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Bacterial resistance and Michael Behe's new book

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laptoppop

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In the thread called "The appearance of design" Shernen wrote:
About bacterial resistance: http://www.ncbi.nlm.nih.gov/sites/en...t_uids=9332013
Policies aimed at alleviating the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents, these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli. Here we present evidence that these genetic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity. We show that second site mutations which compensate for the substantial (14 and 18% per generation) fitness costs of streptomycin resistant (rpsL) mutations in E. coli create a genetic background in which streptomycin sensitive, rpsL+ alleles have a 4-30% per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10,000 generations in the absence of the antibiotic.
(emphases added) There goes your point about antibiotic resistance. Which is shredded in a far less friendly way over at http://mikethemadbiologist.blogspot....evolution.html .
I think I've found what I'm going to ask for for Father's day.... Michael Behe has a brand new book due out today, June 5, 2007: THE EDGE OF EVOLUTION: The Search for the Limits of Darwinism Amazon apparently has it in stock...

From the first link:
Through a combination of experimental evidence, genome research, and mathematical law, Behe analyzes three key case studies of the tens of thousands of generations of malaria, E. coli, and the HIV virus, and the human genomic response to those invaders. We now know exactly what mutations have occurred in the struggle between these parasites and their human hosts. We know their rate of occurrence. We know all possible types of mutations, and their natural rate of occurrence. Armed with all this, it is a simple matter of extrapolation to determine the limits of Darwinian randomness in the entire tree of life on earth.
 

notto

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His math is questionable and there are several reviews online that show this to be the case.

That is why Behe chooses not to publish in peer reviewed journals. His work and cherrypicking doesn't have a good track record on standing up to critical analysis.

Will you actually take the time to seek out reviews of Behe's work and not accept it at face value? After all, the process he follows doesn't force him to adhere to objective and testable methods or conclusions. He can say whatever he wants in his book and it should not be considered evidence that has been validated nor objective without scrutiny.

http://scienceblogs.com/goodmath/2007/05/behes_dreadful_new_book_a_revi_1.php

If you accept Behe as a valid source, do you accept his conclusions about the age of the earth and common descent?
 
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laptoppop

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That is why Behe chooses not to publish in peer reviewed journals. His work and cherrypicking doesn't have a good track record on standing up to critical analysis.

Huh? He has over 35 articles published in peer reviewed biochemistry journals. Please get your facts straight before you start an
[SIZE=-1]argumentum ad hominem attack.[/SIZE].

One should note that Behe accepts common descent... at least for now.:D;) He is not a YEC by any means. I'm thinking that this book could probably best be described as reinforcing the "T" in TE. On the other hand, it also looks like great research into the specifics of these particular bacterial cases.

Here's a review at amazon.com:
The Limits of Random Mutation: An Argument for...., June 3, 2007 By Fritz R. Ward "dayhiker" (Crestline, CA United States) - See all my reviews

What in essence is Darwinian Evolution? Many philosophers would find that a fairly difficult question. For Daniel Dennett, it is a universal solvent that dissolves all non-materialist ideas. For some creationists, it is the root of much evil in the modern world, including racism, war, and a lack of compassion for the poor. For Kenneth Miller, a biologist at Brown University, it is an extraordinarily successful set of explanations for the diversity of life. But for Michael Behe, and one suspects many biologists, Darwinism is simply a series of propositions. These are 1) common descent of life, 2) natural selection (sometimes termed "survival of the fittest") and 3) random mutation at the cellular level driving the changes. The difference between Behe, an advocate of intelligent design, and Miller is simply one of the degree to which each thinks these propositions are applicable in describing life as we observe it. (Readers should note that Behe fully accepts common descent and natural selection. It is the random mutation mechanism that he has difficulty with.)

In this book Behe strikes off in a new direction from his previous work, 'Darwin's Black Box.' Rather than simply explore cellular mechanisms that seem unlikely to arise from chance, Behe instead considers all the areas where evolution seems to function very well. For example, the rise of resistance among certain diseases, notably malaria, to synthetic drugs. Remarkable evolutionary pressures are at work in the struggle between humans and deadly pathogens. Humans who develop an immunity to maleria have a strong evolutionary advantage over those who don't. Similarly, protozoan parasites which can avoid the drugs we use to combat them also have an evolutionary advantage. Indeed, this is common knowledge among all biologists and most of the literate public. Germ resistance of all kinds to drug treatments is the star example of evolution at work.

But what is not so commonly known is that random mutation has severe limits in how effectively it can cope with evolutionary pressure. Indeed, what Behe demonstrates in precise detail is that evolutionary mechanisms are for the most part destructive: a part of the DNA stand is destroyed or replaced with a less efficient coding and the result is a weaker organism, though one which can survive the "trench warfare" of survival with hostile organisms. Thus, for example, humans have developed sickle cell anemia to cope with malaria. This is hardly beneficial, in and of itself, but compared to malarial death, it is a very helpful mutation. Similarly, malaria can rapidly evolve resistance to some drugs, slowly to others (more changes are required, and hence far fewer resistant copies of the cell are likely) but the mutated genes that come from this battle for survival are not optimal. Indeed, like sickle cell anemia, they rapidly die out of the malarial population if not subjected to the pressure of deadly (for the parasite) toxins in the form of antimalarial drugs.

So, while malaria (and several other cases Behe examines) suggests the efficacy of random mutation, it also suggests limits to just how much it can accomplish. Indeed, Behe finds that even two or three simultaneous random changes in DNA sequencing is exceedingly unlikely, and more just about impossible. This is very important because it suggests real limits to the amount of random mutation that could happen among higher mammals. People mistakenly believe that time is the most important factor in allowing for evolutionary change but as Behe demonstrates, population, not time, is what determines successful mutations. Malaria, and even moreso HIV are extraordinarily effective at utilizing evolution. There are a lot of such organisms and they reproduce quickly. Humans, and indeed, all vertebrate and most invertibrate animals, do not. Even given the entire history of life on the planet, it is extremely unlikely that the random mutation proposition of evolution could account for a significant amount of the diversity we witness in the world around us.

Indeed, the situation is even worse than that according to Behe, because the mutations we actually observe in nature are almost always destructive or at a very minimum, sub optimal. They do not build up new structures. Despite strong evolutionary pressure, neither malarial protozoa nor HIV and similar retroviruses have ever developed a single new cellualar structure. Indeed, as Behe tellingly notes, "Until an organism is found that is demonstrated to be much more adept than the malarial parasite at building coherent molecular machinery by random mutation and natural selection, there is no positive reason to believe it can be done. And the best evidence we have from malaria and HIV argues it is biologically unreasonable to think so."(p.155)

So if random mutation does not facilitate change in species, what does? For Behe the answer is clear: non-random mutation. But what causes that? One possibility, of course, is chance. A variant of this possibility is favored by physicists who believe in a multiverse. We are just extraordinarily lucky to have life here, but it looks designed to us. Aside from the fact that there is no evidence for a multiverse, there are logical problems with this solution to the problem of life and the forms it takes on earth. Behe discusses these and then moves on to more serious territory. Should we examine the possibility of a natural law that guides the evolutionary processes of natural selection leading to common descent? In and of itself, Behe finds this approach unappealing. Instead he advocates intelligent design, but in my opinion, especially as described by Behe, this is pretty much indistinguishable from such a natural law. Indeed, many of the natural laws in our universe are at present only explained by the anthropic principle and it is hard to imagine that this one would be any different.

Ultimately, of course, Behe moves from science proper (what we can infer from actual observations of evolution--namely random mutation is insufficient to explain common descent) to more philosophical speculations. What would the designer(s) be like? Can we infer anything about motive? What about the problem of evil? After all, any designer who might have "pre-programed" the possibility of intelligent life into the universe, say us, must also be responsible for malaria as well. These are serious issues and Behe is right to raise them. His critics will no doubt hammer him for it. These speculation are not "scientific" but that doesn't mean they are inappropriate. I think Behe is right when he notes that knowledge need not respect the boundaries we set for it in modern universities. Just because a topic does not yield to scientific inquiry hardly makes it unfit for all inquiry. Moreover, considering other questions will hardly invalidate the scientific portion of Behe's book or the considerable math behind it.

In my opinion this final chapter, where Behe takes on these philosophical questions, is the most important part of the book. It is also the most controversial. Readers will probably come to different conclusions, but Behe's ideas deserve serious consideration. As for the rest of the book, it lives up to its title. There is a clear edge or limit beyond which evolution is a poor mechanism for understanding life on the planet. That line may not be precisely where Behe claims it is, and future research will undoubtedly refine this edge further. But to persist in maintaining no such line exists requires at this point faith. Indeed, the next time a critic of ID suggests that scholars like Behe should be ignored because "they" are religiously motivated, readers would do well to remember that Freud, like Darwin, is largely discredited. But his theory of projection is still valid, much as Darwin's observations still apply to bacteria and anti-biotics. Indeed, I predict such projections will figure very prominently in some reviews of this book. Those with an ideological axe to grind will not appreciate it. Thoughtful readers, on the other hand, will be fascinated with this excellent book.
 
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notto

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Huh? He has over 35 articles published in peer reviewed biochemistry journals. Please get your facts straight before you start an
[SIZE=-1]argumentum ad hominem attack.[/SIZE].

But oddly his ID stuff isn't. Why is that? My argument was not ad hominem. I was stating a fact related to his work and his publishing methods This book is not peer reviewed and is not held to objective scientific, analytical, or mathematical standards.
Here's a review at amazon.com:

So what? I notice that this review doesn't actually critique Behe's work, just accepts it without validation. Exactly the problem with his publishing this way - nobody validates it before it is published.

Did you read the critique of his mathematics?

There are several large problems with his conclusions.
 
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laptoppop

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Yes I read the critique. This particular blog is not exactly unbiased, to put it mildly -- I want to read Dr. Behe's book myself before I trust the analysis in any blog, but particularly this one. I can already see problems in the blog's analysis, but I want to confirm my ideas with the actual book first.
 
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notto

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Yes I read the critique. This particular blog is not exactly unbiased, to put it mildly --
I want to read Dr. Behe's book myself before I trust the analysis in any blog, but particularly this one. I can already see problems in the blog's analysis, but I want to confirm my ideas with the actual book first.

That's great. Let us know what you find. I would be particularly interested if you find any problems with the blogs mathematical analysis. Please show your work and use as much detail as you can.

When you are done with Behe's book, I could suggest some additional books on evolution with favorable reviews on amazon that come to exactly the opposite conclusions of Behe's. Maybe you should read one of those as a followup.

I could also probably dig up a few books on amazon that attribute humans to being the product of transdimensional aliens who will use us for breeding stock in the near future. I'll see if I can find one with a good review.
 
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laptoppop

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That's great. Let us know what you find. I would be particularly interested if you find any problems with the blogs mathematical analysis. Please show your work and use as much detail as you can.

When you are done with Behe's book, I could suggest some additional books on evolution with favorable reviews on amazon that come to exactly the opposite conclusions of Behe's. Maybe you should read one of those as a followup.
I'll try -- I'm a computer geek, not a rigorous mathematician -- but I do OK. In terms of other books, I'm specifically interested in the discussion of these particular bacteria. The review seems to say that the book explains that even in these cases the bacteria in question are less fit after the mutations. If so, that would be fascinating. If not that's OK too. It is also implied that the book develops limits on the rate of mutations, etc. If so, this could have interesting implications on the topic of bariminology and the limits on "kinds".
 
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notto

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I'll try -- I'm a computer geek, not a rigorous mathematician -- but I do OK. In terms of other books, I'm specifically interested in the discussion of these particular bacteria. The review seems to say that the book explains that even in these cases the bacteria in question are less fit after the mutations. If so, that would be fascinating. If not that's OK too. It is also implied that the book develops limits on the rate of mutations, etc. If so, this could have interesting implications on the topic of bariminology and the limits on "kinds".

And it would be a lot more interesting if Behe actually published original research on the subject for peer review or academic scrutiny.

That would be cool but I won't hold my breath.
 
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shernren

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Huh? He has over 35 articles published in peer reviewed biochemistry journals. Please get your facts straight before you start an [SIZE=-1]argumentum ad hominem attack.[/SIZE]

Uh, says who? - as in, source?
 
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theIdi0t

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I have a question. Does anyone know if Behe drops those examples of irreducibly complexity, when they are shown to be reducible? like the eye, and the motor in the cell's flagellum in his subsequent books? Or does he rehash these things over and over again, hoping to find an unknowledgeable prey?

He seems like a decent man, I assume he would abandon one ship when it's sunk, and jump on another one?

Anyone know if this is a case though. It seems that everyone and their mothers killed the eye , and flagellum argument; so has Behe declared some sort of defeat for these two arguments for irreducible complexity?
 
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laptoppop

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I don't know about the eye, but I've looked at the arguments about the flagellum in some detail in the past. The TT-S discussions do not address the irreducible complexity, they just try to postulate a hypothetical evolutionary development path. There are several problems with this supposed path, as I have cited previously in this forum. Beware of folks claiming "victory" when indeed the discussion is ongoing and not conclusive by any means.
 
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theIdi0t

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I don't know about the eye, but I've looked at the arguments about the flagellum in some detail in the past. The TT-S discussions do not address the irreducible complexity, they just try to postulate a hypothetical evolutionary development path. There are several problems with this supposed path, as I have cited previously in this forum. Beware of folks claiming "victory" when indeed the discussion is ongoing and not conclusive by any means.

Have you seen the Ken Miller video on youtube, that breaks down the motor in the cell's flagellum? I couldn't think of a more sound case for a naturally selected structure.

But what I truly wonder, is if creationist understand what Behe is getting at. There's a Bob Barker on evolution article in the Onion, that is floating around here in a thread somewhere, and I think everyone sees the silliness of Bob Barker's case, but that is exactly what Behe's argument is getting at: Evolution explains 99.9% of our biological composition, and God intervened for that additional .1%. God allows the eye to form naturally, but needed to divinely intervene in the construction of the motor in the flagellum?

If you can see the silliness of Bob Barker's argument, why does one not see it in Behe's? I think what happens is that the creationist gets so bent on Behe's examples, that a cloak gets placed over their eyes which does not allow them to see the big picture.

Behe presents a case for irreducible complexity; some group of believers immediately jump on, soon thousands of articles prove the case other wise; Captain Behe abandons ship, while the group of believers drown, unaware the ship had been sinking for some time. The process repeats itself, with Behe finding another ship, it sinks, and few more believers drown.

When does someone realize that there are casualties and no life-preservers, to not board Behe's ship again?
 
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laptoppop

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I'll check out the video. I'll admit what I am expecting to see is speculation without data support -- I'll be pleased if it is different. Of course that's one way I'm particularly pesky -- its not enough to me to have a possible explanation or theory -- I want observed data in support of it. Its too easy for a theory to overlook something. I've designed and built too much electronic hardware and done too much programming to put total faith in a postulated set of steps. There are always things you can look back on and realize in hindsight that you should have seen them earlier.
 
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theIdi0t

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I'll check out the video. I'll admit what I am expecting to see is speculation without data support -- I'll be pleased if it is different.

Well, if you can see why the eye is not irreducibly complex, then you should have no problem seeing why the motor in the flagellum is not irreducibly complex.

Of course that's one way I'm particularly pesky -- its not enough to me to have a possible explanation or theory -- I want observed data in support of it. I've designed and built too much electronic hardware and done too much programming to put total faith in a postulated set of steps. There are always things you can look back on and realize in hindsight that you should have seen them earlier.

:)

...but "kind" works fine for you.
 
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laptoppop

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OK, I watched the video. He misrepresented the position of ID, although it may have been accurate with early ID writings. He claimed that ID says that *all* parts of an IC object need to be useless. This is just not true. Its fine if some of the parts are similar to other parts in other units.

He also failed to mention that more recent evidence points to TT3 structures as being *degraded* flagellum, not precursers.

He failed to account where all the other pieces came from.

In general 6 minutes of happy face evo clap yourself on the back aren't you smart talk.
 
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theIdi0t

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OK, I watched the video. He misrepresented the position of ID, although it may have been accurate with early ID writings. He claimed that ID says that *all* parts of an IC object need to be useless. This is just not true. Its fine if some of the parts are similar to other parts in other units.

hum.......for something to be "irreducibely complex" as ID defines it, the something cannot be in a "reduced complexity" form. Perhaps you can explain why you agree that the eye arguement has been defeated, but not the motor in the cells flagellum. They were both defeated the same way.

He also failed to mention that more recent evidence points to TT3 structures as being *degraded* flagellum, not precursers.

Another play on words. What's the difference between "degraded", "reduced complexity", and "evidence of precursers"
 
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shernren

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:scratch:

OK I'm a little confused here and I have an honest question (no sarcasm). Can someone define Theistic Evolution for me? Or better still what is the difference between TE and ID. Isn't Intelligent Design a form of Theistic Evolution?






+
The lowdown:

TE believes that God's big enough to use evolution to do whatever He wants.
ID believes that God - oops, the Intelligent Designer - must have had to short-circuit evolution at some point or It just wouldn't have gotten what It wanted.
 
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