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Author Topic:   Potential falsifications of the theory of evolution
jar
Member (Idle past 416 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 556 of 968 (601490)
01-20-2011 8:57 PM
Reply to: Message 555 by shadow71
01-20-2011 8:55 PM


Re: Shapiro's use of the word "intelligent"
"Cognitive systems" not cognition.

Anyone so limited that they can only spell a word one way is severely handicapped!

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Taq
Member
Posts: 10045
Joined: 03-06-2009
Member Rating: 5.3


Message 557 of 968 (601491)
01-20-2011 8:58 PM
Reply to: Message 549 by shadow71
01-20-2011 8:38 PM


Re: increased mutation rate is not directed mutation
When he says Molecular compuation network demonstrating biologically useful properties OF SELF-AWARENESS AND DECSION MAKING (emphasis mine) does that not speak of some sort of ability to make decisions based upon what the circumstances present?
You are pulling small phrases out of their context. That seems to be the problem.
I think we would both agree that humans are self-aware and make decisions. However, humans don't decide which mutations are produced in their gametes and which alleles will be passed on to the next generation. Self-awareness and decision making are separate entities from the process of mutation.

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Percy
Member
Posts: 22480
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 558 of 968 (601534)
01-21-2011 7:02 AM
Reply to: Message 542 by molbiogirl
01-20-2011 5:33 PM


Re: Shapiro's use of the word "intelligent"
Asking if there's a "guiding intelligence," referring to cells as "sentient beings," calling them "intelligent," seems like an open invitation to being misunderstood.
--Percy

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molbiogirl
Member (Idle past 2664 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.
http://www.shapiro.bsd.uchicago.edu/shapiro2002.AnnNYAS.pdf
Edited by molbiogirl, : No reason given.

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Replies to this message:
 Message 563 by shadow71, posted 01-22-2011 4:48 PM molbiogirl has replied

shadow71
Member (Idle past 2956 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 560 of 968 (601645)
01-22-2011 4:08 PM
Reply to: Message 544 by Taq
01-20-2011 6:20 PM


Re: The past five decades of research in genetics and molecular biology have brouRe: yawn
Hi Taq,
In reply to your request, here is a paper by Shapiro setting out his history of work.
PubMed Citation
Articles by Shapiro, J. A.
Genetics, Vol. 183, 1205-1214, December 2009, Copyright 2009
doi:10.1534/genetics.109.110007
Letting Escherichia coli Teach Me About Genome Engineering
James A. Shapiro1
Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, Illinois 60637
1 Address for correspondence: Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, 979 E. 57th St., Chicago, IL 60637.
E-mail: jsha@uchicago.edu
Anecdotal, Historical and Critical Commentaries on Genetics
Shadow wrote,
On this board the possibility of a non-Darwinian theory is never considered
taq writes,
Sure it is. The problem is that the evidence just isn't there, or it is overplayed as in the case of both Shapiro and Koonin.
shadow wrote,
He, not me, mentions a possible intelligent cellular action in evolution.
taq wrote,
Based on what evidence?
See above paper, and the impressive list of papers he has written in re "natural genetic engineering",
I have as a trial lawyer in many Product Liability and Med-Mal case retained and qualified many experts.
Shapiro would qualify with ease as an expert in his field.

This message is a reply to:
 Message 544 by Taq, posted 01-20-2011 6:20 PM Taq has replied

Replies to this message:
 Message 564 by Percy, posted 01-22-2011 5:00 PM shadow71 has replied
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shadow71
Member (Idle past 2956 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 561 of 968 (601647)
01-22-2011 4:17 PM
Reply to: Message 552 by Taq
01-20-2011 8:47 PM


Re: increased mutation rate is not directed mutation
SeeShadow post 560

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 Message 552 by Taq, posted 01-20-2011 8:47 PM Taq has not replied

shadow71
Member (Idle past 2956 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 562 of 968 (601648)
01-22-2011 4:32 PM
Reply to: Message 553 by Taq
01-20-2011 8:51 PM


Re: increased mutation rate is not directed mutation
taq writes,
Mutations are still observed to be random with respect to fitness which is the whole point. The cell does not sense antibiotics in the environment and then specifically mutate a specific gene to produce antibiotic resistance, as one example. Instead, random mutations produce the resistance which is then selected for.
Here is a quote from Shapiro an ID chat board Feb. 20, 2003
iarelli
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. When a retrovirus-like element inserts in a new genomic location, it carries with it a defined set of regulatory signals that can affect the reading of nearby DNA sequences in very particular ways. This is an example of non-randomness. In addition, some changes (such as those in the immune system) can be targeted to specific locations by the presence of particular signals in the DNA or by activation of transcription. These phenomena show us that cells are capable of altering their genomes in non-random but not rigidly specified or pre-determined ways.
Here Shapiro seems to go beyond what you have posted above.

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shadow71
Member (Idle past 2956 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 563 of 968 (601650)
01-22-2011 4:48 PM
Reply to: Message 559 by molbiogirl
01-21-2011 12:35 PM


Re: Cognitive systems v. cognition
Here's a definition that I think Shapiro would agree with:
molbiogirl posted,
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.
I can't speak for what Shapiro would agree with, all I can do is post what he wrote, and the above definition does not in my opinion change his opinions and findings.
I never stated Shapiro supported ID.
This thread is Potential falsifications of the theory of evolution.
That is why I posted about Shapiro's findings and opinions. And the following quote is from Shapiro's Boston Review article.
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.

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Replies to this message:
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Percy
Member
Posts: 22480
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 564 of 968 (601651)
01-22-2011 5:00 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
shadow71 writes:
See above paper, and the impressive list of papers he has written in re "natural genetic engineering"
The approach you're taking seems to be:
  1. Find someone who you think has a falsification argument against evolution.
  2. Convince everyone he's so wonderful that he must be right.
An approach you might consider is:
  1. Reach agreement with other participants about what Shapiro is actually saying.
  2. Discuss Shapiro's actual views to determine whether he actually has a falsification argument against evolution.
--Percy

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molbiogirl
Member (Idle past 2664 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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 Message 563 by shadow71, posted 01-22-2011 4:48 PM shadow71 has replied

Replies to this message:
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molbiogirl
Member (Idle past 2664 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 (James A. Shapiro), 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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RAZD
Member (Idle past 1427 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 567 of 968 (601663)
01-22-2011 6:42 PM
Reply to: Message 549 by shadow71
01-20-2011 8:38 PM


Re: increased mutation rate is not directed mutation
Hi again shadow71, sorry but still seem to be reading more into this than exists.
When he says Molecular compuation network demonstrating biologically useful properties OF SELF-AWARENESS AND DECSION MAKING (emphasis mine) does that not speak of some sort of ability to make decisions based upon what the circumstances present?
Please note that the full sentence is:
quote:
One can characterize this surveillance/inducible repair/checkpoint system as a molecular computation network demonstrating biologically useful properties of self-awareness and decision-making.
He is not saying that this is necessarily a conclusion from the data, rather that in his opinion that the behavior actually observed CAN be classified in that manner.
Curiously, I find opinion to be a poor judge of reality, unable to force evidence to fit, no matter how well informed that opinion may be. In this case it may be a little presumptious.
It is very easy to make a primitive computation system with these characteristics. Back in 1964 at university one of the tasks we had was to plug together black boxes to make such a system, a primitive, simplistic computer. The black boxes came in two flavors: the AND gates required both inputs to be positive to issue a positive output, while the OR gates require either input to be positive to issue a positive output. The task was to emulate a mechanical soda machine, detect the value of the money input in a variety of ways and output the proper soda and any change (this was back when soda was 10 cents a can).
This is not earth shaking intelligence, nor is it significant self-directing decision making, it is a response mechanism that makes a variety of different responses in reaction to a variety of different inputs. It does not come up with novel new solutions to brand new input situations.
Evolution, over billions of years, has given all evolved life the results of billions x billions of trial and error experiments, with the results of successful experiments passed on and built on. It would be shocking (to me anyway) if this did not involve evolution of the ways and means that evolution responds to a variety of different inputs with different learned results, including allowing increased mutations in areas where they have been more beneficial in the past.
How do you interpret the statement that "...that cells have molecular computing networks which process information about internal operations and about the external enviroment to make DECISIONS controlling growth, movent, and differentiation...
This clearly speaks of decision making processes .
In the same way that the black box soda machine has a decision making process, responding to a variety of different inputs with a variety of response outputs that have been tried in the past, and where the successful trial offspring survived. One of these is increased rate of mutation, another may be to increase reproduction, and another may be to limit increased mutations to segments that are not life threatening.
It does not come up with novel new solutions to brand new input situations, and it does not decide or direct what mutations would be best.
Enjoy.

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This message is a reply to:
 Message 549 by shadow71, posted 01-20-2011 8:38 PM shadow71 has replied

Replies to this message:
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barbara
Member (Idle past 4824 days)
Posts: 167
Joined: 07-19-2010


Message 568 of 968 (601676)
01-22-2011 11:36 PM
Reply to: Message 567 by RAZD
01-22-2011 6:42 PM


Re: increased mutation rate is not directed mutation
There is no man made device or machine that is built to make decisions. Every step is designed to work if all of its parts are working properly in the order of how it was suppose to function.
In a living body form of life it is regulated in all of its parts and systems that also allow it to function without any other mechanism required to operate it. The problem of accepting this as developing by randomly attracting all of its components together by circumstances that allowed this organized system to emerge as the end result over time without any directed mechanism with the ability to communicate its direction is going to be met with disbelief.
If we are going to accept the fact that mutations are random and no living entity is exempt from this rule and every individual in a lifetime will experience a large number of mutations in their genes that eventually kills you if predation doesn't get to you first then the word "mutations" doesn't explain evolution very well.
When people generally are trying to understand how species can change into another species with a different body plan over time, they don't want to hear the word mutations. Especially when all you hear is how mutations causes disease factors in populations.
At this point in time, science cannot identify any mutation specifically to a gene or a set of genes that can be connected to its morphology that is evidence of one body plan emerging a different morphology structure of another body plan and give its identity of those creatures.
The point is by using the word mutations as the answer for changes then the entire genome is nothing but mutations, therefore it would be impossible to identify differences in any of the genes in that we all came from a common ancestor.
How would you identify when a gene became neutral, deleterious, or beneficial without a set of genes in their original form to compare it too? We do not have the first body plan organisms genetic sequences as the base of your comparison group.
Genetic studies are producing too many false/positive results which indicate the model that is being used is worthless. Until most of the biodiversity has their genes sequenced and logged that perhaps more meaningful patterns will emerge.
Sometimes the best response is to say,"We just do not know enough yet to make any solid determination regarding mutations"

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Coyote
Member (Idle past 2128 days)
Posts: 6117
Joined: 01-12-2008


Message 569 of 968 (601678)
01-22-2011 11:54 PM
Reply to: Message 568 by barbara
01-22-2011 11:36 PM


Re: increased mutation rate is not directed mutation
Sometimes the best response is to say,"We just do not know enough yet to make any solid determination regarding mutations"
Based on your post, I would change that to: "Creationists just do not know enough yet to make any solid determination regarding mutations."

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

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 Message 568 by barbara, posted 01-22-2011 11:36 PM barbara has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 570 of 968 (601688)
01-23-2011 4:40 AM
Reply to: Message 568 by barbara
01-22-2011 11:36 PM


Reconstructing ancestral genomes
If we are going to accept the fact that mutations are random and no living entity is exempt from this rule and every individual in a lifetime will experience a large number of mutations in their genes that eventually kills you if predation doesn't get to you first then the word "mutations" doesn't explain evolution very well.
Well obviously, but no one says that 'mutation==evolution', mutation is one process involved in evolution.
In asexual unicellular organism there is a strong case to be made that 'mutation==evolution' since a) there is no separation of germ line and soma as there is in more complex metazoa, i.e. vertebrates. B) There is only 1 genome copy per organism unlike even multicellular asexuals which lack a discrete soma/germ line distinction. Therefore evolution is effectively lamarckian in such organisms with any mutation acquired during its lifetime passed onto its 'daughters'.
When we look at something like vertebrates however the disjunction between mutation and evolution is clear and makes your question look pretty much incoherent. You are essentially indulging in that favourite of creationist pastimes, creating a strawman of evolutionary theory. Only a tiny small subset of the mutations a complex multicellular organims like man experiences could ever contriubte to evolution, these are the mutations that effect the germ cells and of those only a miniscule fraction will ever have an actual chance to contribute to the development of new offspring. If you think of a human having 2 children then even in women where things are less wasteful that represents 2 out of 1-2 million oocytes initally present in the germ line.
It is also worth pointing out that your assumption that predation and some sort of genetic breakdown are the only two ways to die seems pretty specious. There are plenty of accidental ways to die that don't involve genetics or predation.
The point is by using the word mutations as the answer for changes then the entire genome is nothing but mutations, therefore it would be impossible to identify differences in any of the genes in that we all came from a common ancestor.
Well we do identify such differences, so clearly you are wrong. If you mean that identifying such differences doesn't allow us to perfectly reconstruct the ancestral genome then you have some point.
What it does do is give us a great deal of insight into the geenral structure of the ancestral genome. The exact detail of which specific nucleotide out of the descendant genomes was present in their common ancestor is harder than looking at the diversification of gene families and the reorganisation of genomic architecture, but not impossible. If you have a reasonably diverse group like the primates then a simple consensus approach give yo a good likelihood of finding the corrct ancestral sequence, i.e. if you have 8 descendant species and 6 of them have an A at 1 position and 2 have a T then A is the most likely ancestral nucleotide.
Obviously as you get further and further back it gets harder and harder reconciling all the descendant lineages. But it is still an active field of research and your assertion that it is impossible is therefore strange.
What may be impossible is to ever define a latest universal common ancestor (LUCA) genome. Some origins of life researchers, Carl Woese for one, have suggested that early in the development of cellular life horizontal gene transfer was so pervasive that it may make it next to impossible to construct a single robust LUCA genome.
But if the real problems don't set in until the earliest cellular life then the vast majority of evolutionary biologists are unlikely to be crying into their pillows much.
TTFN,
WK

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