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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
AVS:
I’m still waiting for the info that “refuted” me from that book by the way. =)
Um, no. You're not. You've already admitted that "it's all just chemistry." Now when you finally manage to get your grubby little penny-pinching paws on a copy of that book, perhaps from your local university library, you can show us how it contradicts your assertion that "it's all just chemistry." But don't expect me to hold my breath.Mung
May 6, 2014
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Piotr: I have just seen that in your blog there is a discussion on function which has interesting connections with my post on functional information. Let me say that I did not copy the example of the stone from your post there: I read it only now. :)gpuccio
May 4, 2014
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Piotr: Thank you for your beautiful explanations about languages. That is really a fascinating discipline. My view about the evolution of languages s that it is a special kind of designed process, in the sense that it is the result of multiple design acts by multiple designers. And, obviously, many random or algorithmic processes influence the results too. But language comes from intelligent conscious beings, and is mainly the result of understanding and purpose. IOWs, of design.gpuccio
May 4, 2014
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Piotr @ 165 explained
One could say that Turkish is more synthetic than English, but there are languages with a still higher morpheme/word ratio. Has your friend considered learning Eskimo or Cherokee?
Thank you. I've lost touch with him, but I've always wondered about the structures and capabilities of different languages. Would you say that that languages came into being purely by chance or is it more likely that they have intelligence as their source? I was just reminded that children sometimes invent their own languages. -QQuerius
May 4, 2014
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They are old molecules, obviously.
exactly! You don't get proteins without them, you don't even get protein domains without them. All this talk of how proteins can evolve from short sequences into longer sequences doesn't seem to mean much if it cannot explain them.Mung
May 4, 2014
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Funny Mungy, although my point is that Joe is wrong for the most part. For starters, there is really no such thing as a "small" protein enzyme. Catalase is relatively small, and yet is made up of multiple subunits, each over 50kDa. Also, "adding amino acids" is just about as likely to either HAVE an effect, or NOT HAVE an effect, on substrate binding. In fact, in the lab, proteins are often expressed with entire fluorescent protein constructs engineered into their sequence and they still function properly the majority of the time. I'm still waiting for the info that "refuted" me from that book by the way. =)AVS
May 4, 2014
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Mung: I have always brought up aminoacyl-tRNA synthetases! I (like UB) am a big fan of aminoacyl-tRNA synthetases (or, more correctly, ligases). They are 20 wonderful molecules, divides in two classes. And they are long, big and complex. And, obviously, they have no precursors. Here are some lengths in humans: Class I: Arginine: 660 AAs Cysteine: 748 AAs Leucine: 1176 AAs Class II: Alanine: 968 AAs Asparagine: 548 AAs Glycine: 739 AAs They are old molecules, obviously. Even their "evolution" after their appearance is perplexing, and there are many problems, usually intepreted as HGT.gpuccio
May 4, 2014
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Transfer RNA DatabasesMung
May 4, 2014
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A quote for Upright BiPed:
The linkage of an amino acid to a tRNA is crucial for two reasons. First, the attachment of a given amino acid to a particular tRNA establishes the genetic code. - Aminoacyl-Transfer RNA Synthetases Read the Genetic Code
gpuccio, I am lazy and don't want to read through your past posts :) Did you bring up aminoacyl-tRNA synthetase? How short are they, how specific are they, how important are they, what are their precursors?Mung
May 4, 2014
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Piotr and all: Stimulated by the discussion here, I have just made a post on functional information.gpuccio
May 4, 2014
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AVS:
You sure about that Joe, or are you just talking out of your rear-end?
Well, at least we now know where your ear is. Joe:
Doug Axe goes over this in his essay in “The Nature of Nature” see catalase (for example)
Well joe, perhaps AVS has never heard of Douglas Axe and just can't be bothered to spend the time or money to become familiar. Reminds me of his demand that I debate him over the contents of a book he can't be bothered to read.Mung
May 4, 2014
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Figure 1 shows the distribution of protein chain lengths for all proteins known to be involved in enzymatic functions in E. coli, either alone or in combination with other proteins. The mode of the distribution shows that the most common length of these proteins is around 300 amino acid residues, with the higher mean and median lengths reflecting the existence of numerous protein chains that are much longer than this. - Douglas Axe. The Nature of Protein Folds: Quantifying the Difficulty of an Unguided Search Through Protein Space
Mung
May 4, 2014
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Joe:
Unbelievable that you just cannot extend Spetner’s ideas to include orfan genes.
There's certainly nothing in Spetner that would lead me to extend his ideas to include orphan genes. In fact, having completed my re-reading of his chapter seven, his NREH (nonrandom evolutionary hypothesis) precludes me from doing so.Mung
May 4, 2014
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I don’t understand how common descent could be partial. Are you saying that all human languages started from a single common source, but later somehow branched into major families, and were subsequently modified by common use and disuse, borrowing, and innovation?
No, I mean that we don't know if there was a single source. We start with modern and historically documented languages and classify them in the same family if we have evidence of relationship. There are, for instance, 400+ Indo-European languages, and we can demonstrate they had a common ancestor a few thousand years ago. There are 30+ Turkic languages, and they are also descended from a common ancestor. But we do not know "beyond reasonable doubt" if the Turkic and Indo-European families go back to a single historical source. That's why I call this kind of common descent "partial", not "universal". Given the limited evidence that we have, we can reconstruct many common ancestors -- one for each family -- but not a single one for all of them. Note that people have probably used languages for hundreds of millennia, but writing was invented little more than 5000 years ago, and our best reconstructive methods reach back possibly twice as deep. We can probe only a thin slice of the total history of spoken language.
I was once told by a colleague that a scientist of our acquaintance chose to learn Turkish, because he considered it nearly a perfect synthetic language. In your opinion, why might he have concluded this, or would you disagree?
A "synthetic" language is one in which a word typically contains many morphemes, while an "isolating" language prefers words that can't be decomposed into morphemes. Chinese is an extreme example of the latter, but there's actually a continuum of types rather than a clearcut isolating vs. synthetic dichotomy. One could say that Turkish is more synthetic than English, but there are languages with a still higher morpheme/word ratio. Has your friend considered learning Eskimo or Cherokee?Piotr
May 4, 2014
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Piotr, Thanks for your explanation.
. . . and there is good evidence of partial common descent in linguistics.
I don't understand how common descent could be partial. Are you saying that all human languages started from a single common source, but later somehow branched into major families, and were subsequently modified by common use and disuse, borrowing, and innovation? I was once told by a colleague that a scientist of our acquaintance chose to learn Turkish, because he considered it nearly a perfect synthetic language. In your opinion, why might he have concluded this, or would you disagree? Just curious, that's all. -QQuerius
May 4, 2014
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@Querius:
That you’re skeptical of a single origin of all languages might convey to you why some of us are skeptical of a single point of the origin of life.
We go where the evidence leads us. There is good evidence of universal common descent in biology, and there is good evidence of partial common descent in linguistics. Sometimes we manage to assign more members to an already established linguistic family. For example, Indo-European has grown since the 19th century because a couple of new branches (Anatolian and Tocharian) were discovered, both of them branching off at the root of the family-tree. The Semitic family (whose members are Hebrew, Phoenician, Arabic, Aramaic, Amharic and Akkadian, among others) is now regarded as part of a much larger genetic unit, including also Old Egyptian as well as several language groups in the Sahara and Sahel regions of North Africa (Berber, Cushitic, Chadic, and more speculatively Omotic). We call this extended "superfamily" Afroasiatic. But still there are scores of families (from tiny ones to giants with hundreds of members) whose external relationships remain unknown at present. Do you think the most commonly used languages are evolving in complexity? The "overall" complexity of a language is hard to define and measure. Of you look at its various components, like phonology, syntax, lexicon, and inflectional or derivative morphology, their complexity may increase or decrease historically. For example, Modern English has lost nearly all the declensional and conjugational endings still used in Old English, but its syntax has become more complicated in some ways, e.g. thanks to the development of structures like the complex tenses (not only I write and I wrote, but also I have written, I will be writing, I would have been writing, etc.). They were not deliberately "designed" by anybody in one fell swoop, but appeared gradually and became grammaticalised slowly over the centuries until they settled into a stable system (as recently as 300 years ago a construction like the road is being repaired would have been considered ungrammatical). And of course the lexicon of Modern English has grown enormously since the Middle Ages, mostly through borrowing.Piotr
May 4, 2014
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I was also going to ask Joe if new proteins necessarily required new chaperones (or maybe some of those already available could do, eh?). I leave aside the question if chaperones actually help proteins "to find their functional shape", since it isn't quite the issue here.Piotr
May 4, 2014
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"Adding amino acids to an existing small protein would just block its substrate and render it useless." You sure about that Joe, or are you just talking out of your rear-end?AVS
May 4, 2014
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OK Mung, seeing that you are trapped in a box, then it is MY "built-in responses to environmental cues" that builds ORFan genes. Unbelievable that you just cannot extend Spetner's ideas to include orfan genes. Orfans were found in 1996 and the book was already written and on its way to publicationJoe
May 4, 2014
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Mung: The implication is the same both for orphan genes and for any other protein, orphan or not: Any protein of some functional complexity, when it appears for the first time, with sequence, structure and function unrelated to what already exists (which is true for at least the 2000 superfamilies in SCOP), cannot be explained neither by random processes of variation (any kind of random variation) nor by any known algorithm (like NS). The only possible explanation is guided variation by design. Quite an implicaton, I would say.gpuccio
May 4, 2014
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Axe:
The elucidation of the genetic code in the late 1960's provided a precise framework for understanding the effects of genetic mutations on protein sequences. ...The code had made it clear that the vast set of possible proteins, each of which could conceivably be constructed by genetic mutations, is far too large to have actually been sampled to any significant extent in the history of life.
What is the implication for the origin of orphan genes?Mung
May 3, 2014
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Joe quotes Douglas Axe from The Nature of Nature. There is no entry in the index for ORFan gene or orphan gene or taxonomically restricted gene. So far my reading of Spetner (quotes @ 160) offers no YEC explanation for orphan genes. Will the chapter by AXE likewise fail to provide the missing explanation?Mung
May 3, 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).
Spetner:
My speculation here is speculative. - p. 184
Spetner:
...nonrandom adaptive variation, arising from an environmental signal turning ON an already present set of genes, is hard to account for. - p. 191
Spetner:
I suggest that other organisms also may have latent parts of their genome dedicated to be adaptive to a certain set of environmental conditions that may arise. Then environment can then supply a cue that will turn ON the latent section that will make the organism adaptive. - p. 192
This is not an explanation for ORFan genes. At best it assumes their existence rather than explaining their existence.Mung
May 3, 2014
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Joe, what I am trying to get you to understand, in my fumbling and no doubt irritating way, is that whether evolution is guided or not hardly matters if there is a mechanistic explanation.Mung
May 3, 2014
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Hi Joe, I tend to agree with your analysis. I intend to read that chapter (again?) in The Nature of Nature. But guided by what? According to YEC's, God is not guiding these changes. So there's no "intelligent design intervention" going on. Evolution does not require the guiding hand of God. Materialists and Atheists and YEC's find common ground! What odd bedfellows =pMung
May 3, 2014
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Mung- Adding amino acids to an existing small protein would just block its substrate and render it useless. And long proteins require chaperones to find their functional shape. So unless the process is guided such that the simultaneous changes Axe discusses occur, it doesn't have a chance of doing something useful.Joe
May 3, 2014
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Is it somehow more probable that proteins should gain in length and function by adding additional "modules," or that they simply arise de novo, and why?Mung
May 3, 2014
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Upright BiPed, what with Piotr being a linguist, you're probably going to have to spell it out for him. :)Mung
May 3, 2014
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Thank you for your comments to my questions, Piotr. Through a variety of circumstances, I've been exposed to several languages. I've always been fascinated by how different that they can be conceptually. For example, the Navajo language being so verb heavy. That you're skeptical of a single origin of all languages might convey to you why some of us are skeptical of a single point of the origin of life. Do you think the most commonly used languages are evolving in complexity? -QQuerius
May 3, 2014
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Piotr, While it's true you''ve not "declared" a lack if interest in the physical properties I've brought up to you, but you've most certainly demonstrated it. Three days ago you declared on this forum that duplication and origin of life are separate topics. When I pointed out to you that they both are dependent on these same unique material conditions, you showed the same general disinterest then. That's fine, you are not required to be curious. I'll leave it alone.Upright BiPed
May 3, 2014
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