If we include a wider group of organisms for comparison say the vertebrates and the invertebrates then the limbs of these two groups are not homologous since the last common ancestor of these two groups was limbless. Limbs evolved independently in these two groups. They are analogous structures.
But analogous structures can still be built by genes which are homologous!
Evolution is a tinkerer and uses the same gene networks to build new structures with similar functions in different groups of distantly related organisms.
PZ Myers explains this concept of deep homology and the consequences for understanding how evolution works in an article for Seed Magazine:
Evolution is a tinkerer that cobbles together new functions from old
ones, and the genome is a kind of parts bin of recyclable elements.
When new features evolve, the parts in the bin are co-opted to operate
in new roles. As a result, the same parts appear in anatomically and
evolutionarily distinct structures because it is faster and easier to
reuse an old gene network that almost does what is needed, than it is
to spend another few million years evolving a distinct gene for the
function.
This makes these master genes precisely analogous to the stock of
goods found in a hobbyist’s electronics store. Standard
subunits—oscillators, op-amps, field effect transistors, switches,
rheostats, and so forth—will get incorporated into many different kinds
of projects; whether she is building a radio or a synthesizer or a
burglar alarm, the hobbyist will find it easier to just grab an
oscillator integrated circuit off the shelf than to design her own. We
could sample devices built by different hobbyists with different
purposes, and when we rummaged about in their insides, we would find
the same subunits incorporated into novel, larger assemblies.
An important concept - homology- explained elegantly using ...an analogy ...he.. he...
Tip: 3QuarksDailyRead the rest here....
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