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Author Topic:   Does the Darwinian theory require modification or replacement?
shadow71
Member (Idle past 2934 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 652 of 760 (622453)
07-03-2011 9:41 AM
Reply to: Message 618 by JonF
06-25-2011 6:00 PM


Re: Changing to another undefined term doesn't really help
Shadow71 writes:
I cannot accept that these functions are randomly performed
JonF writes:
Reality is not affected by what you can or cannot accept.
Please read my message 643 where I present proof of dedicated, nonrandom, beneficial change and tell me if that is reality.

This message is a reply to:
 Message 618 by JonF, posted 06-25-2011 6:00 PM JonF has replied

Replies to this message:
 Message 661 by JonF, posted 07-03-2011 1:16 PM shadow71 has replied

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


Message 653 of 760 (622454)
07-03-2011 9:45 AM
Reply to: Message 619 by AZPaul3
06-25-2011 10:15 PM


Re: Natural Engineering
AZPaul3 writes:
Shapiro's natural genetic engineering is based upon a process that relies on escalating random mutation at the genome based upon a biochemical cascade from an outside stimulus to a specific locus in the genome developed over billions of years of intra-cellular trial-and-error (read mutation and selection).
Shapiro's natural genetic engineering is based upon a process that you seem hell-bent to misrepresent.
If Shapiro and Wright and Pigliucci are right then these unplanned natural mechanisms will become additional vectors of hereditary change within the Theory of Evolution. Descent with modification, random mutation and natural selection, will not have been overturned.
In message 643 I present evidence of dedicated, nonrandom, beneficial change. Do acknowledge that the papers show that?
What if any effect does this proof have on the modification of the MS?
Finally, am I misrepresenting Shapiro in message 643?

This message is a reply to:
 Message 619 by AZPaul3, posted 06-25-2011 10:15 PM AZPaul3 has replied

Replies to this message:
 Message 655 by Percy, posted 07-03-2011 9:54 AM shadow71 has replied
 Message 676 by AZPaul3, posted 07-04-2011 6:29 PM shadow71 has replied

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


Message 654 of 760 (622455)
07-03-2011 9:52 AM
Reply to: Message 621 by Percy
06-26-2011 8:38 AM


Re: More misrepresentation.
Percy writes:
Again: modifications to evolution and/or genetics would not have any impact on the modern synthesis. The modern synthesis combines the two fields and evolution and genetics, and so it automatically includes all new developments in those fields.
In message 643 I presented papers showing dedicated, nonrandom, beneficial change.
Do you consider these findings consistent within the Modern Synthesis?
If so would you agree that the MS does not rule out a planned process?

This message is a reply to:
 Message 621 by Percy, posted 06-26-2011 8:38 AM Percy has replied

Replies to this message:
 Message 663 by Percy, posted 07-04-2011 6:48 AM shadow71 has seen this message but not replied

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


Message 656 of 760 (622458)
07-03-2011 10:09 AM
Reply to: Message 655 by Percy
07-03-2011 9:54 AM


Re: Natural Engineering
Percy writes:
Could you read the article and quote those portions you think are describing "dedicated, nonrandom, beneficial change"?
In message 643 I stated that Shapiro in his book cited these 2 papers as evidence of "dedicated, nonrandom, beneficial change."
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.
The CRISPR system is an elegant, effective, and fluid mechanism of defense against foreign genetic elements (Fig. 4). It is rightly described as an adaptive immune system, which evolved long before its famed namesake. Interestingly, CRISPR's ability to acquire a resistance phenotype and pass it to progeny could be construed an example of a soft, or Lamarckian, mode of inheritance. One could also view this from a conventional Darwinian perspective, where pressure exerted by the environment simply selects the fittest. However, armed with knowledge of the molecular basis of this response, CRISPR-cas does seem to fit more firmly with a Lamarckian paradigm, in essence because increases in fitness do not rely on random mutations but on a much more specific acquisition of genetic information from environmental sources.

This message is a reply to:
 Message 655 by Percy, posted 07-03-2011 9:54 AM Percy has replied

Replies to this message:
 Message 657 by jar, posted 07-03-2011 10:14 AM shadow71 has replied
 Message 660 by Percy, posted 07-03-2011 11:46 AM shadow71 has replied

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


Message 658 of 760 (622462)
07-03-2011 10:40 AM
Reply to: Message 657 by jar
07-03-2011 10:14 AM


Re: Natural Engineering
jar writes:
Please point out where your quote
mentions "dedicated, nonrandom, beneficial change"?
"..., CRISPR-cas does seem to fit more firmly with a Lamarckian paradigm, in essence because increases in fitness do not rely on random mutations but on a much more specific acquisition of genetic information from environmental sources."
Dedicated =specific acquistion of genetic information.
nonrandom=do not rely on random mutations.
beneficial= inceases in fitness.

This message is a reply to:
 Message 657 by jar, posted 07-03-2011 10:14 AM jar has replied

Replies to this message:
 Message 659 by jar, posted 07-03-2011 10:53 AM shadow71 has replied

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


Message 669 of 760 (622511)
07-04-2011 11:28 AM
Reply to: Message 659 by jar
07-03-2011 10:53 AM


Re: Natural Engineering
jar writes:
Does the term "dedicated, nonrandom, beneficial change" appear in your quote.
A simple yes or no should suffice.
Do you disagree that the CRISPR System they discuss in the paper, are in the authors opinion dedicated, nonrandom, and beneficial?

This message is a reply to:
 Message 659 by jar, posted 07-03-2011 10:53 AM jar has replied

Replies to this message:
 Message 670 by jar, posted 07-04-2011 11:45 AM shadow71 has seen this message but not replied

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


Message 671 of 760 (622514)
07-04-2011 12:15 PM
Reply to: Message 660 by Percy
07-03-2011 11:46 AM


Re: Natural Engineering
Percy writes:
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."
I read the other paper I linked in my message. I understand what they are saying about the highly adaptive resistance mechanisms that recognize and destroy the invader. I understand they are saying they are nonrandom and beneficial.
So I assumed Shapiro would not misrepresent the other paper he cited. Do you disagree with the findings that the CRISPR System they discuss is a dedicated, nonrandom and beneficial system?
I have read all or most of Shapiro's papers and his new book. I understand his biological findings, even though if I were to look at them microscopically I would not know what I was looking at. I am not a biologist, but I can read and understand what the authors are saying about their findings.
I read many papers and books about the theory of evolution by all the major supporters of their particular interpretation. After all my reading I concluded that evolution could not be an accidental, random process guided by natural selection as per Dawkins, Coyne et. al.
I read the IDs papers and didn't accept the fact that it was a Science that should be taught in the schools, but their philosphy made sense to me.
I then read Shapiro and, by the way, he is not an Idealogue, not an ID proponent. He sets out his findings, explains what they mean w/o resorting to teleology.
I am of the opinion that Shaprio is a very qualifed expert in this field and his findings make sense to me. So from his papers and book it is my opinion that Evolution is a planned created process, just as an atheist such as Dawkins finds it is a accidental process which happens to agree with his Atheism.
Could Dawkins ever find or believe that evolultion was planned? So he doing what you say I am doing. Intrepreting his findngs to agree with his belief.
Percy writes:
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.
I do understand his findings as he told me in the e-mail answers I posted.
Many people on this board will never accept the findings of the CRISPR papers and other findings that lead to dedicated, nonrandom, beneficial changes.
That does not conform to their belief.
Percy writes:
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."
This was also my intrepretation after I read Shapiro's book, read the Karginov and Hannon paper and looked at the Abstract I linked.
That the process developed over time through descent, modification and selection I have no problem with.
After accepting these findings I believe we should think about how this could happen.
Is it totally accidental and random?
Is it planned?
Does it operate like an Engineered system as Shapiro states?
Which is more logical?
I go with planned, am I wrong ,and if so ,what is the basis for the opinion I am wrong?

This message is a reply to:
 Message 660 by Percy, posted 07-03-2011 11:46 AM Percy has replied

Replies to this message:
 Message 674 by Percy, posted 07-04-2011 2:07 PM shadow71 has replied
 Message 701 by Taq, posted 07-07-2011 11:25 AM shadow71 has replied

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


Message 672 of 760 (622517)
07-04-2011 12:30 PM
Reply to: Message 661 by JonF
07-03-2011 1:16 PM


Re: Changing to another undefined term doesn't really help
JonF writes:
The information in the paper you linked to appears to me to be reality. It is not anything that challenges the modern synthesis, or that is evidence of directed mutation or directed evolution.
Karginov & Hannon," The CRISPR system: small RNA-guided defense in bacteria and archaea" writes:
Perhaps the most important difference is that CRISPR seems dedicated to protection against exogenous invaders, whereas the piRNA pathway is tasked to recognize endogenous parasites.
The authors believe it is directed mutation.

This message is a reply to:
 Message 661 by JonF, posted 07-03-2011 1:16 PM JonF has not replied

Replies to this message:
 Message 673 by jar, posted 07-04-2011 12:33 PM shadow71 has seen this message but not replied

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


Message 684 of 760 (622636)
07-05-2011 4:55 PM
Reply to: Message 646 by Taq
06-30-2011 5:09 PM


Re: Pretty much an irrelevant question.
Taq writes:
If which mutations are nonrandom? If 99.999% of mutations are random with a few examples of specialized systems that insert viral DNA into palindromic sequences would the entire theory need to be rewritten, or would a footnote do?
I take it you agree that the papers Shapiro referred to in his book and I cited on this board re CRISPR System is a process of nonrandom mutations for fitness.
If so does this process fit into the theory of evolution as it is known today?

This message is a reply to:
 Message 646 by Taq, posted 06-30-2011 5:09 PM Taq has not replied

Replies to this message:
 Message 689 by Wounded King, posted 07-05-2011 5:38 PM shadow71 has not replied

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


Message 685 of 760 (622638)
07-05-2011 5:04 PM
Reply to: Message 674 by Percy
07-04-2011 2:07 PM


Re: Natural Engineering
Percy writes:
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.
What I am saying is that the whole process of evolution may in fact be planned.
Obviously I cannot prove that, nor can you disprove it.
But if in fact the process of evolution is planned then it still can be a natural process, planned by a Supernatural being.

This message is a reply to:
 Message 674 by Percy, posted 07-04-2011 2:07 PM Percy has replied

Replies to this message:
 Message 686 by Straggler, posted 07-05-2011 5:20 PM shadow71 has not replied
 Message 688 by jar, posted 07-05-2011 5:29 PM shadow71 has not replied
 Message 691 by Percy, posted 07-05-2011 9:14 PM shadow71 has not replied

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


Message 687 of 760 (622641)
07-05-2011 5:21 PM
Reply to: Message 676 by AZPaul3
07-04-2011 6:29 PM


Re: Natural Engineering
AZPaul3 writes:
The mechanism appears to be specific to specific classes of pathogens and thus can be called dedicated. The evolved processes have been developed and put in place by random trial and error over many millions of years and are thus now non-randomly invoked by the presence of the specific pathogens.
Not trying to be a jerk, but can you show by data that the processes have been developed and put in place by RANDOM TRIAL AND ERROR over many millions of years and are thus now nonrandomly invoked by the presence of the specific pathogens?
Or is this merely the assumption that that is how evolution works?
It seems to me to be a contradiction that the presence of specific pathogens would suddenly lead to a nonrandom process.

This message is a reply to:
 Message 676 by AZPaul3, posted 07-04-2011 6:29 PM AZPaul3 has replied

Replies to this message:
 Message 690 by AZPaul3, posted 07-05-2011 6:00 PM shadow71 has not replied

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


Message 697 of 760 (622852)
07-06-2011 7:37 PM


Towards a new evolutinary theory
We have discussed Pigluicci's ES paper and he concludes that the theory of evolution does not need a new paradigm. Here is a paper entitled:
"Towards a New Evolutionary Theory" by Julio E Perez, Carmen Alfonsi & Carlos Muflioz who come to a different conclusion from Pigluicci while discussing mostly the same processes not addressed in the MS.
here is the link:
Interciencia – Revista Interciencia
Here is the conclusion that I throw out for discussion.
Perez et. al. writes:
Though widely accepted as the official scientific explanation for evolution, exerting great influence on both our interpretation of biodiversity and our understanding of the world, modern synthesis lacks some major elements, to wit: endosymbiosis, reticulate evolution, the modern synthesis of embryonic development and evolution (evo-devo), epigenesis, phenotypic plasticity, evolvability; which involve several evolutionary mechanisms such as: fusion of genomes and gene fragments, methylation of DNA, tool kits, regulatiory cis-elements, hybridization and polyploidy. It is also necessary to include different sources of genetic variation, not only mutations. All this knowledge underscores the necessity to develop a new evolutionary theory, a coherent alternative to modern synthesis.
Evolution can occur incrementally through small changes (genetic drift and natural selection) or abruptly through hybridization, endosymbiosis, and changes in gene regulation. The environment plays an important role in the evolution of organisms, through epigenesis. Current knowledge allows for the rejection of the central dogma of biology. Although it seems that the study of macroevolution is not an extrapolation and magnification of the events that occur within populations and species, these events cannot be decoupled, since the population in which macroevolution occurs is the same population that evolves at the microevolutionary level.
Evolutionary innovations do not seem to arise at random; on the contrary, they seem to have originated from non-random processes based on the epigenetic system. As a consequence of these developments, especially that of epigenetic inheritance, a new and wider definition of evolution seems necessary, one that would be the result of several mechanisms that change both the genetic and epigenetic compositions of populations.
The integration of evo-devo with the synthetic theory seems difficult or impossible. The synthetic theory is based mainly on population dynamics, on the correlation of phenotypic variation with statistical gene frequencies in populations, whereas evo-devo explains phenotypic change through alterations in developmental mechanisms, whether they are adaptive or not.
As a final conclusion, we think that a new evolutionary theory is needed.
Any opinions on whether these scientists are correct or Pigluicci is correct. Does the MS include the issues mentioned here as part of what Percy says is Darwin + genetics? Or does the theory of evolution need a modficaton, a new paradigm, that includes and explains:
Endosymbiosis
Reticulate evolution
Embryonic devopment and evo-devo
epigenesis
Phenotypic plasticity
Evolvability etc.?
Edited by Admin, : Fix formatting.

Replies to this message:
 Message 698 by Dr Adequate, posted 07-06-2011 10:48 PM shadow71 has not replied
 Message 703 by Taq, posted 07-07-2011 11:38 AM shadow71 has seen this message but not replied
 Message 704 by molbiogirl, posted 07-07-2011 11:40 AM shadow71 has replied

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


Message 705 of 760 (622944)
07-07-2011 1:28 PM
Reply to: Message 701 by Taq
07-07-2011 11:25 AM


Re: Natural Engineering
Taq writes:
Do you disagree that the CRISPR system only produces mutations within the CRISPR DNA? Do you also agree that eukaryotes like ourselves lack CRISPR regions?
I have no basis to disagree with those statements. But I understand the CRISPR Systems were not discovered until apporx 1987.
There is now more research in the area, so perhaps new discoveries will be forthcoming.
Do you disagree with the findings that the CRISPR System discussed in the paper is dedicated, nonrandom and beneficial?
--------------------------------------------------------------------------------

This message is a reply to:
 Message 701 by Taq, posted 07-07-2011 11:25 AM Taq has replied

Replies to this message:
 Message 708 by Percy, posted 07-07-2011 2:29 PM shadow71 has replied
 Message 709 by Taq, posted 07-08-2011 12:05 AM shadow71 has replied

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


Message 706 of 760 (622946)
07-07-2011 1:31 PM
Reply to: Message 704 by molbiogirl
07-07-2011 11:40 AM


Re: You're really reaching now
molbiogirl writes:
And a paper that hasn't been cited? At all? Ever?
By an author whose paper The Risks of Tilapia Culture in Venuzeula got more cites than the paper you quoted?
By an author who, in nearly 30 years of publishing, manages, at best, 2 cites for one of his papers on aquaculture?
Way to pick em, dude.
Do you have any criticisms of the science in the paper?

This message is a reply to:
 Message 704 by molbiogirl, posted 07-07-2011 11:40 AM molbiogirl has replied

Replies to this message:
 Message 707 by molbiogirl, posted 07-07-2011 2:17 PM shadow71 has replied

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


Message 710 of 760 (623211)
07-08-2011 3:55 PM
Reply to: Message 707 by molbiogirl
07-07-2011 2:17 PM


Re: You're really reaching now
molbiogirl writes:
There is no science in the paper. It's a review.
Do you have any criticisms of his interpretation and review of the biology he discuses?

This message is a reply to:
 Message 707 by molbiogirl, posted 07-07-2011 2:17 PM molbiogirl has replied

Replies to this message:
 Message 712 by molbiogirl, posted 07-08-2011 4:07 PM shadow71 has not replied

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