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Author Topic:   An ID hypothesis: Front-loaded Evolution
Taq
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Posts: 8525
Joined: 03-06-2009
Member Rating: 5.0


Message 76 of 216 (653492)
02-21-2012 5:47 PM
Reply to: Message 73 by Genomicus
02-21-2012 5:32 PM


Am I the only one that is puzzled by this discrepancy of statements?

Perhaps you could focus on what I said in response to what you said? I think I am allowed to disagree with other posters.

You said that life was front-loaded for eyes at the root of the tree. I responded by pointing out that, if evolution is true, then we should find the basal genes at the earliest nodes of the tree. Those genes were then modified through mutation and selection over time through evolution. You are actually taking the predictions that the theory of evolution makes and then claiming that it is evidence for ID front loading instead. That makes no sense.


This message is a reply to:
 Message 73 by Genomicus, posted 02-21-2012 5:32 PM Genomicus has not replied

Replies to this message:
 Message 88 by Percy, posted 02-22-2012 11:59 AM Taq has replied

  
Dr Adequate
Member (Idle past 373 days)
Posts: 16112
Joined: 07-20-2006


(1)
Message 77 of 216 (653493)
02-21-2012 5:50 PM
Reply to: Message 75 by Genomicus
02-21-2012 5:38 PM


Re: Into the swamps...
As Bluejay predicted, I am effectively getting swamped with responses. So is there anyone who would especially like me to respond to their points?

Well, speaking for myself, I would especially like you to respond to my points.

But it doesn't really matter. So long as eventually you get round to explaining your ideas by and by, that's fine. So long as you keep on trying to get round to this or that explanation of your idea, no-one really cares if you'll produce the explanation right now, right away, or later. Do it in your own time.

We evolutionists may be a bit mean in some ways (I know I am) but I think we'll all give you as much time as you like to think of your own hypothesis.


This message is a reply to:
 Message 75 by Genomicus, posted 02-21-2012 5:38 PM Genomicus has not replied

  
Taq
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Posts: 8525
Joined: 03-06-2009
Member Rating: 5.0


Message 78 of 216 (653494)
02-21-2012 5:52 PM
Reply to: Message 75 by Genomicus
02-21-2012 5:38 PM


Re: Into the swamps...
As Bluejay predicted, I am effectively getting swamped with responses.

That's what happens when you push ideas that are poorly defined and unevidenced.

So is there anyone who would especially like me to respond to their points?

Look for common themes amongst the different posts, summarize them, and then address them. One of the common themes right now is trying to find a way to differentiate between ID front loading and the expected results from natural mechanism, most notably evolution. I would also suggest that you stop using vague terms that are completely subjective.

I am not a moderator, so these are just friendly suggestions.


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bluegenes
Member (Idle past 1799 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 79 of 216 (653497)
02-21-2012 6:09 PM
Reply to: Message 75 by Genomicus
02-21-2012 5:38 PM


Re: Into the swamps...
Genomicus writes:

As Bluejay predicted, I am effectively getting swamped with responses. So is there anyone who would especially like me to respond to their points? I do owe bluegenes a response, though, so responding to his post is priority.

No hurry for me Genomicus, and I know I'm busy for the next couple of days anyway. The general point that I made on the other thread and that others are making here might be a good priority, as Taq suggests above. That is, the predictions that would differ from those of evolutionary theory. As you know, I don't think the standard code is any use to you at all in this respect, but I expect you'll disagree, and I'm sure you have other claims as well.


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Trixie
Member (Idle past 3028 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


(1)
Message 80 of 216 (653500)
02-21-2012 6:36 PM
Reply to: Message 74 by Genomicus
02-21-2012 5:33 PM


I understand that you feel snowed under, but you didn't really address my post. You said

Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.

It does not show this at all. It shows that the ability to regulate the expression of genes has remained crucial from prokayotes to humans, since it is the regulatory part of PAX6 which shows homology and in fact the whole family of PAX genes show homology with prokaryotic transcription facors, hardly surprising given that a common method of regulating gene expression is DNA sequence-specific binding by these proteins. Some bacterial TFs can bind to host cell DNA and alter genexpression of the host cel in order to increase their own pathogenic effects, for example Xanthomonas, as mentioned in the article below.

Take all the time you want in addressing this.

For a good overview of transcription factors, anyone interested can go to http://en.wikipedia.org/wiki/Transcription_factors where there's plenty of information.


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 Message 74 by Genomicus, posted 02-21-2012 5:33 PM Genomicus has not replied

  
Blue Jay
Member (Idle past 2019 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 81 of 216 (653515)
02-22-2012 12:09 AM
Reply to: Message 64 by Genomicus
02-20-2012 10:24 PM


Hi, Genomicus.

Like everybody else, I don't think there's any rush to respond to me. I'll still be here whenever you get around to responding.

Genomicus writes:

Do note, too, that the more specific the front-loading objective, the less likely it is that that objective will evolve multiple times.

The more specific the objective, the less likely the objective is to be met at all using a crude technique like front-loading. I find it highly dubious to suggest that something as specific as an eye could feasibly be front-loaded at all for this exact reason.

Unfortunately, I think this is going to leave you in a conundrum: only the most basic, fundamental characteristics that have broad utility for a wide diversity of organisms could be front-loaded. But, the prevalence of those characteristics is expected under anybody's model of the origin and history of life. So front-loading without specific objectives would make no unique predictions, and would thus be untestable.

Genomicus writes:

Well, you wouldn't expect eyes in prokaryotes, now would you?

Why not? Otherwise, you've got a gene that has to persist for a very long time with minimal change due to mutation, while not fulfilling its eye-related functions. If you suggest that it could fill another function in the interim, you'd have to accept that it would be undergoing selection for that other function, which leaves no guarantee that it would still be serviceable in eye development once an organism capable of using it to develop eyes evolved.

Surely we have to accept that front-loaded eyes are a dubious proposition.

Genomicus writes:

Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life.

But only the animals seem able to actually evolve eyes, because they evolved them several times, and no other group did. Doesn't this suggest that the capacity doesn't exist at the base of the tree?


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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Genomicus
Member (Idle past 1263 days)
Posts: 852
Joined: 02-15-2012


Message 82 of 216 (653522)
02-22-2012 5:03 AM
Reply to: Message 57 by bluegenes
02-20-2012 9:13 AM


Re: The best of error minimizing codes?
Yes, that's the answer I was expecting, but it was optimization for error minimization that you mention in the O.P. In fact, the paper suggests that the standard code is frozen some way off even its local fitness peak so far as error correction is concerned. However, the other improved error minimization peaks are so numerous that it would seem unlikely that there aren't those that would achieve better all round balanced function (or more rational design) than the one we've got. The designers had a lot of choice.

I have read the paper you cited earlier. Their conclusions are in direct contradiction with the conclusions of Freeland et al.

Novozhilov et al. conclude that:
"The standard code appears to be the result of partial optimization of a random code for robustness to errors of translation. The reason the code is not fully optimized could be the trade-off between the beneficial effect of increasing robustness to translation errors and the deleterious effect of codon series reassignment that becomes increasingly severe with growing complexity of the evolving system."

While Freeland et al. state that:
"Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space."

Why is there this discrepancy? IMHO, the answer is that these two different studies used different methodologies. Novozhilov et al. primarily use the Gilis scoring matrix to arrive at their results, while Freeland et al. use the PAM74-100 substitution matrix. The Gilis scoring matrix is based on protein stability, while the PAM matrix is based on observed amino acid substitution frequencies. Given that the PAM matrix more accurately portrays amino acid similarity from an evolutionary perspective (that is, the PAM matrix shows amino acid similarities based on what amino acid substitutions have been accepted by natural selection over evolutionary time), while the Gilis scoring matrix portrays amino acid similarities on the basis of protein stability, IMHO Freeland et al.'s conclusions are more biologically realistic from the perspective of evolution. Also, on the side, I don't think Novozhilov et al. consider biosynthetic restrictions on the genetic code, while Freeland et al. do - again, making their results more realistic.

Furthermore, the results of a 2009 paper fly right in the face of the conclusions of Novozhilov et al. A study by Butler et al., 2009 (Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement), used Monte Carlo simulation to assess the optimality of the genetic code, concluding with:
"The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor." (Emphasis added)

Thus, I must disagree with the argument that the genetic code is only "partially optimized." It is extremely optimized for error minimization, and as Freeland et al., 2000, point out, it is very close to the global optimum across plausible parameter space.

It fits the scenario of an initial random functional code evolving to become optimized, and hitting a local peak on the fitness landscape fairly quickly then getting frozen. The paper suggests that random codes hit their local optimums easily and quickly.

A couple of points to be made here:

1) An extremely optimized genetic code, like the standard genetic code, wouldn't seem to be terribly advantageous to unicellular organisms, in contrast to less optimized genetic codes. Radical substitutions would be far more likely to be non-deleterious in unicellular organisms than in complex, multi-cellular organisms. In fact, a less optimized code might be more advantageous for unicellular organisms, in one sense: it would accelerate the rate of protein evolution.
As I explained earlier:
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.

2) Secondly, our different perspectives on the level of optimization come into play here. I view the genetic code as extremely optimal, in agreement with Freeland et al. and Butler et al. The evolution of genetic code optimality, AFAIK, is thought to be Gaussian, instead of linear. This means that there really would be plenty of room for alternative, less optimal codes to branch off, creating a phylogenetic tree of genetic codes, with sub-optimal codes in basal lineages. It doesn't seem all that likely that a highly optimized genetic code will quickly evolve from a random code. You'd also have to gradually incorporate all 20 amino acids. Yet there is also no phylogenetic tree of genetic codes, with gradually increasing numbers of amino acids.

There's quite a gulf between your view and that of the side-loaders.

True.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 57 by bluegenes, posted 02-20-2012 9:13 AM bluegenes has replied

Replies to this message:
 Message 83 by Wounded King, posted 02-22-2012 11:00 AM Genomicus has replied
 Message 85 by Dr Adequate, posted 02-22-2012 11:21 AM Genomicus has replied
 Message 87 by Taq, posted 02-22-2012 11:48 AM Genomicus has not replied
 Message 178 by bluegenes, posted 02-27-2012 5:46 AM Genomicus has not replied

  
Wounded King
Member (Idle past 3416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 83 of 216 (653533)
02-22-2012 11:00 AM
Reply to: Message 82 by Genomicus
02-22-2012 5:03 AM


Re: The best of error minimizing codes?
Given that the PAM matrix more accurately portrays amino acid similarity from an evolutionary perspective (that is, the PAM matrix shows amino acid similarities based on what amino acid substitutions have been accepted by natural selection over evolutionary time)

Massimo Di Giulio (2001) argues that this actually makes approaches such as Freeland's tautological since the nature of the genetic code has had a significant effect on the distribution of amino acid substitutions making it far from an independent measure of the optimisation of that code.

TTFN,

WK


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 Message 82 by Genomicus, posted 02-22-2012 5:03 AM Genomicus has replied

Replies to this message:
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jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.0


Message 84 of 216 (653535)
02-22-2012 11:15 AM
Reply to: Message 83 by Wounded King
02-22-2012 11:00 AM


Re: The best of error minimizing codes?
I'm curious if you have read Freeland's 2010 paper I quoted from and linked to way back up thread and if so what significance it might have related to what Freeland says today.

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

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Replies to this message:
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Dr Adequate
Member (Idle past 373 days)
Posts: 16112
Joined: 07-20-2006


Message 85 of 216 (653536)
02-22-2012 11:21 AM
Reply to: Message 82 by Genomicus
02-22-2012 5:03 AM


Re: The best of error minimizing codes?
I have read the paper you cited earlier. Their conclusions are in direct contradiction with the conclusions of Freeland et al.

Wait ... scientists are disagreeing about something? This has hardly ever happened before.

Seriously, you wish to turn biology on its head and show that our most fundamental ideas about it are wrong. I admire your ambition. But you cannot achieve this with reference to evidence that is itself speculative and unproven. According to your hypothesis (if you fudge it a bit) it would be jolly nice if the genetic code was globally optimal. But no-one has proved this to be the case. The fact that some people have speculated that this is the case is not a reason to throw over Darwinism and start believing in front-loaded evolution instead.


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 Message 82 by Genomicus, posted 02-22-2012 5:03 AM Genomicus has replied

Replies to this message:
 Message 109 by Genomicus, posted 02-23-2012 11:08 PM Dr Adequate has replied

  
Percy
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Posts: 20989
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.5


Message 86 of 216 (653541)
02-22-2012 11:43 AM
Reply to: Message 63 by Omnivorous
02-20-2012 8:32 PM


Re: Presto!
Didn't CS misunderstand this as a complement? And didn't you misunderstand CS as endorsing Genomicus's characterization of ad hoc? What I thought CS was saying was that optimal replacing sub-optimal is precisely what we would expect of a process of successive selection over generations, meaning that it isn't ad hoc at all.

Apologies if the misunderstandings are all mine...

--Percy


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Taq
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Posts: 8525
Joined: 03-06-2009
Member Rating: 5.0


Message 87 of 216 (653543)
02-22-2012 11:48 AM
Reply to: Message 82 by Genomicus
02-22-2012 5:03 AM


Re: The best of error minimizing codes?
1) An extremely optimized genetic code, like the standard genetic code, wouldn't seem to be terribly advantageous to unicellular organisms, in contrast to less optimized genetic codes. Radical substitutions would be far more likely to be non-deleterious in unicellular organisms than in complex, multi-cellular organisms.

You need to support these two assertions with actual evidence.

It doesn't seem all that likely that a highly optimized genetic code will quickly evolve from a random code.

This assertion needs support as well.


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Percy
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Posts: 20989
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.5


Message 88 of 216 (653544)
02-22-2012 11:59 AM
Reply to: Message 76 by Taq
02-21-2012 5:47 PM


Taq writes:

Perhaps you could focus on what I said in response to what you said? I think I am allowed to disagree with other posters.

I don't think you and Mr. Jack are disagreeing. Mr. Jack said that we should expect to find some of our genes represented in the descendants of ancient bacteria, and we do. And you were responding to the example of a specific gene, saying that we should expect to find it in earlier ancestors.

What you actually said was that we should expect to find it in the "earliest ancestors", which implies ancient prokaryotes or before, but of course many of our genes arose later. That may be why Genomicus thinks he sees a contradiction.

The message for Genomicus is that all genes in existence today stem from a process of random mutation and natural selection. Some genes are of recent origin, some of ancient origin. We should expect to find some of our genes in the descendants of ancient archaea, some in the descendants of ancient prokaryotes, some in the descendants of ancient eukaryotes, some in the descendants of ancient fish, some in the descendants of ancient amphibians, some in the descendants of ancient mammals, and some in the descendants of ancient apes. And that's exactly what we find.

Were there frontloading we would expect to see the remnants of that frontloading still hanging around in some lineages, but we don't.

--Percy


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Taq
Member
Posts: 8525
Joined: 03-06-2009
Member Rating: 5.0


Message 89 of 216 (653550)
02-22-2012 1:04 PM
Reply to: Message 88 by Percy
02-22-2012 11:59 AM


What you actually said was that we should expect to find it in the "earliest ancestors", which implies ancient prokaryotes or before, but of course many of our genes arose later. That may be why Genomicus thinks he sees a contradiction.

Yes, I didn't make that very clear. By "earliest ancestor" I meant the common ancestor of a given clade. A homologous feature shared by the entire clade should be found in the earliest ancestor of that clade if evolution is true. Therefore, of the modern organisms that have PAX6 the common ancestor of those organisms should also have the ancestral gene that was modified through time in that lineage.

It seems to me that this is what evolution predicts. I don't see how ID can take this prediction and claim that it is really evidence of front loading. I also sense a dependency on the Sharpshooter Fallacy in that ID proponents assume that the results of evolution that we see today were an intended result when in fact the results could have been quite different. I think it was Stephen J Gould who said something to the effect of "if we replayed the tape of evolution we would not expect anything close to what we see now".

To use an analogy, one could claim that Latin was front-loaded to produce modern French. Afterall, the root words in modern French can be found in ancient Latin. This ignores the fact that if replayed history and started a whole new time line that we probably would not end up with modern French. Which words are adopted and changes in pronunciation are very choatic when it comes to the development of languages.


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Omnivorous
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Posts: 3851
From: Adirondackia
Joined: 07-21-2005


(2)
Message 90 of 216 (653587)
02-22-2012 8:43 PM
Reply to: Message 86 by Percy
02-22-2012 11:43 AM


Re: Presto!
Percy writes:

Didn't CS misunderstand this as a complement?

It was a sincere compliment. I think the general excitement at engaging an intelligent, articulate IDist has allowed a fair amount of circularity and hand-waving to go unremarked. I was pleased to see CS challenge something I had raised an eyebrow at but was too lazy to engage.

And didn't you misunderstand CS as endorsing Genomicus's characterization of ad hoc?

No, I understood CS to be saying, as you did, that "optimal replacing sub-optimal is precisely what we would expect of a process of successive selection over generations, meaning that it isn't ad hoc at all." I took Genomicus' dismissal of that as an attempt to poison the well with a bit of hand-waving.

Apologies if the misunderstandings are all mine...

None needed, Percy. You think and write with uncommon clarity. My default position is that if you are unsure of my meaning, I didn't state it clearly.

Sometimes, perhaps, I should turn the sardonic dial down.


"If you can keep your head while those around you are losing theirs, you can collect a lot of heads."

This message is a reply to:
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