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Many genes relatively new, scientists find

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Science writer Carl Zimmer in the New York Times on recent discoveries in the ongoing evolution of genes:

New genes were long thought to derive from duplications or mistakes in older genes. But small mutations can also form new genes from scratch.

For some scientists, like Dr. Tautz, the data pointed to an inescapable conclusion: Orphan genes had not been passed down through the generations for billions of years. They had come into existence much later.

“It’s almost like Sherlock Holmes,” said Dr. Tautz, citing the detective’s famous dictum: “When you have eliminated the impossible, whatever remains, however improbable, must be the truth.”

Dr. Begun and his colleagues renamed orphan genes “de novo genes,” from the Latin for new. He found that many of his fellow scientists weren’t ready to accept this idea.

Can’t think why not, can you? 😉

While many de novo genes ultimately vanish, some cling to existence and take on essential jobs. Dr. Tautz said the rise of these genes might be as important a factor in evolution as gene duplication.

Now how will this affect attempts to construct evolutionary histories via genome mapping?

More Zimmer on the genome:

One gets the impression that the guy who thought our genomes were in some sense “us” spoke too quickly.

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Comments
Piotr, The designers and builders we know of do so one piece at a time. IOW your "predictions" are pure nonsense wrt random origins. No one in ID would expect a new gene in one generation. Also yours has the issue of once you have a functioning short protein there isn't any known mechanism for adding to that sequence in such a way as to produce a totally new function with a longer chain. Not only that once you get to long chains (AA-wise) a chaperone is required in order to get a proper functioning fold. As for gene duplication there just isn't enough time for accidental genetic changes to duplicate a gene, build a binding site and alter it in such a way as to change the function. The whole issue boils down to the origin of life. It is only if life arose via accidents and chance events would infer evolution is so driven. OTOH if the OoL was designed then we would infer that it was designed to evolve and evolved by design.Joe
May 1, 2014
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It predicts that just cuz you say so? No, the predictions aren't mine. They follow from the model, but in order to understand how and why you'd have to do some reading, and I suspect you can't be bothered.Piotr
May 1, 2014
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@Joe: Of course it is testable. Are you suffing from a reading comprehension problem? How many times shall I repeat that I have suggested a way to test it? The evidence so far is compatible with "random origin", so the hypothesis stands unfalsified. Now if you think you have some evidence of special design in orphan genes (using my suggestion or anything else), why don't you present it, Mr Scientific? If you just keep repeating the same thing, I'll ignore you henceforth.Piotr
May 1, 2014
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Piotr:
It predicts that the transcripts young de novo genes will be relatively short, yielding simple products like non-coding RNAs of small proteins. It makes other predictions too, e.g. that de novo genes will be cis-regulated rather than trans-regulated, that they will have few if any paralogues, etc.
It predicts that just cuz you say so? You realize that you actually have to have some evidence as to why blind watchmaker evolution predicts that.Joe
May 1, 2014
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The null still needs to be tested. If it cannot be tested then it is rejected. The point being is there isn't any reason to falsify something tat cannot be tested in the first place. It's as if you have no clue wrt science.Joe
May 1, 2014
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The null hypothesis is the default position. You can reject it (or fail to reject it) if you propose an alternative hypothesis making more specific assertions, suggested by the data. I have offered one way in which you could disprove the "random origin" scenario. It predicts that the transcripts young de novo genes will be relatively short, yielding simple products like non-coding RNAs of small proteins. It makes other predictions too, e.g. that de novo genes will be cis-regulated rather than trans-regulated, that they will have few if any paralogues, etc. Go ahead, falsify it.Piotr
May 1, 2014
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Piotr:
I can tell science from propaganda
Doubtful.Joe
May 1, 2014
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Piotr:
The null hypothesis about the origin of de novo genes in this case is the random generation of transcribed sequences that accidentally acquire a function, since it makes no arbitrary assumptions and is compatible with known facts (see the article I linked).
I invite you to test that null hypothesis. I also invite you to produce a testable model based on it. If you either cannot or refuse to we will understand why.Joe
May 1, 2014
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gpuccio: Of course you have read those things. That is standard darwinist propaganda. Unfortunately, nothing of that is true or supported by facts. Shall I stop taking you seriously before we actually discuss anything? Read what you've just written. I gave you a link to a review article by highly respected experts on orphan genes, published in one of the best science journals, and you dismiss it off-hand as "darwinist propaganda" and a rigmarole of lies. Does it ever occur to you that if it weren't for people who do actual scientific research and write such stuff, you (I mean ID proponents) would not even know of orphan genes and their functions? How can you, on the one hand, call someone's results not true and unsupported by facts, and at the same time hijack them for your own purposes? It simply makes no sense. I am not a biochemist, but I am an academic worker engaged in research. I can tell science from propaganda, and I detect more of the latter in your three sentences above (note, for example, the agitprop application of the term "darwinist") than in the article in question.Piotr
May 1, 2014
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@Joe The null hypothesis about the origin of de novo genes in this case is the random generation of transcribed sequences that accidentally acquire a function, since it makes no arbitrary assumptions and is compatible with known facts (see the article I linked). I invite you to falsify the null hypothesis and propose a more convincing scenario. For example, if you could show me a young orphan gene that encodes for a large and highly complex multi-domain protein involved in some really important interactions, I'd agree that the spontaneous rise of such a structure by accident is not a satisfactory explanation.Piotr
May 1, 2014
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Joe:
Piotr, How was it determined that the ORFan genes arose by accident? My bet it was just a bald declaration, no science involved
It's a good bet. You would certainly win. :) The simple facts are that we can observe some non coidng regions becoming functional ORFs at a certain point of natural history, if that will be confirmed. That is against all probabilistic considerations. Unless, obviously, the evolution of the sequence is intelligently guided. Usually, the non coding region becomes an ORF when it is ready to be translated, and to express the function. Until then, NS can act in no way, and only pure chance or design can be responsible. What would you bet on? :)gpuccio
May 1, 2014
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Piotr: Thank you for the kind answer. Of course you have read those things. That is standard darwinist propaganda. Unfortunately, nothing of that is true or supported by facts. However, you certainly believe those things in good faith. I can only encourage you to read more, and with a critical spirit. Read also something specific of what is posted here, especially the more technical interventions. If you are interested, you could look at my recent posts here: https://uncommondescent.com/intelligent-design/cambrian-shrimps-heart-more-complex-than-modern-one for example, #57 and following (it's a long discussion with rhampton7)gpuccio
May 1, 2014
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There isn't enough time for the blind watchmaker to A) duplicate a gene and B) have that gene changed for a different function and expressed. As Lenski has demonstrated duplicate genes do not necessarily, contra Art Hunt, have their promoters and binding sites duplicated.Joe
May 1, 2014
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Piotr, Again with the ERVs that no one knows if they were ERVs. "It looks like part of an ERV to me" is not science.Joe
May 1, 2014
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Piotr, How was it determined that the ORFan genes arose by accident? My bet it was just a bald declaration, no science involvedJoe
May 1, 2014
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So is it incorrect to say that ORFan genes are found only in a single species? It doesn't matter from the evolutionary perspective. You may replace 'species' with 'lineage' or 'clade'. Here's Tautz & Domazet-Lošo's definition:
Genes that lack homologues in other lineages — that is, they cannot be linked by overall similarity or shared domains to genes or gene families known from other organisms.
It doesn't say that an orphan gene must be restricted to one species (only of the youngest orphan genes will be; some may even be restricted to populations within a species). Large and old taxa also have genes with no external homologues (200+ in primates, including humans). The term "taxonomically restricted gene" (TRG) is used of them, and at least in some cases it can be demonstrated that they are old "orphan genes". As in the case or ERVs, those that we share with e.g. baboons are a subset of those we share with gibbons, and these in turn are a subset of those shared with chimps/bonobos.Piotr
May 1, 2014
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Mung, Nice quote mine of Spetner. The part you quoted has nothing to do with what I am saying. Spetner also talks about long term changes, Mung. It's as if y6ou have turned into an evoJoe
May 1, 2014
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I am curious: what is your personal idea about the appearance of complex functional de novo genes, especially from non coding sequences? I don't know enough about biochemistry to offer an original personal idea. Here's my tuppenceworth based on what I've read: the accidental formation of a new "RNA gene", complete with regulatory elements, is not at all unlikely. Again, in most cases it will be non-coding RNA which may or may not become co-opted for doing something useful. In extremely rare cases it may be translated into a protein (short, simple and relatively unstructured in the case of young genes, which doesn't rule out certain kinds of functionality). If any of those products (non-coding RNA or peptide) confers an appreciable advantage, positive selection will eventually conserve it, so it may gradually develop into something more complex and more functional, or even give rise to a new gene family. If it turns out to be deleterious, purifying selection will prevent its spread. It may also evolve neutrally or nearly neutrally (not everything that regularly gets transcribed has a function).Piotr
May 1, 2014
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Mung: I agree that the "turning of genes ON or OFF as they are needed" is an important mechanism of environmental adaptation, probably epigenetic, but sometimes due to simple genetic variation, and has nothing to do with the appearance of new complex functional genes. Many so called examples of "darwinian evolution" are of that kind, including the appearance of nylonase and the famous case of citrate in Lenski's experiment. In those two cases, the "adaptation" is genetic, and could be explained as the result or simple random variation + NS (but it could still be algorithmic in some way). In other cases, the adaptation is probably due to the working of intelligent epigenetic algorithms.gpuccio
May 1, 2014
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Piotr: I have appreciated your interventions. You seem a reasonable interlocutor, a precious thing indeed. I am curious: what is your personal idea about the appearance of complex functional de novo genes, especially from non coding sequences?gpuccio
May 1, 2014
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Mung: A few tentative answers from my point of view. De novo genes appear throughout the course of natural history. In a strict sense, we call them ORFans if they remain restricted to one species or group of species. But, in another sense, each new protein superfamily (at least) is a de novo gene when it appears for the first time, even if after it remains common to many species which appear after. Each de novo gene, if functional and complex, requires the active intervention of a designer for its first appearance. There is increasing evidence that at least some de novo genes arise gradually from non coding sequences, without any possible intervention of NS, from a process which can only be explained as guided intelligent variation. We will see if that evidence is confirmed and validated by new data. There is no special reason to believe that the process has stopped.gpuccio
May 1, 2014
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Mung: I don’t recall is interacting before. Hope you’ll stick around. What’s your interest in ID? I often lurk here out of curiosity. Nice talking to you guys. You can guess we disagree about most of this stuff, but I promise to be civil and patient.Piotr
May 1, 2014
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Jehu:
Orphans are inconsistent with common descent but consistent with created kinds.
Why? How? And SO? My point is that if one is going to state or imply that ORFan genes support young earth creationism that an actual argument needs to be put forth. Why aren't ORFan genes consistent with Old Earth Creationism? How are ORFan genes "consistent with created kinds" if they appear within different "kinds" of created kinds? Do ORFan genes require God's direct intervention? If so, why? If not, why not? Is God still creating new species? If so, why is God not still creating new "kinds"?Mung
April 30, 2014
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Joe:
What part of “built-in responses to environmental cues” can’t produce ORFan genes?
Spetner:
The system turns genes ON or OFF as they are needed, but makes no permanent change in the genome. - p. 182
Does that answer your question?Mung
April 30, 2014
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Mung:
Hi Joe, there’s no entry in the index to Spetner’s book for ORFan gene, orphan gene, species-specific gene or taxonomically restricted gene. I’ll re-read the chapter on non-random variation.
So you can't put 2 and 2 together? :) What part of "built-in responses to environmental cues" can't produce ORFan genes?Joe
April 30, 2014
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Piotr:
That was wrong: they are ERVs, and there was nothing to correct in the first place.
They just look like ERVs- remnants of ERVs.
Please explain the method of design, and why the result looks for all the world as if it were produced by common descent (including features that evolve neutrally and have no identifiable function, like those defunct and decaying ERV sequences).
I don't know the method of design and the result doesn't look as if it were produced by common descent. You don't even know what pattern universal common descent would produce.Joe
April 30, 2014
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Mung,
So do YEC’s use orphan genes to help determine the created kinds? Do you have any references? If so, how do they support young earth creationism?
Orphans are inconsistent with common descent but consistent with created kinds. I don't know if anybody has done a study of orphans as they relate to baraminology.Jehu
April 30, 2014
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Hi Piotr, I don't recall is interacting before. Hope you'll stick around. What's your interest in ID?Mung
April 30, 2014
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Jehu:
I think the proper creationist answer would be, there are no orthologous genes outside of a baramin (created kind).
So do YEC's use orphan genes to help determine the created kinds? Do you have any references? If so, how do they support young earth creationism?Mung
April 30, 2014
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Mung:
How do young earth creationists explain ORFan genes?
Joe:
YECs explain ORFan genes by way of non-random evolution, ie “built-in responses to environmental cues” (Spetner 1997).
Hi Joe, there's no entry in the index to Spetner's book for ORFan gene, orphan gene, species-specific gene or taxonomically restricted gene. I'll re-read the chapter on non-random variation. Jehu:
You are kidding right? Creationists explain ORFans easily. They were created by God.
No I'm not kidding. I'd like to know. Some YEC's seem to think they are evidence for young earth creationism and I'd like to know how and why they come to that conclusion. So far I asked the question and received two very different answers. Most YEC's, afiak, don't think God is still creating new species. You seem to be one who does. Do you believe God is still creating new species and that's why ORFan genes arise? Or is are they a result of evolution, like Joe says, just not random evolution? Some YEC's are anti-evolution, others accept evolution within kinds. I am just trying to figure it all out so I can understand how ORFan genes support young earth creationism (if at all).Mung
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