The Bacterial Flagellum Revisited

The accumulation of small heritable changes within populations over time.

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Re: The Bacterial Flagellum Revisited

#101  Postby hotshoe » Jul 23, 2010 12:26 am

CharlieM wrote:
Shrunk wrote:
Please demonstrate, in precise detail down to the molecular level, the process by which the flagellar hook was "designed".

<snip non-response>


RIghto, now please show in detail how the "mind" physically arranged the sequences in the order they needed to be in, and how the "mind" physically transferred the sequence to the bacterium, and integrated it into the rest of the cell function. Oh, and for extra credit please show the preliminary sketches and the lab test models of the sequences before the final design was adopted.
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Re: The Bacterial Flagellum Revisited

#102  Postby CharlieM » Jul 23, 2010 12:40 am

Rumraket:
Well to be honest I don't even think the evolution of the hook poses much of a problem and a possible solution is quite simple.


I would say that the more technology advances and the closer we can look at these things, the less likely that the solution is simple.


http://www.nanonet.go.jp/english/mailmag/pdf/011a.pdf:
When Prof. Namba’s group attached a 40 nm fluorescence bead to the flagellar motor and observed the motor rotation, the group was surprised to see large and rapid fluctuations of the rotation speed. The key to revealing the mystery of the motor must be hidden behind the thermal fluctuation of the protein structure, which is still so far from understanding. “The atoms constituting proteins do fluctuate but the average positions of individual atoms are very precisely determined with an accuracy of sub-angstrom level. That is why individual proteins can properly identify partner molecules to bind and get assembled into the higher order structures of living organisms. The fluctuations of protein structure, that’s what makes living organisms function in such sophisticated and well regulated ways. I am willing to dedicate my entire life to the hard work unveiling the mysterious world of protein structure and function.”


Rumraket:
This duplicated rod is straight to begin with and is slowly accumulating mutations making it bend while retaining structure. Remember, these are individual molecules sticking together entirely by intermolecular attraction forces. It is not unreasonable to postulate that this complex can undergo a very slight twist without breaking. And the proto-flagellum was propably quite slowly rotating. What is now left for evolution to do is simply to filther through mutations for improved function over generations. The pro-flagellum before a bent hook as we see it today arrived, was providing motility already, but it was poor at it. But poor is better than none at all.


Poor motility is no use if it is not strong enough to overcome Brownian motion.

Bending a rod does not give you a universal joint. Ask an engineer to make you a mock up of the flagellum with just a bent tube where the hook should be and he'll say. "no problem". But ask him to make one with a universal joint and you'll have him scratching his head.
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Re: The Bacterial Flagellum Revisited

#103  Postby Shrunk » Jul 23, 2010 12:41 am

CharlieM wrote: If we look at human engineering over the centuries, in the early days human involvement was hands-on throughout the process of manufacture and function of machines. The more we advance the less direct involvement there is. In other words, if we didn't know better, it wouldn't always be obvious that there was a human involved at all. But one thing we can be sure about is that all the machines around us had their origin in human minds.


So your evidence that the flagellum was designed is that we have no evidence that it was designed.

Thank you for playing. Good night, everyone.
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Re: The Bacterial Flagellum Revisited

#104  Postby Shrunk » Jul 23, 2010 12:50 am

CharlieM wrote:
Bending a rod does not give you a universal joint. Ask an engineer to make you a mock up of the flagellum with just a bent tube where the hook should be and he'll say. "no problem". But ask him to make one with a universal joint and you'll have him scratching his head.


This has to be one of my favourite creationist arguments:

"To our knowledge, no intelligent being is capable of designing x. Therefore, x can only have been designed by an intelligent being."
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Re: The Bacterial Flagellum Revisited

#105  Postby hotshoe » Jul 23, 2010 12:59 am

Shrunk wrote:
CharlieM wrote:
Bending a rod does not give you a universal joint. Ask an engineer to make you a mock up of the flagellum with just a bent tube where the hook should be and he'll say. "no problem". But ask him to make one with a universal joint and you'll have him scratching his head.


This has to be one of my favourite creationist arguments:

"To our knowledge, no intelligent being is capable of designing x. Therefore, x can only have been designed by an intelligent being."


The funniest part is, CharlieM said it without a hint of irony.

Oh, CharlieM's designer is a real special one, no doubt. No doubt.
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Re: The Bacterial Flagellum Revisited

#106  Postby CharlieM » Jul 23, 2010 2:58 am

Shrunk:
This has to be one of my favourite creationist arguments:

"To our knowledge, no intelligent being is capable of designing x. Therefore, x can only have been designed by an intelligent being."


If someone scratches their head over a problem, it does not mean that they won't eventually solve it, just that it will take a lot of mental effort and deep thought to accomplish.

Its funny that nature is always one step ahead of us. The industrial revolution came along and nature was a mechanism. It turned out to be much more. The computer age came along and nature was understood as the product of an underlying computer-like code. It is much more than this. The invention of the wheel has been hailed as a marvelous human achievement. Well, nature beat us to it. We didn't know that nature has beaten us to the invention of the electric motor until recently.

So we use our advancing intelligence to design x and lo and behold nature has already designed x.

Bio-mimicry is becoming a popular endeavor as we realize the wonderful inventions that nature has produced.

I find that anyone whose cherished belief is being questioned responds with emotionally-charged replies, so I'll await the Spock-like logical responses. ;)

Must rush. TTFN.
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Re: The Bacterial Flagellum Revisited

#107  Postby DanDare » Jul 23, 2010 6:35 am

CharlieM wrote:
Shrunk:
This has to be one of my favourite creationist arguments:

"To our knowledge, no intelligent being is capable of designing x. Therefore, x can only have been designed by an intelligent being."


If someone scratches their head over a problem, it does not mean that they won't eventually solve it, just that it will take a lot of mental effort and deep thought to accomplish.

Its funny that nature is always one step ahead of us. The industrial revolution came along and nature was a mechanism. It turned out to be much more. The computer age came along and nature was understood as the product of an underlying computer-like code. It is much more than this. The invention of the wheel has been hailed as a marvelous human achievement. Well, nature beat us to it. We didn't know that nature has beaten us to the invention of the electric motor until recently.

So we use our advancing intelligence to design x and lo and behold nature has already designed x.

Bio-mimicry is becoming a popular endeavor as we realize the wonderful inventions that nature has produced.

I find that anyone whose cherished belief is being questioned responds with emotionally-charged replies, so I'll await the Spock-like logical responses. ;)

Must rush. TTFN.

I'm sorry Captain, I don't see your point. Natural phenomena of complexity pre-date human designs of similar complexity that is true. It is illogical to then state that therefore the natural phenomena are not natural after all. Live long, and prosper.
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Re: The Bacterial Flagellum Revisited

#108  Postby Rumraket » Jul 23, 2010 7:09 am

CharlieM wrote:
Rumraket:
Well to be honest I don't even think the evolution of the hook poses much of a problem and a possible solution is quite simple.


I would say that the more technology advances and the closer we can look at these things, the less likely that the solution is simple.


http://www.nanonet.go.jp/english/mailmag/pdf/011a.pdf:
When Prof. Namba’s group attached a 40 nm fluorescence bead to the flagellar motor and observed the motor rotation, the group was surprised to see large and rapid fluctuations of the rotation speed. The key to revealing the mystery of the motor must be hidden behind the thermal fluctuation of the protein structure, which is still so far from understanding. “The atoms constituting proteins do fluctuate but the average positions of individual atoms are very precisely determined with an accuracy of sub-angstrom level. That is why individual proteins can properly identify partner molecules to bind and get assembled into the higher order structures of living organisms. The fluctuations of protein structure, that’s what makes living organisms function in such sophisticated and well regulated ways. I am willing to dedicate my entire life to the hard work unveiling the mysterious world of protein structure and function.”

You keep piling up gaps in our knowledge as evidence of design. They're not. Please grasp this elementary concept. It seems to me the ID community's entire approach to biology is "oh man this is so complex, see how complex that is? Man... that is SO complex... gawd dun it".

Rumraket:
This duplicated rod is straight to begin with and is slowly accumulating mutations making it bend while retaining structure. Remember, these are individual molecules sticking together entirely by intermolecular attraction forces. It is not unreasonable to postulate that this complex can undergo a very slight twist without breaking. And the proto-flagellum was propably quite slowly rotating. What is now left for evolution to do is simply to filther through mutations for improved function over generations. The pro-flagellum before a bent hook as we see it today arrived, was providing motility already, but it was poor at it. But poor is better than none at all.


Poor motility is no use if it is not strong enough to overcome Brownian motion.

Bending a rod does not give you a universal joint. Ask an engineer to make you a mock up of the flagellum with just a bent tube where the hook should be and he'll say. "no problem". But ask him to make one with a universal joint and you'll have him scratching his head.

That's because a macroscopic tube is made up of untold quintillions of atoms more or less randomly arranged. Or let me put it this way, the spatial arrangement of the molecules in the construction of a manmade tube is not really undergoing continued selection over generations for their transfer into a universal join. The difference of mechanism between human engineering and evolution by mutation+natural selection is vastly different and simply not comparable.

At the molecular level there is not really such a thing as a "tube". Everything is lumpy and sticks together by intermolecular electromagnetic forces. Your comparison fails because of these differences in behavior at the molecular level. Many molecules are already inherently flexible "objects", and a secreted adhesion protein is especially such a molecule. Additionally, the hook protein is a mutated duplication of the rod protein, which is itself already a mutated adhesion protein for structural strength. You are making the mistake of thinking that the hook protein had to accumulate mutations on it's own from something completely unrelated that never had a function as a tubular-shaped structural component.

These are microscopic molecules, not macroscopic human-made objects. And while the fundamental forces binding them together are the same, because of the vast size differences, their behaviors are vastly different.
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Re: The Bacterial Flagellum Revisited

#109  Postby Rumraket » Jul 23, 2010 7:18 am

Shrunk wrote:
CharlieM wrote: If we look at human engineering over the centuries, in the early days human involvement was hands-on throughout the process of manufacture and function of machines. The more we advance the less direct involvement there is. In other words, if we didn't know better, it wouldn't always be obvious that there was a human involved at all. But one thing we can be sure about is that all the machines around us had their origin in human minds.


So your evidence that the flagellum was designed is that we have no evidence that it was designed.

Thank you for playing. Good night, everyone.

R O F L. Well said. Basically he's saying that the less evidence we see of the involvement of designers, the more it is evidence of design.
Oh... My... God. I'ts impossible to have a discussion when you approach the subject with such a mindset. I mean, how could you even possibly be convinced otherwise?
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Re: The Bacterial Flagellum Revisited

#110  Postby CharlieM » Jul 23, 2010 8:54 am

Colonel Dare:
I'm sorry Captain, I don't see your point. Natural phenomena of complexity pre-date human designs of similar complexity that is true. It is illogical to then state that therefore the natural phenomena are not natural after all. Live long, and prosper.


JW von Goethe on nature:
She has always thought and always thinks; though not as a man, but as Nature. She broods over an all-comprehending idea, which no searching can find out.

Mankind dwell in her and she in them. With all men she plays a game for love, and rejoices the more they win. With many, her moves are so hidden, that the game is over before they know it.

That which is most unnatural is still Nature; the stupidest philistinism has a touch of her genius. Whoso cannot see her everywhere, sees her nowhere rightly.
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Re: The Bacterial Flagellum Revisited

#111  Postby CharlieM » Jul 23, 2010 9:41 am

Rumraket:
You keep piling up gaps in our knowledge as evidence of design.


Not gaps, no. Remember a quote I provided several posts back. Here is an excerpt,

A three-dimensional structural similarity search using software DALI25 resulted in no match for domain D1, confirming its unique fold.


This is the kind of knowledge that is available to us these days. We see a complex structure such as this domain of protein FlgE and we know that this has to be inserted or developed from a similar protein to it and its homologs. It would take lots of mutations to achieve this unless we assume that it arrived fully formed and inserted itself in just the right place. Can random changes search through all the available combinations of forms and eventually hit a form that will do the job. You think yes, I think no, I would say its directed.

Rumraket:
Additionally, the hook protein is a mutated duplication of the rod protein, which is itself already a mutated adhesion protein for structural strength. You are making the mistake of thinking that the hook protein had to accumulate mutations on it's own from something completely unrelated that never had a function as a tubular-shaped structural component.


I still don't think you are getting the universal joint thing.

Its no use just having a structure that is elastic in its longitudinal axis. Think of the hook like a muscle in your body, it can contract but it needs a nerve signal to do so. A protein in the hook won't just expand or contract on its own. It needs a signal or an outside force to do this and this signal or force needs to keep the expansions and contractions in time with the speed of the motor or the tail will be flailing all over the place. This is one more complexity of the system that I would very much like to see an explanation of. So if there are any experts out there with any ideas please share them.
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Re: The Bacterial Flagellum Revisited

#112  Postby Rumraket » Jul 23, 2010 10:56 am

CharlieM wrote:
A three-dimensional structural similarity search using software DALI25 resulted in no match for domain D1, confirming its unique fold.

This is the kind of knowledge that is available to us these days. We see a complex structure such as this domain of protein FlgE and we know that this has to be inserted or developed from a similar protein to it and its homologs.

Wherefrom it doesn't logically follow that it was designed, at all. It doesn't even hint at it, all it says is that the protein fold, it's 3-dimensional structure, is unique among accessed protein folds by the software. The fact still remains that FlgE is homologous in it's sequence to the rod, cap and filament proteins.
There is of course also the fact that we have yet to sequence the entirety of bacterial genomes in their diversities, we have barely begun to scratch the surface.

For example, regarding the search for T3 export systems back in 2003 Matzke had these facts for digestion:
http://www.talkdesign.org/faqs/flagellum.html#origin
If type III virulence systems are derived from flagella, what is the basis for hypothesizing a type III secretion system ancestral to flagella? The question would be resolved if nonflagellar homologs of the type III export apparatus were to be discovered in other bacterial phyla, performing functions that would be useful in a pre-eukaryote world. That such an observation has not yet been made is a valid point against the present model, but at the same time serves as a prediction: the model will be considerably strengthened if a such a homolog is discovered. For the moment, it is easy enough to explain the lack of discovery of such a homolog on the basis of lack of data. Knowledge of microbial diversity is quite poor (Whitman et al., 1998): far less than 1% of bacteria extant in a particular environment are readily culturable (Hayward, 2000). Cultivation-independent surveys of prokaryote diversity based on environmental rRNA sequencing commonly discover deeply-branching microbes previously unknown to science (DeLong and Pace, 2001), and that certain groups are unexpectedly ubiquitous (Karner et al., 2001). In addition, only a fraction of cultured microbes have been studied in any substantial biochemical or genetic detail, and this subsample is heavily skewed towards pathogens and convenient model organisms. Of the ~112 complete bacterial genomes sequenced as of July 2003 (http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub_g.html), at least two-thirds are pathogens, mutualists, or commensals of multicellular eukaryotes. Many of the free-living bacteria that have been sequenced are extremophiles or are used in industrial applications


CharlieM wrote:It would take lots of mutations to achieve this unless we assume that it arrived fully formed and inserted itself in just the right place. Can random changes search through all the available combinations of forms and eventually hit a form that will do the job.

You are making the mistake of thinking that natural selection is working with some kind of goal in mind. Mutations happen. Most of them are neutral, some a beneficial, some are deleterious. Organisms that recieve deleterious mutations die out. Organisms that recieve beneficial mutations, whatever their nature, have increased chance of passing on to the next generation.
There is no end goal in mind. Whatever works, works and gets selected for. You are looking at the end product now, but it was never planned. Therefore, every single mutation is as impropable as the next... none of them are "special" and have to be "searched for".
To claim that the beneficial mutations are so impropable as to be virtually impossible implies you must know the total amount of beneficial, deleterious and neutral mutations. In addition to the total amount of relevant bacteria, and for how long they have existed. There is no reason to expect that the FlgE protein folds are the only possible protein folds capable of making a molecular universal joint.

Remember, natural selection was not selecting for mutations that would result in a modern bacterial flagellum. Natural selection simply selected anything that worked in a beneficial way. Intermediate steps were beneficial and that's why they stayed. Now it just so happens that the result we see today is a flagellum.

CharlieM wrote:You think yes, I think no, I would say its directed.

With no evidence whatsoever to back it up, making it completely unfalsifiable. You can of couse think anything you want, just don't expect it to be taught as science.

CharlieM wrote:I still don't think you are getting the universal joint thing.

I get it perfectly. All I have to do is look at this site to understand it's wonderful construction. http://molvis.sdsc.edu/flagellar_hook/index.htm

However, I don't think you get the difference between molecular sized object and macroscopic human-made tubes.

CharlieM wrote:Its no use just having a structure that is elastic in its longitudinal axis.

Molecules and their interactions are not really equal to macroscopic objects.

CharlieM wrote:Think of the hook like a muscle in your body, it can contract but it needs a nerve signal to do so. A protein in the hook won't just expand or contract on its own. It needs a signal or an outside force to do this and this signal or force needs to keep the expansions and contractions in time with the speed of the motor or the tail will be flailing all over the place. This is one more complexity of the system that I would very much like to see an explanation of. So if there are any experts out there with any ideas please share them.

Translation : It's so complex, I can't fathom how complex it is. See how complex it is? It's incredibly complex... how could that ever evolve? Surely it's so complex that it couldn't... therefore goddidit.
These are simply made-up hurdles of yours for us to ponder over and are entirely without substance.

CharlieM wrote:A protein in the hook won't just expand or contract on its own.

Well, no... but in the vicinity of other molecules it will.

CharlieM wrote:It needs a signal or an outside force to do this

Yes, those are the other molecules of the hook.

CharlieM wrote:and this signal or force needs to keep the expansions and contractions in time with the speed of the motor or the tail will be flailing all over the place.

Yeah it's called the electromagnetic force and it's propagating throuch a stack of molecules. The molecules have evolved in such a way as to respond to the one next to it. Nothing hugely complex about it I'm afraid. The molecules basically consist of two interacting ends with a joint between them. The interacting ends "stick" together, as is painfully obvious from that link I gave above, and they can bend across the joint. Viola!
This is also quite easy to infer from the structural comparisons between the hook protein FlgE and the Rod protein FlgG :
The differences mostly consist of changes to the two interacting "lumps" at either end of the protein, and the insertion of the "joint" in the middle. They even used the model of the FlgE hook protein as a basis for a model of the FlgG protein in this paper:
The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution
http://genesdev.cshlp.org/content/21/18/2326.full.pdf+html

Modeling the FlgG structure based on homology with FlgE
Filamentous rod structures resulted from single amino acid substitutions in FlgG. This suggested a simple mechanism leading to the cessation of FlgG-rod growth and provided an important clue to the design of the flagellar structure. The FlgG amino acid sequence was shown to have a high degree of identity with the flagellar hook protein (FlgE), which is assembled just after FlgG-rod completion (Homma et al. 1990). Predicted secondary structure analysis shown in Figure 3A suggests that these proteins have a high degree of structural identity as well. This allowed the modeling of the filamentous rod mutations on a three-dimensional FlgG structure. There are two significant differences between the FlgG-rod and FlgE-hook sequences. First, the FlgG-rod has an insertion of 18 amino acids (residues 46–65 of FlgG) not present in FlgE, where the majority of the filamentous rod mutations occurred (amino acids 52–66). Second, FlgE-hook has two insertions of 16 amino acids and a stretch of 146 amino acids in the middle of the protein that is not present in FlgG (Fig. 3A). The structure of FlgE has been determined (Samatey et al. 2004). We modeled the FlgG-rod sequence onto the FlgE-hook structure that had previously been solved (Fig. 3B; Samatey et al. 2004). Unfortunately, the first 70 amino acids of FlgE-hook were not structured, which corresponds to the first 90 amino acids in FlgG, and where a number of filamentous rod mutations were located (amino acids 52–66 of FlgG). However, two filamentous rod mutant sites that include the G183R/G183W and S197L mutations, reside close to each other at the very bottom of the predicted FlgG structural model, and two other filamentous rod mutant sites that include the D117Y, G132R, and G133V mutations, are located close to each other in the middle of the structure (Fig. 3B). This allowed us to propose mechanisms for FlgG stop-polymerization. The 52- to 66-amino-acid region of one FlgG subunit could interact with the bottom region of a second FlgG subunit stacked on top of it at residues G183 and S197 to stop FlgG polymerization. The isolation of mutants at positions D117 and G132 would indicate an effect of these residues on this interaction.


Edit : Cleaned up the post a little.
Last edited by Rumraket on Jul 23, 2010 11:30 am, edited 4 times in total.
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Re: The Bacterial Flagellum Revisited

#113  Postby Shrunk » Jul 23, 2010 11:08 am

CharlieM wrote:
Shrunk:
This has to be one of my favourite creationist arguments:

"To our knowledge, no intelligent being is capable of designing x. Therefore, x can only have been designed by an intelligent being."


If someone scratches their head over a problem, it does not mean that they won't eventually solve it, just that it will take a lot of mental effort and deep thought to accomplish.

Its funny that nature is always one step ahead of us. The industrial revolution came along and nature was a mechanism. It turned out to be much more. The computer age came along and nature was understood as the product of an underlying computer-like code. It is much more than this. The invention of the wheel has been hailed as a marvelous human achievement. Well, nature beat us to it. We didn't know that nature has beaten us to the invention of the electric motor until recently.

So we use our advancing intelligence to design x and lo and behold nature has already designed x.

Bio-mimicry is becoming a popular endeavor as we realize the wonderful inventions that nature has produced.

I find that anyone whose cherished belief is being questioned responds with emotionally-charged replies, so I'll await the Spock-like logical responses. ;)

Must rush. TTFN.



You still failed to understand my point. Your initial claim was presented as evidence for intelligent design. Yet what it demonstrated was that the most intelligent "designer" we know of, human beings, are still not able to create an object of such complexity. From this you conclude that there must exist an even more intelligent designer somewhere that is capable of designing it. But that's just a presupposition on your part. The alternative explantaion, and the one that is supported by literally millions of pieces of evidence, is that it arose from a process that doesn't require a designer.

LIve long and prosper.
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Re: The Bacterial Flagellum Revisited

#114  Postby talkietoaster » Mar 31, 2011 9:14 am

Rumraket wrote:
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.


Of course, evolution show be at the speed of the Futurama. LoL

Why is it everytime you give an example of a life form on the planet with an explanation of the process, a creationist / ID type always goes but it never happened to my hamster? (i know hamster wasn't used its just a way of me saying insert animal) :think:
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Re: The Bacterial Flagellum Revisited

#115  Postby Calilasseia » Jun 16, 2011 10:27 pm

Heh, every time you breed your pets, evolution is happening. Because genes are being shuffled, and variation is being disseminated across generations. Sometimes, that variation is significant. See the Double Tail mutation in Betta splendens for an example, or for that matter just about every colour and finnage variation extant in aquarium guppies, mollies, platies and swordtails. None of those were "designed". What happened in every instance, was that the mutation showed up in breeding stock, and aquarists decided to preserve the mutation in question for aesthetic reasons. Basically, aquarium livebearers nowadays are effectively the result of over 60 years of selection of the prettiest, though how "prettiest" was defined depended upon the arbitrary whim of the aquarists involved. Personally, I think balloon mollies look hideous, but someone must have liked them enough for them to end up in the aquarium trade.

But the point remains that in all instances, what happened was the following:

[1] A mutation appeared in breeding stock that happened to attract the attention of the aquarist breeding the fishes;

[2] The aquarist breeding the fishes selected the mutant to breed from (just as nature selects which individuals in a population are going to breed and which aren't);

[3] The mutation was thus fixed in that particular line of inheritance.

In the case of the Double Tail mutation in Betta splendens (another fish that has exhibited a wide range of colour and finnage mutants that aquarists have selectively bred and fixed), the history of this is well known. It first appeared in breeding stocks in the 1970s, and was fixed in breeding stocks by aquarists who liked the look of Double Tail Bettas. Indeed, the mutation has been traced to a single gene, that exhibits classic Mendelian single-factor recessive inheritance. The Double Tail mutation has been known to aquarists interested in Bettas for 35 years, and consequently, aquarists have known how to combine the Double Tail trait with a variety of colours. I've even seen, in one of my tropical fish magazines, a photo of a "melano black" Double Tail male, which is especially difficult to produce because all melano black females are infertile, so you have to engage in a little ingenuity to combine those two traits. But, it's possible, and I have the magazine photo establishing this.

The funny part of all this being of course, that creationists think evolution couldn't happen just because they need it not to happen in order to preserve their adherence to their masturbation fantasy of a doctrine, yet the aquarium trade effectively uses Darwinian principles to bring new finnage and colour forms to market.
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Re: The Bacterial Flagellum Revisited

#116  Postby ramseyoptom » Jun 16, 2011 10:35 pm

Calilasseia wrote:[3] The mutation was thus fixed in that particular line of inheritance.

The funny part of all this being of course, that creationists think evolution couldn't happen just because they need it not to happen in order to preserve their adherence to their masturbation fantasy of a doctrine, yet the aquarium trade effectively uses Darwinian principles to bring new finnage and colour forms to market.


As did Pigeon Fanciers in the 19th Century, and I wonder who used them as examples of evolution in action??

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Re: The Bacterial Flagellum Revisited

#117  Postby Hardcoreathiest » Jul 30, 2011 7:19 pm

CharlieM wrote:
PhiloKGB:
How have you come to understand that evolution proceeds by using "archetypal plan[s]" with "instructions" inbuilt? Your argument appears to assume facts not in evidence and Matzke's is therefore preferable on that basis alone.


I look at the same facts that he does. We both believe that homology points to a relationship. Matzke assumes that this relationship comes about by fortuitous changes being selected. I believe that the changes are more directed and that the plasticity of protein structure is being used in a creative manner. I would say that the evidence points more towards the assumptions that I am making. If you propose that two functional proteins are the unplanned "offspring" of a single protein, you need to look at the search space needed to be sampled, the regulatory changes that need to accompany the new function, the various connections that need to be considered in order for the proteins to be installed in their new roles. Where in the organisms of the earth are all the functionless proteins or proteins with an inefficient function waiting to slot into a new system that evolution has brought forth? Has anyone observed a biological system becoming more efficient over time as natural selection working on changes makes the necessary tweeks. And if the hook protein FlgE had no functionless precursors what was the path in the diversification between it and its homologs? If you try to make a hook out of proteins that don't have the specific properties of FlgE and you will no doubt end up breaking the flagellar drive. And there is no evidence whatsoever of a pre-existing universal joint being co-opted and slotted into place in the drive train.

Goal directed development is something we see all the time. We see it every time an individual organism grows from an egg or a seed. The fact that self-aware creative beings have appeared on the earth is no accident just as it is no accident that I developed from a fertilized egg (no matter what my mother says).

CharlieM:
I was talking about natural selection on its own. I know things are different when mutations are taken into account. My point was that natural selection cannot create novelty it only removes or lets through what is already there.

PhiloKGB:
This is pure bullshit, an assertion which can only be made by those merely Google-educated who nonetheless consider themselves experts.


I don't know why you think I consider myself an expert. I came here to learn and I think the best way to learn is to share your opinions with those who you know are going to disagree with them and to see what they come back with.

If you think what I said is bullshit can you explain to me how natural selection on its own can create anything that was not already there waiting to be selected?

:coffee:
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Re: The Bacterial Flagellum Revisited

#118  Postby LjSpike » Apr 09, 2016 9:52 am

This Muller (please excuse the lack of accents, I can't be bothered to head over to the unicode char search), is that the same Muller as in the Muller-Urey experiment (of directing electricity into a mixture of various compounds to see if amino acids and eventually life could form...)?
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Re: The Bacterial Flagellum Revisited

#119  Postby campermon » Apr 09, 2016 12:16 pm

LjSpike wrote:This Muller (please excuse the lack of accents, I can't be bothered to head over to the unicode char search), is that the same Muller as in the Muller-Urey experiment (of directing electricity into a mixture of various compounds to see if amino acids and eventually life could form...)?


I belive it was 'Miller-Urey'. So not the same dude. :)
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Re: The Bacterial Flagellum Revisited

#120  Postby Greyman » Apr 09, 2016 1:15 pm

Hermann Joseph Müller (December 21, 1890 – April 5, 1967)

Stanley Lloyd Miller (March 7, 1930 – May 20, 2007)
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