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


Message 67 of 172 (666167)
06-22-2012 10:39 PM
Reply to: Message 63 by Dr Adequate
06-22-2012 12:48 AM


Re: The Ubiquitin Story
Well, no they don't. For example, according to this, the ThiS gene which you mention "plays a central role in thiamin biosynthesis". Unlike ubiquitin, which does something completely different.
Yes, but, from the same paper you cite:
"Although ThiS shares only 14% sequence identity with ubiquitin, it possesses the ubiquitin fold. This structural homology, combined with established functional similarities involving sulfur chemistry, demonstrates that the eukaryotic ubiquitin and the prokaryotic ThiS evolved from a common ancestor. This illustrates how structure determination is essential in establishing evolutionary links between proteins in which structure and function have been conserved through eons of evolution despite loss of sequence identity."
I admit that it was a bit of a stretch to say that these proteins carry out analogous functions. But they have key functional similarities.
Well, because the descent of different proteins doing different things from a common ancestor is Darwinian. If each protein was separately front-loaded into LUCA, that would be an instance of front-loading.
Yes, but loading up the first genomes with proteins similar to ubiquitin would ensure that they'd be around before the appearance of Metazoa, so the front-loaders wouldn't have to depend on the blind watchmaker to "just happen" to find ubiquitin, allowing the origin of Metazoa.
Changing my mind when presented with new data is hardly moving the goalposts, it's what people are meant to do.
Well, yes, but you actually expect a robust phylogeny of ubiquitin and its prokaryotic homologs?
If you're going to admit common descent of ThiS, MOAD, and the ubiquitin family, then a protein closely related to ubiquitin isn't necessary. Why not start with something more like ThiS? In which case, why not start with something pretty much like a prokaryote? The more homologies you claim, the greater the power you cede to purely Darwinian processes, and the less the need to "stack the deck".
ThiS, MOAD, and ubiquitin are all structurally related, so you'd need to load the genome with a structurally similar protein. I have no idea where you're going with "The more homologies you claim, the greater the power you cede to purely Darwinian processes, and the less the need to 'stack the deck'."
(Consider if you showed me that all proteins were homologues descended from a single common ancestor. Would that be a point in favor of FLE?)
Okay, by this do you mean that, e.g., cytochrome c, hemoglobin, insulin, etc., are (in this hypothetical scenario) all descended from a common ancestor?
If you are prepared to say that without front-loading of the different genes, but just Darwininly (is that a word?) ThiS and ubiquitin descended from a common ancestor, when they do completely different things and have only 14% of their gene in common (according to WP) then I don't see why you should also think that there is any need whatsoever for any form of foresightful front-loading to produce eukaryotes.
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).
Anyhew, I'll be back after the weekend and respond to the other posts.

This message is a reply to:
 Message 63 by Dr Adequate, posted 06-22-2012 12:48 AM Dr Adequate has replied

Replies to this message:
 Message 68 by Dr Adequate, posted 06-23-2012 1:21 AM Genomicus has replied
 Message 69 by Dr Jack, posted 06-23-2012 8:53 AM Genomicus has not replied
 Message 71 by New Cat's Eye, posted 06-25-2012 11:38 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 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 1941 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 replied

Replies to this message:
 Message 85 by Dr Adequate, posted 06-26-2012 1:30 AM Genomicus has not replied

  
Genomicus
Member (Idle past 1941 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 replied

Replies to this message:
 Message 86 by PaulK, posted 06-26-2012 1:36 AM Genomicus has not replied
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Genomicus
Member (Idle past 1941 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 replied

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

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


Message 94 of 172 (666371)
06-26-2012 1:29 PM
Reply to: Message 71 by New Cat's Eye
06-25-2012 11:38 AM


Re: The Ubiquitin Story
Nice thread, Geno.
Thanks.
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?
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.

This message is a reply to:
 Message 71 by New Cat's Eye, posted 06-25-2012 11:38 AM New Cat's Eye has replied

Replies to this message:
 Message 95 by jar, posted 06-26-2012 1:36 PM Genomicus has replied
 Message 99 by New Cat's Eye, posted 06-26-2012 2:15 PM Genomicus has not replied

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


Message 96 of 172 (666378)
06-26-2012 2:00 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. The Texas Sharpshooter falacy is where a sharpshooter makes the claim that he can hit a target the size of a quarter from 1,000 yards away on the first try. The sharpshooter fires his shot into a crowded suburb, finds the bullet hole (presumably in the side of a house), and draws a quarter sized bull's eye around the bullet hole. Voila, amazing sharpshooting exhibition, right?
From Wikipedia:
"The Texas sharpshooter fallacy is a logical fallacy in which pieces of information that have no relationship to one another are called out for their similarities, and that similarity is used for claiming the existence of a pattern. This fallacy is the philosophical/rhetorical application of the multiple comparisons problem in statistics, and apophenia in cognitive psychology. It is related to the clustering illusion, which refers to the tendency in human cognition to interpret patterns in randomness where none actually exist.
The name comes from a joke about a Texan who fires some shots at the side of a barn, then paints a target centered on the biggest cluster of hits and claims to be a sharpshooter."
And:
"The Texas sharpshooter fallacy often arises when a person has a large amount of data at their disposal, but only focuses on a small subset of that data. Random chance may give all the elements in that subset some kind of common property (or pair of common properties, when arguing for correlation). If the person fails to account for the likelihood of finding some subset in the large data with some common property strictly by chance alone, that person is likely committing a Texas Sharpshooter fallacy."
Now that we've defined our terms, I ask the following question: in what way do I have "a large amount of data at their disposal, but only focuses on a small subset of that data. Random chance may give all the elements in that subset some kind of common property"?
This is exactly what FLE is. It assumes that the biodiversity we see today is the biodiversity that was intended. Genomicus is drawing the bull's eye around the bullet hole. What Genomicus just can't understand is that eukaryotes DID NOT NEED TO EVOLVE. There is nothing in the history of life that requires the existence of eukaryotes, much less eukaryotes with calmodulin. NOTHING. It is a happenstance of occurences that resulted in eukaryotes evolving. If we went back in time before eukaryotes emerged could we use FLE to predict that eukaryotes would emerge, and that they would all require calmodulin? No. Genomicus has not put forward one methodology within FLE for predicting which proteins will become important in future lineages. None. All FLE does is look at what did evolve and then claim that this was the target. This is Texas Sharpshooting.
One of the premises of Darwinian theory is that all species are related by common ancestry. Meanwhile, the premise of the front-loading hypothesis is that the Metazoa etc. that we see today was the result of intent. If we take this as a basic premise of our hypothesis, we can then develop testable predictions. Confirmation of those predictions strengthens the hypothesis.
Suppose, for example, that we received a radio signal from space that consisted of a long string of prime numbers. From here, it would be perfectly reasonable to hypothesize that the sequence of the radio signal was the intended outcome by some alien intelligence. And this allows us to make testable predictions. For example, we might predict that after the first 50 prime numbers, the 51th prime number will appear next. Etc. As far as I can tell, FLE is similar. The FLE hypothesizes that the eukaryotes and Metazoa that we see today are an intended outcome. Taking this as our basic premise, predictions can be gleaned and tested.
Even worse, the predictions of FLE are exactly what we would predict from the non-teleological process of evolution.
Please read the OP and respond to the specific points I make there, where I argue that there is a prediction of the FLE that we would not make from the non-teleological model.

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

Replies to this message:
 Message 102 by Taq, posted 06-26-2012 3:24 PM Genomicus has not replied

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


Message 97 of 172 (666379)
06-26-2012 2:03 PM
Reply to: Message 95 by jar
06-26-2012 1:36 PM


Re: The Ubiquitin Story
Is there any reason to think it is inevitable for any fold to arise?
Unless there are specific initial conditions, I would answer "no."
I mean it's obvious that the trend of evolution will be towards greater complexity but beyond that, is there anything that seems inevitable?
Well, for example, I would say the evolution of anti-biotic resistance to certain drugs is pretty inevitable.

This message is a reply to:
 Message 95 by jar, posted 06-26-2012 1:36 PM jar has replied

Replies to this message:
 Message 98 by jar, posted 06-26-2012 2:07 PM Genomicus has not replied

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


Message 103 of 172 (666395)
06-26-2012 3:53 PM
Reply to: Message 73 by Taq
06-25-2012 12:50 PM


From here we can make a prediction: key eukaryotic proteins will share deep homology with functional but unnecessary prokaryotic proteins.
This is also what we would expect from non-teleological processes like evolution. In fact, Hermann Muller predicted that evolution would produce these relationships clear back in 1918...
No, Hermann Muller predicted that traits that are at first merely beneficial can become necessary. He did not predict anything at all along the lines that crucial eukaryotic proteins will share deep homology with functional but unnecessary (for life) prokaryotic proteins.
You also make the mistake of equating unnecessary with useless.
No. From the OP:
"So, by 'unnecessary but functional' I mean a gene that is not required by the basic prokaryote cell plan but does carry out a functional role in the LUCA."
One of the MAJOR problems with your model is assuming that a minimalistic genome comprised of only "necessary" proteins would be viable. It wouldn't.
Yes, it would be. At one point, under the non-teleological model, life consisted of only a few genes. In arguing against the possibility that the LUCA could have, under the non-telic model, consisted of only a minimal genome, you are going against what a number of scientific papers have proposed or implied.
For example:
"...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." ("A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective," 2006)
And:
"We argue that there is a commonality of mechanisms and protein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal set of genes thought to represent the genome of the LUCA." ("DNA repair systems in archaea: mementos from the last universal common ancestor?" 1999)
Also:
"One hands-on approach to trying to uncover the biology of the LUCA has been to look for genes that are universal that is, genes that all life forms possess. Once a list of these genes has been made, they also lead to another possibility: perhaps this list encapsulates the essence of cellular life the minimum number of genes required to make a cell. In 1996, with the sequences of the first two bacterial genomes (Mycoplasma genitalium & Haemophilus influenzae) in hand, Arcady Mushegian & Eugene Koonin [Mushegian & Koonin 1996] tried exactly this...
...they tentatively concluded that LUCA stored its genetic information in RNA, not DNA, and made suggestions on how to further reduce the number of genes in their minimal genome. The work heralded the arrival of comparative genome studies, and there is no doubt that a good number of the genes in their 256-strong list do date back to the LUCA."
(My Name is LUCAThe Last Universal Common Ancestor, Anthony Poole)
That RNA, and not DNA, was present in the LUCA is compatible with non-teleological evolution but isn't compatible with FLE.
All of this demonstrates that, not only is it compatible with non-teleological evolution that the LUCA had a minimal genome, but it's not at all unlikely from that perspective.

This message is a reply to:
 Message 73 by Taq, posted 06-25-2012 12:50 PM Taq has replied

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


Message 105 of 172 (666398)
06-26-2012 4:24 PM
Reply to: Message 75 by Taq
06-25-2012 3:55 PM


IOW, FLE is nothing more than the hope of some supernatural guidance in a nominally non-teleologic process.
Since when did the supernatural, gods, deities, etc., enter this discussion?

This message is a reply to:
 Message 75 by Taq, posted 06-25-2012 3:55 PM Taq has replied

Replies to this message:
 Message 106 by Taq, posted 06-26-2012 4:49 PM Genomicus has not replied

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


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


Re: The Ubiquitin Story
What other structural similarities do they have?
The paper I cited describes the structural similarities between ubiquitin and its prokaryotic homologs.
This one fold seems to have been conserved. The rest, not so much. The function of the proteins, not at all.
Yet it is the basic structure of a protein that determines its function - along with the proteins it interacts with, of course. My point is that loading the first genomes with an ubiquitin-related fold allows it to be easily co-opted into the role used by eukaryotes.

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

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

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


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


Re: I predict "No LUCA"!
I wasn't suggesting that the frontloaders would load only eukaryotes. The more, the merrier, and the higher the chances of metazoa.
Understood.
The last point doesn't really fit very well with the first two, does it? It would also mean that, far from frontloading a prokaryote LUCA with eukaryotes in mind, the frontloaders (FLs) would presumably have had terraforming prokaryotes in mind when designing their eukaryote LUCA. Why not make sure by designing the proks as well? The more, the merrier, and the better the chances.....
Quite right. I personally favor the hypothesis that the LUCA was prokaryotic, and not eukaryotic, although some researchers say that the LUCA was more of a eukaryote precisely because of its complexity and the large number of proteins its genome encoded. This is fully compatible with front-loading.
Why wouldn't the "logic of frontloading" predict actual ubiquitin in the proks?
Because the mutations do happen, and over deep time, a protein sequence can change quite extensively - to the point that it is no longer the original protein (but structurally similar, nonetheless, and this is what matters).
There's also a problem here that Mr. Jack hinted at in a post above. Ubiquitin being ubiquitous in eukaryotes does not necessarily mean that it's necessary for metazoa, or that the fold is necessary. It could just be a "frozen accident".
The universal distribution of ubiquitin among eukaryotes strongly implies that it is necessary for eukaryotic existence, does it not? True, it could be a "frozen accident." But the front-loaders aren't going to gamble their chances on accidents. It would be far better design logic just to put that protein fold into the first cells.

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

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

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


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


Quite right. If the intent was for metazoans to arise in the future, why not make them straight away?
Metazoans don't survive that well in an environment like that of the early, hostile earth ya know.
Do you want oxygen in the atmosphere? Dump some genetically modified algae into the planet's oceans.
Alternatively, you could put some cyanobacteria into the planet's oceans. That's why terra-forming is intimately linked with front-loading. In order to ensure that animals and plants can arrive on the scene later, you have to change the earth such that it is hospitable to animals and plants.

This message is a reply to:
 Message 89 by Taq, posted 06-26-2012 11:32 AM Taq has not replied

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


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


Re: I predict no front-loaders.
No more than the fact that the water fills the hole implies that the hole was necessary for the water. The only thing implied is that ubiquitin was just good enough to work.
So why aren't there any animals or plants etc. that lack ubiquitin?

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

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

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


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


Re: I predict no front-loaders.
Because it was just good enough to work.
Yes, but that does not explain why there are no eukaryote lineages that lack ubiquitin.
And, again, from a front-loading perspective, we would predict ubiquitin homologs in prokaryotes, while we cannot predict this from a non-teleological standpoint.

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

Replies to this message:
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