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Comment by jostmey | Hacker News Reader

As someone with a background in computer programming, I found biology quite frustrating. I wanted to see some underlying structure or meaning in the genetic code. It took me a long time to realize that it wasn't there. Biological systems and their genetic codes are the result of random trial and error filtered through Natural selection. Biological systems clearly have a design because you see the same "form" reappear in each generation, but the design itself is completely random. In other words, the design has to work, but it does not have to be sensible.

To summarize, the design of biological systems is random. It was a hard pill for me to swallow, and an utterly dissatisfying one at that.

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I don't know if you've seen it before, but you may be enjoy this famous paper in Bioengineering called "Refactoring Bacteriophage T7": http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681472/

One of my favorite things about experimenting like this is that I learn new things from logical systems I create. Spin things differently and you learn a whole new set of ideas. I had no idea how much junk code that biology would allow in genetics until I made this thing.

> To summarize, the design of biological systems is random. It was a hard pill for me to swallow.

There are so many things about our universe that are very non-random, such as the physical laws, and more specifically the spherical shapes of planets/stars, the flatness of their surfaces, the flow of energy from stars to planets, etc.

An analogy could be that life forms randomly evolving with these constraints are like water particles randomly floating through a river. There are plenty of variations in where the particles can go, but they flow in a general direction.

I guess I was trying to draw a distinction between biological systems and man made machines. I find the difference striking. I can look at a car engine, and if I stare at it long enough, I can make sense of it. The engine makes sense to me not just because it was designed by another human but also because its design is non-random. When I stare at the protein KcsA, which is the biological system that I study, I cannot make sense of its design. My conclusion is that its design is an outcome of chance. The protein works and has a design but it is not one that I can figure out.

Man made machines have a rational design. Biological systems have an "irrational" design. The most striking characteristic of a randomly designed system is that you cannot restart it. Once you shut it off it dies permanently.

  >  The most striking characteristic of a randomly designed
  > system is that you cannot restart it. Once you shut it off
  > it dies permanently.

I don't see how that is a consequence of the underlying design principle. There are many organisms that survive de-facto death through freezing etc. You could also engineer machines to not be restartable, and under certain circumstances that may be a desirable feature. There's no connection between what you call rational or irrational design and restarting.

Moreover, there are natural mechanisms with "sensible" design. To me, the mammalian retina is very carefully calibrated, perfectly understandable machinery implementing various filters and feature extraction networks. Examples abound.

Yes saying it is that random is like to expect nature to build a complex organism like us by only being like a monkey typing randomly on the keyboard of chemistry, physics etc... and be able to create that.

Even if it was the case then the earth would be full of defective cells to animals across the whole tree of life with only a few working well. It's not what we find when we mine the earth or what we have today.

But even still with a "keyboard" that complex.. You will need more than billions of years to accomplish something that complex randomly.

You can see this with a sim called DarwinBots. Hand-crafted code is as clever as it can be. Code evolved from zero is a bunch of gibberish that just happens to hit the right spots here and there. The key is reverse engineering what effect the evolved code is actually going after.

Ironically, the theoretically optimal programs for computers would not be sensible for human understanding as well, so it is probably not that different.

You sure? How do you know? Is this based on research or gut-feeling? (if it's the former I'd be real curious to read about it)

So essentially, we are "shakespeare" produced unknowingly by the infinitum of proverbial (and literal) monkeys :)

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