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Author
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Topic: Evolution caught in the act?
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Michael J. Behe
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Member # 44
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posted 23. February 2004 20:13
This topic has been moved to the Literature Review Forum:
http://www.iscid.org/boards/ubb-get_topic-f-18-t-000029
In a recent news story, called “Evolution caught in the act”, featured on a website called “ www.innovations-report.com ”, the work of some University of Michigan and University of Texas researchers is highlighted. The story excitedly remarks that the researchers:
“... used a strain of mutant bacteria ... that had lost their ability to make disulfide bonds. These disulfides are critical for the ability of the bacteria’s propeller-like swimming motor, the flagellum, to work. The researchers then put these non-swimming bugs to the test by placing them on a dish of food where, once they had exhausted the food they could reach, they either had to repair that broken motor or starve to death on the spot.
...
“To the researchers’ surprise, a mutant carrying only two amino acid changes, amounting to less than 2 percent of the total number of amino acids in thioredoxin, restored the ability of the bacteria to move. The altered thioredoxin was able to carry out disulfide bond formation in numerous other bacterial proteins all by itself, without relying on any of the components of the natural disulfide bond pathway. The mutant bug managed to solve the problem in time and swim away from starvation and multiply.”
The breathless writing (typical for press releases) makes it sound as if something akin to Darwinian evolution was rebuilding a shattered bacterial flagellum. But if you go to the trouble to look up the paper (Masip et al, “An *engineered* pathway for the formation of protein disulfide bonds,”Science 303, 1185 (2004)) you find that, as per usual, the “random evolution” part is all hype.
The authors deliberately deleted a cellular system that normally adds a disulfide bond (don't worry about exactly what that is) to a certain protein that is part of the bacterial flagellum. The bacteria then were unable to swim, since they could not make normal flagella. Our intelligent engineers then went to work to find another protein that would do the job of the disulfide-making system they eliminated. They decided that a good candidate would be a protein called thioredoxin, because they knew it had a structure similar to one of the components of the trashed system, and has the basic chemical material needed for the job. However, thioredoxin normally stays inside the cell, whereas the old machinery operates outside the cell membrane. To overcome this problem the workers deliberately added a signal from another protein that is normally targeted to outside the cell, for the express purpose of getting thioredoxin into the right place. Well, nonetheless the exported thioredoxin didn't work. The workers then scratched their heads and thought, "Well, the critical part of thioredoxin is a four amino acid sequence containing the business end of the protein, which actually does the chemistry to make the disulfide bond. Let's use laboratory molecular biological techniques to make a whole bunch of mutants *in just those four residues* and see if any work." They did just that, and then fished out a couple that work, which were able to perform the step to make the flagellar protein and allow the bacteria to swim again.
The mutations were certainly not random. Quite the opposite. The workers added mutations they needed for a proper background in which to look for what they wanted, and then focused on exactly the part of the protein they wanted to substitute which they thought would help it do the job. If this is Darwinian evolution, then there's not a whole lot of difference between Darwinism and deliberate intelligent design.
Someone might ask, "How did the bacteria know which tools to mutate?" The answer is that the bacteria didn't know at all. The researchers knew. The researchers chose a *very* specific region of a *very* specific protein to zero in on.
As a project in deliberate protein engineering, the work is interesting. As an analogy to Darwinian evolution, the work makes a good case for intelligent design.
[ 24. February 2004, 10:40: Message edited by: Moderator ]
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Pim van Meurs
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Member # 541
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posted 23. February 2004 23:56
Hi Mike good to see you contribute to the ISCID forum. You raise some interesting issues and I agree that press releases seldomly represent arguments to their fullest scientific details. Which is why publications in scientific journals need to be looked at. I have gotten a copy of the paper which is quite interesting
quote:
We have engineered a pathway for the formation of disulfide bonds. By imposing evolutionary pressure, we isolated mutations that changed thioredoxin, which is a monomeric disulfide reductase, into a [2Fe-2S] bridged dimer capable
of catalyzing O2-dependent sulfhydryl oxidation in vitro. Expression of the mutant protein in Escherichia coli with oxidizing cytoplasm and secretion via the Tat pathway restored disulfide bond formation in strains that lacked the complete periplasmic oxidative machinery (DsbA and DsbB). The evolution of [2Fe-2S] thioredoxin illustrates how mutations within an existing scaffold can add a cofactor and markedly change protein function.
What I think is interesting is how they showed how a relatively simple mutation within an existing scaffoled added a cofactor and changed protein function.
The real relevance of these experiments are that they:
".. have, in essence, caught evolution in the act of adding an iron sulfur cluster to thioredoxin, enabling it to act as a thiol oxidant. Our results show that the acquisition of cofactors is evolutionarily a rather simple process, and our ability to generate an artificial pathway for oxidative protein folding highlights the plasticity of redox metabolism."
While undoubtably some intelligent design was needed to conduct these experiments, it is interesting to focus on their evolutionary relevance.
Given evolutionary pressure, thioredoxin mutants have been isolated which restored the motility in these cells.
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warren_bergerson
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Member # 262
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posted 24. February 2004 07:36
This experiment appears to illustrate at least three key elements of evolutionary change processes not explained or accounted for by traditional Darwinian theory. First, as Mike points out, the experiment shows that evolutionary change can be produced by intelligent design or engineering processes. Second it demonstrates that external design processes can impact, influence, or control evolutionary change. Finally, it demonstrates a type of evolutionary change that could not have occurred by RM&NS type processes within the time constraints necessary for survival. It might also be noted that this points out the importance of the distinction between experimental results and the interpretation of experimental results.
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Evan
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Member # 164
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posted 24. February 2004 08:21
I have two quick comments I would like to make this morning (time is short):
First, Dr. Behe wrote
quote:
The mutations were certainly not random. Quite the opposite. The workers added mutations they needed for a proper background in which to look for what they wanted, and then focused on exactly the part of the protein they wanted to substitute which they thought would help it do the job. If this is Darwinian evolution, then there's not a whole lot of difference between Darwinism and deliberate intelligent design.
Someone might ask, "How did the bacteria know which tools to mutate?" The answer is that the bacteria didn't know at all. The researchers knew. The researchers chose a *very* specific region of a *very* specific protein to zero in on.
As a project in deliberate protein engineering, the work is interesting. As an analogy to Darwinian evolution, the work makes a good case for intelligent design.
I have heard this argument before - it goes something like this: any lab experiment (or computer situation) can tell us nothing about what natural processes can do because the role of an intelligent agent (a human being) in setting up the experiment adds an element that necessarily turns the situation into an example of intelligent design.
But this can’t be right. One of the things an experimenter must do is simplify the situation and reduce the number of variables present so as to focus on the single variable or small number of variables under consideration. Experiments are “intelligently designed” to help us find out how the natural world works - I can’t see how it could be otherwise. To rule out any results that follow from such as experiment would seem to negate the possibility of doing any research on how natural processes accomplish what they do.
The question I would ask Dr. Behe is this: if experiments such as this are insufficient to investigate the potential and nature of the development of “Darwinian pathways” because of the involvement of an intelligent human being in setting them up, how would you propose that we do study the issue?
Secondly, assuming as I do that this objection about the intelligent design of the experiment invalidated any conclusions about evolution, I have this to say:
It appears to me that once the situation was set up, the existing function of the gene's product got re-worked into something entirely new in the world, and useful to the species. Nobody designed the new form of thioredoxin -- nobody other than the selective pressure. A new and useful biochemical mechanism, consequent to nothing more than mutation and selection imposed by the environment one, arose spontaneously (even though the environment for this was due to an experiment.)
It seems to me that this creation of biological novelty (and hence "new information") is precisely what many ID theorists say can’t be accomplished by natural processes. Sure, it’s very small - but what else would you expect from a short experiment in a laboratory?
The challenge for the ID theorist is to compute some probabilities here. If the probability of this small change is high (which could be investigated both by repeating the experiment and by perhaps catching sub-steps in the development of the new pathway), then we would be moving, perhaps, towards a method for eventually distinguishing design from non-designed things. With that in mind, I would think (or at least hope) that Dr. Behe would take more interest in this type of experiment and its relationship to the possibility (or impossibility) of irreducibly complex things arising via natural processes rather than dismissing the experiment as fatally flawed precisely because it was an experiment.
[ 24. February 2004, 09:25: Message edited by: Evan ]
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Paul A. Nelson
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Member # 26
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posted 24. February 2004 09:52
Evan wrote:
quote:
I would think (or at least hope) that Dr. Behe would take more interest in this type of experiment and its relationship to the possibility (or impossibility) of irreducibly complex things arising via natural processes rather than dismissing the experiment as fatally flawed precisely because it was an experiment.
Is that really what Mike is saying above -- i.e., "I don't buy it because it's an experiment"?
No. Mike writes:
quote:
They decided that a good candidate would be a protein called thioredoxin, because they knew it had a structure similar to one of the components of the trashed system, and has the basic chemical material needed for the job. However, thioredoxin normally stays inside the cell, whereas the old machinery operates outside the cell membrane. To overcome this problem the workers deliberately added a signal from another protein that is normally targeted to outside the cell, for the express purpose of getting thioredoxin into the right place. Well, nonetheless the exported thioredoxin didn't work. The workers then scratched their heads and thought, "Well, the critical part of thioredoxin is a four amino acid sequence containing the business end of the protein, which actually does the chemistry to make the disulfide bond. Let's use laboratory molecular biological techniques to make a whole bunch of mutants *in just those four residues* and see if any work." They did just that, and then fished out a couple that work, which were able to perform the step to make the flagellar protein and allow the bacteria to swim again.
Mike is saying that this is a biologically, or evolutionarily, unrealistic experiment -- a line of critique common in the origin-of-life literature (see, e.g., many of Leslie Orgel's papers).
[ 24. February 2004, 10:01: Message edited by: Paul A. Nelson ]
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Evan
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Member # 164
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posted 24. February 2004 10:09
Thank you for bringing up this more substantive issue.
However, it should be clear from my post that I didn’t mean to say that this all Mike is saying is that "I don't buy it because it's an experiment." However, this is one of the things he did say, and I think that issue bears discussion.
The other issue, which is related, is to what extent the experiment is biologically relevant. Yes, the experimenters zeroed in on a particular site (thus “intelligently designing” a part of the solution), but also the bacteria reached a solution that was not pre-planned, was unexpected, and taught the researchers something about a possible biological structure. Thinking about what this means, how to fit it into design theory vis a vis probabilities, and thinking about how to refine this type of experiment to learn more about what is biologically relevant outside of the laboratory ought to be the goal of our analysis of this paper.
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Moderator
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Member # 1
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posted 24. February 2004 10:34
This topic is not appropriate for Brainstorms: where positive contributions/brainstorms are welcome (not just critiques). I've moved the thread to the Literature Review section of our site:
http://www.iscid.org/boards/ubb-get_topic-f-18-t-000029
Posts that do not contribute to the discussion but merely advocate or act as a .html"cheerleading" service, will be deleted.
[ 24. February 2004, 10:40: Message edited by: Moderator ]
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