Sythesizing perfect magnetite crystals

_{William Dembski

January 12, 2006

Intelligent Design}

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[From an engineer friend of mine–what’s the evolutionary explanation for the synthesis of perfect magnetite crystals in bacteria?] I’m in Houston at a custom short course (all week long) in nanotechnology for [snip] given by a group of profs at Rice Univ. It’s been a very intensive course, but very informative. One interesting thing that came up was the description of a bacteria that is able to synthesize an approximately linear array of the most perfect crystals of magnetite (better than any that experts have been able to do thus far) internally, which it uses to align itself with the earth’s magnetic field so that it can navigate with respect to the oxygen gradient in the mud in which it lives. See Blakemore and Frankel, “Magnetic Navigation in Bacteria” Scientific American, 245(6), pp. 58-65, 1981. If this ain’t design, I haven’t seen it.

Comments

Patrick, I see your point. What I'm trying to demonstrate is an inconsistancy on the part of Darwinists. On one hand they claim that life is a barrier to any design inference because of the genome but on the other hand, when it serves their purposes, they deny the explanatory power of the genomoe. In any event, what we are dealing with may be substantially different than what I thought. A friend tells me that these sort of artificial compounds contain both the structure and a mirror image of the structure. If this is the case with artificial astaxanthan, it would be structurally identical to natural astaxanthan except it would ALSO contain an astaxanthan that is exactly the reverse of natural astaxanthan. The reverse form would need a completely different set of enzymes to synthesize it. So it looks like a discovery of the reverse compound, with no prior knowledge of the existence of designed astaxanthan AND with no knowledge of any artificial compounds, may be enough to infer design. The main argument would be a lack of selectable function-- the very argument that woctor was laying out! In fact, woctor laid out quite a case for design inference here. I hope he won't mind me cribbing from him. The scientists who discovered the reverse astaxanthan in the fish probably knew about artificial astaxanthan in the feed. That taints our results... Fortunately, we can look at a hypothetical scenario and use woctor's arguments to infer design. Let's say that woctor goes to the store one day and buys some salmon. Now woctor doesn't know anything about the existence of designed astaxanthan and let's say that he also knows nothing about artificial compounds containing structurally reverse forms. woctor is our perfect test control subject. woctor takes the salmon and, in keeping with his daily routine, cuts off a piece and takes it to his laboratory to extract astaxanthan. What he finds is two different astaxanthan forms. There is the regular form that he knows all too well, but there is also something else. It is a reverse form of the structure. Where did this come from? woctor starts to think. After careful analysis, he jumps from his seat and reaches for the phone. His friend RyanLarsen answers, "hello?" "Ryan, this is woctor, my salmon has astaxanthan that I think may have been designed!" How can he suspect such a thing? Well, to quote from him, "one, the mutation would have had to come to dominate the wild red algae population... two, this change in the algal genome would have had to have been unnoticed by scientists" "If itÃ¢â‚¬â„¢s not better for the algae then there is no reason to expect such a mutation, if it occurred at all, to spread throughout the population. It would just die out."(note: the mirror-image astaxanthan doesn't appear capable of delivering any benefit) And thus it is. woctor has been able to infer design for an organic compound that he had extracted from a dead fish. It turns out, in our hypothetical scenario, that life is not a barrier to design inference after all. What's more, the principles are similar to IC-- an inability on the part of nature to select for a functional benefit.RyanLarsen_{January 17, 2006
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"IÃ¢â‚¬â„¢ve appreciated your interest in this thread. I donÃ¢â‚¬â„¢t see the same problem that you do, however." I'm just saying that ID MIGHT generate a false negative since the informational bits related to the difference between the regular version of astaxanthan and the particular synthetic form of astaxanthan might not be enough to be considered CSI. Nor is it likely to be IC. As I said ID is stringent. If ID had been used instead of a weaker form of design detection it's POSSIBLE that the illegal activity would have been missed. So, ASSUMING a false negative would in fact be generated (I don't know), I suppose ID opponents could argue that ID is too stringent for some common cases but I'm not sure how that'd help them. ;) See this thread: https://uncommondescent.com/index.php/archives/348Patrick_{January 16, 2006
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Patrick, Consider this. What is the significance of the designed astaxanthan? It creates a narrow "target" (as woctor might say). But the significance is the size of the target, not the details of why it is narrow. IC structures are a far narrower target for natural selection, so the two are analogous. Just think about it.RyanLarsen_{January 16, 2006
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Patrick, I've appreciated your interest in this thread. I don't see the same problem that you do, however. If you go through and read what I've written I hope you'll understand why.RyanLarsen_{January 16, 2006
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Hi, woctor! You wrote: "First let me note that you ignored the other two reasons I gave above..." Nope, didn't do that. You were arguing that it was improbable and I agreed. No need to get into specifics. You might have missed that. You wrote: "If itÃ¢â‚¬â„¢s not better for the algae then there is no reason to expect such a mutation, if it occurred at all, to spread throughout the population. It would just die out." Now you're sounding like an ID enthusiast. Would you agree that this principle applies to irreducibly complex structures? You wrote: "not even the most hardcore design proponents insist that there is one, and only one, set of proteins that can be used to form a structure with a complicated function (like the flagellum)." Sure. Like Behe said, all sorts of things can be used in a mousetrap. They just have to be well-matched. After all, I was talking about how well they needed to match or, you might say, fit together. In the case of something like the flagellum, you can't just shove any ol' enzyme in there and say, "that'll do!" It has to be a perfect match. But it looks like you've proven me right-- you deny the improbability of it. The question is, why? You wrote: "because natural selection does not operate with long-term targets in mind, it could have arrived at a different useful structure based on the flagellar precursors." So random changes to the genome can account for the flagellum-- you have no problem with that, even though you are unable to lay out actual specifics to back yourself up-- but a minor twist in the orientation of astaxanthan is out of the question? Sounds like you're being selective in your claims regarding nature's capabilities. You wrote: "The astaxanthan design inference depends on the fact that we have known synthetic astaxanthan to compare against." There's a little more to it. It's a matter of probability. If it were highly probable that the natural astaxanthan would mutate to "match" the orientation of the designed astaxanthan, there would be no design inference. But it's improbable. Just like the enzymes in the flagellum binding and fitting so well (that's in addition to their ability to serve their functional purpose). That's highly improbable. Yet, for some unknown reason, you argue as though one is a big deal but the other is a piece of cake. Of course, the vastly more improbable one is the piece of cake. Sorry, you can't have your cake and eat it too. You can't hold that life is a barrier to design inference on one hand and then deny the explanatory power of genome on the other. If you have a selectable pathway for the evolution of the flagellum, let's hear it. Otherwise, it poses a far bigger problem than the probability of natural astaxanthan matching up with synthetic.RyanLarsen_{January 16, 2006
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"Even Patrick acknowledges that your example is not relevant to the ID vs. NDE debate." Actually, I said "might" and that someone would need to run the calculations. Unfortunately that's not something we can do with the limited information available in this post; we'd need to research the subject further. "Patrick, to use your phrase, Ã¢â‚¬Å“please try reading the literatureÃ¢â‚¬Â before criticizing those of us who already have." Sorry, I should have been completely clear when I mentioned the positive case in this instance. I just assumed you'd figure it out for yourself. One of the positive cases for ID is the observation of the ways designers act when designing. Intelligent agents often Ã¢â‚¬Ëœre-useÃ¢â‚¬â„¢ functional components. Said another way: an intelligent agent would likely not invent a new form of astaxanthan but reuse the already existing form for their illegal fish operation. How in this instance does the astaxanthan found in the illegal fish not display the characteristics of design? So, no, I didn't misuse "positive case". Also, take these "points" you made: "I would point out that nobody has determined that the algae would be better off with the second form of astaxanthan. If itÃ¢â‚¬â„¢s not better for the algae then there is no reason to expect such a mutation, if it occurred at all, to spread throughout the population. It would just die out. Moreover, even if the second form of astaxanthan were advantageous to the algae, it isnÃ¢â‚¬â„¢t necessarily the *only* advantageous variant. A mutation for any other beneficial variant would also be expected to spread throughout the population. Natural selection does not Ã¢â‚¬Å“targetÃ¢â‚¬Â a specific form of astaxanthan. It uses whatever it stumbles across that works." That's exactly the type of information that would come into consideration when using the explanatory filter. But you don't provide a good argument against the design detection itself. You're just hypothesizing about the possibilites related to generating this specific form of astaxanthan. "Third, not even the most hardcore design proponents insist that there is one, and only one, set of proteins that can be used to form a structure with a complicated function (like the flagellum). There are many possible protein combinations with the same function, and thus many possible genomic variants which can achieve the specified function. The Ã¢â‚¬Å“targetÃ¢â‚¬Â isnÃ¢â‚¬â„¢t nearly as small as youÃ¢â‚¬â„¢d like to believe." I'm not sure why you're bringing this up since we're unlikely to dispute it (variance in proteins for function). Just show us a real world example of the various systems coopted to form the 40 components needed for the flagellum. "Fourth, because natural selection does not operate with long-term targets in mind, it could have arrived at a different useful structure based on the flagellar precursors. There was nothing inevitable about the flagellum evolving at that particular time." Congrats. You just weaved a just-so story based upon indirect Darwinian pathways.Patrick_{January 16, 2006
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Patrick wrote: "I see too many problems with woctorÃ¢â‚¬â„¢s argument for it to be valid overall..." I'd be grateful if you could point them out to me. The only objection you've raised so far in this thread is due to a misunderstanding of ID on your part, as I explain below. "...but to be fair IÃ¢â‚¬â„¢ve been thinking on this subject over the night and he might have a point that this example is Ã¢â‚¬Å“not relevant to the ID vs. NDE debateÃ¢â‚¬Â..." Thank you. But I should mention that's not just *a* point, that's pretty much the *entire* point I've been making in my comments: Ryan's example is not relevant to the ID vs. NDE explanation of complicated living structures. "And unless IÃ¢â‚¬â„¢m misunderstanding ID myself (Bill?) that is what is known as a positive case for designÃ¢â‚¬Â¦. What, you didnÃ¢â‚¬â„¢t think that design argument relied entirely on the negative case that itÃ¢â‚¬â„¢s improbable that unguided nature produced this second type of astaxanthan? Please try reading the literature before wasting your time with such arguments." It's not a good sign when an opponent of intelligent design has to explain ID to a supporter, but here goes. What Professor Dembski means by a positive case for design is not "we've seen something being designed by humans, therefore we know it was designed" but rather "we see something that displays the characteristics of design (i.e. CSI), therefore we conclude it was designed." Patrick, to use your phrase, "please try reading the literature" before criticizing those of us who already have.woctor_{January 16, 2006
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Ryan wrote: "Amazing that you would realize how improbable it is that the natural astaxanthan would be mutated to Ã¢â‚¬Å“matchÃ¢â‚¬Â the designed astaxanthan, but you seem to deny the improbability of enzymes matching up perfectly in something like the flagellum." First let me note that you ignored the other two reasons I gave above for why the scientists made the design inference in this case. Those reasons stand independently of the third reason, which is the one you are challenging. Regarding your challenge, I would point out that nobody has determined that the algae would be better off with the second form of astaxanthan. If it's not better for the algae then there is no reason to expect such a mutation, if it occurred at all, to spread throughout the population. It would just die out. Moreover, even if the second form of astaxanthan were advantageous to the algae, it isn't necessarily the *only* advantageous variant. A mutation for any other beneficial variant would also be expected to spread throughout the population. Natural selection does not "target" a specific form of astaxanthan. It uses whatever it stumbles across that works. Third, not even the most hardcore design proponents insist that there is one, and only one, set of proteins that can be used to form a structure with a complicated function (like the flagellum). There are many possible protein combinations with the same function, and thus many possible genomic variants which can achieve the specified function. The "target" isn't nearly as small as you'd like to believe. Fourth, because natural selection does not operate with long-term targets in mind, it could have arrived at a different useful structure based on the flagellar precursors. There was nothing inevitable about the flagellum evolving at that particular time. "So, you see, we agree. An inference of design can be made and it is a matter of probability or deciding what explanation is best." We agree that the synthetic astaxanthan is designed. We don't agree on the relevance of this design inference to the larger and far more important question of inferring design from the complexity of living structures. The astaxanthan design inference depends on the fact that we have known synthetic astaxanthan to compare against. The vast majority of design inferences that ID would "like" to make have no such synthetic examples to draw upon. And as I pointed out earlier, having a synthetic example of something does not prove that the natural counterpart was designed. Even Patrick acknowledges that your example is not relevant to the ID vs. NDE debate.woctor_{January 16, 2006
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Ryan: I see too many problems with woctor's argument for it to be valid overall but to be fair I've been thinking on this subject over the night and he might have a point that this example is "not relevant to the ID vs. NDE debate" though obviously I disagree that there somehow exists a "biological barrier" for design arguments in general. This situation employs a weaker form of the design argument and while it worked in this case ID is more stringent. I haven't calculated the informational bits but it's possible ID might produce a false negative in this instance. If someone has the spare time they can do a more thorough investigation and see if that's the case.Patrick_{January 16, 2006
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So you think it's too improbable? You're just giving up and going with design? Amazing that you would realize how improbable it is that the natural astaxanthan would be mutated to "match" the designed astaxanthan, but you seem to deny the improbability of enzymes matching up perfectly in something like the flagellum. So, you see, we agree. An inference of design can be made and it is a matter of probability or deciding what explanation is best. Life is not a barrier to that.RyanLarsen_{January 16, 2006
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Ryan, If all you are claiming is that we can identify designed substances in animal or human bodies, then of course I agree with you, and so would just about every Darwinian on the planet. We test people's blood for the presence of synthetic drugs, we test their tissues for exposure to synthetic carcinogens, etc. The situation is exactly the same as for astaxanthan: we detect a substance, we already know that the substance does not occur in nature but can be produced by humans, so we infer that we have found designed substances. True, but trivial, and not relevant to the ID vs. NDE debate. The challenge for ID is to demonstrate that a particular biological structure was designed by a non-human designer. Imagine that humans are one day able to design, from scratch, a perfect replica of the bacterial flagellum. Will that mean that the original flagellum was designed? Of course not. The "life barrier" remains even when there is an artificial example of the structure in question. In the specific case of astaxanthan, you ask why the scientists were so quick to assume that the astaxanthan was designed and not the result of a genome change in the algal source. Three reasons: one, the mutation would have had to come to dominate the wild red algae population in order to make the salmon appear as if they were farmed, two, this change in the algal genome would have had to have been unnoticed by scientists, and three, the odds are low that a mutation or mutations would produce a form of astaxanthan identical to the synthetic form.woctor_{January 15, 2006
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woctor, I welcome your comments. You are quite correct that the inference of design was not made using the methods of Behe and Dembski. But you are admitting that design is a better explanation for where the organic structures extracted from the fish came from. The confusion is that you've switched the argument to "knowledge of a potential designer" and away from the question of whether life poses a barrier. It is true that knowledge of the existence of designed astaxanthan was necessary to the inference, but it is irrelevant to the question at hand. You have to understand the "life is a barrier" argument. Supposedly, the existence of a genome negates design inference because all organic structures can be attributed to changes in the genome. No matter how unlikely those changes may be (like the flagellum), the improbability is down-played by Darwinists. Astaxanthan with a slightly different orientation would be a miniscule genome leap compared with irreducibly complex structures like the flagellum. And yet, when it was discovered in fish that were said to be "wild," all of a sudden the odds of the astaxanthan resulting from a slight genome change were too overwhelming to even be considered as a possibility. You wouldn't even consider it seriously, now would you? So, what happened to the "life is a barrier" argument? All of a sudden, the invoking of the argument would be an embarrassment. Life, then, is not truly a barrier to the invoking of design. You may argue, "but they had a better explanation than random genome change!" Exactly. When we start dealing with a much higher order of complexity than the orientation of astaxanthan, the direct knowledge of a specific potential designer becomes less and less necessary. But, again, that's a different issue than the life barrier one. Let's keep them separate.RyanLarsen_{January 15, 2006
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"The design inference in this case depends on already knowing that humans designed the second form of astaxanthan." And unless I'm misunderstanding ID myself (Bill?) that is what is known as a positive case for design.... What, you didn't think that design argument relied entirely on the negative case that it's improbable that unguided nature produced this second type of astaxanthan? Please try reading the literature before wasting your time with such arguments.Patrick_{January 15, 2006
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RyanLarsen wrote: "How did they know it was a form not found in nature? They didnÃ¢â‚¬â„¢t. They just thought that design was a BETTER EXPLANATION." Sorry to butt in, but I think I see what Bradcliffe is trying to say, and I want to amplify and elaborate on his point: 1. The astaxanthan found in wild salmon is of one type. 2. Synthetic astaxanthan is of a second type. 3. Wild salmon do not contain the second type of astaxanthan. 4. Red algae (which the wild salmon feed on) contain only the first type of astaxanthan. 5. If a salmon contains the second type, scientists conclude that it was farmed, not wild. Why? Because the second type is not found in wild salmon, but it IS known to be manufactured by humans and fed to farmed salmon. How do the scientists know that the astaxanthan is designed? Because it is identical to synthetic astaxanthan, which they have never seen in the wild, but which they know to be produced by humans. The point is, there is nothing about the structure of the synthetic astaxanthan itself that makes scientists think it couldn't be produced by unguided nature. They conclude it was designed just because they know that humans did design and produce it, and that identical natural forms have never been found. The design inference in this case depends on already knowing that humans designed the second form of astaxanthan. Now consider the bacterial flagellum, where there is no human-designed version to compare against the natural version. The astaxanthan argument no longer applies, and life is as much a "barrier to the design inference" as before.woctor_{January 15, 2006
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More to the point: When a new species of plant is discovered in a far-off jungle, does the scientific community declare that since it had never been discovered before, it must have been designed by the explorers? No. They found the astaxanthan in nature. They found it in a fish. That's natural. But they still claimed that it had been designed. Hope that clears things up.RyanLarsen_{January 14, 2006
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bradcliffe1 writes: "...it was a form not found in nature" Ryan says: How did they know it was a form not found in nature? They didn't. They just thought that design was a BETTER EXPLANATION.RyanLarsen_{January 14, 2006
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To say that it could have evolved but it hasn't yet in this case is not much of an argument. You just don't like the fact that it's possible to detect design in biology and will argue "anything" in order to maintain that position. Or, of course, the message you're receiving now might have been randomly generated by my computer ala your argument.Patrick_{January 14, 2006
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Ryan, Again, I point out that they knew the astaxanthan was synthetic simply because it was a form not found in nature. Beyond that, there was nothing about the astaxanthan that showed it was designed, and no reason to believe it could not in principle be produced by a living organism with the proper genes. Your example thus does not succeed in showing that life is not a barrier to the design inference.bradcliffe1_{January 13, 2006
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Thanks Charlie! clbell, the question of how likely a necessary genome change would be is largely irrelevant. The question I asked that you quote should have been left out of my post. The point I'm making is that scientists extracted an organic compound from a fish and declared that it had been intelligently designed~ that no genome had been responsible for it. That goes for algae as well as salmon genomes. No one questioned their finding. Therefore, unless the NAS wants to challenge the findings, the biological line is not a barrier to design inference (Yockey and others have claimed that when the biological line is crossed design inference can never be made because any organic compounds can be attributed to the genome). I apologize for the confusion.RyanLarsen_{January 13, 2006
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Maybe not lost but not necessarily profound either. "why couldnÃ¢â‚¬â„¢t a red algae genome have evolved to produce a slightly different astaxanthan?" http://www.fz-juelich.de/ptj/datapool/page/462/IGB_Alge1.jpg It's not so easy. Let's say one particular red algae "organism" has a astaxanthan mutation. It may mean that it leaves a distaste in the mouth of the fish or gives it heartburn. Or even less likely, lets say it killed the fish. Guess what? The algae still died and is not able to pass on that mutation which means it's very difficult if not unlikely that this kind of evolution would occur. It's actually more likely that the salmon would evolve to allow it process the astaxanthan which was toxic to it's ancestors.clbell_{January 13, 2006
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Don't worry Ryan. Your point is not lost, and I think it is a good one.Charlie_{January 13, 2006
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Hello again, Intelligent design science doesn't speculate as to the nature of the designer but, yes, humans design the fish feed with the man-made astaxanthan (which, as far as I know, is not irreducibly complex~ adn I'm not claiming that the scientists in this instance were practicing the design inference methods of Behe and Dembski). Doesn't change the fact that these scientists found organic compounds in fish and asserted that nature did not create them but that they were designed. Life, therefore, is not a barrier to design inference. No one speculated that the red algae genome had changed to account for it.RyanLarsen_{January 12, 2006
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Ryan, Let me try to understand. Wild salmon have one type of astaxanthan and farmed salmon have another. Scientist can tell the difference between the two types. Correct? And it sounds to me that the farmed salmon contain the compound from the feed given to them, correct? So the "designers" in this story are humans, correct?cholera_{January 12, 2006
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Ryan, I think they figured out that the astaxanthan was synthetic, not because it had any characteristics which suggested design, but rather because it was of a type not found in nature. If they did not already know about astaxanthan's natural forms, they would not have been able to infer design in the case of the synthetic astaxanthan.bradcliffe1_{January 12, 2006
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Hi cholera, I don't know enough about the structure of astaxanthan to tell you whether the difference in structure of designed astaxanthan could be more beneficial to the algae. What I can tell you is that scientists in the lab determined that an organic structure (astaxanthan) found in the fish had been intelligently designed. No one questioned their credentials as scientists or challenged their findings. You could question their science if you want, but for now I'll go with their findings which ultimately indicate that the living world is not a barrier to design inference.RyanLarsen_{January 12, 2006
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I'm not sure I follow? You ask why couldn't red algae produce different astaxanthan? Could not the difference in the chemical give the algae a particular advantage?cholera_{January 12, 2006
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If someone wants to argue that something like magnetite crystals can be accounted for in the genome, then I have a story that, in principle, relates~ if you'll bear with me, it's a good one. I got thinking about this when I read the Yockey link that was recently given on this blog. Yockey lays down a claim that design can not be inferred in living things because they have a genome. To him, living organisms present a unique barrier to design inference. His exact quote was: "Machines require an Ã¢â‚¬Å“Intelligent DesignerÃ¢â‚¬Â to existÃ¢â‚¬â€or evolveÃ¢â‚¬â€because they do not have a genome. Living things do not require an ad hoc Ã¢â‚¬Å“Intelligent DesignerÃ¢â‚¬Â to live AND EVOLVE because they DO have a genome."(from Hubert Yockey blog thing, capitalization of "and evolve" added) I have an example that proves that biological organisms are NOT a barrier to design inference. I recall hearing that, back in the 1990's, there was a fish scam. Farmed salmon were being sold as wild salmon because wild salmon fetches a higher price. The scam was eventually busted because scientists were able to differentiate between the wild salmon and the farmed salmon in the lab. Here's how: Astaxanthan is a little antioxidant synthesized by red algae. Salmon feed off the algae in the wild, and absorb the astaxanthan for their own biochemical use. Farmed salmon are fed a man-made fish meal that includes man-made astaxanthan. Astaxanthan made by algae is slightly different from designed astaxanthan. In the lab, scientists were able to show that the salmon being marketed as wild had designed astaxanthan in them and, therefore, had lived on a farm. So the question is, why couldn't a red algae genome have evolved to produce a slightly different astaxanthan? If a lowly bacteria is able to synthesize the most perfect crystals of magnetite, then what is to prevent algae from accomplishing this small feat? And yet, we all agree that this little organic structure found in the salmon must have been designed.RyanLarsen_{January 12, 2006
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Yeah, that's way too complicated. Must be a designer.cholerae_{January 12, 2006
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