The Wiring Problem: How a Brain Gets Built

An adult human brain holds about 86 billion neurons. The genome that builds it has about 20,000 genes that code for proteins.

Each of those neurons connects to many others, often thousands, so the brain carries on the order of 100 trillion synapses. Published estimates run from about 10¹⁴ to 10¹⁵, so treat the figure as an order of magnitude. The genes are fewer than the neurons by a factor of millions and fewer than the synapses by a factor of billions. Most of them are also busy running the ordinary business of a cell. Yet human brains come out wired in much the same way, one after another.

That is the question this course keeps asking: “How are these neural circuits assembled during embryonic and postnatal development?”

The wiring problem: a few labels, many rules

Start with the numbers. The neuron count comes from a 2009 study by Frederico Azevedo, Suzana Herculano-Houzel and colleagues, who counted cell nuclei in the brains of four adult men and found 86.1 billion neurons, give or take about 8 billion. It is an estimate from a small sample, and it is the best direct count we have.

Now suppose the genome tried to label every neuron. Labels turn out to be cheap. Take 72 genes and let each be either on or off in a given cell. They can be combined in 2⁷² ways:

labels = 2ⁿ for n on-off genes; 2⁷² ≈ 4.7 × 10²¹, which is more than 10¹⁰ times the number of neurons

Families of genes that could do this exist. The clustered protocadherins are three neighbouring gene clusters holding more than 50 genes in the human genome, and the Eph receptors and their ephrin ligands, membrane proteins that sort cells by contact, number around twenty between the two sides.

The trouble is in the connections. A unique tag says which cell a neuron is. It says nothing about which of the other 86 billion cells it should connect to. In 2003 Bente Pakkenberg and colleagues estimated about 1.5 × 10¹⁴ synapses in the human neocortex alone. A list with one instruction per synapse would be billions of times longer than the list of genes. The information that wires a brain has to be compressed into rules that apply in many places at once.

Here is an analogy. A city cannot hand every driver a written route to every address. It posts street names that change in order and a few rules of the road, and drivers find their own way. Development does something similar, with three strategies this course will meet again and again.

• Graded and combinatorial labels. A molecule whose amount rises smoothly across a tissue gives every cell a different value without a separate gene for each. Two or three gradients at right angles act like map coordinates.
• Local rules that give global order. A growth cone, the moving tip of a growing axon, senses only its immediate surroundings. Simple local rules (grow toward more of a cue, avoid another, stop where a suitable partner is found) can still build a map that spans millimetres.
• Overproduce, then select. Make more neurons and more connections than the finished circuit will keep, then remove the wrong ones. The removal uses information, such as which connections are active together, that the tissue measures after the connections form, so the genome never has to store it.

Cues that guide these steps act at different ranges, from direct contact between membranes to molecules that spread through tissue, as that lesson described for signals in general.

What the simplest circuit teaches

A neural circuit is a population of neurons joined by synapses to carry out a specific function. The simplest one you can feel is the knee-jerk, or stretch reflex.

Tap the tendon below the kneecap and the quadriceps muscle on the front of the thigh is stretched. Stretch receptors in that muscle excite sensory neurons, whose cell bodies sit in a ganglion beside the spinal cord. In the cord, each sensory axon excites the motor neurons that drive the quadriceps, and the muscle contracts. The same sensory axon also excites an inhibitory interneuron, which silences the motor neurons of the hamstring, the opposing muscle on the back of the thigh. The leg kicks.

This tiny circuit carries six lessons that hold for every circuit in the course:

1. Neurons work in circuits, not alone.
2. The direction in which information flows matters.
3. Neurons come in many kinds: sensory, motor and interneurons here, each with its own shape.
4. The information is carried as electrical signals.
5. Connections are either excitatory or inhibitory.
6. Connections are selective and precise. The sensory neuron excites its own muscle’s motor neurons and, through the interneuron, inhibits those of the opposing muscle.

The last lesson is the developmental one. Every one of those connections had to be made during development, with the right partner and the right sign.

How many kinds of neurons must be wired? Take one class, the retinal ganglion cells that carry signals from eye to brain. Early anatomists sorted them into a few classes by shape. A 2002 survey of 520 mouse retinal ganglion cells sorted them by shape into four main groups, and a 2019 single-cell survey of gene expression in mouse reported 46 types, so the count depends on the method. Each type has its own targets.

A circuit that works while it is being built

Compare a “Neural Circuits vs. Electronic Circuits” build. An electronic circuit is useless until the last component is soldered in, and once it is finished its wiring does not change with use. A developing neural circuit works while it is being built. Embryonic neurons fire, and connections made early carry signals while later ones are still growing. Those signals, and later experience, help decide which connections stay.

One way to see this is to count synapses across a human life. In 1979 Peter Huttenlocher counted synapses by electron microscopy in a region of human frontal cortex, in tissue from people of many ages. Synapse density was already high at birth, rose during infancy, peaked at about one to two years of age at roughly half again the adult value, and then declined through childhood and adolescence. The cortex appears to make more synapses than it keeps and to keep the ones that are selected. The course returns to this, and to what happens “when assembly goes wrong”, in later lessons.

Animals with small nervous systems show what a detailed wiring diagram looks like. In 1986 John White, Eileen Southgate, Nichol Thomson and Sydney Brenner reconstructed the whole nervous system of the worm Caenorhabditis elegans from serial electron micrographs: 302 neurons in the adult hermaphrodite, with thousands of synapses. Even there, with every cell named, the genome does not appear to specify each connection one by one.

The roadmap: from induction to refinement

“Neural circuits develop in several steps.” The course follows them in order:

1. Induction. Part of the ectoderm, the embryo’s outer layer of cells, is told to become neural tissue.
2. Patterning. That tissue is divided into regions along its long axis and from back to belly.
3. Generation of neurons and glia. Dividing precursors make neurons and their support cells, the glia, in a set order.
4. Migration. Young neurons move from where they were born to where they will work.
5. Axon growth and guidance. Each neuron sends out an axon, which steers toward its target.
6. Target selection. The axon picks a region, then particular cells within it.
7. Naturally occurring death. Many of the neurons made die, shaped by competition for support from their targets.
8. Synapse formation. Contacts become working synapses.
9. Activity-dependent refinement. Use sharpens the connections and removes some.

The steps overlap in time, and many of them reuse the same signals: Wnt, BMP, Hedgehog and Notch, the pathways of the Cell Signaling course.

The course gathers them into three acts. Act 1 is coalescence: where cells go, and how scattered migrating cells gather into ganglia and layers. Act 2 is guidance: how axons find their targets. Act 3 is competition: who survives. That act opens with the question “Why make neurons just to kill them?”, and with nerve growth factor, a protein made by targets that neurons compete for, which that lesson traced to its discovery.

Design problem

You have about 20,000 genes and must wire a visual system in which each retinal axon ends at the right point in the brain, preserving the layout of the retina. Propose two strategies that need far fewer than one gene per connection. Then design one experiment that tells whether a given connection is set by genes or by activity.