2

Genotype, Phenotype, and Environment

13

isolated from each other, because of behavioural patterns, as if they were living on

different continents, and if we apply our definition, we are forced to assert that the

groups belong to different species (even though they are all taxonomically classified

as Homo sapiens).

The concept of reproductive isolation is of little use when species reproduce

asexually (such as bacteria); in this case, a criterion based on the possibility of

significant exchange of genetic material with other organisms may have to be used. ²

Another difficulty in defining “species” in terms of associating them with

autonomously reproducing DNA is that not only are there well-defined organisms

such as coral or lichen in which two “species” are actually living together in insep-

arable symbiosis, but we ourselves host about 10 Superscript 1410¹⁴ unicellular organisms, mostly

bacteria, which comfortably outnumber the 10 Superscript 1310¹³ or so of our own cells.

A very striking characteristic of living organisms is that they are able to maintain

their being in changing surroundings. It is doubtful whether any artificial machine

can survive over as wide a range of conditions as man, for example. “Survival” means

that the essential variables of the organism are maintained within certain limits. This

maintenance (homeostasis) requires regulation of the vital processes.

Problem. Pirie (1937) asserts that the terms “life” and “living” are meaningless.

Provide a critique of the arguments. Attempt to formulate a definition of life. Find

exceptions.

Figure 2.1 highlights the principle objects of investigation of bioinformatics. The

field could be said to have begun with individual gene (and hence protein) sequences;

typical problems addressed were the extraction of phyologenies from comparing

sequences of the same protein over a wide range of different species and the identi-

fication of a gene of unknown function by comparison with the knowledge base of

sequences of known function, via the inferential route:

sequence homology ⇒ structural homology ⇒ functional homology.

(2.1)

Genetic “texts” lend themselves particularly well to being encoded on a computer

and the comparison of different texts can be rapid and efficient. It is much more labo-

rious to establish homology of, say, anatomical structure. Firstly the measurements

themselves are far more difficult than the nowadays largely automated sequencing

of DNA. Then there is the giant problem of representation in a form that can be

encoded on a computer. Only when that is achieved can the power of the computer

be exploited.

Apropos expression (2.1), there are, however, plenty of examples of structurally

similar proteins with different sequences or functionally different proteins with sim-

ilar structures. Associated with these endeavours are technical problems of setting

up and maintaining databases of sequences and structures.

2 See also Chap. 5.