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Author Topic:   Deep Homology and Front-loading
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 34 of 172 (666042)
06-21-2012 11:54 AM
Reply to: Message 33 by Dr Adequate
06-21-2012 11:14 AM


Well, in that you didn't actually answer it.
Is this your question?
You can produce as many cases as you like of things that are essential to eukaryotes and merely useful to prokaryotes. Knock yourself out. It doesn't help
But is there anything in FLE that predicts that such a thing should exist? Would it not be compatible with FLE that everything that's essential to eukaryotes should also be essential to prokaryotes? Where does FLE rule that out?
If so, then you might want to elaborate. Because reading it from here, it looks like you're basically saying "is there anything in common descent that predicts ERVs should exist? Would it not be compatible with common descent that ERVs do not exist? Where does common descent rule that out?" Ignoring, of course, the simple observation that ERVs do in fact exist, and from this observation we can generate a prediction.
True. But your claim was that (in this respect) FLE had greater specificity than Darwinism. If you now admit that FLE could have been done so that there'd be no homology at all between eukaryote and prokaryote proteins, then your point has vanished. We might see homology, we might see none. Or we could see any degree of homology, depending on how much overlap there would be between the two gene sets. Also, the overlap could have only included absolutely essential proteins. Your "either/or prediction" is that in the case of any given protein, either we'll see homology between eukaryotes and prokaryotes or we won't. That seems to cover everything. Adieu predictive specificity.
A couple of points:
1. The same thing could be said for Darwinian evolution. There's nothing in Darwinian evolution preventing the LUCA from having parallel gene sets, is there?
2. More importantly (I suppose a case could be made that it's unlikely from a Darwinian standpoint to have parallel gene sets in LUCA), the predictive value of the FLE does not lie only in the homology aspect, but in the fact that this homology is shared with prokaryotic proteins that are unnecessary for life.
So, we could summarize the FLE predictions in this manner:
a. Either crucial proteins in eukaryotes will share deep homology with prokaryotic proteins that are functional but unnecessary, and phylogenies will show that prokaryotes and eukaryotes are related,
b. Or phylogenies will indicate that eukaryotes and prokaryotes arose independently.
Simply put, FLE predicts that either (a) eukaryotes and prokaryotes are evolutionarily related - in which case, the prediction that key eukaryotic proteins will share deep homology with prokaryotic proteins naturally follows, or (b) eukaryotes emerged independently from prokaryotes.
Confirmation of either of these two general predictions wouldn't boost the case for front-loading because non-teleological evolution also makes those predictions. However, from these predictions we can glean other predictions, predictions that are made exclusively by the front-loading hypothesis, and thus confirmation of these predictions is what we're looking for.
If you admit the mechanisms, you admit the possibility of every such scenario.
All the Darwinian scenarios are possible, but that doesn't mean they actually happened in the past. And FLE requires that the possibility of the LUCA having only a minimal genome is not actually what happened.
Well, we can't see LUCA. You have no reason to suppose that, just because the histone genes are not absolutely essential to modern prokaryotes, they were not absolutely essential to LUCA. Maybe in this respect it was more like a eukaryote.
Do you agree that the basic prokaryotic cell plan does not require all the proteins necessary for the eukaryote and multicellular life? If so, then you must admit that it is possible that the LUCA did not require eukaryotic proteins. That this possibility was not manifested, however, is what front-loading argues. In other words, under non-teleological evolution, it is possible for the LUCA to have been structured such that it did not require key eukaryotic proteins. But if this is found to be the case, and moreover it is discovered that the LUCA did not in fact have key eukaryotic proteins, FLE is effectively falsified? Make sense?
BTW, I have no idea where you're getting the information about these proteins.
I'm not quite sure what information you're referring to.
For the record: after plowing through some literature, I discovered that histones actually aren't universally required by eukaryotes, being absent in a number of fungi (the paper I read was from 1971 though, so things very possibly have changed since then).

This message is a reply to:
 Message 33 by Dr Adequate, posted 06-21-2012 11:14 AM Dr Adequate has replied

Replies to this message:
 Message 35 by Dr Adequate, posted 06-21-2012 12:50 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 38 of 172 (666055)
06-21-2012 4:05 PM
Reply to: Message 35 by Dr Adequate
06-21-2012 12:50 PM


Given that ERVs exist, we can predict something else, namely the pattern of their distribution. But what you're doing is given that histone homologues exist in prokaryotes, you're predicting the existence of histone homologues in prokaryotes.
No, I'm not. It goes like this: given that protein X is required for eukaryotic existence, I predict that protein X likewise exists in prokaryotes, which is expected from front-loading. So, no, it's not a giraffophile designer. I'm using histone as an example because we know it's present in both eukaryotes and prokaryotes. But there are a number of important eukaryotic proteins that we only find in eukaryotes (e.g., Pax-6), but - given front-loading - I expect we'll eventually find functional homologs in prokaryotes.
Now, how does the non-teleological model explain the origin of Pax-6? The same way it explains the origin of nylonase or T-urf13, and the like. Or maybe small blocks of functional protein modules were randomly mixed and matched, "just happening" to result in Pax-6. So we really wouldn't predict deep homology (i.e., statistically significant similarity) of Pax-6 with prokaryotic proteins under the non-teleological model.
The question was: "Would it not be compatible with FLE that everything that's essential to eukaryotes should also be essential to prokaryotes? Where does FLE rule that out?"
Now, your solution seems to be to add in, ad hoc, the hypothesis that the designer didn't design things that way. Also apparently he likes giraffes but not unicorns.
Sigh. I keep answering this question. Is it true or is it false that proteins required by eukaryotes are not required for the existence of carbon-based life (more specifically, DNA-based life)? If that is true, then we have our FLE prediction: proteins universally required by eukaryotes will share deep homology with proteins in prokaryotes that are not required for the existence of life.
To see that this is so, consider the case in which the homologous proteins were in fact all essential. Would that be cause for us to say: "Front loading definitely didn't occur, then. If there was a designer, there would definitely be inessential proteins in prokaryotes homologous to essential proteins in eukaryotes. We now know for certain that life had no designer and that LUCA was in no way a product of intelligence"?
I think you're missing a crucial point. You say "consider the case in which the homologous proteins were in fact all essential." I assume by that you mean that these proteins are essential to both eukaryotes and prokaryotes. But it is an objective fact that eukaryotes require proteins that are not required by all types of prokaryotic life forms. And from here is where we get our prediction.
My point was this. You suppose that LUCA had inessential proteins. You point to histones as an example of this. That LUCA had histone-like proteins you (rightly) deduce from the fact that they (or their homologues) are present in both prokaryotes and eukaryotes. But you also seem to be claiming that we know they were inessential to LUCA...
No, that's not the point. Whether they are inessential to LUCA specifically is not relevant. What's relevant is whether these proteins are essential to all prokaryotic life forms.
Again, I'll condense the prediction down to this:
1. FLE involves loading the first genomes with proteins that will later be used by eukaryotes - proteins that are required for the rise of eukaryotes (e.g., calmodulin), but are not required for the existence of prokaryotes.
2. FLE therefore predicts that eukaryotic proteins will share deep homology with proteins in prokaryotes that are functional but unnecessary for the existence of prokaryotic life forms as a whole, regardless of whether for some reason or another LUCA required these proteins.

This message is a reply to:
 Message 35 by Dr Adequate, posted 06-21-2012 12:50 PM Dr Adequate has replied

Replies to this message:
 Message 40 by Dr Adequate, posted 06-21-2012 4:37 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 39 of 172 (666056)
06-21-2012 4:18 PM
Reply to: Message 36 by PaulK
06-21-2012 1:16 PM


That's the assumption that I am challenging. Given that we know that proteins may have multiple uses, plus the possibility of near variants having still more uses 250 different proteins should give you quite a range of options to encourage the development of complex life.
And:
All we need is a set of proteins that will work as a minimal life form while strongly encouraging the development of more complex life forms. You say that it can't be done, not even by your hypothetical designers, with their unknown capabilities. But I'm still waiting to see a real reason.
Actually, PaulK, the burden of proof is on you to provide evidence for the assertion that one can design a gene set that both functions as part of the minimum genome and also encourages the development of Metazoa etc. (incidentally, such a strategy for front-loading would be a pretty clumsy design since with only 250 genes you'd have to front-load the appearance of a whole bunch of proteins necessary for the rise of eukaryotes and Metazoa).
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 36 by PaulK, posted 06-21-2012 1:16 PM PaulK has replied

Replies to this message:
 Message 42 by PaulK, posted 06-21-2012 5:05 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 41 of 172 (666058)
06-21-2012 4:38 PM
Reply to: Message 37 by bluegenes
06-21-2012 2:15 PM


Re: I predict "No LUCA"!
For one thing, Genomicus, I don't think your predictions make sense on more than one level. Surely the best way to front load a planet "stacking the deck" in favour of multicellular life would be to include eukaryotes along with prokaryotes, and to have as many of each as possible. Also, if there were forms of multicellular life that could be engineered to live and photosynthesise in the early seas, then those would be included. So, a reasonable prediction might seem to be "no LUCA" on such a planet.
What do you mean by "no LUCA"? Do you mean that modern life would have evolved from a pool of different species? I have no problem with that, and I don't think the scientific evidence does either.
Bacteria are by far the best terra-formers, so there's a good reason why they'd be in the original pool. Simple eukaryotes (i.e., "eukaryotes" that had not yet undergone the endosymbiosis event) may have been present as well.
I think what you're doing with your predictions is a bit like one of our "sideloading" I.D. types suggesting a hypothesis to explain turtles after having observed their existence.
Well, we've got a lot of key proteins in eukaryotes that are not found in prokaryotes. So we can actually make a prediction from FLE that isn't ad hoc, namely that we'll find homologs of these proteins in prokaryotes. Note that Darwinian evolution doesn't really predict this (I explain the rationale for this statement in my latest reply to Dr Adequate).
Can the general idea of front loading make any specific predictions when we know nothing about actual process and nothing about the level of technical knowledge the designers had?
Well, in the first place I'm taking supernatural, omnipotent designers off the table.

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 Message 37 by bluegenes, posted 06-21-2012 2:15 PM bluegenes has replied

Replies to this message:
 Message 43 by Dr Adequate, posted 06-21-2012 5:25 PM Genomicus has replied
 Message 45 by bluegenes, posted 06-21-2012 7:28 PM Genomicus has replied
 Message 47 by Dr Adequate, posted 06-21-2012 8:51 PM Genomicus has not replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 44 of 172 (666072)
06-21-2012 6:31 PM
Reply to: Message 40 by Dr Adequate
06-21-2012 4:37 PM


But that isn't a prediction of FLE as such, is it? If prokaryotes lacked histone homologues, you'd just shrug and say that they dropped out of the prokaryote lineage just as (I presume you would have to say) the ability to synthesize peptidoglycan dropped out of the eukaryote lineage.
I find it suspicious that when I said "Evolution predicts that if the bacterial flagellum evolved, a number of its components will share similarity with proteins that are more ancient than the bacterial flagellum" you made no issue of it. Yet, now that we are discussing FLE you're bringing up the possibility of homologs being lost in various lineages.
In other words, if you want to bring up that aspect of all of this, then you've got to admit that Darwinian evolution actually doesn't predict that the bacterial flagellar components will share homology with more ancient systems. Kewl.
Why would you have to admit this? Precisely because these homologous counterparts could have been loss over deep time, erasing any evidence of pre-cursor homologs to the bacterial flagellum system. You sure you want to go down that path, Dr Adequate?
Let me put it another way. Go ahead and argue that since proteins can be lost over deep time, FLE actually doesn't predict that key eukaryotic proteins will share homology with prokaryotic proteins. But, at the same time, you have to be consistent and admit therefore that any homology the flagellar system shares with more ancient systems isn't evidence for the evolution of the flagellum, precisely because, by your argument, evolution does not predict this homology.
I'll respond to your other points later.

This message is a reply to:
 Message 40 by Dr Adequate, posted 06-21-2012 4:37 PM Dr Adequate has replied

Replies to this message:
 Message 46 by Dr Adequate, posted 06-21-2012 8:49 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 48 of 172 (666089)
06-21-2012 9:26 PM
Reply to: Message 46 by Dr Adequate
06-21-2012 8:49 PM


I never said it did. You did. There is in fact no a priori reason why they should still be hanging around. They might well have been lost instead. There's nothing in Darwinism per se that says this shouldn't have happened. If you want to admit that you were wrong about this too, go right ahead.
So, given that, by your own admission, Darwinian evolution doesn't predict that the flagellum will share similarity with more ancient systems, any such similarity isn't evidence that the flagellum evolved (which is interesting, because it means there's not a scrap of evidence that the bacterial flagellum evolved). You might want to take that up with the numerous scientific papers that are under the impression that the similarities between the flagellum and more ancient systems (e.g., the ATP synthase) is evidence that the flagellum evolved.

This message is a reply to:
 Message 46 by Dr Adequate, posted 06-21-2012 8:49 PM Dr Adequate has replied

Replies to this message:
 Message 49 by Dr Adequate, posted 06-21-2012 9:42 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 50 of 172 (666095)
06-21-2012 10:14 PM
Reply to: Message 49 by Dr Adequate
06-21-2012 9:42 PM


Re: Evidence And Prediction
I said that it's not a prediction of Darwinism that we should be able to find it, not that it's of no significance if we do.
There's a difference.
Okay. Understood (although you're going to find a lot of Darwinians that say that the hypothesis that the bacterial flagellum evolved predicts that it will share homology with systems that pre-date it; Nick Matzke, the guy who wrote an exhaustive essay on the evolution of the flagellum, is an example - but this is an aside).
However, I take issue with this statement of yours:
If prokaryotes lacked histone homologues, you'd just shrug and say that they dropped out of the prokaryote lineage just as (I presume you would have to say) the ability to synthesize peptidoglycan dropped out of the eukaryote lineage.
This is hypothetically possible, but it's really, really not likely for a fully functional protein in prokaryotes to be lost across all prokaryotic lineages.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 49 by Dr Adequate, posted 06-21-2012 9:42 PM Dr Adequate has replied

Replies to this message:
 Message 53 by Dr Adequate, posted 06-21-2012 10:28 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 51 of 172 (666096)
06-21-2012 10:17 PM
Reply to: Message 42 by PaulK
06-21-2012 5:05 PM


The hypothetical designers would be free to choose any set of proteins that would work. They would, for instance be completely free to choose completely unrelated proteins. They would NOT be limited to using the proteins used by Earthly life.
Quite right. But they have to include the 250 or so genes necessary for carbon-based life forms to exist. And they'd add extra genes to the original genomes so that front-loading could follow.
250 proteins is quite a large number.
Okay, let me get your position right: are you suggesting that the designers could engineer the 250 genes needed for life such that they also favor the trajectory of evolution in the direction of Metazoa etc.?
For your argument to be truthful you need a consistent standard for "prediction".
That is you need a satisfactory standard that YOUR views satisfy, while the arguments from the evolutionary side do not.
That is rather difficult when your view is just an assumption that seems intuitive.
So, do you have a stronger argument that actually deals with the issues, or are you just going to evade the problem ?
Not sure what you mean by all of the above. Care to elaborate?
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 42 by PaulK, posted 06-21-2012 5:05 PM PaulK has replied

Replies to this message:
 Message 65 by PaulK, posted 06-22-2012 1:32 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 52 of 172 (666097)
06-21-2012 10:26 PM
Reply to: Message 43 by Dr Adequate
06-21-2012 5:25 PM


The Ubiquitin Story
Dr Adequate brought up the example of ubiquitin, which is a very crucial protein among eukaryotes. This is evidenced by its universal distribution among eukaryotes and tightly conserved sequence identity across taxa (e.g., there is 96% sequence identity between human ubiquitin and yeast ubiquitin). Dr Adequate is quite correct when he says that ubiquitin is essential to eukaryotes.
Based on the logic of front-loading, I'd predict that ubiquitin shares deep homology with a prokaryotic protein.
But what does Darwinian evolution predict? Dr Adequate, do you think we'll find a prokaryotic homolog of ubiquitin one of these days? Why or why not? I'm quite curious as to your answer.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 43 by Dr Adequate, posted 06-21-2012 5:25 PM Dr Adequate has replied

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 Message 55 by Dr Adequate, posted 06-21-2012 10:45 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 54 of 172 (666100)
06-21-2012 10:37 PM
Reply to: Message 53 by Dr Adequate
06-21-2012 10:28 PM


Re: Evidence And Prediction
Yeah, but you can only say that because you know that it is a fully functional protein in prokaryotes --- if it had disappeared, you could quite legitimately have said: "Ah well then, I'm gonna guess that it wasn't any use to prokaryotes". You wouldn't have said: "Oh, in that case FLE falls apart, because I have such insight into biochemistry and so on that I know that if it had been present in LUCA it would certainly have been conserved in prokaryotes." (Maybe it would certainly have been conserved, but the only evidence we have for the is the post-hoc observation that it was --- no-one, I believe, is smart enough to figure this out from first principles, so you wouldn't have known this to be the case.)
Except that front-loading requires that if there's a key protein in eukaryotes, then that protein would have originally been given a function in the LUCA, so that it is retained. In other words, it'd be a horrible, horrible design strategy to load up the LUCA with a functionless protein that will only later find function in eukaryotes. In fact, that really wouldn't be front-loading any more - at least, not front-loading a la Mike Gene.

This message is a reply to:
 Message 53 by Dr Adequate, posted 06-21-2012 10:28 PM Dr Adequate has replied

Replies to this message:
 Message 56 by Dr Adequate, posted 06-21-2012 10:53 PM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 57 of 172 (666105)
06-21-2012 11:20 PM
Reply to: Message 55 by Dr Adequate
06-21-2012 10:45 PM


Re: The Ubiquitin Story
I'd say no, for these reasons:
(1) According to the paper I linked to, no-one's found one yet in all the prokarotes that we've sequenced.
(2) Presumably scientists have deliberately sequenced a wide range of prokaryotes rather than looking again and again at one small clade of them.
This suggests that the use of prokaryotic ubiquitin-like protein and the non-use of ubiquitin is basal in prokaryotes, so it would be bizarre to find a branch of the prokaryotes that used ubiquitin...I'd come to the same conclusion if I believed in FLE. If, as the evidence suggest, ubiquitin was not present in basal archaea or eubacteria, then it would be odd for it to turn up in some branch of them looking all homologous but actually just being analogous, and so far as I can see FLE would tell us the same thing.
Sequence homology isn't everything - especially when you consider the small size of ubiquitin (which means that it's more difficult to find a statistically significant database match among prokaryotes). You have to consider structural homology, and look at the bigger picture. Interestingly, a study from way back in 2003 did just that and found evidence of ubiquitin homologs among prokaryotes.
According to a study by Bienkowska et al. (2003):
"The question of protein homology versus analogy arises when proteins share a common function or a common structural fold without any statistically significant amino acid sequence similarity. Even though two or more proteins do not have similar sequences but share a common fold and the same or closely related function, they are assumed to be homologs, descendant from a common ancestor. The problem of homolog identification is compounded in the case of proteins of 100 or less amino acids...In an effort to identify distant homologs of the many ubiquitin proteins, we have developed a combined structure and sequence similarity approach that attempts to overcome the above limitations of homolog identification. This approach results in the identification of 90 probable ubiquitin-related proteins, including examples from the two prokaryotic domains of life, Archaea and Bacteria."
And:
"Using our search method, in addition to known homologs, we have identified 90 small proteins from the sequenced genomes of Archaea, Bacteria, C.elegans and A.thaliana that are predicted to be similar in structure...Seven sequences were identified as 2Fe—2S ferredoxins and 21 were identified as members of the MoaD/This superfamily. Further analysis of the structural alignments and alignments of MoaD and ThiS COGs lead us to the selection of three genes as coding for ubiquitin‐related proteins. Given the conservation of the structural position of functionally important lysine, we propose that archeal proteins AF0737, MTH1743 and aq_025a are distant homologs of ubiquitin."
All of this is very cool, of course, and is what we'd expect from front-loading: in a world without ubiquitin (or a closely related homolog), eukaryotes might not arise. Thus, we'd want to load the first genomes with ubiquitin, ensuring the origin of eukaryotes and animals, plants, etc.

Structural alignment of ubiquitin and a possible archaeal homolog.

Thus we can see that, despite deep time, traces of homology between ubiquitin and prokaryotic proteins can be found. And this is what we'd expect from front-loading. On the other hand, Darwinian logic doesn't allow us to make this prediction. Darwinian evolution has been very comfortable with the fact that, prior to the era of robust structural analyses, no prokaryotic homolog of ubiquitin was known.
References
Jadwiga R. Bienkowska, Hyman Hartman, Temple F. Smith. A search method for homologs of small proteins. Ubiquitin‐like proteins in prokaryotic cells? Protein Eng. (2003) 16 (12): 897-904.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 55 by Dr Adequate, posted 06-21-2012 10:45 PM Dr Adequate has replied

Replies to this message:
 Message 59 by Dr Adequate, posted 06-22-2012 12:08 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 58 of 172 (666106)
06-21-2012 11:26 PM
Reply to: Message 56 by Dr Adequate
06-21-2012 10:53 PM


Re: Evidence And Prediction
A function in the LUCA, yes, but not necessarily in all its descendants. Surely (stop me if I'm wrong) the whole idea of FLE is that the LUCA contains genetic information that is differently lost in different lines of descent. If everything that was useful to the LUCA was conserved in all its descendants, in what would the E in FLE consist?
Well, in the first place, nothing in the idea of FLE says that genetic information has be differentially lost across lines of descent. FLE is simply about stacking the deck so that the origin of eukaryotes (and Metazoa etc.) is made probable by providing the necessary machinery for their origin. The "evolution" part of FLE is natural selection and random mutation acting in combination with the initial, designed states, making the origin of complex life forms probable.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 56 by Dr Adequate, posted 06-21-2012 10:53 PM Dr Adequate has replied

Replies to this message:
 Message 60 by Dr Adequate, posted 06-22-2012 12:20 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 61 of 172 (666110)
06-22-2012 12:22 AM
Reply to: Message 59 by Dr Adequate
06-22-2012 12:08 AM


Re: The Ubiquitin Story
Distant indeed --- between proteins which do different things and have only a small amount of their sequence in common. Homology? Well maybe --- if you're a Darwinian. But do you want to suggest that these different proteins adapted to doing different things have a common ancestor?
Actually, these proteins carry out analogous functions. And, again, sequence isn't everything. Structural homology is also important, and it's more likely to be detected given the deep-time involved. I really have no idea why you think that one has to be a Darwinian in order to accept the view that these proteins are homologous.
I'd have expected more front-loading of information and less Darwinian evolution.
Huh? You do know that front-loading works with the blind watchmaker, and not against it? So I'm not sure how to make sense out of "more front-loading of information and less Darwinian evolution."
And yet you have no evidence that ubiquitin was the common ancestor of this protein family, if it is one.
Well, the structural evidence coupled to other clues does indicate that these proteins are likely homologous. At any rate, now you're moving the goal-posts. First, you said that ubiquitin has no prokaryotic homologs (inconsistent with FLE), while structural analyses suggest otherwise. And now you want us to actually build a phylogeny of all these distantly related proteins to determine if the common ancestor was ubiquitin.
Anyway, you wouldn't have to load the first cells with ubiquitin itself. You'd simply need to load them with closely related proteins, so that when eukaryotes do appear on the scene of life, they can easily co-opt the proto-ubiquitin into its modern role.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 59 by Dr Adequate, posted 06-22-2012 12:08 AM Dr Adequate has replied

Replies to this message:
 Message 63 by Dr Adequate, posted 06-22-2012 12:48 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 62 of 172 (666111)
06-22-2012 12:24 AM
Reply to: Message 60 by Dr Adequate
06-22-2012 12:20 AM


Re: Evidence And Prediction
So you believe that all extant species descended from a common ancestor by purely Darwinian mechanisms?
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?
Well, I hate to break it to you, but someone got in ahead of you there ... it was Darwin. This is certainly not what is usually understood by front-loaded evolution.
Okay. What is your understanding of front-loading? I'm taking Mike Gene's position here, by the way.

This message is a reply to:
 Message 60 by Dr Adequate, posted 06-22-2012 12:20 AM Dr Adequate has replied

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 Message 64 by Dr Adequate, posted 06-22-2012 12:56 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 66 of 172 (666166)
06-22-2012 10:16 PM
Reply to: Message 45 by bluegenes
06-21-2012 7:28 PM


Re: I predict "No LUCA"!
I'm suggesting that, on any hypothetical planet that was front loaded with the deck stacked in favour of multicellular life, the equivalent of eukaryotes and whatever simple multicellular organisms that could survive should be there.
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. 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.
But why does FLE predict this? As we've agreed, the frontloaders could've made their own eukaryotes. Also, as Darwinian processes take place after the frontloading, then why should we expect all important proteins in modern eukaryotes to have homologues in modern prokaryotes even if the FrontLoaders didn't think of making their own eukaryotes?
I think I've already explained the rationale for this prediction in the OP, but, briefly, given that modern eukaryotes would have been front-loaded under my hypothesis, you'd need to ensure that the genes necessary for their origin would be present before their origin, i.e., in prokaryotes. So you'd load the genomes up with proteins that are necessary for the rise of eukaryotes. And we can detect this by looking for homologs of key eukaryotic proteins in prokaryotes. For example, Pax-6 (an important eukaryotic protein) has no known real prokaryotic homolog AFAIK. From the perspective of front-loading, then, I predict that one of these days we'll find a prokaryotic homolog of Pax-6.
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.
Me too. For an evidence based case, it's best to assume biological aliens. However, as I suggested, this still makes it hard to make predictions when we know nothing of their technical ability and the processes used. Intuitively, it does at least give us a reason why, being multicellular life forms themselves, they might be interested in the kind of project you're suggesting!
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.
Of course, critics of your hypothesis might wonder, if it took 4,000,000,000 yrs for intelligent biologists to emerge from this "stacked-deck" biosphere, how long it took for them to emerge on their "unstacked-deck" planet.
Well, there's a lot of time for the nanotechnologists to emerge on a planet that is older then the earth.
Maybe we can at least get a Sci-fi novel out of this, if nothing else.

This message is a reply to:
 Message 45 by bluegenes, posted 06-21-2012 7:28 PM bluegenes has replied

Replies to this message:
 Message 87 by bluegenes, posted 06-26-2012 8:24 AM Genomicus has replied

  
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