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Author Topic:   Design Framework for Evolution
New Cat's Eye
Inactive Member


(1)
Message 21 of 81 (698862)
05-10-2013 9:59 AM
Reply to: Message 18 by Albert de Roos
05-10-2013 7:12 AM


I consider macroevolution basically everything before the Cambrium. Microevolution is the small things in evolution, like beak size, different insect species, adaptation to enviroment. Microevolution is more adaptation than real evolution, which is for me the addition of new functions and the increase in complexity.
The really big events in evolution are the origin of Life, the origin of the first cell, multicellularity, the origin of sex, origin of insect metamorphosis etc. Neodarwinism is rather useless here.
Then you should stop using the word Macroevolution, its already taken and has a particular meaning.
How about Bioemergence, or something. That way, when people see you write that Neodarwinism doesn't have anything to do with Bioemergence, they won't be so confused.

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


(1)
Message 23 of 81 (698870)
05-10-2013 10:34 AM
Reply to: Message 22 by onifre
05-10-2013 10:10 AM


How about how sea dwelling vertebrate developed into free thinking homosapiens over a span of over 500 million years? Surely that is a macroevolutionary jump.
Inasmuch as a snail "jumps" from one end of a log to the other

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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 replied

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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 replied

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

  
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 replied

Replies to this message:
 Message 42 by Genomicus, posted 05-14-2013 12:45 AM New Cat's Eye has replied
 Message 48 by Albert de Roos, posted 05-14-2013 4:24 AM New Cat's Eye has not replied

  
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:
 Message 42 by Genomicus, posted 05-14-2013 12:45 AM Genomicus has replied

Replies to this message:
 Message 67 by Genomicus, posted 05-16-2013 1:01 AM New Cat's Eye 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

  
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

  
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

  
New Cat's Eye
Inactive Member


Message 78 of 81 (699921)
05-28-2013 11:02 AM
Reply to: Message 67 by Genomicus
05-16-2013 1:01 AM


From the perspective of the genome, we are not looking at salt crystals, since the genome encodes the information needed to construct molecular machinery. When I say "genome," I do not mean merely the nucleic acids, but the information as well.
The nucleotides need no more "information" to form the genome than sodium and chloride need to form salt crystals. Its still spontaneous chemical reactions that are following the laws of physics, its just a lot more complicated. You wouldn't bring up the information needed for the salt to know where the next molecule goes to form the complex crystalline structure, would you?

This message is a reply to:
 Message 67 by Genomicus, posted 05-16-2013 1:01 AM Genomicus has replied

Replies to this message:
 Message 79 by Genomicus, posted 06-03-2013 4:39 PM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


Message 80 of 81 (700495)
06-03-2013 4:52 PM
Reply to: Message 79 by Genomicus
06-03-2013 4:39 PM


The nucleotides need no more "information" to form the genome than sodium and chloride need to form salt crystals.
Yes. But the genome conveys the information needed to construct protein sequences.
No more than the conditions "convey" to the salt the info needed to construct crystals.
This information is not purely chemical;
Yes, it is. Which part isn't?
while mRNA translation operates according to the rules governing chemical interactions, there is no chemical law that states that, for example, the codon ATG must encode methionine.
Given the conditions, the codon will end up yielding the amino acid just like given the conditions, the salt will crystalize.

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