Which is falsifiable?

[Wall-dog]

but you shouldn't limit your reading to only anti-evolutionist ideals if you want to learn about evolution (no matter what your intention is).

Zenith,

You are correct, and I do try to keep an open mind. Maybe the way I learned that evolution was not sound has something to do with my outlook on it. I grew up thinking that evolution was infallible. I mean, it had all but been proven. You've got all of these different really impressive skulls and diagrams and pictures and make it look really convincing. I'd read about it but only passively and when I hit an area that didn't sound logical to me I just assumed that someone had a good answer to my question and let it go.

Then I read Lee Strobel's The Case for Faith, followed by his The Case for Christ and his The Case for a Creator. That wasn't enough to convince me that ID was more than just fluffed-up propaganda, but it was enough to get me to look at Michael Behe's Darwin's Black Box, and Michael Denton's Evolution: A Theory in Crisis.

This lead to an interest in some of their other works, and Michael Behe has worked very closely with William Dembski. Hence an interest in Dembski.

The more I read about ID, the more it makes logical sense to me. And the flaws are not fluffed-over as they so often are with evolution. Many scientists just scoff at ID as 'unscientific' and say nothing but many try very hard to refute it. So there is plenty of material to read that is critical of ID. But logically I have not seen anything yet that would lead me to the conclusion that ID is not a sound theory.

When I began to read about evolution from a more critical perspective though, I found my self saying lots of things like 'Holy <insert explative>!' I was shocked that I'd been blindly following a theory in spite of some of the things I was reading. It could be that because I feel like I was bamboozled in school into believing evolution was much more sound than it really is that I am more critical of it than I should be. I hope that is not the case. I hope I do still have an open mind.

[BGoodForGoodSake]

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?

Perfect!
=)

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.

It's not simple, we were talking about the modification or creation of new proteins. This assumes that this process you just refered to already exists. Proteins do not self assemble, they require the sequencing of amino acids. Once an amino acid chain is formed, the various charges will cause it to fold and refold and begin interactions with other proteins.

In other words as long as the proteins described above exist as above changes in protein sequence will account for new features.

The "molecular machine" which unwinds the DNA is a protein which binds to start codons. Various interactions with other proteins and factors determine which genes are accessed.

A ribosome is a conglomeration of RNA and protein. It is required in RNA transcription. Prokaryotes and Mitochondria have their own types of ribosomes.

The final "machine" which does the folding is simply a protein interaction, albiet a very important one. Not all proteins require this step. It is an enzymatic action.

But that's besides the point, the mechanism we are discussing assumes that all this is in place. A change in DNA sequence does not alter this process, only the final product.

[Wall-dog]

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.

[Wall-dog]

Let me clarify my question further...

You are implying that we can get new necessary proteins as a product of protein creation. In order for that to be possible, the process of creating proteins has to be capable of making mistakes in sequencing amino acids. That's central to natural selection - replication with modification. I'd like you to illustrate how that can happen in a chemical process. Proteins don't give birth to new proteins so the replication you envision doesn't seem to occur and without replication you get no modification. Rather you would get the same proteins over and over again. And if the proteins assemble based entirely on chemical interactions, you would expect the cell to look like a salt crystal so the question of self-assembly is an important one both at the amino-acid level and at the level of proteins being delivered to the precise locations where they are needed.

[BGoodForGoodSake]

BeGood,

If it is a simple method of chemical reaction, then shouldn't the protein strands be repetitous in nature?

By what do you base this assumption? When you look at the simpler code of viruses they do look like crystals.
http://www-micro.msb.le.ac.uk/109/structure.html
There are many genes encoded in the DNA of living organisms. So you shouldn't expect repetition in the overall cell, although in many cases this is what you get.
The bacterial flagellum tail for instance
http://www.aip.org/png/2002/174.htm

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.

Salt crystals are formed from ionic bonds between sodium and chlorine, there isn't much room for variation.

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?

These are two different things. You are now talking about DNA sequence.

We were discussing how amino acid chains, once formed, fold in on themselves.

And why would the sequence stop before all of the amino acids available were used?

There is a stop codon which limits the length of the mRNA.
http://www.biochem.northwestern.edu/hol ... codon.html

Also natural systems have built in feedback loops which prevent loops from going out of control. Think of these as sentinal controlled loops.

Negative Feedback
http://en.wikipedia.org/wiki/Negative_feedback

You don't get a genetic message with self-organization. You get a repetitive pattern.

Again you're confusing protein systhesis with genetics and heredity.

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

Changes in protein structure can occur when there is a change in DNA.

Studying diseases and how malfuntions in the system lead to the symptoms might help you to understand better.
http://www.sciencedaily.com/releases/20 ... 130917.htm
http://www.bmb.psu.edu/faculty/koc/koc.html

[BGoodForGoodSake]

Let me clarify my question further...

You are implying that we can get new necessary proteins as a product of protein creation.

No, I stated clearly changes in DNA will lead to new proteins.

In order for that to be possible, the process of creating proteins has to be capable of making mistakes in sequencing amino acids.

Again no, the change occurs in the code. In the DNA.

And if the proteins assemble based entirely on chemical interactions, you would expect the cell to look like a salt crystal so the question of self-assembly is an important one both at the amino-acid level and at the level of proteins being delivered to the precise locations where they are needed.

Amino acid chain are based on mRNA which in turn is based on DNA. Each gene has a different sequence, thus a different resulting amino acid chain.
http://en.wikipedia.org/wiki/Protein_folding

Each amino acid is defferent, and has different affinities and charges due to their chemical structure. By linking them together the protein will fold in on it self and certain areas of the protein will be reactive. This is refered to as the active site.

[Wall-dog]

By what do you base this assumption? When you look at the simpler code of viruses they do look like crystals.
http://www-micro.msb.le.ac.uk/109/structure.html

Perhaps you should read your sources before you post links:

Matrix Proteins: These are internal virion proteins whose function is effectively to link the internal nucleocapsid assembly

Glycoproteins: These are transmembrane proteins, anchored to the membrane by a hydrophobic domain & can be subdivided into two types, by their function:

External Glycoproteins - Anchored in the envelope by a single transmembrane domain. Most of the structure of the protein is on the outside of the membrane, with a relatively short internal tail. Often individual monomers associate to form the 'spikes' visible on the surface of many enveloped viruses in the electron microscope. Such proteins are the major antigens of enveloped viruses.

Transport Channels - This class of proteins contains multiple hydrophobic transmembrane domains, forming a protein-lined channel through the envelope, which enables the virus to alter the permeability of the membrane, e.g. ion-channels.

That's not the description of a crystal. Just because some viruses may superficially look like crystals doesn't mean they form like them. A virus is nothing like a crystal. Your own source very clearly shows that. Or maybe you were hoping I'd only look at the pictures...

There are many genes encoded in the DNA of living organisms. So you shouldn't expect repetition in the overall cell, although in many cases this is what you get.
The bacterial flagellum tail for instance
http://www.aip.org/png/2002/174.htm

This source does not support you either.

Bacteria swim in viscous liquid environments by rotating helical propellers called flagella.

The bacterial flagellum is a nanomachine made of about 25 different proteins, each of them in multiple copies ranging from a few to tens of thousands. It is constructed by self-assembly of these large numbers of proteins, each into a different part that exerts a different function, such as a rotary motor, bushing, drive shaft, rotation-switch regulator, universal joint, helical propeller, and rotary promoter for self-assembly.

Flagellar proteins are synthesized within the cell body and transported through a long, narrow central channel in the flagellum to its distal (outer) end, where they self-assemble to construct complex nano-scale structures efficiently, with the help of the flagellar cap as the assembly promoter. The rotary motor, with a diameter of only 30 to 40 nm, drives the rotation of the flagellum at around 300 Hz, at a power level of 10-16 W with energy conversion efficiency close to 100 %.

The structural designs and functional mechanisms to be revealed in the complex machinery of the bacterial flagellum could provide many novel technologies that would become a basis for future nanotechnology, from which we should be able to find many useful applications.

Could you please stop making statements and then posting links to websites that don't support your contentions? You should only post links if the linked material says what you claim it says.

But I think I've gotten what I was looking for. Proteins don't just form themselves. You need DNA. And what is DNA? A library of designs for creating proteins.

What tells the proteins where to go after they are formed?

No, I stated clearly changes in DNA will lead to new proteins.

How does the DNA change? For that matter, how do you explain the existence of DNA?

[sandy_mcd]

Let me clarify my question further... 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. ... And if the proteins assemble based entirely on chemical interactions, you would expect the cell to look like a salt crystal

1) You seem to be confusing molecular conformation with crystal symmetry.
a) Elements combine to form molecules or ions. Many of these are flexible and can adopt many different (essentially infinite for some large molecules) geometric arrangements which are very similar in energy.
b) Crystals are a symmetric arrangement of molecules or ions. A basic motif is simply repeated by translation in three dimensions as you say above. ["It has been said the the beauty of crystals lies in the planeness of their faces."] There are only 230 different possible ways of arranging entities in a crystal; not all of these are known by example.
A protein is a long stringy molecule. Like a garden hose or extension cord, its natural state is not stretched out but jumbled together. Unlike the former, a protein however (usually?) adopts only one specific configuration. Some proteins can self-assemble, even in vitro, others need the help of chaperones. [This is an area of current research and is probably more complicated than you imagine.] It is this conformation that Bgood is referring to, not the packing of proteins in crystals as in your salt analogy. Proteins, by the way, can only crystallize in one of 65 different ways.
2) Salt is a simple substance. Since it is only sodium and chloride ions, the individual parts (Na+ and Cl-) cannot adopt different conformations the way a much larger molecule with many atoms like a protein can.
3) Salt has strong interactions. The electrostatic forces between ions in a salt crystal are much stronger than the weaker hydrogen bond, dipole, van der Waals, and other forces which determine the molecular and crystal conformations of proteins. The chemical interactions in salt are quite different and vastly simpler than those within a protein molecule.

Here is a picture of a small rigid benzene molecule with 6 carbons and 6 hydrogens,

It can only have one conformation.

Here is a hexane molecule with 6 carbons and 14 hydrogens which can adopt many different conformations
Here is another view of the hexane molecule; the molecule can be rotated about bonds (illustrated by the little cylinders) to generate different geometric onformations


A protein is a much larger moleculer. Here is a schematic of the 3-dimensional structure of a protein


So in short, the expectation that proteins should resemble salt crystals is seen to be unreasonable.

[sandy_mcd]

Perhaps you should read your sources before you post links:That's not the description of a crystal. Just because some viruses may superficially look like crystals doesn't mean they form like them. A virus is nothing like a crystal. Your own source very clearly shows that. Or maybe you were hoping I'd only look at the pictures...

I'm not quite sure I agree with or even understand what Bgood was saying, but there is some semblance between viruses and crystals. Crystals are a symmetric arrangement of smaller subunits and according to Bgood's source (you have to read all of it)

Francis Crick & James Watson (1956), were the first to suggest that virus capsids are composed of numerous identical protein sub-units arranged either in helical or cubic (=icosahedral) symmetry.
In order to construct a capsid from repeated subunits, a virus must 'know the rules' which dictate how these are arranged. For an icosahedron, the rules are based on the rotational symmetry of the solid, which is known as 2-3-5 symmetry:
* An axis of two-fold rotational symmetry through the centre of each edge
* An axis of three-fold rotational symmetry through the centre of each face
* An axis of five-fold rotational symmetry through the centre of each corner (vertex)

The description is quite similar to the arrangement of crystals. [And note the names of the researchers: presumably the same Crick and Watson of DNA crystallographic fame.] [Of course, as I am sure you are well aware, classic crystals cannot have 5-fold rotation axes. But the recent field of quasi-crystals is based on materials which do possess 5-fold symmetry.]

Here's another interesting quote from the same reference:

In 1957, Fraenkel-Conrat & Williams showed that when mixtures of purified tobacco mosaic virus (TMV) RNA & coat protein were incubated together, virus particles formed. The discovery that virus particles could form spontaneously from purified subunits without any extraneous information indicated that the particle was in the free energy minimum state & was therefore the favoured structure of the components. This stability is an important feature of the virus particle.

So here is a complex structure which forms spontaneously.

[sandy_mcd]

And if the proteins assemble based entirely on chemical interactions, you would expect the cell to look like a salt crystal

Oops, my bad. I see that the second quote of yours is not directly related. I thought you were still on the topic of protein self-assembly. But you want a cell to look like a salt crystal. [Actually that's worse than my original interpretation.] Cells contain water and thousands of different substances. Why should they resemble crystals? In fact, cells contain a fair amount of salt. But the salt is not in the form of crystals either; it is dissolved in solution as ions.
People who want to get crystal structures of proteins first have to isolate the proteins and grow crystals. This is a complicated process which can take years and often doesn't succeed. So either people who study protein structures are totally lacking in lab skills or else assembling proteins into a crystalline array is an extremely difficult task.

[Wall-dog]

Sandy,

It goes deeper than that. BeGood is trying to argue that flagella self-assemble. He's trying to make viruses look like crystals because crystals do self-assemble and while his link does show a crystal-like external appearance for viruses, the similarity is superficial at best. BeGood's first reference clearly shows that this similarity is superficial, so I stand by what I said about his reference not supporting his conclusion.

I haven't posted a rebuttal yet. I want to clarify BeGood's argument first so we can develop some common-ground as a basis for further discussion. BeGood is arguing that flagella self-assemble. Rather than have him say that I don't know what I am talking about as the basis for that, I want to make sure that the basics of his argument are firmly established and then I'll rebutt whatever is left. Otherwise we'll just end up arguing in circles as we have done in the past which invariably leads to negativity and ad-hominum attacks.

I'm also starting to pay much more attention to the what BeGood's sources actually say since he posts select details from his sources and then makes his own conclusions rather than posting the conclusions and then linking back so people can look at where the conclusions came from. I want to make sure that BeGood's references say what he says they say. It's just too easy to take data out of context or to make conclusions that are not really supportable and when you post a link it implies that those conclusions are supported by the scientists who conducted the study.

Really I think that BeGood's argument here will fall on it's own even without rebuttal. I haven't seen any scientist ever say that flagellum are the result of self-assembly in the manner BeGood suggests.

[BGoodForGoodSake]

Sandy,

It goes deeper than that. BeGood is trying to argue that flagella self-assemble. He's trying to make viruses look like crystals because crystals do self-assemble and while his link does show a crystal-like external appearance for viruses, the similarity is superficial at best. BeGood's first reference clearly shows that this similarity is superficial, so I stand by what I said about his reference not supporting his conclusion.

Why are you so frustrating?

I am not trying to show viruses are like crystals. You stated the following.

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.

So I stated simply that proteins have much more complex interactions than ionic compounds. And as a side not I pointed you to how some viral structures are a result of repeating protein formation which ressemble crystals. Forgive me for thinking you would be able to differentiate illustration from disputation. I am not trying to argue with you here, I am only adding facts which I thought were applicable to the discussion.

Due to past discussion I refuse to argue with you.

[BGoodForGoodSake]

I haven't posted a rebuttal yet. I want to clarify BeGood's argument first so we can develop some common-ground as a basis for further discussion. BeGood is arguing that flagella self-assemble. Rather than have him say that I don't know what I am talking about as the basis for that, I want to make sure that the basics of his argument are firmly established and then I'll rebutt whatever is left.

I am not arguing with you here! I'm just providing references. Cells reproduce on their own, this includes bacteria, and this includes bacterial components such as the flagella. Do you disagree?

I'm also starting to pay much more attention to the what BeGood's sources actually say since he posts select details from his sources and then makes his own conclusions rather than posting the conclusions and then linking back so people can look at where the conclusions came from. I want to make sure that BeGood's references say what he says they say. It's just too easy to take data out of context or to make conclusions that are not really supportable and when you post a link it implies that those conclusions are supported by the scientists who conducted the study.

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

Really I think that BeGood's argument here will fall on it's own even without rebuttal. I haven't seen any scientist ever say that flagellum are the result of self-assembly in the manner BeGood suggests.

What manner are we talking about here? Perhaps you misunderstood? Please explain your understanding of my "argument" so that I might clarify or correct myself as necessary.

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

Here is a link to wikipedia which explicitly states this.
http://en.wikipedia.org/wiki/Flagellum
Although I don't normally recommend this sort of source I put it here because this is the type of source you seem to be requesting.

As a final note to think that chemical reaction can only lead to simple formations like salt crystals is to ignore the fields of organic chemistry and materials science.

A chemical reaction can create complex molecules from teflon and rayon to hemoglobin, and insulin.

[Wall-dog]

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.

[sandy_mcd]

BeGood is trying to argue that flagella self-assemble. ...
This source [http://www.aip.org/png/2002/174.htm] does not support you either.

Self-Assembly of Bacterial Flagella
The bacterial flagellum is ... constructed by self-assembly of these large numbers of proteins, each into a different part that exerts a different function, such as a rotary motor, bushing, drive shaft, rotation-switch regulator, universal joint, helical propeller, and rotary promoter for self-assembly.

I realize Bgood and I aren't the sharpest tacks in the road, but even I can see why he might think this site supports his argument.