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Author Topic:   Design Framework for Evolution
Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 46 of 81 (699069)
05-14-2013 4:09 AM
Reply to: Message 37 by New Cat's Eye
05-13-2013 2:13 PM


Re: Scattered Thoughts
Catholic Scientist: What about when species evolve towards less complexity? Like those cave fish that lost their eyeballs, or birds that have vestigial wings?
Interesting examples. I would consider those to be adaptations or maybe streamlining examples.

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Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 47 of 81 (699070)
05-14-2013 4:16 AM
Reply to: Message 38 by New Cat's Eye
05-13-2013 2:23 PM


catholic scientist: 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.""
No offense at all, especially in the light of your comments. Life is a nanomachine and it behaves as one. It is as simple as that. It does nog get messy and illogical, only when you don't understand that it is a machine it gets messy and illogical.
Catholic scientist: 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.""
This is exactly what I dispute (and explain on my website). There is logic in assembling the parts of Life. Of course there is logic, otherwise it would not work. There are only limited possibilities to assemble things in evolution. Many 'scientists'tend to forget the principles of functional continuity in Evolution. A major mistake.

This message is a reply to:
 Message 38 by New Cat's Eye, posted 05-13-2013 2:23 PM New Cat's Eye has replied

Replies to this message:
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Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 48 of 81 (699071)
05-14-2013 4:24 AM
Reply to: Message 40 by New Cat's Eye
05-13-2013 3:50 PM


Catholic scientists: "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."
Again, this is what is disputed. But indeed, this is the basic premise of current evolutionary science. But evolution is not a chemostat, it is a molecular machine with molecules at its basis.
Catholic scientist: "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."
Design-by-contract means that other components of the system can always rely on the interfaces that were initially used. For biology, it means that you can not change things that evolved earlier in evolution. Imagine you would change the genetic code. It would mean that all proteins (downstream) would change and nothing would work anymore. That is why the genetic code has never changed (or changed only within very limited effects). The genetic code has not adapted to become a perfect code, the rest of Life has adapted to the existing genetic code.

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Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 49 of 81 (699072)
05-14-2013 4:36 AM
Reply to: Message 41 by AZPaul3
05-13-2013 5:11 PM


AZPaul3: "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!"
A basic misunderstanding in applying engineering and you seem to confuse engineering principles with a conscious designer. Evolution is not freeform and functionality was put on layer-by-layer. This puts many constraints on the ultimate outcome.
Compare it to current computer legacy systems. The old systems at the core of many banking systems for instance do not conform to current design principles and we would find them now overly complex, but they work and we cannot change them easily. Still it is engineering and we have overcome the 'silly legacy systems' by encapsulating them so that we hide the complexity. And you can only understand how legacy systems work by applying engineering principles.

This message is a reply to:
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Replies to this message:
 Message 50 by AZPaul3, posted 05-14-2013 7:53 AM Albert de Roos has replied

  
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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New Cat's Eye
Inactive Member


Message 51 of 81 (699078)
05-14-2013 10:08 AM
Reply to: Message 42 by Genomicus
05-14-2013 12:45 AM


By that argument, then at the heart of all of technologies is simple chemistry.
Well, no. My motorcycle can't ride itself. But my stomach will dissolve a carrot all on its own. Salt crystals will just grow spontaneously, but my Legos don't put themselves together.
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.
But from that perspective its just chemistry. You're looking at salt crystals, not Legos.
The core structures of the bacterial flagellum and the F-ATPase are perfectly suited to performing their respective functions.
And that's because all the one's that didn't work that well were selected against, or not selected for.
That is, there is a logic to the arrangement of the parts of these machines
But you're looking at it in hind-sight and getting tricked into thinking there's more there than there is.
Let me paing an analogy. I'm working in a grocery store and go to the apple bin. It full of all kinds of qualities of apples. I go through them one by one and keep all the really nice looking apples and then throw away all the bad looking ones. Then you come into the store and see the bin of apples and go: "Holy cow, the guy who buys the fruit for this store an amazingly logical purchaser. Look how he bought only the best looking apples and not one shitty one!" Little did you realize, he bought all kinds of shitty ones but they just didn't get selected to stay in the bin.

This message is a reply to:
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Replies to this message:
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NoNukes
Inactive Member


Message 52 of 81 (699079)
05-14-2013 10:19 AM
Reply to: Message 45 by Albert de Roos
05-14-2013 4:05 AM


Re: Whose proposal is it anyway...
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.
Here is what you did say:
Classical terms such as natural selection and random mutation seem irrelevant or useless at a macroevolutionary scale.
Quite frankly, because you use non-standard terms, it is unreasonably difficult to figure out exactly what you are saying, but it does appear to me that irrelevant and useless are quite contrary to "meaningful".
What you seem to be saying with your software analogy, is that evolution works on whatever is already designed.
I don't see any software features built into biological designs that drive new designs. I am asking that you point them out, but instead you simply say 'they are built into the genome'. Okay, but where? Give me an example of the genome itself giving direction for addition of improvement to spur on evolution.
Under the theory of evolution 'direction' comes from primarily from the environment and not from the genome. There may indeed be a few counter examples, involving things like an increased mutation rate at certain sites in reaction to stimulus like starvation, but generally speaking, but is there a case to be made that wings and fins develop in response to some programming in the genome? If so, where is the support for that?
Edited by NoNukes, : No reason given.

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 45 by Albert de Roos, posted 05-14-2013 4:05 AM Albert de Roos has replied

Replies to this message:
 Message 55 by Albert de Roos, posted 05-14-2013 1:43 PM NoNukes has replied

  
New Cat's Eye
Inactive Member


Message 53 of 81 (699081)
05-14-2013 10:29 AM
Reply to: Message 47 by Albert de Roos
05-14-2013 4:16 AM


This is exactly what I dispute (and explain on my website).
Then get to it. Go ahead and dispute it. Quote the relevant parts of your website here and lets debate them.
Honestly, you're approach seems way too Lamarckian to be correct.

This message is a reply to:
 Message 47 by Albert de Roos, posted 05-14-2013 4:16 AM Albert de Roos has replied

Replies to this message:
 Message 56 by Albert de Roos, posted 05-14-2013 1:50 PM New Cat's Eye has replied

  
Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 54 of 81 (699105)
05-14-2013 1:11 PM
Reply to: Message 50 by AZPaul3
05-14-2013 7:53 AM


AZPaul3: "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."
So we agree to a certain point.
I do not like the terms overly complex or energy inefficient, because they imply a certain goal and the terms are quite anthropomorph (that is why you sound like Life has a designer). Also, you and others seem to use the words 'mess' and 'wasteful', as a way to show that Life is not designed by a designer. 'Mess' and 'wasteful' have no place in science.
In software design, but also in other system designs, the layering is recognized as a design patterns. If you want the system to always work during evolution (the concept of functional continuity, it would imply that earlier layers must be kept intact. From this, you can deduce the actual path of evolution, by peeling of layer by layer and carefully look at the relation and dependencies between the layers. That process is called reverse engineering.
If you look at the origin of the nucleus, I have deduced the steps. I see the dependencies between functional layers and previous layers. Has evolutionary science produced a framework that can predict (deduce) certain steps in evolution? I never saw one. Anything goes in evolutionary science as long as someone comes up with some sort of fitness goal. And hey, if things don't match up, you just terms like 'neutral evolution' and 'genetic drift' or 'hopeful monsters'.

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Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 55 of 81 (699115)
05-14-2013 1:43 PM
Reply to: Message 52 by NoNukes
05-14-2013 10:19 AM


Re: Whose proposal is it anyway...
NoNukes: "What you seem to be saying with your software analogy, is that evolution works on whatever is already designed. "
Evolution works on whatever is already -implemented-. All the previous layers may have evolved by chance events and based on a selection process, but did thet did occurr according to specific rules. These rules that are implied in the design frmaework can be used to deduce the actual steps.
I would not use the words random and natural, because they are difficult terms and are of no use in predicting the steps taken in evolution. Brownian motion is random, but can be used to give a direction to a molecule. I also assume a selection process, but they do not have to be natural.
NoNukes: "Okay, but where? Give me an example of the genome itself giving direction for addition of improvement to spur on evolution."
First, you have to be careful to use the word 'improvement', because improve implies that something was not good and that you know what would be better. I think more along the lines of a machine that increases in complexity without an external driving force (like environment). It is intrinsic.
Some examples that would explain the 'self-evolving':
-Telomerase is an enzyme that actively extends the chromosomes. Evolution-wise, this may create new virgin DNA that can be used for the creation of new genes.
-Active recombination and formation of new genes by randomly recombining exons and genes with the use of active cut-and-ligase enzymes.
-Crossing-over in sexual reproduction. Although the initial events leading to crossing over be be random, the result is an organism with an active recombination mechanism. Inequal crossing-over can drastiscally increase genome size.
I know that these things are difficult to prove, but they must be seen in the context of the self-evolving molecular machine.
Wings and fins would have evolved not because there was some fitness advantage, but due to an intrinsic recombination process in which all possible kinds of extremities (wings, fins, legs) are continuously explored. Viable new organism with rudimentary wings could then evolve into functional wings using RM+NS, but the origin of the wings would lie in another process.

This message is a reply to:
 Message 52 by NoNukes, posted 05-14-2013 10:19 AM NoNukes has replied

Replies to this message:
 Message 62 by NoNukes, posted 05-14-2013 11:22 PM Albert de Roos has replied

  
Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 56 of 81 (699116)
05-14-2013 1:50 PM
Reply to: Message 53 by New Cat's Eye
05-14-2013 10:29 AM


Catholic scientist: "Then get to it. Go ahead and dispute it. Quote the relevant parts of your website here and lets debate them."
I dispute that Life must be seen as a set of chemical reactions, but instead Life must be seen as a molecular machine that follows certain rules. I depict a new framework for evolution with different paradigms.
New Paradigms
1. Evolution can be modeled on a design framework
2. Life evolved inside-out
3. Ontology reflects Phylogeny
Evolution can be modeled on a design framework
The design framework on which the new theory was built can be best described using the design-by-contract methodology from software development. It represents an object-oriented programming where systems can expand as long as existing interfaces must remain intact. Such a system can only expand by refining existing interfaces and implementing new interfaces. Dependencies in the system on interfaces prevents modification of functionality and lead to legacy systems. From the dependencies in the system, one can deduce the evolution of the system.
Life evolved inside-out
It proposes that the first entity of Life was the replicating of DNA, representing also the first life cycle. This replicating (cycling) DNA that started to produce ribozymes including ribosomes subunits and later proteins organized in a nucleolus. The nucleosus wrapped itself in a protein matrix and was surrounded by the nuclear lamina. On this nuclear lamina, the nuclear envelope evolved giving rise to the nucleus as the first cell. Outside of the nucleus, again a protein matrix, the cytoskeleton was formed onto which an additional membrane fused, the plasma membrane.
Ontology reflects phylogeny
The eukaryote cell acquired the capability to fuse with another cell which duplicated its DNA content, resulting in a life cycle that contained both a haploid and a diploid stage. In higher eukaryotes multicellularity evolves in the diploid stage by a progressive mitosis of the fertilized egg and a postponement of the sexual maturity of the germ cells. Early decisions in egg division decide the fate map of the mature organism and represent strong branching point in evolution. Overall, evolution is seen as the addition over time of extra functionality on top of the original life cycle of replicating DNA.

This message is a reply to:
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Replies to this message:
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New Cat's Eye
Inactive Member


Message 57 of 81 (699117)
05-14-2013 2:16 PM
Reply to: Message 56 by Albert de Roos
05-14-2013 1:50 PM


I dispute that Life must be seen as a set of chemical reactions, but instead Life must be seen as a molecular machine that follows certain rules. I depict a new framework for evolution with different paradigms.
Why should I think that life should be seen that way and why should I think your paradigm is correct?

This message is a reply to:
 Message 56 by Albert de Roos, posted 05-14-2013 1:50 PM Albert de Roos has replied

Replies to this message:
 Message 58 by Albert de Roos, posted 05-14-2013 2:56 PM New Cat's Eye has replied

  
Albert de Roos
Junior Member (Idle past 3970 days)
Posts: 25
Joined: 05-02-2013


Message 58 of 81 (699118)
05-14-2013 2:56 PM
Reply to: Message 57 by New Cat's Eye
05-14-2013 2:16 PM


catholic scientist: "Why should I think that life should be seen that way and why should I think your paradigm is correct?"
Because my framework gives actual molecular mechanisms for evolution and I guess we are both here to find out how Life evolved. It also makes sense (to me in any case) that Life is an evolving molecular machine and should be treated that way.
My paradigms must of course be seen in the light of scientific advance. They can be tested. Because I present a concrete (design) framework, it is also up for discussion. For instance, people may argue that functional continuity may be reached by other mechanisms and scenario's.
But test the framework yourself. Try to come up with a logical sequence of events that give rise to the eukaryotic cell. Then look at my explanation and you can decide for yourself which one is better.

This message is a reply to:
 Message 57 by New Cat's Eye, posted 05-14-2013 2:16 PM New Cat's Eye has replied

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New Cat's Eye
Inactive Member


Message 59 of 81 (699119)
05-14-2013 3:16 PM
Reply to: Message 58 by Albert de Roos
05-14-2013 2:56 PM


Because my framework gives actual molecular mechanisms for evolution...
What is the mechanism?
Regardless, the mechanism of evolution that secures the changes to the species doesn't happen at the molecular level. Selection operates on the phenotypes in the population, not on molecules.
...and I guess we are both here to find out how Life evolved. It also makes sense (to me in any case) that Life is an evolving molecular machine and should be treated that way.
My paradigms must of course be seen in the light of scientific advance. They can be tested. Because I present a concrete (design) framework, it is also up for discussion. For instance, people may argue that functional continuity may be reached by other mechanisms and scenario's.
But test the framework yourself. Try to come up with a logical sequence of events that give rise to the eukaryotic cell. Then look at my explanation and you can decide for yourself which one is better.
I'm still wondering why I should think that you are correct.

This message is a reply to:
 Message 58 by Albert de Roos, posted 05-14-2013 2:56 PM Albert de Roos has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 60 of 81 (699133)
05-14-2013 5:30 PM
Reply to: Message 35 by Albert de Roos
05-13-2013 12:50 PM


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.
That's not how software development works. When software designers pull bits and pieces from other programs as units, combine and mix them, or come up with completely novel code. Their iterations need not produce a nested hierarchy.
This is not what we see in life. We do not see wholesale swapping of design units across designs like we do with software development. Instead, we see a nested hierarchy, the very opposite of what we would expect from a design paradigm.
Even more, it is the physical characteristics of DNA that carry information. For example, stem-loop structures can form in DNA and control transcription. The physical interactions with DNA and transcription factors can control embryonic development. This just doesn't happen with software. Software code does not physically react with itself to produce tertiary structures.
Quite frankly, software does not have a lot in common with DNA.

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

Replies to this message:
 Message 63 by Albert de Roos, posted 05-15-2013 10:44 AM Taq has replied

  
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