in the study, told The Scientist in an e-mail.
Is that right? How come we only find out about these problems when they are "solved"? Now that they think they have an answer they are willing to admit that they didn't know the answer up until now. But that's not what they taught us in school! Does anyone remember being told by scientists that the Darwinian evolutionary de novo origin of genes was thought to be virtually impossible up until now? This is the kind of honesty that IDers and creationists want to see in the science books!!! And, not only when they think they have an answer, even before they have the answer. But I guess this kind of brutal honesty is just not possible for them. They fear the mileage that their opponents will get from it so instead of being honest, they make bold claims and state that evolution is a fact. Anyone smell a rat here? I don't know enough about this claim to evaluate it properly, but my guess is that it still doesn't solve their problem.tjguy
January 23, 2014
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