Chapter 16

Environment and Ecology

Any organism is indissociably embedded in an environment (which is ultimately a

source of entropy—or negentropy if one prefers that term). Development does not

follow a preordained program encoded in the organism’s genes but is influenced by

its environment, which may be assumed to be continually varying. Among physical

parameters, temperature is a source of significant variation in the environment of

most organisms, which have developed appropriate mechanisms for surviving tem-

perature fluctuations. Gravity is not only an important parameter for astronauts and

cosmonauts; every time an organism enters water its gravity is diluted roughly sixfold

(corresponding to moving from Earth to the moon), and this difference has played a

key rôle in the development of organisms. ¹

In contrast to the small number of relevant physical parameters, relevant environ-

mental chemical parameters have an almost immeasurable variety. Common human

beverages such as coffee and wine contain hundreds of complex organic molecules.

The sequence of exposures to chemical substances is called the exposome.

A snapshot of the exposome would be a column vector upper CCCC, the components c Subscript ici of

which would represent the concentrations of chemicals in the environment. Under

controlled conditions, some substances engender well-defined responses. For exam-

ple, it is well known that retinoic acid induces stem cells to differentiate into neurons.

Hence

a equals chi c 1 commaa = χc1,

(16.1)

where aa is the attribute of “neuronness”, chiχ the susceptibility of the cell to be trans-

formed into a neuron in the presence of retinoic acid, and c 1c1 the concentration of

retinoic acid. Probably in this case, the output should be binarized such that a equals 1a = 1

(neuron) if the right-hand side exceeds a certain threshold, and otherwise a equals 0a = 0

(unchanged stem cell). Clearly, Eq. (16.1) can be generalized to deal with multiple

substances and multiple attributes, thus

1 Nishihara (2002).

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J. Ramsden, Bioinformatics, Computational Biology,

https://doi.org/10.1007/978-3-030-45607-8_16

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