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Author Topic:   Design Framework for Evolution
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 16 of 81 (698787)
05-09-2013 2:17 PM
Reply to: Message 15 by Pressie
05-09-2013 4:59 AM


I completely disagree. It very relevant to discuss what life is in this discussion.
Albert de Roos has already stated what he considers life: a replicating genome. Do viruses have replicating genomes? Yes, but that replication is often contingent on the host. There is debate within the biology community on the subject of whether or not viruses should be considered life. I don't think that debate can be resolved here. So by de Roos's definition of life, it would seem that an independently replicating genome constitutes life. If I understand him correctly, viruses by themselves are not considered life, inasmuch as transposons are not.

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NoNukes
Inactive Member


Message 17 of 81 (698837)
05-09-2013 11:12 PM
Reply to: Message 14 by Albert de Roos
05-09-2013 3:53 AM


macroevolution because they do not explain the origin of Life
Your use of the term 'macroevolution' seems unconventional. Would you mind stating your definition explicitly?
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 14 by Albert de Roos, posted 05-09-2013 3:53 AM Albert de Roos has replied

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


Message 18 of 81 (698849)
05-10-2013 7:12 AM
Reply to: Message 17 by NoNukes
05-09-2013 11:12 PM


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.

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Replies to this message:
 Message 19 by onifre, posted 05-10-2013 9:31 AM Albert de Roos has replied
 Message 21 by New Cat's Eye, posted 05-10-2013 9:59 AM Albert de Roos has not replied

  
onifre
Member (Idle past 2951 days)
Posts: 4854
From: Dark Side of the Moon
Joined: 02-20-2008


Message 19 of 81 (698858)
05-10-2013 9:31 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.
I believe it's Cambrian.
So going from ocean dwelling vertebrate and invertebrate to dinos, from dinos to birds and from small mammals to homosapiens is what you consider microevolution? This all happened after the Cambrian period.
- Oni
Edited by onifre, : No reason given.

This message is a reply to:
 Message 18 by Albert de Roos, posted 05-10-2013 7:12 AM Albert de Roos has replied

Replies to this message:
 Message 20 by Albert de Roos, posted 05-10-2013 9:51 AM onifre has replied
 Message 24 by Genomicus, posted 05-10-2013 1:17 PM onifre has not replied

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


Message 20 of 81 (698860)
05-10-2013 9:51 AM
Reply to: Message 19 by onifre
05-10-2013 9:31 AM


"So going from ocean dwelling vertebrate and invertebrate to dinos, from dinos to birds and from small mammals to homosapiens is what you consider microevolution? This all happened after the Cambrian period."
My point is basically that I find it more relevant for evolution how cells and multicellular organisms originated in the first place, than how a four legged creature with a spine developed into a slight more complex four-legged creature with a spine.
Once you have a cell, the rest is almost trivial. It is all more of the same, recombinations on common themes. Real macroevolution happened at the microlevel. How did cells evolve, that is the real question.
I guess 99% of the gene families that are present now, originated before the Cambrian (or Cambrium in Dutch). Then the rest would be microevolution. Also, no real new system designs after the Cambrian.

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 Message 19 by onifre, posted 05-10-2013 9:31 AM onifre has replied

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 Message 22 by onifre, posted 05-10-2013 10:10 AM Albert de Roos has not replied

  
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:
 Message 18 by Albert de Roos, posted 05-10-2013 7:12 AM Albert de Roos has not replied

  
onifre
Member (Idle past 2951 days)
Posts: 4854
From: Dark Side of the Moon
Joined: 02-20-2008


Message 22 of 81 (698868)
05-10-2013 10:10 AM
Reply to: Message 20 by Albert de Roos
05-10-2013 9:51 AM


My point is basically that I find it more relevant for evolution how cells and multicellular organisms originated in the first place
So you like the pre-Cambrian period. But aren't those all still microevolutionary changes?
Than how a four legged creature with a spine developed into a slight more complex four-legged creature with a spine.
That's only a small time period. 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.
How did cells evolve, that is the real question.
That is a great question. But you're not using the terms "macro" and "micro" evolution properly.
Also, no real new system designs after the Cambrian.
What about consciousness?
- Oni

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 Message 20 by Albert de Roos, posted 05-10-2013 9:51 AM Albert de Roos has not replied

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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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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 24 of 81 (698905)
05-10-2013 1:17 PM
Reply to: Message 19 by onifre
05-10-2013 9:31 AM


I believe it's Cambrian.
Not in Dutch, and de Roos's PhD education was done in the Netherlands. Just saying
Added in edit: never mind. This has already been pointed out.
Edited by Genomicus, : No reason given.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 25 of 81 (698908)
05-10-2013 1:25 PM
Reply to: Message 6 by Albert de Roos
05-07-2013 6:17 AM


Hi Albert de Roos,
Yes, that is true, it does not directly invoke an intelligent designer, but also does not preclude it. Based on my reverse engineering, I propose a mechanistic scenario of how the eukaryotic cell was put together.
You have applied your design-by-contract approach to things like the origin of life and the origin of the eukaryotic cell. But what about the origin of molecular machines, like, say, the bacterial flagellum? I suggest that the design-by-contract approach would show a possible evolutionary pathway, but if the flagellum was engineered, then that evolutionary pathway would not be an accurate portrayal of what happened in evolutionary history. The two competing hypotheses could be tested using something like molecular clocks.
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?

This message is a reply to:
 Message 6 by Albert de Roos, posted 05-07-2013 6:17 AM Albert de Roos has replied

Replies to this message:
 Message 31 by Albert de Roos, posted 05-11-2013 8:48 AM Genomicus has not replied

  
AZPaul3
Member
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

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


Message 27 of 81 (698928)
05-10-2013 5:45 PM
Reply to: Message 26 by AZPaul3
05-10-2013 4:56 PM


Re: Scattered Thoughts
AZPaul3. Thank you for your (albeit rather condescending ) post.
1. You say that I bring nothing new. I propose a stepwise and detailed mechanistic scenario for the origin of Life based on well-defined design framework. I for instance propose, or rather deduce, that the nucleus was the first cellular entity. That is quite new, is it not? Have you even read my website?
2. Of course I use different terms that do not coincide with the current definitions. It is a different framework that I use. A lot of people seem to define macroevolution based on macroscopic differences, but in engineering terms, that is a mistake. Evolutionary speaking, the effort is in the cell biology. From nothing to a eukaryotic cell, from a cell to multicellularity.
3. Maybe mainstream evolutionary science is a better term than neodarwinism. I just use it as a general term for anything that has been brought up in the last decades. I do not see a coherent theory, no mechanistic scenario. To me it looks more like a religion than anything else.
4. "Evolution says nothing about the origin of Life". Excuse me? 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.
You say that nothing in evolution has any predictive value. It makes your entire framework non-predictive and therefore non-scientific and trivial. At least my theory is based on a predictive framework and on my framework, you can predict evolutionary scenarios. You can also falsify the theory.

This message is a reply to:
 Message 26 by AZPaul3, posted 05-10-2013 4:56 PM AZPaul3 has replied

Replies to this message:
 Message 29 by AZPaul3, posted 05-10-2013 8:56 PM Albert de Roos has replied

  
shadow71
Member (Idle past 2934 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 28 of 81 (698931)
05-10-2013 7:36 PM
Reply to: Message 6 by Albert de Roos
05-07-2013 6:17 AM


albert de Roos writes:
Hi genomicus. Yes, that is true, it does not directly invoke an intelligent designer, but also does not preclude it. Based on my reverse engineering, I propose a mechanistic scenario of how the eukaryotic cell was put together. However, when one arrives at the driving forces for this behavior, it gets a lot more difficult. Classical terms such as natural selection and random mutation seem irrelevant or useless at a macroevolutionary scale. For now, I assume that energy input in the form of day/night and seasonal changes can explain evolution, but at the moment we miss some parts of the equation.
Although not strictly revelant to your orgin of life theory, it seems that your evolutionary theory is consistent with that of James A. Shapiro of the University of Chicago. His life's work set forth in his book "Evolution: A view from the 21st Century"describes "natural genetic engineering" a theory that seems to be accepted by your theory of evolution.
Are you familar with Shapiro's work?, and do you agree with his rejection of the random nature of genetic change by natural selection theory?
Edited by shadow71, : No reason given.
Edited by shadow71, : No reason given.

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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

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

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


Message 30 of 81 (698954)
05-11-2013 8:37 AM
Reply to: Message 29 by AZPaul3
05-10-2013 8:56 PM


Re: Scattered Thoughts
AZPaul3,
I use a completely different framework from mainstream evolutionary science, that is why I use different terms. Mine is based on design paradigms and my definitions come from engineering. Microevolution and microevolutions are indeed different terms for me. They are worthless in another framework. The same as terms like genetic drift or neutral evolution are irrelevant for my research.
For me, the origins discussion is essential in evolution. And as I explained on my website, the early stages in evolution will define the constraints and possibilities later in evolution. There are strict rules in evolution that determine the path of evolution. That's why the origins question equals macroevolution in my design framework.
-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)
I am interested in evolution (and I am quite satisfied with current population genetics to explain adaptation. A lot of people like me have come to the conclusion that current evolutionary theories do not explain evolution at all. As soon as you start to translate evolutionary scenario's into real mechanistic steps, you run into trouble. If you don't address the origins question, you cover only the last 1% of evolution, speaking in system terms.
I am interested in the mechanistics of the evolution of the eukaryotic cell. Is current evolutionary science going to help me in this effort. No, because there is no real framework. Anything goes. Will population genetics tell me how the nucleus was assembled during evolution? I believe engineering science is giving me the answers.
For instance, I give a rather detailed mechanistic explanation of the origin of the eukaryotic cell, indicating that the nucleus was the predecessor of our eukaryotic cell. That is quite a big difference from what you read in the textbook. How the eukaryotic cell was assembled during evolution matters enormously. Cancer is uncontrolled cell growth of eukaryotic cells, and the cell cycle regulators originated very early in evolution. Only if you understand the evolution of the eukaryotic cell, you will start to understand the cell cycle.

This message is a reply to:
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Replies to this message:
 Message 37 by New Cat's Eye, posted 05-13-2013 2:13 PM Albert de Roos has replied

  
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