1. EE 194 Advanced VLSI Spring 2018 Tufts University
Instructor: Joel Grodstein
Lecture 8: Biological computing

2. EE 194/Adv. VLSI Joel Grodstein
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. EE 194/Adv. VLSI Joel Grodstein
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. EE 194/Adv. VLSI Joel Grodstein
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-
lacI promoter
lacI
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
Glucose → less CAP
lacI -
CAP +
lac promoter
lacY
lacZ
EE 194/Adv. VLSI Joel Grodstein

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

9. EE 194/Adv. VLSI Joel Grodstein
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. EE 194/Adv. VLSI Joel Grodstein
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. EE 194/Adv. VLSI Joel Grodstein
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. EE 194/Adv. VLSI Joel Grodstein
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