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Author Topic:   Deep Homology and Front-loading
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 49 of 172 (666092)
06-21-2012 9:42 PM
Reply to: Message 48 by Genomicus
06-21-2012 9:26 PM


Evidence And Prediction
So, given that, by your own admission, Darwinian evolution doesn't predict that the flagellum will share similarity with more ancient systems, any such similarity isn't evidence that the flagellum evolved ...
No, that's not what I said.
I said that it's not a prediction of Darwinism that we should be able to find it, not that it's of no significance if we do.
There's a difference.
If my house is burgled, and we find the fingerprints of notorious burglar John Smith all over my stuff, this is evidence that he was the criminal.
However, the hypothesis that he's the criminal does not predict that we'll find his fingerprints. 'Cos he could have worn gloves, or wiped every surface clean, or set fire to the house. The hypothesis "John is guilty" predicts that we won't find proof of his innocence, but not that we will find all conceivable proofs of his guilt. This is why, if there was other evidence of his guilt (such as being caught with my valuables) his lawyer wouldn't be able to say: "But I can prove he's innocent --- none of his fingerprints were found at the scene!"
The same with Darwinism. It predicts that we won't find evidence against it. If does not predict that we will find all the evidence we could ever imagine in favor of it. Finding functional subsystems of the flagellum is nice; so is finding Smith's fingerprints. But it's not a prediction.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 48 by Genomicus, posted 06-21-2012 9:26 PM Genomicus has replied

Replies to this message:
 Message 50 by Genomicus, posted 06-21-2012 10:14 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 53 of 172 (666098)
06-21-2012 10:28 PM
Reply to: Message 50 by Genomicus
06-21-2012 10:14 PM


Re: Evidence And Prediction
Okay. Understood (although you're going to find a lot of Darwinians that say that the hypothesis that the bacterial flagellum evolved predicts that it will share homology with systems that pre-date it ...
Well, it does predict similarities with systems that predate it, but not that they'll still be around now for us to look at them. In the same way, we don't expect to find primitive birds still flapping about with teeth and gastralia and lots of caudal vertebrae. It would be wonderful if we could find one (creationists would claim that this disproved evolution, but then they're idiots) but Darwinism gives us no particular expectation that we will; and in fact we haven't. Luckily, we have the fossil record.
This is hypothetically possible, but it's really, really not likely for a fully functional protein in prokaryotes to be loss across all prokaryotic lineages.
Yeah, but you can only say that because you know that it is a fully functional protein in prokaryotes --- if it had disappeared, you could quite legitimately have said: "Ah well then, I'm gonna guess that it wasn't any use to prokaryotes". You wouldn't have said: "Oh, in that case FLE falls apart, because I have such insight into biochemistry and so on that I know that if it had been present in LUCA it would certainly have been conserved in prokaryotes." (Maybe it would certainly have been conserved, but the only evidence we have for the is the post-hoc observation that it was --- no-one, I believe, is smart enough to figure this out from first principles, so you wouldn't have known this to be the case.)
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 50 by Genomicus, posted 06-21-2012 10:14 PM Genomicus has replied

Replies to this message:
 Message 54 by Genomicus, posted 06-21-2012 10:37 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 55 of 172 (666101)
06-21-2012 10:45 PM
Reply to: Message 52 by Genomicus
06-21-2012 10:26 PM


Re: The Ubiquitin Story
Dr Adequate brought up the example of ubiquitin, which is a very crucial protein among eukaryotes. This is evidenced by its universal distribution among eukaryotes and tightly conserved sequence identity across taxa (e.g., there is 96% sequence identity between human ubiquitin and yeast ubiquitin). Dr Adequate is quite correct when he says that ubiquitin is essential to eukaryotes.
Based on the logic of front-loading, I'd predict that ubiquitin shares deep homology with a prokaryotic protein.
But what does Darwinian evolution predict? Dr Adequate, do you think we'll find a prokaryotic homolog of ubiquitin one of these days? Why or why not? I'm quite curious as to your answer.
I'd say no, for these reasons:
(1) According to the paper I linked to, no-one's found one yet in all the prokarotes that we've sequenced.
(2) Presumably scientists have deliberately sequenced a wide range of prokaryotes rather than looking again and again at one small clade of them.
This suggests that the use of prokaryotic ubiquitin-like protein and the non-use of ubiquitin is basal in prokaryotes, so it would be bizarre to find a branch of the prokaryotes that used ubiquitin.
This is not particularly a Darwinian answer, just an evolutionary answer --- I'd come to the same conclusion if I believed in FLE. If, as the evidence suggest, ubiquitin was not present in basal archaea or eubacteria, then it would be odd for it to turn up in some branch of them looking all homologous but actually just being analogous, and so far as I can see FLE would tell us the same thing.
(I suppose it might happen by lateral gene transfer. But I suspect that such a transfer, if it occurred, would be selected against.)

This message is a reply to:
 Message 52 by Genomicus, posted 06-21-2012 10:26 PM Genomicus has replied

Replies to this message:
 Message 57 by Genomicus, posted 06-21-2012 11:20 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 56 of 172 (666102)
06-21-2012 10:53 PM
Reply to: Message 54 by Genomicus
06-21-2012 10:37 PM


Re: Evidence And Prediction
Except that front-loading requires that if there's a key protein in eukaryotes, then that protein would have originally been given a function in the LUCA, so that it is retained.
A function in the LUCA, yes, but not necessarily in all its descendants. Surely (stop me if I'm wrong) the whole idea of FLE is that the LUCA contains genetic information that is differently lost in different lines of descent. If everything that was useful to the LUCA was conserved in all its descendants, in what would the E in FLE consist?
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 54 by Genomicus, posted 06-21-2012 10:37 PM Genomicus has replied

Replies to this message:
 Message 58 by Genomicus, posted 06-21-2012 11:26 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 59 of 172 (666107)
06-22-2012 12:08 AM
Reply to: Message 57 by Genomicus
06-21-2012 11:20 PM


Re: The Ubiquitin Story
Distant homology. Distant indeed --- between proteins which do different things and have only a small amount of their sequence in common. Homology? Well maybe --- if you're a Darwinian. But do you want to suggest that these different proteins adapted to doing different things have a common ancestor?
All of this is very cool, of course, and is what we'd expect from front-loading ...
No ... no, I'd have expected more front-loading of information and less Darwinian evolution.
Thus, we'd want to load the first genomes with ubiquitin ...
And yet you have no evidence that ubiquitin was the common ancestor of this protein family, if it is one.

This message is a reply to:
 Message 57 by Genomicus, posted 06-21-2012 11:20 PM Genomicus has replied

Replies to this message:
 Message 61 by Genomicus, posted 06-22-2012 12:22 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 60 of 172 (666109)
06-22-2012 12:20 AM
Reply to: Message 58 by Genomicus
06-21-2012 11:26 PM


Re: Evidence And Prediction
Well, in the first place, nothing in the idea of FLE says that genetic information has be differentially lost across lines of descent. FLE is simply about stacking the deck so that the origin of eukaryotes (and Metazoa etc.) is made probable by providing the necessary machinery for their origin. The "evolution" part of FLE is natural selection and random mutation acting in combination with the initial, designed states ...
So you believe that all extant species descended from a common ancestor by purely Darwinian mechanisms? Well, I hate to break it to you, but someone got in ahead of you there ... it was Darwin. This is certainly not what is usually understood by front-loaded evolution.

This message is a reply to:
 Message 58 by Genomicus, posted 06-21-2012 11:26 PM Genomicus has replied

Replies to this message:
 Message 62 by Genomicus, posted 06-22-2012 12:24 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 63 of 172 (666113)
06-22-2012 12:48 AM
Reply to: Message 61 by Genomicus
06-22-2012 12:22 AM


Re: The Ubiquitin Story
Actually, these proteins carry out analogous functions.
Well, no they don't. For example, according to this, the ThiS gene which you mention "plays a central role in thiamin biosynthesis". Unlike ubiquitin, which does something completely different. In fact, he writes: "Comparison with surface features of ubiquitin and ubiquitin homologs SUMO-1, RUB-1 and NEDD8 suggest how Nature has utilized this single fold to incorporate similar chemistry into a broad array of highly specific biological processes." The homologues do "highly specific" different things. And MoaD, which you also cite, is apparently "involved in molybdenum cofactor (Moco) biosynthesis".
I really have no idea why you think that one has to be a Darwinian in order to accept the view that these proteins are homologous.
Well, because the descent of different proteins doing different things from a common ancestor is Darwinian. If each protein was separately front-loaded into LUCA, that would be an instance of front-loading.
Well, the structural evidence coupled to other clues does indicate that these proteins are likely homologous. At any rate, now you're moving the goal-posts. First, you said that ubiquitin has no prokaryotic homologs (inconsistent with FLE) ...
The paper I found said that there were no prokaryotic homologues. Changing my mind when presented with new data is hardly moving the goalposts, it's what people are meant to do.
Anyway, you wouldn't have to load the first cells with ubiquitin itself. You'd simply need to load them with closely related proteins, so that when eukaryotes do appear on the scene of life, they can easily co-opt the proto-ubiquitin into its modern role.
If you're going to admit common descent of ThiS, MOAD, and the ubiquitin family, then a protein closely related to ubiquitin isn't necessary. Why not start with something more like ThiS? In which case, why not start with something pretty much like a prokaryote? The more homologies you claim, the greater the power you cede to purely Darwinian processes, and the less the need to "stack the deck".
(Consider if you showed me that all proteins were homologues descended from a single common ancestor. Would that be a point in favor of FLE?)
If you are prepared to say that without front-loading of the different genes, but just Darwininly (is that a word?) ThiS and ubiquitin descended from a common ancestor, when they do completely different things and have only 14% of their gene in common (according to WP) then I don't see why you should also think that there is any need whatsoever for any form of foresightful front-loading to produce eukaryotes.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 61 by Genomicus, posted 06-22-2012 12:22 AM Genomicus has replied

Replies to this message:
 Message 67 by Genomicus, posted 06-22-2012 10:39 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 64 of 172 (666114)
06-22-2012 12:56 AM
Reply to: Message 62 by Genomicus
06-22-2012 12:24 AM


Re: Evidence And Prediction
Yes. What did you think my position was? That intelligent intervention occurred for the origin of all species or that the origin of species was "programmed" somehow?
That's what it usually means. Typically, it is proposed as an origin for genetic information other than a Darwinian one. This involves information being differentially lost from different lineages. If you are prepared to admit that purely Darwinian processes can add useful new information to the pool, then really what's the need to front-load anything? Just start with something that's alive, and then let mutation, selection, etc, take it from there.

This message is a reply to:
 Message 62 by Genomicus, posted 06-22-2012 12:24 AM Genomicus has replied

Replies to this message:
 Message 81 by Genomicus, posted 06-25-2012 9:24 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(2)
Message 68 of 172 (666169)
06-23-2012 1:21 AM
Reply to: Message 67 by Genomicus
06-22-2012 10:39 PM


Re: The Ubiquitin Story
I admit that it was a bit of a stretch to say that these proteins carry out analogous functions. But they have key functional similarities.
Presumably involving the structural similarity they have in common.
But they do do radically different things.
Yes, but loading up the first genomes with proteins similar to ubiquitin would ensure that they'd be around before the appearance of Metazoa, so the front-loaders wouldn't have to depend on the blind watchmaker to "just happen" to find ubiquitin, allowing the origin of Metazoa.
Well, how similar? If members of this superduper protein family can differ by as much as 86% in their structure, and can differ completely as to the role they play in the cell, and if you're prepared to put that down to Darwinian mechanisms, then the blind watchmaker is starting to look pretty good at his job, isn't he?
Well, yes, but you actually expect a robust phylogeny of ubiquitin and its prokaryotic homologs?
I don't follow you.
ThiS, MOAD, and ubiquitin are all structurally related, so you'd need to load the genome with a structurally similar protein. I have no idea where you're going with "The more homologies you claim, the greater the power you cede to purely Darwinian processes, and the less the need to 'stack the deck'."
Well, you claim, do you not, that after LUCA the designers just let Darwinian processes get on with it. And you claim, do you not, that ThiS and MOAD and the ubiquitin family are all homologues rather than being separately front-loaded, don't you? In which case you ascribe the differences between them in form and function to the blind watchmaker, don't you? In which case, as I say, he must be quite good at his job.
Well, having admitted that much, does it seem so implausible that the blind watchmaker is also responsible for producing the one thing that ThiS and MOAD and ubiquitin do have in common, at some period prior to LUCA? Once you've said that known and observable processes such as mutation and natural selection can do so much to the form and function of proteins, why postulate an extra unobserved hypothetical mechanism to do one little bit more?
As I said in another post, FLE is usually the choice of people who have fallen for bad arguments for the impotence of Darwinian mechanisms. You, on the other hand, seem to think that these mechanisms are very powerful.
There are those who think that building the Great Pyramid was so far beyond the ability of ancient Egyptians that the work must have been done by space aliens. There are those who think that building the Great Pyramid was well within Egyptian capacities. But what would you say to someone who said: "I think that aliens started the Egyptians off by laying the first layer of stones, but I'm confident that they could easily have finished the rest themselves"? I think you'd say something along the lines of: "If you have such confidence in ancient Egyptian technology, why drag any aliens into it?"
Okay, by this do you mean that, e.g., cytochrome c, hemoglobin, insulin, etc., are (in this hypothetical scenario) all descended from a common ancestor?
Yes. If that was the case, would it be a point in favor of FLE or a point against it?
Precisely because without putting a protein that is structurally similar to ubiquitin in the first genomes, you'd have to depend on the blind watchmaker to tinker around with the existing folds, and "just happen" to come up with a protein that is structurally similar to ubiquitin (and also happens to have the necessary sulfur chemistry).
The "and" there is superfluous. If you admit that all the homologues really are homologues, then the only respect in which the parent molecule has to be similar to ubiquitin is in possessing the one property that the homologues actually have in common. After that you just step back and let the blind watchmaker do his non-magic.

This message is a reply to:
 Message 67 by Genomicus, posted 06-22-2012 10:39 PM Genomicus has replied

Replies to this message:
 Message 83 by Genomicus, posted 06-25-2012 10:19 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 70 of 172 (666199)
06-23-2012 9:49 PM
Reply to: Message 69 by Dr Jack
06-23-2012 8:53 AM


Re: The Ubiquitin Story
I didn't follow that, I don't see why Genomicus would.

This message is a reply to:
 Message 69 by Dr Jack, posted 06-23-2012 8:53 AM Dr Jack has seen this message but not replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(2)
Message 84 of 172 (666325)
06-25-2012 10:54 PM
Reply to: Message 83 by Genomicus
06-25-2012 10:19 PM


Re: The Ubiquitin Story
The proteins belonging to this "superduper" protein family do not differ by as much as 86% in their structure, but in their sequence identity. There's a crucial difference.
If it's crucial, please tell me more about it. What other structural similarities do they have?
Tinkering around with an already existing fold is hardly coming up with a novel fold, ya know.
I never said it was.
This one fold seems to have been conserved. The rest, not so much. The function of the proteins, not at all.
Given that there are many possible protein folds that have not been "found" by evolution in the history of life on earth, ubiquitin could have been one of those structures that never arose - in which case, eukaryotes might very possibly not have arisen.
Are we approaching the Texan Sharpshooter Fallacy?

This message is a reply to:
 Message 83 by Genomicus, posted 06-25-2012 10:19 PM Genomicus has replied

Replies to this message:
 Message 107 by Genomicus, posted 06-26-2012 6:07 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 85 of 172 (666326)
06-26-2012 1:30 AM
Reply to: Message 81 by Genomicus
06-25-2012 9:24 PM


Re: Evidence And Prediction
Actually, given that Darwinian evolution is perfectly capable of generating new information (e.g., gene and genome duplication, etc.), I wouldn't want to argue for a hypothesis that suggests that Darwinian mechanisms can't generate new information. The front-loading hypothesis that I'm discussing, and the one that Mike Gene supports, has to do with simply building the first cells in such a way that subsequent evolution is heavily biased towards chosen trajectories.
Well, I refer you to my analogy of the ancient Egyptians.
I'm really having a hard time understanding why anyone should think what you apparently think. If you suppose that Darwinian processes were sufficient to take LUCA and give rise to such diverse productions as an oak tree and a giraffe and a butterfly, then I don't see why you should cavil at the proposition that LUCA itself is a product of Darwinian evolution. Who swallows a camel but strains at a gnat?

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Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 127 of 172 (666483)
06-27-2012 5:44 PM
Reply to: Message 107 by Genomicus
06-26-2012 6:07 PM


Re: The Ubiquitin Story
The paper I cited describes the structural similarities between ubiquitin and its prokaryotic homologs.
Yes, it was more of a rhetorical question.
If you concede that they are actually homologues, then you concede that the blind watchmaker created all (or all but a few) of the other functional parts of these various superfamilies of proteins? So why would you object to the proposition that the blind watchmaker is also responsible for the one part they have in common?

This message is a reply to:
 Message 107 by Genomicus, posted 06-26-2012 6:07 PM Genomicus has replied

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 Message 136 by Genomicus, posted 06-28-2012 2:16 PM Dr Adequate has not replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


Message 130 of 172 (666495)
06-28-2012 1:27 AM
Reply to: Message 129 by Genomicus
06-27-2012 8:16 PM


Re: The Ubiquitin Story
Also, in a more a global sense, FLE predicts that key eukaryotic proteins will share deep homology with prokaryotic proteins that are not part of the essential gene set.
But as we have seen, it doesn't. The objections to this claim are as cogent this week as they were last week.

This message is a reply to:
 Message 129 by Genomicus, posted 06-27-2012 8:16 PM Genomicus has replied

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 Message 137 by Genomicus, posted 06-28-2012 2:35 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 275 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 156 of 172 (666928)
07-01-2012 12:12 PM
Reply to: Message 137 by Genomicus
06-28-2012 2:35 PM


1. Non-teleological evolution predicts that key eukaryotic genes will share homology with functional but unnecessary proteins. Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome.
Actually, no. As I have pointed out, the fact that a protein is functional but unnecessary in modern prokaryotes does not mean that it was unnecessary in LUCA. The fact that LUCA was a prokaryote in the sense of not-having-a-nucleus does not necessarily mean that its cellular economy was more like modern prokaryotes with respect to the function of (for example) histone-like proteins.
(By analogy, the first amphibians certainly had an amphibian lifestyle. But we know that in some respects they were more like modern reptiles than like modern amphibians.)
Interestingly, however, a number of papers have proposed that the LUCA did, in fact, have only a minimal genome ...
... and a number have proposed that it didn't.
... demonstrating that this is perfectly reasonable under the non-telic model.
Quite.
The designers could have engineered the minimal gene set such that it also front-loads the Metazoa we see. But this is actually quite unlikely, as you'd probably have to substantially modify the necessary genes, in which case they're no longer retaining their original function, and wouldn't be functioning as a minimal gene set.
But now you seem to be back to the error of the "giraffophile designer". (If I understand you correctly, stop me if I'm wrong.) Based on evidence which suggests that the genome was minimal, you conclude that the front-loading must have been front-loading of a minimal gene set, from which you conclude that we should have evidence that the genome was minimal.
But if it was certain (and it is far from certain) that LUCA's genome was minimal, then you couldn't hold that up as a prediction of your hypothesis when you're also using it as data to decide exactly what your hypothesis is.
You need to go: "Front loading, therefore I predict a minimal genome for LUCA"; not: "Front loading, and a minimal genome for LUCA, therefore a front-loaded minimal genome for LUCA, therefore I predict a minimal genome for LUCA."
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 137 by Genomicus, posted 06-28-2012 2:35 PM Genomicus has replied

Replies to this message:
 Message 167 by Genomicus, posted 07-08-2012 9:49 AM Dr Adequate has replied

  
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