Protein structures and intelligent design

In keeping with my theme of the complexity of (sub)cellular life, I offer more evidence as to why the naturllistic explanation of abiogenesis and macro-evolution falls short and involves many assumptions and extrapolations, which IMO, are not proof of naturallistic creation. But instead proof of the need for an intelligent designer.

(1) much time + small changes = large changes

It is this thinking which allows many to extrapolate small evolutionary changes that are observed (microevolution) to rather large evolutionary changes (macroevolution). Thus, we can explain the later in terms of the former simply by adding enough time.

This is basically the theory of macro-evolution, but there are flaws in this logic.

I think this is a crucial point. More and more biologists are arguing that morphological evolution is driven by changes in regulatory elements. In fact, some have even proposed that alterations in the patterns of gene regulation have been far more important in evolution than changes in protein function. But what does this mean? It would mean that all of the fossil evidence is largely the consequence of trivial evolutionary events that have little meaning for the origin of much cellular machinery. If most of evolution and the fossil record can be explained by changing the pattern of gene expression, then most of evolution and the fossil record is not relevant to questions about the origin of those genes or the basic process of gene expression itself. (1) might be vindicated at the level of organismic evolution, but at a very high price. That price being that almost all of the evidence of evolution now becomes irrelevant to the deeper aspects of life

macro-evolution is speculative at best:

If one desires to extrapolate small changes into large changes by simply adding time, one requires independent evidence to justify this move. The problem is that we really don't know how evolution occurs. And when talking about the evolution of the mammalian middle ear bones, we should not forget that we are still basically in the dark in trying to explain how both a mammalian and reptilian zygote actually develops the middle ear and jaw bones, respectively. Without this knowledge, attempts to explain such a transition as a function of a series of small, incremental changes stretched across time are rooted in ignorance. That is, we don't truly understand neither the process of development nor the process of evolution and without such knowledge, there is no reason to think we are on safe ground when employing (1).

Now as i've stated earlier, I do not believe that evidence for micro-evolution is by proxy evidence for macro-evolution(species to species). That is simply an assumption/theory that doesn't seem to fit all the facts.

When we take into account irreducible complexity(the inability of a mechanism to function in its 'pre-evolved' state), the astronomical odds of forming these protein structures(cellular machinery) by chance protein folding, etc.......leaves me with the belief that these traits scream of design and in fact the theory of intelligent design is based on what we see in nature and in our labs.

Now of course you can disagree, but to say that ID is not based on emperical science data is wholly unfounded. You may disagree with the conclusion, but its no less valid, IMO, to the widely accepted assumptions made by natural abiogenesis and macro-evolution.

check here for more detailed info.

Originally posted by Rren
What Byrd said:

He then abuses inductive thinking. Using his form of simplistic inductive reasoning, we can also argue:
* rabbits are carbon based life forms just like humans
* rabbits run around on land just like humans
* rabbits eat vegetables just like humans
* rabbits breathe air just like humans
* rabbits hear sounds just like humans
* rabbits are found in human households just like humans
*** THEREFORE - Rabbits Are Humans

This is what Dr. Rana said:

Experts in inductive thinking will point out that the more objects taking part in an analogy, the more sound the conclusion arrived at through analogical reasoning.

from my original post top

Isn't the key here "the more objects taking part in an analogy" you had rabbits and humans in your example, am I missing something here? Doesn't he base his conclusion on inductive thinking 'protocols' and there are many of these structures not just a couple examples, so does that not add further weight to his analogy?

No, because he's using SELECTIVE examples. I could add a lot more things about rabbits to make them seem to be the same as humans. All I have to do is select a set of the right kinds of examples.

I could even go into the basic chemistry:
* gastric juices in rabbits are mainly hydrochloric acid -- just like humans
* DNA in rabbits is made up of adensoene -- just like humans
* Rabbit livers have mannan-binding protein -- just like humans

.. and so on and so forth, rather endlessly.

This doesn't make a rabbit a human, of course, but if I carefully select my examples I might convince someone that rabbits and humans are almost the same thing.

Some forms of analogous reasoning are accepted in SOME sciences. For instance, if I'm on an archaeological dig here in Texas and if I find an object made of beads strung on a leather cord and the cord is long enough to pull over someone's head and is indeed found with a skeleton, I can use analogous reasoning to say this article was put around the individual's neck and was propbably a necklace.

But I can't say, "oh, well it's obviously a Danegeld treasure necklace and worn by a person of importance and evidence of Danes in Texas":
scholar.google.com...

Originally posted by Rren
Now as i've stated earlier, I do not believe that evidence for micro-evolution is by proxy evidence for macro-evolution(species to species). That is simply an assumption/theory that doesn't seem to fit all the facts.

Then you're saying you don't believe that creatures (even with selective breeding) never get so completely different from their original ancestors that they are a new species?

Erm... what do you define as a "species"? Is it the same definition I use?

By the way, Darwin used the "difficult to tell sometimes where one species begins and another leaves off" as part of his proof of evolution:
dkrizanc.web.wesleyan.edu...

When we take into account irreducible complexity(the inability of a mechanism to function in its 'pre-evolved' state),

Could you explain this? As far as I know, there's no "pre-evolved" states unless you count raw materials.

the astronomical odds of forming these protein structures(cellular machinery) by chance protein folding, etc.......leaves me with the belief that these traits scream of design and in fact the theory of intelligent design is based on what we see in nature and in our labs.

What we see in our labs is clearly designed. Look at the way that atoms spell out things -- like the "IBM" in the photo down the page. Yes, this is a scanning electron microscope; a scan, not a true image. But that's what the microscope output looks like in real life: science.howstuffworks.com...

Designed structures don't look like evolved structres. For one thing, a designed structure doesn't have bits and pieces in it that do NOT contribute to the function of the object. Replications don't introduce flaws, either... the first 2005 Honda Accord to roll off the factory floor will look just like the last 2005 Honda Accord (with a difference in paint color and standard options, perhaps.)

Designed organisms would produce a single species of zebra instead of three (each with different numbers of chromosomes):
www.waterlandfarm.com...

There wouldn't be three different species of elephants:
www.awionline.org...

Or two species of giraffe:
encarta.msn.com...

Or THREE different species of spotted bass in Missouri alone!
www.conservation.state.mo.us...

...and so on and so forth. These species ARE different and it's more than just a little bit of color change (in many cases, as with the zebras, they look superficially the same but the chromosomes are completely different).

ID would suggest that the species was designed just once and then allowed to spread. There's no mechanism for it forming different but similar species.

posted by Byrd:

quote: When we take into account irreducible complexity(the inability of a mechanism to function in its 'pre-evolved' state),
Could you explain this? As far as I know, there's no "pre-evolved" states unless you count raw materials.

I probably said that wrong, I was trying to ask about the evolution of the cell. Here it is from Michael Behe(i believe he coined the phrase):

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. Link

As I understand it, the naturallistic theory is that the 'precursor system' was functional, only we have not discovered its function yet. But I argue; That is not scientifically substantiated and in many cases it has in fact been shown to be the opposite, ie not probable/possible.

Here is an example:

A single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning."

IC describes a system whose function is dependent on the interaction of multiple components, such that the removal of even one component results in the complete loss of function. IC can thus be represented as follows:

A + B + C + D ® F

where A,B,C, and D represent specific components (gene products) and F represents the function that is elicited by the interaction of these four parts. From this observation, it is commonly argued that that F could not possibly evolve, as F requires the presence of all four components. In other words, there would be no selective advantage of having parts A, B, and D compared to an organism having only parts A and B. Why? Because both combinations fail to elicit the function.

The basic flaw in this argument is as follows: While it is true that function F requires components A, B, C, and D to exist, it does not follow therefore that parts A,B,C, and D require function F to exist. And it is this basic flaw that has been exploited by the opponents of ID. There are three basic routes to circumvent the IC obstacle. Yet, while they exploit the inability to prove the impossible, whether they account for general explanations for the evolutionary origin of IC systems is highly doubtful. To see this, let's go back to the original IC formula, yet make one modification and discuss systems in which F is dependent on an IC state. That is, the function can only exist if multiple gene products interact with each other.more details and examples here

Now i'm not suggesting here that evolution(macro) or even naturally occuring abiogenesis is bunk or has been disproven. All things being equal anything is possible(and many people, more knowing than I, have spent lifetimes researching this). But the more we learn it seems the less probable it is for these things to have occured naturally, life seems to get more complex the closer we look, and by evolutionary definition shouldnt we see the opposite?

Also offf topic a little here Byrd, you've said that you work in anthropology(I think I got the right field). I'vw always wondered if things evolve why do we see so many different species in the same places, why wouldn't evolution eventually lead to some sort of super life form or maybe only a few? Not to be antagonistic here, i've always wondered that and wasn't sure what the explanation was......Thanks

(edit)forgot to answer this:

byrd: Erm... what do you define as a "species"? Is it the same definition I use?

reptile, mammal, amphibian etc..is that not correct?







[edit on 4-5-2005 by Rren]

Originally posted by Rren
It would mean that all of the fossil evidence is largely the consequence of trivial evolutionary events that have little meaning for the origin of much cellular machinery. If most of evolution and the fossil record can be explained by changing the pattern of gene expression, then most of evolution and the fossil record is not relevant to questions about the origin of those genes or the basic process of gene expression itself. (1) might be vindicated at the level of organismic evolution, but at a very high price. That price being that almost all of the evidence of evolution now becomes irrelevant to the deeper aspects of life

*shrug* Ok. I mean, if thats how behe see's it, if he thinks things like arhaeopteryx and the dino-birds aren't relevant to macro-evolution *shurg*, ok. he's a biochemist, so he tends to think that biochemical stuff is 'the focus'.
Behe, BTW, accepts the evolution of lots of things, like as in from ape to man.
[quoteIf one desires to extrapolate small changes into large changes by simply adding time, one requires independent evidence to justify this move
Why?? We see a process going on in the world today, evolution. We look at the fossil record, and see a pattern that is nicely explained by evolution operating over great time, or rather, a pattern thats best explained by evolution. What's Behes answer? Literally, "god did it". Any tough problem we come across, a chemical system in primitive cells that is amazingly complex, 'it must've been made by god, because its so complex'. Thats not very good reasoning. People thought that the eye was far to complex to have evovled, and yet, upon examination, we can see lots of fully functional, yet quite intermediate, eyes in naturea and the fossil record.

And when talking about the evolution of the mammalian middle ear bones, we should not forget that we are still basically in the dark in trying to explain how both a mammalian and reptilian zygote actually develops the middle ear and jaw bones, respectively. Without this knowledge, attempts to explain such a transition as a function of a series of small, incremental changes stretched across time are rooted in ignorance.

Not for nothing, but Behe's entire methodology is a programme for ignorance. He doesn't know how the various species involved were able to develop, in their ontogeny, the materials for the bones. Therefore, it happened by divine fiat. Why? Its a non sequitor, it does not follow. What we have in the fossil record is a 'progression' of forms that seem to show the evolution of various jawbones into modern ear bones, slowly and over millenia. Why would that require divine intervention? Why do we need to know the details of the genetic mechanism that results in smaller and more posteriorly placed jawbones?? There is variation in populations, natural selection acts upon it, causing adaptation. Organisms who, 'freakishly', have slightly smaller or more posterior jaw bones were able to better make use of vibrations (that any bone can pick up) than some of the other members of their population. If this gives them an advantage (and its easy to see that it can), then they had more offspring, and their 'type' came to dominate the population over time in terms of their greater numbers. Variation, meanwhile, is causing everything to vary, in all directions. Some have even better 'hearing' adaptions, others worse, the ones with better hearing abilities were able to have more offspring because of this, and the process repeats. Why would it require divine intervention at any stage of the process? And why would we be able to detect that divine intervention anyway?

Now of course you can disagree, but to say that ID is not based on emperical science data is wholly unfounded.

If it was, then it'd be great. ID held out a great promise, a real possiblity, 'lets see if we can scientifically detect design. We can tell, easily, that a plane is designed. Why? Because it seems to be tailored for functions, and if we pull it apart, it just won't work. Can the same logic apply to organism?" It was a decent idea. However, Darwin demonstrated that you can't apply that logic a long time ago. Behe
's thinking is a 'revival' of some aspects of natural theology, but still aspects that were considered and rejected a long time ago. Having a function does not make an object designed. Natural Selection will inherently make 'objects' that serve a function, called adaptations. Natural Selections simultaneously provides and explanation for how complex structures can arise by 'steps'. Also, look at airplanes. We can see that airplanes get designed, we know before hand that they were designed. The only way a plane can come about is if someone builds it. Its not touchable by natural selection. Organisms, however, are. If there were wild populations of planes flitting about the sky, mating, reproducing, living in variable populations, evolving, sure then things would be really weird. But there aren't. What we do have is organisms existing in the world, doing just that. Its possible that god made them and then just let them run free, but what reason is there to think that?

When we take into account irreducible complexity

Irreducible Complexity does not exist. That, perhaps, is the crux of the matter. ID is a pseud-science, Irredicible Complexity, sounds like some labcoat's way of making something thats common sense out of whack. But it has no scientific reality or meaning. Thats the problem. Most 'ID' terms (literally, 'jargon') are bunk. They make it seem like they are saying something, but the terms are not operationally defined, ie, not workable.
IF, hypothetically, there really were things like Irreducible Complexity and Complex Specified Information, then things woudl be really different.

reptile, mammal, amphibian etc..is that not correct?

Strictly, these are what's known as 'grades' of animals. 'Aves is a clade of animals that includes 'birds'. "reptile" is actually a rather confusing term, because all 'reptiles' may not actuallyl be descended from the same original 'stock', and because birds and mammals evolved from reptiles (ie reptile isn't whats called 'monophyletic').

But, regardless, a species is somethign like the rex part in Tyrannosaurus rex. Or the sapiens part of Homo sapiens. The first part is the genus, its 'nested' within the genus. So the evolution of new species is something that we actually can see in the lab and wild, and, striclty, doesn't even require adapations, just isolation. A species is a real thing, it has an objective existence (as opposed to 'reptile grade', which is just a human concept). There are biological mechanisms which reinforce and hold a species together as a species, and also mechanisms that evolve an organism into a new species. There are no mechanisms, however, that prevent a 'grade' or 'kind' of animal from becomming another. IOW, while its 'difficult' for scales to evolve into feathers, there is no 'kind barrier' that has to be crossed and overcome.

Ahh, my first thread...hello sweetie, long time no see.

Ok Darwin says this about falsifing his theory: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”

First question: Why doesn't that read, I have demonstrated that (protein strucure X..or whatever) has been formed by these numerous, successive, slight modifications....therefore my theory of natural selection doesn't break down". Ya know what i mean? Every attempt made to falsify natural selection as the mechanism that built these molecular machines (ex. bacterial flagellum) is just thrown out. If an evolutionist can't provide us with the numerous, successive, slight modifications that 'built' the structure than how exactly would one falsify it? If ya'll want to talk about airtight un-falsifiable theories, well that's natural selection (atleast as it pertains to micro-biology).

Darwin had no idea what the cell actually looked like, heck up until a few decades ago science thought the cell was an unremarkable blob of protoplasym..did they not? We now know that statement to be grossly inaccurate, yet we want to use a 100 year old theory to account for the complexity found in a single cell (which the theorist didn't know was there). Darwin's comment on how to falsify NS works when you're talking about the finch or some such but breaks down on the microscopic level..any attempt to do so (ex., behe IRC bacterial flagellum) is thrown out without every having been refuted. Maybe i'm just not up on all the theories/explainations...so i'll give some examples and hopefully you guys can give me a link to the theory of numerous, successive, slight modifications used to 'build' them. If you guys are going to arbitrarily throw out every attempt to falsify by saying; "we don't know how it happened, but we're sure it did happen that way"...well that's as bad as "GOD did it" is it not?

Alrighty then, here we go.......

All images taken from: www.arn.org... Molecular machines Museum (u.n.o.).

The Bacterial Flagellum

[align=center][/center]

Comprised of (atleast) three parts a paddle, a rotor, and a motor. Described as a rotary propellor, each part in the flagellar motor is absolutely necessary for the whole to function (ie., irreducibly complex). It is, for all intent and purpose, an outboard motor...not motor "like" mind you but an actual biological motor. More sophisticated and complex than any man is capable of building. I mean come on! Capable of 100,000 RPM can stop on a molecular dime (a quarter turn) and reverse its direction back up to 100,00 RPM just as quick. If it looks like a motor, sounds like a motor, talks like a motor...well it's a motor imo, not "motor like".

Michael Behe puts it this way in his book Darwins Black Box (p.73) (emphasis Rren)

In summary, as biochemists have begun to examine apparently simple structures like cilia and flagella, they have discovered staggering complexity, with dozens or even hundreds of precisely tailored parts. It is very likely that many of the parts we have not considered here are required for any cilium to function in a cell. As the number of required parts increases, the difficulty of gradually putting the system together skyrockets, and the likelihood of indirect scenarios plummets. Darwin looks more and more forlorn. New research on the roles of the auxiliary proteins cannot simplify the irreducibly complex syetem. The intransigence of the problem cannot be alleviated; it will only get worse. Darwinian theory has given no explanation for the cilium or flagellum. The overwhelming complexity of the swimming systems push us to think it may never give an explanation.

Is Behe incorrect that "Darwinian theory has given no explaination..."? If so please explain. What is the step by step process, via natural selection, that produced the flagellum, falsifing the ID claim that it's irreducibly complex and supporting NS.... meeting Darwin's standards for verifing it was built via NS.


Ok moving on.....

The Cilium

[align=center] [/align]
Click here for Schematic illustration of a Cilium

From: "Molecular Machines: Experimental Support for the Design Inference" by Michael J. Behe.

The components of cilia are single molecules. This means that there are no more black boxes to invoke; the complexity of the cilium is final, fundamental. And just as scientists, when they began to learn the complexities of the cell, realized how silly it was to think that life arose spontaneously in a single step or a few steps from ocean mud, so too we now realize that the complex cilium can not be reached in a single step or a few steps. But since the complexity of the cilium is irreducible, then it can not have functional precursors. Since the irreducibly complex cilium can not have functional precursors it can not be produced by natural selection, which requires a continuum of function to work. Natural selection is powerless when there is no function to select. We can go further and say that, if the cilium can not be produced by natural selection, then the cilium was designed.

(emphasis - Rren)

What is the step by step process, via natural selection, that produced the Cilium, falsifing the ID claim that it's irreducibly complex and supporting NS.... meeting Darwin's standards for verifing it was built via NS.

Adenosine Triphosphate Synthase Molecule

[align=center][/align]

ATP: The Perfect Energy Currency for the Cell By: Jerry Bergman, Ph.D.

Abstract
The major energy currency molecule of the cell, ATP, is evaluated in the context of creationism. This complex molecule is critical for all life from the simplest to the most complex. It is only one of millions of enormously intricate nanomachines that needs to have been designed in order for life to exist on earth. This motor is an excellent example of irreducible complexity because it is necessary in its entirety in order for even the simplest form of life to survive.

(emphasis -Rren)Please give me the step by step process responsible for the ATP molecule, via natural selection, that refutes the ID claim that it's irreducibly complex...meeting Darwin's standards for verifing it was built via NS.

I don't know how one is supposed to falsify NS as a mechanism capable of building these molecular machines, if evolutionists are unwilling to accept evidence to the contrary but at the same time provide no evidence to support the contention that these machines were built via; "... numerous, successive, slight modifications". Makes you wonder who's pushing an airtight, untestable, un-falsifiable theory, heck you guys are just replacing "GOD did it" with "Natural Selection did it", without actually explaining how NS did it. ID has experimental, evidential support for its claims, what do you guys have outside of unsubstantiated conjecture ie., The same mechanism capable of give a Finch a "better" beak is also capable of building these protein structures (molecular machines)...only please don't ask us to back that up we can't...but we're confident that we are right and you (IDists) are wrong. Now that's good science.

These examples are just a few among the many thousands of intricate, well-designed, molecular machines found inside of any cell. Irreducible complexity as stated by Behe; "a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." essentially falsifies NS as the mechanism capable of building these machines...does it not? It's evidential, is it not. It's experimental, is it not? I mean how much evidence to the contrary will it take before the ID model is atleast given some respect as a possible alternative?

And don't get me started on the evolutionary model that explains where DNA comes from..."We now understand that each human DNA molecule is comprised of chemical bases arranged in approximately 3 billion precise sequences. Even the DNA molecule for the single-celled bacterium, E. coli, contains enough information to fill all the books in any of the world's largest libraries."[ Source ] I'm sure it's just the product of "... numerous, successive, slight modifications" too, right? I mean can you even have natural selection before you have DNA?


Here's a paper you may want to take a look at: Molecular Machines: Experimental Support for the Design Inference By: Michael Behe

PS can anyone tell me what i'm doing wrong with the BB code to align images? Thanks.



[edit on 30-11-2005 by Rren]

Originally posted by Rren
Adenosine Triphosphate Synthase Molecule

[align=center]

[/align]

ATP: The Perfect Energy Currency for the Cell By: Jerry Bergman, Ph.D.

Abstract
The major energy currency molecule of the cell, ATP, is evaluated in the context of creationism. This complex molecule is critical for all life from the simplest to the most complex. It is only one of millions of enormously intricate nanomachines that needs to have been designed in order for life to exist on earth. This motor is an excellent example of irreducible complexity because it is necessary in its entirety in order for even the simplest form of life to survive.

(emphasis -Rren)Please give me the step by step process responsible for the ATP molecule, via natural selection, that refutes the ID claim that it's irreducibly complex...meeting Darwin's standards for verifing it was built via NS.

Ahhhh yes…. the ATP Synthase… did you put this here just for me Rren?

As you are aware, [sniff] this is very near and dear to my heart [sniff], as my doctoral dissertation was based on this particular enzyme.

This is an amazing protein machine; and indeed protein machine is a totally appropriate description. This enzyme is in fact a biological rotary motor, and at the time I was really up on this stuff, was the ONLY known example of a direct conversion of mechanical energy to chemical energy in the form of ATP.

And in terms of Irreducible Complexity (IC), as described by Behe, et al., the protein is a monument to this on both an intramolecular and intermolecular level, as well as intra and intersystemic levels. Now, I’m on a roll… …. Gonna run with this for awhile.

This molecule uses the electrochemical gradient generated by proton transport of various electron transport apparatus, to generate ATP from Adenosine diphosphate (ADP) and inorganic phosphate (Pi). It conducts the diffusion of protons through the cell membrane, and in the process, harnesses the energy released to synthesize ATP. The really neat part is that as the protons flow through the protein, a portion of the protein rotates, actually spins around… a Japanese group was the first to visualize this using a fluorescently labeled actin filament. Rotation assays are pretty common stuff now… I actually was involved in the development of a rotation detection assay using gold nanorods and plane polarized light… but I digress.

Popular opinion states that the gamma subunit, which runs through pretty much the entire length of the protein, and the c-subunit oligomer rotate as the enzyme mediates proton flux through the membrane. Personally, and I should mention that I am practically completely alone in my opinion on this, I think the alpha-beta hexamer is a more likely candidate for rotation in vivo. Irrespective of which segment rotates, rotation has been confirmed. The rotation acts to change the shape of the alpha and beta subunits as it occurs. The shape of the subunits is altered such that ADP + Pi form ATP. The process of using the passive diffusion of electrochemical gradients to form chemical energy in the form of ATP is called chemiosmosis.

Now the enzyme at in its simplest form has a minimum of 9 unique subnits. These subunits combine in a stoichiometric ratio such that, generally the protein in its simplest form consists of at least 25 interacting parts. The thing is though that each of these parts is necessary for the protein to function in its job of energy production. There is no reasonable mechanism to describe the gradual development of a protein such as this. The subunits by themselves have no job, function, or purpose. In fact, free alpha and beta subunits would actually hydrolyze ATP. Furthermore, this protein is considered to be one of the most ancient of all proteins, ie: it’s thought to have been around pretty much since the simplest of life forms existed.

Finally, not only is this protein itself a monument to complexity, it exists at the end of a pathway that involves multiple other complex proteins, specifically, those of the electron transport chain. The ETC is also considered to be very ancient. While many of the proteins within the ETC are not as complex in terms of overall stoichiometry and subunit composition, they are in fact equally unlikely to arise via random processes.

The proteins of the ETC contain co-factors that facilitate the transfer electrons, and subsequent harvesting of energy as the electrons fall down an energy gradient; electron Donor/acceptor species are arranged in order of increasing electronegativity (affinity for electrons). Firstly, that the co-factors are specific enough and arranged in such a manner to facilitate the flow of electrons is astonishing. These co-factors have to be arranged within angstroms of each other to be effective. Furthermore, not only is the distance critical, the orientation of the cofactors is equally important. Any anisotropy whatsoever will greatly hinder electron flow. By the way, one of the ways cyanide kills is by blocking electron flow in ETC’s. Finally, ETC’s are composed of many such proteins that must maintain not only a specific proximal distance, but a specific order within the membrane. All of these things: the pathways to synthesize co-factors, the specific locations of the co factors within the protein, the specific order of the proteins within the membranes, and finally the specific function of the proteins had to be tightly coordinated, and develop at ‘about’ the same time for any of this to work. If I am wrong, please call me on this.

Now… it’s all well and good to say that these systems could have been co-opted from other systems, and theoretically it could have happened. Of course, there exists no reasonable explanation of how this could have happened. I challenge ANYONE on ATS to find a reasonable explanation and post it here for discussion. The problem with co-opting this system from other systems is that this is likely to be one of the most ancient and fundamental of all life processes. What systems were in place prior to the advent of a ‘biological power station’ so to speak. Building a car is great, but wouldn’t have been much good if there were no fuel to run it.

Life seems to exist only because of a series of interdependent and profoundly interconnected pathways. Nothing about these pathways suggests that any portions of them evolved in a piecemeal fashion. Furthermore nothing about biological pathways in general suggests that are even capable of evolving in a step by step fashion…hence the name pathway.

Matzke attempts to utilize an argument based in part on the ATP Synthase in an attempt to describe a mechanism of flagellar development based on Darwinian mechanisms. The argument is incredibly weak, and substantiated only the mind of Matzke, and maybe the people at TO. But in any case, actual discussions of mechanisms by which these systems could have come about based on NDT, are not only severely lacking, but are not likely to be even approaching reasonable, which is why they don’t exist in the literature. The only place you find such descriptions in on line… there’s a reason for that.

This fundamental lack of an explanation is what IDT stems from. This recognized inability for NDT to account for biological complexity is a huge part of the reason IDT exists. Despite what the popular media would have people believe IDT is not fueled by ignorance. Chances are, if I didn’t know as much as I do about biology, I’d be an evolutionist…I’d probably write letters to the editor about ‘Christian conspiracies,’ IDT being unscientific, and evolution being an undeniable fact. I was BEFORE I got my Ph.D.. Now, I have to state: I do believe that NDT, self-organization, and abiogenesis theories are all inadequate for the explanations of biological origins, even when considered as a ‘unified theory.’

That’s why I am open to new hypotheses/theories.

Hoo boy... There's a lot to talk about here... I don't know where to begin.

I liked the idea of "irreducible complexity" the first time around, when it was predicted by evolution supporter Hermann J. Muller in 1939 and called "interlocking complexity." (Source)

"Irreducibly complex" is at most passable description of certain functioning proteins and other organic structures, but it doesn't inherently imply a creative designer. Put simply, the conclusion is illogical. It doesn't follow. Let's unattach the idea from "design" for the moment and talk about these functional proteins with respect to their level of reducibility.

Deep inside Matt's ATP synthase harangue exists an interesting point or two. It is true that there is little written about the evolutionary processes of metabolic pathways. We're currently exploring the possible step by step evolution of complex biochemical pathways. It's a work in progress. However, we're not ready to throw our hands up and say "Ya got me. It must be DESIGNED that way. Yeah," and then wipe our sweatty brows.

Speaking of which, I'm sure that the ID crowd is familiar with the recent discovery about the man-made chemical PCP (pentachlorophenol).

Furthermore recently [j] a novel metabolic pathway, that degrades the toxic chemical pentachlorophenol (PCP), has been discovered in a bacteria called Sphingomonas chlorophenolica. This pathway provides the only source of carbon for the bacteria. This metabolic degradation requires three enzymes. The removal of any one of these enzymes will kill the bacteria, as it no longer has any carbon source. This is thus an irreducibly complex process. However PCP is a man-made chemical that is not known to exist naturally and, get this, PCP was first introduced into the environment only in 1936. Thus the bacteria must have evolved this irreducibly complex metabolic pathway less than 65 years ago! Shelley D. Copley [35] had suggested that this pathway evolved through the co-option of enzymes already used in other pre-existing pathways.

Sure, it's difficult to explain a step-by-step evolution of ATP synthase at the moment. We are not so callously vain that we presume to have all the answers, but, as I said, neither are we immediately given to throwing our hands up and going on vacation. It may appear that evolutionary theory "breaks down" in microbiological examination, but I believe that what we're really seeing is a simple lag period between discovery and explanation.

Zip

[edit on 12/1/2005 by Zipdot]

Originally posted by Zipdot
I liked the idea of "irreducible complexity" the first time around, when it was predicted by evolution supporter Hermann J. Muller in 1939 and called "interlocking complexity." (Source)

You were around in 1939?

Deep inside Matt's ATP synthase harangue exists an interesting point or two. It is true that there is little written about the evolutionary processes of metabolic pathways. We're currently exploring the possible step by step evolution of complex biochemical pathways. It's a work in progress. However, we're not ready to throw our hands up and say "Ya got me. It must be DESIGNED that way. Yeah," and then wipe our sweatty brows.

This completely obfuscates the point. I have made this point repeatedly, and I believe I’ve made it you personally. No one in the ID community suggests throwing up their hands and stating that we shouldn’t study something because it’s IC. IC serves as a basis for hypothesis formation, not as an end. I know it’s lots of fun to go along with popular opinions, but deliberately making the issue unclear doesn’t add to the discussion.

When has an opponent of ID said they shouldn’t study something because it’s IC?

Obviously thinking that ATP synthase is IC didn’t deter my own work on the enzyme, why do you insist that must be the outcome of an IC hypothesis?

Speaking of which, I'm sure that the ID crowd is familiar with the recent discovery about the man-made chemical PCP (pentachlorophenol).

I am actually not familiar with it yet, but will be by next week. Got any good primary refs?

Sure, it's difficult to explain a step-by-step evolution of ATP synthase at the moment. We are not so callously vain that we presume to have all the answers, but, as I said, neither are we immediately given to throwing our hands up and going on vacation. It may appear that evolutionary theory "breaks down" in microbiological examination, but I believe that what we're really seeing is a simple lag period between discovery and explanation.

Okay, so WHO specifically is throwing up their hands and going on vacation? As I mentioned, IC is a basis for hypothesis formation, not an end to the quest for knowledge.

Zip, if you want to talk philosophy of science, let’s do it. Why must continue to obscure the relevant issues with statements have absolutely no relevance on the topic at hand.
Behe and Dembski don’t think research should cease on allegedly IC systems, why do you insist on putting those words in the mouths of the ID community?

BTW, where specifically are we exploring the step by step evolution of complex metabolic pathways… specifically?


[edit on 1-12-2005 by mattison0922]

Okay... so I looked up some refs. on the PCP degradation pathway. I read the most recent review, which isn't really all that recent (1999), and a couple of other more recent primary documents. While I don't have a complete grasp of the situation, ie: I've not actually looked at any gene sequences myself, nor did I study the data in the two primary articles. Irrespective of this, it's pretty clear what's likely to have happened here.

Originally posted by Zipdot
Speaking of which, I'm sure that the ID crowd is familiar with the recent discovery about the man-made chemical PCP (pentachlorophenol).

I'm not sure what you're definition of recent is, but from what I can see the literature on this topic goes back at least 40 years. Did you happen to look into refs such as This One?

When I first ran the search, I was surprised that I'd not heard of this particular example. I've never seen it addressed in any of the standard apologetics literature from either side of the argument. As I read through the review it quickly became clear why I not seen any discussions/rebuttals in the apologetics literature from either side.

Zip, this is an incredibly poor example in support of your position. Let’s discuss your quoted material and reveal not only why this is such a poor example, but also, the author’s poor understanding of the commonly accepted definition of IC. Fun, Fun, Fun!!!!!

Rather than split the quote up, I have reproduced it in it’s entirety below and will address it in a single rebuttal.

Furthermore recently [j] a novel metabolic pathway, that degrades the toxic chemical pentachlorophenol (PCP), has been discovered in a bacteria called Sphingomonas chlorophenolica. This pathway provides the only source of carbon for the bacteria. This metabolic degradation requires three enzymes. The removal of any one of these enzymes will kill the bacteria, as it no longer has any carbon source. This is thus an irreducibly complex process. However PCP is a man-made chemical that is not known to exist naturally and, get this, PCP was first introduced into the environment only in 1936. Thus the bacteria must have evolved this irreducibly complex metabolic pathway less than 65 years ago! Shelley D. Copley [35] had suggested that this pathway evolved through the co-option of enzymes already used in other pre-existing pathways.

First of all, I again have to wonder about the author’s definition of the term recent… 65 years ago? Perhaps this person WAS doing science back then, but it seems pretty unlikely. Personally, I wouldn’t judge a pathway with at least a 65 year old history as being recent. I wouldn’t describe PCR as a recent development either though.

Secondly, the fact that this source describes the bacteria as using only PCP as it’s carbon source doesn’t say much. Actually, this little blurb isn’t reliable enough to really judge whether or not the bacteria must live exclusively off of this substrate. I will look into this, but it won't change the essence or effectiveness of the arguement even if this is the case.

Let me say this though, in the four papers that are sitting here in front of me, the language is very specific, “exhibits PCP degrading Activity...,” “is capable of degradation of PCP by a novel pathway…,” etc.

So far nothing I’ve read says that it must be used as it’s sole C source. Perhaps you can provide the link to where you pulled that quote from. Even if it is the only source of C, it’s doubtful that’s always been the case, and there is likely to be evidence of this… again, I’d appreciate knowing the source of this quote.

PCP is a man-made chemical, this much is true. However the chemical in fact does bear distinct resemblance to numerous naturally occurring biological quinones. Without really looking into it, likely analogs include CoEnzyme Q10, Plastoquinone, Vitamin E2, actually pretty much the entire vitamin E series (tocopherols), tocoquinone, etc. How many other existing analogs do I need to cite? I’m sure a quick over the metabolic pathways chart (with structures of many molecules ) will yield many more candidates.

So irrespective of whether or not PCP was first introduced into the environment in 1936, it’s a poor example as there are many existing biological analogs.

Finally, look at the authors concluding statement… wait I’ll quote it for you: “Shelley D. Copley [35] had suggested that this pathway evolved through the co-option of enzymes already used in other pre-existing pathways.”

This statement disqualifies this system as being IC. Perhaps you should review the definition of IC. An IC system is a system that is not likely to have evolved from a pre-existing system. The very fact that they stated this demonstrates a complete lack of understanding of the definition of IC.

If you’d actually bothered to read any of the papers associated with this particular example, you’d realize that there are several candidates for homologs of the PCP degrading enzymes. In fact, some of the native homologous enzymes do in fact exhibit weak catabolic activities against PCP.

This is a stellar example of natural selection, but hardly any type of refutation of the concept of ID as an Origins theory.

To move on to a couple of other points in your post:

It may appear that evolutionary theory "breaks down" in microbiological examination, but I believe that what we're really seeing is a simple lag period between discovery and explanation.

Okay... so what? You – in your profoundly qualified status as a scientist – judge science to be in a lag period. Generally one of the best ways to get out of one of these slumps is to approach the problem from a different perspective. However, you seem completely opposed to the idea of change. Tell me very specifically: How does Behe, Dembski, Gonzales, Minnich, or whoever pursuing there own alternative hypotheses, using entirely naturalistic methodology threaten you or ‘science’ in general?

You’ve made no convincing arguments as to the superiority of NDT and similar presuppositions; you’ve demonstrated a significant misunderstanding of the basic concepts and premises of IDT, and finally, the arguments presented thus far have been so far off base, we’ve spent most time simply clearing up misconceptions.

Deep inside Matt's ATP synthase harangue exists an interesting point or two.

While, I may be verbose, and I completely acknowledge digressing from the topic at hand, I will say this: At least what I am writing is not written from ignorance. I’ve got actual experience in the fields I discuss. In addition, I actually tend to read about the topics that interest me. I actually have a desire to make an informed opinion. Personally, I enjoy things that make me think critically and challenge my belief system. I would imagine that most who tend to comment on this topic here haven’t even read The Origin, or most of the other major works they like to refer to. Despite the motto of ‘Deny Ignorance,’ IMO, with respect to the O & C forum, there is an overwhelming amount of willful ignorance. Which books about IDT have you read, Zip?

Zip, what have you got to lose if the ID theorists start doing experiments, and testing their hypotheses?

[edit by mattison0922 to remove uncalled for ad hominem attack]
[edit on 1-12-2005 by mattison0922]

[edit on 1-12-2005 by mattison0922]

Originally posted by mattison0922
Another rebuttal attempted from a practically completely ignorant position with respect to the topic at hand.

This is extremely uncalled for. I just lost a lot of respect for you. We're just talking here. This is not the debate forum. I offhanded you a few things to consider, I did not "rebut" your "arguement."

Zip

This message is for everybody.

Kindly refrain from personal attacks when debating this topic. They add NOTHING to the discussion at hand and if you feel the need to resort to an ad hominem type attack, perhaps your position is not well supported

Originally posted by Zipdot

Originally posted by mattison0922
Another rebuttal attempted from a practically completely ignorant position with respect to the topic at hand.

This is extremely uncalled for. I just lost a lot of respect for you. We're just talking here. This is not the debate forum. I offhanded you a few things to consider, I did not "rebut" your "arguement."

Zip

Perhaps you're right... I shouldn't have stated my position in such an adversarial tone. In fact, both of my posts may have been written with a somewhat adversarial tone.

I apologize for perhaps not presenting my points in a manner that's more appropriate.

However, and perhaps I am being too sensitive here, I felt your referring to my earlier post as a 'harangue' was a negative way to portray the info. While it could have been better organized, I did write it off the top of my head. While you think I may have been rambling, I felt the info was relevant to my point.

I felt the overall 'flavor' of your post was somewhat mocking towards me. Again, I apologize if I've misconstrued your statements and intentions.

Please accept my apology for my overly hostile/condescending tone.

Thanks, Matt. I quite enjoy your discourses and I'm really glad that we are all coming together here. I think we've all been given to swelling passionately and fervously about this incessantly fascinating subject at one time or another, so nothing more needs to be said about that.

As an FSME, I am attempting a campaign for cohesiveness, which I think has largely been achieved. More and more, in our forum, we are seeing concessions and willingness to accept alternative ideas. I want you to know that when I used the word "harangue," I meant in in its secondary, non-condescending definition, which merely speaks to the heartfelt intensity that characterized for your love of ATP.

I've got to run, because my pops is in town tonight.

Zip

Originally posted by Zipdot
Thanks, Matt. I quite enjoy your discourses and I'm really glad that we are all coming together here. I think we've all been given to swelling passionately and fervously about this incessantly fascinating subject at one time or another, so nothing more needs to be said about that.

No... Thank you. I too enjoy our discussions, and thanks for your gracious handling of the situation.

As an FSME, I am attempting a campaign for cohesiveness, which I think has largely been achieved. More and more, in our forum, we are seeing concessions and willingness to accept alternative ideas.

Agreed... and your effort is noble. It appears that you have in fact earned your FMSE title, are completely deserving of said title, and in fact more qualified for the position than myself.

I want you to know that when I used the word "harangue," I meant in in its secondary, non-condescending definition,

I appreciate your clarification

which merely speaks to the heartfelt intensity that characterized for your love of ATP.

Ok... I admit it I do... I LOVE ATP!!! I want to shout it from the mountaintops. Hell, I want to get it tattooed on my forearm.

You have voted mattison0922 for the Way Above Top Secret award. You have two more votes this month.

*waves to Mattison and Zipdot* Rock on guys. I'm reading but know better to engage in a highly technical discussion with people who clearly know more than I do. I've not had any exposure to ID, and feel the university somewhat 'cheated' me by knowing about it and not teaching it.

Originally posted by saint4God

You have voted mattison0922 for the Way Above Top Secret award. You have two more votes this month.

Saint! I've been wondering about you... I owe you something... promise I'll get it to you. Thanks for your vote of confidence despite my despicable behavior... of which I've eliminated most of the evidence. You might not have been so quick to cast that vote had I not.

*waves to Mattison and Zipdot* Rock on guys. I'm reading but know better to engage in a highly technical discussion with people who clearly know more than I do. I've not had any exposure to ID, and feel the university somewhat 'cheated' me by knowing about it and not teaching it.

You bring up a relevant point, and something that I feel is worth mentioning. Don't blame your university for not teaching IDT. You might not believe I am going to say this, but universities currently don't really have much to teach in terms of IDT. IDT is a relatively new origins hypothesis. As you are aware I'm sure, the theory is hotly debated and emotions tend to be strong on one side of the arguement or the other. As a result, not many professors, researchers, etc. have embraced the theory. While IDT serves as a totally legitimate basis for hypothesis formation, we've yet to see much activity in this department, ie: IDT is currently not producing much in terms of hard data.

My prediction is that as more young professors become tenured and have a reasonable amount of job security, you'll see more scientists 'coming out' so to speak. When this happens, the movement can actually begin to build some scientific momentum instead of purely philosophical momentum. As this happens, the theory is likely to become more accepted by mainstream science in general.

That's when IDT will really start to appear not only in texts, but actually in science classes. IMO, this is the only legitimate route for the theory to take. If people mandate the theory be taught, it's lost a certain amount of credibility already.

Strong arming school districts and in fact dictating that something must be taught, IMO, goes against the natural flow of education (Please note KS, doesn't state IDT must be taught). No one is insisting that we update the physics texts with the most recent, speculative, and untested hypotheses. Why should this be the case with biological origins? Whether or not IDT is accepted as a legitimate alternative to current origins theories, and is ultimately taught in mainstream science classes should rest on the merits and accomplishments of IDT itself. I predict that it in fact can produce meaningful data, and eventually will. But the success or failure of the theory should rest solely on the merit of the theory, not on political motivations.

Originally posted by mattison0922
Saint! I've been wondering about you... I owe you something... promise I'll get it to you.

Me? I hope it doesn't tick

Originally posted by mattison0922
Thanks for your vote of confidence despite my despicable behavior... of which I've eliminated most of the evidence. You might not have been so quick to cast that vote had I not.

I get a bad case of foot-in-mouth disease myself now and then. The word "saint" isn't synonymous with "perfect". Good to see all is forgiven and can move on.

Originally posted by mattison0922
You bring up a relevant point, and something that I feel is worth mentioning. Don't blame your university for not teaching IDT. You might not believe I am going to say this, but universities currently don't really have much to teach in terms of IDT. IDT is a relatively new origins hypothesis. As you are aware I'm sure, the theory is hotly debated and emotions tend to be strong on one side of the arguement or the other. As a result, not many professors, researchers, etc. have embraced the theory. While IDT serves as a totally legitimate basis for hypothesis formation, we've yet to see much activity in this department, ie: IDT is currently not producing much in terms of hard data.

Okay, perhaps I'd been a bit unfair in my expectations...but I still owe them a 1/3 value of my house and was hoping to get something a little more special than the evolution ramrod when they had gaps needing to be filled . I heard you say something once that I've never heard a professor say before. It was "I don't know" and that my friend, shows a open-mindedness and love for the science while others hide under a veil of pride and ostentatiousness. On top of that you went back to review material and research before making an assessment. If you taugh a class just on that, then I think the scientific community would reap great benefits from the practice.

Originally posted by mattison0922
But the success or failure of the theory should rest solely on the merit of the theory, not on political motivations.

I'm with it. As it should be with any theory I think. I'd be interested to see not only theory, but ideas being taught and discussed as well, to go through the mental exercise of it to see if it makes sense or consider all possibilities. But call an apple and apple, not a thought a theory...as...we...seem to see with another "theory".

Okay - this isn't really on topic, and I just scanned only the first post.

BUT - the examples in the first post all fit with what might be described as "fractal design."

Originally posted by soficrow
Okay - this isn't really on topic, and I just scanned only the first post.

BUT - the examples in the first post all fit with what might be described as "fractal design."

Sofi, your example escapes me. I can't for the life of me come up with a way that a biological rotary motor can be considered a fractal. Can please elaborate? Thanks.