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Author Topic:   Does the Darwinian theory require modification or replacement?
Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 631 of 760 (621639)
06-27-2011 4:40 PM
Reply to: Message 607 by zi ko
06-25-2011 11:03 AM


Re: Pretty much an irrelevant question.
Shapiro treats the matter very serioucly and scientifically.He does'nt give any Teleology meaning in his nonrandomness.

They way you treat Shapiro's work is not serious and seriously unscientific. I even spent an hour or so reading through a Wright paper that you suggested, and then you refused to discuss the particlulars with me. In that paper I demonstrated that the mutations cited by Wright are in fact random with respect to fitness.

Also, you need to define what is nonrandom. Cite a specific mechanism that Shapiro discusses, and then show how it is nonrandom with respect to fitness.


This message is a reply to:
 Message 607 by zi ko, posted 06-25-2011 11:03 AM zi ko has responded

Replies to this message:
 Message 632 by zi ko, posted 06-28-2011 12:54 PM Taq has responded

zi ko
Member (Idle past 1701 days)
Posts: 578
Joined: 01-18-2011


Message 632 of 760 (621724)
06-28-2011 12:54 PM
Reply to: Message 631 by Taq
06-27-2011 4:40 PM


Sorry . I didn't intent to.
As i have said in other thread i can accept mutation randomness in respect to fitness. But as other mechanisms previous in time to mutation lead to somehow in directed by environment random mutations, or propably to other type of genome altering(engineering systems, HGT ) then the result can be what we say as function driven evolution.


Information: It is time its undeservedly neglectet powerful role to evolution to be restored.
This message is a reply to:
 Message 631 by Taq, posted 06-27-2011 4:40 PM Taq has responded

Replies to this message:
 Message 633 by Taq, posted 06-28-2011 2:51 PM zi ko has not yet responded

  
Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 633 of 760 (621746)
06-28-2011 2:51 PM
Reply to: Message 632 by zi ko
06-28-2011 12:54 PM


As i have said in other thread i can accept mutation randomness in respect to fitness.

Since the Modern Synthesis proposes that mutations are random with respect to fitness would you also agree that the theory does not need modification or replacement?

But as other mechanisms previous in time to mutation lead to somehow in directed by environment random mutations, or propably to other type of genome altering(engineering systems, HGT ) then the result can be what we say as function driven evolution.

Where in the Modern Synthesis does it state that all cellular mechanisms must be undirected?


This message is a reply to:
 Message 632 by zi ko, posted 06-28-2011 12:54 PM zi ko has not yet responded

shadow71
Member (Idle past 1015 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 634 of 760 (621762)
06-28-2011 7:47 PM
Reply to: Message 603 by zi ko
06-24-2011 4:29 AM


Re: Puzzled
ziko writes:


I agree. All recent fidings in evolution biology tent to support this view.but this does not mean that we have to accept inevitably Supernatural interfearence. It can be other evolutional mechanisms than could "make the decisions",as e.g Neural System, (www.sleepgadgetabs.com) in metazoa with neural tissue, or engineering systems and maybe other systems yet unkown ,in bacteria.

I agree with your statement that nonrandom mutation does not necessarily mean Creation by a Supernatural being. My point is that to state absoutely that all mutations are random for fitness is dogmatic and not provable.


This message is a reply to:
 Message 603 by zi ko, posted 06-24-2011 4:29 AM zi ko has not yet responded

Replies to this message:
 Message 637 by Taq, posted 06-28-2011 8:16 PM shadow71 has acknowledged this reply

  
shadow71
Member (Idle past 1015 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 635 of 760 (621763)
06-28-2011 7:59 PM
Reply to: Message 606 by Taq
06-24-2011 11:24 AM


Re: Changing to another undefined term doesn't really help
Taq writes:


The mutations that Shapiro talks about are random with respect to fitness as I have pointed out time after time. On top of that, these random mutations are subject to selection. How could they not be? Can you point to any paper written by Shapiro where detrimental mutations are passed on at the same rate as beneficial mutations?

Here is a quote from Shapiro's book "Evolution, A View from the 21st Century"

James A. Shapiro writes:

A Major assertion of many traditional thinkers about evolution and mutation is that living cells cannot make specific, adaptive use of their natural genetic engineering capacities. They make this assertion to protect their view of evolution as the product of random, undirected genome changes. But their position is philosophical, not scientific, nor is it based on empirical observations."

He goes on to give examples of cells that can integrate processes of genome restructuring to serve adaptive needs in normal life cycles. He states there is no scientific basis on which to argue cells cannot use functional capacities to produce evolutionary novelties.

This is clearly a statement that mutations are non-random with respect to fitness.

Do you agree that mutations can be nonrandom with regard to fitness?

--------------------------------------------------------------------------------


This message is a reply to:
 Message 606 by Taq, posted 06-24-2011 11:24 AM Taq has responded

Replies to this message:
 Message 636 by Taq, posted 06-28-2011 8:13 PM shadow71 has acknowledged this reply

  
Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 636 of 760 (621764)
06-28-2011 8:13 PM
Reply to: Message 635 by shadow71
06-28-2011 7:59 PM


Re: Changing to another undefined term doesn't really help
Here is a quote from Shapiro's book "Evolution, A View from the 21st Century"

I am more interested in data found in peer reviewed scientific journals that backs what you are claiming.

He goes on to give examples of cells that can integrate processes of genome restructuring to serve adaptive needs in normal life cycles.

How is this restructuring inherited by the next generation? How is this restructuring specific to an environmental stimuli? Do bacteria produce specific mutations in specific genes in response to antibiotics, and only those mutations?

He states there is no scientific basis on which to argue cells cannot use functional capacities to produce evolutionary novelties.

You are talking past us. We agree that these "functional capacities" produce evolutionary novelties. What you seem to miss is that these functional capacities do not produce specific mutations in response to specific stimuli, and only those mutations. Rather, these functional capacities produce mutations throughout the genome and are random with respect to fitness.

Do you agree that mutations can be nonrandom with regard to fitness?

No I don't, and I have the data from peer reviewed papers to back it up. Do you?

Edited by Taq, : No reason given.


This message is a reply to:
 Message 635 by shadow71, posted 06-28-2011 7:59 PM shadow71 has acknowledged this reply

Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 637 of 760 (621765)
06-28-2011 8:16 PM
Reply to: Message 634 by shadow71
06-28-2011 7:47 PM


Re: Puzzled
I agree with your statement that nonrandom mutation does not necessarily mean Creation by a Supernatural being. My point is that to state absoutely that all mutations are random for fitness is dogmatic and not provable.

All of the data I have seen demonstrates that the mutations observed in the study were random with respect to fitness. I will gladly accept data showing otherwise. When are you going to present this data?


This message is a reply to:
 Message 634 by shadow71, posted 06-28-2011 7:47 PM shadow71 has acknowledged this reply

Replies to this message:
 Message 648 by zi ko, posted 07-01-2011 4:11 PM Taq has responded

shadow71
Member (Idle past 1015 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 638 of 760 (621902)
06-29-2011 2:18 PM
Reply to: Message 630 by Taq
06-27-2011 4:35 PM


Re: Pretty much an irrelevant question.
Shapiro's Book writes:

Because genome evolution is multilevel, amplifying, and combinatorial in nature, the end results are complex hierarchical structues with characteristic system architectures. Genomes are sophisticated data storage organelles integrated into the cellular and multicellular life cycles of each distinct organism. Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations"

Taq writes:


Can you? You are the one who keeps citing Shapiro when you claim that mutations are nonrandom. You tell us, and be specific where it concerns the supporting data.

Would you agree that Shapiro in the above quote from his book is proposing that mutations for fitness may be other than random?

If so I will cite you to his examples of non-random mutations for fitness.
If not we should agree to disagree.


This message is a reply to:
 Message 630 by Taq, posted 06-27-2011 4:35 PM Taq has responded

Replies to this message:
 Message 639 by New Cat's Eye, posted 06-29-2011 2:35 PM shadow71 has responded
 Message 640 by Taq, posted 06-29-2011 4:24 PM shadow71 has responded

  
New Cat's Eye
Inactive Member


Message 639 of 760 (621903)
06-29-2011 2:35 PM
Reply to: Message 638 by shadow71
06-29-2011 2:18 PM


Re: Pretty much an irrelevant question.
Would you agree that Shapiro in the above quote from his book is proposing that mutations for fitness may be other than random?

Yes, but it doesn't require modification or replacement of the current Theory of Evolution because it is still random with respect to fitness.

This has been explained to you for over 100's of posts over the last few months.

If so I will cite you to his examples of non-random mutations for fitness.

Cite away!


This message is a reply to:
 Message 638 by shadow71, posted 06-29-2011 2:18 PM shadow71 has responded

Replies to this message:
 Message 645 by shadow71, posted 06-30-2011 5:05 PM New Cat's Eye has responded

Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 640 of 760 (621929)
06-29-2011 4:24 PM
Reply to: Message 638 by shadow71
06-29-2011 2:18 PM


Re: Pretty much an irrelevant question.
If so I will cite you to his examples of non-random mutations for fitness.

Please do. I have asked for this multiple times. Please reference the data as it is found in the peer reviewed papers.

Added by edit at a much later time point:

You might want to use "Letting Escherichia coli Teach Me About Genome Engineering" written by Shapiro. In this essay he actually references peer reviewed papers that supposedly support his claims. Those referenced peer reviewed papers will contain the data you need.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 638 by shadow71, posted 06-29-2011 2:18 PM shadow71 has responded

Replies to this message:
 Message 643 by shadow71, posted 06-30-2011 4:42 PM Taq has responded

pandion
Member (Idle past 1081 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 641 of 760 (621998)
06-30-2011 1:38 AM


Does the Darwinian theory require modification or replacement?

The clearest and simplest answer is yes, it does.


Replies to this message:
 Message 642 by Taq, posted 06-30-2011 1:41 AM pandion has not yet responded

Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 642 of 760 (621999)
06-30-2011 1:41 AM
Reply to: Message 641 by pandion
06-30-2011 1:38 AM


Does the Darwinian theory require modification or replacement?

The clearest and simplest answer is yes, it does.

Why does it need modification or replacement? Your reply was not clear at all.


This message is a reply to:
 Message 641 by pandion, posted 06-30-2011 1:38 AM pandion has not yet responded

shadow71
Member (Idle past 1015 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 643 of 760 (622104)
06-30-2011 4:42 PM
Reply to: Message 640 by Taq
06-29-2011 4:24 PM


CRISPR/Cas, the Immune System of Bacteria and Re: Pretty much an irrelevant question.
Taq writes:


Please do. I have asked for this multiple times. Please reference the data as it is found in the peer reviewed papers.

Shapiro cites the paper below as an example of dedicated, nonrandom, beneficial change .

Another paper in re CRISPR is found at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186 which specifically says the changes are nonrandom.

CRISPR/Cas, the Immune System of Bacteria and Archaea
Philippe Horvath1,* and Rodolphe Barrangou2,*
+ Author Affiliations

1Danisco France SAS, BP10, F-86220 Dang-Saint-Romain, France.
2Danisco USA, Inc., 3329 Agriculture Drive, Madison, WI 53716, USA.
*To whom correspondence should be addressed. E-mail: philippe.horvath@danisco.com (P.H.), rodolphe.barrangou@danisco.com (R.B.)
Abstract
Microbes rely on diverse defense mechanisms that allow them to withstand viral predation and exposure to invading nucleic acid. In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner. These hypervariable loci take up genetic material from invasive elements and build up inheritable DNA-encoded immunity over time. Conversely, viruses have devised mutational escape strategies that allow them to circumvent the CRISPR/Cas system, albeit at a cost. CRISPR features may be exploited for typing purposes, epidemiological studies, host-virus ecological surveys, building specific immunity against undesirable genetic elements, and enhancing viral resistance in domesticated microbes


This message is a reply to:
 Message 640 by Taq, posted 06-29-2011 4:24 PM Taq has responded

Replies to this message:
 Message 644 by Taq, posted 06-30-2011 5:02 PM shadow71 has not yet responded

  
Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 3.1


Message 644 of 760 (622108)
06-30-2011 5:02 PM
Reply to: Message 643 by shadow71
06-30-2011 4:42 PM


Re: CRISPR/Cas, the Immune System of Bacteria and Re: Pretty much an irrelevant question.
Shapiro cites the paper below as an example of dedicated, nonrandom, beneficial change .

This is perfect. This is the exception that proves the rule.

The paper you cited was not available for free, so I would direct your attention to this paper:

http://www.biochemj.org/bj/imps/pdf/BJ20110901.pdf

It is the same system you are pointing to, and it details the molecular mechanisms that produce the mutations.

In this case, we have an entire operon devoted to inserting phage DNA into a specific area of the genome. I will gladly accept this example as directed mutations.

The problem, however, is that an entire set of proteins is devoted to specifically mutating this section of DNA, and it is very specialized. What you have pointed out is the very reason that random mutations are so prevalent in evolving organisms. How large would the bacterial genome need to be in order to guide mutations for the entire genome? For each protein devoted to guiding mutations you also need another set of proteins devoted to mutating that protein, and so forth.

Also, is the CRISPR system important for anything other than phage resistance? Nope. This system does not guide mutations for the evolution of new enzymes involved in metabolism, for example. On top of that, this system is not seen in eukaryotes.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 643 by shadow71, posted 06-30-2011 4:42 PM shadow71 has not yet responded

shadow71
Member (Idle past 1015 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 645 of 760 (622109)
06-30-2011 5:05 PM
Reply to: Message 639 by New Cat's Eye
06-29-2011 2:35 PM


Re: Pretty much an irrelevant question.
Catholic Scientist writes:


Yes, but it doesn't require modification or replacement of the current Theory of Evolution because it is still random with respect to fitness.

Cite away!

There are 2 cites in my message 643 in reply to Taq.

If in fact mutations are nonrandom with respect to fitness, would you consider that the theory as we know it today needs modification?


This message is a reply to:
 Message 639 by New Cat's Eye, posted 06-29-2011 2:35 PM New Cat's Eye has responded

Replies to this message:
 Message 646 by Taq, posted 06-30-2011 5:09 PM shadow71 has responded
 Message 647 by New Cat's Eye, posted 06-30-2011 5:19 PM shadow71 has acknowledged this reply

  
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