Comments on: Fins Limbs and Gills (And how they evolved) https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/ Wed, 22 Apr 2009 18:34:21 +0000 hourly 1 https://wordpress.org/?v=6.4.6 By: AK https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534583 Wed, 22 Apr 2009 18:34:21 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534583 @Jason Thibeault, NewEnglandBob:

I’ve been working on a post on the subject, too much to put in a comment. See my How Smart is the Cell? Part II: The Gene Activation network as an Analog Computer.

You may want to start with part I…

]]> By: NewEnglandBob https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534582 Mon, 20 Apr 2009 07:56:07 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534582 Actually, there is more analogy to an analog computer, which I did get to use in college, just before my 30+ year career in software. Tweaking those knobs could show a ‘butterfly’ effect cascade at the output.

]]> By: Jason Thibeault https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534581 Mon, 20 Apr 2009 07:33:07 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534581 Indeed — reality has a lot more margin for error, what with copying fidelity and the timing of the chemical reactions. The closest a computer could come to this is to multithread to the n-th degree to allow simultaneous processing of every chemical reaction. Abstracting genetics to a computer language is helpful in my own understanding, but I do understand it’s only an abstraction. In discussions on genetics with my girlfriend who is most certainly not a computer programmer, any time I pull out a computer analogy, she usually replies with “…what?” Where she “got it” before, my analogy usually just confuses and annoys her.

Still though, there are some lessons to be learned from the analogy, or there wouldn’t have been so much buzz from the EvoLisa project around January. And it wouldn’t have driven me to rewrite the same program in Python, with an actual population size and varying selection pressures (shameless self plug — not that it’s worth looking at). Nor would better programmers, like cdk007 on Youtube, have come up with a program putting the lie to the “blind watchmaker” stuff from the creationists’ camp.

]]> By: RBH https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534580 Mon, 20 Apr 2009 01:35:16 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534580 Tempting though it is, ‘ware of pushing the computer metaphor too far. At that level it’s chemistry, not coding. One sees computer folks get themselves into awful twists pushing the metaphor way past where it’s helpful. GilDodgen at Uncommonly Dense comes immediately to mind.

]]> By: NewEnglandBob https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534579 Sun, 19 Apr 2009 22:52:16 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534579 Jason, there already is an interpreter for DNA and it is called life.
I think you are focusing too much on the DNA itself and not at all on the proteins and enzymes.

DNA is more like a macro language and the numerous proteins are the macros, to be called upon to do the actual work, with timing and concurrency of utmost importance.

]]> By: Jason Thibeault https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534578 Sun, 19 Apr 2009 21:45:47 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534578 To further my own analogy, what if we could one day write an interpreter for DNA? We’d basically have to code for physics, chemistry, an environment conducive to reproduction and life itself, so we’d be writing a virtual reality program unparalleled by anything but reality itself, so that would basically make us God for this reality.

O NOES WHAT IF WE ARE THE SIMULATION!!1one

]]> By: Jason Thibeault https://gregladen.com/blog/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534577 Sun, 19 Apr 2009 21:42:14 +0000 http://scienceblogs.com/gregladen/2009/04/19/fins-limbs-and-gills-and-how-t/#comment-534577 As a computer guy who only recently discovered how awesome genetics is (and who in fact occasionally wonders if he missed his calling in life, and who also finds talking in third person to be quite irritating to readers), I’ve been drawing parallels between DNA and code for a computer in my mind that probably aren’t really analogous. Figured I’d try one out on someone who actually knows something about biology.

This sounds a lot like a subroutine that is called with different variables based on where in the code it’s called from. My understanding is that the DNA around something that codes for a particular feature can affect the outcome, even if it’s not directly involved in the code for that feature; like how one sequence of code can actually code for several different enzymes depending on where the read starts, one chunk of code that creates an appendage can be altered by what’s to either side of that code. Since DNA isn’t like a real computer language, I envision it more like an esoteric programming language like Malbolge or Brainf***, where tiny mutations in the code can cause all sorts of drastic results in the end product.

What do you think, sir? It’s damn cool either way.

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