Friday, March 17, 2006

Back to the Golf Course.



(Previous Post)

Some readers did not "get" my golf course analogy. I find it helpful to clarify my thinking so I will have another go to explain it.....









Imagine a 2-dimensional protein gel for a particular protein.

Imagine that a change in its amino acid sequence will change it’s position on the gel.



Thus for a 150 amino acid protein there are 20^150 positions spread out to cover a wide area on the gel.

Then imagine for each variant of that protein you can measure its “selective advantage” for a particular organism.

Then imagine you can plot these selective advantages on the 2-Dimensional gel to give a “contour” map of the protein’s functionality.



Then imagine that the current structure and function of the protein is the hole in a golf course and the contour map that you have is the terrain of the golf course with the selective advantages going downwards towards the hole.

As I said in this post the two models of protein function origin look for different contour maps for protein functionality.

The RMNS model would hope to find a large catchment area for protein functionality. The ID model would hope to find a sharp distinction between function and no function with relatively few variants having a function.

To understand the IC argument you have to imagine several of these golf courses being played independently with the requirement that the protein golf ball on each golf course arrives in its respective hole at the same time.

6 Comments:

Blogger beervolcano said...

Thus for a 150 amino acid protein there are 150 ^ 20 positions spread out to cover a wide area on the gel.

Do you mean there are 150^20 different peptides, each with a unique amino acid sequence?

Maybe I'm wrong, but wouldn't it be something more like 20^150 ?

That's something like 10^195, which means that any one amino acid sequence has a 1 in 10^195 chance in occuring (based on a completely random amino acid selection.) This is far below (above?) William Dembski's Explanatory Filter of 10^150, which means, to him, that any one of those amino acid sequences arising is practically impossible.


This sounds like it's beside the point, but it's not entirely.

Anyway, I think I see what you are getting at. It's still not the best analogy. To be more accurate to biology, any golf course would have different types of holes each having a different score and there are many many many golf balls all on the same course. Sometimes a hole (function) pops up where none was before, depending on what other holes may or may not be there.

I don't think you meant to have two different golf courses in your analogy. There is only one golf course (biology). There are many many many holes on this golf course and many many many many golf balls.

Regardless of the topology of the golf course, for there to be functioning biological structures and processes, balls have to fall into the holes.

Your saying that to have a bacterial flagellum, there needs to be some kind of goofy golf hole at the golf course. To score at this hole, the golfer would have to shoot multiple balls into multiple holes simultaneously. And that to have eubacterial flagella, archeal flagella, and eukaryotic flagella, you need to perform this feat 3 times with three different arranements of holes? Since the ID model has a very Intelligent (omnipotent?) Designer indeed, this is no problem for it.

What this analogy doesn't take into account is that to make the shot at the goofy golf hole, the golfer doesn't need to sink the multiple balls simultaneously.

Wait, maybe you are saying that the hole is the unique protein, and when the ball (which represents what?) lands in the hole, that particular protein is selected for?

I don't know, the whole thing is confusing.

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Let's just look at it this way.

There are many examples of channel proteins that bridge cell membranes and act as little gates that allow selective transport of nutrients in and waste out, or to maintain pH gradients. Some bacteria have channel proteins that gate protons out of their cells when they are produced by the cell's metabolism. If you have this totally functional structure in place, then all you would need is for a random distribution of occasional mutations to this structure. A mutation in the structure wouldn't necessarily shut down the function entirely. Some might cause cell death and would not be passed on. But, one mutated pore (all it takes is one) would have a mutation that caused the outer part to undergo a rotation when channelling protons out of the cell. If this rotation leads to motility, then that one bacterium has an advantage over others , which it will pass on to it's progeny. If it doesn't have a distinct advantage, but it still didn't kill the bacterium, then the mutation is functionally neutral and will still be passed on to progeny. Eventually subsequent mutations in said progeny might produce some advantage, such as motility, and those would survive and reproduce more often. Thank God there are bazillions of said progeny to choose from.

Since there are analogous but not homologous structures in archea as well as eukaryotes, then this sort of thing doesn't seem so far fetched. What sounds far fethced (to anyone without preconceived notions about God and how he might meddle with His Creation) is that an omnipotent being put those structures onto microbes to give them a survival advantage over other microbes. OR maybe an ancient alien put them there for biological warfare and they are still present because they gave the microbes a selective advantage. These are extraordinary claims.

9:56 pm  
Blogger Andrew Rowell said...

You are correct of course 20^150.

10:42 pm  
Blogger Ed Darrell said...

Been awfully quiet here for a couple of weeks . . . S'up?

4:26 am  
Anonymous Hipath said...

My brain hurts from reading that

11:33 am  
Blogger Andrew Rowell said...

Hipath,

Apologies for brain pain,

It is an upside down fitness lanscape.

1:05 pm  
Anonymous Anonymous said...

If there are 20^150 possible 150 peptide proteins, aren't more than one of them good for something? If we're shooting for useful and random, shouldn't we also consider substrings of these 20^150 combinations that are useful proteins and might promote later combination? It just seems like the topography may be sharp, but there should also be a lot more than one hole.

3:02 pm  

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