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Author Topic:   An ID hypothesis: Front-loaded Evolution
New Cat's Eye
Inactive Member


Message 61 of 216 (653387)
02-20-2012 3:15 PM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc.

Wait, why? Isn't that exactly what is expected to have happened?


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Replies to this message:
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Dr Adequate
Member (Idle past 3 days)
Posts: 16112
Joined: 07-20-2006


Message 62 of 216 (653396)
02-20-2012 4:16 PM
Reply to: Message 53 by Genomicus
02-20-2012 12:08 AM


Re: The best of error minimizing codes?
As we learn more about the functions of the genetic code, it becomes ever clearer that the degeneracy in the genetic code is not exploited in such a way as to optimize one function, but rather to optimize a combination of several different functions simultaneously. Looking deeper into the structure of the code, we wonder what other remarkable properties it may bear. While our understanding of the genetic code has increased substantially over the last decades, it seems that exciting discoveries are waiting to be made.

Full optimization of one function may significantly reduce the optimization of another. Thus, a balance would have to be made between various functions.

So it might be optimal ... based on criteria that we haven't discovered yet?

Well yes, and the aliens might descend in their spaceship and say: "Yeah, you got us, we bukkaked your planet with directed panspermia". But maybe we should confine ourselves to the evidence we have now rather than evidence we might discover in the future.

The genetic code is, nevertheless, at a local optimum for error minimization. And the absence of a phylogenetic tree like I describe in my essay, and the fact that this highly optimized genetic code is nearly universal, points to front-loading.

Given that local optimization is exactly what evolution does, no it doesn't, particularly.

The prokaryote LUCA could easily have had a thoroughly sub-optimal genetic code.

Could have, perhaps. But unless you can say would have, which you can't, that's not much of a point.

According to your own scheme the LUCA could also have had a thoroughly sub-optimal genetic code, programmed to get better and better in its descendants as time progressed. Why not? So apparently even being able to look at LUCA would not distinguish between the two hypotheses. Perhaps you should think of something that would.


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Omnivorous
Member (Idle past 396 days)
Posts: 3811
From: Adirondackia
Joined: 07-21-2005


Message 63 of 216 (653409)
02-20-2012 8:32 PM
Reply to: Message 61 by New Cat's Eye
02-20-2012 3:15 PM


Presto!
CS writes:

Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc.

Wait, why? Isn't that exactly what is expected to have happened?

With one magical pass, a successful prediction by the ToE that predates the front-loading hypothesis becomes a lame, ad hoc response to the front-loading hypothesis.

Give that CS fella a cigar.

Edited by Omnivorous, : too many cigars


"If you can keep your head while those around you are losing theirs, you can collect a lot of heads."

This message is a reply to:
 Message 61 by New Cat's Eye, posted 02-20-2012 3:15 PM New Cat's Eye has responded

Replies to this message:
 Message 66 by New Cat's Eye, posted 02-21-2012 11:10 AM Omnivorous has responded
 Message 86 by Percy, posted 02-22-2012 11:43 AM Omnivorous has responded

  
Genomicus
Member (Idle past 728 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 64 of 216 (653417)
02-20-2012 10:24 PM
Reply to: Message 60 by Blue Jay
02-20-2012 3:08 PM


Well, I wasn't trying to put forward an example yet: I was trying to establish a conceptual principle whereby we could test the predictions of FLE.

Well, I think that you are basically correct that we should lineages evolving multiple times if front-loading has occurred: this does not, however, mean that we should each lineage exactly as the other. We might find analogs of those lineages. I'd expect such multiple evolution to be more noticeable at the molecular/gene level than at the morphological level - since the driving force behind front-loading is at the genomic level.

Still, with some biological features, like blood, it would evolve multiple times only under specific circumstances.

Do note, too, that the more specific the front-loading objective, the less likely it is that that objective will evolve multiple times.

So, based only the single criterion I proposed, I would regard multicellularity as potentially consistent with the front-loaded evolution hypothesis.

IMHO, it's not "potentially consistent" with front-loaded evolution, but rather it's a clue in favor of the idea that multicellularity was front-loaded.

My concern with the specific example here (eyes) is that the bias in trajectory only emerges in one "later branch" of the Tree of Life (Metazoa).

Well, you wouldn't expect eyes in prokaryotes, now would you?

So, it seems that the capacity to develop eyes isn't rooted at the base of the Tree of Life, but at the base of the animal branch of the Tree of Life.

Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.

Unless FLE allows for front-loading within individual branches of the tree, and not exclusively at the base of the tree, I think the proper conclusion is that eyes probably were not front-loaded.

The base of the tree contains the necessary information to shape future evolution, and it would contain the genes "anticipating" the evolution of Metazoa; for example, genes (or homologs) needed for eye function would be encoded in the first genomes such that when Metazoa do appear on the scene, eyes can develop.

I will accept your "deep-time" argument if you withdraw your objections to the similar argument in relation to sub-optimal genetic codes.

My "deep time argument" was more of a musing. Lineages can be lost through deep time, but this would be an ad hoc rationalization. Still, even though, for example, animals have not evolved multiple times independently AFAIK, you have to consider this in a broader context. While this might be a clue counting against front-loading, you would also have to consider the evidence favoring the idea that animals were front-loaded.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


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New Cat's Eye
Inactive Member


Message 65 of 216 (653459)
02-21-2012 11:09 AM
Reply to: Message 64 by Genomicus
02-20-2012 10:24 PM


Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.

But with the ToE, we wouldn't expect a gene to come about from nothing. Its going to have to be a modification of a previous gene. Your evidence is consistent with the ToE so it doesn't suggest front-loading over it.

I have a hypothesis that gravity is caused by little invisible angels dancing on top of everything. If I let go of a ball, and it falls to floor, then that suggests that there are little invisible angels dancing on everything, right?

This is from my Message 61:

quote:
Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc.

Wait, why? Isn't that exactly what is expected to have happened?

I'm still wondering why you call that "ad hoc" and why you think it is.

Further, I don't see any reason or evidence to think that some ancient aliens seeded our planet*. What you've got is the idea that something like that happened, and then you're looking for evidence that would be consistent with that happening. You can do that all day, but if that same evidence is consistent with a better idea, then that idea's gonna stay on top until you overturn it. A better approach would be trying to prove that front-loading did NOT happen. What would you expect to find if there was no front-loading and can you find that?

*The only reason I can think of to introduce front-loading would be to leave room for introducing god into the equation. What other reason is there?


This message is a reply to:
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New Cat's Eye
Inactive Member


Message 66 of 216 (653460)
02-21-2012 11:10 AM
Reply to: Message 63 by Omnivorous
02-20-2012 8:32 PM


Re: Presto!
Thanks for the kudos, Omni. I hope Geno explains himself.

Oh, and if you're getting me a cigar, please take all the tobacco out of it and replace it with weed. Thanks.


This message is a reply to:
 Message 63 by Omnivorous, posted 02-20-2012 8:32 PM Omnivorous has responded

Replies to this message:
 Message 69 by Omnivorous, posted 02-21-2012 3:13 PM New Cat's Eye has acknowledged this reply

  
Dr Adequate
Member (Idle past 3 days)
Posts: 16112
Joined: 07-20-2006


Message 67 of 216 (653469)
02-21-2012 2:15 PM


Some Objections
Infinite Regress

One usual case made against front-loading is that while a gene was waiting to become useful, it would be turned into nonsense by genetic drift. I note with pleasure that you have proposed that these genes would be doing something else useful until they were converted to different genes by some pre-programmed process.

But then what about the genes that pre-program the process? To take a concrete instance, the genes that say what genetic changes must be made to turn a land animal into a whale.

Now, these genes themselves must have been doing something else all the time before whales evolved; for two reasons. First, if they'd been saying all along: "Now evolve into whales" then we'd have got whales much sooner. Second, because if they hadn't been doing something, then they themselves would have been turned into nonsense by genetic drift.

But then we need a third set of genes to tell these genes to turn into genes telling other genes to turn into whale genes. And these genes must have had a function other than that, for the same reason that the turn-into-whale genes must have had another function.

Which means that there must have been a fourth set of genes affecting the third set of genes ...

And so on and so forth.

Timing

And then there's the question of timing. How do the genes know: "OK, now it's whale time!" Whatever the genes were for making whales evolve, they were, by your hypothesis, always present from LUCA on down. How do they know when to spring into action? Must there not have been a causal factor external to the genome, causing changes in the genome, to make it start producing whales?

Branching

You haven't answered my question about this, so let me ask it again. According to your hypothesis, LUCA must have had genes to turn it into a whale, and a spider, and an oak tree, and a camel. So what decides which it will actually do?

Ultra-Lamarckism

The only way out that I can see for you is a sort of ultra-Lamarckism. The genes should be able to look around themselves and say: "Hey, I'm in a desert. Better turn into a camel!"; or "Hey, the dinosaurs have gone extinct. It's time for adaptive radiation of mammals!" or "OK, lobsters have been done, so I'd better turn into a tree instead" and change accordingly.

But we have no evidence that genes can respond to environmental feedback in this way. Indeed, where would be the feedback? How could the prospective ancestor of trees know about the existence of lobsters?

Meanwhile we do have known mechanisms that explain ordinary Darwinian evolution.

Edited by Dr Adequate, : No reason given.


Replies to this message:
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PaulK
Member
Posts: 16734
Joined: 01-10-2003
Member Rating: 2.9


Message 68 of 216 (653471)
02-21-2012 2:47 PM
Reply to: Message 67 by Dr Adequate
02-21-2012 2:15 PM


Re: Some Objections
quote:

One usual case made against front-loading is that while a gene was waiting to become useful, it would be turned into nonsense by genetic drift. I note with pleasure that you have proposed that these genes would be doing something else useful until they were converted to different genes by some pre-programmed process.

There's another issue here, too. Selection will keep the genes adequate at performing their function in the life that currently exists. It will not protect them from changes which are neutral with regard to that function. "Front-loaded" information is still hard to protect even in this scenario.


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Omnivorous
Member (Idle past 396 days)
Posts: 3811
From: Adirondackia
Joined: 07-21-2005


(3)
Message 69 of 216 (653473)
02-21-2012 3:13 PM
Reply to: Message 66 by New Cat's Eye
02-21-2012 11:10 AM


Re: Presto!
CS writes:

Oh, and if you're getting me a cigar, please take all the tobacco out of it and replace it with weed. Thanks.

The old man tottered into his basement cave. His favorite cat, the gray one with the strong Abyssinian cast who spoke only in chirps and trills, looked up quizzically from the terrarium lid, warmed by the tri-spectrum LED lights below.

He glanced inside the glass enclosure approvingly, admiring both the latest pillar-like specimens there and the slow-growing, ground-hugging clusters. He made a mental note to water the morning glory seedlings and Mexican mint cuttings in the window boxes upstairs.

The cat watched him closely. From a small drawer in the battered desk he produced a compressed ball of catnip and sent it rolling across the room. The cat crowed, her pitch almost ultrasonic, nearly inaudible, and raced after it. She always moves like a killer, he thought--more a fellow hunter than a pet.

He sat, opened a browser window , peered at the list of replies and clicked the first. His eyebrows rose. He frowned.

"Young man," he typed, "I've been in this game for almost 50 years."

"None of my cigars contain tobacco."

The very idea.


"If you can keep your head while those around you are losing theirs, you can collect a lot of heads."

This message is a reply to:
 Message 66 by New Cat's Eye, posted 02-21-2012 11:10 AM New Cat's Eye has acknowledged this reply

  
Trixie
Member (Idle past 2493 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


(1)
Message 70 of 216 (653475)
02-21-2012 3:25 PM
Reply to: Message 64 by Genomicus
02-20-2012 10:24 PM


You might want to do your PSI-BLAST before making claims about what it will find. The results are pretty much what you get with a BLASTP.

Interestingly, the conserved domain is in the first 140-odd amino acid residues. It's a helix-turn-helix DNA binding domain required for regulation of gene expression.

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.(Lifted straight from the description of HTH_ARSR)

Even then it's only a part of the PAX6 which is similar.

So it's hardly surprising that it's found from prokaryotes to humans - there's very strong selection pressure to conserve these areas which control gene expression.


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jar
Member
Posts: 33179
From: Texas!!
Joined: 04-20-2004
Member Rating: 4.3


Message 71 of 216 (653477)
02-21-2012 3:42 PM
Reply to: Message 70 by Trixie
02-21-2012 3:25 PM


Selection pressure
It's really important to emphasize that there is evidence that it is selection pressure driving the conservation while NO evidence has ever been presented for any, plan, any planning process, any planner or any method for the planner to influence genomes.

Anyone so limited that they can only spell a word one way is severely handicapped!

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Taq
Member
Posts: 8469
Joined: 03-06-2009
Member Rating: 6.0


Message 72 of 216 (653479)
02-21-2012 3:51 PM
Reply to: Message 64 by Genomicus
02-20-2012 10:24 PM


Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life.

Yes, that is exactly what we would expect to see if evolution is true. There is nothing front loaded about it. Evolution is descent with modification. Of course the earliest ancestors are going to have the genes that were later modified through random mutation and natural selection. Where else would you expect to find them?

While this might be a clue counting against front-loading, you would also have to consider the evidence favoring the idea that animals were front-loaded.

The evidence you have presented for front loading is exactly what we would expect to find from the process of random mutations filtered through selection. You might as well claim that the Grand Canyon is encoded in the rain clouds that hover over the Colorado Plateau which means that the Colorado River is front loaded to produce the specific features of the Grand Canyon.


This message is a reply to:
 Message 64 by Genomicus, posted 02-20-2012 10:24 PM Genomicus has responded

Replies to this message:
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Genomicus
Member (Idle past 728 days)
Posts: 852
Joined: 02-15-2012


Message 73 of 216 (653486)
02-21-2012 5:32 PM
Reply to: Message 72 by Taq
02-21-2012 3:51 PM


Mr Jack said:
I'd suggest that your hypothesis should lead to us seeing many, probably most, such multi-cellular genes in prokaryotes - we don't. There are some, yes, but most are not found in bacteria; a few more in Archaea and a decent portion in single-celled Eukarya or in multi-cellular but simply differentiated Eukarya. It seems to me that if front-loading was true we would expect a majority of such genes to be present in all species, would you agree?

Taq said:

Yes, that is exactly what we would expect to see if evolution is true. There is nothing front loaded about it. Evolution is descent with modification. Of course the earliest ancestors are going to have the genes that were later modified through random mutation and natural selection. Where else would you expect to find them?

Am I the only one that is puzzled by this discrepancy of statements?


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Genomicus
Member (Idle past 728 days)
Posts: 852
Joined: 02-15-2012


Message 74 of 216 (653487)
02-21-2012 5:33 PM
Reply to: Message 70 by Trixie
02-21-2012 3:25 PM


You might want to do your PSI-BLAST before making claims about what it will find. The results are pretty much what you get with a BLASTP.

Possibly, but PSI-BLAST uses a different scoring system than blastp. Just a thought.


This message is a reply to:
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Genomicus
Member (Idle past 728 days)
Posts: 852
Joined: 02-15-2012


Message 75 of 216 (653489)
02-21-2012 5:38 PM


Into the swamps...
As Bluejay predicted, I am effectively getting swamped with responses. So is there anyone who would especially like me to respond to their points? I do owe bluegenes a response, though, so responding to his post is priority.

Replies to this message:
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