What I taught today: gene regulation and signaling

Today was more context and a bit of a caution for my developmental biology course. I warned them that we’d be primarily talking about animals and plants (and mostly animals at that), but that actually, all of the general processes we’re describing are found in bacteria and other single-celled organisms — that in a lot of ways, microbiology is actually another developmental biology course. Yes, I went there: developmental biologists tend to be imperialists who see all the other sciences as mere subsets of the one true science. Of course, you could also take that as developmental biology being a synthetic discipline that steals bits and pieces from everywhere…

So the primary lessons today were reviews of stuff these students should have gotten in cell and molecular biology, with bits of biochemistry and microbiology thrown in. We talked about genes getting switched on and off, and the example I used was the classic: the lac operon in E. coli. What? You don’t know about it? It’s a beautiful system, in which the bacterium switches on the genes needed for digesting the sugar lactose only when the sugar is available in the environment. I showed this nice little 3 minute video:

Switching genes on and off? That’s development! It gets a little more intricate in multicellular animals, but all of the fundamental logic is right there in E. coli: activators and repressors, positive and negative feedback, the boolean logic of gene regulation. I also mentioned that when we’re reading Carroll’s Endless Forms Most Beautiful, he’s going to make a big deal out of exactly this kind of regulation, but I want them to remember that it’s not unique to butterflies or fruit flies or frogs, it’s a common theme in all kinds of diverse cells.

We then talked about cell signaling. How does a cell know which genes are supposed to be off and on? It interacts with its environment (as in the lac operon) or its neighbors to make decisions about activity. To illustrate that, we went through quorum sensing and biofilms — again, cell signaling is not unique to animal development, it was all worked out in principle in single-celled organisms. I gave them a little foreshadowing and mentioned that we’d be discussing Sonic Hedgehog and Notch and Delta later in the course, classic examples of signaling in multicellular systems, but in bacteria we have things like hapR and AHL signaling.

Finally, I raised the issue of a phenomenon we’ll be talking about on Wednesday: patterning. Why aren’t your arms growing from your hips, why don’t you have fingers on your feet instead of toes, why are your eyes paired and on the front of your head? Because there is positional information in the embryo that can be read by cells and tissues and lead to development of appropriate structures in their proper places. But once more, this is not unique to multicellular animals. A paramecium, for instance, is not a generic blob, but has a definite shape and orientation; it has organelles in predictable places, and is covered with a nearly crystalline lattice of cilia with specific axes of orientation. I showed them choanoflagellates and pointed out that these protists, representing a multicellular precursor, had a specific shape and a collar organ in a specific functional location: how do they know how to do that?

That’s the question we’ll be asking next. I warned them too that I won’t be lecturing at them on Wednesday, so they’d better have their morning coffee. I’m expecting them to read a review paper on positional information in embryos (pdf), and I’m going to make them explain it all to me for a change.

Slides for this talk (pdf)

For Wednesday:

Kerszberg M, Wolpert L (2007) Specifying Positional Information in the Embryo: Looking Beyond Morphogens. Cell 130(2):205–209.

The Ubiquity of Exaptation

On Thursday, I gave a talk at the University of Minnesota at the request of the CASH group on a rather broad subject: evolution and development of the nervous system. That’s a rather big umbrella, and I had to narrow it down a lot. I say, a lot. The details of this subject are voluminous and complex, and this was a lecture to a general audience, so I couldn’t even assume a basic science background. So I had to think a bit.

I started the process of working up this talk by asking a basic question: how did something as complex as the nervous system form? That’s actually not a difficult problem — evolution excels at generating complexity — but I knew from experience that the first hurdle to overcome would be a common assumption, the idea that it was all the product of

purposeful processes, ranging from adaptationist compulsion to god’s own intent — that drive organisms to produce smarter creatures. I decided that what I wanted to make clear is that the origin of many fundamental traits of the nervous system is by way of chance and historical constraints, that the primitive utility of some of the things we take for granted in the physiology of the brain does not lie in anything even close to cognition. The roots of the nervous system are in surprisingly rocky ground for brains, and selection’s role has been to sculpt the gnarly, weird branches of chance into a graceful and useful shape.

So I put together a talk called The Ubiquity of Exaptation (2.7M pdf). The barebones presentation itself might not be very informative, I’m afraid, since it’s a lot of pictures and diagrams, so I’ll try to give a brief summary of the argument here.

The subtitle of the talk is “Nothing evolved for a purpose”, and I mean that most seriously. Evolved innovations find utility in promoting survival, and can be honed by selection, but they aren’t put there in the organism for a purpose. The rule in evolution is exaptation, the cooption of elements for use in new properties, with a following shift in function. It’s difficult to just explain, so I picked three examples from the evolution of the nervous system that I hoped would clarify the point. The three were 1) the electrical properties of the cell membrane, which are really a byproduct of mechanisms of maintaining salt balance; 2) synaptic signaling, which coopts cellular machinery that evolved for secretion and detecting external signals; and 3) pathfinding by neurons, the process that generates patterned connectivity between cells, and which uses the same mechanisms of cellular motility that we find in free-living single celled organisms.

  1. Excitability. This was the toughest of the three to explain, because I wasn’t talking to an audience of biophysicists. Our neurons (actually, all of our cells; even egg cells have interesting electrical properties) maintain an electrical potential, a voltage, across their membranes that you can measure with very tiny electrodes. This voltage undergoes short, sharp transient changes that produce action potentials, waves of current that move down the length of the cell. How do they do that? Where did this amazing electrical trick come from?

    The explanation lies in a common problem. Our cells have membranes that are permeable to water, and they also must contain a collection of proteins that are not present in the external environment. The presence of these functional solutes inside the cell should create an osmotic gradient, so that water would flow in constantly, trying to dilute the interior to be iso-osmotic (the same concentration) as the outside. Some cells have different ways to cope: one way is to build cell walls that retain the concentration in the interior with pressure; another is to have specialized organelles to constantly pump out water. Our cells use a clever and rather lazy scheme: they compensate for the high internal concentration of essential proteins by creating a high external concentration of some other substance, which is impermeant to the cell membrane. Water has the same concentration inside and outside, but there are different distributions of solutes inside and outside.

    What we use to generate these differential distributions are ionic salts, charged molecules. Positively charged sodium ions are high in concentration outside, while positively charged potassium ions and negatively (on average) charged proteins are high in concentration on the inside. Because these are charged ions, their distribution also coincidentally sets up a voltage difference. I confess, I did show the audience the Goldman equation, which is a little scary, but I reassured them that they didn’t have to calculate it — they just needed to understand that the arrangements of salts in cells and the extracellular space generates a voltage that is simply derived from the physical and chemical properties of the situation.

    We use variations in these voltages to send electrical signals down the length of our nerves, but they initially evolved as a mechanism to cope with maintaining our salt balance. We’re also used to thinking of these electrical abilities as being part of a complicated nervous apparatus, but initially, they found utility in single-celled organisms. As an example, I described the behavior of paramecia. The paramecium swims about by beating cilia, like little oars; the membrane of the paramecium maintains an electrical potential, and also contains selectively permeable ion channels that can be switched open or closed. When the organism bumps into an obstacle, the channels open, calcium rushes in as the potential changes, and the cilia all reverse the direction of their beating, making the paramecium tumble backwards. The electrical properties of your brain are also functionally useful to single-celled organisms.

    I concluded this section by trying to reassure everyone that their brain is something more than just a collection of paramecia swimming about. Although the general properties of the membrane are the same, evolution has also refined and expanded the capabilities of the neuronal membrane: there are many different kinds of ion channels, which we can see by their homology to one another are also products of evolution, and each one is specialized in unique ways to add flexibility to the behavioral repertoire of the cell. The origins of the electrical properties are a byproduct of salt homeostasis, but once that little bit of function is available, selection can amplify and hone the response of the system to get some remarkably sophisticated results.

  2. Synaptic signaling. Shuttling electrical signals across the membrane of a cell is one thing, but a nervous system is another: that requires that multiple cells send signals to one another. A wave of current flowing through a membrane in one cell needs to be transmitted to an adjacent cell, and the way we do that is through specialized connections called synapses. A chemical synapse is a specialized junction between two cells: on one side, the presynaptic side, a change in membrane voltage triggers the release of chemicals into the extracellular space; on the recieving side, the post-synaptic side, there are localized collections of receptors for that chemical signal, and when they bind the chemical (called a neurotransmitter), they cause changes in the membrane voltage on their side.

    Once again, the cell simply reuses machinery that evolved for other purposes to carry out these functions. Cells use a secretory apparatus all over the place; we package up hormones or enzymes or other chemicals into small balloons of membrane called vesicles, and we can export them to the outside of the cell by simply fusing the vesicle with the cell membrane. Lots our cells do this, not just neurons, and it’s also a common function in single celled organisms. Brewer’s yeast, for instance, contain significant pieces of the membrane-associated signaling complex, or MASC, althogh they of course don’t make true synapses, which requires two cells working together in a complementary fashion.

    I described the situation in Trichoplax, an extremely simple multicellular organism which only has four cell types. The Trichoplax genome has been sequenced, and found to contain a surprising number of the proteins used in synaptic signaling…but it doesn’t have a brain or any kind of nervous system, and none of its four cell types are neurons. What a mindless slug like Trichoplax uses these proteins for is secretion: it makes digestive enzymes, not neurotransmitters, and sprays them out onto the substrate to dissolve its food. Again, in more derived organisms with nervous systems, they have simply coopted this machinery to use in signaling between neurons.

    As usual, I had to make sure that nobody came away from this thinking their brain was a conglomeration of Trichoplax squirting digestive enzymes around. Yeast, choanoflagellates, and sponges have very primitive precursors to the synapse; we can look at the evolutionary history of the structure and see extensive refinement and elaboration. The modern vertebrate synapse is built from over 1500 different proteins — it’s grown and grown and grown from its simpler beginnings.

  3. Pathfinding. How do we make circuits of neurons? I’ve just explained how we can conduct electrical signals down single cells, and how pairs of cells can communicate with each other, but we also need to be able to connect up neurons in reliable and useful ways, making complex patterned arrangements of cells in the brain. We actually know a fair amount about how neurons in the developing nervous system do that.

    Young nerve cells form a structure called the growth cone, an amoeboid process that contains growing pieces of the cell skeleton (fibers made of proteins like tubulin and actin), enzymes that act as motor proteins, cytoplasm, and membrane. These structures move: veils of membrane called lamellopodia flutter about, antennae-like rods called filopodia extend and probe the environment, and the whole bloblike mass expands in particular directions by the bulk flow of cytoplasm. The cell body stays in place, usually, and it sends out this little engine of movement that trundles away, leaving an axon behind it.

    “Amoeboid” is the magic word. The growth cone uses the same cellular machinery single-celled organisms use for movement on a substrate. Once again, exaptation strikes, and the processes that amoebae use to move and find microorganismal prey are the same ones that the cells in your brain used to lay down pathways of circuitry in your brain.

    Furthermore, there is no grand blueprint of the brain anywhere in the system. Growing neurons are best thought of as simple cellular automata which contain a fairly simple set of rules that lead them to follow entirely local cues to a final destination. I described some of the work that David Bentley did years ago (and also some of my old grasshopper work) that showed that not only can the cues be identified in the environment, but that experimental ablation of those intermediate targets can produce cells that are very confused and make erroneous navigational decisions.

    We also contain a great many possible signals: long- and short-range cues, signals that attract or repel, and also signals that can change gene expression inside the neuron and change its behavior in even more complicated ways. It’s still at its core an elaboration of behaviors found in protists and even bacteria; we are looking at amazingly powerful emergent behaviors that arise from simple mechanisms.

And that was the story. Properties of the nervous system that are key to its function and that many of us naively regard as unique to neurons are actually expanded, elaborated, specialized versions of properties that are also present in organisms that lack brains, nervous systems, or even neurons…and that aren’t even multicellular. This is precisely what we’d expect from evolutionary origins, that everything would have its source in simpler precursors. Furthermore, it’s a mistake to try and shoehorn those precursors into necessarily filling the same functions as their descendants today. Cooption is the rule. Even the brains of which we are so proud are byblows of more fundamental functions, like homeostasis, feeding, and locomotion.

My inner Bennett Cerf

These will
keep you groaning all day.

A fellow accidentally ingested some alpha-L-glucose and discovered that he had no ill effects. Apparently he was ambidextrose.

A bloke walks into a pub, and asks for a pint of Adenosinetriphosphate. The barman says “That’ll be 80p (ATP) please!”
(note 100p = £1, and ATP is short for Adenosinetriphosphate, but you already knew that.)

Some genetic researchers were studying Acinonyx jubatus to find out why he had a high abnormal sperm count. They gave a group of these animals a histocompatibility (tissue-type) test.

“This is singular,” observed one to the other. “Every one of these cats gave the same answers.”

“Aw,” drawled the other, “they’re all a bunch of cheetahs.

Did you hear about the biologist who had twins? She baptized one and kept the other as a control.

Q: What tool is used to measure a hole in the head?

A: A Phineas gage.

Q: Why didn’t the dendrochronologist get married?

A: All he ever dated was trees!

Q: What is the only thing worse than a mecium?
A: A Paramecium

Q: What does the H. in Jesus H. Christ stand for?

A: In order of increasing groans:

1: Hallowed.

2: Harold. (As in, “Harold be thy name.)

3: Haploid. (Best of all.)

Q: As what did the antibody go to the Halloween costume party?

A: As an “immunogobulin”.

Q: What’s a biologists definition of a graph?

A: An animal with a long neck

Adenine proposing to guanine:”You know dear, mismatches are made in heaven”.

What did one thermophilic bacteriologist say online to another?

“I think you are really hot. Your PCR mine?”

There are some happy sciences, but others are not so happy. A case in point concerns embryologists who tend to be a morose and saddened group than most. No wonder. One of the first things they learn is that our lives are ova before they’ve begun.

A red blood cell walked into a busy restaurant. The hostess asked, “Would you like to sit at the bar?”

The red cell answered, “No thanks, I’ll just circulate.

How do you recognize a native American cell biologist?

He lives in ATP!

They were the first to attempt to colonize Mars. They knew it would be difficult , but they were determined to succeed.

They had landed with grass seeds to plant and embryos of horse, sheep and cattle. But the grass wouldn’t grow, and none of the calves survived. The horses and sheep were doing well, but there not enough animals to meet their needs.

So they sent a message to earth asking for more sheep and horses and a replacement for the cattle and grass. They particularly wanted an animal that could be used as meat in place of beef.

Earth radioed back asking if venison would be satisfactory and the colonists replied it was.

Finally a space shuttle arrived with the needed supplies. The bill of lading was rushed to the leader of the colony who then spoke to his consul, “we got everything we asked for,” he shouted. . . . “They sent mare zygotes and doe zygotes and little lambs and ivy.”