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Author Topic:   Deep Homology and Front-loading
jar
Member
Posts: 28460
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.7


Message 121 of 172 (666461)
06-27-2012 2:14 PM
Reply to: Message 118 by Genomicus
06-27-2012 1:59 PM


Re: I predict no intended outcome
Nonsense, and the overwhelming evidence is that there was no intended outcome.

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

This message is a reply to:
 Message 118 by Genomicus, posted 06-27-2012 1:59 PM Genomicus has not yet responded

  
PaulK
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Posts: 12452
Joined: 01-10-2003
Member Rating: 2.5


Message 122 of 172 (666462)
06-27-2012 2:19 PM
Reply to: Message 116 by Genomicus
06-27-2012 1:48 PM


Re: The Ubiquitin Story
quote:

However, if we follow the line of thought that Metazoa were, in fact, the intended outcome of front-loading, from here we can make real predictions that are not made by the non-teleological model. The non-telic view of life does not require that prokaryotes have ubiquitin homologs.

I disagree. If ubiquitin is essential to eukaryotic life, and if eukaryotes and prokaryotes have a common ancestor then non-telic evolution predicts that at least some prokaryotes should have a ubiquitin homolog.

The reasoning as follows:

If eukaryotes are descended from prokaryotes then ubiquitin must have evolved in the prokaryotic ancestors of eukaryotes (because essential proteins don't just appear at the exact moment that they are needed)

If prokaryotes are descended from eukaryotes then ubiquitin must have been present in the ancestors of all prokaryotes and lost through evolution, after the divide between the two Kingdoms.


This message is a reply to:
 Message 116 by Genomicus, posted 06-27-2012 1:48 PM Genomicus has responded

Replies to this message:
 Message 128 by Genomicus, posted 06-27-2012 7:46 PM PaulK has responded

    
New Cat's Eye
Member
Posts: 11185
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.6


Message 123 of 172 (666463)
06-27-2012 2:25 PM
Reply to: Message 120 by Genomicus
06-27-2012 2:04 PM


Re: The Ubiquitin Story
If my Rain Dance causes the rain, then I predict that it will rain after I do my dance. It did rain after I did my dance, therefore that strengthens the theory that my Rain Dance causes the rain.

No, because rain is predicted from plain ole' meteorology.

You haven't explained why I shouldn't expect the prevalence of Ubiquitin under the standard evolutionary model.


This message is a reply to:
 Message 120 by Genomicus, posted 06-27-2012 2:04 PM Genomicus has responded

Replies to this message:
 Message 129 by Genomicus, posted 06-27-2012 8:16 PM New Cat's Eye has responded

  
Taq
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Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 124 of 172 (666466)
06-27-2012 2:42 PM
Reply to: Message 116 by Genomicus
06-27-2012 1:48 PM


Re: The Ubiquitin Story
If we assume, for sake of argument, that the Metazoa we see today was the intended outcome of a front-loading scheme, we can make testable predictions regarding biotic reality.

If you assume your conclusion then you can not make testable predictions. That's the problem.

However, if we follow the line of thought that Metazoa were, in fact, the intended outcome of front-loading, from here we can make real predictions that are not made by the non-teleological model.

Those predictions exactly mirror non-teleological models. FLE states that modern genes descended from ancient genes. Non-teleological models make the SAME PREDICTION.

The non-telic view of life does not require that prokaryotes have ubiquitin homologs.

The non-telic view of weather does not require that it rain in Dallas, TX today. However, it is certainly a possibility for non-telic meteorology, is it not? The same for ubiquitin homologs. Non-telic mechanisms are clearly capable of co-opting ancestral genes for roles in subsequent generations.


This message is a reply to:
 Message 116 by Genomicus, posted 06-27-2012 1:48 PM Genomicus has responded

Replies to this message:
 Message 135 by Genomicus, posted 06-28-2012 2:04 PM Taq has responded
 Message 159 by Genomicus, posted 07-03-2012 12:31 PM Taq has responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 125 of 172 (666467)
06-27-2012 2:43 PM
Reply to: Message 120 by Genomicus
06-27-2012 2:04 PM


Re: The Ubiquitin Story
No, because rain is predicted from plain ole' meteorology.

Shared genes between eukaryotes and prokaryotes are predicted from plain ole' evolution.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 120 by Genomicus, posted 06-27-2012 2:04 PM Genomicus has not yet responded

  
Dr Jack
Member
Posts: 3500
From: Leicester, England
Joined: 07-14-2003


Message 126 of 172 (666480)
06-27-2012 4:58 PM
Reply to: Message 109 by Genomicus
06-27-2012 1:10 PM


Ubiquitin is not special
The universal distribution of ubiquitin among eukaryotes strongly implies that it is necessary for eukaryotic existence, does it not?

It implies that our Eukaryotes require it, yes, but it doesn't imply that life like a Eukaryote requires it. There's no reason to think that we couldn't engineer a Eukaryote so that it used a different molecule in place of ubiquitin, it'd just need every protein that interacts with it to be re-worked - which is why evolution can't do it.

Ubiquitin is a signalling molecule, not an enzyme, it's functionality lies in its interaction with other proteins, not it anything inherent to its structure (well, it needs to be small, easily synthesized and capable of being combined into chains but that leaves literally thousands of possibilities).


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Dr Adequate
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Posts: 15485
Joined: 07-20-2006
Member Rating: 3.9


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 responded

Replies to this message:
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Genomicus
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Posts: 781
Joined: 02-15-2012
Member Rating: 4.6


Message 128 of 172 (666488)
06-27-2012 7:46 PM
Reply to: Message 122 by PaulK
06-27-2012 2:19 PM


Re: The Ubiquitin Story
I disagree. If ubiquitin is essential to eukaryotic life, and if eukaryotes and prokaryotes have a common ancestor then non-telic evolution predicts that at least some prokaryotes should have a ubiquitin homolog.

And:

The reasoning as follows:

If eukaryotes are descended from prokaryotes then ubiquitin must have evolved in the prokaryotic ancestors of eukaryotes (because essential proteins don't just appear at the exact moment that they are needed)

If prokaryotes are descended from eukaryotes then ubiquitin must have been present in the ancestors of all prokaryotes and lost through evolution, after the divide between the two Kingdoms.

Non-teleological evolution does not predict that ubiquitin will have a prokaryotic homolog because the ubiquitin gene could easily have been pieced together from different pieces of DNA, in much the same way that T-urf13 evolved. In such a scenario, given the deep-time involved and the fact that this protein would have been cobbled together from short stretches of DNA, we would almost certainly not be able to trace this homology in prokaryotes - and, of course, structural analyses wouldn't reveal any homologs of ubiquitin in prokaryotes.

On the other hand, if eukaryotes were front-loaded, the designers wouldn't depend on simple accidents to "just happen" to cobble ubiquitin together from a variety of motifs, indels, chunks of functional modules, etc. The first genomes would have a structurally-related protein, such that the ubiquitin fold is already in place prior to the origin of eukaryotes.


This message is a reply to:
 Message 122 by PaulK, posted 06-27-2012 2:19 PM PaulK has responded

Replies to this message:
 Message 131 by PaulK, posted 06-28-2012 1:37 AM Genomicus has responded
 Message 133 by Taq, posted 06-28-2012 11:23 AM Genomicus has responded

  
Genomicus
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Posts: 781
Joined: 02-15-2012
Member Rating: 4.6


Message 129 of 172 (666490)
06-27-2012 8:16 PM
Reply to: Message 123 by New Cat's Eye
06-27-2012 2:25 PM


Re: The Ubiquitin Story
You haven't explained why I shouldn't expect the prevalence of Ubiquitin under the standard evolutionary model.

More specifically, why the current theory does not predict the presence of ubiquitin homologs in prokaryotes. See my latest reply to PaulK for reasons why we don't expect this under the standard evolutionary model.

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. Although we can't predict exactly what proteins will share homology with functional but unnecessary prokaryotic proteins, we can predict the above in a general sense.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 123 by New Cat's Eye, posted 06-27-2012 2:25 PM New Cat's Eye has responded

Replies to this message:
 Message 130 by Dr Adequate, posted 06-28-2012 1:27 AM Genomicus has responded
 Message 132 by New Cat's Eye, posted 06-28-2012 9:44 AM Genomicus has responded
 Message 134 by Taq, posted 06-28-2012 11:25 AM Genomicus has not yet responded

  
Dr Adequate
Member
Posts: 15485
Joined: 07-20-2006
Member Rating: 3.9


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 responded

Replies to this message:
 Message 137 by Genomicus, posted 06-28-2012 2:35 PM Dr Adequate has responded

  
PaulK
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Posts: 12452
Joined: 01-10-2003
Member Rating: 2.5


Message 131 of 172 (666496)
06-28-2012 1:37 AM
Reply to: Message 128 by Genomicus
06-27-2012 7:46 PM


Re: The Ubiquitin Story
quote:

Non-teleological evolution does not predict that ubiquitin will have a prokaryotic homolog because the ubiquitin gene could easily have been pieced together from different pieces of DNA, in much the same way that T-urf13 evolved.

That doesn't affect my reasoning, though. HOW ubiquitin appeared is not an issue. WHEN it appeared in the evolutionary history of eukaryotes and prokaryotes is the issue. And my argument covers that.

quote:

In such a scenario, given the deep-time involved and the fact that this protein would have been cobbled together from short stretches of DNA, we would almost certainly not be able to trace this homology in prokaryotes - and, of course, structural analyses wouldn't reveal any homologs of ubiquitin in prokaryotes.

This fails to address my argument. If ubiquitin is truly essential for eukaryotes then this patching together almost certainly appeared in a prokaryote - the alternative is vanishingly unlikely. As I said, genes don't magically appear in the first organism that needs them. Therefore there must have been prokaryotes with ubiquitin even in your scenario. So why wouldn't we expect to find homologues ?


This message is a reply to:
 Message 128 by Genomicus, posted 06-27-2012 7:46 PM Genomicus has responded

Replies to this message:
 Message 146 by Genomicus, posted 06-29-2012 2:07 PM PaulK has responded

    
New Cat's Eye
Member
Posts: 11185
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.6


Message 132 of 172 (666514)
06-28-2012 9:44 AM
Reply to: Message 129 by Genomicus
06-27-2012 8:16 PM


Re: The Ubiquitin Story
More specifically, why the current theory does not predict the presence of ubiquitin homologs in prokaryotes.

I think it does. If eukaryotes evolved from prokaryotes, and all eukaryotes have ubiquitin, then there should be something like ubiquitin in prokaryotes that it evolved from.

See my latest reply to PaulK for reasons why we don't expect this under the standard evolutionary model.

You reason seems to be: "it could have happened differently".

quote:
Non-teleological evolution does not predict that ubiquitin will have a prokaryotic homolog because the ubiquitin gene could easily have been pieced together from different pieces of DNA, in much the same way that T-urf13 evolved.

That isn't a reason to not suspect a ubiquitin homolog in prokaryotes. And what makes you think that ubiquitin could have evolved like T-urf13 did? Ubiquitin is a protein and T-urf13 is a gene... wait, are you looking for a homolog to the ubiquitin protein or the ubiquitin gene?

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.

Hold on... the front loaders could have done it differently! Right?

Although we can't predict exactly what proteins will share homology with functional but unnecessary prokaryotic proteins, we can predict the above in a general sense.

Sure, but in the same way: if my Rain Dance works, we can predict in the general sense that the rain that came afterwards was caused by it.


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

Replies to this message:
 Message 143 by Genomicus, posted 06-29-2012 1:50 PM New Cat's Eye has not yet responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 133 of 172 (666530)
06-28-2012 11:23 AM
Reply to: Message 128 by Genomicus
06-27-2012 7:46 PM


Re: The Ubiquitin Story
Non-teleological evolution does not predict that ubiquitin will have a prokaryotic homolog because the ubiquitin gene could easily have been pieced together from different pieces of DNA, in much the same way that T-urf13 evolved.

Non-teleological meteorology does not predict that it will rain in Dallas, TX today because it could just as easily not rain today. Therefore, if it rains it is due to rain fairies.

Do you think this is a valid argument? I sure don't. While non-teleological meteorology does not require that specific areas get rain at specific times, it can easily accomodate these observations. In the same way, evolution does not predict that specific proteins will become necessary in future generations. Rather, it accomodates such observations. Ubiquitin fits this model. Non-teleological evolution can easily co-opt a gene in ancestors to fill a necessary role in descendants. That is what it does. You are trying to falsify evolution by pointing to the very observations that it can produce. That makes no sense.

Better yet, please show that it is impossible for non-teleological evolution to create these observations.


This message is a reply to:
 Message 128 by Genomicus, posted 06-27-2012 7:46 PM Genomicus has responded

Replies to this message:
 Message 144 by Genomicus, posted 06-29-2012 1:54 PM Taq has responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 134 of 172 (666531)
06-28-2012 11:25 AM
Reply to: Message 129 by Genomicus
06-27-2012 8:16 PM


Re: The Ubiquitin Story
More specifically, why the current theory does not predict the presence of ubiquitin homologs in prokaryotes.

It predicts descent with modification, which is exactly what we observe.

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.

This does not differentiate FLE from non-teleological evolution since evolution can produce this same pattern.


This message is a reply to:
 Message 129 by Genomicus, posted 06-27-2012 8:16 PM Genomicus has not yet responded

  
Genomicus
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Posts: 781
Joined: 02-15-2012
Member Rating: 4.6


Message 135 of 172 (666554)
06-28-2012 2:04 PM
Reply to: Message 124 by Taq
06-27-2012 2:42 PM


Re: The Ubiquitin Story
If you assume your conclusion then you can not make testable predictions. That's the problem.

Okay, here's a simple true/false question: If the Metazoa we see today was the intended outcome of a front-loading scenario, could we make testable predictions from this premise?

Those predictions exactly mirror non-teleological models. FLE states that modern genes descended from ancient genes. Non-teleological models make the SAME PREDICTION.

No, non-teleological models do not predict that crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins. I've explained why many times, but here it is again: under the non-telic model, it is completely reasonable for the LUCA to have no more than a minimal genome. I have supported this contention with references to the scientific literature.

For example:
"...a recent analysis of 37,402 protein families across 184 genomes inferred that a CCF [core conserved function] composed of ~1400 gene families was present in LUCA. This estimate challenged the widely held view of a minimal genome containing ~300 genes supported by previous in-silico or in-vivo analyses.

...This indicates that in contrast to early hypotheses, LUCA was far from being a minimal cell because its genome was far from a minimal genome." (emphasis added; from "Origins and Evolution of Life: An Astrobiological Perspective," Muriel Gargaud, Purificación López-Garcěa, Hervč Martin, Cambridge University Press, 2011)

Read that carefully, then tell me that it's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.

The non-telic view of weather does not require that it rain in Dallas, TX today. However, it is certainly a possibility for non-telic meteorology, is it not? The same for ubiquitin homologs. Non-telic mechanisms are clearly capable of co-opting ancestral genes for roles in subsequent generations.

The issue here really isn't whether the non-telic view of life can potentially explain the observation that crucial eukaryotic proteins share deep homology with functional but unnecessary prokaryotic proteins. The real issue is whether the non-teleological model predicts this.


This message is a reply to:
 Message 124 by Taq, posted 06-27-2012 2:42 PM Taq has responded

Replies to this message:
 Message 138 by PaulK, posted 06-28-2012 2:47 PM Genomicus has not yet responded
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