Today in my class we talked for a while about epigenetics. I used it as an example of a term we’d encountered more than once in our ecological developmental biology course, but that has some complicated ambiguity and fuzziness that has led to all kinds of weird popular confusions about the subject. I was also using it as an example of critical analysis of a paper, as I discussed yesterday, and it was a lead-up to having the students discuss papers on relevant topics they were interested in — so we spent most of our time talking about other things.

But I’m going to talk now about just this one paper I read. You see, Larry Moran and I have been having this long-running disagreement about epigenetics — nothing hostile, just an occasional cocked eyebrow in each other’s direction — which you can see on display in this article by Larry on epigenetics, in which he disagrees with my definition of epigenetics, back in 2008. Here’s my definition:

Epigenetics is the study of heritable traits that are not dependent on the primary sequence of DNA.

And here’s the definition used in Gilbert’s text:

…molecular processes around DNA that regulate genome activity that are independent DNA sequence and are mitotically stable.

And here’s Larry’s objection:

Here’s the problem. If this is epigenetics then what’s the point? When I was growing up we had a perfectly good term for these phenomena—it was regulation of gene expression. Why is there a movement among animal developmental biologists to use “epigenetics” to refer to a well-understood phenomenon?

While I agree that “epigenetics” is a huge, broad, diverse category of phenomena, I think he’s overlooking a key point to claim it is synonymous with gene regulation. It is gene regulation that is heritable and mitotically stable. It’s still far too open-ended, but it’s not just any old example of gene regulation.

It’s also clear and consistent. Larry challenges us with eight instances of regulatory phenomena and asks which ones qualify as epigenetic. Easy. 1, 2, 6, 7, 8. Those are the ones where he specifically mentions multi-generational inheritance of a regulatory state. 3, 4, and 5 describe responses within a single cell in a single generation (5 is sneaky, though: Drosophila oocytes are having gene expression modified in ways that might be transmitted through multiple generations — it’s just that those cells are being loaded with bicoid RNA, not having their bicoid genes being set to a sex-specific state).

I am also comfortable with the idea that inheritance of the regulatory state of the lac operon is an example of epigenetics. It’s arguable whether that’s a useful category, but it does fit the definition.

So one approach that could be taken is to come up with a more specific or more practical definition.

Larry has a more recent article in which he agrees with a new paper by Deans and Maggert that tries to do exactly that. It also takes a much appreciated historical approach, giving the various definitions that have been wafting about since the 1930s. For instance, here’s Waddington’s ancient physiological definition:

the branch of biology that studies the causal interactions between genes and their products which bring the phenotype into being

Yes, I agree — that would simply be gene regulation nowadays. You can’t blame us wicked developmental biologists for promoting that one, though, because we don’t use it anymore.

Now we favor the Holliday definition:

the study of changes in gene function that are mitotically and/or meiotically heritable and that do not entail change in DNA sequence.

To me, “heritable” is the magic word that makes all the difference. This, however, is not enough for Deans and Maggert. They want to add more focus, often a good thing, and narrow the definition. I was not happy with their argument, and thought it poorly made, though. See if you can find what was objectionable in this section of their paper (I highlighted it to make it easy, an epigenetic modification that does not change the sequence of the letters in the text.)

We don’t feel that it is possible to reconcile Waddington’s focus on gene regulation with Holliday’s more specific criteria within one field and still maintain the level of clarity needed to produce a useful definition. The efforts to preserve a relationship between these two conceptualizations have been impaired by the fact that there are just too many phenomena, with too few mechanistic connections, to categorize into one field. Also, among the definitions that do maintain the requirement of heritability, we feel that many lack the detail to be functionally useful in directing the testing of specific hypotheses, particularly as it relates to the location or site (cytoplasm or nucleus) of epigenetic phenomena. To mitigate these shortcomings, we advocate defining epigenetics as “the study of phenomena and mechanisms that cause chromosome-bound, heritable changes to gene expression that are not dependent on changes to DNA sequence.”

We feel that this definition makes a strong distinction between gene regulation (Waddington’s definition) and epigenetic inheritance (Holliday’s definition), and also emphasizes that epigenetic phenomena must deal exclusively with chromosome-bound changes. By making these distinctions, we have efficiently separated expressional changes caused by cytoplasmic compounds, which are more closely tied to gene regulation, from those which occur on, or in close association to, the chromosome. Doing so makes the focus of the field much clearer and identifies epigenetic mechanisms more explicitly.

We feel that this definition touches on several important elements not encompassed by other definitions, yet commonly implied in most uses. To further explain the reasoning behind our definition, as well as its utility for improving epigenetic research, we would like to offer a clarification and a test.

Yeesh. I don’t feel that your personall feelings are a strong argument, and I cringed when I hit that page. At least edit it to remove the emphasis on your personal discomfort; just say that the old definitions lack detail, rather than that you feel they lack detail.

So let’s pull out their shiny new definition.

the study of phenomena and mechanisms that cause chromosome-bound, heritable changes to gene expression that are not dependent on changes to DNA sequence

Well. All this fuss for a single change, the addition of the phrase chromosome-bound. That’s it. I agree, it does narrow the topic, but it’s still covering an awful lot of territory. I’m not feelin’ it. I have the impression that the primary virtue of the new definition is that it reduces a class of phenomena to a subset that many people are comfortable studying already, and in part reinforces a gene-centered perspective on cellular behavior.

It also leaves me wondering…what about the inheritance of cytoplasmic or membrane-bound factors that induce consistent changes in gene expression in daughter cells? The gene regulation aspect may be mundane, but it’s the inheritance that is interesting. Under the Deans and Maggert definition, this is no longer under the umbrella of epigenetics — it’s something different for which we have no general name now.

It makes Larry happier, though.

I think this is a useful definition. Nobody cares if dividing E. coli cells inherit molecules of lac repressor and continue to repress the lac operon. That’s a trivial form of epigenetics that never posed a threat to our understanding of evolution.

That’s odd. I do care that the lac repressor is cytoplasmically inherited, but then my primary interests, in the most general form, would be in the patterns of stability and change in cellular properties, rather than the metabolism of sugar. Telling me that I should only pay attention to inherited proteins or methylation states that are directly bound to DNA seems arbitrary.

I also don’t consider “poses a threat to our understanding of evolution” to be a relevant criterion. I agree that lac repressors don’t challenge evolutionary theory, but neither do heritable histone modifications or methylation. I’m one of those people who think epigenetics (even under the old definition!) is important and interesting, but doesn’t affect evolutionary theory much at all.

Larry and I agree.

Methylation is trivial.

Well then, if inheritance of the lac operon is such a trivial form of epigenetics that it should be excluded from the definition, then we apparently need yet another definition that excludes the triviality of methylation.

Or, really, we should recognize that “trivial” is not a good reason to exclude something.

I will still second Larry’s argument that none of this stuff overthrows modern evolutionary theory in any way. It would require extremely persistent inheritance of an epigenetic state over many generations to have those kinds of repercussions.

(The Gilbert text does mention one significant effect: the toadflax plant, Linaria vulgaris, has a radically different flower morph, Peloria, that Linnaeus himself classified as a different species. As it turns out, they only differ in the methylation state of the cycloidea gene, but the DNA sequence is identical. This is a case of an epigenetic change persisting for hundreds of generations. It’s a rare case, though, and also…would still definitely fall under the Deans and Maggert definition.)

In class last week, we continued our discussion of developmental plasticity and began to talk about epigenetics, and in particular, the underlying molecular mechanisms for epigenetic inheritance. In addition, students had to discuss papers on plasticity that they’d researched. Some of the topics covered were: sneaker males and alternative reproductive strategies; aggression in dog breeds, how much is genetic and how much is training; temperature-dependent and behavior-dependent sex determination in reptiles and fish; and physiological responses to variations in gravity (someone has put pregnant rats in a centrifuge and looked at the effects of 2 gravities on development). It was all fun stuff, and I made the students do all the work. Perfect!

This week they have another assignment. There’s a common problem in student writing about science: they tend to describe what a paper says. That makes for very boring reading, I’m sorry to say — if I just wanted to know what was in the paper, I could read it myself, after all. So this week they’ve been asked to write a critical analysis of a science paper relevant to the course. This is a routine skill that needs to be cultivated and practiced.

What’s involved? You first have to identify a key question or assertion in the paper, or even in a short section of the paper, and ask yourself if the authors have adequately defended the claim. Even if you agree with the claim, and think it’s eminently reasonable, you have to approach it as a critic and try to tear it down.

I’m going to try to lead by example, so I have given them a couple of papers to read ahead of time. One is “Novelty and Innovation in the History of Life” by Douglas Erwin, which makes an argument that should be familiar to the students, because we’ve already talked about some of the concepts. Here’s the abstract:

The history of life as documented by the fossil record encompasses evolutionary diversifications at scales ranging from the Ediacaran–Cambrian explosion of animal life and the invasion of land by vascular plants, insects and vertebrates to the diversification of flowering plants over the past 100 million years and the radiation of horses. Morphological novelty and innovation has been a recurrent theme. The architects of the modern synthesis of evolutionary theory made three claims about evolutionary novelty and innovation: first, that all diversifications in the history of life represent adaptive radiations; second, that adaptive radiations are driven principally by ecological opportunity rather than by the supply of new morphological novelties, thus the primary questions about novelty and innovation focus on their ecological and evolutionary success; and third, that the rate of morphological divergence between taxa was more rapid early in the history of a clade but slowed over time as ecological opportunities declined. These claims have strongly influenced subsequent generations of evolutionary biologists, yet over the past two decades each has been challenged by data from the fossil record, by the results of comparative phylogenetic analyses and through insights from evolutionary developmental biology. Consequently a broader view of novelty and innovation is required. An outstanding issue for future work is identifying the circumstances associated with different styles of diversification and whether their frequency has changed through the history of life.

Let’s take that apart. Erwin is saying that there are some long-held assumptions in evolutionary biology that he is going to suggest are possibly invalid. Those assumptions are:

1. Diversity is the product of adaptive radiations;

2. Radiations are driven by ecological opportunities; and

3. Most morphological variants emerge early, in the process of filling open niches.

He’s going to propose alternative processes.

1. Initially non-adaptive variants are going to generate morphological diversity;

2. Novel forms construct the niches that they will fill; and

3. Variation is a constant event in a lineage.

I am predisposed to like those new perspectives, and I’m also biased by the evidence we’ve discussed in class, that ecology and development are in a constant state of reciprocal feedback. But rather than reporting and describing this paper as something that reinforces my views, I need to examine it critically. Does Erwin adequately support his claims? Are there significant questions he does not address? He’s also given us a list of sources of evidence that he’ll use to challenge orthodoxy: “the fossil record, by the results of comparative phylogenetic analyses and through insights from evolutionary developmental biology”. Does he succeed?

I’m just going to consider his first point, whether it is adaptive variation that drives radiations (lesson for students: focus. Better to do one thing well than 3 things poorly). His evidence in this section comes primarily from analysis of the fossil record, which is going to raise some objections.

Erwin does not deny the existence of adaptive radiations, and wisely begins by discussing known examples. He cites the work on Galapagos finches, where we have strong evidence of morphology being shaped by adaptive necessity. He also discusses cichlids, where variations in the environment have clearly played a role in, for instance, feeding adaptations. To then argue for alternative mechanisms using the fossil record is problematic: adaptive radiations are seen in cases where you’ve got close-up, fine-grained observations of single clades, but the evidence for adaptation fades when you use a more coarse-grained, less well-sampled method?

One piece of evidence presented is basically an absence-of-evidence argument. There is a lack of evidence of character displacement in the fossil record. Character displacement is the shift in morphology away from each other from two similar species competing in an overlapping range; it ought to be seen if two populations are adapting to avoid competition.

His argument that solutions to adaptive problems can exist for milllions of years without a radiation occurring is more interesting. He points to Anolis lizards in the Caribbean that converge on similar strategies when they evolve on different islands as an indication that the potential for particular morphologies is present in the species before they find themself with fresh opportunities on a new island. The carnivore fossil record shows a limited repertoire of optimal feeding strategies, which canids exploited repeatedly. Sea urchins have been evolving to follow similar feeding patterns repeatedly, as well.

It’s a somewhat frustrating argument, though. He’s trying to show that a radiation can’t have been driven by the acquisition of an adaptation if the adaptation had existed for long periods previously without a radiation. I can see the point, but one could argue that the radiation depended on both the prior potential in the organism and ecological circumstance, which is part of his second point…which makes point #1 and point #2 codependent on one another.

I’d have to say that I wasn’t entirely satisfied that he’d supported his first conclusion to my satisfaction. It’s also the case that he’s arguing that both adaptive and non-adaptive radiations occur, meaning it’s a quantitative question of which of the two is most important under what conditions, and he hasn’t done anything to measure that balance. I don’t reject the hypothesis, but I also don’t think the work has been done to confirm it — yet. He concludes the whole paper by predicting that gene regulatory networks are characterized by stability, so morphological novelties may be based on features established outside the core GRNs, and are thus more flexible. I don’t know. That’s definitely well outside anything you could figure out with fossils, so it’s going to require a different approach.

That’s how I’m going to talk about a paper I enjoyed with my students (and you Pharyngula readers think I’m harsh with my mere movie reviews). I’m also going to discuss a second paper on epigenetics that I didn’t care much for — the heart of the paper is a painful exercise in writing about how they feel about certain definitions of epigenetics which made me snarl — but I still think it made some valid points.

That’s really the purpose of the whole exercise. Stop treating science papers as holy writ that you can’t challenge; think critically about everything, and try to find logical holes that can be plugged with better evidence. That’s how science gets better and better. These are smart students and they just need to learn that they can actually disagree with Famous Scientists.

The real challenge, too, is that my plan is to talk about these examples for maybe 15 minutes, and then put the students into groups to discuss the papers they’ll have brought with them, trying to punch holes in them. It might be fun. It might be difficult and frustrating. As mentioned, one of the annoyances of student writing is that too often they think of it as reporting, describing what’s in it rather than engaging with the ideas with their very own brain and questioning what the paper says.

Hey, maybe I shouldn’t call it “reporting” since that’s also what journalists should be doing, but too often aren’t. Reciting summaries credulously shouldn’t be what either scientists or journalists do.

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Erwin DH (2015) Novelty and Innovation in the History of Life. Curr Biol 5;25(19):R930-40.

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.