Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 127 (8774 total)
Current session began: 
Page Loaded: 07-21-2017 12:43 PM
391 online now:
DrJones*, JonF, NoNukes, PaulK, ringo, Tangle, Tanypteryx, Taq, vimesey, xongsmith (10 members, 381 visitors)
Chatting now:  Chat room empty
Newest Member: Tom Larkin
Upcoming Birthdays: anglagard
Post Volume:
Total: 814,334 Year: 18,940/21,208 Month: 1,699/3,111 Week: 494/707 Day: 70/120 Hour: 1/15

Announcements: Reporting debate problems OR discussing moderation actions/inactions


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Prev1
...
789
10
1112Next
Author Topic:   Deep Homology and Front-loading
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 136 of 172 (666556)
06-28-2012 2:16 PM
Reply to: Message 127 by Dr Adequate
06-27-2012 5:44 PM


Re: The Ubiquitin Story
If you concede that they are actually homologues, then you concede that the blind watchmaker created all (or all but a few) of the other functional parts of these various superfamilies of proteins? So why would you object to the proposition that the blind watchmaker is also responsible for the one part they have in common?

Well, at this point, I'm not trying to argue against the capabilities of the blind watchmaker. I'm simply trying to develop a prediction that is made by FLE but is not made by the non-teleological model. Based on FLE, we would predict that there exists prokaryotic homologs of ubiquitin, and confirmation of that prediction is a point in favor of FLE, regardless of the possibility that the blind watchmaker could have "stumbled" upon the basic ubiquitin fold.


This message is a reply to:
 Message 127 by Dr Adequate, posted 06-27-2012 5:44 PM Dr Adequate has not yet responded

  
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 137 of 172 (666557)
06-28-2012 2:35 PM
Reply to: Message 130 by Dr Adequate
06-28-2012 1:27 AM


Re: The Ubiquitin Story
But as we have seen, it doesn't. The objections to this claim are as cogent this week as they were last week.

AFAICT, the objections seem to revolve around the following points:

1. Non-teleological evolution predicts that key eukaryotic genes will share homology with functional but unnecessary proteins. Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome. Interestingly, however, a number of papers have proposed that the LUCA did, in fact, have only a minimal genome, demonstrating that this is perfectly reasonable under the non-telic model.

2. The designers could have engineered the minimal gene set such that it also front-loads the Metazoa we see. But this is actually quite unlikely, as you'd probably have to substantially modify the necessary genes, in which case they're no longer retaining their original function, and wouldn't be functioning as a minimal gene set.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 130 by Dr Adequate, posted 06-28-2012 1:27 AM Dr Adequate has responded

Replies to this message:
 Message 140 by Taq, posted 06-28-2012 3:06 PM Genomicus has not yet responded
 Message 156 by Dr Adequate, posted 07-01-2012 12:12 PM Genomicus has responded

  
PaulK
Member
Posts: 12863
Joined: 01-10-2003
Member Rating: 3.4


Message 138 of 172 (666558)
06-28-2012 2:47 PM
Reply to: Message 135 by Genomicus
06-28-2012 2:04 PM


Re: The Ubiquitin Story
quote:

Okay, here's a simple true/false question: If the Metazoa we see today was the intended outcome of a front-loading scenario, could we make testable predictions from this premise?

I don't think so. I would add that that hypothesis assumes too much - it would be much better to construct a plausible scenario and make predictions from that.

quote:

No, non-teleological models do not predict that crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins. I've explained why many times, but here it is again: under the non-telic model, it is completely reasonable for the LUCA to have no more than a minimal genome. I have supported this contention with references to the scientific literature.

Firstly we note that neither you nor your sources present any reasoning to support this assumption.

Secondly, we must note that evolution is not a goal-directed process and as such it seems somewhat unlikely that the first cell would have acquired only those genes absolutely necessary to form a cell.

Thirdly we wouldn't expect the LUCA to be the first cell. And it's even less reasonable to expect there to be no ancestors shared between eukaryotes and some prokaryote since the LUCA, which could also produce deep homologies.

quote:

...This indicates that in contrast to early hypotheses, LUCA was far from being a minimal cell because its genome was far from a minimal genome." (emphasis added; from "Origins and Evolution of Life: An Astrobiological Perspective," Muriel Gargaud, Purificación López-Garcìa, Hervè Martin, Cambridge University Press, 2011)

Read that carefully, then tell me that it's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.


ALright. It's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.

Seriously all you have is a claim about "early hypotheses" with no indication of how they were arrived at. Where's the reasoning that would make them reasonable ?

quote:

The issue here really isn't whether the non-telic view of life can potentially explain the observation that crucial eukaryotic proteins share deep homology with functional but unnecessary prokaryotic proteins. The real issue is whether the non-teleological model predicts this.


And whether FLE predicts it. That's another of your claims that is somewhat lacking in support.

Edited by PaulK, : No reason given.


This message is a reply to:
 Message 135 by Genomicus, posted 06-28-2012 2:04 PM Genomicus has not yet responded

    
Taq
Member
Posts: 6795
Joined: 03-06-2009
Member Rating: 3.9


Message 139 of 172 (666559)
06-28-2012 3:03 PM
Reply to: Message 135 by Genomicus
06-28-2012 2:04 PM


Re: The Ubiquitin Story
Okay, here's a simple true/false question: If the Metazoa we see today was the intended outcome of a front-loading scenario, could we make testable predictions from this premise?

In order to be testable predictions they would need to differ from the assumption and differ from known natural mechanisms that you are seeking to replace. So far, you have fulfilled none of these requirements.

No, non-teleological models do not predict that crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins.

Just like non-teleological meteorology does not predict that it has to rain on July 15th, 2016 in Dallas, TX. However, rain that day is consistent with non-teleological meteorology. In the same way, "crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins" is also consistent with non-teleological evolutionary mechanisms.

It is incumbent on you to show that non-teleological mechanisms can not co-opt proteins in subsequent generations.

Read that carefully, then tell me that it's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.

It's not reasonable under non-teleological models for LUCA to have a minimalist genome. LUCA is a product of many rounds of evolution. LUCA will contain genes that are unnecessary for life by necessary for outcompeting other organisms in a given environment.

What you label unnecessary proteins are beneficial proteins to the organism that carries them. That is why they have been preserved for 3 billion years of evolution. Can non-teleological mechanisms preserve beneficial proteins? Yes. Therefore, it is not a valid testable prediction for FLE.

Can non-teleological mechanisms co-opt beneficial mutations for new purposes through random mutation and natural selection so that they are necessary genes in subsequent generations? Yes, absolutely. This too is not a valid testable prediction for FLE because it does not differentiate FLE from non-teleological processes.

The issue here really isn't whether the non-telic view of life can potentially explain the observation that crucial eukaryotic proteins share deep homology with functional but unnecessary prokaryotic proteins.

Yes, it is. If non-teleological mechanisms can produce the observations then FLE is not supported.


This message is a reply to:
 Message 135 by Genomicus, posted 06-28-2012 2:04 PM Genomicus has not yet responded

  
Taq
Member
Posts: 6795
Joined: 03-06-2009
Member Rating: 3.9


Message 140 of 172 (666560)
06-28-2012 3:06 PM
Reply to: Message 137 by Genomicus
06-28-2012 2:35 PM


Re: The Ubiquitin Story
1. Non-teleological evolution predicts that key eukaryotic genes will share homology with functional but unnecessary proteins. Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome. Interestingly, however, a number of papers have proposed that the LUCA did, in fact, have only a minimal genome, demonstrating that this is perfectly reasonable under the non-telic model.

A minimal genome for what function? LUCA did not have a single base codon system as the evidence suggests was the case for the first life. Instead, LUCA had a three base codon system, with some 3rd base wobble. Already, LUCA is not a minimalist genome, and we have only looked at the tRNA's.


This message is a reply to:
 Message 137 by Genomicus, posted 06-28-2012 2:35 PM Genomicus has not yet responded

  
bluegenes
Member
Posts: 3119
From: U.K.
Joined: 01-24-2007
Member Rating: 3.3


Message 141 of 172 (666596)
06-28-2012 9:13 PM
Reply to: Message 109 by Genomicus
06-27-2012 1:10 PM


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

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.

So, you're agreeing that the frontloaders could have designed a eukaryote. And:

Geno writes:

The universal distribution of ubiquitin among eukaryotes strongly implies that it is necessary for eukaryotic existence, does it not?

I think it implies that it's part of a useful system in them. But that doesn't mean that a complex eukaryote-like cell couldn't have formed in different ways, and couldn't have used different proteins for a similar function.

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.

I like this:

But the front-loaders aren't going to gamble their chances on accidents.

It's exactly what you're suggesting they did do. Let's look at your scenario. The FLs design a prokaryote with the metazoa in mind. They say to themselves: "at some point in the future, two descendents of our LUCA will combine in a way that will form a more complex cell which potentially could evolve into metazoa. These two particular descendents, maybe hundreds of millions of years down the line, maybe more than a billion, will contain all the proteins that we've put into the LUCA for their use."

If that's not gambling, what is?

I'd suggest that the frontloaders wouldn't be able to predict anything as specific as our eukaryotes. They might well know from their own life system that endosymbiotic events that produce useful functions could happen if their prokaryotes bubble away for long enough. But what they can't know is, if they do get lucky and get a more complex cell, specifically how it would form.

If they were trying to maximise the probability of metazoa, they would know that it would require something like mitochondria to power it. Surely that's what we'd expect to see frontloaded, isn't it? Any thing else seems like heavy gambling.


This message is a reply to:
 Message 109 by Genomicus, posted 06-27-2012 1:10 PM Genomicus has responded

Replies to this message:
 Message 162 by Genomicus, posted 07-03-2012 1:56 PM bluegenes has not yet responded

  
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 142 of 172 (666675)
06-29-2012 1:41 PM


The LUCA and the minimal genome
A number of you seem to be under the impression that it’s really not reasonable for the LUCA to have had a minimal genome under the non-teleological model. Interestingly, the mainstream scientific literature doesn’t seem to agree with you.

For example:

quote:
Two questions that should be closely related have historically been studied with very different approaches. One is what constitutes a minimal living system, whether minimal cell or minimal self-contained ecosystem. The other is what actual system was the last universal common ancestor (LUCA) of all modern cells. As the LUCA is supposed to have been a bottleneck through which all life passed before diversifying into modern forms, it is treated as a self-sufficient organism and would be a candidate for a minimal cell.
(Experimental Search for Minimal Organisms and the Last Universal Common Ancestor, 2006, Complexity: DOI 10.1002/cplx.20154)

And:

quote:
The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes.
(The proteomic complexity and rise of the primordial ancestor of diversified life, 2011)

Progenotes, incidentally, are even more minimal than a minimal cell.

Also:

quote:
Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics.

(A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective, 2006)

And:

quote:
A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199-214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403-414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5' and 3' halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5' and 3' halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5' and 3' halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed.
(The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA), 2006)

So this study proposes that (a) tRNA genes arose after the LUCA, and (b) that protein-coding genes have a polyphyletic origin, which means that they similarly arose after the LUCA. This, in turn, implies that the LUCA was quite a simple organism indeed, lacking tRNA genes and other genes.

Furthermore:

quote:
However, several other components of the DNA replication machinery, such as the sliding clamp plus the clamp loader ATPase and the DNA ligase, as well as enzymes of DNA precursor biosynthesis – ribonucleotide reductase and thymidylate kinase – are homologous in all prokaryotes, which led to the proposal that LUCA had a retrovirus-like replication cycle…Because RNA molecules are fragile compared with DNA, and no RNA virus with a monopartite genome O30 kb has been described, it has been suggested that the genome of LUCA consisted of a set of co-inherited RNA segments, each coding for one or a few proteins. The retrovirus-like genetic cycle of LUCA would account for a set of multiplying, competing, functionally diversifying and recombining molecules without demanding the complexity of a fully fledged prokaryotic genome.
(On the origin of genomes and cells within inorganic compartments, 2005)

Thus we see that, according to this paper, the LUCA was (a) virus-like in its replication and genomic architecture, (b) LUCA was simpler than a fully-fledged prokaryotic genome. Also, if you take a look at their Figure 1, you will observe that just before the origin of the LUCA we have limited gene accretion, origin of proto-operons (that’s a far cry from encoding needless complexity), etc. And just after the origin of the LUCA, we still don’t have DNA genomes. In other words, this paper proposes that LUCA was quite simple (yet, for some odd reason – using the logic of a number of you here – this simple LUCA would have encoded globins, gephyrin, calmodulin, thymidine phosphorylase, etc.).

Also:

quote:
Nothing concrete can be said apropos LUCA’s physical appearance, but the common ancestor can be perceived as a molecular entity invested with information qualities. For instance it can be conceived as a member of a phylogenetic line of descent without an organismal corporeal existence, without genealogy, similar to single genes of the RNA world, loosely united in a network with the evolvable gene clustering that in time encoded chaperone proteins, known as enzymes, to develop into a growing functioning metabolism. Epigrammatically, this had to be a simple genetic entity, without a real intermediary metabolism to accompany its beginning. In this view, I see LUCA as deprived of complex protein capabilities as the result of a deficient information processing apparatus. For example, complex proteins, like primases, helicases, DNA polymerases and other familiar enzymes in membrane and nuclear compartments, are out of the question. The replication process that we see in today’s eukaryotes could not have existed. Only chaperone proteins can be expected from this common and communal ancestor. It was nothing but a genetic network of RNA genetic units in total Darwinian “war” among themselves; this was the first theater of selfish genes, with little or no-intermediate metabolism. LUCA “lived” without any of the cell compartments, totally at the mercy of lateral “abuses” from nearby oligonucleotides, molecular parasites that endangered its “incipient library”.
(Evolution without speciation but with selection: LUCA, the Last Universal Common Ancestor in Gilbert's RNA world, 2003)

That sounds like a sophisticated organism deployed for front-loading, doesn’t it?

And:

quote:
The archaeal sequences are highly homologous to those of the eukaryotic Rad2 family and they cluster with genes of the FEN-1 subfamily, which are known to be involved in DNA replication and repair in eukaryotes. 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.

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

The Point
The point is not that the LUCA was, in fact, a simple cell with a minimal genome. The point is that it is perfectly reasonable, acceptable, and logical for the LUCA to have had a minimal genome, based on the non-teleological scenario for the origin of life.

This makes comments like…

LUCA did not have a single base codon system as the evidence suggests was the case for the first life. Instead, LUCA had a three base codon system, with some 3rd base wobble. Already, LUCA is not a minimalist genome, and we have only looked at the tRNA's.

…slightly irrelevant. The point here is not what the LUCA actually was, but what it could have logically been, under the non-telic framework.
By the way, by “minimal genome” I am not referring to the genetic code but to the genome, Taq. There’s a difference, ya know.

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

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


Replies to this message:
 Message 145 by New Cat's Eye, posted 06-29-2012 1:58 PM Genomicus has responded
 Message 150 by PaulK, posted 06-29-2012 4:35 PM Genomicus has responded

  
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 143 of 172 (666678)
06-29-2012 1:50 PM
Reply to: Message 132 by New Cat's Eye
06-28-2012 9:44 AM


Re: The Ubiquitin Story
You reason seems to be: "it could have happened differently".

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

That isn't a reason to not suspect a ubiquitin homolog in prokaryotes. And what makes you think that ubiquitin could have evolved like T-urf13 did? Ubiquitin is a protein and T-urf13 is a gene... wait, are you looking for a homolog to the ubiquitin protein or the ubiquitin gene?

Huh?

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


This message is a reply to:
 Message 132 by New Cat's Eye, posted 06-28-2012 9:44 AM New Cat's Eye has not yet responded

  
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 144 of 172 (666680)
06-29-2012 1:54 PM
Reply to: Message 133 by Taq
06-28-2012 11:23 AM


Re: The Ubiquitin Story
Non-teleological meteorology does not predict that it will rain in Dallas, TX today because it could just as easily not rain today. Therefore, if it rains it is due to rain fairies.

Nope, because there is nothing in the "rain fairy hypothesis" that says it must rain today in Dallas, TX, and therefore that "hypothesis" doesn't predict that it will rain in Dallas today.

In the same way, evolution does not predict that specific proteins will become necessary in future generations. Rather, it accomodates such observations. Ubiquitin fits this model. Non-teleological evolution can easily co-opt a gene in ancestors to fill a necessary role in descendants. That is what it does. You are trying to falsify evolution by pointing to the very observations that it can produce. That makes no sense.

Your problem is that you still think I'm looking for something that Darwinian evolution cannot explain. That's not what FLE is about. It's about making testable predictions that Darwinian evolution does not make. That Darwinian evolution can explain an observation does not mean it predicts it. And if another hypothesis predicts that observation, then that hypothesis is strengthened.


This message is a reply to:
 Message 133 by Taq, posted 06-28-2012 11:23 AM Taq has responded

Replies to this message:
 Message 158 by Taq, posted 07-02-2012 12:07 PM Genomicus has not yet responded

  
New Cat's Eye
Member
Posts: 11538
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.7


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


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

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

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

It took me about 7 minutes to find three:

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

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

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

This message is a reply to:
 Message 142 by Genomicus, posted 06-29-2012 1:41 PM Genomicus has responded

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

  
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 146 of 172 (666685)
06-29-2012 2:07 PM
Reply to: Message 131 by PaulK
06-28-2012 1:37 AM


Re: The Ubiquitin Story
That doesn't affect my reasoning, though. HOW ubiquitin appeared is not an issue. WHEN it appeared in the evolutionary history of eukaryotes and prokaryotes is the issue. And my argument covers that.

Ubiquitin could have appeared shortly before the origin of eukaryotes. In which case, it could have easily been lost in the few prokaryotic lineages in which it first arose.


This message is a reply to:
 Message 131 by PaulK, posted 06-28-2012 1:37 AM PaulK has responded

Replies to this message:
 Message 148 by PaulK, posted 06-29-2012 2:15 PM Genomicus has responded

  
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.9


Message 147 of 172 (666688)
06-29-2012 2:10 PM
Reply to: Message 145 by New Cat's Eye
06-29-2012 1:58 PM


Re: The LUCA and the minimal genome
It took me about 7 minutes to find three...

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


This message is a reply to:
 Message 145 by New Cat's Eye, posted 06-29-2012 1:58 PM New Cat's Eye has responded

Replies to this message:
 Message 149 by New Cat's Eye, posted 06-29-2012 2:42 PM Genomicus has responded

  
PaulK
Member
Posts: 12863
Joined: 01-10-2003
Member Rating: 3.4


Message 148 of 172 (666691)
06-29-2012 2:15 PM
Reply to: Message 146 by Genomicus
06-29-2012 2:07 PM


Re: The Ubiquitin Story
So *IF* it appeared only shortly before eukaryotes arrived it MIGHT have been lost. That doesn't mean that we don't expect to see homologues.

Of course if it was as useful to prokaryotes then that wouldn't be likely to happen. Of course we wouldn't expect to see only distantly related homologues in prokaryotes either. So ubiquitin hardly supports your ideas.


This message is a reply to:
 Message 146 by Genomicus, posted 06-29-2012 2:07 PM Genomicus has responded

Replies to this message:
 Message 151 by Genomicus, posted 06-29-2012 8:56 PM PaulK has responded

    
New Cat's Eye
Member
Posts: 11538
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.7


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


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

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

Quite right.

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

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

Why would it be lost?

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

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

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

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


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

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


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

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

  
PaulK
Member
Posts: 12863
Joined: 01-10-2003
Member Rating: 3.4


Message 150 of 172 (666757)
06-29-2012 4:35 PM
Reply to: Message 142 by Genomicus
06-29-2012 1:41 PM


Re: The LUCA and the minimal genome
quote:

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

I think that I have a paper that about qualifies - and I note that you have yet to find one paper that actually ARGUES otherwise rather than, for instance, stating that it was assumed.

Even if you judge otherwise this paper at least argues that a non-minimal genome is more reasonable and calls the reasonableness of the assumption of a minimal genome into question:


We think moreover that there are general lessons to be learned from evolutionary biology studied at different organismal levels. For example, discussing the Cambrian radiations of primitive animals, Balavoine and Adoutte (1998) stressed ‘the traditional intellectual bias for increasing complexity in evolution’ and Adoutte et al. (1999) concluded that ‘animal diversification… must have been triggered primarily by external factors acting on a “preadapted” (meaning possessing many features prone to further speciation or functional cooption), already genetically complex metazoan’ (our emphasis). The parallel with the problem discussed here is obvious. The fuzzy organization of a redundant genome inherited from the progenotic era, made of scattered domains or subdomains separated by interstitial sequences must have been a far better substrate for further evolution than a prokaryote-like genome, which would have had to acquire several capital novelties and constantly increase in complexity

About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal


This message is a reply to:
 Message 142 by Genomicus, posted 06-29-2012 1:41 PM Genomicus has responded

Replies to this message:
 Message 153 by Genomicus, posted 06-29-2012 9:16 PM PaulK has responded

    
Prev1
...
789
10
1112Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2015 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2017