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Author Topic:   Does the Darwinian theory require modification or replacement?
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 660 of 760 (622464)
07-03-2011 11:46 AM
Reply to: Message 656 by shadow71
07-03-2011 10:09 AM


Re: Natural Engineering
shadow71 writes:
The following is a quote from the paper I linked to online.
I cannot gain access to the full paper of the Abstract Shapiro cited, but I accept his judgment as to what it means.
If you merely accept what Shapiro tells you the paper means instead of understanding what it actually says then you can't really discuss it, can you. All you can do is go off and find more Shapiro to quote at us. Your whole approach in this thread isn't that you've examined Shapiro's references and concluded that he's correct. Your approach is merely, "Shapiro's claims agree with what I already believe, so I'll just assume he's correct without trying to understand the evidence he cites."
But if you don't understand Shapiro's references, how are you going to discuss them? Seriously, this is a big problem for you. How are you going to convince other people that Shapiro is right about something you don't understand? This isn't due to any shortcomings on your part. How would anybody anywhere ever convince other people of things they don't themselves understand? All they can do is hope the people they are talking to can become convinced without understanding what it is they are being convinced of.
But the people you're discussing with here aren't willing to accept things they don't understand. If you want to convince anyone here then you're going to have to understand Shapiro first. That means understanding not just his claims, which you have a fair grasp of, but also the evidence and rationale behind his claims.
Here the link to that paper again: The CRISPR system: small RNA-guided defense in bacteria and archaea. Let's see if we can find where Shapiro might think it supports his claim of "dedicated, nonrandom, beneficial change."
The word "nonrandom" or "non-random" or even "non random" never appears in the paper.
But search for "random" and we can find two occurrences, so let's try to get a handle on why Shapiro thinks the paper supports his position.
First we need to understand what CRISPR's are. Looking up CRISPR at Wikipedia (I recommend reading at least the introductory paragraph and giving the diagram a good, long look) we see that it stands for Clustered Regularly Interspaced Short Palindromic Repeats. CRISPR's are specific gene locations in DNA "containing multiple short direct repeats...CRISPR functions as a prokaryotic immune system..."
Okay, enough of that excerpt, it's pretty technical. But I've looked up the terms and boiled it down, and in lay terms I can tell you that CRISPR's are one type of a bacteria's defense mechanism against infection by viruses.
So let's quote a small portion of the article that includes the first appearance of the word "random":
Thus, during the acquisition of a defensive repertoire, the CRISPR machinery appears to select sequences from the phage genome and incorporate these as novel spacers (Fig. 2B). The selection is not random.
This says that the sequences that are inserted as spacers are not selected at random, so let's see if we can figure out how the selection is not random. This article itself is pretty tough for me to follow, we need WK's help, but I think I can figure out some of this.
The article uses the term "proto-spacer" to refer to a DNA sequence in the virus genome of the virus that is attempting to infect the bacteria (they use the term phages in the article, instead of viruses). The authors think their evidence suggests that the spacers inserted at a CRISPR location are selected by a process driven by proteins that can recognize the specific sequences in viruses that confer immunity.
Is this a "dedicated, nonrandom beneficial change" to the bacteria's genome? I would answer, "Yes."
Is it a genetic mechanism that evolved over time through a process of descent with modification and natural selection (in particular, the recognition proteins)? I would again answer, "Yes."
We've known for a very long time about viruses' ability to insert genetic material into cells that adds to or replaces DNA in the cell's nucleus to take over the cell's machinery, usually to produce more copies of the virus. This detailed understanding we're developing of the CRISPR mechanisms that allow bacteria to develop resistance to viral infection is new, but it seems to fit perfectly within both modern genetics and evolutionary theory.
--Percy

This message is a reply to:
 Message 656 by shadow71, posted 07-03-2011 10:09 AM shadow71 has replied

Replies to this message:
 Message 662 by zi ko, posted 07-04-2011 2:17 AM Percy has replied
 Message 668 by Wounded King, posted 07-04-2011 9:35 AM Percy has seen this message but not replied
 Message 671 by shadow71, posted 07-04-2011 12:15 PM Percy has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 663 of 760 (622495)
07-04-2011 6:48 AM
Reply to: Message 654 by shadow71
07-03-2011 9:52 AM


Re: More misrepresentation.
shadow71 writes:
If so would you agree that the MS does not rule out a planned process?
The modern synthesis combines evolutionary theory with genetics. If in fact the causes of species change over time actually include an intelligent designer who plans and implements genomic changes then the modern synthesis would need to be either expanded or replaced.
Shapiro does not claim to have identified an intelligent designer. I earlier said that I thought you had a fair grasp of Shapiro's claims, and I chose that characterization carefully. I would have instead said you had an excellent grasp of Shapiro's claims if you didn't see an intelligent designer in his claims of directedness and non-randomness. As my Message 660 makes clear by interpreting that CRISPR paper for you, the "dedicated, nonrandom, beneficial" processes Shapiro calls attention to are not an intelligent designer at work, but are merely the operation of genetic and cellular processes that were produced by evolution. If you doubt this then send Shapiro another email with this exact question:
Do you believe the genetic and cellular processes identified in the CRISPR papers you cite came about through evolutionary processes or through the action of an intelligent designer?
--Percy
Edited by Percy, : Typo.

This message is a reply to:
 Message 654 by shadow71, posted 07-03-2011 9:52 AM shadow71 has seen this message but not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 664 of 760 (622496)
07-04-2011 7:02 AM
Reply to: Message 662 by zi ko
07-04-2011 2:17 AM


Re: Natural Engineering
Hi Zi Ko,
I would be glad to provide my opinion but instead find that my attention is fully taken up by your odd juxtaposition of quotes. Why on Earth did you quote Wright in such a way as to make it seem she was stating that Darwin shared Dobzhansky's views about eye evolution, when what she actually said was that Darwin shared some of Lamarck's views about the inheritance of acquired characteristics?
AbE: For reference for anyone reading this, here's the paper Zi Ko is quoting from: A Biochemical Mechanism for Nonrandom Mutations and Evolution
--Percy
Edited by Percy, : Provide reference.

This message is a reply to:
 Message 662 by zi ko, posted 07-04-2011 2:17 AM zi ko has replied

Replies to this message:
 Message 665 by zi ko, posted 07-04-2011 8:43 AM Percy has replied
 Message 667 by Meddle, posted 07-04-2011 9:26 AM Percy has seen this message but not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 666 of 760 (622502)
07-04-2011 8:56 AM
Reply to: Message 665 by zi ko
07-04-2011 8:43 AM


Re: Natural Engineering
Hi Zi Ko,
Thanks for the clarification, that helps a little. Here's your original question:
zi ko writes:
These of of course are not proofs that there is directed evolution driven by information,not only by random mutations and natural selection.
But i think they pose seriously the relative question. What is your opinion ?
If by directed evolution you mean an outside agency that plans and implements genomic changes then I see no evidence of it myself, nor any evidence that Larmarck, Darwin or Dobzhansky subscribed to such ideas.
But if by directed evolution you mean mechanisms that evolve to facilitate more rapid adaptation, that possibility was recognized long before examples were ever identified.
--Percy

This message is a reply to:
 Message 665 by zi ko, posted 07-04-2011 8:43 AM zi ko has replied

Replies to this message:
 Message 675 by zi ko, posted 07-04-2011 5:21 PM Percy has seen this message but not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 674 of 760 (622527)
07-04-2011 2:07 PM
Reply to: Message 671 by shadow71
07-04-2011 12:15 PM


Re: Natural Engineering
Hi Shadow,
First you say:
shadow71 writes:
That the process developed over time through descent, modification and selection I have no problem with.
Then you say:
I go with planned, am I wrong ,and if so ,what is the basis for the opinion I am wrong?
Descent, modification and selection are natural processes. Planned and implemented by some entity is not a natural process. You seem to be trying to have it both ways.
Many people on this board will never accept the findings of the CRISPR papers and other findings that lead to dedicated, nonrandom, beneficial changes.
All people of science at this forum provisionally accept any legitimate scientific finding. The resistance to your arguments isn't about the evolution of processes that aid adaptation. I'm sure very few people here have any problem with the CRISPR papers. The problems stem from your interpretation of Shapiro's comments as supporting direction and planning.
--Percy

This message is a reply to:
 Message 671 by shadow71, posted 07-04-2011 12:15 PM shadow71 has replied

Replies to this message:
 Message 685 by shadow71, posted 07-05-2011 5:04 PM Percy has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 680 of 760 (622596)
07-05-2011 10:10 AM
Reply to: Message 679 by zi ko
07-05-2011 8:54 AM


Re: Answers
zi ko writes:
What are the data for this random trial and error procedure?
This is a reference to evolution. Evolution by means of descent with modification and natural selection is a trial and error process. Trials are performed on random modifications, selection weeds out the "errors".
--Percy

This message is a reply to:
 Message 679 by zi ko, posted 07-05-2011 8:54 AM zi ko has replied

Replies to this message:
 Message 681 by zi ko, posted 07-05-2011 11:21 AM Percy has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 682 of 760 (622614)
07-05-2011 12:30 PM
Reply to: Message 681 by zi ko
07-05-2011 11:21 AM


Re: Answers
zi ko writes:
Are there ny data that exclude any information participation in procedure of evolution?
When scientists purposefully omit data from consideration in order to promote their own personal agenda they're always very careful to make sure it can't be detected.
Seriously, an information theoretic perspective is just one among many, and it isn't often the best one. For most problems in evolutionary theory, approaching them at the information theoretic level would be like calculating the path of a rolling ball through an analysis at the atomic level.
I share your fascination with information theory, but it isn't the best solution for every problem.
--Percy

This message is a reply to:
 Message 681 by zi ko, posted 07-05-2011 11:21 AM zi ko has not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 691 of 760 (622666)
07-05-2011 9:14 PM
Reply to: Message 685 by shadow71
07-05-2011 5:04 PM


Re: Natural Engineering
shadow71 writes:
Obviously I cannot prove that, nor can you disprove it.
Hypotheses that can't be proved or disproved, i.e., cannot be tested, are not science.
WK brought out a good point, that while CRISPR spacer insertion results in beneficial mutations, it also results in many non-beneficial mutations. Those bacteria receiving the beneficial mutations become better represented in later generations. Throwing spacers at random in and around the proximal point of gene loci is better than completely random mutations of any type anywhere, but doesn't in any way resemble an intelligent designer personally splicing the spacers in at precisely the right place. It much more resembles what a process of trial and error might come up with as a modest improvement over completely random. In other words, CRISPR spacer insertion is a Rube Goldberg kind of device, not an elegant design carefully rendered by an intelligent designer.
--Percy

This message is a reply to:
 Message 685 by shadow71, posted 07-05-2011 5:04 PM shadow71 has not replied

Replies to this message:
 Message 692 by Wounded King, posted 07-06-2011 4:54 AM Percy has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 693 of 760 (622723)
07-06-2011 7:34 AM
Reply to: Message 692 by Wounded King
07-06-2011 4:54 AM


Re: Random or not?
Wounded King writes:
Throwing spacers at random in and around the proximal point of gene loci is better than completely random mutations of any type anywhere
Just to clarify, I don't think the insertion site into the bacterial genome is as non-specific as you seem to be making out here...
I think I arrived at that interpretation after reading things like this in the paper (The CRISPR system: small RNA-guided defense in bacteria and archaea): "In each case, as predicted by evolutionary analyses, the insertion(s) occurred proximal to the leader." The paper uses the word "proximal" a lot, and I interpreted that to mean that insertion is not at a very specific point, but at a point near a very specific point, i.e., the leader.
The excerpt you quoted from Al-Attar et al., 2011 seems to be saying somewhat the same thing: "...suggested that proto-spacers are integrated into the CRISPR array randomly and irrespective of strand polarity (Shah et al., 2009; Mills et al., 2010). Similar findings were also made in Escherichia and Salmonella (Touchon and Rocha, 2010)."
I grant the ambiguity, and I'm aware of my greater potential for drawing incorrect conclusions in a field where I'm a foreigner, but my interpretation is also consistent with what we know of evolution and life itself as a messy and error-prone process.
--Percy
Edited by Percy, : Add forgotten parenthesis, add a clarifying leading clause to the last sentence.

This message is a reply to:
 Message 692 by Wounded King, posted 07-06-2011 4:54 AM Wounded King has replied

Replies to this message:
 Message 694 by Wounded King, posted 07-06-2011 8:48 AM Percy has seen this message but not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 708 of 760 (622956)
07-07-2011 2:29 PM
Reply to: Message 705 by shadow71
07-07-2011 1:28 PM


Re: Natural Engineering
sahdow71 writes:
Do you disagree with the findings that the CRISPR System discussed in the paper is dedicated, nonrandom and beneficial?
You must have this posted permanently on your clipboard for quick pasting into messages. There are parrots and broken records less annoying.
WK and I (okay, okay, mostly WK) posted some fairly technical information and some interpretation, maybe we could, oh, I don't know, discuss it?
--Percy

This message is a reply to:
 Message 705 by shadow71, posted 07-07-2011 1:28 PM shadow71 has replied

Replies to this message:
 Message 711 by shadow71, posted 07-08-2011 4:03 PM Percy has seen this message but not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 717 of 760 (623307)
07-09-2011 9:43 AM
Reply to: Message 715 by shadow71
07-09-2011 8:59 AM


Re: Definition of Evolution
Hi Shadow71,
WK just said this in the message prior to yours:
WK writes:
So if you want to actually discuss the CRISPR system nothing is stopping you, but you seem once again simply to tell us what other people have said and rely on that to carry your argument.
It's ironic that the very next message is you once again quoting someone.
Instead of you polling us over and over again about whether we agree with this quote or that quote, perhaps you could present evidence and argument supporting the quote and then discuss the answers.
--Percy

This message is a reply to:
 Message 715 by shadow71, posted 07-09-2011 8:59 AM shadow71 has replied

Replies to this message:
 Message 719 by shadow71, posted 07-09-2011 9:51 AM Percy has seen this message but not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 723 of 760 (623427)
07-10-2011 10:35 AM
Reply to: Message 722 by zi ko
07-10-2011 9:56 AM


Re: Definition of Evolution
zi ko writes:
Ithink this interacting means information flow from parasite to the host. Doesn't it lead to my information theory?
You have an idea in your head that you think is information theory, but you do not yourself have an information theory, and you haven't yet acquainted yourself with the information theory used by people in that field, the one initiated by Claude Shannon.
--Percy
Edited by Percy, : Typo.

This message is a reply to:
 Message 722 by zi ko, posted 07-10-2011 9:56 AM zi ko has replied

Replies to this message:
 Message 724 by zi ko, posted 07-10-2011 2:33 PM Percy has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 726 of 760 (623466)
07-10-2011 6:17 PM
Reply to: Message 724 by zi ko
07-10-2011 2:33 PM


Re: Definition of Evolution
zi ko writes:
I think it is entirely different thing. Idont call my theory information theory , but theory of evolution based on information.
I was going to suggest that you propose a new thread. Then I read WK's message, and he has noticed that you're trying to shift discussion onto this topic in three different threads, so now I think that proposing a new thread is an even better idea. You can do that over in Proposed New Topics.
--Percy

This message is a reply to:
 Message 724 by zi ko, posted 07-10-2011 2:33 PM zi ko has not replied

Replies to this message:
 Message 727 by Wounded King, posted 07-10-2011 6:35 PM Percy has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 728 of 760 (623473)
07-10-2011 7:39 PM
Reply to: Message 727 by Wounded King
07-10-2011 6:35 PM


Re: Definition of Evolution
Sorry, I researched it as much as I had time for.
--Percy

This message is a reply to:
 Message 727 by Wounded King, posted 07-10-2011 6:35 PM Wounded King has not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 731 of 760 (624300)
07-17-2011 6:32 AM
Reply to: Message 730 by zi ko
07-16-2011 11:14 AM


Re: Zi Ko's definition of information
You don't define information here, and when requested to do so you refer us to your webpage where you also don't define information.
Just as here, you're still confusing information with knowledge.
Why can't you just use Shannon information?
--Percy

This message is a reply to:
 Message 730 by zi ko, posted 07-16-2011 11:14 AM zi ko has replied

Replies to this message:
 Message 732 by zi ko, posted 07-17-2011 9:50 AM Percy has replied

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