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Author Topic:   Deep Homology and Front-loading
Taq
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Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 106 of 172 (666401)
06-26-2012 4:49 PM
Reply to: Message 105 by Genomicus
06-26-2012 4:24 PM


Since when did the supernatural, gods, deities, etc., enter this discussion?

When purpose is assigned to natural processes. That is usually where such discussions lead. Perhaps I have jumped the gun on this one . . . time will tell.


This message is a reply to:
 Message 105 by Genomicus, posted 06-26-2012 4:24 PM Genomicus has not yet responded

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


Message 107 of 172 (666410)
06-26-2012 6:07 PM
Reply to: Message 84 by Dr Adequate
06-25-2012 10:54 PM


Re: The Ubiquitin Story
What other structural similarities do they have?

The paper I cited describes the structural similarities between ubiquitin and its prokaryotic homologs.

This one fold seems to have been conserved. The rest, not so much. The function of the proteins, not at all.

Yet it is the basic structure of a protein that determines its function - along with the proteins it interacts with, of course. My point is that loading the first genomes with an ubiquitin-related fold allows it to be easily co-opted into the role used by eukaryotes.


This message is a reply to:
 Message 84 by Dr Adequate, posted 06-25-2012 10:54 PM Dr Adequate has responded

Replies to this message:
 Message 108 by Taq, posted 06-27-2012 10:54 AM Genomicus has not yet responded
 Message 127 by Dr Adequate, posted 06-27-2012 5:44 PM Genomicus has responded

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


Message 108 of 172 (666436)
06-27-2012 10:54 AM
Reply to: Message 107 by Genomicus
06-26-2012 6:07 PM


Re: The Ubiquitin Story
My point is that loading the first genomes with an ubiquitin-related fold allows it to be easily co-opted into the role used by eukaryotes.

This is true no matter what the origin of ubiquitin is, and is easily accomplished by non-teleological processes.


This message is a reply to:
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Genomicus
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Joined: 02-15-2012
Member Rating: 4.6


Message 109 of 172 (666448)
06-27-2012 1:10 PM
Reply to: Message 87 by bluegenes
06-26-2012 8:24 AM


Re: I predict "No LUCA"!
I wasn't suggesting that the frontloaders would load only eukaryotes. The more, the merrier, and the higher the chances of metazoa.

Understood.

The last point doesn't really fit very well with the first two, does it? It would also mean that, far from frontloading a prokaryote LUCA with eukaryotes in mind, the frontloaders (FLs) would presumably have had terraforming prokaryotes in mind when designing their eukaryote LUCA. Why not make sure by designing the proks as well? The more, the merrier, and the better the chances.....

Quite right. I personally favor the hypothesis that the LUCA was prokaryotic, and not eukaryotic, although some researchers say that the LUCA was more of a eukaryote precisely because of its complexity and the large number of proteins its genome encoded. This is fully compatible with front-loading.

Why wouldn't the "logic of frontloading" predict actual ubiquitin in the proks?

Because the mutations do happen, and over deep time, a protein sequence can change quite extensively - to the point that it is no longer the original protein (but structurally similar, nonetheless, and this is what matters).

There's also a problem here that Mr. Jack hinted at in a post above. Ubiquitin being ubiquitous in eukaryotes does not necessarily mean that it's necessary for metazoa, or that the fold is necessary. It could just be a "frozen accident".

The universal distribution of ubiquitin among eukaryotes strongly implies that it is necessary for eukaryotic existence, does it not? True, it could be a "frozen accident." But the front-loaders aren't going to gamble their chances on accidents. It would be far better design logic just to put that protein fold into the first cells.


This message is a reply to:
 Message 87 by bluegenes, posted 06-26-2012 8:24 AM bluegenes has responded

Replies to this message:
 Message 110 by jar, posted 06-27-2012 1:17 PM Genomicus has responded
 Message 126 by Dr Jack, posted 06-27-2012 4:58 PM Genomicus has not yet responded
 Message 141 by bluegenes, posted 06-28-2012 9:13 PM Genomicus has responded

  
jar
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Posts: 28427
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.6


Message 110 of 172 (666449)
06-27-2012 1:17 PM
Reply to: Message 109 by Genomicus
06-27-2012 1:10 PM


I predict no front-loaders.
The universal distribution of ubiquitin among eukaryotes strongly implies that it is necessary for eukaryotic existence, does it not?

No more than the fact that the water fills the hole implies that the hole was necessary for the water. The only thing implied is that ubiquitin was just good enough to work.

True, it could be a "frozen accident." But the front-loaders aren't going to gamble their chances on accidents. It would be far better design logic just to put that protein fold into the first cells.

But there is evidence of the existence of accidents while no one has ever presented any evidence of the existence of the front-loaders.


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

This message is a reply to:
 Message 109 by Genomicus, posted 06-27-2012 1:10 PM Genomicus has responded

Replies to this message:
 Message 112 by Genomicus, posted 06-27-2012 1:26 PM jar has responded

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


Message 111 of 172 (666450)
06-27-2012 1:25 PM
Reply to: Message 89 by Taq
06-26-2012 11:32 AM


Quite right. If the intent was for metazoans to arise in the future, why not make them straight away?

Metazoans don't survive that well in an environment like that of the early, hostile earth ya know.

Do you want oxygen in the atmosphere? Dump some genetically modified algae into the planet's oceans.

Alternatively, you could put some cyanobacteria into the planet's oceans. That's why terra-forming is intimately linked with front-loading. In order to ensure that animals and plants can arrive on the scene later, you have to change the earth such that it is hospitable to animals and plants.


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 Message 89 by Taq, posted 06-26-2012 11:32 AM Taq has not yet responded

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


Message 112 of 172 (666451)
06-27-2012 1:26 PM
Reply to: Message 110 by jar
06-27-2012 1:17 PM


Re: I predict no front-loaders.
No more than the fact that the water fills the hole implies that the hole was necessary for the water. The only thing implied is that ubiquitin was just good enough to work.

So why aren't there any animals or plants etc. that lack ubiquitin?


This message is a reply to:
 Message 110 by jar, posted 06-27-2012 1:17 PM jar has responded

Replies to this message:
 Message 113 by jar, posted 06-27-2012 1:34 PM Genomicus has responded

  
jar
Member
Posts: 28427
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.6


Message 113 of 172 (666453)
06-27-2012 1:34 PM
Reply to: Message 112 by Genomicus
06-27-2012 1:26 PM


Re: I predict no front-loaders.
Because it was just good enough to work. As you said, a "frozen accident".

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

This message is a reply to:
 Message 112 by Genomicus, posted 06-27-2012 1:26 PM Genomicus has responded

Replies to this message:
 Message 114 by Genomicus, posted 06-27-2012 1:37 PM jar has responded

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


Message 114 of 172 (666454)
06-27-2012 1:37 PM
Reply to: Message 113 by jar
06-27-2012 1:34 PM


Re: I predict no front-loaders.
Because it was just good enough to work.

Yes, but that does not explain why there are no eukaryote lineages that lack ubiquitin.

And, again, from a front-loading perspective, we would predict ubiquitin homologs in prokaryotes, while we cannot predict this from a non-teleological standpoint.


This message is a reply to:
 Message 113 by jar, posted 06-27-2012 1:34 PM jar has responded

Replies to this message:
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jar
Member
Posts: 28427
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.6


Message 115 of 172 (666455)
06-27-2012 1:38 PM
Reply to: Message 114 by Genomicus
06-27-2012 1:37 PM


Re: I predict no front-loaders.
But there is evidence of accidents and no evidence of front-loaders.

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

This message is a reply to:
 Message 114 by Genomicus, posted 06-27-2012 1:37 PM Genomicus has not yet responded

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


Message 116 of 172 (666456)
06-27-2012 1:48 PM
Reply to: Message 90 by Taq
06-26-2012 11:38 AM


Re: The Ubiquitin Story
How did you determine that ubiquitin structure was intended for use in metazoans? How did you rule out the possibility that other proteins were destined for this role, but evolution caused ubiquitin to fill this role instead.

That's not really the issue IMHO. 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. This is the point. Confirmation of those predictions strengthens the above thesis.

Now, you might rightly ask why we should assume that Metazoa were the intended outcome of front-loading, instead of, say, a race of flying spaghetti monsters. But here is where fallible intuition comes into play. If we were to seed another planet with life, and front-load objectives into existence, we would likely choose plants and animals. This, of course, is not evidence that Metazoa were the intended outcome of front-loading - I am well aware of that. 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. Darwinian evolution has been very comfortable with the fact that, prior to structural analyses, there were no known prokaryotic homologs of ubiquitin. Yet front-loading predicts exactly this.


This message is a reply to:
 Message 90 by Taq, posted 06-26-2012 11:38 AM Taq has responded

Replies to this message:
 Message 117 by jar, posted 06-27-2012 1:53 PM Genomicus has responded
 Message 119 by New Cat's Eye, posted 06-27-2012 2:01 PM Genomicus has responded
 Message 122 by PaulK, posted 06-27-2012 2:19 PM Genomicus has responded
 Message 124 by Taq, posted 06-27-2012 2:42 PM Genomicus has responded

  
jar
Member
Posts: 28427
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.6


Message 117 of 172 (666457)
06-27-2012 1:53 PM
Reply to: Message 116 by Genomicus
06-27-2012 1:48 PM


I predict no intended outcome
Why should anyone assume that there was ANY intended outcome?

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

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 118 by Genomicus, posted 06-27-2012 1:59 PM jar has responded

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


Message 118 of 172 (666458)
06-27-2012 1:59 PM
Reply to: Message 117 by jar
06-27-2012 1:53 PM


Re: I predict no intended outcome
There are clues that teleology has played a role in the history of life on earth, so this offers a subtle hint that maybe there was an intended outcome.
This message is a reply to:
 Message 117 by jar, posted 06-27-2012 1:53 PM jar has responded

Replies to this message:
 Message 121 by jar, posted 06-27-2012 2:14 PM Genomicus has not yet responded

  
New Cat's Eye
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Posts: 11174
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.7


Message 119 of 172 (666459)
06-27-2012 2:01 PM
Reply to: Message 116 by Genomicus
06-27-2012 1:48 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.

Would that lead you to believe in Rain Dances?


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 120 by Genomicus, posted 06-27-2012 2:04 PM New Cat's Eye has responded

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


Message 120 of 172 (666460)
06-27-2012 2:04 PM
Reply to: Message 119 by New Cat's Eye
06-27-2012 2:01 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.


This message is a reply to:
 Message 119 by New Cat's Eye, posted 06-27-2012 2:01 PM New Cat's Eye has responded

Replies to this message:
 Message 123 by New Cat's Eye, posted 06-27-2012 2:25 PM Genomicus has responded
 Message 125 by Taq, posted 06-27-2012 2:43 PM Genomicus has not yet responded

  
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