Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 155 (8122 total)
Current session began: 
Page Loaded: 09-19-2014 9:54 PM
125 online now:
JonF, Percy (Admin) (2 members, 123 visitors)
Chatting now:  Chat room empty
Newest Member: taiji2
Happy Birthday: AdminPhat
Post Volume:
Total: 736,248 Year: 22,089/28,606 Month: 1,176/1,410 Week: 378/524 Day: 45/36 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Prev1
2
3456
...
51NextFF
Author Topic:   Does the Darwinian theory require modification or replacement?
NoNukes
Member
Posts: 5284
From: Central NC USA
Joined: 08-13-2010
Member Rating: 1.6


Message 16 of 760 (609100)
03-16-2011 3:55 PM
Reply to: Message 11 by shadow71
03-16-2011 1:50 PM


Puzzled
shadow71 writes:

he difference is that these are driven by information in the cell, not by purely mechanical processes.

'Driven' implies way more determinism than Shapiro suggests. Non random is not the opposite of completely determined by. Is Shapiro saying anything more that that some mutations may have a greater likelihood than others? Does that even translate to a greater likelihood of a beneficial mutation occurring relative to a given environment.

And is even this observation meaningful unless there link between an outside stimulus and a mutation. In particular how might that work for macroscopic animals?. How would either being eaten or not being eaten by a saber-tooth tiger stimulate a non random beneficial mutation based on information in a reproductive cell.


This message is a reply to:
 Message 11 by shadow71, posted 03-16-2011 1:50 PM shadow71 has responded

Replies to this message:
 Message 22 by shadow71, posted 03-16-2011 5:08 PM NoNukes has responded

  
Taq
Member
Posts: 5219
Joined: 03-06-2009
Member Rating: 2.8


Message 17 of 760 (609102)
03-16-2011 4:29 PM
Reply to: Message 15 by slevesque
03-16-2011 3:48 PM


Yeah well I perfectly understand that, I was just saying that hypothetically speaking, what shadow71 proposes would entails a drastic revision, not simply 'details'

At this point, such observations would be limited to very special cases. Is it possible that there is a very rare bacteria, found in the soil of southern Italy, that changes one base in one gene in response to the presence of a phosphorylated protein released by another very rare fungus? I suppose this is possible, but once again this would be a very special case. It is not the norm. Experiment after experiment has demonstrated random mutation for a very wide variety of mechanisms, even those spoken of by Shapiro.

So would finding a few specific and special cases of guided mutation throw out all of the mountains of data demonstrating random mutation? I would say no. The special cases are footnotes. Even comparisons of genomes demonstrates different rates of synonymous to non-synonymous changes, hallmarks of random mutation and selection. Do we throw out a theory that describes 99.99999% of the evolutionary history of genomes because that 0.00001% is guided by environment? Again, I would say no.


This message is a reply to:
 Message 15 by slevesque, posted 03-16-2011 3:48 PM slevesque has responded

Replies to this message:
 Message 20 by slevesque, posted 03-16-2011 4:52 PM Taq has not yet responded

shadow71
Member
Posts: 704
From: Joliet, il, USA
Joined: 08-31-2010


Message 18 of 760 (609103)
03-16-2011 4:42 PM
Reply to: Message 8 by Taq
03-16-2011 11:18 AM


taq writes;

Should the Modern Synthesis change? Of course. It has not stopped changing in the last 70 years. It will continue to change. It has to change. Will we need to chuck the theory altogether? No one has found a reason to yet. The fundamentals of the theory are still widely accepted: mutations are blind to fitness and natural selection is blind to sequence and design. Even Shapiro agrees with this fundamental tenet of the Modern Synthesis. The rest are just details which do change over time.

Here is where I have a hard time with Shapiro. In the following quote from www.mobilednajournal.com/content/1/1/4 he writes :

Although there remain many gaps in our knowledge, we are now in a position to outline a distinctively 21st century scenario for evolutionary change. The scenario includes the following elements:

(1) hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering;

((3) ecologically-triggered cell and genome restructurings produce organisms which, at some frequency, will possess novel adaptive features that suit the altered environment. Novel adaptive features can be complex from the beginning because they result from processes that operate on pre-existing functional systems, whose components can be amplified and rearranged in new combinations. Competition for resources (purifying selection) serves to eliminate those novel system architectures that are not functional in the new ecology;

(4) once ecological stability has been achieved, natural genetic engineering functions are silenced, the tempo of innovation abates, and microevolution can occur to fine-tune recent evolutionary inventions through successions of minor changes.

It appears to me that he is saying that the suddent abrupt changes are nonrandom and performed by natural genetic engineering. Once that is finished then micro evolution, ie Darwinian evolution takes over.

Note he says "a distinctively 21st century scenario for evolutionary change."


This message is a reply to:
 Message 8 by Taq, posted 03-16-2011 11:18 AM Taq has responded

Replies to this message:
 Message 21 by Taq, posted 03-16-2011 5:01 PM shadow71 has acknowledged this reply

  
shadow71
Member
Posts: 704
From: Joliet, il, USA
Joined: 08-31-2010


Message 19 of 760 (609104)
03-16-2011 4:52 PM
Reply to: Message 13 by jar
03-16-2011 2:22 PM


Re: Pretty much an irrelevant question.
jar writes;

If and when there is enough evidence for others to take Shapiro seriously, it's possible that the Theory will change again, but never to the extent that Intelligent Design or Special Creation will be more than stuff to laugh about.

He is talking about natural genetic engineering that is nonrandom as I point out in reply to message 8 by taq.

If in fact the theory does change in accord with Shapiro and others who are researching about a 21st century theory of evolution that does not rely on random mutation, but rather information in the cell that engineers change then Special Creation will become something that Science will have to deal with.


This message is a reply to:
 Message 13 by jar, posted 03-16-2011 2:22 PM jar has responded

Replies to this message:
 Message 25 by jar, posted 03-16-2011 6:12 PM shadow71 has responded
 Message 27 by Dr Adequate, posted 03-16-2011 8:53 PM shadow71 has acknowledged this reply
 Message 473 by zi ko, posted 05-02-2011 9:55 AM shadow71 has not yet responded

  
slevesque
Member (Idle past 1072 days)
Posts: 1456
Joined: 05-14-2009


Message 20 of 760 (609105)
03-16-2011 4:52 PM
Reply to: Message 17 by Taq
03-16-2011 4:29 PM


And I totally agree with you

I guess I hsould have bolded the 'hypothetically'


This message is a reply to:
 Message 17 by Taq, posted 03-16-2011 4:29 PM Taq has not yet responded

Taq
Member
Posts: 5219
Joined: 03-06-2009
Member Rating: 2.8


Message 21 of 760 (609107)
03-16-2011 5:01 PM
Reply to: Message 18 by shadow71
03-16-2011 4:42 PM


It appears to me that he is saying that the suddent abrupt changes are nonrandom and performed by natural genetic engineering.

All of this hinges on how Shapiro defines "nonrandom" as it relates to the process of mutation. Unfortunately, Shapiro defines random mutations as those caused by a breakdown in the replication process whereas nonrandom mutations are defined as mutations caused by transposons and genetic recombination. This is not the same type of randomness/nonrandomness that the Modern Synthesis is talking about.

IOW, Shapiro is using personal definitions for these terms.


This message is a reply to:
 Message 18 by shadow71, posted 03-16-2011 4:42 PM shadow71 has acknowledged this reply

Replies to this message:
 Message 30 by NoNukes, posted 03-17-2011 1:59 AM Taq has responded

shadow71
Member
Posts: 704
From: Joliet, il, USA
Joined: 08-31-2010


Message 22 of 760 (609109)
03-16-2011 5:08 PM
Reply to: Message 16 by NoNukes
03-16-2011 3:55 PM


Re: Puzzled
NoNukes writes;

'Driven' implies way more determinism than Shapiro suggests. Non random is not the opposite of completely determined by. Is Shapiro saying anything more that that some mutations may have a greater likelihood than others? Does that even translate to a greater likelihood of a beneficial mutation occurring relative to a given environment.

Shapiro "Revisiting the Central Dogma in the 21st Century"

writes:

Genome System Architecture

By flexible analogy with electronic information-
processing systems, we need to recognize
that every genome has a system architecture
which makes it possible for cells to access
and utilize the information stored there. It has
been argued elsewhere that each genome serves
as a read-write (RW) memory system on multiple
time scales:24,138
1. Within the cell cycle by adjustment of
DNA binding protein complexes;
2. Over several cell cycles by chromatin reformatting;
3. Over evolutionary time by natural genetic
engineering.
As with electronic systems, different system
architecturesmay accomplish similar functions.
Thus genomes may differ in their functional
architectures from one taxonomic group to
another. The idea of genome system architecture
facilitating information utilization can
be applied to thinking about existing genomes
and also to the potential for generating novel
genomes in the face of inevitable but unpredictable
challenges.

When he talks about system architecture and read write memory systems this is not random and is as close to deterministic as you can get without using the word.


This message is a reply to:
 Message 16 by NoNukes, posted 03-16-2011 3:55 PM NoNukes has responded

Replies to this message:
 Message 23 by NoNukes, posted 03-16-2011 5:24 PM shadow71 has acknowledged this reply
 Message 24 by Taq, posted 03-16-2011 5:26 PM shadow71 has responded

  
NoNukes
Member
Posts: 5284
From: Central NC USA
Joined: 08-13-2010
Member Rating: 1.6


Message 23 of 760 (609112)
03-16-2011 5:24 PM
Reply to: Message 22 by shadow71
03-16-2011 5:08 PM


Re: Puzzled
shadow71 writes:

When he talks about system architecture and read write memory systems this is not random and is as close to deterministic as you can get without using the word.

If you could explain to me why read write memory system implies a deterministic mutation process I'd sure appreciate it. The quoted paragraph merely says that cells access stored information.

I'm familiar with the information systems Shapiro refers to in his analogy, but there is no reason to believe that mutations or errors in those system ought to occur deterministically. Where does Shapiro suggest anything more than non-random mutations?

Uh.. Never mind. I see some of the answers to my questions in the paper.

Edited by NoNukes, : Correction.


This message is a reply to:
 Message 22 by shadow71, posted 03-16-2011 5:08 PM shadow71 has acknowledged this reply

Replies to this message:
 Message 474 by zi ko, posted 05-02-2011 10:33 AM NoNukes has acknowledged this reply

  
Taq
Member
Posts: 5219
Joined: 03-06-2009
Member Rating: 2.8


Message 24 of 760 (609113)
03-16-2011 5:26 PM
Reply to: Message 22 by shadow71
03-16-2011 5:08 PM


Re: Puzzled
When he talks about system architecture and read write memory systems this is not random and is as close to deterministic as you can get without using the word.

What is not random? Chromatin binding? DNA binding complexes? Protein-DNA interactions? DNA methylation? What specifically is not random?


This message is a reply to:
 Message 22 by shadow71, posted 03-16-2011 5:08 PM shadow71 has responded

Replies to this message:
 Message 34 by shadow71, posted 03-17-2011 2:40 PM Taq has responded
 Message 475 by zi ko, posted 05-02-2011 10:45 AM Taq has not yet responded

jar
Member
Posts: 24664
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.1


Message 25 of 760 (609123)
03-16-2011 6:12 PM
Reply to: Message 19 by shadow71
03-16-2011 4:52 PM


Re: Pretty much an irrelevant question.
shadow71 writes:

jar writes;

If and when there is enough evidence for others to take Shapiro seriously, it's possible that the Theory will change again, but never to the extent that Intelligent Design or Special Creation will be more than stuff to laugh about.

He is talking about natural genetic engineering that is nonrandom as I point out in reply to message 8 by taq.

If in fact the theory does change in accord with Shapiro and others who are researching about a 21st century theory of evolution that does not rely on random mutation, but rather information in the cell that engineers change then Special Creation will become something that Science will have to deal with.

Fortunately, it is simply that you totally misunderstand what he is saying and Special Creation will never be more 5than a joke and something for Christian con men to use to keep the gold coming in.


Anyone so limited that they can only spell a word one way is severely handicapped!
This message is a reply to:
 Message 19 by shadow71, posted 03-16-2011 4:52 PM shadow71 has responded

Replies to this message:
 Message 35 by shadow71, posted 03-17-2011 2:49 PM jar has responded

Dr Adequate
Member
Posts: 12745
Joined: 07-20-2006
Member Rating: 2.3


Message 26 of 760 (609136)
03-16-2011 8:51 PM
Reply to: Message 11 by shadow71
03-16-2011 1:50 PM


The difference is that these are driven by information in the cell, not by purely mechanical processes.

This is a false dichotomy. You can talk about "information in the cell" all you want; but the fact remains that the changes are made to an actual physical sequence of DNA in accordance with the laws of chemistry.


This message is a reply to:
 Message 11 by shadow71, posted 03-16-2011 1:50 PM shadow71 has responded

Replies to this message:
 Message 37 by shadow71, posted 03-17-2011 3:05 PM Dr Adequate has not yet responded

Dr Adequate
Member
Posts: 12745
Joined: 07-20-2006
Member Rating: 2.3


Message 27 of 760 (609137)
03-16-2011 8:53 PM
Reply to: Message 19 by shadow71
03-16-2011 4:52 PM


Re: Pretty much an irrelevant question.
If in fact the theory does change in accord with Shapiro and others who are researching about a 21st century theory of evolution that does not rely on random mutation, but rather information in the cell that engineers change then Special Creation will become something that Science will have to deal with.

No it won't. One more actual known physical mechanism contributing to evolution would not be a reason to put more credence in imaginary supernatural mechanisms.


This message is a reply to:
 Message 19 by shadow71, posted 03-16-2011 4:52 PM shadow71 has acknowledged this reply

Replies to this message:
 Message 29 by Coyote, posted 03-16-2011 9:09 PM Dr Adequate has not yet responded
 Message 476 by zi ko, posted 05-02-2011 11:15 AM Dr Adequate has not yet responded

Dr Adequate
Member
Posts: 12745
Joined: 07-20-2006
Member Rating: 2.3


Message 28 of 760 (609138)
03-16-2011 9:01 PM
Reply to: Message 12 by slevesque
03-16-2011 1:52 PM


This is because you effectively touch upon one of the two basic principles.

Well no, not really.

As I explained in the last thread on this, the fact that mutations are random is actually a problem for evolution. The genius of Darwin was to realize that the law of natural selection surmounts this problem. The theory of evolution explains how evolution happens despite variation being random. It doesn't depend on the randomness, it explains how even though variation is random evolution still manages to happen.

If it turns out that some variation is Lamarckian, that's all grease to the wheels of evolution.


This message is a reply to:
 Message 12 by slevesque, posted 03-16-2011 1:52 PM slevesque has not yet responded

Coyote
Member
Posts: 4707
Joined: 01-12-2008
Member Rating: 2.2


(1)
Message 29 of 760 (609141)
03-16-2011 9:09 PM
Reply to: Message 27 by Dr Adequate
03-16-2011 8:53 PM


Re: Pretty much an irrelevant question.
Dr Adequate writes:

If in fact the theory does change in accord with Shapiro and others who are researching about a 21st century theory of evolution that does not rely on random mutation, but rather information in the cell that engineers change then Special Creation will become something that Science will have to deal with.

No it won't. One more actual known physical mechanism contributing to evolution would not be a reason to put more credence in imaginary supernatural mechanisms.


This is typical of the approach to evolution that creationists take: they latch on to any point they can stretch enough to make it appear that 1) science may be wrong, or 2) that this poor little stretched-out point supports creationism.

Creationists seem to think that if a particular point within the broad theory of evolution is revised that they come out ahead. Unfortunately for them, this is incorrect. The more the theory of evolution is poked and prodded and corrected the stronger the theory becomes! That is exactly the opposite of what they want, but they still think that by grabbing at little threads and shaking them like a terrier does a rat that they are getting somewhere.

Secondly, by stretching ideas or facts beyond all recognition (and the similar technique of making things up) they just show that they are deliberately distorting what everyone else knows to be accurate. Good examples are placing Noah's flood at 4,350 years ago and at the k-t boundary and at the Cambrian. Another is using the flood at 4,350 years ago to recalibrate radiocarbon dates to come out the way they want. Still another is claiming that residual C14 in dinosaur bones shows they are young. All incorrect, but each of these examples is widely believed by some subset of creationists. They can't even agree among themselves!

Given all of this, any modifications or corrections to the theory of evolution won't be coming from the efforts of creationists. Their only chance to get everyone to believe the same way is for one of those subgroups to establish a religious dictatorship and reestablish the Inquisition.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
This message is a reply to:
 Message 27 by Dr Adequate, posted 03-16-2011 8:53 PM Dr Adequate has not yet responded

NoNukes
Member
Posts: 5284
From: Central NC USA
Joined: 08-13-2010
Member Rating: 1.6


Message 30 of 760 (609150)
03-17-2011 1:59 AM
Reply to: Message 21 by Taq
03-16-2011 5:01 PM


Genetic Engineering
Shapiro's paper is way over my head. But Shapiro seems to be saying that some mutations are triggered by environmental stresses and that these particular stresses produce mutations that are more likely than mere random mutation to be responsive to the stress. Table I of the pair gives a list of stimuli and response mechanisms for various organism along with pointers to substantiating papers.

While I don't see the connection to special creation, since even the presence of "genetic engineering" systems in a cell is attributed to evolution, I also don't see how Shapiro is simply misusing the term nonrandom.

For example, Shapiro states the following on page 24

quote:
In fact, we possess counter-examples to randomness in those cases where DNA change has evolved to be a part of the normal life cycle, as in yeast mating-type switching,132 postzygotic macronuclear development in ciliated protozoa,154 and immune system development in vertebrates.130 In those cases, we have even identified some of the molecular mechanisms involved in making the algorithmic searches that ensure reliability in the DNA changes.

This message is a reply to:
 Message 21 by Taq, posted 03-16-2011 5:01 PM Taq has responded

Replies to this message:
 Message 31 by Wounded King, posted 03-17-2011 3:43 AM NoNukes has acknowledged this reply
 Message 33 by Taq, posted 03-17-2011 11:21 AM NoNukes has acknowledged this reply

  
Prev1
2
3456
...
51NextFF
Newer Topic | Older Topic
Jump to:


Copyright 2001-2014 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2014