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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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AdminNosy
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Message 2 of 136 (367877)
12-05-2006 10:04 PM


Thread moved here from the Proposed New Topics forum.
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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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jjburklo
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Message 4 of 136 (373303)
12-31-2006 11:52 PM
Reply to: Message 1 by RAZD
12-05-2006 9:46 PM


For now I will only touch on the second half of your post about the gaining of information. I would not necessarily call this a gain an information more then it is simply a rearrangement of existing information. The bacteria rearranged existing information to be able to break down lactose. I'll refer you to another paper on the Evolutionary Potential of the ebgA gene (the replacement gene for the lacZ gene which was deleted).

http://mbe.oxfordjournals.org/cgi/reprint/12/3/514.pdf

Interestingly, the study finds that if the lacZ gene and ebgA gene are deleted there is no chance of utilization of lactose. There is also a 35.5% sequence identity between the 2 genes as well as the proteins sharing 13 of 15 active site residues, giving credence, at least to me, that no new information has been provided rather there has simply been a rearrangement of existing information. Also, quite interesting is that the wild-type enzyme of ebgA is quite ineffective in utilizing lactose and its analog lactulose. So ineffective that these sugars cannot be utilized for growth when the operon is expressed constitutively at a level that the ebg protein constitutes 5% of the cells soluble protein (the ebgR- repressor gene was removed).

The evolutionary potential of the gene was then tested when the detla lacZ ebgR- is subject to selection on a plate of lactose. Only 2 phenotypic classes of single step spontaneous mutations were obtained, Class I and class II. Class I will grow on lactose but not on lactulose, and class II will grown on lactose but on only moderately on lactulose. No other class was found to utilize lactose or lactulose. 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.


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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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jjburklo
Inactive Member


Message 6 of 136 (373448)
01-01-2007 2:50 PM
Reply to: Message 5 by RAZD
01-01-2007 12:44 PM


Re: A > B and C = A therefore C > B
quote:
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.

No, I'm comparing a known system(which in my opinion did not evolve) that utilizes lactose and lactulose with a system that in the words of those that composed the study provides an "evolutionary constraint" to the utilization of lactose and lactulose in the absence of the lacZ gene under their particular solution and under their experimental conditions. My point is simply that your example is hardly concrete. I would divulge deeper into this but its the New Years and I'm going to spend the rest of it with my family. Happy New Year to you and thanks for the debate.

Edited by jjburklo, : No reason given.


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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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AnswersInGenitals
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Message 8 of 136 (373513)
01-01-2007 8:31 PM
Reply to: Message 7 by RAZD
01-01-2007 4:08 PM


I have a vague recollection of performing experiments along these lines in a molecular biology class many, many years ago. The purpose of the experiments was to confirm that the bacteria's acquired ability to metabolize lactose was due to random mutations and not due to its 'remembering' a preexisting function that had been disabled. In these experiments, lactose incompetent E. coli were grown on a glucose medium, where they thrived and the glucose was slowly replaced with lactose. This killed almost all the bacteria, but if the switch to lactose was slow enough, a few colonies of lactose competent bacteria would emerge and spread over the lactose infused petri dish.

That the change in the bacteria to lactose competence was due to random mutations was established in two ways. First, several samples were run with varying rates of conversion from glucose to lactose. If the switch was too fast, all the bacteria died and no lactose competence emerged. If the switch over was slower, the few colonies with lactose competence emerged as described above. If the emergence was due to re-learning an existing capability and only a few bacteria survived the switch over, that just meant that some bacteria were faster learners than others. Using a very gradual switch over would allow all the bacteria time to 'learn' the new competency and (almost) all would survive. But even with extremely slow switch over, almost all the bacteria died and only a few competent strains emerged. A detail statistical analysis (which was one of the main points of the exercise) showed that the 're-learning' conjecture was not supported and a random process was involved.

The second set of experiments was even more direct proof (particularly for those uneasy with the statistical analysis.) Another set of glucose to lactose switch over experiments were performed, but this time, some of the samples were exposed to various levels of mutagenic agents: ultra-violet light, gamma-rays from a cobalt 60 source, and the chemical mutagen Na3N (sodium azide, the same stuff used to inflate automobile air bags!) The mutagens increased the rate at which the lactose competent colonies emerged in precisely the way predicted for a random mutation process.

As I said, this is a vague memory from long ago - I'm not even sure we performed these experiments as described or just read about them - so if anyone can correct me if I erred in my description or has any more concrete references , I would be interested in seeing them. It would also be interesting to know if anybody has sequenced the genomes of the bacteria before and after the lactose competence was acquired to show that it was not due to a disabled capability and to show the details of the genetic changes. In the meantime it is amusing to see the evolution deniers plunge into the 'information' issue and then try to rationalize that the loss or gain of critical competences does connote not connote a change of information or that the order of symbols in a sequence is not germain to that sequences information content. The logical extension of this is that there is no significant difference between being alive and being dead since there is no information loss involved.

On the other hand, I have to admit that the lactose competent colonies were still of "bacteria kind".

Edited by AnswersInGenitals, : because the voices told me to.


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RAZD
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Posts: 18767
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Joined: 03-14-2004
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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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Fallen
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Posts: 38
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Message 11 of 136 (414341)
08-03-2007 9:07 PM


Would you mind linking to those threads? As someone who is considering joining/creating a discussion on this topic, I would like to know what has been said so far.
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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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Siggy
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Posts: 15
Joined: 09-09-2007


Message 13 of 136 (420826)
09-09-2007 5:28 PM


i have one little problem with your beginning argument sir. Mr Hall's experiments eliminated the power of IC machines to prove anything. 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.

the idea is simple, and i do agree that micro evolution can do such things, but if you remove one piece of a Lego building, any moron can try every piece until one fits correctly, but try removing 5 or how about all of them?

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.

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?


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Chiroptera
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Message 14 of 136 (420830)
09-09-2007 5:39 PM
Reply to: Message 13 by Siggy
09-09-2007 5:28 PM


Hello, Siggy, and welcome to EvC.

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 not true. Consider, for example, A and B are parts of a simple "IC" system. Then C is added -- C is not necessary, but it does help make the process a little bit better. ABC is better than AB alone. But then a mutation turns A into A'. A' works with the combination BC much, much better than A did -- A'BC is much, much better than ABC. The only problem is, if you take away C then A'B doesn't work at all. Thus, it appears as if A'BC is completely irreducible. But it's not -- you just don't currently see how A'BC evolved from simpler, reducible precursors.

So it is not really the case that you can look at a system and tell that it absolutely could not have evolved.

-

but if you have 1% of the machine, can evolution fill in the difference?

Sure. If that 1% works just good enough to impart a reproductive advantage to the possessor, then it will be selected for.

-

And I couldn't resist:

the idea is simple, and i do agree that micro evolution can do such things, but if you remove one piece of a Lego building, any moron can try every piece until one fits correctly, but try removing 5 or how about all of them?

Great! You have just disproved the "Living organisms are made of Legos" theory. And so science advances.


I could tell you what I've read about evolution, the big-bang, super-universes, quantum foam, and all that stuff. Eventually you'd ask a question I can't answer, then I'd have to go look it up. Even If I had the time for that shit, in the end you'd ask a question science hasn't answered yet. So let's save time and skip ahead to "I don't know." -- jhuger
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RAZD
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Member Rating: 3.8


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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This message is a reply to:
 Message 13 by Siggy, posted 09-09-2007 5:28 PM Siggy has responded

Replies to this message:
 Message 17 by Siggy, posted 09-09-2007 6:34 PM RAZD has responded

  
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