Frêsh Fish

Wednesday, July 23, 2014

A Lot Is Missing

If Life is a groping in the dark, doing this and that in random fashions, the evidence for this is missing. There should be evidence of more diversity in the biochemical - the cell and its components -record. Across the spectrum there is no from the ground up. We have not been able to provide evidence of a chain of major transitions from one biochemical way of doing something to another. No - from simple to complex. Things seem to have just arrived, rather complete. All life shares the same biochemical transmission mechanisms. All of the simpler ways of doing things are missing. It is as if many organs and functions arrived complete.

An argument can be made that when a "better" way of doing something evolved that it completely replaced the "older" more "simplistic" way. This could happen in a very restrictive environment where resources are very scare. But primitive Earth had an abundance of space and resources.

Another puzzle is initially how simple the building blocks of Life are. Four letters taken 3 at a time.

When you first start to look at genetics it is amazing that DNA is composed of just 4 nucleotides. It seems that there just as easily could be 10 or 15 or even 1,000,000,000. I do not know enough about the nucleotides - C,A,T,G - to appreciate why 4 and only 4 would be sufficient and desirable. All DNA is composed of long linear sequences of 4 different nucleotides. Why not more nucleotides? Why not less? I suspect 2 nucleotides would be the minimum.

4 nucleotides is probably a minimum. With 2 nucleotides the amount of genetic material for many life forms would exceed the capacity of its cells. There are biochemical restrictions on how large a cell can be.

These four nucleotides are evaluated 3 nucleotides at a time - condom - to yield what has been defined to be amino acids. Again why not 10, or 7 or 53?

In the beginning 4 and then 3 and then 20 - very intellectually seductive - so simple that even a ape could probably be trained to do it. For sure a caveman.

We go 4, 3, 20 and then POW!! 25,000 proteins squished and folded in a gazillion ways.

Tuesday, July 22, 2014

Lehninger - Principles of Biochemistry

I am starting to read the above. Lots and lots. The book must weight +10 lbs.
Looked at the diagrams for the nucleic acids - CATG - Cytosine, Adenine, Thymine, Guanin - and for RNA - U - Uracil. Nucleic acids bond with each other in special ways. Adenine bonds with Thymine. Cytosine bonds with Guanin. In RNA Uracil replaces Thymine and bonds with Adenine.

C and T are the pyrimidine bases and look less complex than the purine bases A and G. I say less complex because the diagrams for C and T look less involved.

I know very little organic chemistry, but visual speculation suggests that perhaps C and T and maybe U were pushed together to form A and G.

We are invoking a principle of manifestation, that stuffs evolves from simple to complex. Just as with scientific lore that hydrogen and helium came first and then in time the heavier elements.

The thought being pursed is why we need 4 or 5 letters in our genetic alphabet to engender life.

2 letters can yield fidelity. Can anything interesting be done with 2 letters.

DNA more than Information

There is a very strong nexus between the terms DNA and information. If you encounter the pairing enough times you forget that this information does something. To better understand the need for letters you have to appreciate what the information in DNA does. The information in DNA - amino acids - arrange energy packets in certain ways.

The Genetic Code is not as abstract as our alphabet and letters and words. The arrangement of the base pairs has meaning in and of itself.

Next - look at combinations of amino acids that make up proteins

And here in lies the rub.

Description for Figure 1-2 - "Diverse lining organisms share common chemical features. Birds, beasts, plants, and soil microorganisms share, with humans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors."

With our sole reliance on random processes and natural selections, I would expect more diversity. How is it that we do not find life anywhere using a different genetic arrangement?

There is a difference here between the theory of evolution with random mutation and natural selection and the evolution of life. The evolution of life pertains to how existing things combined. There is an inherent way in which things combine - Lehninger refers to this as "the molecular logic of life".