Little kids as scientists, scientists as little kids

My wife likes to point out that our nearly-2-year-old son is the ultimate scientist...something that could be said of all young children. Starting with nothing but boundless curiosity and awe, they are able, with time, to figure out what this world around them is and how it works. You can see it in their eyes as they soak up every bit of information around them.

So you can see why the following made me both nod and chuckle:

"Over the past ten years, developmental psychologists have increasingly used the model of scientific theory change to characterize cognitive development. I have called this idea the "theory theory. It has been consistently productive in explaining the child's developing understanding of the mind and the world. ... The analogy to science has two aspects. First, children's knowledge is structured in a theory-like way, and second, that knowledge changes in a way that is analogous to theory change in science.

"This theory formation system may have evolved specifically to allow human children to learn. Human beings' evolutionary advantage stems from our ability to adapt our behavior to a very wide variety of environments. In turn, this depends on our ability to learn swiftly and efficiently about the particular physical and social environment we grow up in. Their long, protected immaturity gives human children an opportunity to infer the particular structure of the world around them. The powerful and flexible theory formation abilities we see in childhood may have evolved to make this learning possible. In this view, science takes advantage of these basic abilities in a more socially organized way and applies them to new types of problems and domains. Science is thus a kind of epiphenomenon of cognitive development. It is not that children are little scientists but that scientists are big children."

As you might imagine, I added the emphasizing bold and italics. It makes me wonder if Shakespeare had it wrong, that "second childishness" doesn't mark the seventh age of man, but the beginnings of graduate school.

[Many thanks to my ever-vigilant father-in-law for sending this in, via National Review Online. For the whole article, go down to your local library and look up: A. Gopnik (2000). Explanation as orgasm and the drive for causal understanding: The evolution, function and phenomenology of the theory-formation system. In F. Keil & R. Wilson (Eds.) Cognition and explanation. Cambridge, Mass: MIT Press.]

Getting in touch with your -ome

Since the human genome project was completed (a feat that, according to some, was actually accomplished 3 times), the sound "-ome" has been emanating softly from laboratories around the globe. But it has nothing to do with meditation and everything to do with, well, everything.

The suffix "-ome" (a corruption of Greek, Latin, or English, depending on who you ask) refers to the organization of complete collections of aspects or features of biology, such as genes (the genome), proteins (the proteome), and so on. Each covers the total catalog of that particular feature for some point of reference, like the dog genome or the transcriptome of a white blood cells, and can form the basis for its own field of study (hence genomics and proteomics). This is the realm of computational biology and bioinformatics, where researchers can produce thousands or millions of data points per experiment, and where biologists spend large amounts of time in the presence of specialists from such fields as mathematics and theoretical physics, fields long used to crunching lots and lots of numbers.

So how many "-omes" are there? Well the list is big, and seemingly getting bigger all the time. Every branch of the biological sciences seems to have its own set of "-omes" nowadays, with more being proposed all the time. The ones I hear about most often are:

• Genome (the total catalog of genes within a cell or organism; studied via genomics)
• Proteome (the total catalog of proteins within a cell or organism; studied via proteomics)
• Transcriptome (the total catalog of RNA transcripts produced by the genes within a cell or organism)
• Kinome (the total catalog of kinases within a cell or organism)
• Reglome (the total catalog of genes controlled or influenced by a particular pathway, gene, or protein within a cell or organism)
• Metabolome (the total catalog of metabolites within a cell or organism; studied via metabolomics)
• Interactome (the total catalog of gene or protein interactions within a cell or organism)

And while the proliferation of "-omes" strikes some as a little silly or even dangerous (and it does lead me to ask, do we have to redefine economics?), I actually find it refreshing because it really does signal a sea change in ways of thinking about biology. Each -omic field take a large scale, integrated view of an aspect of biology. And the field of bioinformatics exists today to integrate data from different "-omes" (usually genomics and proteomics these days) into a clearer, holistics picture of what makes the total biology of a cell or organisms. I guess you could call that the bioinforome.

A holistic biology. Sounds pretty zen. Ommmmmm.........

[Credit for the photo of the worm protein interactome goes to Harvard Medical School. Wikipedia also has quite a bit to say on the subject of "-omes"...take a look here and here. Oh, and apparently "comics" doesn't count as an "omic" science.]