Jun 18 2011

Genetics as an Interactive Sport

“For your information, I would like to ask a question.”
—Samuel Goldwyn

From an evolutionary point of view, in order for something to carry information, there must first be some sort of “receiver” that reacts to the source of information and interprets it. Through its reaction and interpretation, the receiver’s functional state is changed in a way that is related to the form and organization of the source. Receivers usually have no intentionality in themselves, although it often benefits from the results. Like receivers, most sources do not change when a receiver reacts to and acquires information from them. Humans for example, don’t change much reading one recipe or another. Your computers don’t change physically if you change whatever software you are running on it.

What is information?

A common definition of information is “the knowledge of specific events or situations that has been gathered or received by communication.” (1) Communication is the change of information from one state to another. Only a minute fraction of the energy used by most living systems is employed for information processing. In living systems theory when communications are processed they often shift from one matter-energy state to another, from one sort of marker to another. Matter-energy and information always flow together.

For our needs, information means that a stretch of DNA embodies in an encoded form the particular amino acid sequence for a polypeptide chain. It could just as well be said that a particular DNA sequence provides the code of a regulatory protein to attach to itself, thereby perhaps stopping the transcription of another gene in another stretch of code.

By asking certain questions about the information dynamics of a particular system of heredity transmission, we can help pinpoint similarities and differences. For example, we think of DNA as a “linear” sequence of units (the nucleotides A, T, C, and G) in which any site in the sequence can be occupied by any one of the four possible nucleotides. These nucleotides are interchangeable; replacing one nucleotide in the sequence with another will not influence the sequence to nucleotides that come before or after it. This means that quite a large number of sequences are possible. A sequence of 100 nucleotides, made up of four nucleotides will be capable of producing 4100 different sequences. Even at this graspable level, we are producing unfathomable numbers: This is a number greater than the total number of atoms in our galaxy! (2)

Another peculiar property of DNA is that, much like a photocopier, it will reproduce The Gettysburg Address or a Rorschach Drawing with the same degree of fidelity: DNA has a fundamental indifference to what is being replicated. The combination of its vast capability for possible variations and its inherent indifference to the outcome of replication means that DNA can provide a lot of raw material for natural selection. The downside is that many nonsensical and useless DNA variations can also be generated.

Control of Gene Activity. A: The product of gene P binds to the control region of gene Q and prevents transcription. B: A regulatory molecule associates with the product of gene P, which changes it to a nonfunctional shape, making it unable to bind to gene Q. Gene Q is now transcribed and the mRNA translated into a protein. (after Jablonka and Lamb, 2005).

Control of the process of gene transcription affects patterns of gene expression and, thereby, allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. A protein involved in regulating gene expression is called a regulatory protein or regulatory molecule. It is usually bound to a DNA binding site that is typically located near the gene’s promoter site Regulatory proteins often bind with a regulatory binding site to switch a gene on (activator) or to shut off a gene (repressor). Generally, as the organism grows more sophisticated, their cellular protein regulation becomes more complicated and many activators and repressors working together can control many of our genes. A major feature of multicellular animals is the use of morphogen gradients, which in effect provide a “global positioning system” that tells a cell where in the body it is, and subsequently what sort of cell to become. A gene that is turned on in one cell may make a product that leaves the cell and diffuses through adjacent cells, entering them and turning on genes only when it is present above a certain threshold level. These cells are thus induced into a new fate, and they may even generate other morphogens that signal back to the original cell.

Cells are mostly the mRNA’s and proteins that arise from gene expression. These mRNA and proteins interact with each other with various degrees of specificity. Some diffuse around the cell. Others are bound to cell membranes, interacting with molecules in the environment. Still others pass through cell membranes and mediate long-range signals to other cells in a multi-cellular organism. These molecules and their interactions comprise a gene regulatory network

Cells are mostly the mRNA and proteins that arise from gene expression. These mRNA and proteins interact with each other with various degrees of specificity. Some diffuse around the cell. Others are bound to cell membranes, interacting with molecules in the environment. Still others pass through cell membranes and mediate long-range signals to other cells in a multi-cellular organism. These molecules and their interactions comprise a gene regulatory network

Over longer distances, morphogens may use the active process of signal transduction. Such signaling controls embryogenesis and maintains and regulates adult bodies through feedback processes. The loss of such feedback because of a mutation can be responsible for the cell proliferation that is seen in cancer. In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs. It has been suggested that, because biological molecular interactions are intrinsically stochastic (random), gene networks are the result of cellular processes and not their cause.

Thus, molecular networks are not the cause but the result of cellular processes because these latter restrict the stochastic variability of molecular interactions. (3) Genes are ruled by probabilistic mechanisms allowing cells to differentiate stochastically: Man may be a machine but he is a random one. (4)

This realization leads us to my second favorite definition of information, courtesy of Shu-Kun Lin (b. 1957):

“Information is the amount of the data after data compression.”

  1. Miller JG. Living Systems. McGraw Hill New York, NY (1978)
  2. Jablonka E and Lamb M. Evolution in Four Dimensions. MIT Press, Cambridge MA USA (2005)
  3. Laforge B, Guez D, Martinez M, Kupiec J. Modeling embryogenesis and cancer: an approach based on equilibrium between the autostabilization of stochastic gene expression and the interdependence of cells for proliferation. Progress in Biophysics and Molecular Biology 89 (2005) 93–120
  4. Kupiec J. The Origin of Individuals. World Scientific Publishing Company (2009)

One response so far

One Response to “Genetics as an Interactive Sport”

  1. NICK says:

    awesome

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