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Author Topic:   An ID hypothesis: Front-loaded Evolution
Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 31 of 216 (653271)
02-19-2012 4:40 PM
Reply to: Message 27 by Dr Jack
02-19-2012 4:21 PM


Re: more just plain incorrect assertions.
quote:
Because the selective advantage of a high quality genetic code is high, and the nature of horizontal gene transfer means that there is an advantage in a shared genetic code.

Naturally a high quality genetic code is advantageous. But to argue that the sub-optimal genetic codes disappeared from the scene as a result of the appearance of the highly optimized code is ad hoc. Also note that there might actually be an advantage for prokaryotes to have a sub-optimal genetic code: radical mutations would be more frequent, and this could possibly accelerate evolution. You wouldn't have to go through multiple amino acid substitutions to get to a radically different amino acid. I.e., if you take a look at the PAM1 substitution matrix, there is a 0% probability that an alanine --> tryptophan substitution will occur. So, in order to get alanine to change into tryptophan, it'd have to be like this, for example: alanine --> arginine --> tryptophan. The canonical genetic code, then, is a good system for complex organisms, where radical substitutions will be very likely deleterious. But for bacteria, a sub-optimal genetic code, where radical mutations are far more frequent, this might just be a selective advantage.

In response to the argument that HGT results in a selective advantage for a shared genetic code, I could just as easily respond that HGT reduces the selective advantage for a shared genetic code: horizontally transferred genes can be deleterious if the genes are translated and are incompatible with the genes in the original genome. An important point to realize about HGT is that selfish, mobile elements can be transferred laterally, and so can genes incompatible with the original genome - which means that HGT can be deleterious.

quote:
Living prokaryotes are not ancient throwbacks, they do not represent the vestiges of an ancient world...

While basal lineages are certainly not ancient, in a way they do represent vestiges of an ancient world. Thus, the observation that flagellar genes have been found in deeper-branching bacteria has been used as an argument by various investigators that the bacterial flagellum is more ancient than the type III secretion system.


This message is a reply to:
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Jon
Inactive Member


Message 32 of 216 (653273)
02-19-2012 4:52 PM
Reply to: Message 29 by DWIII
02-19-2012 4:37 PM


Re: Some objections...
If multicellularity (and therefore plants and animals and fungi) was a legitimate goal, why not have started off with it immediately?

My guess is that before the watchmaker went completely blind, he was already a little near-sighted.


Love your enemies!

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Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 33 of 216 (653274)
02-19-2012 4:55 PM
Reply to: Message 23 by Dr Jack
02-19-2012 4:07 PM


quote:
Welcome to EvC...

Thanks - I saw your later message before I saw this one, so I'm replying to this one now.

quote:
How do you intend to test this hypothesis?

We could identify genes important to the development and function of multicellular organisms, and BLAST them against prokaryote genomes, and see if we get any significant hits.

quote:
The trouble with this prediction is that it does not, in fact, differ from the predictions of conventional theory. If a protein exists with homologes in Bacteria, Archaea and Eukarya* then it must have be strongly conserved, otherwise it wouldn't exist in all three domains. Such strongly conserved proteins will trivially be more highly conserved in sequence identity than other proteins.

If a protein exists with homologs in all domains of life, then it does not follow from conventional theory that it must also be highly conserved in sequence identity - not any more so than the average protein. For example, actin has a homolog in prokaryotes: MreB. What does conventional theory say about MreB's degree of sequence conservation, in contrast with other prokaryotic proteins (and without knowing the function of MreB)?

quote:
Interestingly, the 3D shape of proteins is much more highly conserved than sequence identity. I'm not really sure how your justification follows, either.

Yes, but it is sequence identity that, in a large part, determines the tertiary structure of the protein. Thus, ensuring that the sequence identity is well conserved ensures that the basic 3D shape of the protein will be well preserved, which prevents the blind watchmaker from getting in the way of the front-loading objectives by significantly altering the protein's 3D shape.


This message is a reply to:
 Message 23 by Dr Jack, posted 02-19-2012 4:07 PM Dr Jack has replied

Replies to this message:
 Message 37 by Dr Jack, posted 02-19-2012 5:12 PM Genomicus has replied

  
Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 34 of 216 (653278)
02-19-2012 5:01 PM
Reply to: Message 28 by jar
02-19-2012 4:22 PM


Re: more just plain incorrect assertions.
quote:
Okay, so we now know that you admit that there is no universal genetic code.

I already stated that in my first post here, in my essay. I said the "nearly universal genetic code."

That said, I really have little interest in continuing a discussion with you. I'd prefer to spend my time (and I haven't got too much of it) discussing biological origins with the likes of MrJack or DWIII, and not with those of you who seem to be fond of making snide remarks (e.g., "It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god").

Cheerios!


This message is a reply to:
 Message 28 by jar, posted 02-19-2012 4:22 PM jar has replied

Replies to this message:
 Message 35 by jar, posted 02-19-2012 5:07 PM Genomicus has not replied
 Message 36 by Granny Magda, posted 02-19-2012 5:10 PM Genomicus has not replied

  
jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.0


(1)
Message 35 of 216 (653279)
02-19-2012 5:07 PM
Reply to: Message 34 by Genomicus
02-19-2012 5:01 PM


Re: more just plain incorrect assertions.
Although I happen to be a Christian I doubt you can find anywhere I say anything like "(e.g., "It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god")."

However should you ever feel capable of providing either evidence some planner exists or provide a model of how that planner actually "front loads" a genome (for example using really small John Deere tractors) then I look forward to your input.

But until then you have nothing but word salad and I will continue to point out examples of your trying to insert the dime into the little kid's ear.

Edited by jar, : replace " with the missing )


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
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Granny Magda
Member (Idle past 154 days)
Posts: 2384
From: UK
Joined: 11-12-2007


(1)
Message 36 of 216 (653280)
02-19-2012 5:10 PM
Reply to: Message 34 by Genomicus
02-19-2012 5:01 PM


Re: more just plain incorrect assertions.
I'd prefer to spend my time (and I haven't got too much of it) discussing biological origins with the likes of MrJack or DWIII, and not with those of you who seem to be fond of making snide remarks (e.g., "It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god").

It's not my intent to be snide, only to be truthful. I apologise if I have offended you, but I hope you can appreciate that I must call it as I see it. I don't want to soft-soap you, I think that would be patronising and would ultimately do you a disservice.

ID, as a movement, is a form of Christian apologetic. All of its leading lights are Christians, most of its supporters are Christians, the rest Muslims and other theists. There are only one or two non-theistic supporters. We know for a fact that there is a continuity between "creation science" and ID; we have the documents to prove it. So calling this hypothesis an apologetic is simply the truth as far as I am concerned.

Or are you going to tell me that you are not a Christian?

Meanwhile I would appreciate any response to the rest of my post.

Mutate and Survive


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 Message 34 by Genomicus, posted 02-19-2012 5:01 PM Genomicus has not replied

  
Dr Jack
Member (Idle past 1424 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 37 of 216 (653281)
02-19-2012 5:12 PM
Reply to: Message 33 by Genomicus
02-19-2012 4:55 PM


(By the way we usually use [qs]whatever[/qs] rather than [quote]whatever[/quote], which is why our quotes appear in the more prominent light blue blocks and yours just have horizontal bars distinguishing them. Just a quirk of the software )

We could identify genes important to the development and function of multicellular organisms, and BLAST them against prokaryote genomes, and see if we get any significant hits.

Well, I can flat out tell you the answer to that one: we do. The problem for you is that this isn't, in any way, incompatible with conventional theory. Exaptation is common, and well understood. These genes perform important roles in single celled organisms, and are later exapted to perform different roles in multi-cellular organisms. You need to come up with something that will distinguish your front-loaded genes from simple exaptation.

Further, I'd suggest that your hypothesis should lead to us seeing many, probably most, such multi-cellular genes in prokaryotes - we don't. There are some, yes, but most are not found in bacteria; a few more in Archaea and a decent portion in single-celled Eukarya or in multi-cellular but simply differentiated Eukarya. It seems to me that if front-loading was true we would expect a majority of such genes to be present in all species, would you agree?

If a protein exists with homologs in all domains of life, then it does not follow from conventional theory that it must also be highly conserved in sequence identity - not any more so than the average protein.

Of course it does. Highly conserved proteins have higher sequence identities than average proteins whilst, conversely, proteins not under selective pressure rapidly diverge. Proteins shared between the three domains must be highly conserved and thus will tend to have higher sequence identities.

For example, actin has a homolog in prokaryotes: MreB. What does conventional theory say about MreB's degree of sequence conservation, in contrast with other prokaryotic proteins (and without knowing the function of MreB)?

If I knew nothing about MreB I would predict that its sequence identity was higher than other proteins. As I mentioned, 3d structure is more highly conserved than sequence so it's possible that the sequence has entirely altered but it's a less likely possibility.


This message is a reply to:
 Message 33 by Genomicus, posted 02-19-2012 4:55 PM Genomicus has replied

Replies to this message:
 Message 38 by Granny Magda, posted 02-19-2012 5:28 PM Dr Jack has replied
 Message 47 by Genomicus, posted 02-19-2012 6:53 PM Dr Jack has not replied

  
Granny Magda
Member (Idle past 154 days)
Posts: 2384
From: UK
Joined: 11-12-2007


(2)
Message 38 of 216 (653282)
02-19-2012 5:28 PM
Reply to: Message 37 by Dr Jack
02-19-2012 5:12 PM


Miller on Front-Loading
Hi Mr J,

Exaptation is common, and well understood. These genes perform important roles in single celled organisms, and are later exapted to perform different roles in multi-cellular organisms. You need to come up with something that will distinguish your front-loaded genes from simple exaptation.

I found an interesting comment from Ken Miller on this. He suggests that if front-loading were real, we would see the exact opposite of what Genomicus suggests; we would see enormous mutation rates on any front-loading sequences. They would be inactive and thus unchecked by natural selection. Those portion of the genome would be subject to runaway mutation.

quote:
This means that billions of years ago a humble prokaryote was packed with genes that would be turned off for hundreds of millions of years before they produced the eukaryotic cilium, and genes for blood clotting proteins that would pass more than a billion inactive years in genetic "cold storage." And what happens during those billions of years? As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering then hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed.

I have to agree with that. If any gene were front-loaded it would have to have yet further (as yet conveniently undetected) mechanism to guard against this.

Mutate and Survive


This message is a reply to:
 Message 37 by Dr Jack, posted 02-19-2012 5:12 PM Dr Jack has replied

Replies to this message:
 Message 39 by Dr Jack, posted 02-19-2012 5:32 PM Granny Magda has replied
 Message 45 by bluegenes, posted 02-19-2012 6:12 PM Granny Magda has replied

  
Dr Jack
Member (Idle past 1424 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 39 of 216 (653283)
02-19-2012 5:32 PM
Reply to: Message 38 by Granny Magda
02-19-2012 5:28 PM


Re: Miller on Front-Loading
Hi Granny M,

I found an interesting comment from Ken Miller on this. He suggests that if front-loading were real, we would see the exact opposite of what Genomicus suggests; we would see enormous mutation rates on any front-loading sequences. They would be inactive and thus unchecked by natural selection. Those portion of the genome would be subject to runaway mutation.

If I'm understanding Genomicus correctly, this would not apply to his (her? I'm assuming, apologies if I'm wrong) ideas since he is suggesting that these front-loaded genes are active in their original form. His hypothesis is that the nature and selection of the genes present pre-prepares them for later adoption into functions vital for multi-cellular life and a particular form of multi-cellular life at that.

It's not that there is a silent library, it's that the active genes guide life's evolution down a desired path.


This message is a reply to:
 Message 38 by Granny Magda, posted 02-19-2012 5:28 PM Granny Magda has replied

Replies to this message:
 Message 40 by Granny Magda, posted 02-19-2012 5:40 PM Dr Jack has not replied
 Message 41 by jar, posted 02-19-2012 5:41 PM Dr Jack has not replied

  
Granny Magda
Member (Idle past 154 days)
Posts: 2384
From: UK
Joined: 11-12-2007


Message 40 of 216 (653285)
02-19-2012 5:40 PM
Reply to: Message 39 by Dr Jack
02-19-2012 5:32 PM


Re: Miller on Front-Loading
Ooh! Genomicus has a blog! He proposes this answer to the above problem;

quote:
How can this problem be overcome? There’s a pretty simple solution, actually. If proteins A1, B1, and C1 are given functions such that their sequence identity is well conserved, and thus their 3D shapes, this problem is overcome.

Is it just me or does that sound exactly like exaptation?

That's just exaptation, or at least it's indistinguishable from exaptation. So again, the best evidence for front-loading is exactly the same as what we'd see if consensus model evolution were true.

Mutate and Survive


This message is a reply to:
 Message 39 by Dr Jack, posted 02-19-2012 5:32 PM Dr Jack has not replied

  
jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.0


Message 41 of 216 (653286)
02-19-2012 5:41 PM
Reply to: Message 39 by Dr Jack
02-19-2012 5:32 PM


Re: Miller on Front-Loading
It's not that there is a silent library, it's that the active genes guide life's evolution down a desired path.

If so, that is the con as I have tried to point out.

It is that insertion of "desired path" that is without evidence and the magic trick.


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 39 by Dr Jack, posted 02-19-2012 5:32 PM Dr Jack has not replied

  
Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 42 of 216 (653287)
02-19-2012 5:43 PM
Reply to: Message 29 by DWIII
02-19-2012 4:37 PM


Re: Some objections...
quote:
Panspermia, of course, pushes the problem one level deeper.

Although Crick and Orgel abandoned directed panspermia later in their life, this particular quote from their paper is as relevant as ever:
It has also been argued that "infective" theories of the origins of terrestrial life should be rejected because they do no more than transfer the problem of origins to another planet. This view is mistaken; the historical facts are important in their own right. For all we know there may be other types of planet on which the origin of life a6 initio is greatly more probable than on our own. For example, such a planet may possess a mineral, or compound, of crucial catalytic importance, which is rare on Earth.

quote:
Would it necessarily follow that the propagators themselves (of which you talk of) originated by way of earlier directed panspermiatic projects? Where does the chain end, if it ever ends?

No it would not necessarily follow. The front-loading designers may have evolved through non-teleological mechanisms. That's not a problem for front-loading since front-loading isn't so much about finding gaps in the non-teleological theory than in presenting positive evidence in favor of teleology. Also, from a philosophical point of view (I'm no philosopher, so I may very well be cut to shreds here): life might have no historic origin. If the universe is infinite, as many believe, life may also be infinite. I like to think, however, that it is not, 'cause then there'd be a good reason to pursure OoL research.

quote:
And what's so special about multicellularity, then? The vast bulk (by mass) of life on Earth has been, and currently remains, unicellular (bacteria in particular). If multicellularity (and therefore plants and animals and fungi) was a legitimate goal, why not have started off with it immediately?

Complex life forms probably couldn't survive the early, hostile earth. Bacteria are by far the more "survivable" organisms.

quote:
Unfortunately, constructing phylogenic trees requires the existence of intact genetic material, which by and large is not preserved over billions of years; and thus is necessarily limited to currently-living species.

Quite right, but we can still identify ancient systems over more recent systems based on phylogenetic analyses, for example. In other words, if deep-branching organisms (e.g., Firmicutes) had less optimal codes, while later-branching lineages had more optimal genetic codes, this would be a good chunk of evidence against the FLE hypothesis.

quote:
That the various extant alternative genetic codes are derivative from the "universal" code is quite uncontroversial, given that they seem more likely to have arisen via extreme genetic bottlenecks. Unfortunately, this says little to nothing about the actual origins of the universal code itself, except that it shows that even something as hard-wired as the universal genetic code is subject to a possibility of some change under the right circumstances. It is probably reasonable to infer that all known extant life forms one clade with its last common ancestor having had that particular code, but it does not preclude the past existence of other contemporaneous (and currently extinct) clades which had competing codes.

Yea - but that it is possible that competing codes once existed isn't evidence that they did. There's no phylogenetic evidence whatsoever for the view that the canonical, optimized genetic code evolved gradually from sub-optimal codes.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : Lots of typos -.-


This message is a reply to:
 Message 29 by DWIII, posted 02-19-2012 4:37 PM DWIII has seen this message but not replied

  
bluegenes
Member (Idle past 1797 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 43 of 216 (653288)
02-19-2012 6:03 PM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


The best of error minimizing codes?
Hi again, Genomicus.

I hope you'll agree that I was right to suggest a thread specifically for your front loading hypothesis. You may not like all the reactions, but you're certainly getting some!

Genomicus writes:

The genetic code is highly optimized for error minimization (Freeland et al., 2000). This optimal genetic code is nearly universal across all taxa.

There's an interesting thing about this. While our standard code has certainly undergone selection for error minimization, and seems to be close to its local peak on the fitness landscape, there are plenty of higher fitness peaks elsewhere which nature could have hit if it had happened across a different random code to start with.

Looking at this from the I.D. perspective, it seems like bad news. Our standard code seems a very unlikely choice for your rationally designing frontloaders if they were aiming at error minimization.

Here's a 2007 paper that might interest you.

Paper on the rugged fitness landscape of genetic codes

As for your main point about it, I see no reason why any very early more error prone versions should have survived alongside a prokaryote LUCA, and I don't really see the point of your analogy with non-flagellar functional homologies, as these are nothing to do with sub-optimal flagella.

Genomicus writes:

To use front-loading as a working hypothesis, it is assumed that multicellularity was an objective of the front-loading designers, as well as the origin of animals and plants.

Is the suggestion that the front loaders might be able to predict something like the chance endosymbiotic event that seems to have enabled the evolution of eukaryotes? How could they front-load that? And wouldn't they have to have a very clear idea of the future orbit and physical evolution of the planet itself, not to mention the behaviour of the local star which could radically effect things?

I can see many other problems as well, but we've got to start somewhere!

Congratulations on setting out the basic front-loading idea very clearly in your O.P.


This message is a reply to:
 Message 1 by Genomicus, posted 02-19-2012 5:43 AM Genomicus has replied

Replies to this message:
 Message 53 by Genomicus, posted 02-20-2012 12:08 AM bluegenes has replied
 Message 55 by Genomicus, posted 02-20-2012 3:35 AM bluegenes has replied

  
Genomicus
Member (Idle past 1261 days)
Posts: 852
Joined: 02-15-2012


Message 44 of 216 (653289)
02-19-2012 6:04 PM
Reply to: Message 12 by PaulK
02-19-2012 2:16 PM


Re: The obvious problem with front-loading
quote:
Unless preserved by selection the genome can be changed by mutation at a relatively rapid rate. Any "front-loaded" information that isn't actually in use is unlikely to be preserved unchanged for long enough to become useful.

And this is why, under the FLE hypothesis, mRNA transcripts are the sequences that channel evolution, not unexpressed sequences.


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bluegenes
Member (Idle past 1797 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 45 of 216 (653290)
02-19-2012 6:12 PM
Reply to: Message 38 by Granny Magda
02-19-2012 5:28 PM


Re: Miller on Front-Loading
Granny Magda writes:

I found an interesting comment from Ken Miller on this. He suggests that if front-loading were real, we would see the exact opposite of what Genomicus suggests; we would see enormous mutation rates on any front-loading sequences. They would be inactive and thus unchecked by natural selection. Those portion of the genome would be subject to runaway mutation.

Gemonicus is aware of that problem, which is why he describes the genes in prokaryotes intended for later eukaryotes as having function in the prokaryotes and being conserved.


This message is a reply to:
 Message 38 by Granny Magda, posted 02-19-2012 5:28 PM Granny Magda has replied

Replies to this message:
 Message 46 by Granny Magda, posted 02-19-2012 6:44 PM bluegenes has replied

  
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