EE 194 Advanced VLSI

1. EE 194Advanced VLSI Spring 2018 Tufts University Instructor: Joel Grodstein joel.grodstein@tufts.edu Lecture 8: Biological computing

2. Computers are made of… • Transistors. Lots of them! • How many transistors on an Nvidia Volta? • 21 billion! • So many that we don’t really design transistors any more. We don’t even design gates. • We design RTL, or assemble IP. EE 194/Adv. VLSI Joel Grodstein

3. A human computer is made of… • Your body does a lot of computing too. What part of your body does the thinking? • Brain, mostly • Brains are built from … • How many neurons in a brain? • 100B • Similar to a Volta! • Is a Volta 1/5 as powerful as your brain? • A transistor has one input; most gates have 2-3 inputs. • A neuron can have 1000s of inputs; the brain has 100T synapses. • A neuron does substantial analog computation, way more than 1 transistor • Conclusion: all of us are way smarter than a Volta  neurons EE 194/Adv. VLSI Joel Grodstein

4. We’re not talking about brains • Brains are not the only computing machines in biology • Bacteria are smart, too. Really? • Bacteria like to eat sugars: glucose and lactose • Digesting glucose is more efficient; lactose works too • Digesting each sugar requires producing specific enzymes (which cost “money;” i.e., ATP) • Bacteria software: if (there is glucose around) produce glucose enzymes if (there is lactose but not glucose) produce lactose enzymes • And bacteria don’t have a brain. Not one single neuron at all • How can they execute this software? EE 194/Adv. VLSI Joel Grodstein

5. Your body is made of… • Cells. Lots of cells. • 37 trillion human cells (“only” 100B neurons) • many more bacterial cells (a bacteria is just one cell) • What is a cell? Arguably, the smallest part that can reproduce. Which leads us to… • DNA • Every cell in your body has a full copy of your DNA • It’s the software that makes you you. • It’s the key to one type of biological computing: gene regulatory networks. EE 194/Adv. VLSI Joel Grodstein

6. Your body runs on proteins • The cell contains machinery to build most any protein • DNA contains the data structure listing how to build various proteins • DNA also contains the software that controls which proteins get built when EE 194/Adv. VLSI Joel Grodstein

7. The “gates” behind lactose • The proteins lacY and lacZ help digest lactose • The lac promoter says when lacY and lacZ are produced • I.e., when lacI is absent and CAP is present • Glucose metabolism uses up CAP • LacI is produced by another stretch of DNA • active only when lactose is absent lactose - lacI promoter lacI Glucose → less CAP lacI - CAP + lac promoter lacY lacZ EE 194/Adv. VLSI Joel Grodstein

8. We can draw this as gates lacI lactose • The lac promoter is an AND gate • The lacI promoter is inverting lactose • Another inverter for glucose lactose - lacI promoter lacI CAP glucose Glucose → less CAP lacI - CAP + lac promoter lacY lacZ CAP lacI lacY, lacZ EE 194/Adv. VLSI Joel Grodstein

9. Where are the wires? • Note that we did not draw any wires! • VLSI chips have wires that conduct electrons exactly where we want them • Chemicals move randomly in cells by diffusion • Cells have no wires • If we want two inverters, they had better use different chemicals! lacI lactose CAP glucose CAP lacI lacY, lacZ EE 194/Adv. VLSI Joel Grodstein

10. Summary so far • We have digital logic gates made from biological parts (DNA, RNA, proteins) • Your body is full of these; so is a bacteria’s “body.” • Every cell in your body is a sophisticated computing machine, all by itself. • Every bacteria is, too • None of this has anything to do with neurons or brains. EE 194/Adv. VLSI Joel Grodstein

11. Other digital logic in your cells • Our cells have many common patterns of logic • Oscillators. Any idea why? • Set your 24-hour body rhythm (2017 Nobel Prize) • RS latches. • Create memory. Every cell in your body has memory! • Delay lines, pulse generators • Just-in-time manufacturing EE 194/Adv. VLSI Joel Grodstein

12. So what? • Well, it’s cool to understand, I think. • Recombinant DNA technology • We have the ability to go into a single cell and alter its DNA • We can (somewhat) program a bacteria however we like • Our programming ability is limited • 21B transistors on a Volta • A dozen or so gates in a cell (best so far) • So why do we care? EE 194/Adv. VLSI Joel Grodstein

13. Cells can reproduce • When a cell reproduces, its altered DNA gets reproduced • A bacteria may have only a dozen custom gates • but that bacteria can swim in your bloodstream • and reproduce • How fast can bacteria reproduce? • 20-30 minutes for E.coli. • How many bacteria get made in 24 hours? • So, about 50 generations in 24 hours. • 250 is about 1015, or 1000 trillion • And people are working very hard to extend that “dozen” gates up higher. EE 194/Adv. VLSI Joel Grodstein

14. What is the potential for this technology? • Talk about cancer fighter, and recognizing the combination of multiple markers. EE 194/Adv. VLSI Joel Grodstein