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Author Topic:   Design Framework for Evolution
AZPaul3
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Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 26 of 81 (698927)
05-10-2013 4:56 PM


Scattered Thoughts
Albert,
I appreciate the time and effort you put into your web site. It certainly was a learning experience for you in gathering all that information, learning the different processes, then putting the results into writing. The writing part, getting everything in order within your head, is where the real learning occurs in my opinion/experience.
I have a number of issues to bring up.
First, I'm not seeing where you are bringing anything new to the table. The processes you describe in general rather than in the detail we already know exist. The design attributes you describe and the reverse engineering of the processes within the cell has been going on, though in somewhat different form, for the last century. The hierarchies and modular design has already been determined and is to be expected given that evolution can only alter what is already there and cannot backtrack to re-design from scratch. If you're looking to find some design efficiencies within evolution there are none. Since evolution can only take advantage of the processes already developed any new processes must be layered upon the old. The result is some of the most god awful complexity in existence. The Krebs Cycle and the blood clot cascade being two glaring examples. What new concept, new insights, do you bring to us in this exercise?
Second, your semantics are a bit off. You are using your own definitions for micro-, macro- evolution when these have already been set by the discipline. If you were talking to your mirror this would be fine but you are talking with us and the expectation is that you will converse within the accepted semantics. Micro-evolution is the small genotype/phenotype variations that develop in a population and extends to cover the closely related daughter species like wolf-to-dog. Macro-evolution takes the longer view of these populations over many thousands of generations where the genotype/phenotype differences become quite pronounced and identifiable like Hemicyonidae into both Ursidae (bear) and Canidae (wolf). Macro- is lots of micro- accumulated over generations.
And, yes, evolution is the result of both.
Third, lose the neo-darwinism. If you are talking about the history of the theory of evolution then the term is appropriate for that period in the early 20th century when darwinism was melded with mendelian genetics. At this point there is the theory of evolution which entails mutation/selection/drift. There are no other theories of evolution within the discipline. Darwinism and neo-darwinism are older incomplete versions of today's theory.
Fourth, evolution says nothing about the origin of life. It was never designed to address that question. Evolution is the theory of how the vast diversity of life came to be once life had developed and was underway, not before.
the terms random mutation and natural selection are irrelevant for macroevolution because they do not explain the origin of Life, the origin of the cell, the origin of multicellular organisms etc. They also have no mechanistic basis and are non-predictive.
This is not good. If you do not understand the mechanics behind mutation/selection/drift then you need to find out. Also see the second point above. These mechanisms are indeed the most basic elements behind evolution whether micro or macro and, yes, they do explain quite well diversity of cells, multicellularity, sex, insect metamorphosis, and every other biological attribute and biological system on this planet. Also, nothing in evolution has any predictive value except for change and, over extended time, diversity.
Finally, the explosion of diversity we see in the Cambrian relates to body plan, not gene family, whatever that is. In my view the various suites of genomes are evidenced by the class, order, family, genus, species of today's biosystems the vast majority of which evolved since the Cambrian. From where did you get the view that gene families were all developed pre-Cambrian?
All in all you have a good start on learning the mechanisms of the theory of evolution, but you need to standardize your semantics, fill in the holes in your knowledge of evolutionary mechanisms and stop trying to re-invent what has already been done for you.
Edited by AZPaul3, : Oh, let's see. Spelin, syntax, semantics, god just a whole host of stuff.

Replies to this message:
 Message 27 by Albert de Roos, posted 05-10-2013 5:45 PM AZPaul3 has replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 29 of 81 (698934)
05-10-2013 8:56 PM
Reply to: Message 27 by Albert de Roos
05-10-2013 5:45 PM


Re: Scattered Thoughts
Thank you for your (albeit rather condescending ) post.
I did not intend to be condescending, just constructively critical.
Did I read your web site?
Of course I read your web site. Each section in its entirety. I do not go into these things without all the information I can get. I am not unarmed.
On your claim that you are the first to "deduce" the nucleus as the first cellular entity. Sidney Fox and Aleksandr Oparin would disagree with you. Spontaneous generation of limpid membranes has been known for quite some time, and such membranes are speculated to be the first enclosures for the small simple self-replicating molecules of the earliest cells. And these hypotheses are not only decades earlier but much more detailed then you have provided, so , no, your deduction is not very new.
Of course I use different terms that do not coincide with the current definitions. It is a different framework that I use.
I do not mean to sound condescending or harsh but there is no other way to say this, Albert. You do not have the standing or the influence in this discipline to take concepts like micro and macro-evolution and redefine them for your own purposes. These words are taken, have detailed specific meanings and are used in detailed and specific ways. If you want to speak within the discipline you will use the semantics as settled or you will be ignored. If you need to define an new concept then find a new word. You cannot have micro- and macro-evolution. They are taken. There is no flexibility here. You will standardize or be sidelined. These are your options. And do not mistake this as me personally trying to putting up some barrier. I haven't the standing or influence any more than you. This is a reality of scientific discourse.
I do not see a coherent theory, no mechanistic scenario. To me it looks more like a religion than anything else.
Then you have not completed your studies. The mechanisms of evolution (genetic mutation, natural selection, genetic drift, evo-devo, punctuated equilibrium, genetic stasis, Hox genes, etc.) are all there in exceptional detail for you to digest. In doing so you will see how these mechanisms drive the whole of evolution in one of our most detailed, comprehensive and coherent scientific theories.
As if the origin of Life is separated from its evolution. It sounds rather creationist to me. Anyway, genetic drift, neutral evolution, hopeless monsters, Margulis' fairy tales, thet all make no sense to me because they are non-mechanistic.
Now I will be harsh. Your incredulity and ignorance do not change the reality of The Theory of Evolution one bit. Evolution is confined to explaining diversity not origins. You cannot change that no matter how uppity you get. The mechanisms, in detail, are there for you to learn. Do so.
You say that nothing in evolution has any predictive value. It makes your entire framework non-predictive and therefore non-scientific and trivial.
I took your predictive value statement the way we see a lot of our less studied posters use that term, predicting what outcome evolution will produce as in what some population will evolve into next. In this context Evolution cannot be used in any way to predict any specific outcome for some future species.
The theory's predictive value and falsifiablity as used in the formal scientific sense is well known by those who study and understand the discipline. You, obviously, are not there, yet.

This message is a reply to:
 Message 27 by Albert de Roos, posted 05-10-2013 5:45 PM Albert de Roos has replied

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 Message 30 by Albert de Roos, posted 05-11-2013 8:37 AM AZPaul3 has seen this message but not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


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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 Message 39 by Genomicus, posted 05-13-2013 3:17 PM Genomicus has replied

Replies to this message:
 Message 43 by Genomicus, posted 05-14-2013 12:52 AM AZPaul3 has replied
 Message 49 by Albert de Roos, posted 05-14-2013 4:36 AM AZPaul3 has replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


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

This message is a reply to:
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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 50 of 81 (699074)
05-14-2013 7:53 AM
Reply to: Message 49 by Albert de Roos
05-14-2013 4:36 AM


Evolution is not freeform and functionality was put on layer-by-layer.
That is what I said in my post. You forgot to read the sentence just upstream from what you quoted.
The point being that evolution works with what it has, layers new functionality onto the old and after several such events the result can be seen as overly complex, energy inefficient and wasteful ... but it works and that is the only reason such messes remain in the system.
No one said anything about any conscious designer. Where you got that in the post is a bit bewildering.

This message is a reply to:
 Message 49 by Albert de Roos, posted 05-14-2013 4:36 AM Albert de Roos has replied

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 Message 54 by Albert de Roos, posted 05-14-2013 1:11 PM AZPaul3 has seen this message but not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(2)
Message 70 of 81 (699238)
05-16-2013 8:13 AM
Reply to: Message 69 by Panda
05-16-2013 5:34 AM


Panda:
I think they perhaps would have been better writing "could not have found a better design using the material available."
Genomicus:
We may discuss the arguments from homology, etc., but at present the issue is whether the Krebs Cycle is the molecular equivalent of the recurrent laryngeal nerve.
Actually, I think you're both right.
The present Krebs cycle may be as efficient as it can be considering its evolution but not as efficient as a deliberate re-design might achieve.
But thinking on what Genomicus was asking for I now am reticent to put Krebs forward as such an example.
You both win.
And some say these discussions never achieve anything.

This message is a reply to:
 Message 69 by Panda, posted 05-16-2013 5:34 AM Panda has seen this message but not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 77 of 81 (699394)
05-18-2013 1:35 PM
Reply to: Message 76 by Panda
05-18-2013 9:11 AM


I cannot answer than question - my biological knowledge drops me off several streets before that destination.
AZPaul3...it's your turn.
You were not alone on that bus ... nor were you alone when you got off.

This message is a reply to:
 Message 76 by Panda, posted 05-18-2013 9:11 AM Panda has seen this message but not replied

  
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