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Can new genes arise from junk DNA?

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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 molecular equivalent of a mysterious beast discovered in the depths of a remote rainforest, a biological enigma seemingly unrelated to anything else on earth.

The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of so-called junk DNA, or non-coding DNA, the mysterious stretches of DNA between genes. “Genetic function somehow springs into existence,” said David Begun, a biologist at the University of California, Davis. More.

Hmmm. Whenever scientists use terms like “somehow springs into existence,” find your boots, your bicycle lock key, or your car keys.

But this is a good conversation to be having.

Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.

Evolution isn’t what we used to think.

See also: The Myth of Junk DNA

and

Talk to the fossils: Let’s see what they say back.

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Comments
Darwinists are not just mentally ill, they're cowards to boot. Yellow fruitcakes. :-DMapou
August 27, 2015
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Wow, you guys have really lost it... Box, yes, I forgot about your peculiar misunderstanding about natural selection. Leaving that aside, it is true that selection only works on a sequence once it exists. But if de novo genes are not common then then the origin of new functiona sequences from junk DNA can be an exceedingly rare event and still provide us will all the superfamalies we know about. EugeneS, There is no reason to think cells make decisions in the way you describe. If you drop an engineered gene into a genome with the right promoter sequence to express in , say, kidney epithelial cells, it will express that gene in kidney epithelial cell. It's just biochemistry. SA, Nope. I literally can't see anything in there that relate s to anything I've said.wd400
August 27, 2015
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Innovate or Die. Nature is innovative in tooth & claw & feather & thumb. How does the innovation emerge? It's either a random walk in the park, or a guided one. The park sure looks designed though. Mountains of evidence on that design.ppolish
August 27, 2015
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Box - True. In the end, the challenge to explain function got more difficult, not easier.Silver Asiatic
August 27, 2015
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Silver: The idea is “things happened, therefore evolution caused them”. We see a huge space for random search, but this is supposedly not a problem because “it must be easier to find function than we thought”. Proof? “Obviously, evolution already found lots of function”. If there were a a hundred billion different species, this would mean “it’s even easier for evolution find function”.
Indeed. If there were so staggeringly many different species — 99.9% went extinct (the countless posited "intermediate forms") and a multitude of viable organisms that were never allowed to prosper because NS eliminated them for whatever reason — it has to be rather easy to find new biological function. Hence my question to WD400. How can his position allow for the belief that it would be difficult to find biological function in sequence space? IMO he — as a true Darwinian — is compelled to hold the belief that finding biological function is a walk in the park. Which is, needless to say, absurd.Box
August 27, 2015
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The idea is "things happened, therefore evolution caused them". We see a huge space for random search, but this is supposedly not a problem because "it must be easier to find function than we thought". Proof? "Obviously, evolution already found lots of function". If there were a a hundred billion different species, this would mean "it's even easier for evolution find function". Then we have the theory itself, which "predicts what happened in history by adjusting itself to new observations". My New Ultimate Theory (NUT) is that the entire cosmos is made from blue plastic. Proof? Here's some blue plastic. See? The NUT is validated! Look, the sky is blue - it's probably plastic. The NUT wins again! Wait, this thing is yellow. No problem! The NUT accommodates that. Yellow is a color and so is blue. Hey, this other thing is not plastic. Well, now we have the neo-NUT. Same theory, of course. It states: "The entire cosmos is made from something with some kind of color or not, which might or not be plastic." The Root core of the New Ultimate Theory always stands, everybody accepts it: "The entire cosmos is." Only an Idiot would deny that. Everything else is just incidental detail, subject to change. That's just the way science works. :-)Silver Asiatic
August 27, 2015
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WD400, "Why? I honestly can’t work out why someone would think this. I mean, that 99% of species are dead tells you that there are lots of ways to be alive, it doesn’t tell you anything about how many ways there are to not be alive, does it?" Another example of quasi-scientific equivocation. "Many", "a lot", "lots of". Any living system is a functional hierarchically organized whole. The fact that living organisms die out is irrelevant to the question of biological function. You guys need to show how biological functionality, which is in its essence decision making, arises without recourse to decision making. Random shuffling, gene duplication etc are biological functions themselves. I.e. all this is used in a context of decision making. The cell decides to do something. The simple yet profound intuition behind this is that the cell is doing it for a reason. BTW, this kind of intuition is traditional in science. All this glaringly intelligent behaviour cannot just emerge simply by virtue of replication errors and a coarse grained filter of natural selection. On the contrary, it must be loaded. Natural selection cannot decide, nor can random variation, nor can their combination. Law and Chance are not up to the task of explaining the presence of Logic that uses Law and Chance in order to achieve utility. The biggest challenge for you guys is to explain naturalistically the emergence of decision making in the living organisms. There is no such explanation available so far, only question begging.EugeneS
August 27, 2015
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WD400: I think biologically functional sequences don’t arise from one-of random sampling sequence space but by natural selection (...).
How? A la Dawkins Weasel? Natural selection needs biologically functional sequences in order to have something to select on. It doesn't make sense to say that natural selection produces biologically functional sequences. Natural selection produces zero information — instead it subtracts massive amounts of information.Box
August 27, 2015
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@75 My challenge still stands. Anybody? It all comes down to whether you got gonads or not. And if you don't, can you grow a pair? Wussies. ahahaha...Mapou
August 26, 2015
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The average size of the nucleotide search space for a single human gene is:
4^23000 !!!!!
I claim that this kills Darwinism dead, period. Can any Darwinist here gather enough gonads to refute this claim? Or are you all a bunch of wussies? And BTW, materialist abiogenesis never even made it to the gates. ahahaha...Mapou
August 26, 2015
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DNA far outclasses anything man has ever created in terms of its ability to store information.
DNA: The Ultimate Hard Drive - Science Magazine, August-16-2012 Excerpt: "When it comes to storing information, hard drives don't hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare." http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html Information Storage in DNA by Wyss Institute - video https://vimeo.com/47615970 Quote from preceding video: "The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA." Sriram Kosuri PhD. - Wyss Institute
Moreover, from just barely starting to scratch the surface of the encoding that is written on DNA, it is discovered that there are multiple layers of overlapping coding on DNA that far, far, outclasses anything man has ever programmed.
Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://www.youtube.com/watch?v=fDB3fMCfk0E In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark): "Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010 'It's becoming extremely problematic to explain how the genome could arise and how these multiple levels of overlapping information could arise, since our best computer programmers can't even conceive of overlapping codes. The genome dwarfs all of the computer information technology that man has developed. So I think that it is very problematic to imagine how you can achieve that through random changes in the code.,,, and there is no Junk DNA in these codes. More and more the genome looks likes a super-super set of programs.,, More and more it looks like top down design and not just bottom up chance discovery of making complex systems.' - Dr. John Sanford - Inventor of the ‘Gene Gun’ - 31 second mark - video http://www.youtube.com/watch?feature=player_detailpage&v=YemLbrCdM_s#t=31s Jeffrey Tomkins, Ph.D., Duons: Parallel Gene Code Defies Evolution, January 6, 2014 Excerpt: The human mind struggles to comprehend the overall complexity of the genetic code—especially the emerging evidence showing that some genes have sections that can be read both forward and backward.3 Some genes overlap parts of other gene in the genome, and now it has been revealed that many genes have areas that contain dual codes within the very same sequence. Even the most advanced computer programmers can’t come close to matching the genetic code’s incredible information density and bewildering complexity. http://www.icr.org/article/7870/
Moreover, the 3-D fractal global architecture present in DNA operation and repair processes would make any computer engineer drool with envy.
3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. per Science Daily
Moreover, bacteria have been shown to reconstruct their own genome after it has been blown to pieces by radiation.
Extreme Genome Repair - 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/ In the lab, scientists coax E. coli to resist radiation damage - March 17, 2014 Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. "We blasted the cultures until 99 percent of the bacteria were dead. Then we'd grow up the survivors and blast them again. We did that twenty times," explains Cox. The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human. http://www.news.wisc.edu/22641 Pond scum smashes genome into over 225k parts, then rebuilds it - Sept. 9, 2014 Excerpt: The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it’s time to mate, https://uncommondescent.com/intelligent-design/pond-scum-smashes-genome-into-over-225k-parts-then-rebuilds-it/
Imagine your computer breaking its hard drive into a quarter million pieces and then putting it back together again. That would be roughly similar to what is happening here. Needless to say, no computer in the world is even close to reconstructing its own hard drive. And yet, despite all this unfathomed complexity being discovered in DNA that our best engineers have not even come close to imitating, wd400 has the sheer audacity to claim, not only that unguided material processes put that unfathomed complexity together, but that the vast majority of information on DNA must be junk. :) For wd400 to state such a thing would be absolutely hilarious for me, instead of just mildly humorous, if it were not for the dire consequences implicit for wd400 in wd400 resolutely setting himself against God as he has apparently chosen to do,,, even to the point of making himself look completely ridiculous by stating such obvious, and over the top, lies about the actual state of the evidence for obvious widespread DNA multi-functionality. Verse:
Romans 1:25 for that they exchanged the truth of God for a lie,,,,
bornagain77
August 26, 2015
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wd400, "The meme that ENCODE proved 80% of the genome has function is, I’m afraid, just rubbish." You got the meme from me? I said, "encode project suggests". They certainly did make that suggestion. They did not provide proof.bFast
August 26, 2015
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I really don't see what any of that has to do with extinct species. My comment simply meant that if do novo genes are common then in suggests that biological function is so dense in the sequence space that random streches of intergenic DNA might fall in to them. I don't think biological function is quite that easy to come by (or at least no the funcions we generally asociated with proteins). Instead I think biologically functional sequences don't arise from one-of random sampling sequence space but by natural selection (and gene duplication and exon shuffling and all that).wd400
August 26, 2015
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WD400:
Box: Seems to me that this [99.9% of all species that have ever lived on Earth are now extinct] shows that in fact a staggering amount of biological function has been found in sequence space.
Why? I honestly can’t work out why someone would think this.
Do you really ask "why?"? You amaze me.
WD400: I mean, that 99% of species are dead tells you that there are lots of ways to be alive, (...)
More precisely, it tells us that "a lot of biological function has been found in sequence space", exactly what I said. Just think of all the intermediate forms — that have never been found ...
WD400: (...) it doesn’t tell you anything about how many ways there are to not be alive, does it?
No, but did I or anyone else even hint at the possibility that it does? And how is this relevant? I sincerely hope that you are not suggesting that there are not many ways of being dead so that therefor the amount of biological function that has been found cannot be said to be "staggering". Suggesting that would be utter madness. Again, lots of biological function has been found in sequence space, now my question is: how does that square with your belief that it is so difficult to find?Box
August 26, 2015
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Describe a formal test that intelligent design in biology.
Rec, it is not difficult to give you such a test, the question is: "Why are you asking?" It is certainly the case that you will never accept the test, nor the results. You will make pointless objections here and lodge irrelevant complaints there - but hell will freeze over before you accept the outcome of a purely empirical test of design in biology. So why even ask? What do you gain by the charade?Upright BiPed
August 26, 2015
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Seems to me that this shows that in fact a staggering amount of biological function has been found in sequence space .
Why? I honestly can't work out why someone would think this. I mean, that 99% of species are dead tells you that there are lots of ways to be alive, it doesn't tell you anything about how many ways there are to not be alive, does it?
My question about regulation was: How do we get to a regulatory system given that a novel gene arises from junk-DNA. How do you envision the steps towards a (novel) regulatory system?
I explained one way -- an element with it's own cis-regulatroy sequences integrates alongside. That way you get expression down stream. Because expression also depends on DNA accessibility and methylation state you end up with tissue-specific expression too.wd400
August 26, 2015
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WD400: I have no clue how you think the two statements above relate to each other, so can’t answer you question.
Really? Let me spell it out for you: If you guys thought that biological function is difficult to find in sequence space, how does that add up with the tremendous amount of species that once roamed the Earth - 99.9% of all species that have ever lived on Earth are now extinct. Seems to me that this shows that in fact a staggering amount of biological function has been found in sequence space and therefor there is no room for the (correct) belief that biological function is difficult to find in sequence space.
WD400: For your question about regulation, for the de novo genes we atually know about (the SMBE talk is not published so I don’t know if the same applies to these) it’s the onset of expression that marks the “birth” of the gene (...)
Unresponsive. Maybe I wasn't clear here also ... My question about regulation was: How do we get to a regulatory system given that a novel gene arises from junk-DNA. How do you envision the steps towards a (novel) regulatory system? 1. We have a novel gene. 2. ... 3. ... ..... ... now we also have a regulatory system.Box
August 26, 2015
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"The meme that ENCODE proved 80% of the genome has function is, I’m afraid, just rubbish. Even the ENCODE group don’t make that claim." Even memes of rubbish serve a purpose WD400. Kind of like junk DNA.ppolish
August 26, 2015
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Notice how the dirt worshippers steer away from the argument that a search space as large as 4^23000 (the search space for a single gene!) kills Darwinism dead? They have no answer to this simple yet devastating argument against their little dirt-worshipping religion. And you know why? They are morons and liars. That's why.Mapou
August 26, 2015
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JDD, The questoin was wetherde novo genes are generally involved in important processes. Of course some non-conserved sequences will be involved in in biologically important process (but even they will be conserved at a population level if their function is sequence related). bFast, "and nothing else" only meant that using only phylogenetic data was helpful. There are other measures that also include biochemistry or population diversity data, which are would be "conservation and some other stuff". The meme that ENCODE proved 80% of the genome has function is, I'm afraid, just rubbish. Even the ENCODE group don't make that claim.wd400
August 26, 2015
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REC, What kind of falsification are you talking about? The origin of life is a one-off event in the natural history of the Earth. Whatever the explanation, it is a matter of plausibility and inference that best fits the available data, not a matter of falsifiability as such. It cannot be falsified in the sense you imply because it was a singular event. The more science progresses, the more data will fit into the design explanatory mode. However, there will always be a loop-hole for believers in fluctuations and frozen accidents just because it was a singular event, despite all the evidence to the contrary: organisms being decision making systems may only have appeared as a result of decision making and nothing else.EugeneS
August 26, 2015
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wd400, "To be clear, I meant by “phylogenetic conservation and nothing else” I mean..." So you are taking back the "and nothing else" part then? Good, it needs to be gone. There certainly is some value in conservation analysis. We, over here, think its a lot less valuable than it is made out to be. ('Seems that phylogenetic conservation confirms value to less than 10% of human dna, when the analysis done by the encode project suggests the number is more like 80%) However, I think that phylogenetic conservation is pretty much useless when analyzing de novo genes, as there is virtually no history to analyze for conservation. wd400, "Then we’ll be able to start testing ideas about their origin." Good. Please test the theory! In the mean time please don't inform me and mine that the theory is as clearly established as gravity.bFast
August 26, 2015
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wd400 - this is where the deception comes in, when it is stated in such a way that conserved sequences are important to infer that if there is a lack of phylogenetic conservation it must not be functionally important. This line of thinking has polluted modem science and is false for 2 reasons: 1) as above, non-conserved proteins demonstrate functional necessity 2) only ~2% of the genome is protein coding yet there is more functional sequence that is non-codingthan thrthere is protein coding (so homology of 2% doesn't say much tbh). No one denies that if something shows conservation it is likely to be of functional importance. However what is contended is that there are also non-conserved sequences which exhibit very important functions (often overlooked because...They are not conserved!). REC - you do realise many IDers are successful scientists with peer reviewed publications and fully understand how science works, don't you?Dr JDD
August 26, 2015
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REC, "Describe a formal test that intelligent design in biology." Begone with your "my theory is better than your theory" argument. It is stupid! Your theory must stand or fall, on its own, against the data. Why bother with a theory that doesn't fit the facts? Because it is better than the other guy's theory (a theory that you are determined not to understand)? The principle of falsification does not require an alternative theory -- period.bFast
August 26, 2015
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"Describe a formal test that intelligent design in biology." How about "appearance of design". Mountains of evidence for "appearance". Algorithm of Appearance of Design. Appearance lol:) https://m.youtube.com/watch?v=Yn_Xarm6Rj8ppolish
August 26, 2015
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To wd400 and REC et al. You people are traitors to your own species. You are the scum of the earth, AFAIC.Mapou
August 26, 2015
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REC:
Describe a formal test that intelligent design in biology.
Here are 4 predictions of intelligent design: 1. The species are organized in a mostly nested hierarchy (i.e., there are many instances of HGT). 2. De novo genes are everywhere. 3. There is no such thing as junk DNA. 4. The genome is organized hierarchically. Falsify those, Mr. Dirt worshipper. And don't bother telling us when you're done. We don't care.
It is cute watching IDers, who generally haven’t a clue about what scientists do, moan over the mangled secondhand bits “news” harvests from other science writers.
You can pack your science up you know where. A stochastic search mechanism (e.g., RM+NS) is useless against a search space as huge as 4^23000, the search space for a single gene. RM+NS is a stupid idea in the bozo category. You people are not scientists. You are all a bunch of freaking morons. Your time in the sun is almost at an end. Wait for it. ahahaha...Mapou
August 26, 2015
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bfast- "Proper science: oh, unexpected data. Here’s a possible explanation. Lets test the explanation to see whether it holds water." Describe a formal test that intelligent design in biology. It is cute watching IDers, who generally haven't a clue about what scientists do, moan over the mangled secondhand bits "news" harvests from other science writers.REC
August 26, 2015
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wd400:
Then we’ll be able to start testing ideas about their origin.
Ha! What possible ideas could you have that do not do away with the Darwinian stochastic search mechanism? Why are you people so dishonest with yourselves and everyone else? The religious fervor of your conviction is duly noted. The end soon cometh. And sooner than y'all think. Wait for it. I've said it before. I'll be watching the whole thing unravel with a beer in one hand, a bag of Cheetos in the other and a smirk on my face. ahahaha...AHAHAHA...ahahaha... PS. I think I'll add a Havana cigar into the mix for good measure. ahahaha...Mapou
August 26, 2015
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Balderdash! That is Darwinistic theory driving research...
To be clear, I meant by "phylogenetic conservation and nothing else" I mean if all you know about a given site in a given protein is how conserved it is, that is a pretty good predictor of how important the site is. That's the basis of scores like SIFT and PolyPhen which are used in labs to predict the severity of mutations every day.
Your method of science: oh, unexpected data. Hah! Here’s a possible explanation. No problem — done.
No. As I said, it will be interesting to read about these apparent de novo genes when the SMBE talk is published. Then we'll be able to start testing ideas about their origin.wd400
August 26, 2015
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