The Bacterial Flagellum Revisited

The accumulation of small heritable changes within populations over time.

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Re: The Bacterial Flagellum Revisited

#21  Postby debunk » Jun 25, 2010 10:23 am

CharlieM wrote:
Debunk:
What you're doing here is calling what amounts to a textbook definition of evolution by natural selection "unsubstantiated belief", never mind the fact that it's an observed phenomenon.


CharlieM:
What I'm calling unsubstantiated belief is the power of evolution by natural selection to produce anything but small changes within a limited area. What observed phenomenon did you have in mind?


The bit you quoted and then called an unsubstantiated belief.

Your Behe quotes change nothing about what I said regarding his arguments.


On the contrary, Behe says quite clearly that he thinks IC systems can not evolve from precursors, and that his conclusion is that they must be designed with the end-product in mind.
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Re: The Bacterial Flagellum Revisited

#22  Postby Rumraket » Jun 25, 2010 11:17 am

CharlieM wrote:
Debunk:
What you're doing here is calling what amounts to a textbook definition of evolution by natural selection "unsubstantiated belief", never mind the fact that it's an observed phenomenon.


CharlieM:
What I'm calling unsubstantiated belief is the power of evolution by natural selection to produce anything but small changes within a limited area. What observed phenomenon did you have in mind?


The fossil record, comparative anatomy, comparative genetics(the tree of life), biogeography etc. etc. etc. You going to handwave it all away with reference to the flagellar hook protein FlgE ?
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Re: The Bacterial Flagellum Revisited

#23  Postby debunk » Jun 25, 2010 2:04 pm

CharlieM wrote:I take it you are referring to my comment, "Note that Behe is not saying that it is impossible for an irreducibly complex system to be assembled by known naturalistic means."

Hotshoe:
That is a serious misreading of Behe's point as far as Intelligent Design.


CharlieM:
I'm only going by what the man himself says. From "Darwin's Black Box":
"There is no magic point of irreducible complexity at which Darwinism is logically impossible. But the hurdles for gradualism become higher and higher as structures are more complex, more interdependent."


From the horse's mouth:

In Darwin’s Black Box (Behe 1996) I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can’t be produced by natural selection acting on random mutation, or any other unintelligent process.
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Re: The Bacterial Flagellum Revisited

#24  Postby hotshoe » Jun 25, 2010 3:53 pm

From the horse's mouth:

Behe wrote:In Darwin’s Black Box (Behe 1996) I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can’t be produced by natural selection acting on random mutation, or any other unintelligent process.



So Charlie M can't claim Behe never said it.
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Re: The Bacterial Flagellum Revisited

#25  Postby ElDiablo » Jun 25, 2010 4:06 pm

debunk wrote:On the contrary, Behe says quite clearly that he thinks IC systems can not evolve from precursors, and that his conclusion is that they must be designed with the end-product in mind.

The crux of the whole BS of ID. God did it.
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Re: The Bacterial Flagellum Revisited

#26  Postby debunk » Jun 25, 2010 4:09 pm

ElDiablo wrote:
debunk wrote:On the contrary, Behe says quite clearly that he thinks IC systems can not evolve from precursors, and that his conclusion is that they must be designed with the end-product in mind.

The crux of the whole BS of ID. God did it.


Indeed, the quote shows precisely what's wrong with ID; it's a false dichotomy. If evolution can't explain it (or if people just claim it can't) that means God THE DESIGNER did it.
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Re: The Bacterial Flagellum Revisited

#27  Postby scruffy » Jun 25, 2010 8:01 pm

CharlieM wrote:
Debunk:
What you're doing here is calling what amounts to a textbook definition of evolution by natural selection "unsubstantiated belief", never mind the fact that it's an observed phenomenon.


CharlieM:
What I'm calling unsubstantiated belief is the power of evolution by natural selection to produce anything but small changes within a limited area. What observed phenomenon did you have in mind?

Your Behe quotes change nothing about what I said regarding his arguments.


I've never understood why it's so difficult for some to go from believing the evidence for short-term, multi-generational adapation via natural selection (for example, the oft quoted example of industrialized moths) to extrapolating this evidence to macro evolutionary change, over evolutionary time-spans. Although we cannot directly observe this phenomena, we can resort to broad comparisons and and direct references from such sources as the paleontological record to make some very strong inferences.

For example, we can trace the evolution of gill arches into ear ossicles and jaw musculature by looking at the ancient jawless fishes (late Triassic), and extrapolating all the way up to current day Opossums. (Wake 1979; Radinsky 1987; Luo 2007; and Francois Jacob 1977)

There are also well documented examples of laboratory recreated Macro evolution in Monkey Flowers (Mimulus). In this example, two species of flowers known to have shared a common ancestor both reproduce via pollination by insects. One species using Bees, the other Hummingbirds. These two distantly related species show some striking differences in flower shape, flower color, sexual organs, etc. all having co-evolved with their respected insect pollinators. From what I understand Schemske and Bradshaw used some modern molecular methods to to recreate this evolution in a controlled laboratory experiment. (Schemske and Bradshaw 1999; Bradshaw and Schemske 2003).


It is one thing to change the color of a moth, and quite another creating an ear ossicle from jaw arches, that I'll give you. One needs to keep in mind though that the former occured over a time-span of a few generations with the latter taking place over the span of millions of years. Cumulative selection over geological time spans is a powerful force, one that us humans are quite incapable of being able to understand. This is what makes studies and evidence like the above so important to our understanding of adaptations via natural selection.

_____________________________________________

EDIT: On a side note, from what I seem to have gathered here is that you (CharlieM) have no problem with limited forms of micro evolutionary change, but reject the notion of macro evolution. My question is what exactly DO you think to be the cause of all the diversity and change in life we see around us?
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Re: The Bacterial Flagellum Revisited

#28  Postby hotshoe » Jun 25, 2010 8:47 pm

jaredennisclark wrote:There are also well documented examples of laboratory recreated Macro evolution in Monkey Flowers (Mimulus). In this example, two species of flowers known to have shared a common ancestor both reproduce via pollination by insects animal pollinators. One species using Bees, the other Hummingbirds. These two distantly related species show some striking differences in flower shape, flower color, sexual organs, etc. all having co-evolved with their respected insect pollinators. From what I understand Schemske and Bradshaw used some modern molecular methods to to recreate this evolution in a controlled laboratory experiment. (Schemske and Bradshaw 1999; Bradshaw and Schemske 2003).

Sorry, not being pedantic; hummingbirds aren't insects - which is exactly why Mimulus is significant in having evolved two completely different pollinator-attracting strategies within such closely related species of flowers.

Your point about the power of evolution is supported by the fact that the species changes in Mimulus must be recent (recent, biologically speaking, although not as in recent human history) since they are native to the very young geological area of the Sierras near Yosemite. So, evolution can produce species-level change within a few thousand or tens of thousands of years. Wouldn't we reasonably calculate that it could produce ten times as much change in 100,000 years ? And 100 times as much change in 1,000,000 years ? Perhaps more importantly, the Mimulus studies provide experimental support that not all evolutionary change has to be imagined as a slow accumulation of minute effects, but can occur by large effect of a single gene change (or the large effects of a few gene changes).

Following up on this, I found their 1999 paper available in full, free:
Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus)

Douglas W. Schemske and H. D. Bradshaw, Jr. wrote:... Two experiments are required to elucidate the genetic architecture of reproductive isolation by pollinator-mediated selection. First, the genetic basis of traits such as flower color, size, shape, and nectar reward must be determined for plant species with different pollinators. Second, the response of wild pollinators to each floral trait must be evaluated in a geographic region where the plant species co-occur. We have completed the first experiment, using linkage mapping with molecular markers to identify quantitative trait loci (QTL) that control complex floral traits in M. lewisii and M. cardinalis. We found that most floral traits had at least one QTL of large effect (explaining >25% of the F2 phenotypic variance), suggesting that pollinator-mediated selection in this system could involve “major” genes (21, 22). Here, we report results from the second experiment, identifying the ecological significance of floral traits and the effect of simple genetic changes on pollinator visitation in nature.

... We tested the hypothesis that adaptation to different pollinators may involve genes with large phenotypic effects by comparing visitation rates as a function of QTL marker genotype for petal carotenoid concentration and nectar volume, the two traits with the greatest impact on bee and hummingbird visitation, respectively (Fig. 2 B). A single Mendelian locus controls the distribution of carotenoid pigments in the petals (20). F2 plants homozygous for the recessive M. cardinalis allele at the yup locus (yellow upper; ref. 20) have carotenoids distributed throughout the petals, and are orange- or red-flowered (Fig. 1 D, E, K, and L), whereas F2s carrying the dominant M. lewisii allele are pink-flowered (Fig. 1 F–J). There was no effect of yup genotype on hummingbird visitation rate (Fig. 3 A), but bee visitation was 80% lower in plants homozygous for the M. cardinalis allele (Fig. 3 B). This clearly shows that genetic variation for petal carotenoid concentration affects bee visitation and supports earlier findings that bees visiting Mimulus species in the section Erythranthe strongly prefer pink over red flowers (26).

... Taken together, our results provide evidence of striking differences in the floral preferences of bees and hummingbirds, and considerable opportunity for the adaptive divergence of floral traits through pollinator-mediated selection. This stands in contrast to recent suggestions that pollinators typically have broad preferences, and are therefore unlikely to contribute to floral evolution or the reproductive isolation of sympatric taxa (25, 34, 35). Floral traits associated with bumblebee and hummingbird pollination, such as petal carotenoid pigments and nectar volume, appear to be under relatively simple genetic control, with major QTLs responsible for pollinator discrimination and reproductive isolation in nature. This work contributes to the growing body of evidence that adaptation may often involve genes of large effect (3, 5, 36–39).


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Re: The Bacterial Flagellum Revisited

#29  Postby CharlieM » Jun 25, 2010 11:56 pm

Jaredennisclark:
I've never understood why it's so difficult for some to go from believing the evidence for short-term, multi-generational adapation via natural selection (for example, the oft quoted example of industrialized moths) to extrapolating this evidence to macro evolutionary change, over evolutionary time-spans.


CharlieM:
That isn't a very convincing example because there is no evolution of form during the change in the moth population. Before the change took place the moth population consisted of both light and dark forms. And after the trees were polluted the population consisted of the same light and dark forms only the ratio of one to the other changed. Not only that but get rid of the pollution and the population returns to its original state. This is not a good example of evolution but it is a good example of plasticity within a form.

Jaredennisclark:
EDIT: On a side note, from what I seem to have gathered here is that you (CharlieM) have no problem with limited forms of micro evolutionary change, but reject the notion of macro evolution. My question is what exactly DO you think to be the cause of all the diversity and change in life we see around us?


CharlieM:
My views are a wee bit unconventional. I look at things mainly from a teleological, holistic perspective. I think there is a lot of wisdom in Blake's words, "To see a World in a Grain of Sand and a Heaven in a Wild Flower."

So to answer your question, I see the diversity of organisms as the individual expression of archetypal forms and not as blind accidents of natural evolution. I have no problem with evolution as such, just with blind, unguided evolution.

J.W. Goethe:
The ever-changing display of plant forms, which I have followed for so many years, awakens increasingly within me the notion: The plant forms which surround us were not all created at some given point in time and then locked into the given form, they have been given a felicitous mobility and plasticity that allows them to grow and adapt themselves to many different conditions in many different places. How they can be brought together under one concept has slowly become
clear to me and that this conception can be enlivened at a higher level [of consciousness]: thus I began to recognize in the sense perceptible form a supersensible archetype.
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Re: The Bacterial Flagellum Revisited

#30  Postby scruffy » Jun 26, 2010 12:13 am

Okay, replace the moth example with whichever other example of micro evolution you DO find convincing. It doesn't change the point of my post, or Hotshoe's reply to my post, both of which you didn't really reply to.

I haven't seen anyone in this thread so far suggesting evolution as a blind, unguided process. No one who seriously understands the theory would assert such a thing. That's a straw-man.. unless of course you weren't accusing anyone here of it. -.-
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Re: The Bacterial Flagellum Revisited

#31  Postby CharlieM » Jun 26, 2010 12:26 am

CharlieM:
What I'm calling unsubstantiated belief is the power of evolution by natural selection to produce anything but small changes within a limited area. What observed phenomenon did you have in mind?


Rumraket:
The fossil record, comparative anatomy, comparative genetics(the tree of life), biogeography etc. etc. etc. You going to handwave it all away with reference to the flagellar hook protein FlgE ?


CharlieM:
Let's say the flagellar proteins FlgB, FlgC, FlgE, FlgF, FlgG and FlgK are homologous and that they all developed from some unknown precursor protein. Why is this evidence that they were formed by some unguided, evolutionary mechanism? My blood cells, neurons, liver cells and skin cells all developed from a common precursor cell. Does it then follow that they were formed by some unguided developmental mechanism? Your list above is good evidence that life changes and develops over time, but it tells us nothing about the cause of the change; whether or not it was brought about by unguided accidents.
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Re: The Bacterial Flagellum Revisited

#32  Postby CharlieM » Jun 26, 2010 12:55 am

Jaredennisclark:
I haven't seen anyone in this thread so far suggesting evolution as a blind, unguided process. No one who seriously understands the theory would assert such a thing.


CharlieM:
Well Richard Dawkins called it the Blind Watchmaker and if it isn't unguided you are getting into the realms of teleology.

I thought Goethe had replied to your Monkey Flower example. As he would say, "they have been given a felicitous mobility and plasticity that allows them to grow and adapt themselves to many different conditions in many different places."
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Re: The Bacterial Flagellum Revisited

#33  Postby Blitzkrebs » Jun 26, 2010 2:35 am

This is not a good example of evolution but it is a good example of plasticity within a form.


You've missed the point. It's an excellent example of natural selection, a critical factor in evolution.
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Re: The Bacterial Flagellum Revisited

#34  Postby Rumraket » Jun 26, 2010 6:08 am

CharlieM wrote:
CharlieM:
What I'm calling unsubstantiated belief is the power of evolution by natural selection to produce anything but small changes within a limited area. What observed phenomenon did you have in mind?


Rumraket:
The fossil record, comparative anatomy, comparative genetics(the tree of life), biogeography etc. etc. etc. You going to handwave it all away with reference to the flagellar hook protein FlgE ?


CharlieM:
Let's say the flagellar proteins FlgB, FlgC, FlgE, FlgF, FlgG and FlgK are homologous and that they all developed from some unknown precursor protein. Why is this evidence that they were formed by some unguided, evolutionary mechanism? My blood cells, neurons, liver cells and skin cells all developed from a common precursor cell. Does it then follow that they were formed by some unguided developmental mechanism? Your list above is good evidence that life changes and develops over time, but it tells us nothing about the cause of the change; whether or not it was brought about by unguided accidents.

You are making the mistake of thinking about any given line of evidence as seperate from the otheres. If you take it all together, observed speciation, observed micro/macro evolution, our knowledge of the workings of genetics and all the other stuff I listed above, plus more, the simple conclusion is that life evolved. And the geological record shows it.

Additionally, the alternative "design" explanation is ludicrous. We have fossils stretching back almost 700 million years before we get to jellyfish stage in life, and before that there is only bacteria. Are we now supposed to believe that intelligent designers returned to earth to finetune living organisms once every, say 100.000 years, over a course of 3.5 billion years just so they can engineer existing life into looking like the slowly evolved? Unless of course, you are now going to say that radiometric dating is false and the change only took place over a course of 6000 years?

Furthermore, I never understood the objection to large-scale speciation in the first place. Creationists often cry about the supposed impossibilites of "macro evolution" with inane references like "We have never observed a fish turn into a cow".

Well, actually.... we have. You did it yourself in nine months. Every fucking animal on earth did. At one point, you, a Blue-Whale, a Bear, an elephant... every fucking mammal was a tiny fishlike creature with a tail inside their mothers womb. And you all turned into a fully grown living member of your extant species, without intervention by any intelligent agent. All you required was time and nutrients. Here you are now... from almost nothing to a huge chunck of flesh. And it was pure, unintelligently guided chemistry and physics. If that can happen... a fish turning into a not-so-much-a-fish-but-with-legs in 20 million years cannot really be said to be a stretch of the imagination.
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Re: The Bacterial Flagellum Revisited

#35  Postby PhiloKGB » Jun 26, 2010 6:29 am

CharlieM wrote:Let's say the flagellar proteins FlgB, FlgC, FlgE, FlgF, FlgG and FlgK are homologous and that they all developed from some unknown precursor protein. Why is this evidence that they were formed by some unguided, evolutionary mechanism? My blood cells, neurons, liver cells and skin cells all developed from a common precursor cell. Does it then follow that they were formed by some unguided developmental mechanism? Your list above is good evidence that life changes and develops over time, but it tells us nothing about the cause of the change; whether or not it was brought about by unguided accidents.

Are you of the 'an evolutionary explanation must provide a mutation-by-mutation reconstruction of a phenotypic change' school of ID-thought? I'm asking because that betrays a perfectly awful understanding of science, and I am extremely reluctant to waste my time on perfectly awful understandings of science.
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Re: The Bacterial Flagellum Revisited

#36  Postby CharlieM » Jun 26, 2010 10:28 am

Blitzkrebs:
You've missed the point. It's an excellent example of natural selection, a critical factor in evolution.


CharlieM:
And the vast majority of ID supporters believe that natural selection happens, as in the case of the Peppered moths or Darwin's finches. Those traits or features which have some sort of selective advantage do well in the population. But they must be already present in the population in order to be chosen. This is more a conservative feedback mechanism than a creative form producing force. My argument lies in the attributes of the creative force not in the selection mechanism.
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Re: The Bacterial Flagellum Revisited

#37  Postby Rumraket » Jun 26, 2010 10:43 am

CharlieM wrote:But they must be already present in the population in order to be chosen.

Yes, and what "makes" them present, so that selection can act on them, is a combination of duplications, random mutations and gene-shufflings. Evolution experiments have shown that mutations, shufflings and geneduplications can create novel information which natural selection can act upon.

CharlieM wrote:This is more a conservative feedback mechanism than a creative form producing force. My argument lies in the attributes of the creative force not in the selection mechanism.

Yes, selection is not the "creating" system, the genetic replication mechanisms like Duplications, mutations and shufflings are. Selection just acts on them once they are in place. Both systems exist and are observed to function : the novel information producing system and the selection for fitness system.

Additionally, we have 500-700 million years of fossils(in correct chronological order), combined with ALL the other lines of evidence to support the theory of evolution. There is nothing left to debate. The "creative force" is a combination of gene-duplications, random mutations and gene-shuffling, the selection is competitive and environmental, the result is what we see. The case is settled.
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Re: The Bacterial Flagellum Revisited

#38  Postby CharlieM » Jun 26, 2010 11:06 am

Rumraket:
You are making the mistake of thinking about any given line of evidence as seperate from the otheres. If you take it all together, observed speciation, observed micro/macro evolution, our knowledge of the workings of genetics and all the other stuff I listed above, plus more, the simple conclusion is that life evolved. And the geological record shows it.


CharlieM:
I am looking at the details while keeping the whole in mind. As you begin to look outward from the half a dozen proteins I mentioned things only get worse for a naturalistic explanation. These proteins need to work together as part of a whole functioning unit in order to be viable. They must be copied in precise numbers, transported to their correct location in sequence and assembled into the right shape, flexibility, strength and position. Thus you have structural proteins, assembly proteins, regulatory proteins and the rest all working together in a precise manner. And many of these proteins have no known homologs.

Granted your list of stuff giving the bigger picture shows that life developed into what we see today. But this does not show that it was some sort of fortuitous accident. We can observe a human developing from a fertilized egg, this does not mean that there was no plan involved. A point you seem to have forgotten (see below).

Rumraket:
Are we now supposed to believe that intelligent designers returned to earth to finetune living organisms once every, say 100.000 years, over a course of 3.5 billion years just so they can engineer existing life into looking like the slowly evolved? Unless of course, you are now going to say that radiometric dating is false and the change only took place over a course of 6000 years?


CharlieM:
This would be a very simplistic view of how "the designers" operated. Its not my view. And I'm happy to accept any timescale that the evidence supplies. Its all relative anyway.

Rumraket:
Furthermore, I never understood the objection to large-scale speciation in the first place. Creationists often cry about the supposed impossibilites of "macro evolution" with inane references like "We have never observed a fish turn into a cow".

Well, actually.... we have. You did it yourself in nine months. Every fucking animal on earth did. At one point, you, a Blue-Whale, a Bear, an elephant... every fucking mammal was a tiny fishlike creature with a tail inside their mothers womb. And you all turned into a fully grown living member of your extant species, without intervention by any intelligent agent. All you required was time and nutrients. Here you are now... from almost nothing to a huge chunck of flesh. And it was pure, unintelligently guided chemistry and physics. If that can happen... a fish turning into a not-so-much-a-fish-but-with-legs in 20 million years cannot really be said to be a stretch of the imagination.


CharlieM:
I think you are forgetting about the plan that was put in place when you were conceived, your DNA. You could have all the time and nutrients you wanted but nothing would have developed without your DNA.
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Re: The Bacterial Flagellum Revisited

#39  Postby Larkus » Jun 26, 2010 11:16 am

CharlieM, do you recognize, that Behe's argument, that the Bacterial Flagellum could not have evolved because it is irreducible complex has been refuted?
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Re: The Bacterial Flagellum Revisited

#40  Postby CharlieM » Jun 26, 2010 11:22 am

PhiloKGB:

Are you of the 'an evolutionary explanation must provide a mutation-by-mutation reconstruction of a phenotypic change' school of ID-thought? I'm asking because that betrays a perfectly awful understanding of science, and I am extremely reluctant to waste my time on perfectly awful understandings of science.


CharlieM:
Only where its needed. You can postulate co-option, its a perfectly reasonable assumption although things would need an awful lot of tweaking. But with something like the flagellar propulsion system (the rod, hook, filament and associated proteins) where there is little evidence of a system to co-opt from then you have to start looking at gene duplications, inversions, individual mutations, things like that. The proteins involved need to be of a very precise structure to function without being detrimental to the life of the organism.
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