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Intelligent Design - Part VI
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Atheist
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PostPosted: Tue Jan 31, 2006 11:45 am    Post subject: Reply with quote

Haha. I'll see what I can do. wink

Out of curiosity, though, would you rather have "In God We Trust" on everything?

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Lebowsk1
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PostPosted: Tue Jan 31, 2006 3:40 pm    Post subject: Reply with quote

No need to have it on the money. I'd certainly be very, very careful about which faces I put on it (safer to have something like the picture of the earth from space or something impersonal like that) and text something like "I solemnly swear in sound mind, body and soul to pay the owner £10" or whatever. No need to go invoking God at every turn, we shouldnt need that.

Ahem... but to stay on topic, here's another review of that Horizon documentary (seems the author of this one feels much the same as I do):

Quote:
BBC's War on Science Looks at Darwinism / Intelligent Design Controversy
A Cambridge University ex has a trenchant review of Horizon's "War on Science," a program looking at the controversy between Darwinism and Intelligent Design. Paul writes:

They didn’t do a bad job, as far as mainstream media go, although they plumped heavily down on the side of the majority opinion in the end. William Dembski, Michael Behe, Steven Meyer and Phil Johnson at least had the opportunity to express their ideas fairly clearly, although they didn’t apparently get the chance to respond to the “refutations” that Kenneth Miller was able to present in the Dover trial and also on the programme. It was also made pretty clear that the analysis of ID proponents, unlike that of creationists, was based on scientific research and analysis, not on scripture, and this fact alone undermined about half the case made against ID in the programme.
The reviewer, Exiled from GROGGS, also commented that "Richard Dawkins made himself look stupid by saying nothing scientific at all – he is still holding the line that you can win a debate by not arguing (or rather, arguing against straw men, as he did in his own recent showcase programme)." And David Attenborough "failed to grasp the difference between being able to detect evidence for design (which is what ID proponents say they are doing) – which is a legitimate pursuit in many fields of science – and coming to a conclusion about the means of design."

Paul's review suggests that, without meaning to, the BBC gave Dawkins and Attenborough just enough rope to, if not hang themselves, then certainly make themselves look pretty tangled up. As the reviewer noted:

There were some choice quotes, which were delivered without a hint of apparent irony. For example, David Attenborough said something along the lines of: “The notion that we are masters of our destiny they [i.e. Theists] find abhorrent.” Well, Mr Attenborough, you might like to consider to what extent you are master of your destiny if you believe that you are a gene machine.
The reviewer also considered the documentary's religion vs. science trope:

The programme used the development of the Dover, PA trial as the framework for the programme. It was well structured, and the issues at stake in the trial were made generally clear. It also managed to avoid some of the mischaracterisations and clichés of the “religion versus science” debate – though it still argued that this was the fundamental dynamic of the debate. It is being made into that by those people opposing ID – but it is a matter of great frustration to people who wish ID to have a hearing that as soon as it is raised, all the anti-ID community put their fingers in their ears and say, “La, la, la. Religion! Religion! I can’t hear you! Religion. La, la, la.”
Paul has other good material on intelligent design at his website, including this two-part series on the Avida program, which purports to model biological macroevolution in a computer environment.

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zero_saiyaman
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PostPosted: Fri Feb 24, 2006 6:37 am    Post subject: Reply with quote

By request, I'll put up some info I have on Irreducible Complexity. Because I haven't been able to do actual research, this synthesis is the best I can do in regards to the hallmark of irreducible complexity that is the Bacterial Flagellum. So, let me put down the info that has been discovered and argued about for decades now to see what you all think about it.

Two primary sources for this presentation:
Video movie of Scott Minnick giving a science seminar on his 18 years of research dedicated to the flagellum titled "Bacterial Flagellum: A paradime for design", Iowa State Univerisy.

And the evolutionary paper "Evolution in (Brownian) space" by N. J. Matzke.

Basics of the presentation and debate on irreducible complexity in the bacterial flagellum:

-"Irreducible complexity: Macromolecular machines have multiple inter-dependant parts. Loss of one componant results in loss of function. Consequently, evolution must explain how the system arose to its present state."
-Nothing to select upon. All pieces needed for function and natural selection requires a currently fully working function to select upon to evolve it.
-Flagellum expression controlled by 50 genes, if one gene is lost, all other genes are no longer expressed. This is seen in Yersinia pestis, aka the Black Plague, where one gene loss from three point mutations left pestis immotile and lacking flagellum. Other Yersinia genus species have flagellum.
-The flagellum is a signal transduction system with short term memory; reversible rotation at over 100,000 rpms with ability to stop within a quarter of a turn. 30 main structual protein types, with many individual proteins of each making up the structure (i.e. 32 motor proteins in motor structure). Proteins are secreted in order that they are assembled from inside of cell out, flagellum fiber grows from tip, not the base. Gateway proteins control order of construction in a "type 3" secretory system.
-Problems in assembly shut down genes that would be expressed later. Mutations in any gene of the basal body (motor and hook) stops filliment expression (200,000 sub units per propeller). FlagM keeps filliment proteins suppressed until the hook is assembled correctly, then it is secreted so exression of filliment can begin; shows timing system in place to dictate construction on a percies, functional, temporal scale.
-Each motor protein has to make four connections to the rotor. Even a few Angstroms (atomic scale distances) off will deactivate the system and thus expression of all other flagellum parts after motor/rotor assemblage.
-Genes are bundled together discretely, and not spread out, and there are no intermediates expressible. This means the flagellum was not co-opted from other systems as if that was the case the genes would be spread out in the genome and not bundled directly together. Also, gene expression is partially controlled by DNA shape conformation at different temperatures, so that the very placement of the genes in the genome is not random but critical and cannot be changed or loss of function will occur.
-Other type three systems had to come after the flagellum (bacteria before eukaryots). There are no real known homologues of the flagellum, most parts are completely unique to the flagellum, only FliI and three others have a sustantial homologue possibility (from a subunit of ATPase for FliI which shares 30% sequence similarity and is the most homologous of the four possibles).

From Brownian paper:
-Hypotheses that flagellum evolved from ATPases for the purpose of bulk flow is proveably wrong; low reynolds make diffusion faster than bulk flow, and stiring action cannot affect brownian motion at those low sizes. All flows dictated by brownian motion at prokaryot sizes.
-Possible hypotheses: secretor first, cap first, cap-secretor
-Secretor first fails in that there are no natural type 3 secretor systems in nature that could have come before the flagellum, all arose later for virulance and are triggered only at 32 degress Celcius by a conformational change in the DNA at that temperature (in a host's endothermic body).
-Cap first fails in that there is no cap structures used in nature nor no purpose for one except substraight adhernace which is not needed for bacteria which rapidly outgrow resources and need to move instead of stay in place. Again, a secretor system is needed to develop the cap, and there are no proto type 3, or homologous, systems.
-Secretor-cap hypothesis: viewed as best one by this paper, but runs into trouble for both reasons of the other. However, said to be able to generate low amounts of motion if tied into a synthase system (motor).
-Other problems: Gram negative bacteria are first; meaning there are two membrains that must be crossed to form a flagellum, and so would two lesser systems. No ATPases bridge both membrains. Complex developmental timing patterns and location patterns. Again, no proto systems or homologues found in nature that could paralell such a archaic system. Problem with that if one gene is lost, all genes are not expressed in the flagellum, meaning that the entire suit must be there for expression, how can a proto system form? No known function still able to be deduced with early proto systems, being costly and fitness reducing on the organism instead of helpful, thus would be weeded out by natural selection even if it could start to develop.

There's the basic data on it all, see what you guys think. Is this an irreducibly complex system, and what would it mean if it is?

Also, because I keep seeing people saying that most mutations are neutral to an organism, here's a graph from my evolution text book (Futuyma D. J. "Evolution" 8th ed. Sinauer associates, INC. Mass: 2005) showing how almost all mutations are slightly deleterous, and slowly build up to incredible reducing power. Next to no mutations are neutral, and even fewer are benefitial in any way. So really, almost all mutations are deleterous.
(Higher selection coefficiant means higher selection against and more fitness reducing. Higher frequency means percent encountered in population over time)

http://i36.photobucket.com/albums/e7/zero_saiyaman/mutations.jpg

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Shaper
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PostPosted: Fri Feb 24, 2006 2:54 pm    Post subject: Reply with quote

So when we're talking about evolution vs design of the flagellum, what is the purpose we're actually assigning it? Are we talking about a flagellum that allows the bacteria to swim or are we talking about smaller flagellum that allow the bacteria to grab on to host cells? I think the functions of different varieties of this system have to be considered before one can actually say without a doubt that it is irreducibly complex and could not have evolved.

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zero_saiyaman
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PostPosted: Sat Feb 25, 2006 8:59 am    Post subject: Reply with quote

Actually, it is one and the same flagellum. Those theories I put up are the best theories out there of how a flagellum system could have arisen. They are all hypothetical systems and do not exist in nature, but having a pathway to investigate allows discussion at least.

The flagellum, however, can be used to adhear to host cells in some species, but it is the same flagellum as is in all bacteria (just a secondary secretion is used after the flagellum is constructed to make the end cap of the fiber sticky. It is the grounds on which the "cap first" hypothesis was formed)

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Lebowsk1
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PostPosted: Sat Feb 25, 2006 2:57 pm    Post subject: Reply with quote

Hm, think about this:

A human being can create a programme and machine that can then go on to create further machines. Like, at a car assembly plant. Cars are assembled by other machines.

But it would be incorrect to say that the cars are the product of blind, impersonal and dead forces like the machines because if you trace the trail of cause and effect all the way back, you end up with an experiencing and thinking consciousness (or several).


I just don't see why the reasoning should be any different for the flagellum. The programme in place to build it is the DNA and associated assembly proteins and the designer of that system is... well, I'll stop there, at the point where we acknowledge a designer.

Although I must say that I am now pretty sure that ID is philosophy of science as opposed to just science. But this is also true of neo-Darwimism surely, so if one is banned from the classroom, so should the other.

(quite pleased with the agreement reached with Dreamer on this subject btw)

Zero: thanks for the info.

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zero_saiyaman
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PostPosted: Tue Feb 28, 2006 8:27 am    Post subject: Reply with quote

You're welcome, though I think it is too technical and obscure to form arguments over and to debate. But at least it is interesting?

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Shaper
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PostPosted: Tue Feb 28, 2006 1:56 pm    Post subject: Reply with quote

I found it interesting, and I didn't know the two types of flagella were actually the same thing (but I guess an arm is an arm and a leg is a leg, so it makes sense to me ^^ )
Anywho, my position is that it's obvious that some systems in nature seem irreducibly complex (to me), but that doesn't mean they couldn't have evolved. For example, perhaps a feature that has one function now had a different function at a different level of that species. But that's the hard part about answering this whole debate, since no one was around to see anything actually be created or rise to another level of species and any evolutionary change we see now is usually so small that we may not even be looking at an evolutionary change, we've just got to make an educated guess about how life really came to be.....
......so I suppose I'm just going to have faith in my belief system, and if science reaches a different answer that what I believe, I'll accept that yes

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zero_saiyaman
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PostPosted: Wed Mar 01, 2006 7:36 am    Post subject: Reply with quote

Good ideas, Josh.

Co-option is the method you are mentioning there, that is where one system, of a certain function, is adapted to serve a different function (further known as an exadaptation). However, the interesting thing about the flagellum genes are that they come in a discrete package. With co-option, you will have genes that code for proteins and features randomly spaced in the genome that become mutated and recruited for another purpose, but they retain their spaced out, random possitions, as theory has it. Also, about half or more of the proteins for the flagellum has no homologues of any sort in nature, which is odd. The greatest homologue happens to be with ATPase, and that is a 30% sequence similarity (so 70% dissimilar).

However, you will certainly find many cases of possible exadaptations (such as taking features used for thermoregulation and co-opting them for flight) in nature. As you say, all these things do come down the principles of philosophy.

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Lebowsk1
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PostPosted: Wed Mar 01, 2006 7:47 am    Post subject: Reply with quote

zero_saiyaman wrote:
Also, about half or more of the proteins for the flagellum has no homologues of any sort in nature, which is odd. The greatest homologue happens to be with ATPase, and that is a 30% sequence similarity (so 70% dissimilar).

Yeah, this is the argument I was using against co-option before. Eventually you are going to have to account for entirely new content because you can only borrow so much from other systems.

I didnt know about the "discrete package" evidence, will surely help me out in future debates. colgate
Quote:
However, you will certainly find many cases of possible exadaptations (such as taking features used for thermoregulation and co-opting them for flight) in nature.

Once again this goes to show that Behe made a great choice in selecting the flagellum as an example of IC. The co-option hypothesis (which is all it is) seems to be applicable to some things, not to others. Those things it is not applicable to need another explanation, and naturalists are running out of wriggle-room...

I mean jeez, maybe we're not just walking sacks of meat eh. Maybe there is something a bit special about us. This debate has effects way beyond science, it's all about how we define ourselves.

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Shaper
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PostPosted: Wed Mar 01, 2006 1:31 pm    Post subject: Reply with quote

Lebowsk1 wrote:

I mean jeez, maybe we're not just walking sacks of meat eh. Maybe there is something a bit special about us. This debate has effects way beyond science, it's all about how we define ourselves.


I'm sure that there are lots of 'naturalists' out there who would be very happy if we were more than just sacks of meat, but they are just interpresting the evidence the bast they can yes
I mean, it's not like people want to live in a universe where you life a life full of chellenges and then die (if that's the way you think of life), only to vanish into non-existence. I'd love it if there were something more to the universe, I just don't know what it is or if it exists yet.

So back to the Flagellum; it seems like a really cool case of IC that where it is entirely possible that co-option didn't happen, but I'd be curious to know how many examples of this we can find, and compare it to features which could evolve through co-option.....I wonder what the ratio would be
nervous
Not that it would be easy to compare or even classify these things, because like zero said, it really comes down to philosophy when your working with these ideas.

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infinite ends
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PostPosted: Sat Mar 04, 2006 2:08 am    Post subject: Reply with quote

hmmmmmm anyone seen the movie "the hitch-hikers guide to the galaxy"? lol reminds me of this, creating worlds and stuff....intellegint creation is a theory, its just sciences interpretation of the christian figure "god", that nature cannot create itself someone had to come up with this its incomprehensive that something advanced as our natural universe and complex could have appeared out of nowhere, but then you run into a problem...if thats not comprehendable then neither is a creator advanced and infinite and intriqute as this mechanical "god". intelligent design is merely a theory, just like darwins crap...for crying out loud even gravity's a theory, thats what makes me unconfident in science or religion...science isnt about being certain its about being uncertain and always prooving yourself wrong...everyone thought the earth was flat, and they were confident because those were THE RESULTS THEY ACHIEVED WITH THE TECNOLOGY AND THINGS AVAILABLE AT THE TIME.next thing we know the earth is round and now today we know the earth is not round but a slight spherical oval...WHEN DOES IT END??? we are just outsmarting ourselves in science, science doesnt discover anything, it just gives an explanation for natural phenomenom, except through observation rather then religion or myth...

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PostPosted: Tue Mar 07, 2006 8:01 pm    Post subject: Reply with quote

I like Richard Dawkin's response to IC...

He points out (In 'Devil's Chaplain') that all species experience freak mutations from time to time. This is only natural. And these disfigured creatures don't die automatically. If they live long enough to breed, their mutation becomes part of the next generation, and can even become an asset down the line.

Slug -> Slug with hardnened calcium on back ->->->-> slugs with most calcium don't get eaten as much ->->->->->->->->->->->->->->->-> Snail

I'm not saying that example is necassarily true (I'm not an expert on slugs...) but it explains the general theory, and fits in with scientific fact.

Not sure if that point had been made, sorry if I'm accidentally parroting.

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Lebowsk1
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PostPosted: Wed Mar 08, 2006 1:26 pm    Post subject: Reply with quote

Hi Rosethorn.

I’m not about to commit the logical fallacy of arguing against the man but let me offer you a bit of personal advice: take everything Dawkins says with a barrel load of salt. I’ve heard him say some ridiculous things in my time, such as “science has explained 99% of biology” and “the only people who support ID are people who know nothing”.

I mean both of these are provably false, ludicrous statements, and he’s just full of this kind of sound and fury (signifying nothing).

But to get to the actual argument, there is a big difference between the kind of example you have cited here (the proposed evolution of a snail's shell) and the kind ID theorists forward (the bacterial flagellum). If indeed a slug can gain what is called ‘functional advantage’ by just having what could be viewed as a partial shell, and you could progress along this evolutionary pathway by gradually increasing the functional advantage each step of the way then fine: it is not impossible that such a thing could evolve. My only two points to make here would be that we should remember this has no effect on the origins of life problem (which still stands) and also that there is still the problem of finding a decent mechanism to initiate the genetic changes.

But with examples like the bacterial flagellum these evolutionary pathways cannot work because you can't get a functional advantage at every step of the way. If the flagellum is truly irreducibly complex (requiring all parts for function) then the gradual addition of one part cannot provide any functional advantage and therefore will be invisible to natural selection. To return to the simple mousetrap example: you can't start with a block of wood and catch a mouse, then add a spring and catch a few more mice, then add the hammer and catch a few more mice until you end up with a full mousetrap. You need the entire lot there from the start to catch any mice. And, according to ID theory, the same applies to certain biological structures including the flagellum.

The theory of irreducible complexity is kind of like a direct response to Darwin’s own statement: “If it could be shown that there exists an organ in nature that could not be formed by numerous slight, successive modifications, then my theory would absolutely break down”. Darwin set the definition for the disproval of his theory: Mike Behe actualised that disproval by identifying such an organ.

But the problem with Dawkins is he doesn’t even engage deeply enough with the debate to understand this situation and so just misses the point entirely.

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