Evolution of the the Bacterial Flagellum

[The Grand Nudger]

Who makes the claim? The point of the precursor system being mentioned is that it shows that a system -like this one- is functional, if not for motility. Handily explaining why "irreducible complexity" -itself- is not an issue worthy of any serious response or consideration, by ignoring this and pretending that it were. When dealing with how any -particular- biological system evolved in the distant past (and especially so if we're talking about something like bacteria) we are more accurately describing ways in which things -could have happened- in most cases. If something -could have happened- in a way that is completely counter to a claim of how something must have happened - the claim is DOA.

You don't need a degree in biology to understand this. We do not need to explain the evolution of the flagellum in unerring specifics to discard the claim of irreducible complexity. Thus, it needn't be any source of irk.

[Cato]

Kim,

I too wish I had deeper knowledge in a great many subjects; however, I am not irked by this. I strongly consider the knowledge and opinion of those who's life work deals with the subject at hand to better my understanding and form my own opinion. Consider the blog you referenced.

PineappleBunny has already pointed out one facet of the blog authors use of the paper. Might I suggest page 6 for an honest assessment of what isn't known, why, and the proposed next steps for further inquiry? Seems the blog author didn't read that far or doesn't understand how science works. Another possibility is that the blog author ignored it in order to invoke the very unscientific and ubiquitous god-botherer gambit of shoving God into spaces of ignorance. Ignorance motivates science by illuminating another avenue of inquiry.

Here's a link to the referenced paper.
http://home.planet.nl/~gkorthof/pdf/Pallen_Matzke.pdf[/align]

[Kim]

The point of the precursor system being mentioned is that it shows that a system -like this one- is functional, if not for motility.

I understand that. Structures that were used for different purposes can be utilized in a different manner. In the case of flagellum, the proteins in the flagellum should be traced back to precursors that were providing a different functionality in the precursor bacteria. In order to prove that, you need to show that the flagellum proteins have homologs. If only 50% have homologs, what is your explanation for the other 50%? So the question is, how did those proteins evolve? How were they incorporated into the flagellum?

[The Grand Nudger]

I understand that. Structures that were used for different purposes can be utilized in a different manner. In the case of flagellum, the proteins in the flagellum should be traced back to precursors that were providing a different functionality in the precursor bacteria. In order to prove that, you need to show that the flagellum proteins have homologs. If only 50% have homologs, what is your explanation for the other 50%?

I told you, alien waffles.

So the question is, how did those proteins evolve? How were they incorporated into the flagellum?

What you're actually asking is more precisely -when and exactly what/where from and to-. As the "how" would be the same for any other example. In either of those cases I can't help you (and the difficulty in establishing such a thing is fairly easy to understand). It would be fantastic to figure that out, though, agreed. Estimating this is one thing, finding a specimen (and determining that the specimen found is the correct specimen) is entirely another.

[popeyespappy]

-Nor are we likely to find much in the way of fossilized bacteria from which something we can sequence is going to be pulled. You know what I think happened, I think that alien waffles genetically engineered the other half of those proteins.

So don't make claim that the bacteria flagellum can be completely explained TODAY by evolution. Say it's a work-in-progress or whatever. Easy enough.

That's the problem Kim. Behe and his ilk claim the bacteria flagellum couldn't possibly have evolved to its current state. They claim evolution doesn't have the necessary mechanisms for that to happen. Then they insert their hypothesis without a shred of evidence to support it. ID isn't a scientific argument for design. It is an argument from ignorance against evolution.

Biologists like Ken Miller don't claim we know the exact evolutionary path the bacteria flagellum took. In fact there is debate among biologists whether the flagellum evolved from a T3SS like structure or the T3SS evolved from a flagellum. Either path is possible and most biologists admit to that. Their argument with Behe is that the mechanisms for the evolutionary process to take either pathway exist. In fact that Behe himself admits as much in his paper Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution.

[Kim]

Cat123, thanks for posting the paper! It explained a lot of things in details. It seems studying the evolution of these systems is just starting and the paper even suggested lab-based experiments to test possible evolutionary pathways to the current flagellum from simpler components.

So why the evolution of these systems was not studied thoroughly before? According to the paper:

However, the flagellar research community has scarcely begun to consider how these systems have evolved. This neglect probably stems from a reluctance to engage in the ‘armchair speculation’ inherent in building evolutionary models, and from a desire to determine how a system works before wondering how it got to be that way.

Now, if you can get a PDF to the 2009 paper (Bacterial flagellar diversity and evolution: seek simplicity and distrust it?) that would be awesome!!

[Rahul]

Who cares if we don't know any homologs yet for those?

All they're doing is saying that we don't know everything yet. Well, no shit.

We still know that we learn more everyday from the scientific Theory of Evolution.

What is the proposed alternative? Hmm?

Because we don't know everything yet that there is to learn by studying evolution then goddidit?

Pbbbht.

Weak. The entire gameplan of Intelligent Design is pathetic.

[pineapplebunnybounce]

The point of the precursor system being mentioned is that it shows that a system -like this one- is functional, if not for motility.

I understand that. Structures that were used for different purposes can be utilized in a different manner. In the case of flagellum, the proteins in the flagellum should be traced back to precursors that were providing a different functionality in the precursor bacteria. In order to prove that, you need to show that the flagellum proteins have homologs. If only 50% have homologs, what is your explanation for the other 50%? So the question is, how did those proteins evolve? How were they incorporated into the flagellum?

It's not really 50%. The blog assumes (and he honestly said that he did), that one of the structures did not evolve first. So proteins with homolog to that structure, he classified as no homolog. And he also quite honestly said that there was a paper that said that structure did evolve first. And the way he calculated the 50% was by counting amino acid lengths. What does that accomplish I really don't understand. Because a protein's homology to another affects the entire protein. Not individual amino acids. It would make more sense to say that we found homology for all the proteins except for these 15. So now we look for homology for these 15. There are 15 homology to look for, however long and short these 15 are, there is still only 15.

And why haven't they found homologous proteins. It's not easy to isolate all proteins in a bacteria, and then get their crystallized structure. it just isn't. the paper clearly stated "none yet known". If they had exhausted all the proteins they'll say they did not find any. It is a hypothesis isn't it? I'm not too informed about the flagellum debate thing, and i don't keep an eye on the research on this field. So yea, if they haven't been able to find all the homology, i would just wait and see. it's a pretty common thing to happen in science.

There is no need to come up with a new hypothesis yet. A hypothesis is proposed, and then it takes time to see if evidence supports it. So far evidence does. "None yet known" isn't sufficient to disprove a theory. It really just means they haven't found any yet, doesn't mean it doesn't exist. But since quite a lot has been found, to say that these do not exist and a new hypothesis is needed is a baseless assumption. And like cato said, i usually would look to what the authors suggest for their next steps, than to say, there are no next steps to be taken, this theory is in trouble. Took them 50 years to find higgs and no one said the theory was disproven, and hey they found higgs

[Kim]

And why haven't they found homologous proteins. It's not easy to isolate all proteins in a bacteria, and then get their crystallized structure. it just isn't. the paper clearly stated "none yet known". If they had exhausted all the proteins they'll say they did not find any. It is a hypothesis isn't it? I'm not too informed about the flagellum debate thing, and i don't keep an eye on the research on this field. So yea, if they haven't been able to find all the homology, i would just wait and see. it's a pretty common thing to happen in science.

That's certainly part of it. However, even if some of the proteins they found (for example FlgBCFG), those are homologous to each other! I'm no biologist, but I thought the purpose is to show homologies with precursor proteins, not flagellum proteins. I know all of this does not make ID more plausible, but to just say "It evolved and that's it" is not enough. Interestingly, this is what the authors said in the paper:

Notwithstanding the good scientific reasons for new forays in this direction, the lack of a scientific literature on flagellar evolution (emphasis mine) also has another undesirable consequence — it leaves open the suspicion among members of the public that maybe there is some mystery here, that maybe the ID proponents do have a point. Although all experts in this field agree that there is nothing to these claims, as Wilkins has recently pointed out , in these politically charged times, it is no longer enough to say, for example, that bacterial flagella evolved and that is that. Instead, scientific experts have to engage with a skeptical public.

[pineapplebunnybounce]

it is homologous to each other, that's in favour of evolution, no? That one flagellum protein along the evolutionary path duplicated and the second one became something slightly different? They haven't found the precursor to both these proteins, which is the same thing as the others they haven't found the precursor for. So yea, my response would be similar.

No of course it's not enough to say it evolved and that's it, if science were a religion that would be sufficient, but it isn't. You need to do research on it. Which I would assume people are doing. My training is in science, not in politics and frankly I give no thoughts to ID/creation, it's so hogwash i can't even. It's really just fairytales with the benefit of mass delusion.

I guess what I'm saying is I'm not sure what solution you're seeking? I've explained why the hypothesis still stands. So a new one is not required, but if one were to present itself then that one needs research to get support from evidence. New evidence doesn't just show up to support the hypothesis we want it to, research has to be done. And this hypothesis may ultimately be falsified and it'll just be another day in science .