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Author
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Topic: Genetic Information
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Micah Sparacio
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Member # 6
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posted 06. March 2003 13:29
I'd like to start this brainstorm by asking a simple question in the hopes of learning from the more informed:
1. What is genetic information?
Here are some follow up questions:
2. Does genetic material have information content?
3. What sort of information does genetic material contain?
4. In James Shapiro's chat, he mentioned that there is information in the cell that is not contained in the nucleus. What role does this information play in cellular functioning?
5. What function does genetic information serve: is it merely algorithmic information that needs to be interpreted or does the genetic information do "stuff" on its own?
6. Finally, does the term "genetic information" rely on a bad analogy?
[Added to post in response to a request for "positive hypotheses"]
Seeing that I'm not a biologist, I may not have all that much to add to the thread, and indeed, all that I may have to add is probably front-loaded into my questions. However, speaking as a philosopher with much to learn:
My position is that a view of the organism as the realization of an "information molecule" is way off course. I've also been intrigued by the way in which Barbara McClintock approached biology in the midst of genetic "information" reductionism. McClintock and her disciples (such as Shapiro) still used the terminology of information, but recognized that genetic information can be thought of as an organ of the organism, not the source of the organism itself. The organism is somewhat in control of its genetic information rather than the genetic information being in control of the organism.
What I'm trying to get at is this: there is a pervasive sense in which DNA and genetic information are thought of as a programming "code", isolated (and in many senses superior) to the organism. My view is that the genetic code may be a toolkit to be used by the organism. In other words, I take an "organism first" view of biology (I think that Michael Denton may take a similar view but from a different angle).
Taking this a bit further, I wonder if our fascination with information technology, and the parallel development of genetic discoveries and computing machines led to an oversimplified view of genetic material as mere information in much the same way that a strict (and very flawed) analogy was made between brains and von neumann computers.
[ 06. March 2003, 14:46: Message edited by: Micah Sparacio ]
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Evan
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Member # 164
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posted 06. March 2003 13:54
Not to be difficult, but my understanding is that the general sentiment is for opening posts to do more than ask questions, but rather to advance ideas, however speculative, for us to brainstorm about.
So, catching the ball and immediately throwing it back to Micah, I ask, what are your answers to these questions? ![[Smile]](smile.gif)
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Micah Sparacio
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Member # 6
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posted 06. March 2003 14:10
My apologies for not following Brainstorms rules.
I'll go back and make some adjustments, but still, I think that the moderators should consider changing the rules a bit...don't you;-) Do brainstorms not sometimes begin with legitimate questions?
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Rex Kerr
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Member # 632
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posted 06. March 2003 19:10
I'm afraid the question is hard to answer, because I don't know what you mean by "information".
So in answer to (6), it is perhaps a bad analogy, or at least imprecise.
Working backwards, I'd suggest to (5) that if we interpret information in the Shannon sense, the genetic information doesn't do stuff on its own, for the most part anyway, but needs to be decoded into a functional molecule (e.g. protein). But really, what do you mean by function? The information has a function relative to the transmission of a set of characteristics from parent to offspring.
(4) There is mitochondrial DNA which is essential for function of mitochondria (and the cell's supply of energy).
(3) What types of information exist? It's hard to classify genetic material into one of those types if you don't know what classes you have to choose from.
(2) DNA has information content in the context of transcription and translation machinery as a channel with all possible sequences as input and all possible proteins as output.
(1) I don't know. I don't ever think about "genetic information" on its own. In the context of a particular question, one can be interested in the information content of a piece of DNA. But what that is varies widely depending on whether you want to know its melting temperature, the sequence of amino acids that could be transcribed/translated from it, the transcription factors that could bind to it, the impact that its loss would have on the phenotype of an organism, and so on.
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Nel
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Member # 614
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posted 10. March 2003 21:17
I'll try to take a stab at one of these
1. What is genetic information?
Can I propose as a definition, genetic information is a component of a molecular system which controls the system through a decoding device that is able to decode the instructions encoded in that component? Adapting from Loewenstein,
DNA = source of information
transcription = encoder
messenger RNA = message
tranlsation machinery/
hormone synthesis/ = transmitter
release apparatus
hormone (or whatever) = signal
DNA-headgate multiplex = decoder or receiver
DNA polymerase = user
This may a bit too reductionist for ID.
[ 10. March 2003, 23:12: Message edited by: Nelson_Alonso ]
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Frances
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Member # 169
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posted 11. March 2003 00:47
The most succesful definition of information and genetics so far seems to be Shannon information. Shannon information is basically the decrease in entropy.
I believe that concepts of mutual information can be used to show how information can increase in an open system which per definition has a non-zero mutual information relationship.
Tom Schneider has been one of the first to apply the concept of Shannon information to the genome and quite succesfully as well.
Schneider applied the concept to binding sites on nucleotide sequences
quote:
Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information ( Rsequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information ( Rfrequency) that would be required to locate the sites given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements.
The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between Rsequence and Rfrequencysuggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome.
His application of information theoretical concepts led to interesting predictions
quote:
DNA sequences to which the OxyR protein binds under oxidizing conditions were analyzed by the sequence logo method, a quantitative graphic technique based on information theory. A sequence logo shows both the sequence conservation and the frequencies of bases at each position in a site. Unlike the consensus sequence, the sequence logo analysis revealed that OxyR should bind to four major grooves of DNA. This was later confirmed by experiments. Detailed interpretation of the sequence logo also allowed the prediction of likely major and minor groove OxyR-DNA base contacts, consistent with available experimental results. Because the sequence logo shows the original base frequencies in a clear, easily interpreted graphic that does not distort the data, highly refined analysis of binding site contacts becomes easy. Not only can these methods be applied to any DNA sequence binding site, they can also be applied to sites on RNA and proteins.
Source: Reading of DNA Sequence Logos: Prediction of Major Groove Binding by Information Theory
Thomas D. Schneider
The most interesting application of this concept can be found in both Evolution of Biological Information
Thomas D. Schneider, Nucleic Acids Res, 28(14): 2794-2799, 2000 and Evolution of Biological Complexity Christoph Adami (Caltech), Charles Ofria (MSU), Travis C. Collier (UCLA) Proc. Nat. Acad. Sci (USA) 97 (2000) 4463.
Adami makes the link between information and the environment which I believe is instrumental in showing how information can increase.
quote:
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that because natural selection forces genomes to behave as a natural ``Maxwell Demon'', within a fixed environment genomic complexity is forced to increase.
Adami has applied some of the concepts in "Selective pressures on genomes in molecular evolution" by Charles Ofria (Michigan State University), Christoph Adami (JPL, Caltech), Travis C. Collier (UCLA) in Quantum Physics; Biological Physics; Neural and Evolutionary Computing; Adaptation and Self-Organizing Systems
quote:
Recently Adami and Cerf (2000) argued that a genomic complexity can be defined rigorously within standard information theory as the information the genome of an organism contains about its environment. Adami et al. (2000) then demonstrated how this complexity must generally increase in simple evolving systems. Here, we focus on the selective pressures of molecular
evolution and how they contribute to the evolution of robust and complex structures. Thus, information theory can be a tool that ties together evolutionary biology and molecular biology.
In What is Complexity Adami addresses some of the questions Micah seems to be interested in. Adami looks at various forms of complexity. Adami also addresses the concept of natural selection and its impact on the information/complexity content of the genome by showing that information tends to increase through selection which acts like a filter.
In the following paper A Theory of Pragmatic Information and Its Application to the Quasi-species Model of Biological Evolution Edward Weinberger applies some of these concepts. Interestingly enough he also addresses a concept called 'agency'
[ 11. March 2003, 01:03: Message edited by: Frances ]
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gedanken
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Member # 594
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posted 11. March 2003 22:59
I and some others were involved in discussion of "information" in context of biology in the thread Shapiro and the Genome. The discussion spanned several pages(interleaved with other issues). The main request to which some responded was in the middle of page 4, and continued to page 5.
I'm not sure that we resolved anything that is agreed to in any universal way, but I made comments of what I thought was basic and common to the definitions of several. I was of course trying to relate to specific points, but this may be relevant to this discussion.
[ 11. March 2003, 23:03: Message edited by: gedanken ]
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