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Author Topic:   Deep Homology and Front-loading
Taq
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Posts: 6461
Joined: 03-06-2009
Member Rating: 4.3


Message 166 of 172 (667178)
07-03-2012 3:59 PM
Reply to: Message 162 by Genomicus
07-03-2012 1:56 PM


Re: I predict "No LUCA"!
Well, we know that endosymbiosis events are not at all implausible occurrences. However, it's not plausible for a specific protein fold to "just happen" to evolve, given that there are many more possible protein folds that could have arisen, many of which would not have contributed to the rise of eukaryotes.

You are assuming that metazoans were the goal. The front loaders may have had different life in mind, but an evolutionary novelty arose that dashed all of their plans. What you keep ignoring is that something other than eukaryotes could have arisen.

If convergent evolution has taught us anything, it is that given specified initial conditions, specific biological objectives can be front-loaded over deep-time.

Actually, it teaches us just the opposite. It teaches us that evolution will find similar solutions from DIFFERENT starting points. That is the opposite of front loading.


This message is a reply to:
 Message 162 by Genomicus, posted 07-03-2012 1:56 PM Genomicus has not yet responded

  
Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 167 of 172 (667495)
07-08-2012 9:49 AM
Reply to: Message 156 by Dr Adequate
07-01-2012 12:12 PM


I'm quite busy with moving at the moment, so apologies for the extremely slow responses.

Anyhew:

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.

You're ignoring the key issue: that, under the non-telic model, LUCA could have been a simple prokaryote that did not require eukaryotic proteins. Is it not true, that under the current theory, the LUCA could easily have been only a simple prokaryote?

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.

No. As I stated in the OP, front-loading requires that the genome of the LUCA be more than a minimal genome. Indeed, some evidence indicates it was minimal. But the idea that the LUCA's genome was minimal is not compatible with front-loading, and thus we can predict that key eukaryotic proteins will share deep homology with prokaryotic proteins that are functional but unnecessary for a minimal genome, which in turn would mean that the LUCA's genome was not minimal.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 156 by Dr Adequate, posted 07-01-2012 12:12 PM Dr Adequate has responded

Replies to this message:
 Message 168 by Dr Adequate, posted 07-08-2012 1:41 PM Genomicus has responded

  
Dr Adequate
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Posts: 15929
Joined: 07-20-2006
Member Rating: 3.8


Message 168 of 172 (667505)
07-08-2012 1:41 PM
Reply to: Message 167 by Genomicus
07-08-2012 9:49 AM


You're ignoring the key issue: that, under the non-telic model, LUCA could have been a simple prokaryote that did not require eukaryotic proteins. Is it not true, that under the current theory, the LUCA could easily have been only a simple prokaryote?

Yes, that's perfectly true, but it's not what you said. What you said was: "Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome." So I pointed out that it does not in fact make that prediction.

No. As I stated in the OP, front-loading requires that the genome of the LUCA be more than a minimal genome. Indeed, some evidence indicates it was minimal. But the idea that the LUCA's genome was minimal is not compatible with front-loading, and thus we can predict that key eukaryotic proteins will share deep homology with prokaryotic proteins that are functional but unnecessary for a minimal genome, which in turn would mean that the LUCA's genome was not minimal.

I must have misunderstood the point I was replying to, then.

I still can't see what you were getting at here.

On the one hand, you say that: "the idea that the LUCA's genome was minimal is not compatible with front-loading" --- i.e. FLE would predict a non-minimal genome.

OTOH, you say that: "the non-telic model predicts that the LUCA did not have a minimal genome".

But weren't you meant to be looking for a prediction that FLE made and Darwinism didn't? You seem to have asserted in separate posts that both of them predict the same thing.


This message is a reply to:
 Message 167 by Genomicus, posted 07-08-2012 9:49 AM Genomicus has responded

Replies to this message:
 Message 169 by Genomicus, posted 07-09-2012 4:42 PM Dr Adequate has responded

  
Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 169 of 172 (667572)
07-09-2012 4:42 PM
Reply to: Message 168 by Dr Adequate
07-08-2012 1:41 PM


Yes, that's perfectly true, but it's not what you said. What you said was: "Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome." So I pointed out that it does not in fact make that prediction.

If I did say that, then I was dreadfully wrong. It would be more accurate to say that: "Essentially then, it is fully compatible under the non-telic model for the LUCA to have only a minimal genome, and it is also fully compatible with that model for the LUCA have more than a minimal genome."

I must have misunderstood the point I was replying to, then.

I still can't see what you were getting at here.

On the one hand, you say that: "the idea that the LUCA's genome was minimal is not compatible with front-loading" --- i.e. FLE would predict a non-minimal genome.

OTOH, you say that: "the non-telic model predicts that the LUCA did not have a minimal genome".

But weren't you meant to be looking for a prediction that FLE made and Darwinism didn't? You seem to have asserted in separate posts that both of them predict the same thing.

Okay. Let me try to explain what I'm trying to get at. The below diagram may help us visualize the situation here.

In this figure, we see two ovals: the blue one represents all the potential biological observations that are compatible with non-teleological evolution. The pink oval represents the potential biological observations that are compatible with FLE. The area of overlap between the two ovals signifies those biological observations that are compatible under both models. Areas with no overlap indicate biological observations that are only compatible in one of the models.

Now, observe that the potential biological observation of a non-minimal genome for the LUCA is compatible with both non-telic evolution and front-loading. However, the observation that the LUCA had only a minimal genome is not compatible with front-loading, while it is compatible with non-telic evolution. And this is where we can generate a testable prediction from the FLE perspective: when it comes to genomic complexity, FLE predicts that the LUCA had a non-minimal genome. Meanwhile, non-telic evolution doesn't predict this.

I have argued from the literature that it is certainly reasonable under the non-telic model for the LUCA to have only a minimal genome. You (Dr Adequate), along with Catholic Scientist, seem to be in agreement with this (i.e., that it is not unreasonable in the non-telic model for the LUCA to have only a minimal genome), while Taq, PaulK, et al., think otherwise. I'd say that the scientific literature, for the most part, supports the former contention: namely, that it is not unreasonable for the LUCA to have only a minimal genome under the current theory.

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 168 by Dr Adequate, posted 07-08-2012 1:41 PM Dr Adequate has responded

Replies to this message:
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 Message 171 by Dr Adequate, posted 07-10-2012 12:25 AM Genomicus has not yet responded

  
PaulK
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Posts: 12688
Joined: 01-10-2003
Member Rating: 2.8


Message 170 of 172 (667575)
07-09-2012 5:06 PM
Reply to: Message 169 by Genomicus
07-09-2012 4:42 PM


I submit to you that, on the contrary, a LUCA that is a minimal prokaryote is MORE likely given FLE than non-telic evolution.

Firstly, non-telic evolution gives us no reason to presume that the LUCA was a prokaryote, while it appears to be an assumption of FLE.

Secondly I have given good reasons to expect that even if the LUCA were a prokaryote it would be very unlikely to have a strictly minimal genome - reasons that do not apply to the artificially engineered life assumed by FLE.

Thirdly your reason for assuming that the FLE LUCA could not have a minimal genome is simply an opinion without much in the way of argumentative support - and in my opinion it ignores the possibilities open to the assumed FLE engineers. It is certain that an artificial prokaryote produced by engineering would be more capable of evolving the current diversity of life than one produced by non-telic evolution, probably to a significant degree.

Finally "deep homology" does not require that the genes in question were present in the LUCA, only that they appeared prior to the split between prokaryotes and eukaryotes. They need only be present in the last common ancestor of eukaryotes and SOME prokaryotes for vertical transmission - and not even that for horizontal transmission from eukaryotes to prokaryotes.


This message is a reply to:
 Message 169 by Genomicus, posted 07-09-2012 4:42 PM Genomicus has not yet responded

    
Dr Adequate
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Posts: 15929
Joined: 07-20-2006
Member Rating: 3.8


Message 171 of 172 (667588)
07-10-2012 12:25 AM
Reply to: Message 169 by Genomicus
07-09-2012 4:42 PM


You (Dr Adequate), along with Catholic Scientist, seem to be in agreement with this (i.e., that it is not unreasonable in the non-telic model for the LUCA to have only a minimal genome) ...

Yes. If I had to put money on it, I think I'd lean towards it being non-minimal. It is, after all, the last universal common ancestor; but this is merely a hunch, and I wouldn't be at all shocked to learn that it was minimal after all.

I'd say that the scientific literature, for the most part, supports the former contention: namely, that it is not unreasonable for the LUCA to have only a minimal genome under the current theory.

Do bear in mind that when they say that, that's not a prediction of the theory, it's an interpretation of the observations in light of the theory. Now since your version of FLE maintains that evolution was Darwinian after LUCA, it follows that if they're right that this is the Darwinian interpretation, it must also by the same token be the interpretation of (your version of) FLE.

To put it another way, if it is consistent with modern observations and with Darwinism to say that LUCA could have been minimal, it is also consistent with your FLE to say that it could have been minimal. So for the sake of your argument, you should be hoping that the scientists who say this are wrong, whereas you seem to be hoping that they're right.

Edited by Dr Adequate, : No reason given.


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 Message 169 by Genomicus, posted 07-09-2012 4:42 PM Genomicus has not yet responded

Replies to this message:
 Message 172 by Dr Adequate, posted 07-10-2012 12:59 PM Dr Adequate has not yet responded

  
Dr Adequate
Member
Posts: 15929
Joined: 07-20-2006
Member Rating: 3.8


Message 172 of 172 (667609)
07-10-2012 12:59 PM
Reply to: Message 171 by Dr Adequate
07-10-2012 12:25 AM


To clarify my point.

When scientists speculate about what LUCA was like, they are not doing so by saying: "Abiogenesis is true, and Darwinian processes reigned between abiogenesis and LUCA, therefore we can deduce such-and-such a thing about LUCA".

Rather, they are saying: "The observations we make of modern organisms are true, and Darwinian processes reigned between LUCA and modern organisms, therefore we can deduce such-and-such a thing about LUCA".

And you agree with their premises.

So if you're going to say that FLE predicts a priori a non-minimal genome for LUCA, then what you would want them to say is that their interpretation is that LUCA had a non-minimal genome.

But I think you're wrong about what FLE predicts. I have no difficulty conceiving of aliens (for example) seeding our planet with organisms with a minimal genome, which then evolved in a Darwinian way to produce the diversity of life we see today. I have no problem with this because I also have no problem with believing that LUCA had a minimal genome, was not seeded by aliens, and produced the same results by the same mechanisms.

The question of whether LUCA was or was not minimal can be decided, if at all (which I doubt very much) not a priori from the competing hypotheses of Darwinism and FLE, but a posteriori from the data about modern organisms that we now have in front of us. Which totally screws your argument.


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