Tuesday, September 27, 2005
Additional Mechanisms of Inheritance
This is mostly a literature review, but Alex Williams has a nice summary of additional modes of inheritance that has surfaced, and has applied some of Gitt's semantic information theory to it. The paper is Inheritance of Biological Information Part I (TJ 19[2] 29-35). Part II is available, but I haven't read it yet.
The main points are as follows:
He points out:
He then explains the five parts of Gitt information theory: statistics, semantics, syntax, pragmatics, and apobetics. Though I have not read Gitt's book, it looks like Williams gave semantics waaay too small of a role. Within computer science, semantics is much more all-encompassing than Williams mentions. What Williams says is true, but there is indeed much more to be said.
He then concludes with Barbieri's semantic view of biology (also available in dead tree format). I have not heard of this work before, but since it is online I will hopefully have the ability to do so shortly. Williams sums up Barbieri as saying that:
I agreed with Williams overall in principle, but I thought there were some things he overlooked.
First of all, he seemed to be trying to fit the changing nature of the genome with the semi-static nature of life, and therefore proposed that the genome is completely changeable while it is the structure of the cell which provides the stasis. This may in fact be true, but it is irrelevant. Codal systems are codal systems, whether they exist within the genome, or within the structure of the cell itself. I don't doubt that we will find parts of cellular structure which will change, too. From the point-of-view of a computer programmer, all information is essentially on equal par. In order for a program to work, you must have a base system, which can then be fitted with attachments. The base system, however it is coded, must necessarily have little change in order for the rest of the system to change in an orderly and consistent manner. In computer programs, both the changing and unchanging parts are stored on the same system (i.e. - program and data). Therefore, saying "the unchanging part is here and the changing part is here" is rather irrelevant and will probably be disproved in short order. The fact is simply that the unchanging part is more important than the changing part, and in fact is specifically what allows the changing parts to change in an orderly fashion.
Kind of along with this, there are many aspects of program semantics that are more than just the mapping of nucleotide sets to amino acids. A good look at type theory in computer science will show a beginning of the semantic information that must be accounted for in any codal system.
However, I do think that his main point -- we are only scratching the surface of inheritance and control of cellular structures, is quite correct.
There was also a note in there about an article discussing drastic chromosomal structure changes in rock hopper wallabies (TJ 17[1] 19-21), which should be of interest.
The main points are as follows:
- the more we study cells, the more complex their biochemistry becomes
- while genes are inherited, the cells themselves have control over genetic expression through epigenetics
- this implies that DNA is more-or-less a "library" of information to be used by cellular processes as needed
- the cell, and not the genes, control inheritance
- cell stability in the face of large genomic change is readily viewable in the bacterial world
- transplanted membranes can be inherited even when transplanted to cells with different DNA
He points out:
For example, a study of the bacterium Escherichia coli over 10,000 generations found that at the end, 'almost every individual had a different genetic fingerprint', yet they were still Escherichia coli. Only if the cell is in control can we explain these observations.
He then explains the five parts of Gitt information theory: statistics, semantics, syntax, pragmatics, and apobetics. Though I have not read Gitt's book, it looks like Williams gave semantics waaay too small of a role. Within computer science, semantics is much more all-encompassing than Williams mentions. What Williams says is true, but there is indeed much more to be said.
He then concludes with Barbieri's semantic view of biology (also available in dead tree format). I have not heard of this work before, but since it is online I will hopefully have the ability to do so shortly. Williams sums up Barbieri as saying that:
- The cell is fundamentally an epigenetic, rather than a genetic, system (the cell is in charge, not the genes)
- Genes provide genetic memories for the cell, but there are other memories, some of which are waiting to be discovered, which participate in cell life, including many aspects of embryological development
- Each memory has a semantic code established
I agreed with Williams overall in principle, but I thought there were some things he overlooked.
First of all, he seemed to be trying to fit the changing nature of the genome with the semi-static nature of life, and therefore proposed that the genome is completely changeable while it is the structure of the cell which provides the stasis. This may in fact be true, but it is irrelevant. Codal systems are codal systems, whether they exist within the genome, or within the structure of the cell itself. I don't doubt that we will find parts of cellular structure which will change, too. From the point-of-view of a computer programmer, all information is essentially on equal par. In order for a program to work, you must have a base system, which can then be fitted with attachments. The base system, however it is coded, must necessarily have little change in order for the rest of the system to change in an orderly and consistent manner. In computer programs, both the changing and unchanging parts are stored on the same system (i.e. - program and data). Therefore, saying "the unchanging part is here and the changing part is here" is rather irrelevant and will probably be disproved in short order. The fact is simply that the unchanging part is more important than the changing part, and in fact is specifically what allows the changing parts to change in an orderly fashion.
Kind of along with this, there are many aspects of program semantics that are more than just the mapping of nucleotide sets to amino acids. A good look at type theory in computer science will show a beginning of the semantic information that must be accounted for in any codal system.
However, I do think that his main point -- we are only scratching the surface of inheritance and control of cellular structures, is quite correct.
There was also a note in there about an article discussing drastic chromosomal structure changes in rock hopper wallabies (TJ 17[1] 19-21), which should be of interest.
Permanent Link posted by crevo @ 5:38 AM 
