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>

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.

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.

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.

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.

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."

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."

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.

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.”

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.

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.

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.

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

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

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.

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.

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.

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

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

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

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.

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

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

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.

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.

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.

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.

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.

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?