grading continues
May. 17th, 2019 12:10 am![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
sciatrix...but at least I'm just doing the extra choice question now, in which students propose a future lab experiment they'd like to do over the course of the (~twelve-week) lab. They're supposed to explain what model system they want to use, the learning objectives the lab would accomplish, and the experimental idea itself.
Here are some of the more entertaining suggestions, organized by category:
Wildly Ambitious And Totally Impractical:
-"we could do an addiction genetics experiment locating a gene implicated in alcohol addiction in mice, including exposing mice to steady alcohol and measuring withdrawal levels!"
-"we could look at epigenetics in fruit flies by exposing successive generations to limited nutrients and seeing how this changes methylomes!"
-"what if we [made up the concept of ChIP-SEQ] and did that on human DNA"
-let's look at gene by environment interactions in zebrafish embryos!
-let's make our own GMO crops in the lab!
-let's genetically modify a line of human T cells that will then express a specific antigen receptor, using viral vectors to modify the cells and then testing them on a cancer line! (bless this student, who ended their answer with "you would need loads of money to pull this off and probably the entire semester for students to make it work, and also waivers for working with viruses--but it would be so cool!!!")
-can we make a hybrid fruit like a tangelo and breed plants for desired traits?
-what if we MADE HUMAN CANCER by targeting p53 and transgenically destroying it in human cell tissue?
Could We Genotype Ourselves More?*
-what if we tested everyone in the lab for a locus controlling how cilantro tastes
-what if we did ancestry testing on ourselves like in 23 and Me
-what if we all checked to see if we were pre-disposed to a disease
-what if we did a forensic hair analysis and then extracted DNA and tested the genes from our hair?
-what if we sampled our skin's microbiome and sequenced it? or our mouths? or other parts of ourselves?
-what if we typed our own blood?
-what if we sequenced everyone and made a phylogenetic tree of the whole class?
-what if we did the same thing but we extracted proteins from our own blood instead?
-what if we tested the whole class for Huntington's?
Entertaining Suggestions
-"what if we repeated the fly lab to study Mendelian assortment but using guinea pigs or mice instead? Then we could pet them."
-"what if instead of using fly eye color we looked at mutations like EXTRA EYES OR MOUTHS"
-"what if we tested to see if vegan/vegetarian products are actually meatless?"
-"use a less-annoying novel organism for inheritance patterns"
-"what if we extracted DNA from all of our pets and did a cladogram of them"
-"could we create illustrations using streaking of bacterial with plasmids incorporating fluorescent proteins onto plates? we could use strains with different colors!"
-"what if we did a species ID lab with fruits so we didn't have to smell the fish smell?"
-"what if everyone genotyped their dogs and then brought in the dogs so we could pet them as we reviewed the results? I like petting dogs."
Actual Potentially Workable Ideas
-"Could we try using CRISPR/CAS in bacteria? It's an important technique, and I think that it would be good for us to understand how it works."
-"What if we cultured the bacteria living on our hands or our cell phones and then did a metabarcoding study on the colonies we isolated?" (probably a little too ambitious, but could be workable)
-"What if we did a mouse experiment where we collect the DNA from different tissues?" I'm going to guess that my students are not going to be proficient enough to play with RNA transcriptomics, but this would definitely be a fun project if I trusted them not to contaminate the RNA.
-"What if we did a study with C. elegans involving checking the motility of two different genotypic lines to show how behaviors can be underlaid by genetic variation?"
-"What if we tested the accuracy of various types of PCR on a human sample?"
-"Could we look at RNAi, maybe in C. elegans?"
*We already do two separate labs involving extracting and isolating students' own DNA, including a modified VNTR/DNA fingerprinting lab and a population genetics lab involving a neutral locus. These tend to be very popular with students when they work, although the fingerprinting lab, which requires students to estimate their allele frequencies in the context of ethnicity, can be a nightmare for us when students don't enter their own data (and we have to put something in on ethnicity) or when students are mixed-race and quite reasonably think that categorizing themselves is kind of dumb. I had one student a few years ago who pointed out that he could easily categorize himself as African, Asian, or European all at once, and what the hell should he put down?
Here are some of the more entertaining suggestions, organized by category:
Wildly Ambitious And Totally Impractical:
-"we could do an addiction genetics experiment locating a gene implicated in alcohol addiction in mice, including exposing mice to steady alcohol and measuring withdrawal levels!"
-"we could look at epigenetics in fruit flies by exposing successive generations to limited nutrients and seeing how this changes methylomes!"
-"what if we [made up the concept of ChIP-SEQ] and did that on human DNA"
-let's look at gene by environment interactions in zebrafish embryos!
-let's make our own GMO crops in the lab!
-let's genetically modify a line of human T cells that will then express a specific antigen receptor, using viral vectors to modify the cells and then testing them on a cancer line! (bless this student, who ended their answer with "you would need loads of money to pull this off and probably the entire semester for students to make it work, and also waivers for working with viruses--but it would be so cool!!!")
-can we make a hybrid fruit like a tangelo and breed plants for desired traits?
-what if we MADE HUMAN CANCER by targeting p53 and transgenically destroying it in human cell tissue?
Could We Genotype Ourselves More?*
-what if we tested everyone in the lab for a locus controlling how cilantro tastes
-what if we did ancestry testing on ourselves like in 23 and Me
-what if we all checked to see if we were pre-disposed to a disease
-what if we did a forensic hair analysis and then extracted DNA and tested the genes from our hair?
-what if we sampled our skin's microbiome and sequenced it? or our mouths? or other parts of ourselves?
-what if we typed our own blood?
-what if we sequenced everyone and made a phylogenetic tree of the whole class?
-what if we did the same thing but we extracted proteins from our own blood instead?
-what if we tested the whole class for Huntington's?
Entertaining Suggestions
-"what if we repeated the fly lab to study Mendelian assortment but using guinea pigs or mice instead? Then we could pet them."
-"what if instead of using fly eye color we looked at mutations like EXTRA EYES OR MOUTHS"
-"what if we tested to see if vegan/vegetarian products are actually meatless?"
-"use a less-annoying novel organism for inheritance patterns"
-"what if we extracted DNA from all of our pets and did a cladogram of them"
-"could we create illustrations using streaking of bacterial with plasmids incorporating fluorescent proteins onto plates? we could use strains with different colors!"
-"what if we did a species ID lab with fruits so we didn't have to smell the fish smell?"
-"what if everyone genotyped their dogs and then brought in the dogs so we could pet them as we reviewed the results? I like petting dogs."
Actual Potentially Workable Ideas
-"Could we try using CRISPR/CAS in bacteria? It's an important technique, and I think that it would be good for us to understand how it works."
-"What if we cultured the bacteria living on our hands or our cell phones and then did a metabarcoding study on the colonies we isolated?" (probably a little too ambitious, but could be workable)
-"What if we did a mouse experiment where we collect the DNA from different tissues?" I'm going to guess that my students are not going to be proficient enough to play with RNA transcriptomics, but this would definitely be a fun project if I trusted them not to contaminate the RNA.
-"What if we did a study with C. elegans involving checking the motility of two different genotypic lines to show how behaviors can be underlaid by genetic variation?"
-"What if we tested the accuracy of various types of PCR on a human sample?"
-"Could we look at RNAi, maybe in C. elegans?"
*We already do two separate labs involving extracting and isolating students' own DNA, including a modified VNTR/DNA fingerprinting lab and a population genetics lab involving a neutral locus. These tend to be very popular with students when they work, although the fingerprinting lab, which requires students to estimate their allele frequencies in the context of ethnicity, can be a nightmare for us when students don't enter their own data (and we have to put something in on ethnicity) or when students are mixed-race and quite reasonably think that categorizing themselves is kind of dumb. I had one student a few years ago who pointed out that he could easily categorize himself as African, Asian, or European all at once, and what the hell should he put down?
OT
Date: 2019-05-19 04:52 am (UTC)Re: OT
Date: 2019-05-20 07:39 pm (UTC)Name's familiar, but I don't know him personally--although the work looks familiar, too. (I love spider behavior work, especially wolf and jumping spiders; they do some really interesting things.)
...come to think of it, I'm pretty sure that this meme (which I have used in legit professional presentations and adore; contains spider) comes back to him in some way. They totally are cute.
And then I found his paper, which I'm giggling about. Based on my experience, I would have generally agreed with his contention that fewer papers on invertebrate behavior are published (although I'm glad he did the number-crunching!), although I'm not sure that I'd say there's a bias against people studying those systems: I'm not sure that this study is designed to test that! Looking at the number of manuscripts accepted on vertebrates vs invertebrates doesn't tell you anything, after all, about the total number submitted, or the total number of people working in the field. And of course if there are more people out there working on vertebrates, they will tend to cite each other more frequently than people working on invertebrates because they're referring back to what is or is not possible within the paradigm of the species system. This is why I've read every single paper that touches on my species of mouse--because I need to know them very well in order to reference and contextualize my own work, even if they're not directly related to my work in the context of the overarching topic. In the same way, folks working on Hawaiian crickets are probably all reading all of the Hawaiian cricket literature, and also more broadly reading a lot of papers about other kinds of crickets to cite them when they're writing about feasibility. But if there are fewer people working in invertebrates and the invertebrates are distantly related--just as I do not read a ton of papers about hyenas to justify the feasibility of my methods, someone working on crickets is not going to read a ton of papers about wolf spiders--you won't get this species-system effect of increased citation.
(I came from invertebrates--I worked on Drosophila, although not melanogaster, in undergrad--and my work is actually heavily influenced by work originally done in rhinoceros beetles, even though I work on vertebrates right now. This is one of only three vertebrate labs I even applied to when I was looking at grad schools, and the only mammalian one--one works with frogs, and one with swallows. I was also looking at labs working with crickets, bedbugs, snails, and more flies, as I recall.)
Oddly enough, I'm submitting a manuscript to Animal Behaviour myself, just as soon as I wrangle my boss into looking at it one last time. I'll probably catch up with him on that tomorrow.
Re: OT
Date: 2019-05-20 08:33 pm (UTC)They totally are cute.
They do have puppy-dog eyes! AWWWWWWWW!
One of the things his work really raises for me is the question of what this research is really for. What are we trying to know, and why?
For instance, if why we, like, as a species, are studying the behavior of other organisms because we want to know what the full range of possibilities are - possibly to contextualize and inform human behavior - then, yes, lack of coverage is a problem. The question of what all those under- or un-studied beetles are up to becomes important, and science should get on that.
But if the purpose of studying the behavior of other organisms is to consider them as representing possible human phenomena - for instance, as I understand it, your own work on singing mice has a lot of obvious import for suggesting possible scopes of the role of leptin in humans – then the less like a human, or less informative of something about humans, an organism is, the less interesting it is to study. The reason for all the D. melanogaster studies is those gloriously big, chunky, easy to see chromosomes; it was like a Fisher-Price My First Organism(tm) kit for the nascent field of genetic analysis, back when.
Now, obviously, the answer is "well, both, and other things too". But that in turn raises the question for me of who the, for want of a better term, consumers of this research are. Yes, other scientists working in the same field, sure; but that's not the justification for pursuing this knowledge, is it? I'm wondering how (and whether) the scientific discoveries on, say, singing mice make it out of the circle of researchers into singing mice and to other scientists who are working on problems that would be usefully informed about what's up with singing mice, who have no idea, not being singing mice scientists (or even animal ethologists) that there is anything pertinent to their work about singing mice.
I mean. Do you know the story about Charles Silverstein's lit review and the removal of homosexuality from the DSM?
Anyways. I take issue with the contention that choice of organism should not proceed choice of question. Yes, there's types of science that absolutely should be conducted question-first. But there's this other type of science which is incredibly important and under-appreciated which proceeds from the question, such as it is, "So what is [species] up to, anyways?" And the idea that that's bad science or illegitimate leaves me both aghast and unsurprised.
The history of medicine – and very specifically the history of mental illness – is littered with studies attempting to explain phenomena which didn't exist. And should really have been proceeded by studies establishing that the phenomenon actually existed. Observational studies. Studies which don't "answer a question" – but do indeed pose one. Studies which document the existence of phenomena and the methodologies for making those observations so that other observers can confirm that the phenomena exist.
The bias in medical science against doing that kind of work is enormous. There's reasons like "wow, that's difficult and expensive to do" for some things, but beyond that, there's this nasty idea that it's not really scientific because it's not experimental.
There's a sneering aphorism I've heard, "All science is either math or butterfly collecting", and it makes me, on behalf of every lepidopterist ever, want to burn down a particle accelorator.
I, uh, oh, sorry, did you want this soapbox back?
Re: OT
Date: 2019-05-20 10:49 pm (UTC)Well, the short answer is that answers vary wildly, but usually come down to "scientists got curious and found a way to justify that we should know this." The longer answer has more to do with the way that we execute funding for scientists and for specific projects. The way this boils down within the field of animal behavior is that most of us in the USA and behavioral ecology are funded by the National Science Foundation (NSF), which exists for pure basic research of the "but how does the world work?" variety and bookmarks a certain amount of money for the fields of evolutionary biology, animal behavior, and so forth each year. However, the NSF has a vastly smaller pot of money available than the National Institutes of Health (NIH), and honestly smaller than the National Institute of Mental Health (NIMH). So if you can make a good case that your research is relevant to understanding human health, you can compete for NIH grants as well as NSF grants, and because there are way more of them, you might have a better shot.
This is how both my current PI and now the other guy working on singing mice have argued at various points that understanding singing mice and their communicatory behavior is the key to understanding autism. (My current PI has wrapped his mind around this being a bad idea; the other gentleman hasn't, which has directly led to me being buttonholed about autism research when I talk about my study system in the goddamn YMCA, which is possibly my least favorite activity ever.) At some point, I will almost certainly make an argument that my work on leptin can Combat The Obesity Epidemic (TM), even though that's not the primary thing that's motivating my research (and insofar as it is involved, I'm thinking about the relationship of body weight to chronic stressors and how/why bodies allocate resources rather than "how do we make people stop being fat" per se). Certain topics within human health have an especially large amount of research money available to them; obesity and autism are both part of that category.
So you kind of get both kinds, and people in this field will sometimes go "fine, I'm going to see if I can't fund my lab and pay my graduate students a summer salary with this grant I've spun to argue that my work will answer this human health question that is sort of tangentially related to my work, if you squint and tilt your head." That usually doesn't mean they're planning to do anything differently in their research, mind you--the motivations that people lay out in the grant applications can sometimes be very, very different to the way they spin their work in presentations to other researchers in the same field. But it is something that really sits in the back of people's minds.
The US does in fact provide a lot of research funding, and I only know a little bit about how it works in Canada and the UK, but I believe it's broadly similar.
for instance, as I understand it, your own work on singing mice has a lot of obvious import for suggesting possible scopes of the role of leptin in humans
LOL, but that's not remotely related to why I got interested in leptin or even, honestly, why I wound up working with singing mice, or why my boss did. (My boss picked them up as a species because he wanted to do fieldwork in Central America and also work on a rodent with some kind of interesting behavior, and he went flipping through a field guide. No lie! And before I joined the lab, we were doing species interactions work with aggression; the move to condition dependence and leptin is something that in a very real way was driven by my interests and the bee I got in my bonnet about a particular paper that was published in Science around the time I started graduate school, and more directly about the talk that researcher gave at the 2012 Evolution conference I saw.) Right now, I'm seeing people begin to talk about leptin in... oh, to my knowledge, three other species in this context, in at least one case I'm going to bet is a direct result of my own lab's work. Those species are weakly electric fish, garter snakes, and tungara frogs.
But that in turn raises the question for me of who the, for want of a better term, consumers of this research are
Often, the direct consumers are intended to be other researchers asking other broad questions about animal behavior--we're a basic field (rather than an applied field), so our questions are focused on "well, how does this work?" rather than "can we solve this problem in the world?" Beyond that point, I think the prevailing assumption is that if something turns out to be applicable in another field, folks there had better be reading very widely and collaborating with people who have different interests and backgrounds so that ideally, someone will notice that and bring it up in their own field. (And people in this field often do read extremely widely themselves, and have areas of expertise that often have overlaps into other areas of biology or sometimes chemistry, physics or mathematics. Especially in sensory biology.)
I'm wondering how (and whether) the scientific discoveries on, say, singing mice make it out of the circle of researchers into singing mice and to other scientists who are working on problems that would be usefully informed about what's up with singing mice, who have no idea, not being singing mice scientists (or even animal ethologists) that there is anything pertinent to their work about singing mice.
In animal ethology, this kind of work is spread very widely across taxonomy. Within the broader question of energy balance and energy allocation, and how sexual signaling evolves, I actually read a lot of literature on teleost fish, crickets, spiders, and beetles in addition to birds and mammals, and in particular I would say mammals make up a comparatively small proportion of the elaborated trait literature I devour because mammalian signaling is so often focused on chemosensory communication, and as a discipline we're way better at studying acoustic and visual signaling. For the most part, within my field we read very widely across taxonomies, which is part of why Rosenthal is making the argument that we don't read enough invertebrate work--he's saying that bird and mammal researchers should be reading as much invertebrate work as anything in vertebrates. I should add, though, that he's making the argument that we should read widely explicitly because we are a field which exists for the sake of understanding natural phenomena rather than for the sake of executing human health outcomes--again, we're a basic research field rather than an applied field. We should be going out and looking at different corners of the animal kingdom just in case there's something cool there. And that's actually very explicitly part of his argument in his paper:
"Understanding the dynamics of behaviour in one taxonomic group is an important goal, but the entire field moves forward only when a series of such studies across a variety of taxa allows leaps in global understanding. For example, testing established theory across new taxonomic groups can lead to the discovery that paradigms established in popular model taxa do not hold generally (e.g. Zuk, Garcia-Gonzalez, Herberstein, & Simmons, 2014). If we restrict the bulk of our research effort to a subset of taxa, we risk drawing conclusions that are invalid at broader scales by assuming that the predominant behaviours in that subset of taxa are universal."
Which boils down to: "look, we need to look at all the taxa, not just the ones closest to us, because they might be doing something different." Let me know if you want/need the full paper; it's actually a pretty fun ride, nearly as fun as the NPR segment.
I mean. Do you know the story about Charles Silverstein's lit review and the removal of homosexuality from the DSM?
In the broad strokes, yes, but I bet you've got a much more rich version of the story than the one I know. If you'd like to, I'd love to hear your version!
And don't mind about the soapbox--I have this conversation very frequently with a dear friend of mine, who is motivated by what we call "natural history" work that is very much about the kind of observational work that you describe. ("Where is this animal found? What eats it? How do we know?" That sort of thing--and I am desperate to work on a species where we actually know that, because the paucity of information on my guys that now exists makes me perpetually sad.) Ironically enough, he is a dyed-in-the-wool bird person who is way more taxonomically attached to his birds than I am.
more as I'm rechecking the NPR piece--you know, I was at Animal Behaviour in 2016. I wasn't exactly firing on all cylinders--I think I was still recovering from my sister's wedding at the time, which was an experience I found traumatic, and I was pretty cognitively beat up at the time. I don't think I went to this talk, but if I'd realized I would have loved it. (I just looked up the program, and I'm pretty sure I went to another track: I still remember going to "Sexual Selection in Fruit Flies: Courtship Interference versus Female Choice" in the slot immediately before it, and I think I went to a talk about multimodal sensory signaling instead. Shame! And, you know, I'd say that I was illustrating his point, except that that fruit fly talk is one of relatively few talks I remember extremely clearly from that conference, and I went out of my way to go listen--and his own talk was in a modeling track, which is not my cup of tea normally... but man, that fruit fly talk was so elegant, and such a thoughtful discussion of the problems inherent in female choice paradigms as applied to fruit flies.)
Come to think of it, I mostly read house mouse papers in order to mine other fields (usually conducted in the context of improving human health!) for information that I can use to make arguments about basic research. And then I read very very widely in a wide variety of species to look at the kinds of questions I actually am interested in and want to answer. That's the way I think it should be.