Evolution is a special kind of (machine) learning

Theoretical computer science has a long history of peering through the algorithmic lens at the brain, mind, and learning. In fact, I would argue that the field was born from the epistemological questions of what can our minds learn of mathematical truth through formal proofs. The perspective became more scientific with McCullock & Pitts’ (1943) introduction of finite state machines as models of neural networks and Turing’s B-type neural networks paving the way for our modern treatment of artificial intelligence and machine learning. The connections to biology, unfortunately, are less pronounced. Turing ventured into the field with his important work on morphogenesis, and I believe that he could have contributed to the study of evolution but did not get the chance. This work was followed up with the use of computers in biology, and with heuristic ideas from evolution entering computer science in the form of genetic algorithms. However, these areas remained non-mathematical, with very few provable statements or non-heuristic reasoning. The task of making strong connections between theoretical computer science and evolutionary biology has been left to our generation.

ValiantAlthough the militia of cstheorists reflecting on biology is small, Leslie Valiant is their standard-bearer for the steady march of theoretical computer science into both learning and evolution. Due in part to his efforts, artificial intelligence and machine learning are such well developed fields that their theory branch has its own name and conferences: computational learning theory (CoLT). Much of CoLT rests on Valiant’s (1984) introduction of probably-approximately correct (PAC) learning which — in spite of its name — is one of the most formal and careful ways to understand learnability. The importance of this model cannot be understated, and resulted in Valiant receiving (among many other distinctions) the 2010 Turing award (i.e. the Nobel prize of computer science). Most importantly, his attention was not confined only to pure cstheory, he took his algorithmic insights into biology, specifically computational neuroscience (see Valiant (1994; 2006) for examples), to understand human thought and learning.

Like any good thinker reflecting on biology, Valiant understands the importance of Dobzhansky’s observation that “nothing in biology makes sense except in the light of evolution”. Even for the algorithmic lens it helps to have this illumination. Any understanding of learning mechanisms like the brain is incomplete without an examination of the evolutionary dynamics that shaped these organs. In the mid-2000s, Valiant embarked on the quest of formalizing some of the insights cstheory can offer evolution, culminating in his PAC-based model of evolvability (Valiant, 2009). Although this paper is one of the most frequently cited on TheEGG, I’ve waited until today to give it a dedicated post.
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Algorithmic view of historicity and separation of scales in biology

A Science publications is one of the best ways to launch your career, especially if it is based on your undergraduate work, part of which you carried out with makeshift equipment in your dorm! That is the story of Thomas M.S. Chang, who in 1956 started experiments (partially carried out in his residence room in McGill’s Douglas Hall) that lead to the creation of the first artificial cell (Chang, 1964). This was — in the words of the 1989 New Scientists — an “elegantly simple and intellectually ambitious” idea that “has grown into a dynamic field of biomedical research and development.” A field that promises to connect biology and computer science by physically realizing John von Neumann’s dream of a self-replication machine.

makingBilayer
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Programming playground: Cells as (quantum) computers?

Nearly a year ago, the previous post in this series introduced a way for programmers to play around with biology: a model that simulated the dynamics of a whole cell at unprecedented levels of details. But what if you want to play with the real thing? Can you program a living cell? Can you compute with molecular biology?

Coccolithophore

Could this single-celled photosynthetic algae be your next computer?

Biology inspired computation can probably be traced back as far back as Turing’s (1948) introduction of B-Type neural networks. However, the molecular biology approach is much more recent with Adleman (1994) proposing DNA computing, and Păun (2000) introducing membrane computing with P-systems. These models caused a stir when they appeared due to the ease of misrepresenting their computational power. If you allow the cells or membranes to carry on exponential rate of reproduction for an arbitrarily long time, then these systems can solve NP-complete problems quickly. In fact, it is not hard to show that this model would allow you to solve PSPACE-complete problems. Of course, in any reasonable setting, your cells can only grow at an exponential rate until they reach the carrying capacity of the environment you are growing them in. If you take this into account then efficient DNA and membrane computing are no more powerful than the usual definition of efficient computation — polynomial time on a Turing machine.

The stirred (i.e. inviscid) nature of membrane and (early approaches to) DNA computing provide substantial constraints for empirical realizations, and scalability of bio-computing. In these early models, regulatory molecules are reused in the self-mixing environment of the cell, and gates correspond to chemical reactions. As such, gates are temporary; and the information carrying molecule must change at every step of the computation to avoid being confused with residue from the previous step. This made implementing some gates such as XNOR — output 1 only if both inputs are the same — experimentally impossible (Tamsir, 2011): how would you tell which input is which and how would the gate know it has received both inputs and not just an abnormally high concentration of the first?

To overcome this, Bonnet et al. (2013) designed a cellular computation model that more closely resembles the von Neumann architecture of the device you are reading this post on. In particular, they introduced a cellular analog of the transistor — the transcriptor. The whimsical name comes from the biology process they hijacked for computation, instead of electric current flowing on copper wires the researchers looked at the “transcriptional current” of RNA polymerase on DNA “wires”. Only if a control signal is present does the transcriptor allow RNA polymerase to flow through it; otherwise it blocks them, just like an electric transistor. By putting several transcriptors together, and choosing their control signals, Bonnet et al. (2013) can implement any logic gate (including the previously unrealized NXOR) just as an electrical engineer would with transistors. What matters most for connecting to quantum computing, is the ability to reliably amplify logical signals. With amplifying gates like AND, OR, and XOR, the authors were able to produce more than a 3-fold increase in control signal. For further details on the transcriptor listen to Drew Endy explain his group’s work:

Taking inspiration from biology is not restricted to classical computation. Vlatko Vedral provides a great summary of bio-inspired quantum computing; start from top down, figure out how biology uses quantum effects at room temperature and try to harness them for computation. The first step here, is to find a non-trivial example of quantum effects in use by a biological system. Conveniently, Engel et al. (2007) showed that photosynthesis provides such an example.

During photosynthesis, an incident photon becomes an ‘exciton’ that has to quickly walk through a maze of interconnected chlorophyll molecules to find a site where its energy can be used to phosphorylate used-up ADP into energy-carrying ATP. Unfortunately, if the exciton follows a classical random walk (i.e. spreads out in proportion to the square root of time) then it cannot reach a binding site before decaying. How does biology solve this? The exciton follows a quantum walk! (Rebentrost et al., 2009)

It is cool to know that we can observe a quantum walk, but can that be useful for computation? My former supervisor Andrew Childs (2009; see also Childs et al., 2013) is noted for showing that if we have control over the Hamiltonian defining our quantum walk then we can use the walk to do universal computation. Controlling the Hamiltonian generating a quantum walk is analogous to designing a graph for a classical walk. Theoretical work is still needed to bridge Rebentrost et al. and Childs, since (as Joe Fitzsimons pointed out on G+) the biological quantum walk is not coherent, and the decoherence that is present might doom any attempt at universal computation. The last ingredient that is needed is a classic controller.

Since the graph we need will depend on the specific problem instance we are trying to solve, we will need a classical computer to control the construction of the graph. This is where I hope synthetic biology results like Bonnet et al. (2013) will be useful. The transcriptors could be used as the classic control with which a problem instance is translated into a specific structure of chlorophyll molecules on which a quantum walk is carried out to do the hard part of the computation. The weak quantum signal from this walk can then be measured by the transcriptor-based controller and amplified into a signal that the experimenter can observe on the level of the behavior (say fluorescence) of the cell. Of course, this requires a ridiculous amount of both fundamental work on quantum computing, and bio-engineering. However, could the future of scalable quantum computers be in the noisy world of biology, instead of the sterility of superconductors, photon benches, or ion-traps?

References

Adleman, L. M. (1994). Molecular computation of solutions to combinatorial problems. Science, 266(5187), 1021-1023.

Bonnet J, Yin P, Ortiz ME, Subsoontorn P, & Endy D (2013). Amplifying Genetic Logic Gates. Science PMID: 23539178

Childs, A. M. (2009). Universal computation by quantum walk. Physical review letters, 102(18), 180501. [ArXiv pdf]

Childs, A. M., Gosset, D., & Webb, Z. (2013). Universal Computation by Multiparticle Quantum Walk. Science, 339(6121), 791-794. [ArXiv pdf]

Engel GS, Calhoun TR, Read EL, Ahn TK, Mancal T, Cheng YC et al. (2007). Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446 (7137): 782–6.

Păun, G. (2000). Computing with membranes. Journal of Computer and System Sciences, 61(1), 108-143.

Rebentrost, P., Mohseni, M., Kassal, I., Lloyd, S., & Aspuru-Guzik, A. (2009). Environment-assisted quantum transport. New Journal of Physics, 11(3), 033003. [ArXiv pdf]

Tamsir, A., Tabor, J. J., & Voigt, C. A. (2011). Robust multicellular computing using genetically encoded NOR gates and chemical/wires/’. Nature, 469(7329), 212-215.