Which is falsifiable?

[sandy_mcd]

He's trying to make viruses look like crystals because crystals do self-assemble ... I haven't posted a rebuttal yet.

In the lull before you rebut Bgood's arguments, would you be so kind as to clarify your clarifications above? As I recall (please correct me if I am wrong), it was you who first brought up the topic of crystals. You went on to say

If the answer was self-organization, shouldn't the result be a repetitive sequence, like A-G-A-G-A-G-A-G-A-G?

I put together several posts illustrating why your writing didn't make any sense to me. Could you please explain what you were really trying to say, perhaps using some of the examples I raised so that I won't be left even more confused?

[Totoro]

BeGood,

I must have misunderstood your post. I thought you were arguing that flagella are the result of self-assembly.

Cells reproduce on their own, this includes bacteria, and this includes bacterial components such as the flagella. Do you disagree?

Yes - I do disagree. Flegella do not reproduce. They are a product of production within the cell - not reproduction on their own.

When have I done this? Please point to a specific instance so that I can rectify the mistake.

I posted two examples earlier. You seemed to be arguing that flagella self-produced like a crystal. I wanted to point out that nothing in your sources implied anything of the sort.

The flagellum is a result of a self assembly process.
http://www.bio.cmu.edu/Courses/03441/Te ... ellum.html
http://www.aip.org/png/2002/174.htm

And you call me frustrating. First you are not arguing and now you say flagellum are the result of a self assembly process. Which is it?

Let us look at your sources though.

Your first source - bio.cmu.edu

Flagellum Assembly
The flagellum of Caulobacter is assembled during development of the swarmer cell. Flagellum biogenesis results in the synthesis of a basal body, hook, and flagellar filament at one pole of the developing swarmer cell. This process involves at least 50 genes, most of which have been oganized into a hierarchy that includes four classes of genes. In this hierarchy, the expression of genes in an earlier class is required for expression of the genes in the subsequent class. Additionally, genes that encode structural components of the flagellum are expressed in the order that their gene products are assembled into their structure . Furthermore, the flagellum itself is sequently assembled from the inside of the cell to the outside.

I see the word 'assembly' in your source, but I don't see the word 'self assembly'. Once again, your own source does not say what you claim it says.

Your AIP.org post does support your contention that flagella are the product of self assembly. I thank you for posting something that actually supports your argument. Unfortunately though it only says that it happens and then gives some pretty computer CAD drawings that show flagella assembly but which do not show self assembly. What I would say about this source is that self-assembly is a very bad hypothesis and my source, as posted, shows not only that the argument for self assembly is bad but also why it is bad. Posting the argument from a credible source is better than what you've posted thus far, but generally speaking specific information in a debate trumps generalities and your source is a three-paragraph assertion that does not tell us how the process occurs. It is conjecture. I'll grant that it is educated conjecture from a reputable source, but as my source tells us that this view exists and what is wrong with it, I would urge you to find something that details the process.

The Wikepedia post also supports you, but let us look at that section in detail:

The components of the flagellum are capable of self-assembly in which the component proteins associate spontaneously without the aid of enzymes or other factors. Both the basal body and the filament have a hollow core, through which the component proteins of the flagellum are able to move into their respective positions. The filament grows at its tip rather than at the base. The basal body has many traits in common with some types of secretory pore which have a hollow rod-like "plug" in their centers extending out through the plasma membrane, and it is thought that bacterial flagella may have evolved from such pores.

Even if the components of the flagellum are capable fo self-assembly, you still have nothing more than a pile of components. What assembles those components? This actually does not refute Dr. Wells at all. In fact, reading the rest of the Wikepedia article shows just how complex the Flagella is, making the argument that the components self-replicated into a working machine sound rather silly.

I am glad that some of your sources really say something along the lines of what you say they say. That is progress. I would ask though that in the future you highlight what you consider the relevant parts as some of the articles you link are very long. Doing so also makes it more difficult for you to mistakingly provide an irrevelant link.

Wow, someone has trouble understanding.

what is this guys problem?

[sandy_mcd]

I haven't seen any scientist ever say that flagellum are the result of self-assembly in the manner BeGood suggests.

So are you having difficulties with the concept of self-assembly or just Bgood's interpretation? Remember, no matter what Bgood writes, the starting point of this thread is

I contend that there is no unintelligent process that could have possibly brought this system about.

Here's a reference, undoubtedly not the most recent, to a scientific view:
Title: Self-assembly and type III protein export of the bacterial flagellum
Author(s): Minamino T, Namba K
Source: JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY 7 (1-2): 5-17 2004
Document Type: Article
Language: English
Cited References: 96 Times Cited: 6 Find Related Records Information
Abstract: The bacterial flagellum is a supramolecular structure consisting of a basal body, a hook and a filament. Most of the flagellar components are translocated across the cytoplasmic membrane by the flagellar type III protein export apparatus in the vicinity of the flagellar base, diffuse down the narrow channel through the nascent structure and self-assemble at its distal end with the help of a cap structure. Flagellar proteins synthesized in the cytoplasm are targeted to the export apparatus with the help of flagellum-specific chaperones and pushed into the channel by an ATPase, whose activity is controlled by its regulator to enable the energy of ATP hydrolysis to be efficiently coupled to the translocation reaction. The export apparatus switches its substrate specificity by monitoring the state of flagellar assembly in the cell exterior, allowing this huge and complex macromolecular assembly to be built efficiently by a highly ordered and well-regulated assembly process. Copyright (C) 2004 S. Karger AG, Basel.
Author Keywords: flagellum; motility; assembly; capping structure; type III protein export; ATPase; chaperone; substrate specificity switch

[BGoodForGoodSake]

BeGood,

I must have misunderstood your post. I thought you were arguing that flagella are the result of self-assembly.

Cells reproduce on their own, this includes bacteria, and this includes bacterial components such as the flagella. Do you disagree?

Yes - I do disagree. Flegella do not reproduce. They are a product of production within the cell - not reproduction on their own.

Why do you focus on the wrong thing? When bacteria reproduce each of the daughter cells forms a flagella. The point is that new a new flagellum does indeed form in this process.

When have I done this? Please point to a specific instance so that I can rectify the mistake.

I posted two examples earlier. You seemed to be arguing that flagella self-produced like a crystal. I wanted to point out that nothing in your sources implied anything of the sort.

You brought up salt crystals trying to state that all self forming things are simple. I was only pointing out that proteins can form repetitions structures as well. But to expect repetition when there are so many molecules involved doesn't make sence.

And you call me frustrating. First you are not arguing and now you say flagellum are the result of a self assembly process. Which is it?

What is your problem with this statement? We have a detailed account of how the flagellum forms. The proteins do self assemble when they are present together. Do you disagree? If you do then how does the flagellum assemble?

Let us look at your sources though.

Your first source - bio.cmu.edu

I see the word 'assembly' in your source, but I don't see the word 'self assembly'. Once again, your own source does not say what you claim it says.

My goodness, so what is it thats doing the assembly?

Your AIP.org post does support your contention that flagella are the product of self assembly. I thank you for posting something that actually supports your argument. Unfortunately though it only says that it happens and then gives some pretty computer CAD drawings that show flagella assembly but which do not show self assembly. What I would say about this source is that self-assembly is a very bad hypothesis and my source, as posted, shows not only that the argument for self assembly is bad but also why it is bad.

How did you reach this conclusion?

Posting the argument from a credible source is better than what you've posted thus far, but generally speaking specific information in a debate trumps generalities and your source is a three-paragraph assertion that does not tell us how the process occurs.

LOL the process is discussed in the first source.

It is conjecture. I'll grant that it is educated conjecture from a reputable source, but as my source tells us that this view exists and what is wrong with it, I would urge you to find something that details the process.

Care to be a little less cryptic?

The Wikepedia post also supports you, but let us look at that section in detail:

Even if the components of the flagellum are capable fo self-assembly, you still have nothing more than a pile of components. What assembles those components?

The gene translation process.

[Wall-dog]

Sandy,

Here's a reference, undoubtedly not the most recent, to a scientific view:
Title: Self-assembly and type III protein export of the bacterial flagellum
Author(s): Minamino T, Namba K
Source: JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY 7 (1-2): 5-17 2004
Document Type: Article
Language: English
Cited References: 96 Times Cited: 6 Find Related Records Information
Abstract: The bacterial flagellum is a supramolecular structure consisting of a basal body, a hook and a filament. Most of the flagellar components are translocated across the cytoplasmic membrane by the flagellar type III protein export apparatus in the vicinity of the flagellar base, diffuse down the narrow channel through the nascent structure and self-assemble at its distal end with the help of a cap structure. Flagellar proteins synthesized in the cytoplasm are targeted to the export apparatus with the help of flagellum-specific chaperones and pushed into the channel by an ATPase, whose activity is controlled by its regulator to enable the energy of ATP hydrolysis to be efficiently coupled to the translocation reaction. The export apparatus switches its substrate specificity by monitoring the state of flagellar assembly in the cell exterior, allowing this huge and complex macromolecular assembly to be built efficiently by a highly ordered and well-regulated assembly process. Copyright (C) 2004 S. Karger AG, Basel.
Author Keywords: flagellum; motility; assembly; capping structure; type III protein export; ATPase; chaperone; substrate specificity switch

My point is that the complexity of this process begs the question of how it occurs but that if you could show a naturalist cause you would largely disprove ID. The topic really wasn't about flagella (flagella being an example of falsifiability - nothing more) but BeGood's first posts went on to try and give natural explanations for the creation of flagella:

Discovering a specific pathway to a specific case is more like forensic investigation.

Identifying a mechanism for change allows one to speculate how the mechanism could have lead to specific examples.

Proteins self assemble according to the charges found on the various amino acids.
http://www.friedli.com/herbs/phytochem/proteins.html
The interactions of these proteins form structures within the cell.
Such as the cell membrane.
http://sun.menloschool.org/~cweaver/cel ... _membrane/
Does the cell membrane require directions for formation?
Not at all the phospholipids have a polar and non polar end. The polar end is attracted to water which is also a polar molecule and the nonpolar is water aversive. Thus leading to the self assembly of a double layered membrane.
http://www.jdaross.mcmail.com/cell2.htm

Changes in amino acid sequence lead to changes in protein shape.
Once this mechanism is identified one can see how new funtionalities can arise. Thus leading to speculation of how specific functionalities could have been originated.
http://jb.asm.org/cgi/content/full/181/ ... d=10572114
http://www.blackwell-synergy.com/links/ ... 01.02195.x

AttentionKMartShoppers wrote:
Biological predestination again? Oh we can have such great fun. So you're trying to say everything is reducible to chemistry.

No, what I am saying is that proteins behave in specific ways, due to their chemical makeup.

They fold in very specific ways due to the interactions of the various charges in the amino acid chain.

Heres a neat article about gene's in general.
http://www.thetech.org/genetics/ask.php?id=106

I'll grant that the topic changes somewhat at that point from the falsifiability of Evolution and ID to an attempt to actually disprove a large portion of ID, but rereading my initial post...

Bacterial flagellum, which are little tiny motor-driven propellors in bacteria capable of spinning at 10,000 RPM, are often called irreducibly complex systems. I contend that there is no unintelligent process that could have possibly brought this system about.

Darwinists have no answer for how the flagellum developed but they say linking it to intelligence is an argument from ignorance and unfalsifiable.

Isn't saying 'evolution did it but we can't explain how yet' also an argument from ignorance?

What is more falsifiable? All a darwinist has to do to disprove this contention is find one unintelligent process and get it to produce flagellum. To disprove the darwinist you would have to prove that none of a potentially infinite number of natural processes could do it.

If Intelligent Design is not falsifiable and evolution is, please explain this.

...I did unintentionally word almost like a dare so I can't really take offense at someone taking me up on it even though doing so does change the topic. I didn't change the topic but I did word the initial post such that the topic's changing was probably inevitable.

How did the discussion of crystals come up? BeGood brought up self-assembly, which invariably leads to crystalline forms (and I guess I'm starting my rebuttal here as well though I really wanted to hammer-out more common ground first). Dr. Stephen Meyer, in the book The Case for a Creator, but Lee Strobel, deals with the topic of self-organization and self-assembly in building proteins:

We'll use proteins as an example. Remember, proteins are composed of a long line of amino acids. The hope was that there would be some forces of attraction between the amino acids that would cause them to line up the way they do and then fold so that the protein can perform the functions that keep a cell alive.

Salt crystals are a good illustration. Chemical forces of attraction cause sodium ions, Na+, to bond wiht chloride ions, Cl-, in order to form highly ordered patterns within a crystal of salt. You get a nice sequence of Na and Cl repeating over and over again. So, yes, there are a lot of cases n chemistry where bonding affinities of different elements will explain the origin of their molecular structure. Kenyon and others hoped this would be the case for proteins and DNA.

...As scientists did experiments, they found that amino acids didn't demonstrate these bonding affinities.

...There were some very, very slight affinities, but they don't coorelate to any of the known patterns of sequencing that we find in functional proteins <My interjection - look at the disorganized illustration in Sandy's 3-d rotating protein above for an illustration of Dr. Meyer's point>. Obviously, that's a major problem - but there was an even bigger theoretical difficulty. Information theorist Hubert Yockey and Chemist Michael Polanyi raised a deeper issue: 'What would happen if we could explain the sequencing in DNA and proteins as a result of self-organization properties? Wouldn't we end up with something like a crystal of salt, where there's merely a repetitive sequence?'

...Consider the genetic information in DNA, which is spelled out by the chemical letters A, C, G, and T. Imagine every time you had an A, it would automatically attract a G. You'd just have a repetitive sequence: A-G-A-G-A-G-A-G. Would that give you a gene that could produce a protein? Absolutely not. Self-organization wouldn't yeild a genetic message, only a repetitive mantra.

Dr. Meyer goes on, but I think this is enough to illustrate pretty clearly both the problems with using self-assembly as an explanation and also why I was pressing BeGood with the questions I was pressing him on. I wanted to hear BeGood for example say clearly that DNA was a prerequisite for creating proteins and particularly the flagella.

quote="Wall-dog"How are the proteins assembled? Does that process require DNA?

BeGood:
In Nature RNA is required to fashion amino acid chains.
http://www.accessexcellence.org/RC/VL/G ... hesis.html

Wall-dog:
BeGood,

Your source seems to say that RNA is necessary for the actual assembly of the proteins. It kind of looks like when transcription occurs, a molecular machine unwinds a section of the DNA helix to get the specific instructions needed for the protein being built. Then another machine copies those instructions to form a messenger RNA. At the end of transcription the RNA strand takes the genetic information from the DNA out of the nucleus and goes to a two-part molecular factory called a ribosome. The ribosome then takes the data from the DNA (delivered by the RNA) and then the amino acids are assembled inside the ribosome into the right sequence or chain, often hundreds of units long. This sequence - which again is determined by the section of DNA being used - determines the type of protein manufactured. Once the chain is finished it is moved from the ribosome to anotehr machine that helps fold it into the precise shape needed for its function. At that point it is a protein, and another molecular machine takes it to the exact location where it is needed.

Does that sound about right?

I ask because you make it sound like you just pour random amino acids into a vat and you get proteins. Your source doesn't make it sound anywhere near that simple.

BeGood:

Perfect!
=)

This is where the subject of salt crystals came up.. My next post:

BeGood,

If it is a simple method of chemical reaction, then shouldn't the protein strands be repetitous in nature? When I think of a salt crystal for example - something which does form because of chemical attractions - sodium ions (Na+) bond with chloride ions (Cl-) and you get highly ordered patterns within the crystal of salt kind of like Na-Cl-Na-Cl-Na-Cl, etc. Of course, that sequence within a salt crystal is three-dimensional, but you get the picture. I don't see the repetitious nature of a salt crystal within a strand of protein.

While there are some slight affinities within amino acids, how can they be said to correlate into any of the sequences that we find in functional proteins?

If the answer was self-organization, shouldn't the result be a repetitive sequence, like A-G-A-G-A-G-A-G-A-G? And why would the sequence stop before all of the amino acids available were used? You don't get a genetic message with self-organization. You get a repetitive pattern.

I don't see how that process could create a protein, much less a flagula.

Now, after reading Meyer's quote, it is probably clear where I was going with that.

I should apologize though for a couple of things. One is that I've allowed and even encouraged this thread to stray from a discussion of whether or not ID or Evolution are falsifiable (for the record I think we showed that neither really are) to a discussion on whether or not natural processes could produce a flagella.

The second, and more important apology, is to BeGood. I've been awfully hard on BeGood for using links that don't really support his position, for taking quotes out of context, and for doing other things that don't necessarily support his position. It was correct for me to point those things out but I've phrased those attacks in ways that had ad-hominem repercussions. Re-reading some of the things I've said one would almost think I'm attacking BeGood's character and at times perhaps even mocking him. My intent is not to attack BeGood's character and it certainly isn't to mock him. I stand by my statements that some of BeGood's links do not say what he says they say but I apologize for phrasing those statements such that they sound like attacks against BeGood rather than attacks against the use of those quotes. My intent is not to personally attack BeGood nor any of the other users of this forum. On other threads (I don't think this one) I've been guilty of getting angry at BeGood for repeatedly calling me unknowledgable and I called him intellectually dishonest several times. I regret saying anything that infers an attack against BeGood's character and if I allowed anger from other threads to influence my conduct on this one I regret that as well.

That said, I don't have a problem with continuing a discussion on whether or not flagella can be naturally explained. Really there are two problems:

1) You may be able to show affinities within a protein that could lead to the creation of a part of the protein, but as Dr. Meyer shows, you can't explain the whole protein that way.

2) Even if you can explain a protein's creation in this manner, that still doesn't explain how those proteins assembled into a flaggellum.

[Wall-dog]

BeGood,

I'll deal with your last post specifically..

What is your problem with this statement? We have a detailed account of how the flagellum forms. The proteins do self assemble when they are present together. Do you disagree? If you do then how does the flagellum assemble?

My goodness, so what is it thats doing the assembly?

For starters, the assembly takes place within the ribosome. Self assembly does not take place. You agreed with that when you agreed that DNA was necessary for the process to occur. The proteins don't just fall into place - they have to be assembled as per the information contained in the DNA. As for the rest, I think the obvious answer is that God wrote the DNA and designed the ribosome, thus God made the assembly of the flagella possible within the cell. The mechanisms are in place because God put them there. This is a religious forum so I'm surprised that possibility didn't suggest itself to you.

Why do you focus on the wrong thing? When bacteria reproduce each of the daughter cells forms a flagella. The point is that new a new flagellum does indeed form in this process.

Since the question is how the first flagellum came about, this doesn't really help.

You brought up salt crystals trying to state that all self forming things are simple. I was only pointing out that proteins can form repetitions structures as well. But to expect repetition when there are so many molecules involved doesn't make sence.

I'm glad we agree. Repetition, and thus self-assembly, doesn't really make sense.

LOL the process is discussed in the first source.

That's not true. The first source says nothing that would imply self-assembly in any way. Where do you read self-assembly into your first source? Your first source really supports Dr. Meyer and Dr. Behe more than it supports your second source.

The gene translation process.

Doesn't the gene translation process infer God?

[BGoodForGoodSake]

BeGood,

What is your problem with this statement? We have a detailed account of how the flagellum forms. The proteins do self assemble when they are present together. Do you disagree? If you do then how does the flagellum assemble?

My goodness, so what is it thats doing the assembly?

For starters, the assembly takes place within the ribosome. Self assembly does not take place.

I am talking about self assembly after a protein has formed. We already agreed the process of transcription and translation must be in place first. The self assembly occurs once the protein is free in the cell.

You agreed with that when you agreed that DNA was necessary for the process to occur. The proteins don't just fall into place - they have to be assembled as per the information contained in the DNA. As for the rest, I think the obvious answer is that God wrote the DNA and designed the ribosome, thus God made the assembly of the flagella possible within the cell. The mechanisms are in place because God put them there. This is a religious forum so I'm surprised that possibility didn't suggest itself to you.

Given this however the mechanisms are self sustained would you not agree?

I think perhaps we should put the entrie process into numbered steps so you don't take a statement and apply it to the incorrect steps.

Lets use the following.
Step 1. Transcription DNA to RNA
Step 2. Translation RNA to amino acid
Step 3. Folding
Step 4. Protein Interactions.
Step 5. Mutation

Now self assembly occurs at step 4. Not 1, 2, or 3.

Why do you focus on the wrong thing? When bacteria reproduce each of the daughter cells forms a flagella. The point is that new a new flagellum does indeed form in this process.

Since the question is how the first flagellum came about, this doesn't really help.

Well lets look at the entire process. Once your confusion lifts it's easy to see that a change in the DNA(step5) will lead to a change in behaviour of the protein interactions(step 4)

You brought up salt crystals trying to state that all self forming things are simple. I was only pointing out that proteins can form repetitions structures as well. But to expect repetition when there are so many molecules involved doesn't make sence.

I'm glad we agree. Repetition, and thus self-assembly, doesn't really make sense.

No the point is that self assemble does not necessarily lead to repetition.

LOL the process is discussed in the first source.

That's not true. The first source says nothing that would imply self-assembly in any way. Where do you read self-assembly into your first source? Your first source really supports Dr. Meyer and Dr. Behe more than it supports your second source.

Again the first post is the mechanism of assembly. Self assembly is a given. Proteins are chemicals and will react and interact when conditions will allow for it. This is due to the 2nd law of thermodynamics and the various charges within a protein. Proteins spontaneously interact just like when you pour salt into water and the salt disolves.
http://ull.chemistry.uakron.edu/genobc/Chapter_19

The gene translation process.

Doesn't the gene translation process infer God?

I'm not arguing against God. You simply asked if there is a mechanism which could have originated the bacterial flagellum.

[sandy_mcd]

How did the discussion of crystals come up? BeGood brought up self-assembly, which invariably leads to crystalline forms (and I guess I'm starting my rebuttal here as well though I really wanted to hammer-out more common ground first). Dr. Stephen Meyer, in the book The Case for a Creator, but Lee Strobel, deals with the topic of self-organization and self-assembly in building proteins:

The hope was that there would be some forces of attraction between the amino acids that would cause them to line up the way they do and then fold so that the protein can perform the functions that keep a cell alive.
Salt crystals are a good illustration. Chemical forces of attraction cause sodium ions, Na+, to bond wiht chloride ions, Cl-, in order to form highly ordered patterns within a crystal of salt.

Thanks for referencing Strobel. [There are no copies at any of our local libraries so I have not read any of his books.] I apologize for attributing this odd analogy to you when you were just copying someone else.
1) I still don't see how molecular self-assembly "invariably" leads to crystalline forms, and what the strong interactions in a simple salt like NaCl have to do with protein folding.
2) But more importantly, are you contending that proteins cannot fold by themselves? I can't see any other possible interpretation of the following from Strobel.

...As scientists did experiments, they found that amino acids didn't demonstrate these bonding affinities.
...There were some very, very slight affinities, but they don't coorelate to any of the known patterns of sequencing that we find in functional proteins

[BGoodForGoodSake]

1) I still don't see how molecular self-assembly "invariably" leads to crystalline forms, and what the strong interactions in a simple salt like NaCl have to do with protein folding.
2) But more importantly, are you contending that proteins cannot fold by themselves? I can't see any other possible interpretation of the following from Strobel.

...As scientists did experiments, they found that amino acids didn't demonstrate these bonding affinities.
...There were some very, very slight affinities, but they don't coorelate to any of the known patterns of sequencing that we find in functional proteins

This is very important amino acids (which I posted on page one of this thread) do not have a special affinity to other amino acids. Meaning that there is no preference. This makes them like different peices of a lego set with each having the ability to connect to any other amino acid in an infinite number of combinations.

Nucleic acids are also the same way, along their backbones.
But of course this is where the confusion comes in, the sequence of nucleic acids is based on the DNA sequence. This effects step 1 transcription.

The nucleic acids do however have an afinity along their covalent bonds. Thus making duplication of DNA possible.

Proteins are a result of step 2 in the process, translation. This step takes advantage of mRNA's affinity to tRNA, and tRNA's affinity to specific aminoacids. This process brings amino acids close together to form a bond. And thus create the amino acid chain.

There is no repetition in the amino acid chain unless the repitition occurs in the DNA itself. And any such repetition would not automatically lead to a crystaline structure.

Now once the amino acid chain has completed and the protein has formed, it is very possible for the resulting proteins to form repeating structures. The flagellum tail itself is a repeating structure as just described. Of course that depends on the properties of the protein itself.
Thus to expect a crystaline structure does not make sence.

The properties of a protein are dependant on its structure. A change in structure can have a profound influence on a proteins function.
http://www.sciencedaily.com/releases/20 ... 060745.htm

[sandy_mcd]

I think I see a major source of confusion. Bgood and his sources are using the term "self-assembly" to refer to the conformation (secondary, tertiary, and quaternary structure) of the protein developing after it has been produced, that is the complex three-dimensional shape that arises from the folding of the one-dimensional polymer string of amino acids; walldog and his people seem to be using the term "self-assembly" to refer to the synthesis (primary structure) of the protein from its constituent amino acids, that is the linking of individual amino acids to form the polymer.

[Wall-dog]

Sandy,

1) I still don't see how molecular self-assembly "invariably" leads to crystalline forms, and what the strong interactions in a simple salt like NaCl have to do with protein folding.

Think about it in terms of me giving you two buckets of compounds. Call compound one 'A' and compound two 'B'. Let us further suppose that these two compounds have a chemical affinity for one another. Now we dump them into a bug tub together. What will happen? They will begin to bond, but they will not bond in irregular patterns because B does not bond to B and A does not bond to A so I'll always get patterns of ABABABABABABAB and so on. You'll have to forgive me for making it a one-dimensional pattern. In real life it would be three-dimensional. But I think you get the picture. That is self assembly and as Dr. Meyer shows, self-assembly always creates patterns. You never get irregularities. Also, self-assembly would require no DNA as the chemicals would assemble themselves without it. This is how crystals form but I would ask you to look at the protein you posted and ask yourself if it makes sense to think that chemical affinities create that kind of an irregular makeup. Self-assembly always creates regular patterns.

Proteins can not be explained that way. The very need for DNA and RNA shows that proteins are not the result of self-assembly.

Furthermore, to create a molecular machine like the flagellum you would need to take several proteins and assemble them. Again though self-assembly always creates regular patterns whereas the molecular machines do not.

Salt crystals are an excellent example of something that does self assemble. What do they have to do with proteins or molecular machines? Nothing - but they do serve as a great contrast when someone tries to argue that self-assembly created something self-assembly can not account for.

Self-assembly did NOT create the flagellum. The truth is that naturalists have no clue how flagellum are created. They can observe the assembly within the cell but they don't really have an explanation for how it works. You can see the real argument when they say things like:

What is your problem with this statement? We have a detailed account of how the flagellum forms. The proteins do self assemble when they are present together. Do you disagree? If you do then how does the flagellum assemble?

My goodness, so what is it thats doing the assembly?

Compare your diagram of a protein to any real-world example of self assembly and then ask yourself if intelligent design doesn't sound like a more practical explanation.

Don't take my word for it. Don't take BeGood's word for it either. Do the research and make your own conclusions. All I would ask is that you do so with an open mind. On that kind of playing field, ID wins.

2) But more importantly, are you contending that proteins cannot fold by themselves? I can't see any other possible interpretation of the following from Strobel.

The ribosome does help the folding process, but with or without ribosomes if you assemble amino-acids into a sequence they will fold. But here is the thing - if you assemble them into a different sequence they will fold differently. Each protein has a unique sequence of amino acids stored in the DNA and carried to the ribosome in RNA.

The critical thing is that you can take the same amino acids but use a different sequence from the DNA and you'll get a different protein. No self-assembly there!

Neo-darwinists will argue that it is self-assembly at the cellular level because the cell does do the assembly, but really that's nothing more than symantecs because they have no explanation for why the differnet pieces do what they do. They make observances and they say well, it works because the ribosome does this and the RNA unwinds the helix and takes a sequence, and so on and so on and so on. But why do these things occur? Where are the chemical affinities that tell the RNA which sequence to pick up? Neo-darwinism has no explination for that unless you accept mere observance as an explanation. The question of 'why' it happens leads to ID. In fact, that is exactly why Dr. Michael Behe says he became a proponent of ID.

BeGood,

I am talking about self assembly after a protein has formed. We already agreed the process of transcription and translation must be in place first. The self assembly occurs once the protein is free in the cell.

Please see my comment above on how this is a symantec argument rather than a practical explanation.

Given this however the mechanisms are self sustained would you not agree?

That's kind of like saying that if we take the mechanics and pit crews and fuel and driver and everything else as givens then a NASCAR car maintains itself and drives itself around the track.

I think perhaps we should put the entrie process into numbered steps so you don't take a statement and apply it to the incorrect steps.

Lets use the following.
Step 1. Transcription DNA to RNA
Step 2. Translation RNA to amino acid
Step 3. Folding
Step 4. Protein Interactions.
Step 5. Mutation

Now self assembly occurs at step 4. Not 1, 2, or 3.

Actually, the folding would occur by itself though the ribosome helps with that process. No self-assembly occurs in step 4, and I would ask that you be very careful in what you infer from step five unless you want to start hearing 'BAM! There's a crocodile!' again.

Well lets look at the entire process. Once your confusion lifts it's easy to see that a change in the DNA(step5) will lead to a change in behaviour of the protein interactions(step 4)

I'm not confused BeGood and calling me confused does not support your argument. All it does is show that you don't have a better argument to make.

No the point is that self assemble does not necessarily lead to repetition.

Source, please?

Again the first post is the mechanism of assembly. Self assembly is a given. Proteins are chemicals and will react and interact when conditions will allow for it. This is due to the 2nd law of thermodynamics and the various charges within a protein. Proteins spontaneously interact just like when you pour salt into water and the salt disolves.
http://ull.chemistry.uakron.edu/genobc/Chapter_19

You just refuted yourself again. The first source shows the mechanism of assembly as being something other than self-assembly. At no point in the first source does anything resembling self-assembly occur. You are mis-applying the second law of thermodynamics.

As for the link you provided going to ull.chemistry.uakron.edu, I actually had to load it four times before I got the joke. I'll post the whole page here:

Proteins

That's it. One word and some links on the left. What were you trying to get out of that? Did the word self-assemble?

I'm not arguing against God. You simply asked if there is a mechanism which could have originated the bacterial flagellum.

You know what is funny? You keep saying that you aren't arguing against God and yet I've never seen you post anything anywhere on this entire forum where you took a pro-God stance. You are always taking the other side.

If you can find a mechanism that could have originated the bacterial flagellum I'd love to hear it. Thus far all I've seen is conjecture that has already been refuted by scientists such as Dr. Michael Behe and Dr. Stephen Meyer.

[Wall-dog]

I think we are all posting at the same time!

I think I see a major source of confusion. Bgood and his sources are using the term "self-assembly" to refer to the conformation (secondary, tertiary, and quaternary structure) of the protein developing after it has been produced, that is the complex three-dimensional shape that arises from the folding of the one-dimensional polymer string of amino acids; walldog and his people seem to be using the term "self-assembly" to refer to the synthesis (primary structure) of the protein from its constituent amino acids, that is the linking of individual amino acids to form the polymer.

It goes even deeper than that. Neo-darwinists including BeGood like to use the term 'self-assembly' to account for anything that occurs within the cell even if the pieces being assembled are being assembled not by just falling into place based on chemical affinities but because they are literally being picked up and carried by other parts of the cell. To truly seperate what is true 'self-assembly' from what is conjecture, ask yourself if you could get the same result without the rest of the cell. In other words, if I took the proteins that together form a flagellum and dumped them into a petri-dish, would I end up with a pile of proteins or a flagellum? This has been tried countless times including by Dr. Behe. You get a pile of proteins. No self-assembly occurs.

[sandy_mcd]

You keep saying that you aren't arguing against God and yet I've never seen you post anything anywhere on this entire forum where you took a pro-God stance. You are always taking the other side.

Bgood is a big boy and can speak for himself, but consider this quote from St Augustine (http://www.holycross.edu/departments/re ... enesis.htm This excerpt is taken from St. Augustine, the Literal Meaning of Genesis. vol. 1, Ancient Christian Writers., vol. 41. Translated and annotated by John Hammond Taylor, S.J. New York: Paulist Press, 1982.):

"Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of this world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he holds to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking non-sense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of the faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men. If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods on facts which they themselves have learnt from experience and the light of reason? Reckless and incompetent expounders of holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books. For then, to defend their utterly foolish and obviously untrue statements, they will try to call upon Holy Scripture for proof and even recite from memory many passages which they think support their position, although “they understand neither what they say nor the things about which they make assertion.” "

[BGoodForGoodSake]

I think that the problem lies in a lack of understanding of the steps of protein synthesis. When I get a chance I'll detail the process here so that we can clear that up first before continuing any discussion.

[sandy_mcd]

This is how crystals form but I would ask you to look at the protein you posted and ask yourself if it makes sense to think that chemical affinities create that kind of an irregular makeup. Self-assembly always creates regular patterns. Proteins can not be explained that way.

This is a pretty reasonable refutation of your statements above. An isolated protein is active in solution. As the concentration of urea increases, the protein loses some of its three-dimensional structure and no longer functions. As the urea is removed, the structure and function return. [Again, you are confusing molecular conformation and crystal packing.] There is no DNA present. There is no RNA present. The protein regains its complex three-dimensional structure on its own, just as virus subunits will spontaneously form viruses.

Figure 11.24. Denaturation and spontaneous renaturation of a small protein. As the urea concentration increases to 8M, the protein becomes denatured by unfolding: its activity decreases and the viscosity of the solution increases. When the urea is removed by dialysis, this small protein re-adopts its folded conformation. The activity of the protein increases back to the original level and the viscosity of the solution decreases.