Irreducible Complexity

THE GALATIAN

The point of the email was not that the components of the flagellum existed in another form in simpler structures of the cell.

Rather, it points out that the combination of proteins found in the flagellum is not irreducibly complex. So the Type III Secretory "syringe" that has the components of the flagellum that can be adapted to motion rather than movement to inject molecules into another cell.

The reason that this sort of motility evolved in bacteria seems clear. The Reynolds number a measure of viscosity related to turbulent flow, is about 1X10^7 for a bacterium, while it is about 1X10^-4 for a sperm cell. Even waving cilia would be inefficient for a bacterium.

Rotation is a more sensible approach when viscosity is to the point that it doesn't matter much how one orients the paddle on a return stroke.

Keeping in mind that there is essentially no inertia for a bacterium in water, due to the low Reynolds number, it's clear that any motion by a structure of the cell would impart a useful unbalanced force on the cell.

Carrier proteins, large protein molecules involved in active transport, work by rotating in the cell membrane. They are powered by the same processes that make the syringe/flagellum assemblies go, but they are much simpler. Nevertheless, they do impart a moment on the cell when they turn, as a portion of the protein is normally protruding from the cell membrane.

The simplest form of locomotion for a cell would then be an active transport molecule that had lost a specific site, and turned freely. Again, because of the viscosity at this scale, even a very short "flagellum" would provide a usable moment. The Type III Secretory Apparatus is on the cell membrane, protruding out into the environment. It moves at the base, because it is used to protrude and expel cell material. But it also has the important elements of a flagellum. It provides a moment when it does move, (because of the low Reynolds number, there is little inertia, so efficiency is not the issue) and it is made of many of the same proteins of the more complex flagellum.

One could object, saying that these have two different "purposes". But the history of evolution has always been not of the appearance of completely new features, but of the reworking of old features to new uses. And here we have an obvious candidate in the form of a moving structure on the surface of the cell that has many of the features of a flagellum.

There's a lot of interesting work to be done here. But it becomes very clear that even the simplest bacterial flagellum is not the simplest form of motility structure possible, and there are a number of possible ways for it to evolve.

[ June 07, 2002, 09:39 AM: Message edited by: Administrator ]

 

JOHN PAUL

Time to bring the water to the horse.

By now we all should be well aware that Behe’s book, Darwin’s Black Box, is a challenge to scientists to objectively demonstrate how apparent IC biochemical systems arose via purely natural processes and to get that work published in peer-reviewed journals. You don’t have to take my word for it all you have to do is to read the book.

Just below what Helen posted from the book, also on page 72:

So what is Behe talking about when he speaks of irreducible complexity?

From page 39 of Darwin’s Black Box

John Paul:
In the Galatian’s example, the structure had a function as that 10-part (protein) piece (which appears to go against Behe’s definition). As I stated in my earlier post we now have to figure out how that 10-protein structure came together in the first place. Is it IC? Then we have to figure out, seeing that this 10-protein structure has a function, what happens to the organism once that function has been removed because of the mutational accumulation that is required for that 10-protein structure to become part of the flagellum. Once that is accomplished we have to figure out where the other parts (proteins) of the flagellum came from and what put all the parts together so that the flagellum would form and function as it does.

More from Behe on IC (Darwin’s Black Box posted earlier in this thread):

*Same elephant mentioned in the article below:

http://www.creationequation.com/Archives/TheBiologist.htm

John Paul:
Here’s another difference between Creationists and evolutionists:

Evolutionists say the apparent design in living organisms is illusory and the apparent sequence of fossils is real and needs to be explained.

Creationists say the apparent design in living organisms is real and needs to be explained and the apparent sequence of fossils is illusory.

How can we be sure of the design in living organisms?

Again, Behe from Darwin’s Black Box:

 

HELEN

Galatian, I'm glad you agree with God's design regarding the flagellum. However your agreement does not mean it evolved. Nor does it mean that proteins somehow switched jobs and that the governing mechanisms in the cell allowed this. I'm sure you know that proteins in the cell are recycled continually for most kinds of cells in most areas. Extra proteins are a useless waste and are dissassembled and the amino acids used again for another protein. The cell of any organism will not produce a new form or function that we have seen. Your example of a changed metabolic pathway is the only example you have and it had to replace one that was disturbed by intelligent designing scientists. The fact that it had a perfectly good metabolic pathway in the first place and also had the ability to replace it when artificially disturbed says nothing about the emergence of a NEW function and form, such as a flagella.

In the meantime, the point of Behe, again, is that any irreducibly complex structure or function cannot function in that way or be what it is unless it is ALL there from the start. Part of a flagellum doesn't work. Part of a blood clotting cascade is a killer without the rest, etc.

 

THE GALATIAN:

That's just what Hall's work on E. coli demonstrated.

"Evolution on a Petri Dish : The evolved B-galactosidase system as a model for studying acquisitive evolution in the lab", Barry G Hall, Evolutionary Biology (1982) #15, pg 85-150.

Mutation produced an entirely new way of utilizing a food source, and then made it irreducibly complex by adding a regulator. Now the system can't work unless both are present. Since Behe declared that to be irreducible complexity, we now have undeniable evidence that IC evolves.

A quick look found these:
(a quote from the report, not the abstract)

Envelope structure of Synechococcus sp. WH8113, a nonflagellated swimming cyanobacterium
Aravinthan DT. Samuel, Jennifer D. Petersen, and Thomas S. ReeseBMC Microbiol. 2001; 1(1): 4

A simpler form of motion, using a primitve "motor", and a simpler protein complex from the cell wall.

Molecular Characterization of fliD Gene Encoding Flagellar Cap and Its Expression among Clostridium difficile Isolates from Different Serogroups
Albert Tasteyre, Tuomo Karjalainen, Véronique Avesani, Michel Delmée, Anne Collignon, Pierre Bourlioux, and Marie-Claude BarcJ Clin Microbiol. 2001 March; 39(3): 11781183

Again, we see other functions for these units, consistent with the evolution of flagella. Here's an interesting one that shows flagella as having an structural function as well as motility:

Borrelia burgdorferi periplasmic flagella have both skeletal and motility functions
Mohammed Abdul Motaleb, Linda Corum, James L. Bono, Abdallah F. Elias, Patricia Rosa, D. Scott Samuels, and Nyles W. Charon
Proc. Natl. Acad. Sci. USA. 2000 September 26; 97(20): 1089910904 ; published online before print September 19, 2000.

Since evolution works by reworking old structures to new uses, this finding is a very interesting breakthrough.

No, Hall's study put an end to that idea. Irreducible Complexity is quite easily evolved.

This one is a stunner. Here one has declared a priori, that anything capable of evolving cannot, by definition, be irreducibly complex. But then, this is nothing but an attempt to deny evolution by definition. As you have seen, irreducibly complex (in the sense that all components must be present for the system to work) featurse do evolve, and rather readily.
And such a definition is impossible to use, since one must prove a negative, i.e. demonstrate that it could not have evolved.

John Paul:

A good question, in more ways than one. Now we know that the typical bacterial flagellum has antecedents, we ask next, "How about the Type III Secretory Apparatus?". And if we can show a simpler antecedent for that, we can keep backing up, presumably to the time when the four forces decoupled and made chemistry possible. To what end?

It's to prove a negative. But science is not in the business of doing that. Nor is religion, as far as I know.

 

THE GALATIAN

Helen:
Galatian, I'm glad you agree with God's design regarding the flagellum.

Of course, as we have discussed before, I believe it is insulting God to suggest that He "designs" like a limited creature. I am, however, continually impressed by the way He created nature to evolve such things.

However your agreement does not mean it evolved.

Of course not. It is, rather, the evidence that counts. The fact that we find a simpler structure in the cell, with the same proteins, demonstrates that the flagellum is not irreducibly complex after all. Of course, we also have to specify which flagellum, since there are several different ones, of differing levels of complexity. It also turns out that bacterial flagella still function as secretory structures, and this works, even in the absence of most parts of the flagellum.

http://minyos.its.rmit.edu.au/~e21092/flagella.htm

Nor does it mean that proteins somehow switched jobs and that the governing mechanisms in the cell allowed this.

Check the link above. There is evidence for just that happening.

I'm sure you know that proteins in the cell are recycled continually for most kinds of cells in most areas. Extra proteins are a useless waste and are dissassembled and the amino acids used again for another protein. The cell of any organism will not produce a new form or function that we have seen.

We certainly have seen numerous examples of that happening. One of the most remarkable is that several genera of bacteria have evolved enzymes capable of digesting nylon oligomers.

http://www.nmsr.org/nylon.htm

Your example of a changed metabolic pathway is the only example you have and it had to replace one that was disturbed by intelligent designing scientists.

That's the nature of evolution; it is indifferent to how the environment actually got changed. But the response is entirely by the sorting of mutations by natural selection. And if you note the example linked above, you'll see that new information, in the form of a frame shift that created a gene to digest nylon oligomeres (moderate-sized nylon polymer) did exactly that.

The fact that it had a perfectly good metabolic pathway in the first place and also had the ability to replace it when artificially disturbed says nothing about the emergence of a NEW function and form, such as a flagella.

See above. There are many other examples. Most of the new genes for antibiotic resistance are like this. In some cases, the precise nature of the mutation is known.

In the meantime, the point of Behe, again, is that any irreducibly complex structure or function cannot function in that way or be what it is unless it is ALL there from the start.

That's what Hall's experiment refuted. The new metabolic pathway is irreducibly complex, because it cannot function without both components present. Yet it evolved by stepwise accumulation of mutations.

Part of a flagellum doesn't work.

Actually, that's not quite true, either. All of them work as secretory structures, even if the other parts are missing. And even the motility function isn't irreducibly complex in most bacteria.

Part of a blood clotting cascade is a killer without the rest, etc.

But since we have observed that irreducible complexity evolves, it doesn't really say anything about evolution. After all, part of the enzyme system in Hall's bacteria won't work either. Yet it evolved.

 

JOHN PAUL

It is now obvious that the galatian hasn’t read Behe’s book Darwin’s Black Box, nor has he read Behe’s responses to his critics which I linked to in the 3rd post of this thread and has been posted since February 24th of this year. This is no way to conduct a debate. In order to debate properly you have to know what it is you are debating against. In this case it is irreducible complexity. If you are going to argue against Behe you have to know what his position is. That would mean reading his material that pertains to this topic. Reading other material by Behe might give you more insight into his position.

Here is the .pdf file of Behe’s responses to his critics. In it he rebuts Miller’s claim (notice it isn’t Hall’s claim) that Hall’s experiment(s) show that irreducibly complex systems can evolve and have been shown to do so.

http://www.iscid.org/papers/Behe_ReplyToCritics_121201.pdf

From the 3rd post of this thread:

 

THE GALATIAN

Actually, that's wrong. Here's one.

I found about 30 different articles on the evolution of ATP, in which the evolution of enzymes for ATP was also discussed. The oldest was published twelve years ago.

[ June 11, 2002, 09:27 AM: Message edited by: Administrator ]

 

HELEN
Galatian, Hall’s work, as described in Evolution on a Petri Dish, from the quotes you have given, and the way you describe it, involved intelligently knocking out one function, keeping the E.coli in optimal living conditions, and then seeing the function be restored via another pathway internally.

At the very least, this tells me that E.coli were designed well enough that they were able to establish alternate metabolic pathways in a pinch to keep themselves going.

Now, if you would care to explain how, in totally natural conditions, like, say, an animal’s gut, E.coli is going to have a pathway knocked out in the first place? Or be in optimal conditions to try to survive?

In short, as this seems to be the only example you have (you have been using it for about four years now), might I suggest that it is not nearly sufficient to show what it is you are wanting it to show? The E.coli is still E.coli. The change evidently did not stay among the E.coli. Both of these results are exactly what would be predicted by the various groups opposed to evolution. And that is because that is what we see continually: basic type is maintained (biological stasis), and in the wild, there is a reversion to wild type, with mutations and variations simply varying around a mean and never heading anywhere by building on top of one another to produce a new type.

And yes, there has been a great deal written about the cilia and flagellum. That is not the point. The point is that the ONLY paper even approaching the possibility of them arising evolutionarily was published the SAME year as Behe’s book, in another language in Europe! Therefore he was right in saying the scientific literature was barren of explanations for the evolutionary process. It was simply taken for granted.

Ken Miller has attempted to show how the flagellum can arise by a series of purely natural processes. His attempt uses impossible protein transfers which somehow stay through how many generations? And then as if that isn’t enough imagination, it turns out the entire scenario is simply a ‘what if’ story with no basis on scientific fact whatsoever. “Theoretical work suggests” is also not enough to show anything actually happened, only that a man can imagine it happening!

Nor is there ANY DATA showing how a more ‘primitive’ means of cellular locomotion is related to cilia or flagellum development.
Your quote involving cell shape does show one interesting point I have made a number of times, though, and that is that the genome does NOT carry all the information regarding cell replication. So a change in the genome itself (mutation) is not enough to even change the shape of your B.bufgdorferi.

Now, about “design”. The opposite is “undesigned.” Are you saying the world is not designed?

Design involves plan. Man is stuck with needing to design sequentially. God is not. This is where your straw man of God not being a designer falls flat. God is God. The plan, or design for the world and humanity did not need step by step incubation in His mind! He invented time! So He is not subject to it.

When we refer to God as the Intelligent Designer (which we do if we are Christian, although the Intelligent Designer may have another identity to someone else), we are not saying God needed to be involved in a mental step-by-step process. We are saying that the world shows evidence of design, intentional, intelligent design. We do know from Genesis that it was created via a step-by-step process, so this would also indicate a grand Design in the mind of God. Therefore it is no insult to God to credit Him with the marvelous beauty, complexity, and interrelationships we see in creation.

 

[Administrator: this includes two emails from Galatian arriving in the same group]

THE GALATIAN

Helen:

Well, you need to remember that Hall never actually "knocked" out anything. He merely found a mutant that had lost the ability to metabolize one particular substance. Having done that, he then simply cultured it in the usual manner, in the presence of that substance.

If he had stupidly done this, would it then count? What if that mutation was never noticed by anyone, and the new pathway evolved. How would that be different? These are certainly good issues you've brought up here, and deserve some discussion.

Although (as you know), I object to the use of "design" because I think it's disrespectful to God, I'm inclined to agree with you that God certainly created living things with an ability to evolve new features in such events. We differ primarily in how far back we think God's creation incorporated such wonders.

Good questions. There's really only one way to lose such a function. A mutation damages the system in such a way that it no longer functions. The reason E. Coli would survive such a mutation is that it does not depend on any one particular substrate for an energy source. Hence it would survive quite readily. What Hall did was put the bacterium in an environment with a good amount of that substrate. Hence, any bacterium gaining the ability to metabolize it again would be at a considerable advantage.

I found out about it last year, I think. It's certainly a great one, though. How often do you actually get to be there when an irreducibly complex system evolves?

Of course you're right; it is. The good part is that it’s an E. Coli with a new, irreducibly complex metabolic pathway.

Heck, even evolutionists like Behe said that it was impossible. But there it is.

I'll pick up on the question of "design" as an attribute of creation later.

* * *

I think it was an understandable oversight. I'm just making the point that the literature has many papers on the evolution of cellular structures.

The fact that we see those "flagella proteins" showing up in simpler moving structures, and that the simplest flagellum would be no more than a single molecule rotating in the cell membrane (of which there are many) is merely evidence that the flagellum could have evolved. We may never know precisely how. But what we don't know for sure is a shaky foundation.

Yes. We know, for example, that the mitochondria, chloroplasts, and other organelles have their own DNA, which is more like bacterial DNA than that of eukaryotes . So that is technically not our genome, even though the information therein is essential to the survival of almost every eukaryotic cell. It's the best evidence that eukaryotes evolved from prokayotes by endosymbiosis.

Do you have any other examples?

It isn't, that's also true. Form in living things is an interaction between genes and the environment. Have you had time to read "On Growth and Form"? D'Arcy Thompson shows that much of the form of living things can be shown to be due to physical forces of the environment. He also shows how the complex "designs" of bee combs and termite mounds can be accomplished by very simple rules for each insect's behavior.

Looks created to me. The reason Paley had to chose a watch in his paper asserting design, was that if he had chosen a created object, no one would conclude it was designed.

If we redefine "design" to exclude planning, then we are no longer insulting God. So, If that's how you define it, then I have no compliant. After all, we say that a man's painting is his "creation", and that probably also is an affront to the creator, unless we redefine "creation". I can see your point, but I think I'll leave "creation " for God's way, and "design" for the things creatures do.

I think any Christian, including theistic evolutionists would agree with you, if you define "design" as you have earlier. It is that "grand design" by which God created everything in one stroke, from which that "stepwise" creation came about.

Hence, you are right, I think, in asserting that God had already provided the means by which E. Coli evolved a new metabolic pathway. The very fabric of living things contains the ability to adapt to environments. I know that you don't think of it that way, but it's really just a different aspect of the same creation.

On that, we can agree. It's always a challenge talking to you, Helen. But it's always a pleasure. Thanks for the input.

 

JOHN PAUL

galatian:
Actually, that's wrong. Here's one.

John Paul:
How did I know that you were going to ignore the pertinent part of the post and instead divert attention away from your unsubstantiated claims? By doing so it would appear that you are abandoning Miller’s premise that Hall’s experiments show that IC can evolve.

BTW, according to Hall we are seeing adaptive mutations in his experiments. Something the modern synthesis (or neo-Darwinism if you prefer) states can’t happen, but what Dr. Spetners non-random evolutionary hypothesis relies on.

John Paul:
The full article can be read here:

http://www.pnas.org/

Click on the Search feature.

Once there enter 171178898 in the box for the DOI:10.10733/pnas. search selection. You can also enter the authors in the appropriate boxes.

What will be clear to anyone reading this is it is not a paper on the Darwinian evolution of the ATP synthase.

One more thing to clear up- Behe’s book Darwin’s Black Box was published in 1996. From the book:

galatian:
A quick look found these:
(a quote from the report, not the abstract)

John Paul:
Now as far as I know, 2000 & 2001 are after 1996. All the galatian has done was to show that it appears scientists are taking up the challenge. That is if these articles really do discuss the evolution of the flagella. Let’s take a look:

The first article, which can be read here:

http://www.biomedcentral.com/1471-2180/1/4

The authors discuss the motile mechanism for Synechococcus sp. WH8113:

And finally:

However flagella is mentioned:

(bold added)

Behe’s challenge was not met by the first article.

The second article can be found here:

http://jcm.asm.org/cgi/content/full/39/3/1178

It basically says that flagellated & non-flagellated bacteria have the Genes fliC & fliD. Although similar they aren’t exact copies.

(bold added)

a little more from the article:

And as you can see the purpose of the article was not to demonstrate how the flagella evolved, just what its possible role is in a certain scenario. It does show that there is interest in the flagella, but Behe wasn’t disputing that.

I am not so sure the last article states what the galatian thinks it does it reference to the evolution of the bacterial flagelum. To read the last article just go to the PNAS search linked to above, enter the first two author’s names as shown plus the first four words of the title and you should get the article. Or enter the DOI number 200221797 .

The link I see in the last article is that the internal periplasmic flagella (allegedly) evolved into the external motility mechanism we are discussing. However upon further investigation I found the following which pretty much wipes out any hope of this organisms’ periplasmic flagella evolving into the flagella we are discussing:

http://www.hsc.wvu.edu/micro/faculty/charon.htm

(bold added)

It can be seen these articles do not say what Galatian claims they say.

 

SCOTT PAGE

A creationist writes:

BTW, according to Hall we are seeing adaptive mutations in his experiments. Something the modern synthesis (or neo-Darwinism if you prefer) states can’t happen, but what Dr. Spetners non-random evolutionary hypothesis relies on.

Is that the same Hall that co-authored this (emphasis mine):

As for Spetner's 'hypothesis', have any creationists been able to find any documentation at all describing anything similar to what Spetner requires in multicellular eukaryotes? That is, where are the before-and-after genetic analyses that demonstrate the changes that would be needed

 

JOHN PAUL

Does Hall’s experiment(s) involving E. coli really show that IC can evolve? According to Dr. Behe the answer is a resounding “No”!

The following can be read in its entirety at the following URLs:

http://www.iscid.org/papers/Behe_ReplyToCritics_121201.pdf

and

http://www.arn.org/docs/behe/mb_trueacidtest.htm

Dr. Behe:
When I first read this section of Miller’s book I was quite impressed by the prospect that actual experiments-not theoretical, “just-so” stories- had produced a genuine, non-trivial counterexample to irreducible complexity. After going back to read Professor Hall’s publications, however, I found that the situation was considerably different. Not only were Hall’s results not what I expected based on Miller’s description, in fact they fit most naturally within a framework of irreducible complexity and intelligent design. The same work that Miller points to as an example of Darwinian prowess I would cite as showing the limits of Darwinism and the need for design.

John Paul:
From this it is obvious that Dr. Behe really wants scientists to take up his challenge. He is as sick of “just-so” stories as the rest of us who, for good reasons, doubt the grand sweep of the ToE.

C. Adaptive Mutation

Dr. Behe:
So what did Barry Hall actually do? To study bacterial evolution in the laboratory, in the mid 1970's Hall produced a strain of E. coli in which the gene for just the beta -galactosidase of the lac operon was deleted. He later wrote:

John Paul:
If, as Behe states, Hall produced that strain with the lac operon deleted, that would be a sign of intelligent intervention (yes even if it was done stupidly). Can anyone link us to Hall’s original paper(s) so we can see if he says how this strain was produced (naturally or with his intervention)?

Thus, contrary to Miller’s own criterion for “a true acid test,” a multipart system was not “wiped out” - only one component of a multipart system was deleted.

John Paul:
Well maybe the deletion of that one component led to the multi-part system’s not functioning correctly (or at all) but that just shows that all the components need to be in place for that multi-part system to function correctly. IOW, if you have an apparent irreducibly complex multi-part system you have to demonstrate how each of those parts arose and then how they came together to form that multi-part system, before you can say the apparent IC of that system is illusory. As anyone can see Hall’s experiment(s) did not do this.

as Hall later wrote:

Dr. Behe:
The mechanism(s) of adaptive mutation are currently unknown. While they are being sorted out, it is misleading to cite results of processes which “violate our most basic assumptions about the randomness of mutations” to argue for Darwinian evolution, as Miller does.

John Paul:
Heck I say bring on all the evidence for adaptive mutations that you can. I am sure Dr. Spetner would appreciate it. It does show how far evolutionists will go to try to refute IC, even including experiments that could show their premise of only random mutations leading to diversity to be questionable.

 

JOHN PAUL

Scott page:
Is that the same Hall that co-authored this (emphasis mine):

John Paul:
Most likely the same guy. No one has said adaptive (or directed) mutations are not natural. They are natural they just aren’t random. Was there a point to citing this article?

AIG discusses the article here:

http://www.answersingenesis.org/docs2002/0408lab_evolution.asp

Or maybe this one:

John Paul:
Again most likely the same guy. And again the debate is random vs. non-random, not adaptive vs. growth-dependent or adaptive vs. natural.

If you are going to post stuff like this it may be a good idea to state the relevance of the material and even post the URL so we can read the whole article without having to search for it. If you are getting this stuff off the internet you are at the website anyway so just give us the link.

Scott Page:
As for Spetner's 'hypothesis', have any creationists been able to find any documentation at all describing anything similar to what Spetner requires in multicellular eukaryotes? That is, where are the before-and-after genetic analyses that demonstrate the changes that would be needed

John Paul:

From Merriam-Webster’s collegiate dictionary ( http://www.m-w.com/ ). NOTE: Definitions for all main words used (ie Hypothesis, Theory and Law) can also be found there be entering the respective word in the proper box or by going to the hypothesis definition and clicking on them.

Grin… If Dr. Spetner’s non-random evolutionary hypothesis had what the evolutionist asks for it would no longer be a hypothesis now would it?

However the theory of evolution is allegedly well beyond the hypothesis stage.

Have any evolutionists been able to find any documentation that random mutations can lead to the vast diversity of life from some genetically unknown single-celled organism that just happened to have the ability to self-replicate? True we know that copying errors occur, but that doesn’t mean they can lead to the grand sweep of evolution required by the ToE. We also know that other mutations occur, but that doesn’t make them random.
Do evolutionists have any evidence, besides our ignorance, that recombination, duplications/ amplifications, insertions, deletions, inversions and transpositions of genetic material are random events?