Synthetic Biology: Engineering Open-Source Software with DNA • Hacker News Board

Re: Synthetic Biology: Engineering Open-Source Software with DNA

#31

Post by madhadron » Tue, Jun 12, 2012, 6:15 PM UTC

jostmey wrote: post #12

How do they prevent the E. Chromi bacteria from eventually being displaced by other non color coding poo bacteria? It seems to me that even if the E. Chromi did work as advertised, that the bacteria would quickly (within days) disappear from your intestinal track. If anything, I would suspect that the E. Chromi would be at an evolutionary disadvantage in the gut. This is because the E. Chromi would be expending effor…

Very important point. E. coli describes a range of organisms that share about 14% of their genome. For comparison, all of primates share over 99%. The strains everyone uses for genetic engineering are derived from strains isolated many decades ago and are incapable of colonizing hosts. They've also been selected over the years to be hysterical (they over respond to any stimulus, since when you're picking colonies to study response, you select the bright, clear one...and if you do it again and again over the years, you select for hysteria).

Poking around, I couldn't find the strain they used. They might have engineered a gut isolate. They might not. Doesn't appear to say anywhere.

Re: Synthetic Biology: Engineering Open-Source Software with DNA

#32

Post by madhadron » Tue, Jun 12, 2012, 6:18 PM UTC

Others have already said this, but let's get it out in the open once and for all:

Biochemistry has no relation to computation.

Neuroscience has no relation to computation.

Anatomy has no relation to computation.

Ecology has no relation to computation.

Someone using an computational image in any of these fields is trying to impart a sense of familiarity for his audience. If you actually want to learn any of these fields, you need to build your thought processes from scratch. No part of you works like a computer.

Re: Synthetic Biology: Engineering Open-Source Software with DNA

#33

Post by refurb » Tue, Jun 12, 2012, 6:31 PM UTC

tempuser007 wrote: post #29

refurb wrote: post #28

Earlier quoted context omitted.

Let me give you the best example I can. Computation chemistry has been going on for decades. Attempts at modeling how molecules behave is still quite primitive. We're talking about modelling the behavior of a object that is comprised of a few dozen atoms. That's it, pretty simple right? We'll the models aren't that good at predicting molecular behavior. Let's move up a step now. Computation chemistry is used heavily…

You see, my feeling is that trying to guess the progress of genetics by extrapolating the complexity and insecurity of the computation chemistry is wrong. As far as I understood, genetics today is a lot about (but not only) identifying which genes (portions of DNA) are responsible of which phenotype (en.wikipedia.org/wiki/Phenotype).Therefore a lot of resources are and were allocated to create a dictionary with genes…

OK, I see your perspective now. I agree that our understanding of how genes encode for proteins is well developed, as are our techniques for "transplanting" a gene from one organism to another.

What we have very little handle on is gene regulation. All those "non-coding" genes that scientists used to think were junk? They are actually used to control gene transcription.

Controlling this is infinitely easier in a simple organism like a hookworm, but the complexities of in human borders on obscene.

Re: Synthetic Biology: Engineering Open-Source Software with DNA

#34

Post by terangdom » Tue, Jun 12, 2012, 7:05 PM UTC

fghh45sdfhr3 wrote: post #22

terangdom wrote: post #19

Earlier quoted context omitted.

My prediction: We can find a subset of proteins such that they do not interfere with each other, and still large enough that they can perform useful functions. It is possible to write threaded software in a way that everything interacts with everything and it is almost impossible to make out how anything works. That's why we don't. The halting problem never stopped us from writing software.

My prediction: We can find a subset of proteins such that they do not interfere with each other, and still large enough that they can perform useful functions. The tiny, tiny amount of bioinformatics knowledge I have makes me think the probability of your prediction is ~ 0.00000000000001%. For non-trivial values of "useful". :) Can you tell me what experience or knowledge lead you to make that prediction?

Now I feel bad, maybe I should have voiced it in a way that sounded less sure. I base it on two things. 1. Similar genes do similar things in different species. 2. There are an incredible amount of possible proteins.

Re: Synthetic Biology: Engineering Open-Source Software with DNA

#35

Post by redwood » Wed, Jun 13, 2012, 8:29 AM UTC

madhadron wrote: post #30

redwood wrote: post #25

Earlier quoted context omitted.

Curious what field and capacity you're working in basic science. I'm considering pivoting out of industry. Studied physics undergrad but quite frankly couldn't cut it to do so post-grad. However I do wonder if another field would be doable for me... but without prereqs I'm not sure how to get onto that path now (I'm not a coder, getting really into bio/chem/neuro/genetics). Been out of uni 6 yrs

You can go into biology with no background. I went from physics and math as an undergrad to a PhD in biology. The first six months were rough, but if you really cut yourself off from your previous field and make yourself understand how the thought process in biology works, you can pick it up fairly quickly. Actually, I suspect that an undergraduate degree in biology might be a liability, since you will have memorized…

Well great to hear you've made a similar transition, and very cool to think that some of the bias coming from traditional lower-level bio training could be looked at as a liability.

I wonder if I can somehow find a way to pivot into bio without going through a university. Would love to somehow get there through industry, perhaps through some of the genome sequencing outfits which have some crossover with the semiconductor industry.

Hadn't heard the Delbruck joke but hah good to hear, if I understand you correctly, that in a sense it'd be easier to swim in bio if I was sinking in physics.