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Author Topic:   Typical ID response to rebuttals?
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 4 of 34 (245825)
09-22-2005 8:12 PM
Reply to: Message 1 by Annafan
09-19-2005 9:18 AM


There are several examples of refutations and counter refutations and counter-counter refutations in the literature
You can read some of them here:
Not a Free Lunch But a Box of Chocolates
A critique of William Dembski's book No Free Lunch
by Richard Wein
Not a Free Lunch
There is also:
The Flagellum Unspun
The Collapse of "Irreducible Complexity"
by Kenneth R. Miller
http://www.millerandlevine.com/km/evol/design2/article.html
More specifically there is the "acid test" -- about a specific IC system that was observed evolving. This of course refutes the proposal that IC must be designed.
{edit}I used to have a link here:
http://biocrs.biomed.brown.edu/Darwin/DI/AcidTest.html
but it doesn't seem to be working.

http://www.millerandlevine.com/km/evol/DI/AcidTest.html {/edit}
This message has been edited by RAZD, 09*25*2005 10:55 AM

we are limited in our ability to understand
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RebelAAmerican.Zen[Deist
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This message is a reply to:
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Replies to this message:
 Message 6 by Funkaloyd, posted 09-24-2005 7:54 AM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 7 of 34 (246102)
09-24-2005 11:37 AM
Reply to: Message 6 by Funkaloyd
09-24-2005 7:54 AM


The Acid Test - IC invalidated by observed evolution.
Thanks. I've saved a copy of it now so I can reference it if need be.
It also let me find the new webpage for the article
http://www.millerandlevine.com/km/evol/DI/AcidTest.html
and I have updated my bookmark
Note that this specific example doesn't refute the concept of IC, it invalidates it as a scientific concept: an IC system was shown to evolve, therefore there is not only no reason to expect any other IC system to be different, there is no need to.
If Behe were {honest\scientific} he would accept that and move on.
This message has been edited by RAZD, 09*24*2005 11:42 AM

we are limited in our ability to understand
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RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
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 Message 8 by Ben!, posted 09-25-2005 10:20 AM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 9 of 34 (246279)
09-25-2005 11:00 AM
Reply to: Message 8 by Ben!
09-25-2005 10:20 AM


Re: The Acid Test - IC invalidated by observed evolution.
It has been raised several times before, but discussed in terms related to this thread, the rebutals and refutations of rebutals, no, not that I am aware of.
I do feel that Ken Miller seems to belabor some points and take others as fully demonstrated when he could provide a little more detail, and that he repeats himself when he could be much more concise, but that could just be me (and I never do that ).
To me the point is that an IC was observed to evolve (whether naturally or under the {intentional\influence\cause} of an experiment is not relevant). Especially as it did not re-evolve the previous IC system but a new one.
What's your take?
This message has been edited by RAZD, 09*25*2005 11:01 AM

we are limited in our ability to understand
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RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 8 by Ben!, posted 09-25-2005 10:20 AM Ben! has replied

Replies to this message:
 Message 10 by Ben!, posted 09-25-2005 1:50 PM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 13 of 34 (246318)
09-25-2005 3:34 PM
Reply to: Message 10 by Ben!
09-25-2005 1:50 PM


Re: The Acid Test - IC invalidated by observed evolution.
How did these bacteria survive with no way to metabolize lactose?
My understanding is that the environment provided marginal sustenance for the bacteria unless it adapted to consume lactose, which was abundant. This would be similar to the one where a bacteria evolves to use nylon as a nutritional source (or oil or toxic waste ...)
What did the "artificial inducer IPTG" actually do?
Promote mutations, according to the study.
Was there any actual "competition" going on?
There was death of non-adaptive organisms, change in adaptive organisms, followed by the next generation. Competition is not necessary between individuals in survival situations for there to be evolutionary processes involved.
the validity of extending these lab results to true evolution (mutation and NATURAL selection).
This could be claimed of every single experiment. Did {mutation\selection} evolution occur (was there change in alleles over time)? Yes. Did this evolution allow the bacteria to consume lactose? Yes. Was this specific mutation caused directly by IPTG? No, according to the study. Would this {study\result} be repeated without IPTG? That is the test of science eh? I'd say probably, given sufficient time. Of course this is where Behe has an opportunity to do real science and invalidate the study.
That the system truly fits "IC" to start with. (want to ignore this quesiton for now)
The study was not originally intended to generate an IC system, it is Ken Miller's observation of it that puts it in this position.
BUT, according to the definition established by Behe, that removal of any one part causes the whole to fail, it is an IC system as it relies on the interaction of three parts working together.
Let's start there. As I learn more about the tests, I can really drill down specific complaints. For the moment, I have to fill in the gaps of knowledge.
.... the usual Ben SOP? ...

we are limited in our ability to understand
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RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 10 by Ben!, posted 09-25-2005 1:50 PM Ben! has replied

Replies to this message:
 Message 14 by Ben!, posted 09-25-2005 3:46 PM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 15 of 34 (246341)
09-25-2005 5:18 PM
Reply to: Message 14 by Ben!
09-25-2005 3:46 PM


Re: The Acid Test - IC invalidated by observed evolution.
Part of the problem is that the article itself is not on-line (as far as I can determine). There are other references to this study in other papers that don't have anything to do with this IC controversy, and one on NCSE has this:
Excursion Chapter 1: The Origin Of Life
http://www.ncseweb.org/...nleitner_what39s_wr_11_24_2004.asp
The evolution of new enzymes and enzymatic functions by mutation and natural selection has been demonstrated in bacterial cultures (Hall, 1982; Mortlock, 1982).
They seem to accept the argument that this involved mutation and natural selection.
There is also this from another discussion forum:
http://www.volconvo.com/forums/showthread.php?t=319
To counter the claim that no beneficial mutation has ever been observed, let's go back to the mid-1970s at the University of Rochester where Professor Barry Hall is conducting an experiment with special strains of E. coli[2]. A typical nutrient of bacteria is lactose, so Hall decided to remove the lacZ gene, responsible for the metabolization of the milk sugar substance. Hall placed one strain in an environment rich in lactose with little nutrient to survive on, and the other strain was placed in an environment with no lactose. The former recovered its ability to metabolize lactose over the course of a few days, with two mutations to preexisting genes along a different operon in the genome from the original. The first mutation produced a beta-galactosidase enzyme (34% homologous to its predecessor), tasked with breaking down lactose via a process of hydrolysis into the two monosaccharides glucose and galactose. This new enzyme was dubbed the ebg, or evolved b-galactosidase enzyme. The second mutation altered the control region, or repressor protein (25% homologous), so that the enzyme may be expressed in the presence of glucose. The second strain displayed no such progress.
(red for emPHASis)
Again, this source does not discuss IC either, but goes on to make some interesting points, one of which is related to the issue of {survival\mutation} here:
John Cairns, et al. (1988) demonstrated with E. coli that stress on an organism, created by a significant threat of survival, increases the rate of mutation. However, this should and does not make "good" or "bad" mutations any more or less likely to occur, you are merely increasing the frequency of mutations period. The disposition of mutations remain proportionate to the mutation rate.
Just increased survival {threat\pressure} has been noticed to "turn up" the mutation rate on several bacterial organisms. Its as if the mutation rate is controlled by some factor having to do with the organisms health?
This does seem to confirm my statement
I also question how much difference there is between mine and Millers?:
... set up conditions where the bacteria would survive (although just barely), and would prosper only if they evolved a system to {consume lactose}
and
... the environment provided marginal sustenance for the bacteria unless it adapted to consume lactose, which was abundant.
both say marginal survival without lactose?
The next quote seems to me to indicate the role of the IPTG was to promote survival of baceria which normally would not survive on their own:
Looking up the growth rate of e. coli (the bacterium used) I found this abstract about another experiment:
Growth-rate recovery of Escherichia coli cultures carrying a multicopy plasmid, by engineering of the pentose-phosphate pathway.
We constructed a high-copy number plasmid carrying the gene for glucose-6-phosphate dehydrogenase, zwf, under the control of an inducible trc promoter (pTRzwf04 plasmid). By transforming a wild-type strain and inducing with IPTG, it was possible to recover growth-rate from 0.46 h(-1) (uninduced) to 0.64 h(-1) (induced). The same transformation in an Escherichia coli zwf(-), allows a growth-rate recovery from 0.43 h(-1) (uninduced) to 0.62 h(-1) (induced).
Looks like they used IPTG to induce faster population growth (by cell division) from ~45% more/hr to ~63% more/hr. This would of course speed up the experiment, but I would think it would also add extra stress to the organism to gather sufficient resources in a shorter time.
I don't see any death at all.
I could be wrong, but my experience (testing e. coli contamination) is that there is normally a portion of cells that die unless specific precautions are taken to reduce that during normal testing of water for contamination.
Apparently all the ones in the other sample died. But more than that, there was no measure of dead cells mentioned so it is hard to quantify, nor does it say there was none. If they expected cell death it would not be a novel factor, but if they didn't expect it then there should be some comment about that other sample eh?
E coli is a well known bacteria and does not form spores when threatened with individual cell death. It usually survives inside intestinal tracts and has lowered survivability at normal temperatures (hence is not widely spread in the environment and thus makes a good marker for fecal pollution, albeit source can be cows as well as people).
organisms being kept alive, but only barely.
But in order for the mutations to be expressed they have to reproduce, multiply, and if the population as a whole is barely able to keep at the same levels but show change over time there has to be {loss\old} as well as {gain\new}.
But that definitely puts limitations on this experimental finding which don't seem to be stated by the book author or you in your original post. If the only evolutionary situation possible for this "IC" system to evolve is when there's no competition between situations, then that's a really important restriction to state
I'm not sure I follow your point. Perhaps we need to define or evaluate your use of "competition" in this matter? Evolution by mutation and {survival\selection to reproduce} is all that is necessary. Competition for {most limiting} resources to {survive\reproduce} would occur but I see that more as first come first served rather than kill for it, outrun etc, competition. Perhaps competition has connotations that blur the picture?
edited format, one typo
This message has been edited by RAZD, 09*25*2005 05:22 PM

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

This message is a reply to:
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 17 of 34 (246375)
09-25-2005 9:06 PM
Reply to: Message 16 by mark24
09-25-2005 8:04 PM


Re: The Acid Test - IC invalidated by observed evolution.
hey Mark.
In running down some of the points of the Hall experiment I also ran across this:
29+ Evidences for Macroevolution: Part 5
Unicellular organisms have evolved the ability to use nylon and pentachlorophenol (which are both unnatural manmade chemicals) as their sole carbon sources (Okada et al. 1983; Orser and Lange 1994). The acquisition of this latter ability entailed the evolution of an entirely novel multienzyme metabolic pathway (Lee et al. 1998).
And this last part (in yellow for emphasis) caught my eye as another multipart system. The citation is:
Lee, S. G., B. D. Yoon, et al. (1998) "Isolation of a novel pentachlorophenol-degrading bacterium, Pseudomonas sp. Bu34." Journal of Applied Microbiology 85: 1-8. {PubMed}
The abstract at PubMed did not discuss the "multienzyme metabolic pathway" so I could not determine if this could be another evolved IC system. Any idea from your end?
Thanks.

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

This message is a reply to:
 Message 16 by mark24, posted 09-25-2005 8:04 PM mark24 has replied

Replies to this message:
 Message 18 by mark24, posted 09-26-2005 9:26 AM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 19 of 34 (246647)
09-26-2005 7:21 PM
Reply to: Message 18 by mark24
09-26-2005 9:26 AM


Re: The Acid Test - IC invalidated by observed evolution.
Oh I know, that's why I wanted to find out more.

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

This message is a reply to:
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 Message 21 by Ben!, posted 09-28-2005 9:04 AM RAZD has not replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 34 of 34 (247117)
09-28-2005 10:36 PM
Reply to: Message 27 by Ben!
09-28-2005 2:27 PM


Re: IC HAS evolved, we've seen it. What's the objection now?
Ben
There has to be justification to jump from this specific scenario to ALL scenarios, and that justification simply hasn't been given.
there is a logical falsehood involved here:
the claim is that an IC system could not evolve, therefore evidence of an IC system is evidence of a designer,
there is an IC system that has been shown to evolve, so this refutes the claim that evidence of an IC system is evidence of a designer.
This does apply to all IC systems, because the premise has been falsified.
There has to be explicit argumentatation about WHY you can generalize from a specific case to a broader range of cases. It isn't a "default" that you can just hang your hat on. And I haven't seen the articles in the website that RAZD quoted, or from RAZD either.
The reason you can generalize is because of the claim of IC to be de facto unrefutable evidence of design. This has been shown to not be the case, the premise is falsified therefore the conclusion is logically invalid.
Every other IC system now defaults to the argument from incredulity (I just can't believe it can evolve) and a lack of personal ability (to envisage such happening).
It is an invalidated hypothesis, and science dictates that it is dismissed as such and we go to the next theory.
but it has to be QUALIFIED. If there is no other food supply, the damn organism would die before it ever evolved this "IC" system.
But has any organism evolved use of a new food supply when the previous one(s) have been eliminated? Or do they normally add food supplies as they are able to expand their sources? Putting an organism is a situation with low normal food supply, but an alternate food source they are not currently using does not make them evolve to use it, but allows this to happen.
Does that help?

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

This message is a reply to:
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