For the naysayers: they've implemented a raytracer in chemical reactions that are executed by dna. Very cool conceptual piece. See linked images, eg (sorry for pasting this horrible url)
(Edit nevermind that, check the link posted by dkural for some more details)
> Synthesize the oligonucleotides from the cube3d.dna file.
OK, so you get a long list of oligonucleotides ordered and shipped. Sounds prohibitively expensive, I guess this is a thought experiment or simulation exercise?
> Arrange the test tubes as shown in the diagram below.
OK, Get a microplate with 384 wells (== test tubes).
> Don't forget to provide the initial concentrations according to the table below.
Dump an oligonucleotide solution into each well? According to what table? There is no "table below". Which oligonucleotide in which well?
> Use a pipette to encode the position (row and column) of each tube to start the computation.
A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?
Is this a joke for biology PHD's?
However, it is far more realizable than some other DNA implementations described in papers.
The idea to publish DNA code on GitHub with CI, tests, linters, badges etc. is obviously a form of joke, but the project itself was done like a serious applied maths research.
Awesome visualisations and super interesting work!
Looking forward to more :D
Why 384? You could get any amount you want, you'd just have to modify the coefficients for row and column accordingly (linear increase with decrease of number per axis).
Imagine if you'd skip every other row and column, the image would still be the same, just lower resolution.
> According to what table? There is no "table below".
CTRL-F environment variables. Click on that.
>A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?
The concentrations are determined by row and column, thus encode position.
The illustration shows this relatively clearly: at row N column M, you put N drops of solution A and M drops of solution B.
This is shown in the picture; you put X drops of one fluid and Y drops of a different fluid, where (X, Y) is the position of a given test tube.
1) Is DNA "computation" turing-complete?
2) Can DNA make the basic digital logic gates, AND, NOT, NOR, etc.?
If neither of those are true, then this is an incredibly silly article and I'm really impressed.
There is mind-blowing paper, that gives exhaustive anwser to this question: https://hal.inria.fr/hal-01519828/document
This paper is about chemical reaction networks, but in 2010 it was shown, that any chemical reaction network is realizable in DNA: https://www.pnas.org/content/pnas/107/12/5393.full.pdf
2) Yes, it was figured out in 2006, how to do logic gates in DNA: https://science.sciencemag.org/content/314/5805/1585
I wouldn't be so quick to make that call. That we don't know how to do it does not mean it can't be done and there is some weak evidence (innate knowledge) that nature has indeed found a way to do this, just that we don't understand it.
I still feel this way although after a lot of googling it's a little better, I wish I had a good book or other resource on it.