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Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

biology.stackexchange.com

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Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#131

Post by alexchamberlain »

roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

Computers only look like they have windows, digital signals and logic gates. It's all just pixels, noisy voltages and imperfect silicon.

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#132

Post by mgfist »

roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

Sounds like many a codebases I've worked on haha

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#133

Post by munificent »

roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

The I think about it is like this: Code is read and maintained by humans, so it is under selection pressure to be comprehensible by human minds.

Reality has no such constraint. If the biological processes of some animal lead to inscrutable irreducibly complex "spaghetti code" but the animal is slightly more likely to produce offspring... the complexity wins. The natural world doesn't care whether or not we can understand it.

(There is, of course, a natural selection pressure going the other direction. Brains that understand the natural world do seem to often be generally more likely to produce offspring, so there's evolutionary pressure for minds to understand the world, but not for the world to be understood by minds.)

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#134

Post by sjducb »

roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

As a biologist who moved into software engineering I love working with actual machines.

You can think of a design, build it and have it work as you expect. You can’t do that in biology.

The reason is that we “understand” how computers work. Our understanding of biology is nowhere near that level. A high percentage of established knowledge is wrong or so incomplete that it’s not useful for designing new systems. This is hard for engineers or even scientists from physics and chemistry to accept.

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#135

Post by bossyTeacher »

munificent wrote: post #133
roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

The I think about it is like this: Code is read and maintained by humans, so it is under selection pressure to be comprehensible by human minds. Reality has no such constraint. If the biological processes of some animal lead to inscrutable irreducibly complex "spaghetti code" but the animal is slightly more likely to produce offspring... the complexity wins. The natural world doesn't care whether or not we can unders…

> Brains that understand the natural world do seem to often be generally more likely to produce offspring

I would argue that the evolutionary pressure only applies to a limited level of understanding of the physical world. Think how many kids people like Stephen Hawkings have and how many poorly educated people have.

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#136

Post by campbel »

munificent wrote: post #133
roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

The I think about it is like this: Code is read and maintained by humans, so it is under selection pressure to be comprehensible by human minds. Reality has no such constraint. If the biological processes of some animal lead to inscrutable irreducibly complex "spaghetti code" but the animal is slightly more likely to produce offspring... the complexity wins. The natural world doesn't care whether or not we can unders…

Yes! Optimal designs may not be "elegant" from the human perspective. Reminds me of these complex computer generated airframe designs https://www.bbc.com/future/article/20181129-the-ai-transform....

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#137

Post by nico »

munificent wrote: post #133
roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

The I think about it is like this: Code is read and maintained by humans, so it is under selection pressure to be comprehensible by human minds. Reality has no such constraint. If the biological processes of some animal lead to inscrutable irreducibly complex "spaghetti code" but the animal is slightly more likely to produce offspring... the complexity wins. The natural world doesn't care whether or not we can unders…

In some way, neural networks and newer ML models seem to be going in this direction. We are starting to get faster/better results with black boxes than with if-else style code

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#138

Post by bossyTeacher »

roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

I would argue that it is only messy because we are looking at the wrong level of abstraction with an incorrect computational model. At the end of the day, if it has inputs and produces outputs, it is a computing device (i.e. a computer).

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#139

Post by mrguyorama »

Karellen wrote: post #45
dawnofdusk wrote: post #3

An interesting question because all of this genetic encoding and expression is probabilistic at its very core (it has to be, otherwise there wouldn't be evolution), whereas it would be very bad if basic operations in a CPU had similar level of error rates. Interesting to me how the top comment has talked about constructing logic gates out of biological circuits. I wonder if anyone has done the opposite, i.e., write a…

> it would be very bad if basic operations in a CPU had similar level of error rates. Given how slow evolution is, and how many times DNA is copied and/or transcribed in any one individual, my intuition is that the error rates for genetic processes are actually incredibly low.

There are numerous correction mechanisms, and other mechanisms that destroy malformed proteins and mRNA chains. Wikipedia claims one out of every 1000 to 100000 amino acids added to a forming protein is wrong. Each ribosome is proceeding to add amino acids to a chain at about 10 per second, and millions (or way more) proteins are being produced all the time.

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#140

Post by Ancapistani »

Karellen wrote: post #45
dawnofdusk wrote: post #3

An interesting question because all of this genetic encoding and expression is probabilistic at its very core (it has to be, otherwise there wouldn't be evolution), whereas it would be very bad if basic operations in a CPU had similar level of error rates. Interesting to me how the top comment has talked about constructing logic gates out of biological circuits. I wonder if anyone has done the opposite, i.e., write a…

> it would be very bad if basic operations in a CPU had similar level of error rates. Given how slow evolution is, and how many times DNA is copied and/or transcribed in any one individual, my intuition is that the error rates for genetic processes are actually incredibly low.

My intuition says that error rates are extremely low, but that errors are common - due to the incredible number of iterations that occur in a very short time period.
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