The Bacterial Flagellum Revisited

The accumulation of small heritable changes within populations over time.

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Re: The Bacterial Flagellum Revisited

#61  Postby PhiloKGB » Jul 01, 2010 12:56 am

CharlieM wrote:Matzke has proposed this model based on his views on how evolution proceeds and this assumes that the type III secretory system is ancestral to the flagellum. I could propose a model based on my understanding of how evolution proceeds in which various bacteria make use of an archetypal plan which contains the "instructions" for making flagellar motility and secretion systems. This plan is expressed variously by different bacteria and sometimes in the same bacterium depending on physical factors. With my plan it doesn't matter which system (type III or Flagellum) came first.

Both our models can fit the observed data. Its our beliefs that determine the model, the data is the same in both cases.

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 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.

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

#62  Postby scruffy » Jul 01, 2010 1:38 am

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 have to agree with you there. I'm having troubles pin pointing exactly what it is that CharlieM is trying to convince us of. It seems to me like the crux of his argument rests on 'archetypal' forms, which to me is bull-shit. Explain to me exactly how this would work. Having a 'program' built into the organism whose eventual goal is to become a sentient self aware human. I don't buy it.

CharlieM: I see the diversity of organisms as the individual expression of archetypal forms and not as blind accidents of natural evolution.


CharlieM: ...Every human being starts out with the potential to be a self-conscious being. Not everyone achieves this potential due to circumstances along the way. Nothing is set in stone.

I believe that the evolution of life is the flowering of consciousness. Life develops to produce entities with awareness, and more than that self-awareness. And its not accidental.

Goethe thought of the archetypal plant as being more real than individual plants and he discovered the inter-maxillary bone in humans because of his ability to see the whole in the parts. He did not see humans as being detached from the rest of life.


I just have a problem when someone just pulls out a 'pre-made' assertion like this and doesn't back it up at all, but yet expects us to discuss as if it were true. Iono, just seems a little pointless to me.

____

CharlieM wrote:Saying I believe in God tells you nothing really. It then comes down to defining what we mean by "God". Other than that, what I believe is not important to the argument, but thanks for showing an interest.


I was just curious is all. You're argument ultimately rests on this belief, so I thought it would be nice to get a full picture of who you 'are'.
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Re: The Bacterial Flagellum Revisited

#63  Postby Rumraket » Jul 01, 2010 4:50 am

CharlieM wrote: Matzke has proposed this model based on his views on how evolution proceeds and this assumes that the type III secretory system is ancestral to the flagellum.

Matzke doesn't have a unique "view" on how evolution works. Matzke is working from the generally accepted parameters of evolutionary theory. It has a number of testable predictions, these predictions are observationally confirmed. Therefore the evolutionary models has empirical support.

CharlieM wrote:I could propose a model based on my understanding of how evolution proceeds in which various bacteria make use of an archetypal plan which contains the "instructions" for making flagellar motility and secretion systems. This plan is expressed variously by different bacteria and sometimes in the same bacterium depending on physical factors. With my plan it doesn't matter which system (type III or Flagellum) came first.

Both our models can fit the observed data. Its our beliefs that determine the model, the data is the same in both cases.

Ahh, another version of the "I can design a machine in such a way that it looks like it evolved"-argument. Well good for you but I'm afraid this doesn't highlight a weakness in evolutionary theory, only the lengths to which you would go in order to cast doubt on evolutionary theory. I can also doctor up the evidence on a crime scene for a murder trial, are we now supposed reject the rule of law?
Essentially, this is an admittance that it looks like the flagellum evolved. Which brings us to the conclusion that IF it was designed, the designer is deliberately decieving us. Nothing we can do in that situtation though.

CharlieM wrote: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.

Yes and as I was saying natural selection acts on stuff with gain or cost. Some things are neutral, some are both gains and costly. If they have higher gain than cost, they will still be positively selected. I think you get the picture.
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Re: The Bacterial Flagellum Revisited

#64  Postby CharlieM » Jul 01, 2010 11:21 pm

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?
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Re: The Bacterial Flagellum Revisited

#65  Postby debunk » Jul 01, 2010 11:53 pm

CharlieM wrote:Has anyone observed a biological system becoming more efficient over time as natural selection working on changes makes the necessary tweeks.


http://en.wikipedia.org/wiki/E._coli_lo ... experiment
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Re: The Bacterial Flagellum Revisited

#66  Postby PhiloKGB » Jul 02, 2010 12:33 am

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.

You mean you and Matzke have equivalent education? No, of course you don't.
We both believe that homology points to a relationship. Matzke assumes that this relationship comes about by fortuitous changes being selected.

It's not an assumption. Science permits inductive conclusions; no one seriously believes each trait needs to be reverse-engineered before we can reasonably conclude evolutionary processes are at work.
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.

Ah, the fallacy of never-enough-detail. The underhanded creationist takes refuge here because he knows that biologists have neither the resources nor the inclination to reverse engineer a pathway for every feature. Moreover, they have absolutely no intention of doing so every time a creationist issues a poorly-considered challenge.
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).

What do we see when a 64-cell blastocyst spontaneously aborts due to a lethal mutation? Is that the proper "direction" for that genome?

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.

It never occurred to me that I could learn by declaring paradigm shifts in disciplines outside my expertise. Nice work if you can get it.
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?

"On its own"? Please tell me you are not so transparently dishonest.
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Re: The Bacterial Flagellum Revisited

#67  Postby Rumraket » Jul 02, 2010 7:26 am

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.

The difference is, Matzke has evidence on his side. We have observed foruitous mutations happen in the laboratory and get selected for.
The E.coli long term evolution experiment is one such instance. I believe Calilasseia has a considerable list of papers that demonstrate this abtly both in the lab and in the wild.

Additionally, your claims are unfalsifiable and therefore unscientific. You can fit your explanation to any observed fact. "I believe what we see here is the product of intentional design" Well how do you know? "Because it looks like what the designer would want it to look". :facepalm2:

I would say that the evidence points more towards the assumptions that I am making.

In which case you are making an unsupported bare assertion. we don't see any designers running around tweaking lifeforms today and there is no evidence around that this happened in the past.

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.

Uhh what? No, I don't need to do all those things. That's ludicrous. Why would that be a requirement?
The hypothesis is that the hook and filament are build by proteins secreted by a secretory system. Therefore the hook and filament proteins should be homologous to the ancestral secreted protein. They are.

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?

What? This is a specious question when I have already told you about geneshufflings and duplications. A gene coding an existing protein can be duplicated, leaving one of them open for mutations resulting in alternate or superior function. Or two, three or more existing genes can be shuffled together into a new and highly functional protein.

Additionally, any given protein has the potential for superior function, depending on the environment. Take hemoglobin in humans for blood oxygen transport. You may argue that this protein is highly functional, but If I move to an area of extreme cold, it's ability to extract and transport oxygen is no longer adequate and it get's difficult to breathe. This leaves hemoglobin open to mutations which can undergo selection for improved function in extreme cold.
There are no "functionless" proteins waiting in a que somewhere. When the environmental and selective pressures change, the already existing and highly functional proteins undergo selection for improved function in their NEW environment.

Has anyone observed a biological system becoming more efficient over time as natural selection working on changes makes the necessary tweeks.

Yes. I'll dig something up later when I get home from work but to get you started, the observed evolution of increasingly effective camouflage in multiple species are some excellent examples.

And if the hook protein FlgE had no functionless precursors what was the path in the diversification between it and its homologs?

This question assumes the precursor must be functionless. Which is ludicrous and flatly wrong. Whatever the precursor proteins function was, as the entire precursor system started serving a motility function, the hook-precursor protein was under selection for increased functionality, in this case successful transfer of torque without breaking. Those that failed, died, those that succeeded didn't.

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.

Big surprise?

And there is no evidence whatsoever of a pre-existing universal joint being co-opted and slotted into place in the drive train.

Which is not the proposed model and therefore a strawman.

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.

Yes, that goal being the construction of bodies from genes evolved through succesive generaitons over hundreds of millions of years, to successfully construct bodies that enhanced their chances of successful replication. Which Is why we have so many vestigial traits and organs and share so many attributes and oddly constructed imperfections with related species. And why ours and every other organism's DNA fits so well in a hirearchial tree of life. Why comparative anatomy, biogeography, embryology, the fossil record and everything else fits so well with the darwinian evolutionary explanation.

The fact that self-aware creative beings have appeared on the earth is no accident

Baseless blind assertion.

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?

Red herring.
We are under no obligation to explain how natural selection can create novel information, when none of us claim it does. Natural selection selects, mutations, gene duplications and geneshufflings CREATE. Please try and grasp this fundamental concept.
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Re: The Bacterial Flagellum Revisited

#68  Postby Calilasseia » Jul 02, 2010 10:22 am

Oh dear. I see someone's erecting the "beneficial mutations don't exist" canard. Yawn. Time for this:

Protein engineering of hydrogenase 3 to enhance hydrogen production by T. Maeda, V. Sanchez-Torres and T. K. Wood, Applied Microbiology and Biotechnology, 79(1): 77-86 (May 2008)

Here's the abstract:

Maeda, Sanchez-Torres & Wood, 2008 wrote:The large subunit (HycE, 569 amino acids) of Escherichia coli hydrogenase 3 produces hydrogen from formate via its Ni-Fe-binding site. In this paper, we engineered HycE for enhanced hydrogen production by an error-prone polymerase chain reaction (epPCR) using a host that lacked hydrogenase activity via the hyaB hybC hycE mutations. ... The best epPCR variant contained eight mutations (S2T, Y50F, I171T, A291V, T366S, V433L, M444I, and L523Q) and had 17-fold higher hydrogen-producing activity than wild-type HycE. In addition, this variant had eightfold higher hydrogen yield from formate compared to wild-type HycE. Deoxyribonucleic acid shuffling using the three most-active HycE variants created a variant that has 23-fold higher hydrogen production and ninefold higher yield on formate due to a 74-amino acid carboxy-terminal truncation. Saturation mutagenesis at T366 of HycE also led to increased hydrogen production via a truncation at this position; hence, 204 amino acids at the carboxy terminus may be deleted to increase hydrogen production by 30-fold. This is the first random protein engineering of a hydrogenase.


So, what did the authors of this paper do?

Basically, they wanted to improve the performance of the hydrogenase-3 enzyme that is used by Escherichia coli, with a view to using it as a commercial producer of hydrogen gas. Now, there were two possible approaches to solving this problem. The first approach would have been to dissect the enzyme, amino acid by amino acid, determine how that enzyme worked based upon its structure, then try and design a better one with a more economical structure with improved performance. However, the authors realised that this process would keep them up to their necks in supercomputer analyses of the molecules for the next 50 years. Needless to say, they wanted a quicker route. So what they did was this. They decided to let evolution do the hard work for them.

Now, in order to understand the neat trick employed here, bear in mind that in order to copy DNA molecules, scientists use what is known as a polymerase enzyme, which is an enzyme that is present (in various forms) in all living organisms. Everything from bacteria to humans possesses a polymerase enzyme of some sort. Indeed, these enzymes were first pressed into service on a large scale in forensic science, where they are used to amplify the contents of a DNA sample, so that there is sufficient material available for gel electrophoresis (the so-called "DNA fingerprinting" technique). However, forensic scientists are interested in eliminating copying errors, so that the amplified DNA fragments are all faithful copies of the original. So, forensic scientists have been looking for high-fidelity polymerase enzymes (and have found them) to perform this task. What the authors of the above paper were interested in was not the production of high-fidelity copies of their hydrogenase gene, but accelerated generation of mutant versions of that gene. So, they deliberately looked for a polymerase enzyme with low copying fidelity in order that mutations would be introduced into the gene population at an accelerated rate.

Once they had their population of mutants, they then tested each of the mutants for efficiency in producing hydrogen. The abject failures were discarded, whilst those that produced hydrogen more efficiently than the original were used as seed material for a second round of the same process - accelerated mutation, followed by selection of the successful mutants. In other words, the classic Darwinian process, just speeded up a little. And, when they did this experimentally in the laboratory, it worked. Not only did their accelerated evolution process produce lots of nice mutants to select from, but it eventually produced a mutant that was thirty times better than the original wild type enzyme at producing hydrogen.

In other words, evolution has been demonstrated experimentally to work in the laboratory and to be capable of producing improvements in a function coded for by a given gene.

And before anyone tries to erect apologetic bullshit to the effect that the above paper somehow supports "design" (despite the fact that, with typical lack of rigour, creationists use the word "design" for two entirely different processes, and perform a duplicitous bait and switch based on this), what happened in the above experiment was this:

[1] Generate lots of mutants;

[2] Test the mutants for competence with respect to the desired function;

[3] Discard the failures;

[4] Use the successful ones as seed material for a repeat round of mutation and selection.

The idea that this supports creationist assertions about "design" is ludicrous. Plus, it nails the lie that beneficial mutations don't exist. Indeed, in vitro evolution, with the fitness function being determined by increased success at production of a given end product, is being harnessed in research laboratories for such tasks as the production of new pharmaceuticals, and large R&D budgets are being expended upon this.

Indeed, that's how nature works - if a gene producing a given product gives an organism a competitive advantage, it is selected for, and if better versions of that gene arise, they are in turn selected for. No magic needed, and certainly no magic man.

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Re: The Bacterial Flagellum Revisited

#69  Postby Shrunk » Jul 02, 2010 11:21 am

PhiloKGB wrote:Ah, the fallacy of never-enough-detail. The underhanded creationist takes refuge here because he knows that biologists have neither the resources nor the inclination to reverse engineer a pathway for every feature. Moreover, they have absolutely no intention of doing so every time a creationist issues a poorly-considered challenge.


It's blatantly hypocritical, as well. There's no point in even asking CharlieM to provide details of the nature of his imagined "designer" or the mechansims by which this "designer" operates. Like all creationists, he'll just shrug his shoulders and say this is irrelevant.
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Re: The Bacterial Flagellum Revisited

#70  Postby hotshoe » Jul 02, 2010 3:54 pm

CharlieM wrote:Has anyone observed a biological system becoming more efficient over time as natural selection working on changes makes the necessary tweeks.

Yes, of course we have.

Breaking news today, Genetic Evidence for High-Altitude Adaptation in Tibet

Tatum S. Simonson, Yingzhong Yang, Chad D. Huff, Haixia Yun, Ga Qin, David J. Witherspoon, Zhenzhong Bai, Felipe R. Lorenzo, Jinchuan Xing, Lynn B. Jorde, Josef T. Prchal, RiLi G wrote:... Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia-response pathways in humans.


Here's a good summary in the popular press:
Cian O'Luanaigh, The Guardian wrote:An international team of researchers compared the DNA of 50 Tibetans with that of 40 Han Chinese and found 34 mutations that have become more common in Tibetans in the 2,750 years since the populations split. More than half of these changes are related to oxygen metabolism.

The gene [EPAS1], which codes for a protein involved in responding to falling oxygen levels and is associated with improved athletic performance in endurance athletes, seems to be the key to Tibetan adaptation to life at high altitude. A mutation in the gene that is thought to affect red blood cell production was present in only 9% of the Han population, but was found in 87% of the Tibetan population.


http://www.guardian.co.uk/science/2010/jul/02/mutation-gene-tibetans-altitude
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Re: The Bacterial Flagellum Revisited

#71  Postby scruffy » Jul 02, 2010 4:28 pm

Not that I've been really contributing to this 'discussion' here, but I'd say this is done. CharlieM's last post just proves that he hasn't taken ANYTHING we've said into consideration. He's making the same mistakes we've already corrected him on many times. Nothing is going to change his mind, he's closed to it. That's just my opinion. :fsm2:
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Re: The Bacterial Flagellum Revisited

#72  Postby hotshoe » Jul 02, 2010 6:50 pm

Not quite "hasn't taken ANYTHING we've said". He took in my suggestion about leaving his name off of each paragraph. By the way, thanks, CharlieM 8-)

Evolutionary science is hard. It's NOT hard to get the basics - variability of traits, differential survival in some population with respect to some environment based on the relative success of those traits, survivors having a chance to pass on their selected traits to offspring, who then repeat cycles of variability and survivorship. (It's so easy to get that I suspect the only reason we had to wait till 1850 for a valid ToE was because of the poisonous effect of religion and its static cosmology, but that's a subject for another thread.)

What's hard is the details. It's hard to work out the molecular basis for a process which was completed a billion years ago. It's hard to establish the correspondence between amino acid sequence and finished protein fold (even though we know it must be highly deterministic as it follows inert laws of chemistry). It's hard to work out the nature of "cellular machinery" when our dichotomous minds alternate between the extremes of "goo" and "machines", such that our perception of the "hook" is colored by the very word itself.

But failure (at this moment) to explain every molecular detail is not sufficient to disprove the basic theory outlined. That's just dumb, like saying I can't have gone to someone else's house, because you can't tell exactly which route I took. Maybe I couldn't just drive straight there; maybe I drove out of town, stole a horse, rode it across the river at a shallow ford, left the horse grazing under a tree and finished my route on foot. What's important is that I started there and ended here. Unless you claim that I was magically and instantaneously poofed from one to the other, we have to conclude there was a continuous physically-possible process in between (even if you don't know what the process was).

So, let's double check what should be the easy step. CharlieM, do you have a problem with the basic outline of evolutionary theory ? You accept common ancestry and descent with modification ?
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Re: The Bacterial Flagellum Revisited

#73  Postby CharlieM » Jul 03, 2010 2:47 am

I'd like to reply to lots of comments and questions directed at me in the past few days. Its a problem finding the time and when I rush replies I find that I usually make a mess of what I want to say. I hope to reply to at least some of them. I'll start with the last one I read.

Hotshoe:
So, let's double check what should be the easy step. CharlieM, do you have a problem with the basic outline of evolutionary theory ? You accept common ancestry and descent with modification ?


I believe that life on earth started with a single cell of some sort and developed into what we now witness, so I have no problem with common ancestry. Descent with modification sound good to me, the original descent being a sort of condensation from above. :lol:

I believe that life is a lot more complex than we imagine, that natural selection fits an organism to its environment and selects from variation in the breeding population. And I do think that some mutations can be beneficial.

I think our main difference of opinion is in how much of the genetic variability is due to chance.
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Re: The Bacterial Flagellum Revisited

#74  Postby PhiloKGB » Jul 03, 2010 3:09 am

CharlieM wrote:I believe that life is a lot more complex than we imagine, that natural selection fits an organism to its environment and selects from variation in the breeding population. And I do think that some mutations can be beneficial.

I think our main difference of opinion is in how much of the genetic variability is due to chance.

It would be a real point in your favor if modern biology was the sort of discipline whereby a non-academically trained individual could issue proclamations that upset the entire fruit industry. But please, tell us more about how you're here to learn.
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Re: The Bacterial Flagellum Revisited

#75  Postby hotshoe » Jul 03, 2010 5:06 am

I don't think academic training matters; what matters is thinking logically and following the scientific method, which has a wonderful track record of weeding out spurious claims

It's a fair point that the main difference is in ascribing how much variability is due to chance. But I'd say it's more than a "difference in opinion". It's not that biologically trained scientists are biased against design, it's that there is no reason to even consider such a possibility unless its proponents can supply evidence that it might even possibly exist. True, it is possible that a designer exists and did set up pre-conditions which allowed for complex life to arise, or even meddled directly in certain tricksy steps. I can't think of a way to disprove that.

But I don't have to disprove that. It's not my case, it's yours. That means you have to supply the evidence. Locating the designer and providing proof of its existence may be beyond your ability, but you have to have at least some evidence of its possible existence other than scraps of poetry. Until you can supply some evidence, I don't have to take a (probably non-existent) designer as a factor in evolutionary theory, any more than I have to take into account Santa's elves or intelligent-falling spirits. That way lies madness, not science.

Actually, locating the designer might be the easier problem to tackle, compared to tackling the questions: what parts did it design, and how did it carry out its work?

How do you support your answer ? What's the measurement of designedness ? Without evidence, your claim is just more poetry, not science.
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Re: The Bacterial Flagellum Revisited

#76  Postby Rumraket » Jul 03, 2010 5:35 am

The biggest problem I have with design "theories" is the claim that they are somehow continously involved in tweaking extant life. This is simply ignorance to me. I can't even begin to describe how ludicrous it sounds.
We see beneficial mutations arrive in laboratory experiments all the time. But are we now supposed to believe a designer sneaked into the lab under the cover of night and darkness and planted the mutations? Gimme a break here.

Now CharlieM is saying he allows *some* beneficial mutations by chance, but not most of it? This just seems like a pathetic attempt to save his design wish. So every time we see a beneficial mutation happen, that's the ones which are due to chance. All the other ones we didn't see, THOSE are the ones which were designed. Riiiight....
It's simply stuffing design into the gaps. This time gaps of history. We cannot go back in time and witness events at the molecular scale, and because we can't do that... that's where the designer is hiding. In the fog of the unknowable past. Or at night, when noone's looking -_-
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Re: The Bacterial Flagellum Revisited

#77  Postby hotshoe » Jul 03, 2010 8:51 am

Rumraket wrote:The biggest problem I have with design "theories" is the claim that they are somehow continously involved in tweaking extant life. This is simply ignorance to me. I can't even begin to describe how ludicrous it sounds.
We see beneficial mutations arrive in laboratory experiments all the time. But are we now supposed to believe a designer sneaked into the lab under the cover of night and darkness and planted the mutations? Gimme a break here.

Now CharlieM is saying he allows *some* beneficial mutations by chance, but not most of it? This just seems like a pathetic attempt to save his design wish. So every time we see a beneficial mutation happen, that's the ones which are due to chance. All the other ones we didn't see, THOSE are the ones which were designed. Riiiight....
It's simply stuffing design into the gaps. This time gaps of history. We cannot go back in time and witness events at the molecular scale, and because we can't do that... that's where the designer is hiding. In the fog of the unknowable past. Or at night, when noone's looking -_-

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Re: The Bacterial Flagellum Revisited

#78  Postby CharlieM » Jul 05, 2010 1:45 am

I wrote:
And if the hook protein FlgE had no functionless precursors what was the path in the diversification between it and its homologs?

Rumraket replied:
This question assumes the precursor must be functionless. Which is ludicrous and flatly wrong. Whatever the precursor proteins function was, as the entire precursor system started serving a motility function, the hook-precursor protein was under selection for increased functionality, in this case successful transfer of torque without breaking. Those that failed, died, those that succeeded didn't


I pose a question asking what must happen given that there is no functionless precursors (sorry for the double negative) in other words a function is assumed in all precursors on the path from common precursor to FlgE and its homologs. You then say my question assumes the precursor must be functionless. You must have read me wrong.

PhiloKGB:
Ah, the fallacy of never-enough-detail. The underhanded creationist takes refuge here because he knows that biologists have neither the resources nor the inclination to reverse engineer a pathway for every feature. Moreover, they have absolutely no intention of doing so every time a creationist issues a poorly-considered challenge.


But I'm not asking for a suggested pathway for every feature, just for FlgE. As homology is so prominant in Matzke's proposed flagellar evolution, surely he could look into the details of just one pathway as an example.

Rumraket:
We cannot go back in time and witness events at the molecular scale, and because we can't do that... that's where the designer is hiding.


You said it yourself, we cannot go back and witness these events. So to state that FlgE and its homologs developed from an unknown precursor through the selection of unguided random events is unfalsifiable and therefore not science as most here see it.

I wrote:
And there is no evidence whatsoever of a pre-existing universal joint being co-opted and slotted into place in the drive train.

Rumraket replied:
Which is not the proposed model and therefore a strawman.


I never said it was the proposed model. I was clarifying that, unlike the TTSS, the hook is not available to be co-opted from elsewhere and so it would seem that it appeared due to the modification of a pre-existing protein. The question is, was the route taken guided or fortuitous? Most people here would say that it was fortuitous but no one has gone into what amino acid changes would need to occur for this to happen. We know the amino acid sequences of FligE and its homologs so we know the sequence differences. Several of these differences will have a minor or no effect in the function of the protein but there will be a vital few which make all the difference. Steps of single amino acid changes along the path are not going to result in a functional protein for every step. So in order to retain functionality, multiple amino acid changes will have to occur together. And changes will have been co-ordinated between the hook protein and related proteins such as hook associated proteins and regulators in order to retain a functioning unit. All this reduces the plausibility of chance events being the cause of the change into a functional universal joint.

Hotshoe writes about the hook:
our perception of the "hook" is colored by the very word itself.

Well mine isn't when I consider the flagellar hook. As far as I'm concerned a hook is a far more simple structure than a universal joint and so the term 'hook' doesn't do justice to the joint in question.

A few evolutionary facts have been given which I presume are supposed to argue against my position. The ones I can recall are:
A monkeyflower turning into a monkeyflower, a peppered moth turning into a peppered moth and hydrogen producing bacteria turning into hydrogen producing bacteria. I have no problem with these examples of evolution.
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Re: The Bacterial Flagellum Revisited

#79  Postby Rumraket » Jul 05, 2010 8:10 am

CharlieM wrote:I pose a question asking what must happen given that there is no functionless precursors (sorry for the double negative) in other words a function is assumed in all precursors on the path from common precursor to FlgE and its homologs. You then say my question assumes the precursor must be functionless. You must have read me wrong.

Fair enough, I misread your question as implying the precursor was functionless.

CharlieM wrote:But I'm not asking for a suggested pathway for every feature, just for FlgE. As homology is so prominant in Matzke's proposed flagellar evolution, surely he could look into the details of just one pathway as an example.

While it might be possible to look at the two proteins and propose a chain of events that happened in between, such an analysis would require huge supercomputer modeling of every step in the chain. This would be extremely expensive and time consuming. Additionally, even if you manage to compute the structure of an intermediary protein, it's still not a guarantee that you will be able to guess it's proper function since this will also require detailed knowledge of it's environment.
So in order to understand every step in the evolution of FlglE, you'd have to understand all the other proteins in the flagellar evolution too.

CharlieM wrote:You said it yourself, we cannot go back and witness these events. So to state that FlgE and its homologs developed from an unknown precursor through the selection of unguided random events is unfalsifiable and therefore not science as most here see it.

No, it's not unfalsifiable. The existence of protein homologues are a testable prediction of evolutionary theory and therefore their supposed nonexistance would falsify the flagellum evolution. This is because the mechanisms are observed to work in the here and now. Mutations/duplications/shufflings with selection acting upon them are an observed and confirmed phenomenon. From this an inference is drawn that the flagellum proteins evolved in the past. Therefore a testable prediction is made from this inference, which has the potential to falsify the evolved model.

Additionally, the evolution of the flagellum would be falsified if it had no genetic basis. That would also mean it was obviously "put" there by an outside agent. It would not specify what did put it there, but it would rule out an evolutionary pathway. Having no genetic basis, but still being present in an organism is actually positive evidence for some kind of "design". It means something other than the internal metabolism of the organism put the device in place. Now this could of course be anything from a virus to a superintelligent alien or whatever. But it would completely rule out an evolutionary model.

The problem with your design inference is that it is truly unfalsifiable. You could observe any feature and conclude it was the work of your designer.

CharlieM wrote:Several of these differences will have a minor or no effect in the function of the protein but there will be a vital few which make all the difference. Steps of single amino acid changes along the path are not going to result in a functional protein for every step. So in order to retain functionality, multiple amino acid changes will have to occur together. And changes will have been co-ordinated between the hook protein and related proteins such as hook associated proteins and regulators in order to retain a functioning unit.

You are making a number of claims here about the FlglE protein evolution which aren't nessecerily true.

CharlieM wrote:Steps of single amino acid changes along the path are not going to result in a functional protein for every step.

Are you implying that the changes are going to result in a protein with loss of function, or simply that the change was neutral and therefore did not result in increased functionality? In addition, I'd like to know how you know this?

CharlieM wrote:So in order to retain functionality, multiple amino acid changes will have to occur together.

This sounds like an implication that the intermediary might have resulted in a loss of function? This would obviously be false. Once again, you are speaking of events you can have no knowledge of?

CharlieM wrote:And changes will have been co-ordinated between the hook protein and related proteins such as hook associated proteins and regulators in order to retain a functioning unit.

So you did those supercomputermodelings? Fascinating. Please share your results.

CharlieM wrote:A few evolutionary facts have been given which I presume are supposed to argue against my position. The ones I can recall are:
A monkeyflower turning into a monkeyflower, a peppered moth turning into a peppered moth and hydrogen producing bacteria turning into hydrogen producing bacteria. I have no problem with these examples of evolution.

Hahaha... the micro/macro evolution canard.
And you are arguing against a bacteria without a flagellum evolving into a bacteria with a flagellum? Great. Sounds like a double standard to me.

It's also worth noting that you more or less ignored the fact that these provided examples directly demonstrate the ability of random mutations with selection acting upon them to result in new and/or increased functionality. You know, the thing you originally specified you had a problem with?

CharlieM wrote: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.


CharlieM wrote:It is blind to the future and, because it only "sees" present fitness, it reduces the variability of the breeding population. Some trait which may be beneficial in a future environment gets weeded out because it is of no present use. So natural selection tends to reduce the variability of the breeding population. A bit like stem cells becoming specialized.


No, what you obviously have a problem with is the fact that you are an ape like the rest of us. You may wish all you want that someone superintelligent made you for a "special" purpose", whatever that is. But the simple fact is that you evolved and noone was around to guide it. You're an ape, get over it. Life can still be enjoyed, you still have a right to live, and nobody thinks any less of you because of it.
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Re: The Bacterial Flagellum Revisited

#80  Postby Calilasseia » Jul 05, 2010 12:14 pm

CharlieM wrote:A few evolutionary facts have been given which I presume are supposed to argue against my position. The ones I can recall are:
A monkeyflower turning into a monkeyflower, a peppered moth turning into a peppered moth and hydrogen producing bacteria turning into hydrogen producing bacteria. I have no problem with these examples of evolution.


This is merely the wholly absurd regurgitation of the "I've never seen a cat give birth to a dog" piece of creationist scientific illiteracy. Which, apart from being scientifically illiterate, is a duplicitous strawman caricature of evolutionary theory erected for mendacious apologetic purposes.

First of all, evolution is based upon inheritance. Therefore, evolutionary theory postulates that organisms inherit characteristics from their ancestors. A postulate for which we have a large body of evidence. It also postulates that when new features arise amongst some of those ancestors, and those new features are positively selectable, they too will be inherited by descendants thereof. However, it also postulates that when isolating mechanisms come into play that split populations into reproductively distinct groups, those groups will diverge. Evolutionary theory postulates that if a population A is split into two populations B and C, with an isolating mechanism erected between them, then individuals belonging to population B will eventually fail to be reproductively compatible with individuals from population C, and vice versa, at which point we have a speciation event. But, those two species share a common ancestor in the form of the individuals of the original population A, and therefore will be nested within the clade that contained population A originally. They won't "transmute" into something totally different. Plus, since these changes take place at the population level, this invalidates at a stroke the fatuous "x turns into y" nonsense of creationists. Oh, and if you think speciation hasn't happened, Dobzhansky produced a speciation event in his laboratory in 1971, and documented it in a paper submitted to Nature.

Trying to use the fact that modern, derived organisms inherit a large collection of derived characteristics from their ancestors, as purported "evidence" against cladogenesis occurring in earlier, simpler, less derived organisms, is mere apologetic duplicity.
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