The Levinthal Paradox 2

In the previous post where I introduced the Levinthal Paradox I mentioned the following http:
http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olprotfold.html

If any of you went there and checked out the information, you would find the following:

"Lubert Stryer (in his classic Biochemistry text), shows a way out of this dilemma by using an analogy of a monkey sitting at a typewriter, and typing this line out of Hamlet: "Me thinks it is like a weasel." Random typing would produce that line after 10⁴⁰ keystrokes on average, but if the correct letters were maintained, the number of keystrokes would be in the realm of a few thousand. Proteins could fold more quickly if they retain native-like intermediates along the way."

This a quote from a university level biochemistry text. Did you notice anything completely lacking in the above analogy? How about 3 or 4 things? If you didn't don't worry. I didn't either, until I began thinking about and analyzing this "way out of this dilemma".

First, "the way out of this dilemma" requires a monkey.A monkey is a very complex living organism that contains 100's, if not 1000's of proteins. (As well as a few hundred other complex organic molecules. Not to mention organ systems.) Where did they get a monkey? How did all of its proteins form, when there is not enough time in the age of the whole universe for ONE, one hundred amino acid protein to form?

Secondly, it requires a typewriter.Some of you reading this may not even know what that is ;-) , but believe me, it is a relatively complex piece of office machinery. They require hundreds of exactly machined and correctly assembled parts. Even if it is only a pre-electric, manual one.

Where did a typewriter come from? What unguided, completely random forces caused it to suddenly appear out of no where? What is the mathematical probability of that happening? And what miraculous force keeps the keys from jamming?

Thirdly, the author tells us "if the correct letters were maintained, the number of keystrokes would be in the realm of a few thousand. " Although this sounds logical, this one, short statement is full of difficulties.

1)The sentence "Me thinks it is like a weasel." requires the existence of a system of communication called "English". In this short sentence there is vocabulary, grammar and syntax that are peculiar to the English language.

Where did this complex communication system come from? That is to say, WHO decided what the correct letters are anyway?

2) The amino acid-protein structure is not a 2 dimensional words on paper construction. Proteins have 3 different levels of structure individually, and proteins interacting with each other form a fourth level of structure. http://en.wikipedia.org/wiki/Proteins#Structure_of_protein
http://en.wikipedia.org/wiki/Protein_structure#Levels_of_protein_structure

The fourth level could possibly be ignored for a solitary, one hundred amino acid protein. However, there is seldom if ever a solitary, one hundred amino acid protein floating in an isolated condition.

You are not just typing random letters and keeping the ones that fit a preselected sentence.Every level of amino acid sequence-protein structure is influenced by the previous level of structure.
http://en.wikipedia.org/wiki/Protein_structure#Protein_folding

When you rearrange "letters" you affect the protein on 3 different levels. And ripping amino acids out to replace them with new ones would totally change the configuration of the previous structure. And therefore, there would be no advantage of keeping the ones "that fit"...none of them would fit in the unintelligible sentence.

Use a poem for an example. It would be as if the letters in a sentence not only affected vocabulary, grammar and syntax, and the length and number of lines, but also the individual letters had an attraction on all the other letters that pulled the poem into a geometric shape, a cube, for example. Changing ONE LETTER would change the entire geometric shape...and in many cases make it entirely worthless.

As a note, the structure of proteins is much more complex than a cube.
http://en.wikipedia.org/wiki/Image:Protein-structure.png

Wikipedia also tells us "A unique polypeptide may have more than one stable folded conformation, which could have a different biological activity, but usually, only one conformation is considered to be the active, or native conformation."
http://en.wikipedia.org/wiki/Protein_structure#Protein_folding (emphasis added)

The "correct" protein in the wrong place would be useless. An incorrectly assembled "protein" in the right place would be the same.


And LAST but not least, their sentence is no where near 100 characters. Even IF you could use a 2 dimensional sentence to represent a protein, their sentence counting the spaces and the period is only 30 characters. Their calculation of the necessary keystrokes should be multiplied by 3.3, just to get it approximately correct. (Not to mention the fact that the sentence requires a capital "m" to make it correct...but I won't even go into that...)

Me thinks their "way out of this dilemma" is a weasel...