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Author Topic:   Design Framework for Evolution
Albert de Roos
Junior Member (Idle past 1945 days)
Posts: 25
Joined: 05-02-2013


Message 31 of 81 (698955)
05-11-2013 8:48 AM
Reply to: Message 25 by Genomicus
05-10-2013 1:25 PM


genomicus: "But what about the origin of molecular machines, like, say, the bacterial flagellum?

I think that the way they are assembled in development could be exactly the way it was assembled in evolution. So basically, you start with either the stator or the rotor and keep adding extra modules to it. I am not sure, I haven't looked into it for a long time. What is important is that the previous stages in evolution should all be functional and preferably with the same functions as the end product. So, if that is movement, you would expect an early truncated flagellum or even the rotor/stator combination to already create movement.

"This brings me to a second question. Your scenario for the origin of the eukaryotic cell seems mechanistically plausible, but what kind of experiments could be done to test your hypothesis? "

Experiments are difficult, but we should further analyze the components of the nucleus and eukaryotic cell and see if they fit. For instance if it was proven that essential nucleolar proteins originated after the nuclear lamina was formed.


This message is a reply to:
 Message 25 by Genomicus, posted 05-10-2013 1:25 PM Genomicus has not yet responded

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 Message 32 by NoNukes, posted 05-11-2013 11:17 PM Albert de Roos has responded

    
NoNukes
Inactive Member


Message 32 of 81 (698976)
05-11-2013 11:17 PM
Reply to: Message 31 by Albert de Roos
05-11-2013 8:48 AM


So basically, you start with either the stator or the rotor and keep adding extra modules to it.

Why would I do such a thing? When would I be finished designing? Who am I?


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
 Message 31 by Albert de Roos, posted 05-11-2013 8:48 AM Albert de Roos has responded

Replies to this message:
 Message 33 by Albert de Roos, posted 05-12-2013 8:00 AM NoNukes has responded

  
Albert de Roos
Junior Member (Idle past 1945 days)
Posts: 25
Joined: 05-02-2013


Message 33 of 81 (698980)
05-12-2013 8:00 AM
Reply to: Message 32 by NoNukes
05-11-2013 11:17 PM


NoNukes: "Why would I do such a thing? When would I be finished designing? Who am I?"

What I am trying to do is reverse engineer the steps in evolution. The flagellum was assembled during evolution and there is a logical way of assembling it, giving the constraints of evolution.

I consider Life an evolving molecular machine and metaphorically I speak from the point of view of an engineer. Seeing the flagellum/nucleus/cell as it is now, what would be the logical way to assemble it. How would you assemble it if you were an engineer, basically.

The questions you ask are valid and represent the driving forces and goal-orientation of Evolution. I don't think that there was a conscious design or an active designer at work. For me, the driving forces are in the life cycle itself and an intrinsic active evolvability built into the genome.

But once you have reversed engineer the steps in evolution (all the way thinking in terms of system designs and design patterns), we can deduce what actually happened and start thinking about the driving forces.

The steps towards the eukaryotic cell that I propose, adding layer on top of layer of extra functionality are a lot easier current evolutionary theories. If you think that a eukaryotic cell with a plasma membrane can generate a nucleus, you will encounter tremendous physical problems. For instance, how would you evolve the essential nuclear pores when there was no nuclear membrane in the first place. This is what you call irreducibly complex. My solution is not reducibly complex.

Imagine a baseball. It consists of several layers. It would be pretty difficult to start with the outside leather and stitching and to try to put in the cork ball in the end. The logical sequence would be from the inside to the outside. I can deduce that without knowing what the purpose of the baseball was, who assembled it or where the subparts came from.

baseball


This message is a reply to:
 Message 32 by NoNukes, posted 05-11-2013 11:17 PM NoNukes has responded

Replies to this message:
 Message 34 by NoNukes, posted 05-12-2013 9:10 AM Albert de Roos has responded
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NoNukes
Inactive Member


Message 34 of 81 (698982)
05-12-2013 9:10 AM
Reply to: Message 33 by Albert de Roos
05-12-2013 8:00 AM


I don't think that there was a conscious design or an active designer at work. For me, the driving forces are in the life cycle itself and an intrinsic active evolvability built into the genome.

I want to pursue the 'driving forces' beyond mere hand waving because these are the forces that substitute for random variation and natural selection that predominate in natural evolution.

Yes, if some force was going to add wings to a wingless creature, perhaps it would do so in a way your model would accept, but in order to see if this force makes more sense than does current theory, does it make sense to explore whether we can find evidence for the forces?


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
 Message 33 by Albert de Roos, posted 05-12-2013 8:00 AM Albert de Roos has responded

Replies to this message:
 Message 35 by Albert de Roos, posted 05-13-2013 12:50 PM NoNukes has responded

  
Albert de Roos
Junior Member (Idle past 1945 days)
Posts: 25
Joined: 05-02-2013


Message 35 of 81 (699027)
05-13-2013 12:50 PM
Reply to: Message 34 by NoNukes
05-12-2013 9:10 AM


NoNukes: "I want to pursue the 'driving forces' beyond mere hand waving because these are the forces that substitute for random variation and natural selection that predominate in natural evolution."

See it as a software program that will create its own extra code with each software development cycle. You start it up, the program adds some extra code in the source code and compiles and sees whether it still works, i.e. whether the extended program can still add code and be complied into a working program that can add automatically to the source code and then compiles, etc.

And testable, I guess. My next project maybe, although my Java skills are a bit rusty.


This message is a reply to:
 Message 34 by NoNukes, posted 05-12-2013 9:10 AM NoNukes has responded

Replies to this message:
 Message 36 by NoNukes, posted 05-13-2013 1:04 PM Albert de Roos has responded
 Message 60 by Taq, posted 05-14-2013 5:30 PM Albert de Roos has responded

    
NoNukes
Inactive Member


Message 36 of 81 (699028)
05-13-2013 1:04 PM
Reply to: Message 35 by Albert de Roos
05-13-2013 12:50 PM


Whose proposal is it anyway...
See it as a software program that will create its own extra code with each software development cycle.

I don't want an analogy with programming. I want to know what in the real world corresponds to your "driving forces" such that no random addition processes are involved and such that natural selection is not a meaningful effect.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
 Message 35 by Albert de Roos, posted 05-13-2013 12:50 PM Albert de Roos has responded

Replies to this message:
 Message 45 by Albert de Roos, posted 05-14-2013 4:05 AM NoNukes has responded

  
New Cat's Eye
Inactive Member


Message 37 of 81 (699034)
05-13-2013 2:13 PM
Reply to: Message 30 by Albert de Roos
05-11-2013 8:37 AM


Re: Scattered Thoughts
-Evolution: The stepwise additions of new functional modules over time (i.e. an increase in complexity)

-Adaptation: The differential use of existing functionality to adapt to changes in the environment (i.e. no or minor change in complexity)

What about when species evolve towards less complexity? Like those cave fish that lost their eyeballs, or birds that have vestigial wings?


This message is a reply to:
 Message 30 by Albert de Roos, posted 05-11-2013 8:37 AM Albert de Roos has responded

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New Cat's Eye
Inactive Member


Message 38 of 81 (699035)
05-13-2013 2:23 PM
Reply to: Message 33 by Albert de Roos
05-12-2013 8:00 AM


I consider Life an evolving molecular machine and metaphorically I speak from the point of view of an engineer.

No offense, but I'd expect an engineer to make a lousy biologist. Life is not a machine nor does it behave like one... it gets messy and illogical.

Seeing the flagellum/nucleus/cell as it is now, what would be the logical way to assemble it. How would you assemble it if you were an engineer, basically.

There is no logic when it comes to assembling parts of life. Basically, whatever is just good enough to make it so the animal doesn't die before it reproduces is what is going to get included in the selection process. That allows for all kinds of ridiculous bullshit. For example, check out the recurrent laryngeal nerve in a giraffe (its the black line on the left that loops all the way under the red line at the bottom only to connect all the way back at the top:

There's nothing logical about it. Its totally wasteful and unecessary. Taking the approach of "how would you assemble it if you were an engineer", is either going to lead you in the wrong direction, or make the engineer out to be a total buffoon.

Imagine a baseball. It consists of several layers. It would be pretty difficult to start with the outside leather and stitching and to try to put in the cork ball in the end.

But with cells, stuff can easily pass through the membrane both inside and out.


This message is a reply to:
 Message 33 by Albert de Roos, posted 05-12-2013 8:00 AM Albert de Roos has responded

Replies to this message:
 Message 39 by Genomicus, posted 05-13-2013 3:17 PM New Cat's Eye has responded
 Message 47 by Albert de Roos, posted 05-14-2013 4:16 AM New Cat's Eye has responded

  
Genomicus
Member
Posts: 852
Joined: 02-15-2012


Message 39 of 81 (699037)
05-13-2013 3:17 PM
Reply to: Message 38 by New Cat's Eye
05-13-2013 2:23 PM


No offense, but I'd expect an engineer to make a lousy biologist. Life is not a machine nor does it behave like one...

That really depends on what part of life, though. The machine analogy works very nicely at the molecular level (e.g., molecular machines actually are machines), and the machine analogy extends into the domain of multicellular life. Does life get "messy and illogical"? I suppose so, but this is the result of billions of years of evolutionary tinkering. At its core, however, life is not illogical from an engineering standpoint.

There is no logic when it comes to assembling parts of life.

That is entirely contingent on what part of life is under consideration. How is the structure of the bacterial flagellum or the F-ATPase illogical?

Basically, whatever is just good enough to make it so the animal doesn't die before it reproduces is what is going to get included in the selection process.

Yet one would be hard-pressed to find the molecular equivalent of the recurrent laryngeal nerve among the core machinery of life. Why is that? Some parts of life do not make much sense from an engineering standpoint; others do.

Imagine a baseball. It consists of several layers. It would be pretty difficult to start with the outside leather and stitching and to try to put in the cork ball in the end.

But with cells, stuff can easily pass through the membrane both inside and out.

I'm pretty sure Albert de Roos was using the baseball as an example of the methodology of the design-by-contract approach; he was not using the baseball as an analogy of how cells work.


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 Message 38 by New Cat's Eye, posted 05-13-2013 2:23 PM New Cat's Eye has responded

Replies to this message:
 Message 40 by New Cat's Eye, posted 05-13-2013 3:50 PM Genomicus has responded
 Message 41 by AZPaul3, posted 05-13-2013 5:11 PM Genomicus has responded

  
New Cat's Eye
Inactive Member


Message 40 of 81 (699039)
05-13-2013 3:50 PM
Reply to: Message 39 by Genomicus
05-13-2013 3:17 PM


That really depends on what part of life, though. The machine analogy works very nicely at the molecular level (e.g., molecular machines actually are machines), and the machine analogy extends into the domain of multicellular life. Does life get "messy and illogical"? I suppose so, but this is the result of billions of years of evolutionary tinkering. At its core, however, life is not illogical from an engineering standpoint.

At its core, life is just chemistry. I wouldn't call spontaneous chemical reactions "machines", but I don't really care to argue the semantics.

That is entirely contingent on what part of life is under consideration. How is the structure of the bacterial flagellum or the F-ATPase illogical?

I'm not sure I understand how to apply logic to a structure. I don't think "logical" is a word we need in evolutionary biology. I only used it because he did.

Yet one would be hard-pressed to find the molecular equivalent of the recurrent laryngeal nerve among the core machinery of life. Why is that? Some parts of life do not make much sense from an engineering standpoint; others do.

Well, as I said, it depends on what is good enough to make it so the organism doesn't die before it reproduces. A bacterium with a bad flagellum is not good enough. Different parts are going to have different strengths of selective pressure. The high pressure stuff doesn't allow for much variation, but for low pressure stuff its about what's just good enough.

My point was that that allows for all kinds of ridiculous bullshit so there's no need to look at it from a "logical" perspective.

I'm pretty sure Albert de Roos was using the baseball as an example of the methodology of the design-by-contract approach; he was not using the baseball as an analogy of how cells work.

Well I may very well have missed his point. I don't see the design-by-contract approach being applicable to biology. There is no contract. Its whatever works goes, where working is reproducing before you die.


This message is a reply to:
 Message 39 by Genomicus, posted 05-13-2013 3:17 PM Genomicus has responded

Replies to this message:
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AZPaul3
Member
Posts: 3518
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.2


Message 41 of 81 (699041)
05-13-2013 5:11 PM
Reply to: Message 39 by Genomicus
05-13-2013 3:17 PM


Yet one would be hard-pressed to find the molecular equivalent of the recurrent laryngeal nerve among the core machinery of life.

Not so hard pressed. Two right off the top of my head (since I used them before in this thread) are the Krebs cycle and the blood clot cascade. Function layered on function wrapped in function layered on function. A kludge like the laryngeal nerve creating a god-awful design any engineer would run screaming out of the room over.

Have we talked any of the intercellular signaling cascades? Talk about screwed up overly complex energy wasting kludges!

Edited by AZPaul3, : cuz


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Replies to this message:
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Genomicus
Member
Posts: 852
Joined: 02-15-2012


Message 42 of 81 (699065)
05-14-2013 12:45 AM
Reply to: Message 40 by New Cat's Eye
05-13-2013 3:50 PM


At its core, life is just chemistry. I wouldn't call spontaneous chemical reactions "machines", but I don't really care to argue the semantics.

By that argument, then at the heart of all of technologies is simple chemistry. This is indeed true, but it misses the point. From the perspective of the genome - that is, when we consider the core features of the genomes of various taxa - life is not "illogical" from an engineering standpoint.

That is entirely contingent on what part of life is under consideration. How is the structure of the bacterial flagellum or the F-ATPase illogical?

I'm not sure I understand how to apply logic to a structure. I don't think "logical" is a word we need in evolutionary biology. I only used it because he did.

The core structures of the bacterial flagellum and the F-ATPase are perfectly suited to performing their respective functions. That is, there is a logic to the arrangement of the parts of these machines - a logic that is defied in, for example, the backward wiring of the mammalian eye.

A bacterium with a bad flagellum is not good enough.

There are plenty of possible arrangement of protein parts that would produce motility. Yet the vast majority of these arrangements would not produce optimal function - that is, the vast majority of the possible arrangements would result in a system that is the molecular equivalent of the recurrent laryngeal nerve. There are many possible protein arrangements that would produce motility and thereby provide an evolutionary advantage. Only a small fraction of these arrangements would make sense from an engineering perspective.

Consider the bacterial flagellum. It is composed of two rings (the MS-ring and the C-ring); the C-ring houses the export apparatus (the flagellum-specific ATPase). FliC monomers (from which the filament is constructed) are exported by the F-ATPase through the FliF pore; other flagellar parts are also transported in this manner (e.g., the hook and junction proteins). Yet during the evolution of this system (specifically, when the F-ATPase associated with the primitive FliF pore), it would have been easy enough for the F1 component of the ATPase to bind partially to the side of the FliF pore (instead of fitting neatly into the "hole" of the pore, as it does in actual flagella), thereby minimally clogging transport of filament proteins. Perfect binding of the ATPase to the FliF pore would not be expected anyway, since evolution is a tinkerer, not an engineer. If this had occurred, the co-opted ATPase would still provide a selectable advantage to the organism by energizing protein transport, so this configuration would be inherited. Subsequent addition of protein parts to the proto-flagellum would occur; these parts would be integrated around the faulty-but-functional ATPase configuration. Thus, if a mutation occurred to place the ATPase directly in conjunction with the FliF pore, the system could no longer function properly. This is because the arrangement of the other protein parts would be scaffolded on the sub-optimal placement of the ATPase.

This illustrates my point: that one would be hard-pressed to find the molecular equivalent of the recurrent laryngeal nerve among the core machinery of life, despite the fact that it is perfectly acceptable on evolutionary grounds.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


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 Message 40 by New Cat's Eye, posted 05-13-2013 3:50 PM New Cat's Eye has responded

Replies to this message:
 Message 51 by New Cat's Eye, posted 05-14-2013 10:08 AM Genomicus has responded

  
Genomicus
Member
Posts: 852
Joined: 02-15-2012


Message 43 of 81 (699066)
05-14-2013 12:52 AM
Reply to: Message 41 by AZPaul3
05-13-2013 5:11 PM


Not so hard pressed. Two right off the top of my head (since I used them before in this thread) are the Krebs cycle and the blood clot cascade. Function layered on function wrapped in function layered on function.

A similar argument was raised in the past. From:

Behe admits that biological systems can best be described as Rube Goldberg mechanisms [note: Behe states that some biological systems (i.e., biochemical cascades) are best described as Rube Goldberg mechanisms]. When you look at the molecular world you see the equivalent of this toothpaste dispenser...Here are cellular apoptosis pathways...

My response was as follows:

You haven't explained what's wrong with the apoptosis pathway. I'm pretty sure each of those proteins play a very useful role in that pathway. Such pathways benefit from cascades so that any stimulus is amplified to an effective degree.

As Kenneth Miller explains (regarding the blood clotting cascade):

"It sure does look pretty, but why a cascade? Why couldn't we have a simpler pathway, like the lobster, where something like tissue factor activated clotting directly? Well, we could, but a complex pathway, even if it drives biochemistry students to distraction, has advantages of its own. For one thing, the multiple steps of the cascade amplify the signal from that first stimulus. If a single active molecule of Factor XII could activate, say, 20 or 30 molecules of Factor XI, then each level of the cascade would multiply the effects of a starting signal. Put 5 or 6 steps in the cascade, and you've amplified a biochemical signal more than a million times. Clotting with fewer steps would still work, but it would take longer to produce a substantial clot, and would be much less responsive to smaller injuries."

The same holds for other biochemical cascades, such as the apoptosis pathway.

I would be interested on hearing your thoughts on where exactly the Krebs Cycle is the molecular equivalent of the recurrent laryngeal nerve. Which step in the Krebs Cycle should be eliminated? How would you design a system that performed the same function as the Krebs Cycle?

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


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 Message 41 by AZPaul3, posted 05-13-2013 5:11 PM AZPaul3 has responded

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 Message 44 by AZPaul3, posted 05-14-2013 3:39 AM Genomicus has responded

  
AZPaul3
Member
Posts: 3518
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.2


Message 44 of 81 (699067)
05-14-2013 3:39 AM
Reply to: Message 43 by Genomicus
05-14-2013 12:52 AM


I would be interesting on hearing your thoughts on where exactly the Krebs Cycle is the molecular equivalent of the recurrent laryngeal nerve. Which step in the Krebs Cycle should be eliminated? How would you design a system that performed the same function as the Krebs Cycle?

No proof of anything, just conjecture. The only evidence to offer is the Krebs cycle itself.

The Krebs Cycle takes glucose and extracts ATP which is used all throughout the cell to power reactions. For instance, ATP sparks the attachment of the various aminos to their tRNAs and then another to dislodge the amino once in position on the mRNA template and then another, maybe two depending, to attach the amino to the growing protein chain. Lots of other uses including RNA and DNA building.

We see in the present Krebs Cycle, which is an aerobic process, the initial primitive anaerobic processes. Not to difficult to figure why since free oxygen wasn't much available for the first 2 billion years of cell evolution. Going further back we see the malate-fumarate-succinate steps which, the speculation goes, may be holdovers from when glucose wasn't so readily available thus relying on simpler compounds to power metabolism. When the abundance of glucose as the food of choice for cells developed these steps provided some advantage for reoxidizing an NADH molecule that came out of the glucose structure and so were retained. In essence glucose became this food of choice because there were processes already in place from simpler molecules. There is even the thought that since glucose is a plant sugar the photosynthetic processes were "geared" to its manufacture because a mechanism for its use was pretty much already in place. Who knows.

Is this the most efficient and effective way to break glucose into ATPs? With the evolutionary holdovers from pre-glucose and anaerobic processes I wouldn't think so, but then I'm not a biochemist. Maybe someone else can answer that question. We also have to remember that evolution has had about 2 billion years to make the present cycle as efficient as it could be made considering what it started with. It is still a kludge built in identifiable stages over 3 billion+ years but it works well enough to keep around.

To answer your last question, if I were god, I personally would have designed a metabolism based on ... you guessed it ... Haagen Dazs Chocolate ice cream. But I'm not god and god wasn't around so we ended up with vegetables.

Some sources: here, here and this pdf here


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Albert de Roos
Junior Member (Idle past 1945 days)
Posts: 25
Joined: 05-02-2013


Message 45 of 81 (699068)
05-14-2013 4:05 AM
Reply to: Message 36 by NoNukes
05-13-2013 1:04 PM


Re: Whose proposal is it anyway...
NoNukes: I don't want an analogy with programming. I want to know what in the real world corresponds to your "driving forces" such that no random addition processes are involved and such that natural selection is not a meaningful effect.

I never said that no random addition processes are involved or that natural selection is not a meaningful effect. I expect them to be involved, but they do not explain evolution. Like gasoline is necessary to work an engine, but does not say anything about how the engine works.

The driving forces I speak about can be built in into the genome. A random mutation process can be exploited to give direction. Mutation-sensitive parts of the DNA for instance.


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Replies to this message:
 Message 52 by NoNukes, posted 05-14-2013 10:19 AM Albert de Roos has responded

    
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