The DNA computer: super hard drive of the future?

Liv­ing com­put­ers are the promise of DNA com­put­ing. This tech­nol­o­gy pro­pos­es to exploit the com­pu­ta­tion­al capa­bil­i­ties of cells, replac­ing sil­i­con sys­tems with biotech­nol­o­gy. Although the approach is still in its infan­cy, it is already arous­ing a mix­ture of won­der and fear.

There are the four sym­bols, based on the nucleotide bases, which are the mol­e­cules that con­sti­tute the DNA alpha­bet. A for ade­nine, T for thymine, C for cyto­sine and G for gua­nine. So, just as we code in bina­ry (0, 1) by play­ing on the dif­fer­ence in elec­tri­cal charge, we can encode infor­ma­tion in A, T, C and G. In prin­ci­ple, the con­cept not par­tic­u­lar­ly com­pli­cat­ed to do. The proof: in 2020, Twist Bio­science, an Amer­i­can com­pa­ny spe­cial­is­ing in DNA syn­the­sis, Net­flix and the Zurich Poly­tech­nic announced that they had encod­ed the entire Ger­man series Bio­hack­ers – which cen­tres its plot on the world of syn­thet­ic biol­o­gy – on only a few strands of DNA. A cut­ting-edge com­mu­ni­ca­tions coup!

In fact, in terms of stor­age, DNA com­put­ers are much bet­ter than elec­tron­ic sys­tems. DNA stores infor­ma­tion for thou­sands, even mil­lions of years with­out any ener­gy input. Fos­sil DNA, for exam­ple, has shown us this. So, in that sense, it is a more sus­tain­able solu­tion, with greater infor­ma­tion den­si­ty and biodegrad­abil­i­ty. But the tech­nol­o­gy will not stop there. With an enzyme that can edit bases, a DNA sequence and cel­lu­lar machin­ery that reads DNA and pro­duces bio­log­i­cal mol­e­cules, we already have a DNA com­put­er. The real chal­lenge is the archi­tec­ture of such sys­tems. Lest we for­get John von Neu­mann, the Hun­gar­i­an-Amer­i­can math­e­mati­cian who enabled mod­ern com­put­ing to emerge by invent­ing an archi­tec­ture enabling proces­sors to com­mu­ni­cate with ran­dom access mem­o­ry (RAM) when he was a con­sul­tant at IBM. This is what DNA com­put­ers need today: an architecture.

DNA mol­e­cules are mem­o­ries. As far as proces­sors are con­cerned, recent work has high­light­ed ‘tran­script hubs’ in stem cells, i.e. regions con­cen­trat­ing a large num­ber of sys­tems for read­ing and con­trol­ling DNA machin­ery. These regions are linked to the organ­i­sa­tion of DNA in space, to the way in which dis­tant sequences of the genome can come togeth­er when the DNA strand folds. They are like the micro­proces­sors in DNA com­put­ers, which can con­trol both access to and the read­ing of dif­fer­ent regions of the genome. Thanks to this dis­cov­ery, we can imag­ine that with­in 10 or 20 years, lab­o­ra­to­ries will have real demon­stra­tors of bio­log­i­cal computers.

DNA is a biodegrad­able mate­r­i­al. How­ev­er, DNA com­put­ers will nev­er entire­ly replace sil­i­con chips. We won’t see DNA tele­phones, for exam­ple. This is because to read infor­ma­tion in DNA with cur­rent sequenc­ing tech­niques we must extract the genet­ic mate­r­i­al from the sam­ple and there­fore destroy the chip or cell that con­tained it. What’s more, to encode the infor­ma­tion requires syn­thet­ic biol­o­gy, which is time-con­sum­ing, cost­ly, and dif­fi­cult to gen­er­ate long frag­ments. A great deal of research is need­ed to improve these processes.

In any case, the research that needs to be car­ried out to imag­ine DNA com­put­ers will be very instruc­tive about how liv­ing things work. In this sense, even if this tech­nol­o­gy nev­er comes to fruition, it will advance our under­stand­ing of life. In the same way that the steam engine made it pos­si­ble to mas­ter the laws of ther­mo­dy­nam­ics, DNA com­put­ers will help us to under­stand the ther­mo­dy­nam­ics of life.

Pro­gram­ming a cell is a way of talk­ing to a life form. By pro­duc­ing trans­mis­si­ble trans­for­ma­tions in these DNA com­put­ers, we will be able to com­mu­ni­cate with liv­ing beings over sev­er­al gen­er­a­tions. DNA is a uni­ver­sal lan­guage between species on Earth. In this sense, isn’t read­ing the DNA of an extinct species a form of com­mu­ni­ca­tion, even if it is one-way? How­ev­er, the lan­guage of liv­ing things is not like a human lan­guage. We shouldn’t hold out too much hope that we can crack jokes with trees or talk to a wool­ly mam­moth as if we were talk­ing to our dog.

DNA com­put­ing has the poten­tial, yes. But is it accept­able? Just because we have the pow­er to do some­thing doesn’t mean we should. Pur­pose is a bioeth­i­cal issue that must not be ignored while we devel­op this tech­nol­o­gy. And this ques­tion is all the more impor­tant because most DNA com­put­ers will not be vis­i­ble. It will be hid­den inside cells, sim­i­lar to those that make up our bod­ies. Only spe­cial­ists will recog­nise the pres­ence of DNA computers. 

Agnès Vernet