Is Biology a Science?

Is Biology a Science?

When reading this polemic, I could not help but think of the genre of articles that compares economics to physical sciences to argue that economics is not a science.

It’s exactly the same of sort of argument: trying to make a disagreement in emphasis into a disagreement in substance (I mean, this isn’t even like the major fights in that other non-science, theoretical physics, where string theory is either the solution or a blind-alley).

At the end of the article, I still don’t understand the anti-selfish gene argument. I see two arguments in this article:

Differences in gene expression can account for large changes in phenotype. Well, duh. My hand is not like my liver even though the cells have the same genome.

The whole genome is a system and genes do not function individually. This is the part of the argument that most feels like the anti-efficient markets polemics I read after Eugene Fama won the Nobel Prize. It’s a complete straw-man. Even in the Selfish Gene book, Dawkins [1] stresses that (1) fitness of a gene is a function of the environment and (2) the most important environment for a gene is the genome in which it is inserted. Genes can be high-fitness by changing the expression of other genes, perhaps conditional on certain environmental cues. How else does gene expression change? It’s genes all the way down [2].

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Let me put it this way: the gene that codes for the light receptors in your eyes would be pretty useless in a species that lives in dark caves. The gene that regulates the expression of other genes would be pretty useless in the absence of those other genes. Even the light receptor gene is pretty useless if you species does not have a nervous system. Was this ever in doubt?

Also, yes, we are no longer trying to look for the gene for autism, the gene for homosexuality, or the gene for X. In as much as these are genetically mediated, these are multi-gene phenomena with complicated environmental interactions. But saying this just says that the gain in fitness of a specific gene is a complicated process, which depends on the whole context, and that is not easy for humans to apprehend it. It does not invalidate the idea of a gene as the basic element that gets selected (in the context of other genes). Only in a fuzzy, mood-affiliation, sense does the systems biology view contradict the selfish gene model. In a non-fuzzy sense, they’re 100% compatible.

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Maybe there is something I’m missing in the anti-selfish gene argument, but having read a few of these, it always feels that the author just does not like the word selfish in the metaphor as it celebrates the wrong kind of human behaviour (as if making a point about the evolution of insects had anything to do with how you should live your life: a locust is a grasshopper therefore you should visit your mother for Thanksgiving).

The author says towards the end:

It’s not a selfish gene or a solitary genome. It’s a social genome.

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Turns out that, just like Economics, Biology is not a science.

[1] I find myself in the unusual position of defending Dawkins, who I generally find a very shallow thinker.
[2] Dawkins says this in the piece. The author is taken by surprise (which just means that he never even understood the view that he’s criticizing) and replies with a non-answer quote. It’s like that old chestnut markets are not efficient because you cannot predict them (actually, the efficient market hypothesis is the idea that you cannot predict markets, so you’ve just argued that gravity is not true because things fall).
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What is a Gene? The Definitive Answer

I think the GenBank file spec gets the definition just right:

gene: A region of biological interest identified as a gene and for which a name has been assigned.

That’s basically it. If people call it a gene, it’s a gene.

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They could mean:

  • a region in the genome that gets transcribed (or translated; but are introns no longer part of it?)
  • the nucleotide or amino-acid code in those regions
  • the “reference” nucleotide code that is expected in that region
  • the homologs of that (or othologs or paralogs or purposefully remaining fuzzy because it’s hard to say what’s what)
  • the regions of genome that cluster together across different organisms
  • a higher level concept that groups several proteins together through inferred orthology
  • (or perhaps even convergent evolution)
  • the protein encoded by the gene (or the general cluster of proteins)

In many discussions, gene is a good word to rationalist taboo. It clears up many mistakes when people are obliged to say what they mean by this tricky word.

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Another good word to taboo is species when the organisms are bacteria

To even use the same word as we have for animals is probably a mistake. We need a word for “bacteria whose rRNA clusters together in nucleotide space” without all of the baggage of species.

And so we would replace a veneral biological concept with a computational definition: progress!