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Author Topic:   The End of Evolution By Means of Natural Selection
Wounded King
Member (Idle past 2171 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 811 of 851 (577114)
08-27-2010 8:33 AM
Reply to: Message 809 by Bolder-dash
08-27-2010 7:32 AM


Re: Zhang and Saier
Where are you claiming these processes, like endosymbiosis, and epigenetic inheritances arose from? Were they random mutations that were selected for through natural selection?
...
How about transposon insertion, where did that "mechanism" come from? Random mutations?

Not quite sure why these highly related questions took the form of two separate posts.

The answer for endosymbiosis and epigenetic inheritance is a mixture of yes and no in both cases.

The initial engulfment part of endosymbiosis is not a random mutation as I would think of it, but the subsequent transfer of genetic material from the engulfed organism to the host which leads to it becoming a subsidiary organelle seems consistent with stochastic genetic processes we are familiar with.

Similarly for epigenetic inheritance it is associated in large part with Modifying enzymes produced by the cell which are viable targets for RM/NS to operate on. The primary sequence of the DNA can also have significant effects on possible patterns of epigenetic modification in terms of providing binding/recognition sites for modifying enzymes. The one element which is clearly distinct from random mutation is the environmental factors which can alter the balance of epigenetic modification.

As to transposon insertion, if anything this is the one which can most clearly be ascribed as the result of processes of RM/NS. The tranposon's transposing activity is a result of its genetic sequence, that sequence can be modified by random mutation causing functional changes in its behaviour. Similarly the insertion sites for a transposon are specific sequences of DNA, often very short motifs which can easily arise randomly.

in the case of the IS5 transposon in the Zhang and Saier paper the recognition site is simply C-(A or T)-A-(A or G) which is not highly specific. The position of this sequence was such that binding of a protein which regulates glycerol metabolism was sufficient to block access of the transposon to the sequence and prevent it inserting under normal conditions.

So many of these mechanisms do indeed involve significant roles for rm and certainly ns in both their origination and their maintenance.

TTFN,

WK


This message is a reply to:
 Message 809 by Bolder-dash, posted 08-27-2010 7:32 AM Bolder-dash has responded

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Bolder-dash
Member (Idle past 1706 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 812 of 851 (577454)
08-28-2010 9:52 PM
Reply to: Message 811 by Wounded King
08-27-2010 8:33 AM


Re: Zhang and Saier
We'll let's summarize what is being said here. When adding in details about the proteins involved, and other tangential matters, it is easy to distract from the real point (sometimes I wonder if that is not your intention).

These "mechanisms", as you are calling them, do possibly have significant origins from random mutations and naturals selection- some even more so than others.

So, according to you, epigenetics originated (significantly or partially?) through random mutations and natural selection. Likewise, endosymbiosis, if it is even a valid concept, was formed through RM and NS, among other things. Of course the fact that endosymbiosis even exists is still just theoretical, so of course the method through which it might have come about, if its even true, is even more suppositional in nature.

Now of course, by your use of the term mechanism, we get to include every process of life, such as breathing, metabolizing food, cell, division, and any other system of organic matter, ...but even with this loose definition of what is an actual mechanism, and what is actually just a process (such as transposson insertion), I still find you parsing the root origins of all of these processes.

The bottom line is, if you say they "could be" partially related to RM and NS what is the other source of origin? Is there another? You are trying to make the argument that RM and NS are not the only mechanisms of the modern evolutionary theory (which I can understand why you are trying to make this escape hatch, because of the difficulties for explaining things by such an unguided process), but isn't it true, that you have nothing else to start with other than those two originators? How can you say that it came from something else? Where else can an intelligent system come from with your theory? It doesn't matter what you use to define as a mechanism of evolution, ultimately by your own theory they can ONLY come from RM & NS in the beginning. Otherwise,please tell me how they can come from something else.

I think, once again, you are trying to run from your own theory, by creating a category of "other mechanisms" (preferably as vague and as flexible as possible), when in truth ANY other origin for a mechanism runs completely contrary to your theory. So we are back to the beginning, your theory ONLY has RM and NS as a base.

Edited by Bolder-dash, : No reason given.


This message is a reply to:
 Message 811 by Wounded King, posted 08-27-2010 8:33 AM Wounded King has not yet responded

Replies to this message:
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Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 813 of 851 (577492)
08-29-2010 8:22 AM
Reply to: Message 812 by Bolder-dash
08-28-2010 9:52 PM


Re: Zhang and Saier
Bolder-dash writes:

So we are back to the beginning, your theory ONLY has RM and NS as a base.

The beginning was Darwin, so evolution didn't even have random mutation when first formulated, only "descent with modification." We only learned about random mutation with the discovery of the structure of DNA, which didn't happen until the 1950's.

Evolutionary research seeks all the mechanisms that contribute to evolution, which is the term we use for what causes life to change over time. Random mutation and natural selection are merely the most prominent. They aren't the only mechanisms. For example, a scientist named Kimura developed the neutral theory of evolution. It explored the possibilities of evolutionary change due to neutral or nearly neutral mutations not affected by natural selection.

If tomorrow someone discovers a new mechanism causing life forms to change over time, it would become part of evolutionary theory (hint, hint, IDists - find a mechanism!). That's because evolution isn't a theory of random mutation and natural selection. It's a theory of the causes of the changes in life over time.

--Percy

Edited by Percy, : Typo.


This message is a reply to:
 Message 812 by Bolder-dash, posted 08-28-2010 9:52 PM Bolder-dash has responded

Replies to this message:
 Message 814 by Bolder-dash, posted 08-29-2010 12:49 PM Percy has responded
 Message 816 by Dr Adequate, posted 08-29-2010 2:50 PM Percy has responded

    
Bolder-dash
Member (Idle past 1706 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 814 of 851 (577522)
08-29-2010 12:49 PM
Reply to: Message 813 by Percy
08-29-2010 8:22 AM


Re: Zhang and Saier
I wasn't asking what the theory said one hundred years ago, or what it might say in another 100 years, I am asking what you are saying today. If you have any other mechanism for evolutionary designed intelligent structures that does not have either RM and NS as its cause, please explain?

If you wish to claim the two mechanisms as 1. Rm and neutral selection, and 2. Rm and Natural selection, ok, make the case if you chose. Please stop using the excuse of ID can't provide a better explanation diversion. If you don't believe in ID why are you using that for a yardstick?


This message is a reply to:
 Message 813 by Percy, posted 08-29-2010 8:22 AM Percy has responded

Replies to this message:
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Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 815 of 851 (577544)
08-29-2010 2:27 PM
Reply to: Message 814 by Bolder-dash
08-29-2010 12:49 PM


Re: Zhang and Saier
Hi Bolder-dash,

The answer you seek was in the message you just replied to where I said:

"If tomorrow someone discovers a new mechanism causing life forms to change over time, it would become part of evolutionary theory (hint, hint, IDists - find a mechanism!). That's because evolution isn't a theory of random mutation and natural selection. It's a theory of the causes of the changes in life over time."

--Percy


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Dr Adequate
Member
Posts: 16085
Joined: 07-20-2006
Member Rating: 10.0


Message 816 of 851 (577549)
08-29-2010 2:50 PM
Reply to: Message 813 by Percy
08-29-2010 8:22 AM


We only learned about random mutation with the discovery of the structure of DNA, which didn't happen until the 1950's.

Surely it isn't necessary to know the molecular structure of DNA, or even that DNA is the hereditary material, to appreciate that random mutations exist.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 813 by Percy, posted 08-29-2010 8:22 AM Percy has responded

Replies to this message:
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Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 817 of 851 (577554)
08-29-2010 3:15 PM
Reply to: Message 816 by Dr Adequate
08-29-2010 2:50 PM


Dr Adequate writes:

Surely it isn't necessary to know the molecular structure of DNA, or even that DNA is the hereditary material, to appreciate that random mutations exist.

Feel free to fill in more detail, there's lots I don't know here. When did the term mutation first come into use? If prior to the discovery of the structure of DNA, what was the definition of mutation at that time? Did the population geneticists of the 1920s think in terms of mutations?

--Percy


This message is a reply to:
 Message 816 by Dr Adequate, posted 08-29-2010 2:50 PM Dr Adequate has not yet responded

Replies to this message:
 Message 818 by bluegenes, posted 08-29-2010 5:49 PM Percy has acknowledged this reply
 Message 819 by Taq, posted 08-30-2010 1:45 PM Percy has responded

    
bluegenes
Member (Idle past 553 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(2)
Message 818 of 851 (577597)
08-29-2010 5:49 PM
Reply to: Message 817 by Percy
08-29-2010 3:15 PM


Early use of "mutations".
Percy writes:

When did the term mutation first come into use? If prior to the discovery of the structure of DNA, what was the definition of mutation at that time? Did the population geneticists of the 1920s think in terms of mutations?

To the last question, yes, they did. Chromosomes were identified in the late 19th century, and the word "gene" to describe active chunks of them was in use by the early 20th century.

By the 1920s, mutation was certainly being used, but I can't answer your first question exactly (it could have been well before).

Here's Sewall Wright a bit later using it in 1932 as if it's already well established: Sewall Wright talking about mutations

Look at the second and third sentences:

quote:

The observed properties of gene mutation - fortuitous in origin, infrequent in occurrence and deleterious when not negligible in effect - seem about as unfavourable as possible for an evolutionary process. Under biparental reproduction, however, a limited number of mutations which are not too injurious to be carried by the species furnish an almost infinite field of possible variations through which the species may work its way under natural selection.


Sewall Wright 1932.

I chose that not particularly early example because the phrase I've highlighted is a long-winded way of saying "random", and clearly indicates Wright's view on the mutations.


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 Message 817 by Percy, posted 08-29-2010 3:15 PM Percy has acknowledged this reply

Replies to this message:
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Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 2.6


(1)
Message 819 of 851 (577807)
08-30-2010 1:45 PM
Reply to: Message 817 by Percy
08-29-2010 3:15 PM


Feel free to fill in more detail, there's lots I don't know here. When did the term mutation first come into use? If prior to the discovery of the structure of DNA, what was the definition of mutation at that time? Did the population geneticists of the 1920s think in terms of mutations?

A mutation was a change in phenotype. Throughthe work done by Luria and Delbruck with their fluctuation assay and the Lederbergs' work with the plate replica experiment it was shown that these changes in phenotype preceded exposure to selection pressure. Specifically, Luria and Delbruck were able to show that mutations leading to bacteriophage resistance occurred prior to the bacteria being exposed to bacteriophage. Their conclusion was that mutations were random with respect to fitness, the same conclusion we hold today. This work was done before the structure of DNA was discovered.


This message is a reply to:
 Message 817 by Percy, posted 08-29-2010 3:15 PM Percy has responded

Replies to this message:
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Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 2.6


Message 820 of 851 (577809)
08-30-2010 1:56 PM
Reply to: Message 812 by Bolder-dash
08-28-2010 9:52 PM


Re: Zhang and Saier
So, according to you, epigenetics originated (significantly or partially?) through random mutations and natural selection.

From the tree of life we know that histones and DNA methylases had to evolve at some point before epigenetics could happen in the eukaryote branch.

Likewise, endosymbiosis, if it is even a valid concept, was formed through RM and NS, among other things.

Again, looking at the tree of life we know that chloroplasts and mitochondria had to evolve during eukaryote evolution. All of the evidence indicates that these structures are derived from the host cell engulfing another cell. Evolution through RM+NS resulted in a relationship that benefitted both the intracellular parasite and the host. We can find the same relationships between macroscopic species as well such as flowering plants and their pollinators, ants and aphids, etc. Evolution favors changes that benefit two different species at once.

You are trying to make the argument that RM and NS are not the only mechanisms of the modern evolutionary theory (which I can understand why you are trying to make this escape hatch, because of the difficulties for explaining things by such an unguided process), but isn't it true, that you have nothing else to start with other than those two originators?

We have all of the different factors that influence how DNA is changed and how the environment shapes the genome of a species from one generation to the next. This can and does include neutral drift and a few examples of non-random mutations. What we don't observe is supernatural deities causing changes in DNA or culling a species based on a genotype.

I think, once again, you are trying to run from your own theory, by creating a category of "other mechanisms" (preferably as vague and as flexible as possible), when in truth ANY other origin for a mechanism runs completely contrary to your theory. So we are back to the beginning, your theory ONLY has RM and NS as a base.

I think you have things a bit backwards. We have observations that the theory must incorporate.

To use an analogy, it is often said that water always flows downhill. This is true, with a few exceptions. For example, in a siphon water can flow uphill for a short stretch. Does this violate the theory that water always flows downhill? If you want to be a stickler, yes it does. However, the general theory works in almost all situations and the exceptions have known explanations.


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Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 821 of 851 (577810)
08-30-2010 1:57 PM
Reply to: Message 819 by Taq
08-30-2010 1:45 PM


Bluegene and Taq,

Neat! Thanks!

--Percy


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Replies to this message:
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Theodoric
Member
Posts: 5954
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 2.6


Message 822 of 851 (577818)
08-30-2010 2:35 PM
Reply to: Message 821 by Percy
08-30-2010 1:57 PM


Bluegene and Taq,

Neat! Thanks!

Right there you show the difference between bolder, archie type posters and those not completely driven by their religious faith. You are willing to conceded and acknowledge you do not know everything and that you can and are willing to learn.

Why can the creo/fundie side admit they might not know everything and actually may be wrong about some things?


This message is a reply to:
 Message 821 by Percy, posted 08-30-2010 1:57 PM Percy has acknowledged this reply

Replies to this message:
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barbara
Member (Idle past 2878 days)
Posts: 167
Joined: 07-19-2010


Message 823 of 851 (580308)
09-08-2010 3:43 PM
Reply to: Message 822 by Theodoric
08-30-2010 2:35 PM


Natural Selection is misleading to the general public
The words chosen to describe the process "natural selection" provokes the debate of being directed or undirected. Couldn't science have been more careful of choosing its words to describe undirected processes?

This is the problem for the general public to fully understand science because science is always implying direction when they explain how cells cooperate, cell signaling, DNA processes, bacteria behavior, species interaction, organization factors, and on and on. What bothers me is that when you read many of the scientific discoveries is that the entire paper is written in details that indicates direction explaining the entire process. Many will end it by stating this an undirected process. When I come across these great explanations to describe life's processes that you can only conclude that it is directed until you read the last statement that says it is undirected, it makes me think that the person who wrote this scientific discovery is completely insane. Right here is where people that are not scientists have trouble in understanding it. I would like nothing better if science can prove without a shadow of a doubt that life is not a directed process.
I see life, from bacteria and all the way up the food chain are all driven by the will to survive and is obviously the directed part. However, bacteria are not restricted and for the most part make up a great deal of the cells living in every life form that are the food web. The mechanism for RM and NS is not yet fully understood especially when microbes have mostly been ignored and excluded when describing the process of evolution in relationship that we are a community of many beings of life in one body.

The story of evolution through RM and NS takes on a different meaning when there is no such thing as an individual being of life. Experimentation done in a science lab using one cell to based its findings on does not produce the same results in the natural world. You are never going to find one cell by itself on the planet.

Making the assumption of what bacteria can and cannot do that is the foundation of which the current theory of evolution is based on is proving to be more incorrect everyday. Directed or undirected is what people really want to know. The problem is if we do get the answer, what kind of impact will it have on mankind's future to survive?


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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004


Message 824 of 851 (580312)
09-08-2010 3:55 PM
Reply to: Message 823 by barbara
09-08-2010 3:43 PM


Re: Natural Selection is misleading to the general public
Directed or undirected is what people really want to know.

Undirected.

It really is that simple.


Anyone so limited that they can only spell a word one way is severely handicapped!
This message is a reply to:
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Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 2.6


Message 825 of 851 (580316)
09-08-2010 4:17 PM
Reply to: Message 823 by barbara
09-08-2010 3:43 PM


Re: Natural Selection is misleading to the general public
This is the problem for the general public to fully understand science because science is always implying direction when they explain how cells cooperate, cell signaling, DNA processes, bacteria behavior, species interaction, organization factors, and on and on. What bothers me is that when you read many of the scientific discoveries is that the entire paper is written in details that indicates direction explaining the entire process.

When the weather man states that the wind is blowing in a specific direction do you take this to mean that an intelligent force is directing it? Do you take this to mean that wind has a goal that it is blowing towards?

Also, of the things you mention above none are natural selection.

When we say that natural selection is undirected we mean that natural selection does not have a specific goal in mind and then shapes creatures towards that goal. This is why we see more than one type of wing, more than one type of eye, etc. There are many solutions to a problem, and natural selection finds these solutions blindly. Natural selection does not see structure. It sees fitness. Natural selection is equally blind when it comes to DNA sequence.

I see life, from bacteria and all the way up the food chain are all driven by the will to survive and is obviously the directed part.

Of course, all of the organisms through time that lacked the will to survive left no offspring so it is kind of expected, is it not?

Also, if this will to survive is directed then why do we have so many different species with so many different adaptations?

The mechanism for RM and NS is not yet fully understood especially when microbes have mostly been ignored and excluded when describing the process of evolution in relationship that we are a community of many beings of life in one body.

What makes you think that RM and NS are not fully understood? Things can be tough to understand for very specific adaptations, but the overall mechanisms are very well understood IMHO. Also, interspecies communication and cooperation is a very active field in microbiology as it relates to such areas as oral and gastrointestinal biofilms.

Making the assumption of what bacteria can and cannot do that is the foundation of which the current theory of evolution is based on is proving to be more incorrect everyday.

I don't think this at all. We observe what bacteria do and don't do, and then draw conclusions from that. What else are we supposed to do?


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