Biology-Engineering Lexicon

It became apparent to me in my committee meeting today, that my hybrid of biology and engineering speak is going to get me in trouble. Most noticeably, there are terms which imply intelligent design, even though I wish to imply no such thing. There are no succinct biology terms to satisfy me, so I will write out the mapping that exists in my head.

Design — The process by which evolution creates something. Design normally implies a conscious process, but this refers to an unconscious one. It still follows the rules of design: a device is made that meets the specifications. See below for more information. Examples: lacZ is designed to break down lactose should be read lacZ has been subjected to sufficiently strong selective pressure to break down lactose and do little else. Conversely, lacZ was not designed to break down maltose should be read there had never been a selective force that pressured lacZ into breaking down maltose (in addition to lactose), therefore, it is unsurprising/expected that it is incapable of doing so.

Constraint/Specification — This refers to the sum environmental conditions of selective advantage. This include more than the selective pressure we think of as the goal. For example, if it is advantageous to transport lysine from the surroundings instead of synthesising it, we can consider the constraints of that situation: there must be a way to take in lysine, lysine should not be able to leak out, this method should not break lysine synthesis, the protein should not be toxic. These are constraints that are created during the evolutionary process. For instance, the constraint that this method should not break lysine synthesis will only become part of our specification if the cell will be subjected to an environment where lysine is not available. One might thing to add the constraint that this method should not allow cytosolic lysine to rise to a toxic level, but it is unlikely that the cell will find itself in such an environment, therefore, there will never be selective pressure to guard against this constraint. Engineering usually requires that specifications be balanced in some way (checking both extremes). Biological specifications only have constrains on the extremes that have been experienced (this is why the sum is important). There is a memory for specification, but it can fade with time unless subjected to occasional selective pressures.

Junk/Garbage — Something presently not of interest/use. Biologists tend to refer to stuff they don't yet understand as junk (e.g., much of that junk DNA is doing something useful, but no one knows what). Where as, from a more engineering point of view, junk can be anything that's not relevant. If I'm looking at protein coding genes, all other genetic sequences, even if they are of known function, become junk. Junk can also refer to unnecessary intermediates. When discussing a signal transduction pathway, I would happily say: a ligand activates a receptor on the surface of the cell which activates a certain gene using some junk in the middle.

Good/Bad Idea — Something selected for/against. Addiction cassettes are a good idea.

(Quantifiably) Weird — Weird generally means unique, unconventional, non-parsimonious, and/or non-obvious. The fact that Bradyrhizobium japonicum only does half of the citric acid cycle in its own cells and the other half in the plant cells is weird/unconventional/non-obvious. I am sure there are many other organisms that do equally weird things, but since I don't know them, I don't know they are weird. This leads to a very difficult comparison for weird. We take the model organisms that we use and assume them to be accurate reflections of all vaguely similar organisms, yet we know this is wrong. Hence, to say that something is weird, contrasts it again the standard cannon we know from the well studied organisms. Given enough research, we may come to realise how far our model organisms are from some kind of consensus. E. coli has already proven to be a problem. It has a very fuzzy definition of species compared with most other bacteria studied. More concerning, only 1 % of microorganisms can be grown in the lab. It would appear that organisms that can be grown in the lab are, themselves, weird. Weird, eh?

Species — Fortunately, microbiologists recognize that they have no good definition for a species. That doesn't stop them from pretending. As I see it, there are two definitions for a species and both are necessary, but we must be careful how we mix them together. I shall dub them the sqecies and the clecies. The squecies is the sequenced species. Basically, you go and get one bacterium. You let it grow and sequence it. You are effectively sequencing one organism. Only 0.004 mutations/division are introduced, so we can ignore the mutations for short times. When you go and download the genome of a species, you're really getting a squecies: the genome of one individual. Given that we can go the same source and isolate another organism that appears to be the same as the first, what is the relation between the two? If we sequence the genome, undoubtedly, this second squecies will be different. Perhaps it will contain all the same genes, but shuffled. That seems equivalent, but we know that position can dramatically affect gene activity. A few crucial point mutation can completely change the character of an organism. Yet, at the same time, it could have large genetic changes and still be the same. Particularly, in the case of virulence, some genes are on mobile elements (e.g., plasmids, transposons). These mobile elements can transfer between different organisms but have different ranges; ranges which do not coincide well with any existing definition of species. So, we need to think of a cloud of probable species, or clecies. This really refers to a nebulous group of genes that are smeared out over a group of cells. I generally have 3 working terms for species: sqecies (usually qualified by in the NCBI database), clecies (usage without a specific strain identifier), or the hybrid mode that is a clecies with a particular squecies as its representative.

Hopefully, this is clearer.

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