Of pigs and people


Calm down, people. Nobody is making human-pig hybrids, even if the news is making a big deal about it. To be honest, I’m not even very impressed with the utility of the experiment, although it is interesting and technically accomplished. It’s being touted as a step in developing pigs with human-derived organs for transplants, and no, I just don’t see it.

The experiments involve xenografts in the blastocyst; that is, they take pluripotent stem cells from one organism, and inject them into the embryos of a different species at a very early stage of development, when the embryo is a hollow ball of cells with an inner cell mass that will eventually become the fetus proper. Then they look for incorporation of the injected cells into the embryo.

It doesn’t always work. The inner cell mass doesn’t necessarily accept these alien cells, or the injected cells don’t thrive in this unusual environment, so you might do the injections, implant the resultant hybrids, and when you open up the host days or weeks later, your injected cells are all gone. It is non-trivial to get this to work, so what they’ve accomplished is technically impressive.

It was a lot of work, too. They injected 2,181 pig blastocysts with human pluripotent stem cells, cultured them in vitro for a few days, and had 2075 embryos that were then implanted in masses of 40-50 embryos into host pigs (which implies that many would be expected to be lost), and collected 186 embryos about 4 weeks later. This is a good yield — I’ve done experiments with much lower rates of success — but the real question is whether any of the human cells were incorporated into the pig embryos.

It worked! They got incorporation of human cells into the pig embryos. Unfortunately, there are a few problems: one is that the embryos with incorporated human cells were significantly retarded in their growth. This ought to be expected; just the timing of development for the two kinds of cells will be out of sync, so I’d actually have expected even greater problems. It’s promising that they got incorporation at all. The other problem is that the incorporation was very low: 0.001% of the embryo’s cells were human. Uh, that’s not very good. If you’re trying to generate organs grown in pigs that have exclusively human antigens, even 99.9% human isn’t going to be good enough — it’s going to trigger an immune response when transplanted.

None of these cells made up the majority of cells in any organ, even; the experiment doesn’t really test the feasibility of accomplishing that, and I suspect that trying to increase the percentage of human cells is going to also increase the incompatibilities and lead to greater and greater rates of developmental failure. They do have some interesting ideas for increasing the rates, though. If the host pig cells are transgenically modified to make them unable to make a pancreas, for instance, any pancreas in the pig would have to be derived from human cells. It would still be infiltrated with pig-derived nerves and blood vessels and connective tissue, though, so that’s insufficient to create a transplant-ready organ.

As pure basic research, it’s a good experiment, and I’ll be interested to see how much further it can go — if nothing else, it’s going to expose evolutionary disparities in development between different mammalian species. The head investigator has an appropriate perspective on it, I think:

Scientific American: So this is very, very basic biology?

JCIB: So I feel that there has been a little bit of exaggeration of where we could go with this now. If you look on the Internet you see images of chimeras between human and animal. And I feel that that’s a little bit of exaggeration. It’s true that it works very nicely between rat and mouse — just this experimental protocol that I am telling you. It’s only a couple of months ago that we have been able to put human cells into another animal. In this case in a mouse and realized that they can differentiate in the three germ layers. The three germ layers are the mesoderm, ectoderm and endoderm that will give rise to the more than 250 different cell types. So that’s a major accomplishment I will say. But from there, dreaming that they will generate a functional structure, I think we’re going to need time and a lot of luck.
So we need to go for a lot of basic research still. It’s my own feeling, of course. There are other people who think that tomorrow we are going to create human organs. And I wish that I am wrong and they are right, but I think it will take time.

Yes! It’s basic research, which is a grand and worthy thing. It’s too bad so much of the press coverage can only grasp it in terms of making organs for human transplantation — I doubt that this approach will ever work for that, but will instead teach us more about development and evolution and molecular biology.

The second week of ecological developmental biology


I’m trying to do weekly assessments of how my new class is going…and also to have a regular record of concerns and successes so I can remind myself of what not to do next time I teach the course. We’re wrapping up a rapid survey of a few developmental systems just to expose them to some of the concepts of the field first; last week we blitzed through early polarity formation and gastrulation. This week we covered neural tube formation and neural crest on Tuesday, and this morning it was limb formation and craniofacial development.

One of my concerns is that it’s really easy for me to dominate the class hour. Yeah, just trigger me with a few phrases like apical ectodermal ridge, progress zone, and zone of polarizing activity, wind me up, and I’ll happily talk about cool experiments and nifty results for a few hours, my eyes glazing over as I forget that those students are there. That’s bad. I have to slap myself out of that habit. And as I mentioned last week, it’s not helping that it’s 8am and the students eyes are a bit glazed over, and I’m concerned about drawing them out to talk more. My ideal class would be one where I just help answer questions for the entire period.

I’m happy to say that, while they aren’t quite at that point yet, the students are warming up and I’ve been getting a few sharp questions, including some that I was unable to answer, which always leaves me overjoyed. Challenging stuff! It’s the best!

It also helped that the last half of today was something completely different: I gave them a short review paper that was rather densely technical on craniofacial development. I warned them that I was throwing them into the deep end of the pool to start with, so we struggled our way through all the acronyms and unexplained syndromes and weird little genes. We puzzled out the molecular basics for common developmental problems, like cleft palate, and more exotic and severe ones like Bartsocas-Papas syndrome (if you read the paper, you might not want to follow up by googling the syndromes, because you’ll encounter lots of tragic children). I learned a few things myself, like how common ribosomopathies are in these craniofacial disorders — there are genes like TCOF1 which produce proteins that act specifically in the nucleolar regions to regulate ribosome expression in specific tissues, and haploinsufficency leads to all kinds of failures in cell migration and differentiation.

I got even more questions. That’s good — I wasn’t looking forward to a semester of talking at nodding heads. I’m beginning to relax a little now.

Next week will be even more of a shock. I won’t be leading the discussions at all — I’ll be the one sitting back and answering questions. Tuesday will be student-led reviews of the stages of human embryonic development, with discussions of clinical correlates. Each student has been assigned a tiny snippet of the sequence to explain to us. Thursday they all have to explain The Triple Helix to me. Next week is all about student engagement!

The first week of Ecological Developmental biology


We’re off to a slow start in my brand new course, largely because I’m in the awkward phase of trying to catch everyone up on the basics before we plunge into the deeper waters, but also because the 8am scheduling is not good for inspiring interaction. Maybe it wasn’t the best decision to begin with a crash course in introductory concepts in developmental biology, because it’s encouraging the students to think that I’m going to do nothing but pour knowledge into their brains, but I’m at a loss to know how to get right into the primary literature without making sure they’re comfortable with the terminology and ideas of the discipline first.

The theme of the first week really was fundamental: polarity. How does a single-celled zygote figure out which end goes up? The students had to read a few chapters from the Gilbert developmental biology text (which is free online, at least in the 6th edition, which is good enough for a quick summary), specifically the chapter on anterior/posterior polarity (which is almost entirely about Drosophila, I added a fair number of examples from Ciona and echinoderms), and the chapter on the organizer in amphibians. That covered a good range, from an organism in which the orientation is pre-specified by maternal RNA (flies) to a case where it’s determined by an environmental interaction — the sperm entry point followed by a cortical rotation reaction (frogs). I also added a bit about mammals, where the decision by the blastula cells to form inner cell mass vs. extra-embryonic membranes is basically a chance event, biased by location in the cluster of early cells.

In all of the examples, though, the key point is that the decisions are not determined exclusively genetically, whatever that would mean, but are contingent on interactions between genes and cytoplasm, which also has structure and pattern, and that that structure may also be influenced by the external environment.

It was fun and familiar to me, but again I’m concerned that when I do most of the work, I’m encouraging passivity in the students. That role is continuing this week, when I give them the stories of neural tube and limb development, as examples of later organ systems that rely on complex interactions. The third week, though, I completely turn the tables on them: they’ve got some reading assignments for that week, and have to do short presentations in class. I’m just going to sit back and ask questions, and hope I don’t get bleary-eyed silence in response.

In my notes for what to do next time I teach this course:

  • Lobby for a better course time. 8am is too damn early for young men and women, even if it is just fine for us oldsters who don’t sleep as much and get up early anyway.

  • This section is a prime candidate for a flipped classroom approach — I could make some short videos ahead of time that they need to watch in their homes, with an accompanying set of questions that they’ll have to discuss in class. The problem there is that in-class responsiveness is one of their weaknesses right now.

  • Later in the course we’ll be trying some different pedagogical approaches: watch for what works best with this group, and maybe revise our crash course section to use that.

I’m a little worried about teaching genetics

I start teaching my genetics class today, and usually I plunge right in to simple Mendelian genetics to get through the easy stuff quickly. I’m making a big change, though, for social and political reasons. In a country rife with neo-Nazis and racism, it’s a bad idea to encourage simplistic thinking about genetics — too many people know a little bit about Mendel’s pea plants (trust me, those traits were chosen for their discontinuous properties and apparent simplicity), a teeny-tiny bit about Darwin and selection, and turn that into sweeping pronouncements about the True Nature of Humanity, as understood by idiots. It’s embarrassing. So I’ve decided to start the genetics course with a little demonstration of humility. Think before you leap to conclusions about how genetics works!

This page on the myths of human genetics is extremely useful for that purpose, so we’re going to go through a few examples right there in the classroom, and show some of the data. There has been a historical tendency to shoehorn traits into a simple Mendelian model, and it’s easy to show that there are cases where that doesn’t work, at all.

We’re also going to take on that popular nonsense about finger lengths, which is just a classic example of overinterpreting tiny amounts of variation (which is still statistically significant!), and making grandiose claims about human nature as derived from a morphological feature. It’s little more than modern palmistry…I’ve even found a page on palmistry that just runs on at length about these ridiculous claims about personality derived from the length of your index finger. And then there’s Joseph Mercola, who claims that you can use finger length to predict your IQ, SAT scores, and of course, autism, in addition to your sexual preferences.

In the end, I’m going to give them a short list of basic intellectual and ethical ideas they ought to have when beginning a study of genetics.

  • Avoid value judgments. What is a flaw to one person might be a virtue to another.

  • Do not concatenate assumptions. An individual might have a particular trait, but it does not imply that they have another, and another, and another, creating a false picture from a single data point.

  • Genetics is a mighty fine hammer; it does not mean everything is a nail. In particular, individuals are the product of gene products interacting with each other and the environment. Don’t disregard one component at the expense of another!

  • Reductionism is essential for a beginning of understanding, but is not sufficient for a thorough understanding. We start simple because that’s what we’re sure of; but our purpose is to build a more accurate model on that foundation, that will inevitably be more complex.

  • We do not understand everything about heredity. An ethical culture refuses to stereotype people on the basis of limited knowledge…or worse, false knowledge.

  • Nullius in verba. Critically assess all claims.

On Monday we’ll review basic Mendelian genetics, which seems to be all students come out of high school knowing anything about (and even at that, they’ll make lots of mistakes). It just seems to me, though, that in the current political climate it is irresponsible to put off a discussion of the limitations of science and ethical concerns until the very end of the course.

Cheap toy failures

The other day, when I was doing some online shopping, an ad popped up for a clip-on microscope for my phone. I thought, “I’m a professional microscopist! I should have a microscope I can carry around in my pocket!” and on a whim, I ordered it. It was only $8, so what the hey.

My dream has not yet been accomplished, I’m sad to report.


First sign of trouble: It claims 60-100x magnification, and looking inside, there’s a cheap plasticky looking lens set well back inside — it’s got maybe a 30mm focal length. Nope, that’s not going to work. I haven’t even tried it yet and I’m doubtful.

Next step is to attach it to your phone, which is really, really easy, using a big clip to clamp it to the camera lens. Except that the clamp is not very solid, and your phone is going to be hanging off to the side. It won’t stay clamped for long. You also just have to eyeball the positioning, since there’s nothing to lock it in alignment with the phone camera lens. Aligning it is a constant struggle. The clamp can’t even hold the phone in place, it certainly won’t hold it in alignment. If you’re lucky enough to get a picture, be prepared for uncontrollable wobbly vignetting.

The next problem: there are a couple of crude, hard to work knobs on the side. One is for magnification: forget it. Set it to the lowest mag, “60x”, and just leave it there. The other is the focus knob, which is also clumsy and hard to turn. Now imagine juggling a loosely held phone clipped to the side of this thing, you’re trying to hold it steady because any wobble will shift the camera lens away from the “microscope”, and you’ll understand that this is a frustrating exercise in imppossibly precise coordination.

So I got it together, pulled out a couple of prepared, stained slides of chick embryo sections, about the easiest targets possible, and tried to take a picture. Nooooope. I briefly saw a few images wander by, afflicted with ghastly spherical and chromatic aberration, but if I moved a finger to click a picture, they’d wander off again. I thought briefly about making it work with a couple of ringstands and some clamps, but realized that the agglomeration would be bigger than my dissecting scope and produce crappier pictures, so there was no point.

Caveat emptor. You get what you pay for. Sometimes less than what you pay for.