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Author Topic:   Deep Homology and Front-loading
Dr Adequate
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Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 46 of 172 (666081)
06-21-2012 8:49 PM
Reply to: Message 44 by Genomicus
06-21-2012 6:31 PM


I find it suspicious that when I said "Evolution predicts that if the bacterial flagellum evolved, a number of its components will share similarity with proteins that are more ancient than the bacterial flagellum" you made no issue of it. Yet, now that we are discussing FLE you're bringing up the possibility of homologs being lost in various lineages.

In other words, if you want to bring up that aspect of all of this, then you've got to admit that Darwinian evolution actually doesn't predict that the bacterial flagellar components will share homology with more ancient systems.

I never said it did. You did. There is in fact no a priori reason why they should still be hanging around. They might well have been lost instead. There's nothing in Darwinism per se that says this shouldn't have happened. If you want to admit that you were wrong about this too, go right ahead.

Edited by Dr Adequate, : No reason given.


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Replies to this message:
 Message 48 by Genomicus, posted 06-21-2012 9:26 PM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 47 of 172 (666082)
06-21-2012 8:51 PM
Reply to: Message 41 by Genomicus
06-21-2012 4:38 PM


Re: I predict "No LUCA"!
What do you mean by "no LUCA"? Do you mean that modern life would have evolved from a pool of different species? I have no problem with that ...

In which case, once again, FLE does not predict any deep homologies at all.


This message is a reply to:
 Message 41 by Genomicus, posted 06-21-2012 4:38 PM Genomicus has not yet responded

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 48 of 172 (666089)
06-21-2012 9:26 PM
Reply to: Message 46 by Dr Adequate
06-21-2012 8:49 PM


I never said it did. You did. There is in fact no a priori reason why they should still be hanging around. They might well have been lost instead. There's nothing in Darwinism per se that says this shouldn't have happened. If you want to admit that you were wrong about this too, go right ahead.

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 (which is interesting, because it means there's not a scrap of evidence that the bacterial flagellum evolved). You might want to take that up with the numerous scientific papers that are under the impression that the similarities between the flagellum and more ancient systems (e.g., the ATP synthase) is evidence that the flagellum evolved.


This message is a reply to:
 Message 46 by Dr Adequate, posted 06-21-2012 8:49 PM Dr Adequate has responded

Replies to this message:
 Message 49 by Dr Adequate, posted 06-21-2012 9:42 PM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


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.


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

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 50 of 172 (666095)
06-21-2012 10:14 PM
Reply to: Message 49 by Dr Adequate
06-21-2012 9:42 PM


Re: Evidence And Prediction
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.

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; Nick Matzke, the guy who wrote an exhaustive essay on the evolution of the flagellum, is an example - but this is an aside).

However, I take issue with this statement of yours:

If prokaryotes lacked histone homologues, you'd just shrug and say that they dropped out of the prokaryote lineage just as (I presume you would have to say) the ability to synthesize peptidoglycan dropped out of the eukaryote lineage.

This is hypothetically possible, but it's really, really not likely for a fully functional protein in prokaryotes to be lost across all prokaryotic lineages.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 49 by Dr Adequate, posted 06-21-2012 9:42 PM Dr Adequate has responded

Replies to this message:
 Message 53 by Dr Adequate, posted 06-21-2012 10:28 PM Genomicus has responded

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 51 of 172 (666096)
06-21-2012 10:17 PM
Reply to: Message 42 by PaulK
06-21-2012 5:05 PM


The hypothetical designers would be free to choose any set of proteins that would work. They would, for instance be completely free to choose completely unrelated proteins. They would NOT be limited to using the proteins used by Earthly life.

Quite right. But they have to include the 250 or so genes necessary for carbon-based life forms to exist. And they'd add extra genes to the original genomes so that front-loading could follow.

250 proteins is quite a large number.

Okay, let me get your position right: are you suggesting that the designers could engineer the 250 genes needed for life such that they also favor the trajectory of evolution in the direction of Metazoa etc.?

For your argument to be truthful you need a consistent standard for "prediction".

That is you need a satisfactory standard that YOUR views satisfy, while the arguments from the evolutionary side do not.

That is rather difficult when your view is just an assumption that seems intuitive.

So, do you have a stronger argument that actually deals with the issues, or are you just going to evade the problem ?

Not sure what you mean by all of the above. Care to elaborate?

Edited by Genomicus, : No reason given.


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 Message 42 by PaulK, posted 06-21-2012 5:05 PM PaulK has responded

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 Message 65 by PaulK, posted 06-22-2012 1:32 AM Genomicus has responded

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 52 of 172 (666097)
06-21-2012 10:26 PM
Reply to: Message 43 by Dr Adequate
06-21-2012 5:25 PM


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.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 43 by Dr Adequate, posted 06-21-2012 5:25 PM Dr Adequate has responded

Replies to this message:
 Message 55 by Dr Adequate, posted 06-21-2012 10:45 PM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


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.


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 Message 50 by Genomicus, posted 06-21-2012 10:14 PM Genomicus has responded

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

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 54 of 172 (666100)
06-21-2012 10:37 PM
Reply to: Message 53 by Dr Adequate
06-21-2012 10:28 PM


Re: Evidence And Prediction
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.)

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. In other words, it'd be a horrible, horrible design strategy to load up the LUCA with a functionless protein that will only later find function in eukaryotes. In fact, that really wouldn't be front-loading any more - at least, not front-loading a la Mike Gene.


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 Message 53 by Dr Adequate, posted 06-21-2012 10:28 PM Dr Adequate has responded

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 Message 56 by Dr Adequate, posted 06-21-2012 10:53 PM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


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.)


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 Message 52 by Genomicus, posted 06-21-2012 10:26 PM Genomicus has responded

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

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


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.


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 Message 58 by Genomicus, posted 06-21-2012 11:26 PM Dr Adequate has responded

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 57 of 172 (666105)
06-21-2012 11:20 PM
Reply to: Message 55 by Dr Adequate
06-21-2012 10:45 PM


Re: The Ubiquitin Story
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...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.

Sequence homology isn't everything - especially when you consider the small size of ubiquitin (which means that it's more difficult to find a statistically significant database match among prokaryotes). You have to consider structural homology, and look at the bigger picture. Interestingly, a study from way back in 2003 did just that and found evidence of ubiquitin homologs among prokaryotes.

According to a study by Bienkowska et al. (2003):

"The question of protein homology versus analogy arises when proteins share a common function or a common structural fold without any statistically significant amino acid sequence similarity. Even though two or more proteins do not have similar sequences but share a common fold and the same or closely related function, they are assumed to be homologs, descendant from a common ancestor. The problem of homolog identification is compounded in the case of proteins of 100 or less amino acids...In an effort to identify distant homologs of the many ubiquitin proteins, we have developed a combined structure and sequence similarity approach that attempts to overcome the above limitations of homolog identification. This approach results in the identification of 90 probable ubiquitin-related proteins, including examples from the two prokaryotic domains of life, Archaea and Bacteria."

And:

"Using our search method, in addition to known homologs, we have identified 90 small proteins from the sequenced genomes of Archaea, Bacteria, C.elegans and A.thaliana that are predicted to be similar in structure...Seven sequences were identified as 2Fe–2S ferredoxins and 21 were identified as members of the MoaD/This superfamily. Further analysis of the structural alignments and alignments of MoaD and ThiS COGs lead us to the selection of three genes as coding for ubiquitin‐related proteins. Given the conservation of the structural position of functionally important lysine, we propose that archeal proteins AF0737, MTH1743 and aq_025a are distant homologs of ubiquitin."

All of this is very cool, of course, and is what we'd expect from front-loading: in a world without ubiquitin (or a closely related homolog), eukaryotes might not arise. Thus, we'd want to load the first genomes with ubiquitin, ensuring the origin of eukaryotes and animals, plants, etc.

Structural alignment of ubiquitin and a possible archaeal homolog.

Thus we can see that, despite deep time, traces of homology between ubiquitin and prokaryotic proteins can be found. And this is what we'd expect from front-loading. On the other hand, Darwinian logic doesn't allow us to make this prediction. Darwinian evolution has been very comfortable with the fact that, prior to the era of robust structural analyses, no prokaryotic homolog of ubiquitin was known.

References

Jadwiga R. Bienkowska, Hyman Hartman, Temple F. Smith. A search method for homologs of small proteins. Ubiquitin‐like proteins in prokaryotic cells? Protein Eng. (2003) 16 (12): 897-904.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 55 by Dr Adequate, posted 06-21-2012 10:45 PM Dr Adequate has responded

Replies to this message:
 Message 59 by Dr Adequate, posted 06-22-2012 12:08 AM Genomicus has responded

  
Genomicus
Member (Idle past 252 days)
Posts: 852
Joined: 02-15-2012


Message 58 of 172 (666106)
06-21-2012 11:26 PM
Reply to: Message 56 by Dr Adequate
06-21-2012 10:53 PM


Re: Evidence And Prediction
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?

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, making the origin of complex life forms probable.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 56 by Dr Adequate, posted 06-21-2012 10:53 PM Dr Adequate has responded

Replies to this message:
 Message 60 by Dr Adequate, posted 06-22-2012 12:20 AM Genomicus has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


(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.


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 Message 57 by Genomicus, posted 06-21-2012 11:20 PM Genomicus has responded

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

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


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 responded

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

  
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