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Author Topic:   Irreducible Complexity, Information Loss and Barry Hall's experiments
RAZD
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Message 1 of 136 (367875)
12-05-2006 9:46 PM


1. Irreducible Complexity


Ken Miller on his website "A True Acid Test" talks about the evolution of an "Irreducibly Complex" mechanism that fits the definition Michael Behe used when he made the term up ("Darwin's Black Box: The Biochemical Challenge to Evolution." - p 39):
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.

The conclusion made by Behe and others is that IF evolution cannot produce them, THEN they must have been made, designed, created.

Let's review the logic of this argument:

  • (P1) complex systems exist in biological organisms where there are multiple parts involved in a process, feature or function, and where the removal of any part of the system renders the whole process non-functional.
  • (P2) if NO such system can evolve then it must be developed by some other process, and then, AND ONLY THEN, the existence of any "IC" system is evidence that "some other process"MUST have occurred.
  • (C1) Therefore such a system MUST be made, designed, created by some other process.

Leaving aside for now the logical fallacy of the false dichotomy (and the fact that precept (P2) of this argument is basically based on ignorance or denial of how such systems could have formed), we can still show that the concept is falsified if we can show that ONE such "IC" system HAS evolved: if ONE such "IC" system evolves then it invalidates the "then AND ONLY THEN" condition that is necessary in order that "some other process" MUST be involved.

Without the "then AND ONLY THEN" condition, the argument is reduced to it MAY have happened on any system where we just don't know whether it evolved or not (thus depending on ignorance of any mechanism to even be considered), and the specific conclusion is invalid (as several other conclusions can be made with equal validity, one of which is "we don't know") ... or at this point it becomes a non-falsifiable concept, a god-of-the-gaps, a moving-goal-post concept that avoids scientific pursuit of answers at all costs. Without the above condition the conclusion becomes

  • (C1b) Therefore such a system MAY or MAY NOT have evolved OR it MAY or MAY NOT have been made, designed, created by some other process, OR the universe may have sprung into existence last thursday fully formed, OR some other answer: we don't know.

This is not a testable conclusion and does not add any intellectual advantage to investigating the biology of the system with only science - the pursuit of knowledge based on what we DO know.

This is why the principle of falsification is used by science.

On to the experiments in question:

As noted in Ken Miller's website, just such an "IC" system was seen, observed, and documented as evolving in a couple of experiments run by Barry Hall:

quote:
In 1982, Barry Hall of the University of Rochester began a series of experiments in which he deleted the bacterial gene for the enzyme beta-galactosidase. The loss of this gene makes it impossible for the bacteria to metabolize the sugar lactose. What happened next? Under appropriate selection conditions Hall found that the bacteria evolved not only the gene for a new beta-galactosidase enzyme (called the evolved beta-galactosidase gene, or ebg), but also a control sequence that switched the new gene on when glucose was present. Finally, a new chemical reaction evolved as well, producing allolactose, the chemical signal that normally switches on the lac permease gene, allowing lactose to flow into the cell.

Does Barry Hall's ebg system fit the definition of irreducible complexity? Absolutely. The three parts of the evolved system are:

(1) A lactose-sensitive ebg repressor protein that controls expression of the galactosidase enzyme
(2) The ebg galactosidase enzyme
(3) The enzyme reaction that induces the lac permease

Unless all three are in place, the system does not function, which is, of course, the key element of an irreducibly complex system.

It's "irreducible" and it evolved. Thus precept (P2) is invalidated, falsified, refuted, and ALL conclusions based on it are invalidate. Q.E.D.

Denial of falsification is not faith, it is delusion: something believed in spite of evidence to the contrary.

2. Information Loss


Another argument common to creationism and IDology is that mutations only result in the loss of "information", and that without a mechanism to gain "information" new systems, functions or features cannot evolve.

Let's review the logic of this argument:

  • (P1) mutations cannot cause an increase in "information."
  • (P2) an increase in "information" is necessary for new mechanisms or functions to evolve.
  • (C1) Therefore new mechanisms or functions cannot evolve.

Leaving aside the fact that "information" is not defined in any way to measure whether or not there is an increase or a decrease in any evolved changes in species over time, we can still show that the concept is falsified if we can show that ONE such mechanism or function has evolved that would require such an increase. In other words, if we can show that either (P1) or (P2) must be invalid then we have shown that the conclusion is invalid.

Now let's look at Barry Hall's experiments again in light of this concept:

An existing "irreducibly complex" system is intentionally disrupted and ceases to function.

According to the equation of new information with the evolution of new functions or mechanisms by precept (2), the intentional loss of a function or mechanism must then also involve the loss of AT LEAST SOME information for that function or mechanism:

quote:
In 1982, Barry Hall of the University of Rochester began a series of experiments in which he deleted the bacterial gene for the enzyme beta-galactosidase. The loss of this gene makes it impossible for the bacteria to metabolize the sugar lactose.

Thus the deletion of the beta-galactosidase gene MUST have involved the loss of AT LEAST SOME information for the function or mechanism of that gene.

Next what we see is that a DIFFERENT "IC" system evolves to replace the original -- the original "IC" system is not repaired or recovered, but a new and different "IC" system evolved.

Ergo new "information" MUST have evolved that was not in the original organism, the "information" for that organism MUST have been increased. Again, this is the principle of falsification used by science - it invalidates either precept (P1) or precept (P2), and therefore invalidates ALL conclusions based on their combination.

We started with a system with some quantity of "information" that -- according to precept (2) -- must have been lost to render it dysfunctional, and then a replacement system evolved.

Either "information" was added (invalidates precept (P1)) OR added "information" was not necessary for the evolution of a feature, function or system (invalidates precept (P2)).

Thus either precept (P1) OR precept (P2) is invalidated, falsified, refuted and ALL conclusions based on their combination are invalidate. Q.E.D.

Denial of falsification is not faith, it is delusion: something believed in spite of evidence to the contrary.

Conclusion


These two experiments by Barry Hall invalidate two pet concepts of creationism and IDology.

This was not the intent of the experiments -- they were done in 1982 and 1983 and well before Behe's book (hardcover published by Free Press August 2, 1996; first paperback edition published by Free Press March 20, 1998) -- the intent was to do science and find answers to questions via the scientific method.

That these experiments invalidate these concepts shows if anything, a lack of intellectual rigor on the part of creationism and IDology, and not any further need for science to investigate either concept.

Enjoy.



Hall's experimental results are available in two papers:
(1) - BG Hall (1982) Evolution on a Petri Dish. The evolved b-galactosidase system as a model for studying acquisitive evolution in the laboratory. Evolutionary Biology 15: 85-150.
(2) - BG Hall (1983) Evolution of new metabolic functions in laboratory organisms, in Evolution of Genes and Proteins, M Nei and RK Koehn (eds.), Sinauer Associates, Sunderland, MA.


Is It Science Forum please.

Edited by Admin, : No reason given.

Edited by Admin, : Fix bad character in title.

Edited by RAZD, : symbols fixed

Edited by RAZD, : urling


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RAZD
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Message 3 of 136 (368136)
12-07-2006 7:33 AM
Reply to: Message 2 by AdminNosy
12-05-2006 10:04 PM


Thanks Ned ... bump for notice ..
Thanks (and welcome back) AdminNosy

I suspect it will get little response from the IDologists and Creationists.


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RAZD
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Message 5 of 136 (373414)
01-01-2007 12:44 PM
Reply to: Message 4 by jjburklo
12-31-2006 11:52 PM


A > B and C = A therefore C > B
I would not necessarily call this a gain an information more then it is simply a rearrangement of existing information.

Irrelevant gibberish. Mental masturbation imh(ysa)o.

You could equally claim that a compilation of every alphabet and numerical system we know then contains all the information in the universe, for all you have to do is rearrange it.

Obviously it is the arrangement that contains the information and not the elements. Rearranging the elements to produce new meaning ADDS information - meaning that did not exist before.

It is the arrangement of 1's and 0's in the binary code that contain the information of your post and mine, not the existence of 1's and 0's.

The point of the post about the Hall experiment is that information was removed, subtracted, deducted, deleted, taken, wiped, zapped, etc.

That information was then replaced by a different system that accomplished the same result, consumption of lactose, in a different way.

In between the bacteria was incapable of processing lactose. It did not have the information to process lactose.

How can you do that without adding information?

A - x = B where x > 0
B + y = C where y = any positive or negative number
C = A : solve for y

you can't get back to the same place without adding something back.

It does not matter how you define "information" to realize that this addition must have happened in this case, or that the concept of "information" is useless, having no impact on restricting what can and what cannot evolve.

... giving credence, at least to me, that no new information has been provided ...

Denial of evidence does not make it go away, nor does it affect the operation of the real world.

The conclusion was that the ebg operon is quite limited in its evolutionary potential. So your example shows not only an "evolved gene" that in wild type has only feeble beta galactosidase activity towards lactose and lactulose, but also an evolved gene who's mutations to increase its activity towards lactose and lactulose, which constitutes a whopping number of 2, are hardly convincing as well.

First, you are comparing and old mechanism that has undergone thousands of years of evolution and natural selection to continually become more robust and capable to one that is only a few years old and has only passed ONE mutation and selection event.

Second, there is no requirement for an evolved system to be robust and universal - all it needs to do is allow the organism to survive and reproduce better than it can without it. This system accomplishes that task.

Again, your impression is irrelvant to the way the world operates.

Enjoy.


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RAZD
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Message 7 of 136 (373469)
01-01-2007 4:08 PM
Reply to: Message 6 by jjburklo
01-01-2007 2:50 PM


Re: A > B and C = A therefore C > B
No, I'm comparing a known system(which in my opinion did not evolve) ...

Your opinion counts for nothing. It does not keep the world from spinning, nor the seasons from progressing. It does not keep life from evolving.

You still cannot escape the irreducibly simple fact that

A > B and
C = A
therefore C > B

Where both A and C contain the "information" for processing Lactose, and B does not.

Either "information" was added or the concept of "information" is useless. It is that simple.

Enjoy.

Edited by RAZD, : No reason given.

Edited by RAZD, : words words words

Edited by RAZD, : rearranged equations for clarity


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RAZD
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Message 9 of 136 (373863)
01-02-2007 11:44 PM
Reply to: Message 8 by AnswersInGenitals
01-01-2007 8:31 PM


I did a google and found some stuff that seemed similar (even some high school experiments on e. coli) but no direct reference in the ones I looked at (and no, I did not look at all of them, so it may be out there somewhere).


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RAZD
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Message 10 of 136 (404753)
06-09-2007 3:52 PM


bump for new people
there are two threads where IC has been raised. This thread discusses some evidence that falsifies it.

Edited by RAZD, : english


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RAZD
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Message 12 of 136 (414378)
08-03-2007 11:26 PM
Reply to: Message 11 by Fallen
08-03-2007 9:07 PM


Welcome to the fray Prodi

Would you mind linking to those threads?

Don't remember specifically (two months ago?), Sorry, but I think that IC would probably have been off-topic, hence re-direction here rather than continue on those threads.

Check Forum Intelligent Design to see current active threads on ID.

Enjoy

ps -- there are two reply buttons, the General one you used and another at the lower right corner of each post -- that one links messages to the one replied to providing continuity (and usually sending an email to the poster)

also check out dbcodes (help) while in reply mode as it has many hints on formating such things as

type [qs]quote boxes are easy[/qs] and it becomes:

quote boxes are easy


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RAZD
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Message 15 of 136 (420833)
09-09-2007 5:49 PM
Reply to: Message 13 by Siggy
09-09-2007 5:28 PM


Welcome to the fray Siggy.

the point isn't for an already working machine to rebuild itself, the point is that starting with nothing, a machine of that complexity cannot evolve.

But evolution doesn't start with nothing. It starts with an existing organism that adapts to changing ecologies & opportunities or dies.

And when we switch the topic to abiogenesis and the development of a possible first life, with only the requirements for a very simple self-replicating system, then you would have to show that an IC system would be required for that (and which could not come together with the same processes that developed life). And we won't know that until life is generated eh?

The point is this; natural selection by its very nature will eliminate parts that do not benefit the organism immediately so unless all of the parts evolved simultaneously natural selection itself would have gotten rid of them.

This is precisely what is falsified by the experiment. Natural selection eliminates parts that are deleterious or lethal, but it is indifferent to ones that are neutral.

if you have 99% of the parts of a machine in working order, i can imagine that under "the correct circumstances," whatever that means, evolution can fill in the rest, but if you have 1% of the machine, can evolution fill in the difference?

Life is not machines. If you have 1% of an organism, but it is independently alive and can replicate then it will continue to evolve. Look at what "machines" evolved from the basic prokaryotes (after a billion years slow start).

Enjoy.


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RAZD
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Message 23 of 136 (420860)
09-09-2007 7:26 PM
Reply to: Message 17 by Siggy
09-09-2007 6:34 PM


Edit Please.
Can you edit your post so the url is not so long? It is forcing the window to be too wide to read. Use "peek mode" in the reply window to copy the coding used here:

Evolutionary Loss of Useless Features: Is it Molecular Noise Suppression?

nothing was in reference to the machine not the organism

Life is not a machine and machine analogies just don't represent what life systems do.

isnt that an origin of life topic?

That is what abiogenesis is.

This is completely not true. thus why evolutionists claim that we are losing "unnecessary" biological parts

http: //links.jstor.org/sici?sici=0003-...

survival of the fittest means eliminating everything that isnt fit, and by its very nature eliminating parts that dont benefit the body immediately

Nope. First off, the elimination of structural features by gradually making them vestigial is due to (a) several mutations being involved and (b) the energy used to make them can be employed to make other features, but this doesn't have to happen.

Second, what we are talking about are neutral mutations in the DNA code -- ones that are not involved in the production of a feature in the phenotype. As such they are not subject to natural selection - which acts on the phenotype of whole individuals - and there is no way for natural selection to touch them.

youre making statements based on your assumptions! that would be like me saying look at how great God is because He made all of this; while this is what I believe i dont make that statement because you dont believe He did, so it means nothing to you.

I would be careful ascribing beliefs to others in any way.

No, I am making statements based on my understanding of evolution and biology, aspects that have been tested and validated.

Life replicates itself, and that makes it fundamentally different from any mechanical device.

Enjoy.


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RAZD
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Message 28 of 136 (514828)
07-13-2009 7:49 AM
Reply to: Message 25 by traderdrew
07-12-2009 2:50 PM


Re: Irreducibly Complexity and a True Acid Test
Hi Traderdrew, thanks for following the link.

Upon reading Razd’s post a second time, I came across a name that I was already familiar with and that is Brown University professor Kenneth Miller. I had to investigate Razd's post because I don’t think it is worth being a proponent of irreducible complexity if it doesn’t have any merit. However, I knew there were some things that didn’t jive and there were some questions and beliefs I had in mind.

Yes, Ken Miller is a biologist at Brown University, and he was a witness for the Dover trial that showed Intelligent Design as taught in Dover was just regurgitated Creationism, religion masquerading as science. Behe was also a witness, and he admitted in court that there were no (repeat no) known "irreducibly complex" systems that could not evolve.

1. Jason Shapiro has discovered and continues to discover an incredible sophistication of life at the cellular level. Michael Behe stated in his latest book that natural genetic engineering makes evolution (not Darwinian) more plausible.

Irrelevant. For one, this is the argument from authority, plus Behe's is the argument from incredulity. Plausibility has nothing to do with what actually happens. How complex things are now is not related to how difficult it is for evolution to accomplish it over billions of years.

2. If the lactose-utilizing system in E. coli is irreducibly complex, then why isn’t the more complex TTSS (type three secretory system) NOT irreducibly complex? (page 61, “Only a Theory” by Kenneth Miller)

Again, irrelevant. What makes something "irreducibly comples" is defined by Behe - any system where the removal of one part renders the system inoperative.

3. When an irreducibly complex system loses any of its parts, it does indeed cease to function. There is no denying this. So why is there a debate on this? The question should be, how long does the system stay non-functional before it is repaired?

Once more, irrelevant. Evolution does not repair systems it replaces them if they are beneficial to improve survival or reproduction. If neither purpose is served, broken systems are not repaired nor replaced. Look at ape vitamin C broken gene.

4. Why didn’t Kenneth Miller use the TTSS along with this argument in his book, “Only a Theory”. I consider this bacterial argument the stronger one since he claims that it produced and irreducibly complex system.

Because there are many systems that have evolved "IC" systems. This is another one.

5. Irreducible complexity is not necessarily a reality. Don’t think for a moment that I have slipped into the dark side. Irreducibly complexity is derived from the neo-Darwinian paradigm and the complexity of microorganisms. It is a way of looking at the complexity of cellular life through neo-Darwinism. I am not a believer in neo-Darwinism. Since I am not, I.C. isn't a filter for intelligent design.

I think you have this backwards. Behe proposed IC as a test of Intelligent Design - as something that could not evolve, and therefore must have had help. Several evolved IC systems - including this one - show that this concept is false and thus is not indicative of Intelligent Design.

When I googled the search term “Michael Behe lactose”I started to find some real answers to my confusion. You can find the Miller / Levine link and Michael Behe links with the same search term.

Of course. You will also see links to Behe's response from the Miller site, as well as a reply that still shows that the critical element of the issue is that an IC system evolved - it does not matter how it evolved, just that a new system is now in place where the removal of any one part renders the remainder inoperative.

This says that only one part of the multipart system that Miller alluded to was wiped out.

Correct, rendering the system inoperative, hence it was an IC system.

The genes apparently came from similar preexisting genes. These genes were probably located somewhere in the so-called junk DNA. We do have two mutations so far.

It is irrelevant where they came from, as the necessarily start with an existing gene. The genes in question were still changed by mutation and selected for by improved survival or reproductive ability - ie evolution.

Sounds like they were sensing what Jason Shapiro discovered and that is “natural genetic engineering”. NGE raised a question from proponents of ID. Where did this sophistication come from? The more sophistication inside the cell, the more things could be tinkered with and therefore, mutations would require more precision and larger effects for natural selection to act upon them.

Again this is a red herring to the issue of evolving an IC system and it is just an argument from incredulity: gosh I can't think how such a "sophisticated" system could have evolved, it MUST be helped by something. Bad logic does not make reality.

Now we have an artificially produced substance called IPTG that was required in order to produce the final results of this experiment otherwise the bacteria would not have been able to use lactose in the wild. We have our third artificially induced mutation produced by human intervention.

Again irrelevant. Evolution operates by mutation and selection. The selection is for greater survival and reproduction in an environment, regardless of the environment.

The issue still remains that a new system evolved that the removal of any one part renders the remaining parts inoperative, hence it is an IC system - an evolved IC system.

I believe Jason Shapiro (from his website) tells us that the genome has sophisticated error correction mechanisms that actively participate in correcting errors arising out of transcription. So when I add this into the picture, it seems to me that it would be very, very unlikely for these three mutations actually being produced in the wild. It is more likely that the results of this experiment were the results of an intelligent designer.

Curiously, your opinion on what is more likely has absolutely no effect on reality, does not alter biological behavior in any way, nor does it change the FACT that an IC system was observed to evolve.

The content below (is similar to but expressed in my own terms) came from Jason Shapiro who is a professor of biochemistry and molecular biology at the Universtiy of Chicago. See the next link below.

http://shapiro.bsd.uchicago.ed.....eeting.pdf

Exonuclease proof reading in the polymerase (that exists in bacteria as well as E. coli) catches and corrects 99.999 percent of the errors as soon as they are made (Kunkel & Bebenek, 2000). If any errors escape the exonuclease, the methyl-directed mismatch repair system detects and fixes over 99% of those errors. (Modrich, 1991) This multilayered proof reading system effectively boosts the error correction precision to over 99.99999999%.

Interestingly, this assertion is refuted in this particular experiment by the FACT that the existing system was not repaired. This repair mechanism only repairs errors, it does not create new systems to replace broken systems. Thus the evolution of a different system to replace the broken system was not put into effect by this repair mechanism.

The Conclusion

The possibility of three simultaneous mutations in these bacteria evolving from neo-Darwinism and maybe even all types of random evolutionary processes seems to be quite impossible without intelligent intervention and guidance.

For one, they were not three simultaneous mutations, but each occurred independently. For seconds, once again your opinion is irrelevant. The fact remains that a system evolved where the removal of any one part renders the whole system inoperative - an IC system.

The fact that an IC system was seen to evolve means that it is absolutely impossible to honestly claim that an IC system cannot evolve.

Enjoy.


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RAZD
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Message 31 of 136 (514898)
07-13-2009 8:28 PM
Reply to: Message 29 by greentwiga
07-13-2009 10:35 AM


Hyjacked gene duplications
Thanks greentwiga,

Then if A', B', and C' disappear, we are left with A,B, and C. Granted it wouldn't happen often, but we do see all these steps happening.

Exactly, it happens often enough that one cannot use the claim that such a system cannot evolve.

It also does not need to involve a whole gene, but just a patch that codes for a certain protein, say one that facilitates the consumption of a previously unused food source. This happens often, without it necessarily being a part of an "IC" system.

One can also say that the theory of evolution predicts the evolution of "IC" systems, as there is no reason to maintain A', B', and C' if they serve no purpose or their original purpose has been superseded by the new function/s.

Enjoy.


we are limited in our ability to understand
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Rebel American Zen Deist
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This message is a reply to:
 Message 29 by greentwiga, posted 07-13-2009 10:35 AM greentwiga has not yet responded

  
RAZD
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Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 32 of 136 (514909)
07-13-2009 10:09 PM
Reply to: Message 30 by traderdrew
07-13-2009 4:10 PM


Sticking to the topic.
Hi again Traderdrew,

Once again, I have searched for a quote like this on the internet and in the Dover trial statements you provided in the other thread. Would you care to show us where it is and exactaly what Behe stated?

I'll have to get back to you on that. It was discussed on another thread here shortly after the cross examination of Behe, but the search engine is a little funky, presumably with the new board. A link that was supposed to be

quote:
EvC Forum: Behe and blood clotting
One of Behe's examples of supposedly un-evolvable irreducibly complex systems is .... In the Dover trial, even after presented with a mountain of evidence ...
www.evcforum.net/cgi-bin/dm.cgi?action=msg&f... - Cached - Similar

Except it lead to http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=10&t=221&m=1

Curiously it doesn't change the fact that an IC system was seen to evolve in the Barry Hall experiment.

It is irrelevant to the discussion directly but other than that, I don't agree with the rest of that. First of all, plausibility suggests the best possible scenario. I have noted that the scientific process doesn't directly look for the truth; it looks for the best explanation by looking for what is false. Since we cannot go back and see how it all occurred, then we should look for the best explanation or conduct experiments that could support historical evidence.

Yes, but the plausibility of an argument is not sufficient on it's own to make a concept scientific, and your personal opinion of what is plausible (or not) is not science.

Irrelevant seems to be your favorite word so far but how does irrelevant information disprove any of the arguments that directly reference information in the main one?

Interestingly, it would not have been used if you had not posted irrelevant material. It is a common ploy of creationists to try to divert the argument with irrelevant material.

Vitamin C is another example of how evolution seems to have deconstructed a system ...

Which is another example of an argument that is not about the development of an IC system in the Barry Hall experiment. This is another diversion attempt. Evolution says natural selection can construct and deconstruct systems, and there is no mechanism known to prevent the construction of systems. That however is a matter for another thread.

You cannot show us how the flagellum evolved from the TTSS. Even my dog knows that you can't evolve the flagellum from a TTSS. The TTSS has 10 parts while the flagellum has 40. Pull out some logos and try to make a model of a flagellum with a model of a TTSS.

Another argument from incredulity. This is also trying to move the goal-post to a different IC system. (ie irrelevant to the specific issue of this thread).

Let's stick to the IC system in Barry Hall's experiment first, and then IF you can refute that an IC system did in fact evolve, we can discuss other IC systems.

You cannot explain in detail nor is there any evidence of a Darwinian step by step process that can produce an IC system.

Don't need to. What we have is an existing IC system (as defined by Behe) that was disabled, and a replacement system evolved. That replacement system just happened to also be an IC system (as defined by Behe).

I can illustrate this in the form of stepping stones. The first two stepping stones were resurrected from genes that divurged from the genome (Hall, 1999) and resurrected by a process known as natural genetic engineering. The stepping stones (mutations) were only made posssible with the inclusion of an artifical substance called IPTG. IPTG was obviously synthesized for specific experimental functions.

The stepping stones were mutations that occurred naturally and that were selected by natural selection within the environment the bacteria was grown in. It does not matter that IPTG was there, as it was not involved in the mutation, it was not involved in the natural selection, so it was not involved in the evolution of the IC system. All that it provided was the marginal survival of the bacteria long enough to take advantage of the lactose when a beneficial muation occurred.

Miller strongly implies that natural selection pieced together the whole pathway in Hall's experiments, but in fact it only replaced one component (and even then it could only replace the component with a spare near-copy of the original component). When two or more components were deleted, or when the bacterium was cultured in the absence of an artificial chemical (called IPTG), no viable bacteria could be recovered. Just as irreducible complexity would predict, when several steps must be taken at once, natural selection is a poor way to proceed. - Michael Behe

Curiously, it does not matter where the original DNA were before the mutation, as any mutation would occur on existing DNA.

Interestingly, the fact that a "spare near-copy" was used still ignores the fact that this specific DNA sequence was unable to provide the missing component without the mutation.

Fascinatingly, the fact that IPTG was used to keep the bacteria marginally alive while the process of evolution took place only means that it was part of the ecology the bacteria was living in, where mutation and natural selection for the use of lactose occurred.

Amazingly, when several steps can be taken in sequence, natural selection is a good way to proceed. This is, in fact, what has occurred.

Incredibly, knocking out two components violates the terms of an IC system as defined by Behe, and we now have almost any system you care to name, that can be so disabled.

Tellingly, we are still left with the fact that an IC system evolved.

Hall has not demonstrated how the lactose function in E. coli lacking both the lacZ and the ebg gene could really evolve from scratch. Where did those genes come from in the first place? Hall believes they existed in the genome 2 billion years ago.

Again, this is irrelevant. The issue is really very simple:

  • an e.coli bacteria could metabolize lactose using an existing IC system.
  • that IC system was disabled by knocking out one of the components (the element that makes it an IC system).
  • the bacterium was kept alive, barely, on a medium that provided just sufficient nutrients for survival, AND that provided lactose.
  • the bacteria evolved the gene for a new beta-galactosidase enzyme (called the evolved beta-galactosidase gene, or ebg),
  • then it evolved the control sequence that switched the new gene on when glucose was present,
  • finally, a new chemical reaction evolved as well, producing allolactose, the chemical signal that normally switches on the lac permease gene, allowing lactose to flow into the cell.

With this system now in place, the e.coli could once again metabolize lactose. The system is also an IC system because if you remove any one of the three elements, the e.coli cannot metabolize lactose.

Despite what I state here, Darwinists will always fall back on the same old excuse. "If we give organisms enough time and chance, they will evolve the same sophistication that we see in life today." Just look at the quote below from the above post.

Irrelevant: an IC system has been observed to evolve. That is the focus of this topic.

I think that this belief should be testable or falsifiable. Science has stated this correct? If it is testable in confluence of neo-Darwinism, then there should be evidence in some places in the past that support that belief. Perhaps rapid evolution at first with slow evolution in the last 500 million years but that is not what happened.

Once again, what you think has no - absolutely no - effect on reality, what actually occurred, nor on what is occurring now.

Aside from that point, most of them don't want to see the math (something I cannot do but I have seen) that shows us the chances of evolving complex biological systems. Never mind the necessity of multiple coherent mutations that compound the odds of creating an IC system. Never mind that natural selection would have to preserve those mutations and cannot initiate them. Never mind that the complexity in the cell would require pin point mutations. Never mind that those mutations would have been mutated in such a way as to provide specific functions. Never mind that sophisticated error correction mechanisms actually correct transcription errors 99.99999999% of the time.

And incredibly, in spite of that irrelevant ramble, and IC system was still seen, observed, confirmed, documented evolving.

In other words, your continued incredulity over what can and cannot evolve is not sufficient arguement to refute the fact that an IC system has been seen, observed, confirmed, documented evolving.

Once again, for the record:

  • an e.coli bacteria could metabolize lactose using an existing IC system.
  • that IC system was disabled by knocking out one of the components (the element that makes it an IC system).
  • the bacterium was kept alive, barely, on a medium that provided just sufficient nutrients for survival, AND that provided lactose.
  • the bacteria evolved the gene for a new beta-galactosidase enzyme (called the evolved beta-galactosidase gene, or ebg),
  • then it evolved the control sequence that switched the new gene on when glucose was present,
  • finally, a new chemical reaction evolved as well, producing allolactose, the chemical signal that normally switches on the lac permease gene, allowing lactose to flow into the cell.

With this system now in place, the e.coli could once again metabolize lactose. The system is also an IC system because if you remove any one of the three elements, the e.coli cannot metabolize lactose.

However, the concept of evolving doesn't contradict my belief system as an "assemblist". I am not a creationist. I am an assemblist.

Incredibly, I don't care what you call yourself, what you need to do is look at the facts that show that, yes indeed, and IC system evolved, and as such the existence of IC systems cannot be used for the god-of-the-gaps argument.

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 30 by traderdrew, posted 07-13-2009 4:10 PM traderdrew has responded

Replies to this message:
 Message 33 by traderdrew, posted 07-14-2009 9:08 AM RAZD has responded

  
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 56 of 136 (515018)
07-14-2009 9:02 PM
Reply to: Message 36 by Phage0070
07-14-2009 11:26 AM


Please stick to the facts
Hi Phage0070, I have trouble with your position, as it is not supported by the definition Behe gave when he first defined IC.

A system which was thought to be irreducibly complex had an element removed, and it did not cease functioning but rather mutated into a working arrangement. Thus, it was proven not to be irreducibly complex.

It did stop functioning. Generations of e.coli lived and died without metabolizing lactose.

The mutations did not repair the old system but developed a new system, with parts that did not exist before, and the method of metabolizing lactose is different from the previous method.

From the previous link on Ken Miller's website:

quote:
In my book I quoted evolutionary biologist Douglas Futuyma's description of these experiments:

"Thus an entire system of lactose utilization had evolved, consisting of changes in enzyme structure enabling hydrolysis of the substrate; alteration of a regulatory gene so that the enzyme can be synthesized in response to the substrate; and the evolution of an enzyme reaction that induces the permease needed for the entry of the substrate. One could not wish for a batter demonstration of the neoDarwinian principle that mutation and natural selection in concert are the source of complex adaptations." [ DJ Futuyma , Evolution, ©1986, Sinauer Associates, Sunderland, MA. pp. 477-478.]

These changes\alterations\mutations are not repairs, but novel to the bacteria in the experiment.

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 ...
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This message is a reply to:
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RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 59 of 136 (515025)
07-14-2009 10:37 PM
Reply to: Message 33 by traderdrew
07-14-2009 9:08 AM


Re: Sticking to the topic/s, and avoiding deceptions.
Hi again traderdrew, seems there is a lot of recent misinformation posted here: let's see if we can clear it up.

What kind of reply is that? You can't be thinking that I think my thoughts are going to influence the outcomes of experiments like that, which are experiments of natural laws. It is important to be in tune with reality.

Exactly, and we know we are in tune with reality when we are not contradicted by the facts.

For instance, Behe's "rebuttal" that you have quoted:

Look what Michael Behe wrote:
Miller also writes, "the ebg gene is actually only 34% homologous to the gene whose activity it replaces (meaning that about 2/3 of the protein is quite different from the galactosidase gene whose function it replaces)". Yet he knows as well as I do that 34% general sequence homology makes it virtually certain that the three-dimensional structures of the two enzymes are essentially identical. And since the active sites (the business end) of the enzymes are much more similar (they are identical in 13 of 15 residues), the ebg enzyme is pretty much a spare copy of the lac enzyme. Thus it seems to me that the taking over of lac galactosidase function by ebg hardly even rises to the level of microevolution.
Once again Miller shows his deceptiveness. Maybe you should be lecturing Miller (not me) on reality.

Fascinatingly, the one being deceptive is Behe: it is irrelevant how similar the genes are, similar is not identical. In fact, it is highly likely that a mutation that results in a similar feature would occur on a similar gene.

Note that if "(they are identical in 13 of 15 residues)" (= 87% identical) is sufficient similarity for one to be a "spare copy" for the other, then a chimpanzee is a "spare copy" of a human (DNA 95% identical).

Curiously, I don't consider 87% identical to be a working spare part - and that would only be the issue if it replaced the original function with a repaired version of the original function. This did not happen.

The fact is that this gene alone - without the mutation - is incapable of producing the necessary function. That means that it is not, cannot be, a "spare" copy. To call it such is to intentionally misrepresent reality.

Fact: if it was a "spare copy" then there would be no need for the mutation. It did not replace the function without the mutation, and even with the mutation it did not repair the function - it still needed the second part.

The other mutation, the second part, involves an even more dissimilar gene:

quote:
The repressor (control) gene is even more different, showing just 25% homology to the lac repressor.

Now you have two genes that are not the same, both being modified by subsequent mutations, and ending up producing a functional lactose metabolizing system.

Fact: these mutation modified genes do not exist in the previous e.coli population, they did not wait to be called upon when the original system blew a flat tire.

Natural selection only replaced one component with a 34% homogenous copy of the original component.

Natural selection did not replace anything. Natural selection does not make components nor cause functions to occur: it selects components and functions that exist in the organism by the increase in survival and reproduction the components or functions provide for the organism.

Mutations replaced two parts to achieve a functioning system, one with 34% homology and one with 25% homology. Don't creationists like to point out that the DNA of bananas is more similar to human DNA that that?

http://www.thingsyoudontneedtoknow.com/dnabananas.html

quote:
It's true. Humans share 50% of their DNA with bananas. Apparently Steve Jones, Professor of Genetics at University College, London is credited with stating this information. Kind of freaky when you think about it. DNA (deoxyribonucleic acid) is what makes us all different, but the difference between us and the next species or even a fruit isn't as significant as you would think.

So a little bit of difference in DNA can add up to a lot of difference in the organism.

I don't want to debate or argue about the subject any further. I think we have both stated what we could state.

In other words, you don't want to admit that an IC system was actually observed to evolve during the experiment.

This is, of course, the #1 ploy of creationism - avoid admitting when you are wrong.

However we are also a little off the original assertion you made on the other thread - see Message 229 - which we still need to address:

quote:
Also, science has never proven that complex specified information was created by any sort of random process or self-organization. Self-organization only gives us redundant information such as crystals.

and your response to my reply Message 240:

quote:
Actually, it has been done several times - see Thread Irreducible Complexity, Information Loss and Barry Hall’s experiments and A True Acid Test. ...

No, that is incorrect. You don't know what I am talking about. I just read your first post on that other thread. I wasn't around to shed some light on it. :-)


This is, after all, what got us here.

Interestingly, this thread not only discusses the fact that an IC system has evolved, but that in the process, information must have been added. The reason is simple: after the lactose mechanism was disabled the organisms were unable to process lactose, even though it was readily available, then a couple of mutations occurred that enabled the bacteria to metabolize lactose - by a different mechanism. This is a novel mechanism utilized by the bacteria in the experiment, a mechanism that does not exist in the outside e.coli population, and thus the addition of ability to use lactose means that information was added.

Message 42

I disagree with you on two things. I believe it did cease functioning. It has to cease functioning for a least a brief amount of time since those biochemical repairs don't occur at the speed of light.

Nor do sequential mutations occur in the same generation. Once again, the system was not repaired, as the original system is still broken\disfunctional\disabled\not working.

1. As I had already stated, when you remove a part of any IC system it has to cease functioning. The questions are, How long did it cease to function? Did Barry Hall have to keep these strains of E. coli alive when the part was removed?

It took several generations, hence the substrate designed to allow the bacteria to exist, but not prosper, while also providing the lactose for the opportunity to evolve a system to increase metabolism, survival and reproduction. It did not need to be lactose, nor did the system evolved need to be an IC system.

Could this only be done using IPTG?

No. As Miller states:

quote:
However, when Hall grew the bacteria under selective conditions designed to favor re-evolved galactosidase activity, Behe cried foul. As he should know, and as Futuyma wrote, "... mutation and natural selection in concert are the source of complex adaptations." All that Hall had done was to set up conditions where the bacteria would survive (although just barely), and would prosper only if they evolved a system to replace the one he had deleted.

All that IPTG provides is an environment where the bacteria could survive and where adaptation to metabolize lactose would result in increased survival and reproduction.

2. Was the system of the E. coli not irreducibly complex to begin with?

It is relatively unimportant to the end result, however the original system was an IC system. One part of a three part system was removed, and the system stopped working, and the bacteria never again used that system to metabolize lactose. This matches Behe's definition of IC.

Other than that, did the complexity increase?

Yes: a new system to metabolize lactose developed by mutation of existing parts, and the new system was selected by the increased survival and reproduction of the bacteria. It's this simple:


  1. The bacteria before the experiment could metabolize lactose.
  2. The bacteria with the disabled gene could not metabolize lactose.
  3. The bacteria with the new mutations can metabolize lactose.

From (A) to (B) is a change in information, "X", where X=A-B, and ...

from (B) to (C) is a change in information, "Y", where Y=B-C, and ...

because (C) = (A) and both ≠ (B), Y = -X ... so either an increase in information occurred, or ...

the change in "information" is irrelevant to the evolution of new features and functions.

As I said above, this is the other issue that this thread addresses.

If it did increase by a little bit, then it was done with intervention.

Are you saying that Barry Hall personally made the mutations on the genes?

If the person who was conducting the experiment didn't intervene, then E. coli would not have been able to hydrolyze lactose.

Except that the two independent mutations occurred after the "intervention" where Hall disabled the gene and placed the bacteria on the culturing medium. Barry Hall did not cause the mutations to occur.

This, of course brings us back to the issue of being "in tune with reality:"

What kind of reply is that? You can't be thinking that I think my thoughts are going to influence the outcomes of experiments like that, which are experiments of natural laws. It is important to be in tune with reality.

Seems you have an issue there to resolve regarding reality.

Amazingly, it now seems my comment was predictive, based on experience, and justified.

At least it would have not been done without simultaneous multiple coherent mutations and that would arguably be entering into the realm of metaphysical miracles.

Which, incredibly, is not the way it happened, so pretending that it did is just another falsehood\lie\fabrication, that you seem to need to tell yourself to avoid dealing with reality. It's a perfect example of someone thinking their opinion alters the reality to suit their belief.

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 33 by traderdrew, posted 07-14-2009 9:08 AM traderdrew has responded

Replies to this message:
 Message 67 by traderdrew, posted 07-15-2009 11:35 AM RAZD has responded

  
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 60 of 136 (515026)
07-14-2009 10:42 PM
Reply to: Message 58 by DevilsAdvocate
07-14-2009 9:21 PM


Junk DNA is off topic
Please stick to the topic, and help traderdrew stick to the topic.
This message is a reply to:
 Message 58 by DevilsAdvocate, posted 07-14-2009 9:21 PM DevilsAdvocate has responded

Replies to this message:
 Message 63 by DevilsAdvocate, posted 07-14-2009 11:07 PM RAZD has acknowledged this reply

  
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