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Author Topic:   Towards a Hypothesis of Molecular Design
Genomicus
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Posts: 813
Joined: 02-15-2012
Member Rating: 3.5


Message 16 of 20 (701303)
06-16-2013 3:26 PM
Reply to: Message 14 by Taq
06-03-2013 4:39 PM


Your design hypothesis is entirely arbitrary. There is no reason to expect one outcome over another. That is the problem.

Other than the fact that some of the alternatives wouldn’t be terribly rational from the perspective of human intelligence (and remember, any design hypothesis must presume an intelligence analogous to our own, since we would have but little hope of detecting the design of an intelligence radically different than our own), arbitrary hypotheses aren’t exactly foreign to science. Some examples:

(1) The Kaluza-Klein theory of the early 20th century which added extra dimensions to general relativity was an attempt to unify gravity and electromagnetism. How was this not an arbitrary model, since this was not the only way to unify gravity and electromagnetism (see, e.g., Hermann Weyl’s gauge theory)?

(2) How are the inflationary and varying speed of light models in cosmology (to explain the horizon problem) not arbitrary?

Hypotheses are models that help with guiding research. By eliminating different hypotheses, it is possible to finally arrive at a hypothesis that is the best explanation for the phenomenon under consideration. So I see no real problem in outlining different hypotheses for the origin of biological cells, provided that those models are testable.


This message is a reply to:
 Message 14 by Taq, posted 06-03-2013 4:39 PM Taq has not yet responded

  
Genomicus
Member
Posts: 813
Joined: 02-15-2012
Member Rating: 3.5


Message 17 of 20 (701304)
06-16-2013 3:28 PM
Reply to: Message 15 by bluegenes
06-06-2013 5:16 AM


Hi bluegenes,
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.

Positive selection would explain an initial rapid substitution rate in a local sense, but it does not address my central argument here, which is that there is no reason why this specific pattern (of positive selection accelerating the substitution rate after duplication) should occur for all components of a system. The problem is compounded significantly the more molecular systems we can take into consideration. Let me reiterate my argument to further clarify this:

In other words, your hypothesis will be hard-pressed to explain why none of the protein components evolved at a nearly-constant molecular clock, when this is not only biologically possible but also seen in a variety of protein sequences. And if some protein parts did evolve and originate at a nearly-constant molecular clock, then this would result in a prediction different from the molecular design hypothesis. We would expect the divergence times of some of the proteins (the ones that originated at a nearly-constant clock) to cluster closely together, and not necessarily in the pattern expected from molecular design…

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. Simply put, an accelerated rate of substitution is not any more likely than a constant substitution rate, 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). 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.

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.

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. To be sure, the use of molecular clocks is probably not the only way to test such a hypothesis (or even the best), and more novel methods should be explored. But that might take just a bit of time to work out.

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?

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).

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.


This message is a reply to:
 Message 15 by bluegenes, posted 06-06-2013 5:16 AM bluegenes has responded

Replies to this message:
 Message 18 by bluegenes, posted 06-20-2013 6:24 AM Genomicus has responded

  
bluegenes
Member
Posts: 2988
From: U.K.
Joined: 01-24-2007
Member Rating: 2.0


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 responded

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

  
Genomicus
Member
Posts: 813
Joined: 02-15-2012
Member Rating: 3.5


Message 19 of 20 (703432)
07-21-2013 12:22 PM
Reply to: Message 18 by bluegenes
06-20-2013 6:24 AM


Hi bluegenes,

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.


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.

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.

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.

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?

.....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?

No, I’m not. The issue here isn’t about paralogs or orthologs. That proteins (such as paralogs) evolve at a different rate does not mean that those paralogs cannot evolve at a constant rate. Again, to make this clear, it’s probably best to use examples.

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.

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.

Both would not be compatible with some proteins in the core flagellum appearing to have about the same age, unless relatively little modification would be required for the new function. This qualifier is necessary and important.

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?

I’m not seeing the dilemma here?

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.

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.

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.

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!

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 18 by bluegenes, posted 06-20-2013 6:24 AM bluegenes has responded

Replies to this message:
 Message 20 by bluegenes, posted 08-26-2013 1:50 AM Genomicus has not yet responded

  
bluegenes
Member
Posts: 2988
From: U.K.
Joined: 01-24-2007
Member Rating: 2.0


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 yet responded

  
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