The New Evolution

Recently, scientists decoded the most complex genome yet found. And no, its not human.

Its not even a mammal. Or for that matter, very big at all.

It's a water flea. This tiny crustacean is 25% more complicated than humans. Yes, you are less interesting than a flea. To a geneticist anyway.

Water Flea Daphnia pulex (water flea), a near-microscopic crustacean that lives in ponds and lakes, has a translucent body and a compound eye.
It's 31,000 genes actually have more in common with human's than any other crustacean. But perhaps the more interesting question is why a flea would have 31,000 genes.
And here is the, very interesting, answer: it can transform in response to stresses — it can develop spines, helmets or neck-teeth (really) in response to predator threats. It changes its gene expression based on the environment around it. And here, our understanding of evolution is, well, evolving.
The old theory of evolution wen't like this (and not all that different from Darwin's original theory): random mutations are constantly occurring, and those random mutations which give an advantage are selected for, as those individuals have more offspring. The other side of the equation, natural selection, basically said that given all of the variations currently in the population, the most effective at reproducing will be selected for. Thus, when external factors change, those more fit for the new conditions will prosper.
Turns out, this is not really the case all of the time.
As "intelligent design" supporters like to point out, it is difficult to explain periods of intense genetic change through random mutation. You see, evolution is something like sailing: hours (or eons) of boredom, followed by moments of sheer panic. And in those moments of sheer panic, lots and lots of interesting things happen. So many interesting things in fact, that in the case of evolution, random mutations during the period of sheer panic can't really explain it.
What the water flea and many other lines of research are teaching us is that the genome is in fact far more capable and interesting than many have believed. In essence, the genome for most organisms has the ability to express a range of different phenotypical attributes. For example, when a moth needs to change their colors, as the peppered moth so famously did in response to the soot of northern England in the industrial revolution, it is becoming apparent that a random mutation did not result in a black moth. Rather, the moths were already capable of expressing a black coloring - it was already genetically coded. When the environment changed, they simply changed which proteins they coded from which genes, and shazam, there were black moths.
The idea that the genome contains not just the current "best of breed" but a whole range of alternatives is completely revolutionary, and really damn cool. We have always thought that much of our genome was "wasted": unused GATCs which were simply old and forgotten code never removed. While this might be true to an extent, it is also possible that some of that code is actually for completely viable alternatives, currently not in use. This is not intuitively that surprising: would rather have subs or no subs when you send your soccer team to the world cup?
Of course, again, this is when the bright sparks over in the Intelligent Design 5-day Find Yourself through God Camp say "but how would the moths know to change over to black? God must have done in." Errr... no.
If I told you I could create an incredibly efficient factory, a factory which turned out just as much product as was needed, every single time. A factory with almost no bottlenecks, only a few errors out of thousands of units, and hell, lets throw in the fact that the product is delivered exactly where it is needed every time. And then I asked you, what would be needed to create this factory? The usual conclusion is that you would need to have someone very intelligent, very capable to design and then run this factory. The more complex, the more impressive, the more efficient I made this hypothetical factory, the more likely you would eventually say you needed someone, something, omnipotent and omniscient to design and run that factory.
Turns out that you need nothing at all.
One of the most amazing, most impressive things about the natural world is that it is all self regulating. The most critical, most interesting pathways critical to life are far far better designed than any factory any human will ever build. Take a look at the ATP pathway, the beauty of the thing is that whenever you run low on ATP, more is automatically called for. In fact, the whole process is self-regulating, running with a level of efficiency that would make Toyota's famed "Just in time manufacturing" akin to 2yr olds playing with blocks. And yet, what regulates it? Itself. More ATP is called for when ATP is used up, in an endless and amazingly efficient loop. Is there any "intelligence" behind this design? No. Just the efficiency of billions of years of evolution.
So then, we have these incredible genomes which give us not just a blueprint of who we are now, but give us the options necessary to rapidly adapt as conditions change. And when those conditions change, we rapidly adapt. It is no different than the many pathways which keep us living and breathing, moving, and thinking: the change in conditions calls for the change in genetic expression.
What chemical pathways are at work you ask. How exactly does it happen? Well, I don't know. But to me, the simplest and most logical answer is the most likely. And that is that these changes in what is expressed are brought on by the factors which create the need for change, in the same way that every other natural system is self-regulating.
Need more proof? Lets go back to our friend, the water flea. Much as the little guy has a mother-lode of G's A's T's and C's, he is not what you would call sentient. Or intelligent. Or really, anything other than a very simple little organism. Yet, when different predators are present, he can 'decide' to change his phenotype. Want even more evidence? It has been discovered that certain slim molds, organisms that are commonly used as the dividing line between alive and not alive can "decide" whether or not to hunt & gather or farm the bacteria they eat. If they area around them is short on their favorite bacteria, they keep some in pods, and then seed a new area, but if there are enough bacteria around, they just go ahead and eat up.
Again - how do they do it? Feedback from the environment around them.

I find this pretty damn incredible. Our genomes are far far more interesting and complicated than we believed, and far more capable. We can evolve over very short periods of time because we already have the codes there, waiting to be used.
Hopefully someone can find the code which gives me wings and lets me fly. I would like that.

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