Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9164 total)
9 online now:
Newest Member: ChatGPT
Post Volume: Total: 916,608 Year: 3,865/9,624 Month: 736/974 Week: 63/286 Day: 63/58 Hour: 10/3


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Towards a Hypothesis of Molecular Design
bluegenes
Member (Idle past 2501 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 6 of 20 (699423)
05-19-2013 11:44 AM
Reply to: Message 1 by Genomicus
05-17-2013 10:08 PM


Genomicus writes:
Prediction 1: Molecular clock analyses of protein sequences of the components of the machine should reveal a specific pattern. Under the Darwinian model, the evolution of a machine like the flagellum proceeds through the stepwise co-option of parts.
Correct. But there are problems with your molecular clock predictions. Firstly, we could put forward an evolutionary hypothesis that the core parts of the ancestral flagellum (an "Ur-flagellum that is ancestor to all the modern variables - there could be millions of these) evolved over less than 1 million years more than 1 billion years ago. Then, all things being equal, it would be impossible to distinguish the relative ages of the diverging proteins by molecular clocks because the actual ages would be 99.9% the same. In addition, the enormous number of generations in an old system like this would mean problems with saturation and parallel mutations on the diverging genes, as well as with changes in the mutation rate of different copies.
The evolution of the core flagellum in less than 1 million years (~2 billion generations of a group of organisms with a very large effective population size) is perfectly plausible. You get from a fish to an elephant in far fewer generations than that!
Geno writes:
this means that we cannot logically predict — from a design perspective — that molecular clocks will demonstrate that all machine components originated at about the same time. This is because if some proteins are modified more substantially than others, it would confuse the molecular clock. Protein components that have undergone more drastic modifications will have the appearance of being more ancient (using a molecular clock), while proteins that are only slightly changed will appear to have originated more recently.
This would also apply with natural selection. Some of the duplicated genes will have had more beneficial mutations that have gone to fixation via positive selection than others after duplication.

This message is a reply to:
 Message 1 by Genomicus, posted 05-17-2013 10:08 PM Genomicus has replied

Replies to this message:
 Message 9 by Genomicus, posted 05-27-2013 3:02 PM bluegenes has replied

  
bluegenes
Member (Idle past 2501 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 7 of 20 (699467)
05-20-2013 11:35 AM
Reply to: Message 1 by Genomicus
05-17-2013 10:08 PM


To explain further.
I.D. hypothesis (A): Intelligent designers design and construct the core flagellum all at the same time more than 1 billion years ago.
I.D. hypothesis (B): Intelligent designers design and construct the core flagellum in a number of stages involving a number of visits to the planet over a very long period of time, with long time gaps between visits.
Evolutionary hypothesis (C): The core flagellum evolves in stages during less than 1 million years more than 1 billion years ago.
Evolutionary hypothesis (D): The core flagellum evolves in stages over a very long period of time, with long time gaps between stages.
With regards to molecular clock related predictions, A and C make the same ones, as do B and D. Research could support one pair of hypotheses over the other, but couldn't distinguish within the pairs AC and BD.

This message is a reply to:
 Message 1 by Genomicus, posted 05-17-2013 10:08 PM Genomicus has not replied

  
bluegenes
Member (Idle past 2501 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 10 of 20 (699900)
05-28-2013 5:33 AM
Reply to: Message 9 by Genomicus
05-27-2013 3:02 PM


Genomicus writes:
Right, but that scenario would still lead to a different set of predictions. The evolutionary scenario you outlined would result in the prediction that the core flagellar proteins all diverged from their non-flagellar homologs at approximately the same time. This is not what the molecular design model I described predicts.
Yes, it does. It predicts the same actual time, but not the same "molecular clock" time because, as you say here:
Genomicus writes:
Instead, the molecular design model predicts different divergence times for different proteins, depending on two factors: their substitution rates and the amount of modification that would be required to change a non-flagellar component into a flagellar component.
And these variants also apply to my specific evolutionary hypothesis. The amount of modification would vary whether achieved by mutation and selection or by design, and substitution rates would vary.
The two hypotheses make the same predictions, and I agree that it's possible that they could be falsified by the application of relaxed molecular clocks if the core flagellum did actually develop over long periods of time with significant gaps in the times of divergence.
Genomicus writes:
Also, while the scenario you postulate is possible under a Darwinian framework, it is not predicted by it. This is a crucial point. While Darwinian evolution might be able to explain any observations that match the predictions of the molecular design hypothesis, it does not predict it.
Neither general evolutionary theory nor a general intelligent design hypothesis make the predictions that your specific I.D. hypothesis and my specific evolutionary hypothesis make.
I gave an example of an I.D. hypothesis that would match the slow, long term evolution of the flagellum (the designers revisiting the planet many times and making adjustments). Another would be more down your street. That is, the front loading of non-flagellar bacteria with functional proteins that could later evolve by duplication and mutation into flagellar proteins.
This is where I think you're going wrong. Every time you make a specific I.D. hypothesis, I can match it with a specific non-telic evolutionary hypothesis. It's no good pointing out that the general theory of evolution does not make the predictions of your specific hypothesis, because neither does the general proposition that life was designed.
But you can make specific I.D. hypotheses that are incompatible with all evolutionary hypotheses. The standard young earth creationist model is an example of this. We cannot make evolutionary hypotheses to fit the prediction that all life should appear suddenly ~6,500 years ago.
So, as you seem to understand that the general proposition of I.D. doesn't make predictions (no biosphere would be incompatible with it), can you "old earth common descent" I.D. advocates make specific I.D. hypotheses that make predictions that cannot also be the predictions of specific evolutionary hypotheses, as the "young earthers" do?

This message is a reply to:
 Message 9 by Genomicus, posted 05-27-2013 3:02 PM Genomicus has replied

Replies to this message:
 Message 12 by Genomicus, posted 06-03-2013 4:30 PM bluegenes has replied

  
bluegenes
Member (Idle past 2501 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 15 of 20 (700707)
06-06-2013 5:16 AM
Reply to: Message 12 by Genomicus
06-03-2013 4:30 PM


Genomicus writes:
However, for your hypothesis to work, you would have to explain why every single component of the system fits with your scenario. For example, if machine X has 24 core components (like the bacterial flagellum does), your hypothesis needs to explain why every single one of them (specifically, the ones that have homologous counterparts, or are fusion proteins) underwent the same pattern of violating the molecular clock in the precise way of undergoing a rapid substitution rate so that they would fit nicely with the rest of the machine parts. Your model needs to explain this, preferably in a non-ad hoc fashion, since we know that protein sequences are perfectly capable of fitting a nearly-constant molecular clock (I don’t think I need to bring up the many examples of protein sequences that conform to a nearly-constant molecular clock).
These proteins have been co-opted into new functions. So, positive selection would explain an initial rapid substitution rate after duplication or fusion.
The hypothesis you're referring to was that the machine parts are 99.9% the same age. That means that we will not be able to tell their order of arrival by molecular clocks, because molecular clocks are not 99.9% accurate. It means that any molecular clock related predictions would be the same as those for an instantly designed "machine", so far as synonymous mutations are concerned.
In your O.P., you point out that the amount of modification required can distort molecular clocks. This applies whether the modification is done by mutation and selection or by engineering.
Geno in the O.P. writes:
this means that we cannot logically predict — from a design perspective — that molecular clocks will demonstrate that all machine components originated at about the same time. This is because if some proteins are modified more substantially than others, it would confuse the molecular clock.
Protein components that have undergone more drastic modifications will have the appearance of being more ancient (using a molecular clock), while proteins that are only slightly changed will appear to have originated more recently. In particular, the design hypothesis predicts that molecular clocks will show that proteins with rapid substitution rates will have a later origin, while proteins with slow substitution rates will have an early origin. We can summarize this prediction in this manner: in general, the slower the substitution rate, the more ancient the protein will appear to be. If a protein has a slow substitution rate, then any modifications to the sequence of that protein will give the appearance of a large amount of time passing by. In contrast, even fairly extensive modifications to a protein with a rapid substitution rate will not significantly affect the molecular clock. To further refine this prediction, we can take into account the amount of modification that would be needed for a given protein.
Indeed, a high neutral substitution rate on both diverging proteins would diminish the effects of adaptation to a new function on one of them. What you're really describing are effects that could easily arise from established evolutionary processes, and would apply under my hypothesis that the core flagellum evolved relatively rapidly. I say "relatively", because one million years does equal 2 billion generations, and I see no reason why it would take anywhere near that many to evolve a flagellum under selection pressure for motility.
Still, you're making by far the best effort to make I.D. hypotheses that make predictions that I've seen on this site, so keep it up. But I think what you may be doing, perhaps unconsciously, is using your knowledge of evolution to identify quite likely evolutionary scenarios, and then deciding that your designers have designed in a way that would fit them.
Once again, why didn't the designers front load the proteins for the core flagellum? Wouldn't it be technically much easier to do this than to front load with metazoa in mind?

This message is a reply to:
 Message 12 by Genomicus, posted 06-03-2013 4:30 PM Genomicus has replied

Replies to this message:
 Message 17 by Genomicus, posted 06-16-2013 3:28 PM bluegenes has replied

  
bluegenes
Member (Idle past 2501 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 18 of 20 (701487)
06-20-2013 6:24 AM
Reply to: Message 17 by Genomicus
06-16-2013 3:28 PM


Genomicus writes:
The problem is that there is the real possibility — even if the bacterial flagellum evolved in a time span of 1 million years — that some of the components evolved in accordance with a nearly-constant molecular clock. It is well known that protein sequences can often evolve at a nearly constant molecular clock. The suggestion that adaptive evolution would accelerate the substitution rate in the initial stages of evolution does not refute this argument because duplicated genes often undergo mostly neutral evolution until they acquire a novel function as a result of that neutral evolution.
Think again. After duplication, the copy that gains a novel function doing so by neutral steps does not mean its rate of change isn't higher than the copy that retains the original function, because the original is constrained by selection, while the wandering copy isn't.
Simply put, an accelerated rate of substitution is not any more likely than a constant substitution rate,...
It is. The fact of gaining a new function makes the acceleration much more likely even if some of the steps are neutral.
.....as evidenced by the many known examples of protein sequences that have evolved according to a molecular clock (it largely depends on context — e.g., the degree of selection pressure for a given function, and even this is contingent on the external environment).
Are you sure you aren't thinking of the examples that relate to orthologs rather than paralogs and/or clocks based exclusively on synonymous mutations?
Geno writes:
And this is where the problem with your hypothesis comes in. Your hypothesis would be able to explain isolated examples of protein components in molecular systems whose relative ages (as determined by molecular clock analyses) match with function, rather than with the time of origin under an evolutionary pathway. But if this pattern is seen in many components in many systems, your hypothesis starts to break down IMHO, because it does not explain why none of these components have originated at a constant (or nearly) constant molecular clock, even though this is a perfectly realistic scenario.
I think you've missed the point that both my scenario and yours mean that the actual times of divergence of are effectively the same. Both would actually be compatible with some proteins in the core flagellum appearing to have about the same age, especially when relatively little modification was required for the new function.
Genomicus writes:
I’m simply trying to identify the necessary consequences of the hypothesis that molecular systems in the first organisms were engineered in a manner similar to the methods used to design our own biotechnology.
Why would advanced designers who have already created organisms and functional proteins from scratch do that?
Geno writes:
Yes, it would be easier to front-load the proteins for the core flagellum than it would be to front-load Metazoa, but what kind of designer would select a limited goal like that? If the human race wished to carry out front-loading on another planet, I don’t think we’d just focus on front-loading a motility device. Instead, we’d probably want to front-load advanced life forms (possibly intelligent life forms).
As I've suggested before, including eukaryotic cells in the original mix would seem to be the best bet for that.
Geno writes:
Finally, there is one prediction here that simply cannot be made under a non-teleological framework. If early prokaryotic molecular systems fit the predictions of the molecular design model, whereas eukaryotic and later-originating prokaryotic systems do not, then this would significantly strengthen the front-loading model (wherein the first cells are engineered, and later life forms are the product of evolution). The molecular design model would offer the necessary insight to check if this pattern is indeed seen in the biological world.
It's always worth remembering how many generations early cellular systems have had to refine themselves.

This message is a reply to:
 Message 17 by Genomicus, posted 06-16-2013 3:28 PM Genomicus has replied

Replies to this message:
 Message 19 by Genomicus, posted 07-21-2013 12:22 PM bluegenes has replied

  
bluegenes
Member (Idle past 2501 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 20 of 20 (705301)
08-26-2013 1:50 AM
Reply to: Message 19 by Genomicus
07-21-2013 12:22 PM


genomicus writes:
First off, my sincerest apologies for the very belated response. I’ve been busy with stuff unrelated to EvC, but now I expect I’ll be able to respond more frequently.
The same to you! I missed this last month.
Geno writes:
Yea, but that’s not my argument. I’m saying that firstly, it is known that protein sequences can evolve at a nearly-constant molecular clock. Secondly, as a consequence, it is possible that, for example, when FliG diverged from MgtE, FliG diverged at a nearly-constant molecular clock. Similarly, it is also possible that when MotA diverged from ExbB, it too diverged at a nearly-constant molecular clock. Moreover, it is perfectly possible for MgtE and ExbB to evolve at a nearly-constant molecular clock (albeit at different rates than FliG and MotA). The result would be that if the flagellum evolved in a million-year timespan, the divergence times of these two sets of proteins should cluster close together.
If the core flagellum had evolved (or was designed) inside a million-year timespan fairly recently, you might well get that effect from a clock using synonymous mutations. But that's no use for deep time.
Geno writes:
Not really, since that’s contingent on selective pressure. Who’s to say that there would be strong selective pressure for this function to evolve?
That's not necessary. When two paralogs diverge and there's neofunctionalization, the initial divergence is usually rapid and asymmetrical because one copy is highly conserved. It performs the original function.
Geno writes:
Suppose MotA and ExbB split off from a common ancestor. MotA is incorporated into a complex motility system, while ExbB is integrated into a simpler transport system. Thus, it’s likely that ExbB would be under less functional constraint in its sequence evolution than MotA. This does not mean that these two proteins cannot evolve in a manner consistent with molecular clocks. It only means that their rate of substitution will differ. For example, ExbB might evolve faster, while still ticking at a constant rate. The same holds for MotA.
Surely "evolving faster" is ticking at a different rate? Tell me, how accurate do you think molecular clocks are over very long periods of time?
Geno writes:
I’m not seeing the dilemma here?
I was wondering why designers who are not our species and are more advanced than us would design in ways similar to us at the moment, rather than, for example, ways more similar to the way we might do our biotechnology in 200 years time, or 500 years time, or in the year 3,800, or ways not similar to anything we would ever do?
Geno writes:
Not necessarily. Eukaryotes, on the whole, aren’t as survivable as prokaryotic organisms. Not only are these cells landing on the hostile environment of the early Earth, but they must also travel through the expanse of space — which is also a hostile environment.
I thought they might design resilient and flexible eukaryotes.
Geno writes:
I’m afraid I’m not seeing how the number of generations of early cellular systems has to do with the above prediction. Could you elaborate? Thanks!
I can't remember what I meant. It's too long ago. As for the prediction, I've just looked back at your O.P., and I still say what I said in my second post:
I.D. hypothesis (A): Intelligent designers design and construct the core flagellum all at the same time more than 1 billion years ago.
I.D. hypothesis (B): Intelligent designers design and construct the core flagellum in a number of stages involving a number of visits to the planet over a very long period of time, with long time gaps between visits.
Evolutionary hypothesis (C): The core flagellum evolves in stages during less than 1 million years more than 1 billion years ago.
Evolutionary hypothesis (D): The core flagellum evolves in stages over a very long period of time, with long time gaps between stages.
With regards to molecular clock related predictions, A and C make the same ones, as do B and D. Research could support one pair of hypotheses over the other, but couldn't distinguish within the pairs AC and BD.

This message is a reply to:
 Message 19 by Genomicus, posted 07-21-2013 12:22 PM Genomicus has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024