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Author Topic:   Potential falsifications of the theory of evolution
Taq
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Message 526 of 968 (601095)
01-18-2011 5:33 PM
Reply to: Message 523 by shadow71
01-18-2011 4:14 PM


Re: The fact of evolution.
The problem I have with saying evolution is a fact is that it assumes the process and the cause of the process are fact. I agree the evolution is a fact, but the cause and the manner of the process is still not fully determined.
The problem lies with the layman understanding of how science works. To the scientist the difference between the fact and theory of evolution is quite clear. Organisms change over time and share a common ancestor. Fact. This change is explained through mutation, selection, and speciation. Theory.
A theory is always a tentative explanation of the facts, to put it succinctly.

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bluegenes
Member (Idle past 2478 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 527 of 968 (601107)
01-18-2011 6:34 PM
Reply to: Message 523 by shadow71
01-18-2011 4:14 PM


Re: The fact of evolution.
shadow71 writes:
The problem I have with saying evolution is a fact is that it assumes the process and the cause of the process are fact. I agree the evolution is a fact, but the cause and the manner of the process is still not fully determined.
One can see historically that evolution has happened but not how or what caused it to happen. That is the theory and theories are not fact.
So what's your problem with people like Coyne, Dawkins and many others stating that evolution is a fact? They do not say that any particular theory of evolution is a fact.
Here are Coyne and Dawkins in a newspaper piece they wrote together in 2005: (my bold):
quote:
Among the controversies that students of evolution commonly face, these are genuinely challenging and of great educational value: neutralism versus selectionism in molecular evolution; adaptationism; group selection; punctuated equilibrium; cladism; "evo-devo"; the "Cambrian Explosion"; mass extinctions; interspecies competition; sympatric speciation; sexual selection; the evolution of sex itself; evolutionary psychology; Darwinian medicine and so on. The point is that all these controversies, and many more, provide fodder for fascinating and lively argument, not just in essays but for student discussions late at night.
All those "controversies" about how evolution actually happens and what has happened in the past "and many more". Note that they mention at least three of the areas that Koonin mentions in the article you linked to.
No-one is claiming that the study of evolutionary biology is finished, or even near its end, when they state that evolution itself is a fact.
More directly on the topic of the thread. Scientific theories can adjust to new information, and evolutionary theory has evolved (appropriately!) over time. Actual falsification of the modern theory requires something that cuts completely across it. I agree with some others on the thread that Koonin slightly overstates his case, although that's common when people have a point to make.
His statement that gene duplications aren't incremental changes seems strange to me, as they happen all the time with little or no apparent effect on the organism involved, meaning that at least most of the time they could certainly be described as "incremental".
There's a much better case for key historic endosymbiotic events being non-gradual, but these seem rare, and gradual change is still the norm.
Discussion on the relative importance of two kinds of natural selection (positive and purifying) do not change the fact that natural selection has been a central plank of the theory for 150 years.
Things that could be described as "neo-Lamarckian" are not really the kind of Lamarckian view that was strongly opposed in the early twentieth century, and Darwin himself was certainly open to Lamarckian ideas.
Much has changed in 150 years, and many processes and details have been incorporated into the mainstream as knowledge increases. But this is nothing dramatic, just the evolution and improvement of a strong theory.

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RAZD
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Posts: 20714
From: the other end of the sidewalk
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Message 528 of 968 (601170)
01-19-2011 12:39 AM
Reply to: Message 521 by shadow71
01-18-2011 3:57 PM


Re: yawn
Hi again shadow71.
I understand this to mean he is saying that major changes are the result of planned, engineered functions in the cell that do not rely on gradual, random changes.
Then you are jumping to a concussion.
(1) hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering;
Non-random does not mean planned. Hydrogen and oxygen do not react and form random combinations, rather there is a very high preponderance of H2O combinations with a smattering of HO and H2O2 some H2 and some O2 and very little else. This is a reality of chemistry, not of planned engineered functions in the atoms.
Biological actions and reactions are similar: the chemical possibilities mean that complete randomness is not possible. This is one of the reasons why the formation of life by chemical reactions is possible.
Again, this is not news. It does not mean that evolution is no longer the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Nor does it mean that the theory, that evolution is sufficient to explain the diversity of life, is invalid when this occurs.
(2) major disruptions of an organism's ecology trigger cell and genome restructuring.
Again, it is common modern knowledge that bacterial organisms react to stress with increased rates of mutations. Whether this is due to a "trigger cell" (or part of a cell) or due to the reduced action of the mechanisms for checking and correcting replication accuracy is moot, as the result is increased mutations.
Change the ecology and organisms change in response, change the ecology drastically and organisms change drastically or go extinct.
This too is not news. It does not mean that evolution is no longer the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Nor does it mean that the theory, that evolution is sufficient to explain the diversity of life, is invalid when this occurs.
(3) ecologically-triggered cell and genome restructurings produce organisms which, at some frequency, will possess novel adaptive features that suit the altered environment.
Repeat: change the ecology and organisms change in response, change the ecology drastically and organisms change drastically or go extinct. This higher rate of mutation and reduced selection will produce more organisms that differ from the original individuals. The possibility of speciation events increases in isolated subpopulations. Again, this is also seen following extinction events (when selection is lowered).
This too is not news. It does not mean that evolution is no longer the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Nor does it mean that the theory, that evolution is sufficient to explain the diversity of life, is invalid when this occurs.
(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.
And yet the increased rate of evolution still occurs by microevolution as well ... it does not mean that evolution is no longer the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Nor does it mean that the theory, that evolution is sufficient to explain the diversity of life, is invalid when this occurs.
This 21st century scenario assumes a major role for the kind of cellular sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel Prize address.
Made 27 years ago?
It also answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties.
You must have missed that part. It is still a natural process, and what it affects is the rate of change. It does not mean that evolution is no longer the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Nor does it mean that the theory, that evolution is sufficient to explain the diversity of life, is invalid when this occurs.
In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science.
At best this is just a(nother) mechanism for the causing changes to hereditary traits, it does not mean that evolution is no longer the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Nor does it mean that the theory, that evolution is sufficient to explain the diversity of life, is invalid when this occurs.
Curiously, the theory of evolution has progressed from the times of Darwin and the early stages of evolutionary science by understanding the mechanisms that are involved, in genetics, in population dynamics, and in many other areas. The new knowledge adds to the bank of information available to modern evolutionary biologists and increases our understanding of how evolution works.
Enjoy.
Edited by RAZD, : clrty

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This message is a reply to:
 Message 521 by shadow71, posted 01-18-2011 3:57 PM shadow71 has replied

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


Message 529 of 968 (601290)
01-19-2011 5:22 PM
Reply to: Message 525 by Taq
01-18-2011 5:29 PM


tag writes,
What neo-Darwinism states is that mutation and selection are independent of one another. That is, mutations are blind to what is good or bad for the individual. This is exactly what we see with mobile DNA elements. They insert all over the place, and the helpful ones are kept through natural selection.
In the paper I posted by James A. Shapiro "Mobile DNA and evolution in the 21st Century" he writes:
"Cell mergers and WGDs are the kinds of events that activate mobile DNA and genome restructuring. In order to fully integrate the genomic findings with our knowledge of mobile DNA, we have to make use of information about the molecular regulation of mobile DNA activities as well as McClintocks's view that cells RESPOND TO SIGNS OF DANGER, FREQUENTLY RESTRUCTURING THEIR GENOMES AS PART OF THE RESPONSE." (EMPHASIS MINE)
This is contra to what you posted above.
I think Shapiro is clearly stating that randon mutation and natural selection are not as clear as traditonal darwinists theorists are saying.

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 Message 525 by Taq, posted 01-18-2011 5:29 PM Taq has replied

Replies to this message:
 Message 530 by RAZD, posted 01-19-2011 5:55 PM shadow71 has replied
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RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 530 of 968 (601297)
01-19-2011 5:55 PM
Reply to: Message 529 by shadow71
01-19-2011 5:22 PM


increased mutation rate is not directed mutation
Hi shadow, do you know what confirmation bias is?
Confirmation bias - Wikipedia
quote:
Confirmation bias (also called confirmatory bias or myside bias) is a tendency for people to favor information that confirms their preconceptions or hypotheses regardless of whether the information is true.[Note 1][1] As a result, people gather evidence and recall information from memory selectively, and interpret it in a biased way. ... They also tend to interpret ambiguous evidence as supporting their existing position. ...
quote:
... cells RESPOND TO SIGNS OF DANGER, FREQUENTLY RESTRUCTURING THEIR GENOMES AS PART OF THE RESPONSE."
(EMPHASIS MINE)
This is contra to what you posted above.
No it isn't.
What you are mistakingly interpreting as directed mutation to counter the danger, is in actuality just an increased rate of mutations, such that the possibility of one that is beneficial in countering the danger can evolve sooner rather than (too) much later.
In other words, organisms have evolved mechanisms that allow them to adjust their rate of mutation in response to changing selective pressures. After 3.5 billion years of life on this planet, and gazillions of opportunities, this should not be a major surprise, and it would certainly be subject to positive selection once it began, because variation in ecologies is the rule rather than the exception.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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This message is a reply to:
 Message 529 by shadow71, posted 01-19-2011 5:22 PM shadow71 has replied

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


Message 531 of 968 (601313)
01-19-2011 7:31 PM
Reply to: Message 528 by RAZD
01-19-2011 12:39 AM


The past five decades of research in genetics and molecular biology have brouRe: yawn
james a. shapiro writes:
The past five decades of research in genetics and molecular biology have brought us revolutionary discoveries. Upsetting the oversimplified views of cellular organization and function held at mid-century, the molecular revolution has revealed an unanticipated realm of complexity and interaction more consistent with computer technology than with the mechanical viewpoint which dominated the field when the neo-Darwinian Modern Synthesis was formulated. The conceptual changes in biology are comparable in magnitude to the transition from classical physics to relativistic and quantum physics.
from razd post 528
shadow writes
I understand this to mean he is saying that major changes are the result of planned, engineered functions in the cell that do not rely on gradual, random changes.
razd writes
Then you are jumping to a concussion.
Above quote was taken from Shapiro letter to Boston Review Feb.10th. 2006

This message is a reply to:
 Message 528 by RAZD, posted 01-19-2011 12:39 AM RAZD has replied

Replies to this message:
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Granny Magda
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Joined: 11-12-2007
Member Rating: 4.0


Message 532 of 968 (601317)
01-19-2011 7:44 PM
Reply to: Message 531 by shadow71
01-19-2011 7:31 PM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
Hi shadow,
james Shapiro writes:
The conceptual changes in biology are comparable in magnitude to the transition from classical physics to relativistic and quantum physics.
This is a good comparison actually. Neither relativity, nor quantum physics rendered Newtonian physics wrong. Classical physics still holds true, in most regards and in most examples. There are situations where it does not apply, yes, but that doesn't invalidate the whole of classical physics, it just refines and expands upon it.
Similarly, recent discoveries in genetics and molecular biology have brought new perspectives to biology. There is much that was unanticipated by biologists back in the Fifties, but that doesn't mean that the Theory of Evolution has been overthrown. It just means refinement and improvement of theory, which is exactly how science is supposed to function.
shadow71 writes:
I understand this to mean he is saying that major changes are the result of planned, engineered functions in the cell that do not rely on gradual, random changes.
Eh? I don't think he is saying that. Where are you even getting that from? From the "more consistent with computer technology" line? That doesn't mean that biology is a product of planned engineering. I agree with RAZD, you are reading too much into such a simple statement.
Mutate and Survive

On two occasions I have been asked, — "Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?" ... I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question. - Charles Babbage

This message is a reply to:
 Message 531 by shadow71, posted 01-19-2011 7:31 PM shadow71 has replied

Replies to this message:
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RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 533 of 968 (601321)
01-19-2011 8:27 PM
Reply to: Message 531 by shadow71
01-19-2011 7:31 PM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
Hi again Shadow71,
Above quote was taken from Shapiro letter to Boston Review Feb.10th. 2006
But your interpretation is not. - can you point to where he even implies "planned" in any way shape or form?
Do the same for "engineered" as not a completely natural process.
If you cannot do this, then you need to accept that your interpretation is not supported by the evidence.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 531 by shadow71, posted 01-19-2011 7:31 PM shadow71 has replied

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


Message 534 of 968 (601420)
01-20-2011 11:58 AM
Reply to: Message 532 by Granny Magda
01-19-2011 7:44 PM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
Granny magda writes,
Eh? I don't think he is saying that. Where are you even getting that from? From the "more consistent with computer technology" line? That doesn't mean that biology is a product of planned engineering. I agree with RAZD, you are reading too much into such a simple statement
James A. Shapiro writes in Boston Review cited earlier:
Unfortunately, readers of Boston Review may remain unaware of this intellectual ferment because the debate about evolution continues to assume the quality of an abstract and philosophical "dialogue of the deaf" between Creationists and Darwinists. Although our knowledge of the molecular details of biological organization is undergoing a revolutionary expansion, open-minded discussions of the impact of these discoveries are all too rare. The possibility of a non-Darwinian, scientific theory of evolution is virtually never considered. In my comments, then, I propose to sketch some developments in contemporary life science that suggest shortcomings in orthodox evolutionary theory and open the door to very different ways of formulating questions about the evolutionary process. After a discussion of technical advances in our views about genome organization and the mechanisms of genetic change, I will focus on a growing convergence between biology and information science which offers the potential for scientific investigation of possible intelligent cellular action in evolution.
On this board the possibility of a non-Darwinian theory is never considered. Those who bring up the possibility are "uneducated". So I read James A. Shapiro and am posting his findings and conclusions.
I agree he is not saying the whole theory is not valid, but he says, changes may be necessary.
He, not me, mentions a possible intelligent cellular action in evolution.
Am I reading too much into this to?
Edited by shadow71, : No reason given.

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


Message 535 of 968 (601423)
01-20-2011 12:06 PM
Reply to: Message 533 by RAZD
01-19-2011 8:27 PM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
Razd writes,
But your interpretation is not. - can you point to where he even implies "planned" in any way shape or form?
Do the same for "engineered" as not a completely natural process.
If you cannot do this, then you need to accept that your interpretation is not supported by the evidence.
Please read my post 534 to Granny Magda.
Shapiro clearly states His belief in a potential of " possible intelligent cellular action in evolution."
I don't know why most of the scientists on this board are adamantly against such a possibilty.
It would not ruin the theory, just bring it into the 21st Century.
Edited by shadow71, : No reason given.
Edited by shadow71, : No reason given.

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


Message 536 of 968 (601427)
01-20-2011 12:14 PM
Reply to: Message 530 by RAZD
01-19-2011 5:55 PM


Re: increased mutation rate is not directed mutation
Razd writes,
--------------------------------------------------------------------------------
Confirmation bias (also called confirmatory bias or myside bias) is a tendency for people to favor information that confirms their preconceptions or hypotheses regardless of whether the information is true.[Note 1][1] As a result, people gather evidence and recall information from memory selectively, and interpret it in a biased way. ... They also tend to interpret ambiguous evidence as supporting their existing position. ...
Would you agree that based on what I posted in Message 534 to Granny Magda, that I may not be suffering from confirmation bias?
Shapiro is not a creationist. He has a very good reputation in the field. I wonder how Jerry Coyne feel about his fellow Univ. of Chicago faculty mate?
I just don't see how Shapiro can be rejected out of hand. I think we will have to wait and see how this develops, and how, if at all , it changes the Darwinian, neo-Darwinian theory.
Edited by shadow71, : No reason given.

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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 537 of 968 (601440)
01-20-2011 1:33 PM
Reply to: Message 534 by shadow71
01-20-2011 11:58 AM


Shapiro's use of the word "intelligent"
I suggest anyone who's interested in Shapiro's use of the word "intelligent" read this thread:
404 Not Found
Here's a summary of Shapiro's definition of "intelligence":
You guys really need to combine this with his March presentation on "A signal-responsive (cognitive) systems view of the genome" - he is not saying cells function as intelligent agents in the sense of teleological, goal planning, high order intelligences.
There is intelligence and intelligence - one can quite reasonably define natural selection itself as an intelligent process in a heuristic sense but that doesn't make it a conscious process, people should not confuse the two, and many natural systems have the properties of being able to go beyond simple stimulus-response.
He is saying we need to think of cellular processes as interactive systems (as we do with neural nets) rather than one way, linear, cause-effect systems.
He is challenging the one way gene centric central dogma by arguing cells have themselves evolved systems for more flexible responses based on "experience" (in the form of epigenetic information amongst other things).
Here's the presentation referenced in the above quote:
http://shapiro.bsd.uchicago.edu/2009.SFI.pdf

This message is a reply to:
 Message 534 by shadow71, posted 01-20-2011 11:58 AM shadow71 has replied

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


Message 538 of 968 (601450)
01-20-2011 3:47 PM
Reply to: Message 537 by molbiogirl
01-20-2011 1:33 PM


Re: Shapiro's use of the word "intelligent"
molbiogirl posts;
You guys really need to combine this with his March presentation on "A signal-responsive (cognitive) systems view of the genome" - he is not saying cells function as intelligent agents in the sense of teleological, goal planning, high order intelligences. There is intelligence and intelligence - one can quite reasonably define Natural selection itself as an intelligent process in a heuristic sense but that doesn't make it a conscious process, people should not confuse the two, and many natural systems have the properties of being able to go beyond simple stimulus-response. He is saying we need to think of cellular processes as interactive systems (as we do with neural nets) rather than one way, linear, cause-effect systems. He is challenging the one way gene centric central dogma by arguing cells have themselves evolved systems for more flexible responses based on "experience" (in the form of epigenetic information amongst other things).
http://shapiro.bsd.uchicago.edu/2009.SFI.pdf
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12-19-2009, 07:24 PM #736167 / #16
The following was posted in reply to Monad's post.
unfortunately the cut and paste was lost, but Figuer did not agree with Monad and suggested shapiro was indeed talking about intelligence in the cell.
I don't know who Monad is but it appears that is Monad's intrepretation and not Shapiro's.
Edited by shadow71, : No reason given.
Edited by shadow71, : No reason given.

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 Message 537 by molbiogirl, posted 01-20-2011 1:33 PM molbiogirl has replied

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


Message 539 of 968 (601451)
01-20-2011 3:52 PM
Reply to: Message 537 by molbiogirl
01-20-2011 1:33 PM


Re: Shapiro's use of the word "intelligent"
Here is post of figuer that I lost
Originally Posted by Monad
he is not saying cells function as intelligent agents in the sense of teleological, goal planning, high order intelligences.
Certainly, it would be in another sense, since the goal planning, teleological capacities of the cell would be minuscule and rudimentary compared to such capacities in a human brain. I do see however that he is indeed suggesting a sort of mental aspect to the cell, which I find quite unproblematic

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Granny Magda
Member
Posts: 2462
From: UK
Joined: 11-12-2007
Member Rating: 4.0


Message 540 of 968 (601456)
01-20-2011 4:48 PM
Reply to: Message 534 by shadow71
01-20-2011 11:58 AM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
James A. Shapiro writes...
For the sake of brevity, I agree with Molbiogirl on this point. Shapiro's use of the phrase "intelligent cellular action" should not be taken as a synonym for "planned, engineered functions in the cell", as you had it.
Certainly there was nothing at all in your previous Shapiro quote that supported this.
On this board the possibility of a non-Darwinian theory is never considered. Those who bring up the possibility are "uneducated".
Oh grow up and drop the martyr complex. I wasn't accusing you of being undereducated, I was suggesting that you were mistaken, You are being over-sensitive.
I agree he is not saying the whole theory is not valid, but he says, changes may be necessary.
And I have no objection to that.
He, not me, mentions a possible intelligent cellular action in evolution.
But it is you, not Shapiro, who has previously sought to use mysteries in biology as a jumping on point for god-of-the-gaps arguments involving the Christian god.
You are attempting to portray Shapiro's words as being in line with your Christian model, but that was not his intent. You are running with his ideas and taking them out of context.
Am I reading too much into this to?
No disrespect, but yeah, I think you are. having read the article, I don't think that Shapiro is saying that there is existing evidence of planning in the genome. He is saying that new perspectives might allow us to test for such a thing, but that is another story.
Mutate and Survive

On two occasions I have been asked, — "Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?" ... I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question. - Charles Babbage

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