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Author Topic:   Deep Homology and Front-loading
New Cat's Eye
Inactive Member


Message 71 of 172 (666269)
06-25-2012 11:38 AM
Reply to: Message 67 by Genomicus
06-22-2012 10:39 PM


Re: The Ubiquitin Story
Nice thread, Geno.

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).

But how unlikely is it, really? Maybe its inevitable, no? Given that its all spontaneous chemistry, and that proteins work because of thier shape, why wouldn't we expect these kinds of similarities even without FLE?


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


(2)
Message 74 of 172 (666294)
06-25-2012 2:35 PM
Reply to: Message 72 by Taq
06-25-2012 12:39 PM


This quote exemplifies the problems with FLE. It is Texas Sharpshooting, plain and simple.

I was noticing that too, but couldn't remember the name of the fallacy. I was thinking that this looked an aweful lot like saying the pothole was designed to fit around the puddle, its just that were zooming in to the individual water molecules interacting with the concrete ones.

I was going to mention to Geno that it looked like he already liked FLE, and then went looking for evidence that can be shoehorned into it, rather than coming to a conclusion of FLE from the evidence that he had found.


This message is a reply to:
 Message 72 by Taq, posted 06-25-2012 12:39 PM Taq has responded

Replies to this message:
 Message 75 by Taq, posted 06-25-2012 3:55 PM New Cat's Eye has responded

  
New Cat's Eye
Inactive Member


(1)
Message 76 of 172 (666303)
06-25-2012 4:57 PM
Reply to: Message 75 by Taq
06-25-2012 3:55 PM


A more scientific approach would be to derive the ancestral genome and then demonstrate from first principles which genes were front loaded without pointing to modern genomes.

So yeah, he seems to be saying that is you work backwards from a protein that's necessary for eukaryotes, but not for prokaryotes, and then if Front Loading did happen, we should see a unneeded homolog for that protein in prokaryotes. I don't see where he explains why we wouldn't expect that under 'darwinian' evolution.

I don't know enough about genetics, how would you derive the ancestral genome?

How would you go about showing that some of the stuff we find in the earliest forms of life contain evidence of incorporating intelligently desinged genomic sequences and/or proteins?


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 Message 75 by Taq, posted 06-25-2012 3:55 PM Taq has responded

Replies to this message:
 Message 77 by Taq, posted 06-25-2012 5:48 PM New Cat's Eye has responded

  
New Cat's Eye
Inactive Member


(1)
Message 79 of 172 (666314)
06-25-2012 8:27 PM
Reply to: Message 77 by Taq
06-25-2012 5:48 PM


The methodology is based on the rules of parsimony where it is assumed that common sequence is ancestral instead of the same independent mutation in several lineages.

With your meaningfully helpful example, that assumption seems shaky at first. But I guess that depends on the size of the sequence. What sizes are we talkin'?

You can also incorporate the phylogeny into the reconstruction. Of course, the more ancient the sequence the more phylogeny and sequence data you will need and the less confidence you will have in the sequence.

More data's great. That makes sense. What determines the size of the sequence?


This message is a reply to:
 Message 77 by Taq, posted 06-25-2012 5:48 PM Taq has responded

Replies to this message:
 Message 88 by Taq, posted 06-26-2012 11:11 AM New Cat's Eye has responded

  
New Cat's Eye
Inactive Member


Message 92 of 172 (666360)
06-26-2012 12:58 PM
Reply to: Message 88 by Taq
06-26-2012 11:11 AM


What are the chances that the same mutation will occur at the same base in 5 different species? Quite slim. It is possible, but improbable.

Doesn't that depend on the length of the sequence?

If were just dealing with AAAA and AAAT, then having AAAT pop up twice isn't all that improbable. (Stats was the only math class I hated and I ain't gonna figure this one) Plus, considering the chemistry of it, some of it ain't even all that random, is it?

As to size . . . as large as possible.

Sweet. E aho laula.

If you are trying to reconstruct the entire ancestral genome then you will try to find ALL of the shared DNA you can. You need to keep in mind that DNA will be lost in different lineages, so phylogenetic information is also important to determine when that deletion occurred.

Seems to me that the phylogeny speeks better, I don't see how you could come to much of a conclusion from the sequences. I'm not liking Geno's approach... but don't get me wrong folks, I'd love to see some good evidence showing some planning involved in the evolution of life on Earth.


This message is a reply to:
 Message 88 by Taq, posted 06-26-2012 11:11 AM Taq has responded

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New Cat's Eye
Inactive Member


Message 93 of 172 (666361)
06-26-2012 1:01 PM
Reply to: Message 87 by bluegenes
06-26-2012 8:24 AM


Re: I predict "No LUCA"!
Ubiquitin being ubiquitous

Just now getting that, thanks.

I don't see how the large presence of ubiquitin would point more towards either FLE or "darwinian" evolution.


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New Cat's Eye
Inactive Member


Message 99 of 172 (666383)
06-26-2012 2:15 PM
Reply to: Message 94 by Genomicus
06-26-2012 1:29 PM


Re: The Ubiquitin Story
I don't think there's anything in the blind watchmaker that makes it inevitable for a specific fold to arise, in the absence of specified initial conditions. I.e., starting with just a few basic folds, there's no real guarantee that the blind watchmaker will be able to piece together a specific novel fold.

The thing in the blind watchmaker is chemistry. Proteins work because of their shape, they get their shape based on the chemistry of their interactions. The blind watchmaker would just offer every possible fold and the ones that work would stick and the ones that didn't would be discarded.

In hind sight, it might look like the ones that stuck were meant to be, but you're not looking at all the ones that didn't make it. That's were the sharpshooting fallacy comes into play. How many folds were tried and how many of those succeeded? If you had a brazillion folds and a handful make the cut, then looking back on only the handful to come to a conclusion of improbability wouldn't be good thinking.

It sure looks like the puddle was designed to fit within the pothole, and when you zoom in it might not make sense why that particular water molecule ended up in that particular place. The water is trying to go everywhere, but gravity pulls it into the puddle. Similarly, the proteins were trying to fold in every shape, but chemisty decides what works and what doesn't.


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New Cat's Eye
Inactive Member


Message 100 of 172 (666384)
06-26-2012 2:18 PM
Reply to: Message 95 by jar
06-26-2012 1:36 PM


Re: The Ubiquitin Story
If you've got a lock and somebody keeps randomly making keys, its inevitable that eventually you'll get a key that unlocks it.
This message is a reply to:
 Message 95 by jar, posted 06-26-2012 1:36 PM jar has acknowledged this reply

  
New Cat's Eye
Inactive Member


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?


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

  
New Cat's Eye
Inactive Member


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

  
New Cat's Eye
Inactive Member


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

  
New Cat's Eye
Inactive Member


(1)
Message 145 of 172 (666681)
06-29-2012 1:58 PM
Reply to: Message 142 by Genomicus
06-29-2012 1:41 PM


Re: The LUCA and the minimal genome
C’mon guys, the least you can do is admit that your view that the LUCA could not have logically had a minimal genome is contradicted by the scientific literature.

People certainly inferred that LUCA had a minimum genome and that inferrence is consistent with the "darwinian" model. But its not necessitated. As we've uncovered more genetic evidence, we've realized that LUCA would have been bigger than we had thought. Which, too, is consistent with the model.

Challenge: find a single paper in the scientific literature that argues that it is not reasonable under the current paradigm for the LUCA to have only a minimal genome.

It took me about 7 minutes to find three:

quote:
Therefore , the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology. source

quote:
Thus LUCA was not a minimal organism but the first modern organism equipped with a DNA genome and the universal genetic code. source

quote:
Results: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote
but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad
range of moderate temperatures, genetically redundant, morphologically and metabolically diverse.source

This message is a reply to:
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Replies to this message:
 Message 147 by Genomicus, posted 06-29-2012 2:10 PM New Cat's Eye has responded

  
New Cat's Eye
Inactive Member


Message 149 of 172 (666702)
06-29-2012 2:42 PM
Reply to: Message 147 by Genomicus
06-29-2012 2:10 PM


Re: The LUCA and the minimal genome
From Message 143:

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

Quite right.

"It could have happened differently" isn't a reason to not suspect a ubiquitin homolog in prokaryotes.

Under the non-teleological model, ubiquitin could have evolved from different stretches of non-coding DNA, which means that any evidence of homology would have been lost over deep-time.

Why would it be lost?

If we find a homolog to the ubiquitin protein, we automatically have found a homolog to the ubiquitin gene.

Not necessarily. You could find homologous proteins without knowing their genes. It looks like you were saying that non-teleological evolution does not predict that the ubiquitin protein will have a prokaryotic homolog because the ubiquitin gene could have arrisen differently. That doesn't necessarily follow.

"Ubiquitin is a protein and T-urf13 is a gene." Yes, and ubiquitin is encoded by a gene, which could have been pieced together in the same way that the T-urf13 gene was.

How do you know the gene that encodes ubiquitin could have arrisen like the T-urf13 gene did?


You did not address my challenge. You provided three studies - of which I was aware - that provide evidence that the LUCA did not have a minimal genome. You did not provide any papers arguing that it is unreasonable for the LUCA to have had a minimal genome under the non-telic model. In other words, find papers that say stuff like "the idea that the LUCA had a minimal genome is not compatible with the 'Darwinian' model."

Who's saying that it was unreasonable to infer a minimal genome for LUCA?


This message is a reply to:
 Message 147 by Genomicus, posted 06-29-2012 2:10 PM Genomicus has responded

Replies to this message:
 Message 152 by Genomicus, posted 06-29-2012 9:12 PM New Cat's Eye has responded

  
New Cat's Eye
Inactive Member


Message 157 of 172 (667017)
07-02-2012 11:20 AM
Reply to: Message 152 by Genomicus
06-29-2012 9:12 PM


Re: The LUCA and the minimal genome
"It could have happened differently" isn't a reason to not suspect a ubiquitin homolog in prokaryotes.

Certainly it is. If it could have happened differently in the non-telic framework, then you don't have a real prediction.

Oh, you mean like a real temporal prediction... Sometimes when people are talking about whether a scientific theory predicts something, they're just meaning that its a valid logical consequence of the theory and not really that the theory was used to forecast a new discovery.

But if that's the case, then FLE didn't predict any of this either, did it?

I'm not following you. If you find a protein that is homologous to ubiquitin, then all you have to do is track down its gene sequence, and voila! you have a gene that is homologous to the ubiquitin gene.

Um, ubiquitin was discovered in, like, 1975. They didn't know how to "track down gene sequences" back then.

And that's the cause of a lot of your issue here. You're using the scientific inferences about the size of LUCA that were before the latest in genetic discoveries. We've learned a lot since then and the scientific position has changed. It wasn't unreasonable for those people in the past to infer a small LUCA, but today, with our current knowledge we now know that it is unreasonable. We've learned that the size of LUCA was a lot larger than we first anticipated.

But the thing is, both the small and large LUCA's are logically consistent with the model, that is, it "predicts" both of them (in the non-temporal sense). What I mean is that either one will work within the model, the model doesn't necessitate either one.

The same goes for FLE. The designers could have done it any number of ways. In your own sense, you don't have a prediction either. And in my sense, we don't have a definative case that your data suggest FLE over the traditional model.

How do you know the gene that encodes ubiquitin could have arrisen like the T-urf13 gene did?

How do you know that it could not have? After all, what's stopping a gene that encoded ubiquitin from arising in the same manner that the T-urf13 gene did?

Oh. You were saying that it could have like it was some fact. Apparently, you're just assuming that it could have. Not all genes can arrise in the same way.

Specifically, who's saying that it is unreasonable under the non-telic model for the LUCA to have a minimal genome.

I'm sure you didn't miss these:

I did miss those, and I prefer to see them in context - aren't they talking about being reasonable today rather than referring to the old inferrences from the past?

If you type [msg=152] , it will become Message 152 and you can link to specific posts within this same thread by their post number. You can also use the message ID number, the dark grey long number next to the Message # of #, with the "mid" tag like this: [mid=666826] if you want to link to messages in other threads, it'll look like this: Message 152. You can also click on the Peek button in the bottom right of any post to see the coding that was entered into the text box.


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