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Author Topic:   Potential falsifications of the theory of evolution
molbiogirl
Member (Idle past 652 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:

http://talkrational.org/showthread.php?t=21194

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 responded

Replies to this message:
 Message 538 by shadow71, posted 01-20-2011 3:47 PM molbiogirl has responded
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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 542 of 968 (601462)
01-20-2011 5:33 PM
Reply to: Message 538 by shadow71
01-20-2011 3:47 PM


Re: Shapiro's use of the word "intelligent"
Sorry for the misunderstanding.

Yes, the quote I provided is a summary of Shapiro's position by someone other than Shapiro.

And yes. There is someone on talkrational who agrees with you, shadow.

However. It is clear from both the article and the presentation that Shapiro is using the term "intelligent" as it is used in information science.

He states that explicitly in the conclusion of his 1997 Boston Review article, A Third Way (Alternatives to Creationism and Darwinism)!

www.shapiro.bsd.uchicago.edu/...ostonReview1997.ThirdWay.pdf

Shapiro writes:

What significance does an emerging interface between biology and information science hold for thinking about evolution? ... Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation.

Emphasis added.

In addition, the title of Shapiro's presentation is A signal-responsive (cognitive) systems view of the genome.

Cognitive systems view of the genome, shadow. Not "intelligently designed genome".

ABE:

Here's another .pdf (from a 2006 talk Shapiro gave) where Shapiro uses "intelligence", "cognition" and "sentience" to refer to sophisticated mechanisms for intercellular communication:

www.shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdf

From the introduction:

Shapiro writes:

This remarkable series of observations requires us to revise basic ideas about biological information processing and recognize that even the smallest cells are sentient beings.

Emphasis added.

From the last paragraph:

Shapiro writes:

The take-home lesson of more than half a century of molecular microbiology is to recognize that bacterial information processing is far more powerful than human technology. The selected examples of bacterial smarts I have given show convincingly that these small cells are incredibly sophisticated at coordinating processes involving millions of individual events and at making them precise and reliable. In addition, the astonishing versatility and mastery bacteria display in managing the biospheres geochemical and thermodynamic transformations indicates that we have a great deal to learn about chemistry, physics and evolution from our small, but very intelligent, prokaryotic relatives.

Emphasis again added.

Edited by molbiogirl, : No reason given.


This message is a reply to:
 Message 538 by shadow71, posted 01-20-2011 3:47 PM shadow71 has responded

Replies to this message:
 Message 555 by shadow71, posted 01-20-2011 8:55 PM molbiogirl has responded
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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 559 of 968 (601555)
01-21-2011 12:35 PM
Reply to: Message 555 by shadow71
01-20-2011 8:55 PM


Cognitive systems v. cognition
Jar is right. Cognitive systems, not cognition.

Here's a definition that I think Shapiro would agree with:

Cognitive system: one that utilizes plausible computational representations of biological processes as a basis for system designs that seek to understand the underlying mechanisms of intercellular communication.

Furthermore, Shapiro has expressly denied that his work supports intelligent design.

http://books.google.com/books?id=MjKkFG8qVjcC&pg=PA18&lpg...

William Dembsky writes:

James Shapiro e-mailed me a few years back saying, "I hear that you are citing me in your talks as supporting ID. " Indeed, it helps to show that evolution is in disarray by citing people like Shapiro who have no truck with ID.

ABE:

Found another anti-ID Shapiro quote:

Shapiro writes:

The possibility that computational control of natural genetic engineering functions can provide an answer to the problems of irreducible complexity and intelligent design deserves to be explored fully. Contrary to the claims of some Creationists, these issues are not scientifically intractable. They require an application of lessons from the fields of artificial intellligence, self-adapting complex systems, and molecular cell biology.

www.shapiro.bsd.uchicago.edu/shapiro2002.AnnNYAS.pdf

Edited by molbiogirl, : No reason given.


This message is a reply to:
 Message 555 by shadow71, posted 01-20-2011 8:55 PM shadow71 has responded

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 Message 563 by shadow71, posted 01-22-2011 4:48 PM molbiogirl has responded

molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 565 of 968 (601653)
01-22-2011 5:45 PM
Reply to: Message 563 by shadow71
01-22-2011 4:48 PM


Re: Cognitive systems v. cognition
Shapiro writes:

The point of this discussion is that our current knowledge of genetic change is fundamentally at variance with neo-Darwinist postulates. We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutation rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures. Inevitably, such a profound advance in awareness of genetic capabilities will dramatically alter our understanding of the evolutionary process. Nonetheless, neo-Darwinist writers like Dawkins continue to ignore or trivialize the new knowledge and insist on gradualism as the only path for evolutionary change.

Just what in the above "falsifies evolution"?


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Replies to this message:
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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 566 of 968 (601656)
01-22-2011 5:58 PM
Reply to: Message 560 by shadow71
01-22-2011 4:08 PM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
shadow writes:

See above paper, and the impressive list of papers he has written in re "natural genetic engineering"

From the ISCID chat between Dembski & Shapiro that you referenced:

http://www.iscid.org/james-shapiro-chat.php

Dembski writes:

Are you confident that non-teleological mechanisms can account for the rise of natural genetic engineering systems, and if so why?

Shapiro writes:

All existing living organisms possess natural genetic engineering capabilities. So they must be pretty fundamental. Any self-organizing evolving system has to have the capacity to alter its information store.

Please note the use of the word evolve.

And again.

Shapiro writes:

We know that cells activate natural genetic engineering functions in response to various inputs, particularly stresses (what McClintock called "genome shock"). In certainly highly evolved situations, like the immune system, the responsiveness of these systems is quite extraordinary.

From later in the chat:

Micah writes:

Dr. Shapiro, are there other researchers/labs that currently exemplify your concept of a 21st century view of evolution?

Shapiro writes:

Goodness. If you look at my web site (http://shapiro.bsd.uchicago.edu), there are several papers available that give lists of references. There are books on the roles of transposable elements in evolution. Springer just published a book on "Evolution as Computation" (Landweber and Winfree, eds), and the NY Academy of Sciences has published a couple of volumes where these ideas have been explored at length (L. Caporale, ed. 1999, "Molecular Strategies in Biological Evolution: and one just published on Epigenesis at the end of 2002).

What in the above "falsifies evolution"?


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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 587 of 968 (601801)
01-24-2011 11:53 AM
Reply to: Message 586 by Percy
01-24-2011 7:13 AM


shadow, define your terms.
Percy, I'd like to second your request.

shadow, before we go any further, please summarize Shapiro's position in your own words. No quotes. Just your own words.

In particular, focus on those aspects of Shapiro's work that "falsify" the current theory of evolution.


This message is a reply to:
 Message 586 by Percy, posted 01-24-2011 7:13 AM Percy has acknowledged this reply

molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 601 of 968 (601977)
01-25-2011 11:59 AM
Reply to: Message 599 by shadow71
01-25-2011 11:43 AM


Shapiro's definition of nonrandom
shadow, we're not going to get very far if you keep quoting half a sentence and pointing to one word. (e.g. Shapiro said INTELLIGENT. Shapiro said FUNDAMENTAL. Shapiro said NONRANDOM.)

Here's what Shapiro means by nonrandom.

shapiro.bsd.uchicago.edu/...MS.RevisitingCentral%20Dogma.pdf

(Table of examples starts on page 16.)

Shapiro writes:

Another inaccurate assertion of conventional wisdom is the idea that DNA changes must occur randomly throughout the genome. Once again, there is a large and growing literature documenting examples (and sometimes clarifying mechanisms) where particular natural genetic engineering systems show decidedly nonrandom specificities of action.

He means "natural genetic engineering".

In the paper I've quoted, Shapiro includes a list of about 50 examples of natural genetic engineering. It's far too long to quote.

But examples include:

DNA damage --> transposon and retrotransposon activation

Heat shock --> IS element activation

Aerobic starvation --> base substitution

I am nearly certain this is not what you understood Shapiro to mean.

What did you understand "nonrandom" to mean?

Edited by molbiogirl, : No reason given.

Edited by Admin, : Fix link.

Edited by Admin, : Refix link.

Edited by Admin, : Fix link again after bug fix.


This message is a reply to:
 Message 599 by shadow71, posted 01-25-2011 11:43 AM shadow71 has responded

Replies to this message:
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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 603 of 968 (601981)
01-25-2011 12:27 PM
Reply to: Message 602 by nwr
01-25-2011 12:18 PM


Broken link
Thank you nwr! I never would have thought of that!
This message is a reply to:
 Message 602 by nwr, posted 01-25-2011 12:18 PM nwr has acknowledged this reply

molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


(1)
Message 617 of 968 (602201)
01-26-2011 6:03 PM
Reply to: Message 612 by shadow71
01-26-2011 3:43 PM


What a mess, shadow
Just a note before I get to googling all of your unattributed Shapiro quotes.

It is common courtesy to provide cites and links to your sources.

For example, when I google your assertion that Shapiro thinks "Mobile DNA movements rather than replication errors serve as the primary engines of protein evolution.", I find this:

shapiro.bsd.uchicago.edu/Shapiro.2010.MobileDNA.pdf

In the future, please provide your cites.

That said.

What is with the laundry list? Reverse transcription? Ribozymes? DNA repair? Shapiro says in the introduction that he is going to review:

technical advances in our views about genome organization and the mechanisms of genetic change

That's all that is, shadow. A list of a some mechanisms.

And then we come to your summary of what Shapiro means:

He accepts descent with modification, but does not accept natural selection and random mutation to the degree that the modern evoluntionists believe.
.I believe he is formulating a theory that does not rely on Random Mutation as a primary player in the evolving of organisms.

That's where you go off the rails.

NOWHERE does Shapiro assert the above.

In fact, here's Shapiro addressing that question directly:

The following text was published in The New York Times, November 10, 1996.

To the Editor: I find myself quoted in Michael J. Behe's Op-Ed article questioning Darwinian explanations for cellular evolution (Oct. 29), leaving the impression that I share his call for a return to religious explanations. This is not my position.

Darwinism and creationism are not the only ways to think about sources of biological function and diversity. The virtue of science is its ability to evolve concepts that render ''miraculous'' aspects of the world comprehensible.

Molecular biology has uncovered complexity in genome structure and cellular function. It has also revealed biochemical systems that cells use to restructure DNA molecules in ways that resemble our own genetic engineering. These systems introduce potentials for rapid genome reorganization and biological feedback into the evolutionary process.

Scientists have the task of exploring how far the operation of natural genetic engineering systems can provide novel ways to account for biological adaptations not explained by random mutation and selection.

James A. Shapiro
Professor of Microbiology
at the University of Chicago.
Chicago, Nov. 5, 1996

http://www.stephenjaygould.org/...e/design/shapiro_behe.html

Take a close look at that last sentence:

Scientists have the task of exploring how far the operation of natural genetic engineering systems can provide novel ways to account for biological adaptations not explained by random mutation and selection.

Let me translate that for you:

There are lots of things that we can explain with random mutation and selection. However, if there is something that we can't explain, I bet we will find the answer in natural genetic engineering.

As a reminder. Shapiro's definition of natural genetic engineering (aka nonrandom changes):

www.shapiro.bsd.uchicago.edu/...evisitingCentral%20Dogma.pdf

Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations106 or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.107110 Genetic change is almost always the result of cellular action on the genome.

And from the ISCID chat:

Masciarelli
I'm curious about "their non-random operations." Does 'non-random' suggest that the very instructions for all possible morphological changes are front loaded or pre-programmed into living things, needing only a given catalyst to get things going?

James Shapiro
No. Non-random means that they operate under certain conditions (e.g. after genome damage or viral infection) and that these systems make characteristic kinds of changes ... These phenomena show us that cells are capable of altering their genomes in non-random but not rigidly specified or pre-determined ways.

Is that clear, shadow?

And when Shapiro says:

Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cell.

He is absolutely NOT saying we CANNOT know but that we DO NOT know. For now.

Remember?

Shapiro writes:

The possibility that computational control of natural genetic engineering functions can provide an answer to the problems of irreducible complexity and intelligent design deserves to be explored fully. Contrary to the claims of some Creationists, these issues are not scientifically intractable. They require an application of lessons from the fields of artificial intellligence, self-adapting complex systems, and molecular cell biology.

Let me translate that for you:

"ID and irreducible complexity are bullshit. We will figure it out."


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 Message 612 by shadow71, posted 01-26-2011 3:43 PM shadow71 has responded

Replies to this message:
 Message 618 by shadow71, posted 01-26-2011 7:23 PM molbiogirl has responded

molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 621 of 968 (602262)
01-27-2011 2:40 AM
Reply to: Message 618 by shadow71
01-26-2011 7:23 PM


Re: What a mess, shadow
shadow, you pulled quotes word for word out of Shapiro's Mobile DNA paper without citing him. That's a no no. It's called plagiarism.

As best as I can tell, you pulled the subheadings from pages 7 & 8 of his Central Dogma paper for your laundry list. The majority of the quotes that follow are from his Mobile DNA paper. However, a couple seem to have come from his Third Way paper.

So yes, a comprehensive list of the papers you failed to cite would be appreciated.

And just a couple of side notes.

I think it's remarkable that Behe, Dembski, and Comfort continue to quote mine Shapiro in order to support ID while at the same time acknowledging that Shapiro doesn't agree with them.

For example. Behe is rather fond of this quote:

Shapiro writes:

There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.

(It's from National Review 16 September 1996 apparently. I can't track it down.)

And yet Behe admits that Shapiro "hopes that they (the biochemical pathways) will be explained by some other non-intelligent mechanism".

http://gene-callahan.blogspot.com/...concession-by-behe.html

Shapiro must get awfully tired of that.

And finally. Let's say, for the sake of argument, Shapiro thinks that "the modern theory isn't acceptable".

So what?

Stephen Jay Gould didn't think that the modern theory was "acceptable" -- so he proposed punctuated equilibrium.

But when punctuated equilibrium or natural genetic engineering (or any other new idea) gains acceptance, it doesn't:

...mean that the theory of evolution by natural selection is wrong.

...mean that the central conclusion of evolutionary theory no longer holds.

...negate previous work on how evolution by natural selection works.

...imply that evolution only happens in rapid bursts or thru natural genetic engineering.


This message is a reply to:
 Message 618 by shadow71, posted 01-26-2011 7:23 PM shadow71 has responded

Replies to this message:
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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 626 of 968 (602302)
01-27-2011 11:32 AM


Let's see if Shapiro agrees
shadow, I've given this some thought.

Let's try another tack.

Let's you and I try to put together your take on Shapiro's view.

1. All mutation is nonrandom.
2. Natural selection works so poorly that essentially it doesn't work at all.
3. All evolution occurs due to cells rearranging their own genomes (aka NGE).
4. Cells are intelligent.

Does this sound about right?

Because, once we've agreed on the language, I'm going to e mail Dr. Shapiro and ask if this is a fair assessment of his work.


Replies to this message:
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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 639 of 968 (602346)
01-27-2011 4:08 PM
Reply to: Message 637 by shadow71
01-27-2011 3:37 PM


Again with the RM & NS
Since my interpretations are invalid, how would you interpert this quotation from Shapiro?

Shapiro merely substitutes "modular units" into the mutation + natural selection = evolution formula.

http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html

Major evolutionary change to the genome occurs by the amplification and rearrangement of pre-existing modules. Old genomic systems are disassembled and new genomic systems are assembled by natural genetic engineering functions that operate via non-random molecular processes.

Note! It's the biochemical pathways that move the modules that are nonrandom. Not the mutation.

Natural selection following genome reorganization eliminates the misfits whose new genetic structures are non-functional. In this sense, natural selection plays an essentially negative role, as postulated by many early thinkers about evolution (e.g. 53). Once organisms with functional new genomes appear, however, natural selection may play a positive role in fine-tuning novel genetic systems by the kind of micro-evolutionary processes currently studied in the laboratory.

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 640 of 968 (602347)
01-27-2011 4:10 PM
Reply to: Message 638 by Taq
01-27-2011 4:02 PM


Thank you, Taq. Well said.
Just between you and me, a lot of what Shapiro goes on and on about sounds an awful lot like "OMG!!! Epigenetics!!11!!"
This message is a reply to:
 Message 638 by Taq, posted 01-27-2011 4:02 PM Taq has responded

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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 645 of 968 (602356)
01-27-2011 4:51 PM
Reply to: Message 644 by shadow71
01-27-2011 4:46 PM


What, no cites?
Come now, shadow.
You promised.

And what say you to writing Shapiro?
Seems a pretty simple way to settle the question, does it not?
And he seems amenable to e mail correspondence with IDists.

Again, I have to refer you to my papers or to a later email correspondence on this issue.

http://www.iscid.org/james-shapiro-postchat.php


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molbiogirl
Member (Idle past 652 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 647 of 968 (602359)
01-27-2011 5:03 PM
Reply to: Message 644 by shadow71
01-27-2011 4:46 PM


Built in?
Let's leave aside RM & NS for a moment.

In the least he is discussing a built in information system in the cell.

Yes. And?

A major problem, often cited by religious and other critics of orthodox evolutionary theory, is how to explain the appearance of complex genomic systems encoding sophisticated multicomponent adaptive features.99, 100 The possibility that computational control of natural genetic engineering functions can provide an answer to the problems of Irreducible Complexity and Intelligent Design deserves to be explored fully. Contrary to the claims of some Creationists,99 these issues are not scientifically intractable. They require an application of lessons from the fields of artificial intellligence, self-adapting complex systems, and molecular cell biology.100, 101

We already have some clues about how to proceed in addressing complex novelties in evolution. As McClintock first demonstrated, insertions of MGEs at distinct genetic loci bring them under coordinate control.8, 64, 66 Thus, we know in principle how multi-locus genomic systems can originate. Once such systems exist, we know that the transcriptional regulatory apparatus is capable of specifically accessing the component loci in response to biologically meaningful signals.

http://shapiro.bsd.uchicago.edu/contextgenome.html

Shapiro sees an evolutionary explanation for these systems.


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