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Author Topic:   Deep Homology and Front-loading
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?


This message is a reply to:
 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

  
Taq
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Posts: 8002
Joined: 03-06-2009
Member Rating: 4.4


(1)
Message 77 of 172 (666307)
06-25-2012 5:48 PM
Reply to: Message 76 by New Cat's Eye
06-25-2012 4:57 PM


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

Through a consensus sequence. Let's say that you had the following three sequences:

seq 1: ATAA
seq 2: AATA
seq 3: AAAC
-------------------
con : AAAA

The consensus sequence would be AAAA since the majority of the three sequences have an A at each position. 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. 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. However, it would seem to be the most obvious starting place for the FLE hypothesis, but it would appear that Geno is starting clear at the other end.

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?

The first thing I would look for is sequences that are designed solely for the benefit of the designer, such as those found in lifeforms that we design (e.g. GM foods).

If I was front loading a genome then I would want to make sure it does the job I want it to do when it gets to that point. That would mean having some sort of mutation protection for that sequence.


This message is a reply to:
 Message 76 by New Cat's Eye, posted 06-25-2012 4:57 PM New Cat's Eye has responded

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 Message 79 by New Cat's Eye, posted 06-25-2012 8:27 PM Taq has responded

  
bluegenes
Member (Idle past 733 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(2)
Message 78 of 172 (666310)
06-25-2012 6:16 PM
Reply to: Message 75 by Taq
06-25-2012 3:55 PM


Taq writes:

IOW, FLE is nothing more than the hope of some supernatural guidance in a nominally non-teleologic process.

To say fair, Genomicus seems to deliberately steer clear of implying the supernatural. The hypothesis is that the deck has been stacked on this planet, but not necessarily on the planet of origin of the designers. Unlike other I.D.ists, he never attacks non-telic abiogenesis with spurious probability arguments, and he never claims that the blind watchmaker couldn't have produced the metazoa (including his designers).

That might seem to make Geno's position difficult, but actually any argument for natural intelligent design (a known phenomenon - we do it) is on an infinitely better footing than one for supernatural design.

But you're right about the sharpshooting. I've been attempting what seem to me more reasonable (if conditional) predictions from the general hypothesis. If the hypothesis is that this planet was seeded with the intent of producing metazoa, then I'd suggest that we should see instant biodiversity and no LUCA, because that would be the best way for the designers to minimize risk of complete extinction. More importantly, we should see the maximum possible engineering of shortcuts towards the production of complex metazoa, given the circumstances of the early planet. So, if geochemists were to discover that eukaryotes appear right at the very first point that life appears, that might seem to be a point in favour of directed panspermia.

So I think Geno's problems go beyond Occam's razor and sharpshooting. I don't think that the most obvious predictions of the hypothesis are supported by current evidence at all. Still, Sci-Fi can be fun.


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

Replies to this message:
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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

  
Genomicus
Member (Idle past 197 days)
Posts: 852
Joined: 02-15-2012


(2)
Message 80 of 172 (666315)
06-25-2012 9:19 PM


Note to foreveryoung
This is a brief off-topic note to the user foreveryoung (since it's off-topic, I'll totally understand if the moderators remove it):

You've "liked" a great number of my posts for no real reason, other than to "artificially" inflate my member rating. I'd far rather that my member rating reflects my actual standing here instead of something that is the result of what is effectively abusing the system of liking posts. I daresay that you didn't read most of the posts that you liked, foreveryoung (you probably did it just because I happen to be an ID proponent, and in your mind any ID proponent's argument is valid, right? No, that's not how it works; I may very well be wrong about something, so you have to use good judgment in what is and what is not a valid argument). I would therefore greatly appreciate it if you removed the "likes" of my posts and did not continue to do abuse the system.

Thank you.


  
Genomicus
Member (Idle past 197 days)
Posts: 852
Joined: 02-15-2012


Message 81 of 172 (666316)
06-25-2012 9:24 PM
Reply to: Message 64 by Dr Adequate
06-22-2012 12:56 AM


Re: Evidence And Prediction
Yes. What did you think my position was? That intelligent intervention occurred for the origin of all species or that the origin of species was "programmed" somehow?

That's what it usually means. Typically, it is proposed as an origin for genetic information other than a Darwinian one. This involves information being differentially lost from different lineages. If you are prepared to admit that purely Darwinian processes can add useful new information to the pool, then really what's the need to front-load anything? Just start with something that's alive, and then let mutation, selection, etc, take it from there.

Actually, given that Darwinian evolution is perfectly capable of generating new information (e.g., gene and genome duplication, etc.), I wouldn't want to argue for a hypothesis that suggests that Darwinian mechanisms can't generate new information. The front-loading hypothesis that I'm discussing, and the one that Mike Gene supports, has to do with simply building the first cells in such a way that subsequent evolution is heavily biased towards chosen trajectories.


This message is a reply to:
 Message 64 by Dr Adequate, posted 06-22-2012 12:56 AM Dr Adequate has responded

Replies to this message:
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Genomicus
Member (Idle past 197 days)
Posts: 852
Joined: 02-15-2012


Message 82 of 172 (666317)
06-25-2012 9:48 PM
Reply to: Message 65 by PaulK
06-22-2012 1:32 AM


Again, you are just repeating your assumption.

It's not exactly an assumption IMHO. It's an argument based on what we know about biology: life requires a fairly specific core set of genes and there is little evidence that those genes, in themselves, favor the appearance of complex life forms.

I am suggesting that it is possible that they might be able to engineer the proteins to favour an evolutionary trajectory that would produce the features that they were interested in, yes. I don't accept that those possibilities are only satisfied by the metazoa as we know them.

Where is the evidence that one can engineer a gene set that not only fills the roles necessary for the existence of life but also favor the appearance of complex life forms?

Your standard for prediction seems to require absolute certainty, because you reject near-certainties as predictions when they come from the evolutionary side.

I have no idea where you got that idea.


This message is a reply to:
 Message 65 by PaulK, posted 06-22-2012 1:32 AM PaulK has responded

Replies to this message:
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Genomicus
Member (Idle past 197 days)
Posts: 852
Joined: 02-15-2012


Message 83 of 172 (666321)
06-25-2012 10:19 PM
Reply to: Message 68 by Dr Adequate
06-23-2012 1:21 AM


Re: The Ubiquitin Story
Well, how similar? If members of this superduper protein family can differ by as much as 86% in their structure, and can differ completely as to the role they play in the cell, and if you're prepared to put that down to Darwinian mechanisms, then the blind watchmaker is starting to look pretty good at his job, isn't he?

The proteins belonging to this "superduper" protein family do not differ by as much as 86% in their structure, but in their sequence identity. There's a crucial difference. You can have proteins that are quite divergent in sequence similarity, but have pretty similar structures.

So, from a front-loading perspective, the designers would load up the first genomes with the basic ubiquitin structure, such that it could be easily co-opted into a role that is necessary for the rise of eukaryotes.

Well, you claim, do you not, that after LUCA the designers just let Darwinian processes get on with it. And you claim, do you not, that ThiS and MOAD and the ubiquitin family are all homologues rather than being separately front-loaded, don't you? In which case you ascribe the differences between them in form and function to the blind watchmaker, don't you? In which case, as I say, he must be quite good at his job.

Tinkering around with an already existing fold is hardly coming up with a novel fold, ya know. With the basic ubiquitin structure in the first genomes, the blind watchmaker would modify it, giving it different functions, etc., - but all of this isn't anything terribly significant. Simple mutations could do the trick. But if you don't put the basic ubiquitin structure in the first genomes, you'd have to depend on Darwinian mechanisms to come up with that structure, prior to the origin of eukaryotes. Given that there are many possible protein folds that have not been "found" by evolution in the history of life on earth, ubiquitin could have been one of those structures that never arose - in which case, eukaryotes might very possibly not have arisen.

Yes. If that was the case, would it be a point in favor of FLE or a point against it?

It would be a point against it because it would mean that there was no front-loading, but that, instead, all these proteins came from the machinery necessary to the existence of life, which means that evolution could have followed any one of numerous other paths, many of which wouldn't lead to eukaryotes. In essence, there wouldn't be any "stacking of the deck."


This message is a reply to:
 Message 68 by Dr Adequate, posted 06-23-2012 1:21 AM Dr Adequate has responded

Replies to this message:
 Message 84 by Dr Adequate, posted 06-25-2012 10:54 PM Genomicus has responded
 Message 90 by Taq, posted 06-26-2012 11:38 AM Genomicus has responded

  
Dr Adequate
Member
Posts: 16101
Joined: 07-20-2006


(2)
Message 84 of 172 (666325)
06-25-2012 10:54 PM
Reply to: Message 83 by Genomicus
06-25-2012 10:19 PM


Re: The Ubiquitin Story
The proteins belonging to this "superduper" protein family do not differ by as much as 86% in their structure, but in their sequence identity. There's a crucial difference.

If it's crucial, please tell me more about it. What other structural similarities do they have?

Tinkering around with an already existing fold is hardly coming up with a novel fold, ya know.

I never said it was.

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

Given that there are many possible protein folds that have not been "found" by evolution in the history of life on earth, ubiquitin could have been one of those structures that never arose - in which case, eukaryotes might very possibly not have arisen.

Are we approaching the Texan Sharpshooter Fallacy?


This message is a reply to:
 Message 83 by Genomicus, posted 06-25-2012 10:19 PM Genomicus has responded

Replies to this message:
 Message 107 by Genomicus, posted 06-26-2012 6:07 PM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16101
Joined: 07-20-2006


Message 85 of 172 (666326)
06-26-2012 1:30 AM
Reply to: Message 81 by Genomicus
06-25-2012 9:24 PM


Re: Evidence And Prediction
Actually, given that Darwinian evolution is perfectly capable of generating new information (e.g., gene and genome duplication, etc.), I wouldn't want to argue for a hypothesis that suggests that Darwinian mechanisms can't generate new information. The front-loading hypothesis that I'm discussing, and the one that Mike Gene supports, has to do with simply building the first cells in such a way that subsequent evolution is heavily biased towards chosen trajectories.

Well, I refer you to my analogy of the ancient Egyptians.

I'm really having a hard time understanding why anyone should think what you apparently think. If you suppose that Darwinian processes were sufficient to take LUCA and give rise to such diverse productions as an oak tree and a giraffe and a butterfly, then I don't see why you should cavil at the proposition that LUCA itself is a product of Darwinian evolution. Who swallows a camel but strains at a gnat?


This message is a reply to:
 Message 81 by Genomicus, posted 06-25-2012 9:24 PM Genomicus has not yet responded

  
PaulK
Member
Posts: 15372
Joined: 01-10-2003
Member Rating: 3.3


Message 86 of 172 (666328)
06-26-2012 1:36 AM
Reply to: Message 82 by Genomicus
06-25-2012 9:48 PM


quote:

It's not exactly an assumption IMHO. It's an argument based on what we know about biology: life requires a fairly specific core set of genes and there is little evidence that those genes, in themselves, favor the appearance of complex life forms.

It would be more accurate to say that Earthly life requires a fairly specific set of genes, and there's little evidence that THOSE genes favour the emergence of complex life forms (although that's more to do with our current ignorance than our knowledge). When we start talking about hypothetical designed life then we're talking about something very different.

quote:

Where is the evidence that one can engineer a gene set that not only fills the roles necessary for the existence of life but also favor the appearance of complex life forms?

Where's the evidence that it can't be done ? Remember that your requirement for a prediction is absolute certainty - an opinion won't cut it. I've given reasons to think that it might be possible and you haven't really answered them. That's not good enough to have a solid prediction even by my standards, let alone yours.

quote:

I have no idea where you got that idea.

Yes, you apologetic types often have problems remembering what you said:

Message 32


...one scenario that is perfectly acceptable under Darwinian evolution is that the LUCA had only a minimal genome. Such a scenario is not, however, compatible with FLE.

According to you the fact that non-telic evolution doesn't absolutely rule out the possibility of a LUCA with a minimal gene set is sufficient to say that it is not a prediction. Therefore FLE must absolutely rule out the possibility that a minimal gene set could be constructed that would provide sufficient guidance for the purposes of it's inventors. Now, without any idea of the limits of design or any clear idea of how that guidance might work or even the purposes of the designers you aren't in a position to do that.

So lets get rid of the double standard. At present there's a stronger case for a LUCA with a non-minimal gene set under the assumption of non-telic evolution than there is under the FLE. That means that it isn't a prediction of FLE that can separate it from standard evolutionary views.


This message is a reply to:
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bluegenes
Member (Idle past 733 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 87 of 172 (666341)
06-26-2012 8:24 AM
Reply to: Message 66 by Genomicus
06-22-2012 10:16 PM


Re: I predict "No LUCA"!
Genomicus writes:

Well, eukaryotes aren't as good terra-formers as bacteria, and for front-loading to work on an originally hostile planet, you'd need to terra-form it such that it'll eventually be friendly to complex life forms, like mice and rabbits and trees (and of course, giraffes) etc.

I wasn't suggesting that the frontloaders would load only eukaryotes. The more, the merrier, and the higher the chances of metazoa.

Also, although some eukaryotes can survive extreme environments, prokaryotes are far at surviving extreme environments. Furthermore, since I envision the first life forms arriving on earth via directed panspermia, the eukaryotes would have to survive the space voyage from their home planet to earth.

One more point. Some researchers have in fact proposed that the LUCA was effectively a eukaryote (albeit lacking mitochondria), with prokaryotes "degenerating" from the LUCA.

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.....

And as for FLs leaving out mitochondria in a eukaryote LUCA when they want to frontload metazoa..... come on, Geno, that can't make sense to you!

Genomicus writes:

Ubiquitin is another example. Prior to structural analyses of various prokaryotic proteins, there were no known prokaryotic homologs of ubiquitin. The logic of front-loading predicts otherwise, and indeed, research has uncovered deep homology between ubiquitin and prokaryotic proteins.

Why wouldn't the "logic of frontloading" predict actual ubiquitin in the proks? 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 letter "a" is ubiquitous in all languages that use Latin letters, and denotes approximately the same sound(s) in them all. That doesn't mean that the Romans intentionally frontloaded the modern languages with it. More importantly, the "a" sign is arbitrary, and the function could be performed just as well by "$" if the correct protocol were in place. Mr. Jack's "lock and key" analogy might be better to illustrate the more directly physical nature of signalling proteins.

Genomicus writes:

I freely admit that much of the time I'm following my intuition when it comes to the hypothesis of front-loading. My intuition is fallible of course, but that's why I'm not asking any of you to accept front-loading as a valid science at the moment. As I stated earlier, there are many hurdles facing the FL hypothesis.

Yes, I understand that your claims are modest. It's refreshing compared to what we're accustomed to with more conventional I.D. ists, and the tentativity should be appreciated by most of us here.

Geno writes:

Well, there's a lot of time for the nanotechnologists to emerge on a planet that is older then the earth.

They've got to be around 4 billion y.a., which gives them from the moment that the universe could first support life up to 4 bya to evolve. I think that the jury is still out on when the universe could first have supported life. If it was as late as 8 bya, the frontloading biologists arrived just as quickly as us without any "deck stacking".


This message is a reply to:
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Replies to this message:
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Taq
Member
Posts: 8002
Joined: 03-06-2009
Member Rating: 4.4


Message 88 of 172 (666349)
06-26-2012 11:11 AM
Reply to: Message 79 by New Cat's Eye
06-25-2012 8:27 PM


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'?

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.

As to size . . . as large as possible. 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.


This message is a reply to:
 Message 79 by New Cat's Eye, posted 06-25-2012 8:27 PM New Cat's Eye has responded

Replies to this message:
 Message 92 by New Cat's Eye, posted 06-26-2012 12:58 PM Taq has responded

  
Taq
Member
Posts: 8002
Joined: 03-06-2009
Member Rating: 4.4


Message 89 of 172 (666351)
06-26-2012 11:32 AM
Reply to: Message 78 by bluegenes
06-25-2012 6:16 PM


To say fair, Genomicus seems to deliberately steer clear of implying the supernatural.

Fair enough. However, we can't have an infinite regress of natural designers. There had to be a first set of natural designers at some point in our Universe's history. Therefore, we already know that non-teleologic natural mechanisms are capable of producing intelligent designers like us. There is every reason to believe that we are those First Designers, the first in a chain of intelligent design.

Perhaps I have jumped the gun in accusing Genomicus of proposing a supernatural teleological force . . . time will tell.

If the hypothesis is that this planet was seeded with the intent of producing metazoa, then I'd suggest that we should see instant biodiversity and no LUCA, because that would be the best way for the designers to minimize risk of complete extinction. More importantly, we should see the maximum possible engineering of shortcuts towards the production of complex metazoa, given the circumstances of the early planet.

Quite right. If the intent was for metazoans to arise in the future, why not make them straight away? We can deduce from our own technological evolution that it would only take a few decades between designing our first prokaryote and our first eukaryote. Even more, we could easily tweek simple metazoans from our own ecosystem to fit the environs of a distant planet. Do you want oxygen in the atmosphere? Dump some genetically modified algae into the planet's oceans.


This message is a reply to:
 Message 78 by bluegenes, posted 06-25-2012 6:16 PM bluegenes has acknowledged this reply

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Taq
Member
Posts: 8002
Joined: 03-06-2009
Member Rating: 4.4


Message 90 of 172 (666352)
06-26-2012 11:38 AM
Reply to: Message 83 by Genomicus
06-25-2012 10:19 PM


Re: The Ubiquitin Story
So, from a front-loading perspective, the designers would load up the first genomes with the basic ubiquitin structure, such that it could be easily co-opted into a role that is necessary for the rise of eukaryotes.

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.

But if you don't put the basic ubiquitin structure in the first genomes, you'd have to depend on Darwinian mechanisms to come up with that structure, prior to the origin of eukaryotes.

This would only be true if the evolution of complex life required the existence of the ubiquitin fold. You haven't shown that anywhere. You are acting as if the biodiversity we see today is the only way it could have been. I see no reason why this is true. If ubiquitin did not evolve and life took a different route towards complex multicellular life then you (or possibly and intelligent being like you) would be talking about how this other protein was front loaded. You are painting the bull's eye around the bullet hole.

Given that there are many possible protein folds that have not been "found" by evolution in the history of life on earth, ubiquitin could have been one of those structures that never arose - in which case, eukaryotes might very possibly not have arisen.

But something else would have.


This message is a reply to:
 Message 83 by Genomicus, posted 06-25-2012 10:19 PM Genomicus has responded

Replies to this message:
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