Let it Go.

Note: Slight trigger warning here. I talk about depression and suicidal thoughts herein. For those who could care less about such things, read on! 

This post was inspired after reading Adam Rubin’s latest ‘Experimental Error’ column in Science Careers. I think it’s one of the posts that makes me nervous to post. I worry that disclosing my (largely) past issues with depression hurts me (even while feeling that literally changing my brain required enormous fortitude and determination on my part). I worry how I probably come off as a whiny and overly sensitive human in a world that does not value sensitivity in any job; I hate feeling like I’m one of those so called ‘orchid’ people…needing fairly specific conditions to thrive (The dreaded response: empathy? compassion? People first? Listening? Learning/education? HAHAHAAHAHA! Most ridiculous things we’ve ever heard of. Get out of this office, we’re about the dollars! //Note: I too, am about dollars on some level, just not to the exclusion of other things; maybe where I differ is wanting to build for the long-term, not the next quarter…something else no longer really valued it seems to me). I realize that the world is full of decent people too. I hope you enjoy this rather experimental essay 

Let it Go.

I want to let go. I want all of us to let it go.

The cold will never bother us if we do. I’m pretty convinced.

Read this and this from Sarah K. Peck and Andrew Rubin, respectively.

We exist in a state of terror as young scientists (or a lot of us do, perhaps some even unaware– the terror can be hard to distinguish from the air we breathe).

We’re frozen with fear.

With the pressure to be perfect.

With the fear of making mistakes.

With the fear that anything but the tenure-track is ‘failure’.

Fearing we’re not one of the super-humans that can ‘make it’ in science.

Vulnerability isn’t allowed (The beginnings of change, innovation, learning, and purpose– not necessarily fabulous wealth/success, but deeper satisfaction in work, definitely).

I spend a lot of time thinking about what makes scientists able to produce high quality work.

The conclusion from my anecdotal experience is a combination of effort, space/time to think, permission to make mistakes, an iterating growth mindset, some autonomy, and an open environment where learning from one another is encouraged and people aren’t afraid to ask for things they need (no, that does not mean always getting them).

And my own watchword here: Don’t become clinically depressed. Learn the signs and if it seems like your emotions have been flattened for a few weeks straight, seek help, nip it in the bud quickly. Believe me you don’t want the feeling that you & the world would be better off if you were dead (in part because you functionally don’t fully see the difference between being alive and being dead), hoping a bus will run you over. That’s not a brain space for doing good science; you can do science, but you certainly won’t be firing on all cylinders. Even now that I’m a lot less depressed, my mind still has those thoughts sometimes. It’s a mental habit I’m trying to get out of still.

Chris Hadfield talks about fear and danger and how to take risks and be prepared.

15-20 years of training in every possible scenario and then you can launch yourself into space. Get started learning the whole system you’ll be working in and you’ll be ready to take chances and put yourself out of this world.

And yet, today’s academic system doesn’t instill that very well (or doesn’t allow the time for that to happen; the long learning phase seems to get clipped off even as experiments get bigger, more technical and more complex).

The work has to get done and yet there seems to be ‘no time’ for training people to do it even though we’re labeled grad students and postdocs; both considered ‘training phases’.

Fantastic mentorship exists and there are people that thrive, but I’m sure we can do better, do better work and improve the scientific enterprise without making a sizable population of participants within it mentally ill (again that does not mean it shouldn’t be hard; science will always be hard work and take effort).

Feedback is often judgmental and harsh, instilling a fixed mindset, believing learning isn’t possible, but that our talent/intelligence is a fixed trait.

Pressure and uncertainty can be paralyzing. One misstep and we’ll be unemployable forever. Nothing but academia is acceptable. Don’t tack against the wind. If you’re not in the lab, you must be wasting time.

And if you can’t do it on your own, don’t bother. Collaborate and be a good citizen, but stand out. Work alone, but as a team.

Being able to learn, problem solve, ask good questions, and perhaps be unleashed to do grow and do great things somewhere won’t happen because you’re convinced you’re an impostor.

Never enough. Ever.

There’s a fog that settles over your mind. You have dead eyes. Helplessness sets in.

I’ve felt all of these things and I’m starting to get to a place where the cold doesn’t bother me anymore.

There’s a space for me somewhere; either in science or not, I don’t know, but it exists and I can rule there, even if it is just me writing for a small audience on my blog.

Let it Go. We’re all human. Fallible and ridiculous creatures.

Take the work, but not yourself, too seriously. Try stuff. Figure out how to do it in small scale first if it’s something new to you that will be big later. And write. Write it all down– take notes.  And don’t be afraid to get your work out there or toss out ideas (guess what, vast majority will be terrible and probably wrong, who cares?).

Always feeling like I did the rational thing hasn’t worked. So I’m trying irrational (to me; often that means leaping without 100% certainty of outcome…obviously I still try to be as informed as possible ).

I adopted a cat a month ago. That makes no logical sense for my life, but I think it was a good decision for the most part.

My joke about this blog has been that it’s about what not to do as a postdoc/academic. I hope it’s helped a few people, mainly me, of course, because I write for myself too (and it has helped me).

Success is not a straight road. It’s a maze with lots of blind turns and dead ends. We won’t all end up in academia, but I’m sure most of us will find satisfying work somewhere, some how.

Let it go. All of us. We’ll likely do better work, help each other more, give better feedback, and not always act so terrified of everything and everyone. Funding is tight, work/life balance doesn’t exist, we don’t know enough to advance to the next phase since you only get hired to do something someone needs done, who can demonstrate they’re awesome in a loud way (never mind if they’ve hastily published crap papers in high profile journals…it’s out there, so they must be good somehow).

I feel passionate enough about studying the ideal knowledge worker that I’d be willing to switch fields and make a study of just how to optimize humans to do science. It’s certainly not a one size fits all formula (e.g. it’ll likely be different for introverts and extroverts), but as with depression, there are likely hallmarks of it as well as individual level manifestations.

Keep going. Get out into the cold. It’s not as bad as you think/feel, we’re wired for survival (take that from a former near-suicidal person). Expose yourself to small ‘dangers’ at first and watch yourself grow. It won’t be pretty. Winter is always coming. Staying in a warm cocoon leads to mere survival whereas the science enterprise not only must survive, but thrive as well (advancement & knowledge is our business). I’m sick of mere survival for myself. Let it go.

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GMO labeling.

I had a creative thought about GM labeling that might also teach people something about the evolutionary past of plants and agriculture (both of which involved extensive genetic modification of plants before what is considered GM came into being in the 1980’s:

CompleteGMLabels
Figure 1. Complete GM history of crop plants. (A) A made up phylogenetic tree of plants, focusing on Zea mays, with notes (small arrows). Small arrow s indicate notes/interesting evolutionary features/sarcastic notes (B) A basic lineage of modern hexaploid wheat. Purple circles indicate areas of modern species, even if there is a GM trait present. ya = years ago.

I believe something like the cartoons in Figure 1 (panel A has made up branches to the dendrogram, but the relationships are basically right. Panel B is a very basic diagram of the species’ genomes that hybridized to form hexaploid wheat) tell the full evolutionary history including any genetic modifications in modern times. If a GM label exists, it has to be more than ‘GMO’…that’s not the important part in a lot of ways; the specific modification is (as in, what trait has been conferred or taken away from the plant through that genetic modification). Heck, maybe with this ‘full’ label, even Monsanto would be in favor of labeling their products since it provides the full picture of plant modification (both the natural and some unnantural).

Some thoughts on GM & companies behind them (& why they’re so loathed by some):

—Yes, Monsanto is a large for-profit biotech company that is part of the industrial agriculture complex that basically owns the US Government and can get whatever policy they want passed (fact is, it still costs $10 million to go through the regulatory hurdles to bring one of their GM crops to market– which is why all GM crops come from large companies…they’re the only ones who can afford to go through the regulatory approval process).

—Monsanto sells a product. It is genuinely useful to some farmers in some places. In other places, less so. Mileage will vary. Now, Monsanto’s marketers would (probably) tell you that GM is a panacea, but it’s not. They’re great for some situations, but right now at least, certainly not ALL situations. But I’m sure scientists are hard at work coming up with new GM products that might genuinely help even more farmers grow higher yielding food on their land.

—A lot of the hate Monsanto gets is exactly why anyone hates a large corporation (or the government)…it’s a big entity that seems to get away with things the rest of us who are *ACTUALLY* people can’t get away with (tax shelters, anyone?).

—The optics of a large company these days are inherently terrible: They own Washington & get all the legislation they want (just see the FCC & Net Neutrality debate) and will do anything to enrich executives at the expense of other employees (& favoring share holders above all). It has little to do with what the company actually does. However, the bad optics don’t matter unless it affects the profits of said company (how many bank CEOs got canned after the financial crisis?). And of course, I’m sure this is a bit of a cartoonish picture of how things actually operate, but there is some validity to it, and that’s kind of sad that people like me have become  so jaded by ‘The Man’, for lack of a better term.

—Boycotts and actual science can work to change a company; Monsanto used to make agent orange…they don’t anymore as far as I know in part due to a changing Ag industry and in no small part due to the shift in the culture at large.

—Monsanto hasn’t done itself many favors by being so opaque about it’s technologies and what their scientists are motivated by; they’re not out to destroy the world, I genuinely think they want to leave it a better place– they have kids and families too, after all.

—Monsanto is keenly aware that if they put out a GM product that is actually dangerous or detrimental, they’re done. Finished as a company, no one will trust them ever again. So they really do extensive testing of their products before releasing them. And they’ve got a great safety record (the environmental degradation is not necessarily due to GM, but simply to agriculture itself…a very disruptive process to the environment…something that I hope they’ll work to improve, after all, no environment & we’re all kinda screwed…).

Labeling issues.

Vermont recently became the first state to mandate GM food labels. There are other proposals and this was recently in ‘The Atlantic’. It’s popular and part of why it’s popular is the simple ‘right of the consumer to know’ what they’re eating. Other states have come close to passing similar legislation. I haven’t followed these debates closely, but here are some of the issues to consider in labeling GM foods:

—What would the genetic engineering label entail? Not all GM crops are the same; scientists can put basically any gene into a plant (we do this for strictly research purposes all the time), so is labeling each modification important? (yes, it is– depending on the gene, a lot of different traits can be conferred to a plant, that is more important than the fact that it’s been genetically modified).

—What ‘counts’ as GM? Agriculture has been practiced for 10,000 years. The crops we grow now are selected varieties for traits that are good for growing a lot of food in a small area…like dwarf wheat, responsible for the Green Revolution; there are some very real genetic modifications that happened in that time…even whole genomes introduced into plants (that’s about 20,000 genes…not just the usual 1 or 2 of today’s GM). And then, of course, evolution shapes plant genomes too; is that genetic modification?

—Nature is messy. So called horizontal gene transfer (a gene passing from one organism to another that aren’t related; in other words, not a direct descendant) happens all the time. Viruses insert DNA into genomes of all kinds of life every day.  Bacteria swap genes constantly, sometimes into eukaryotes like humans and plants, and there are even examples of eukaryotic horizontal gene transfer, the neochrome gene in many ferns originated in an early land plant called a hornwort…and yet anti-GM activists aren’t torching the fern covered forest floors. Natural does not mean good, it means natural. Human-made does not mean bad (often, that’s the case, but not always), it means human-made.

Wrap up.

So does a GM label have to incorporate both modern and traditional GM? Should it include all of the genetic, natural and evolutionary history of a plant we eat? Consumers have a right to know where their food comes from, after all. My Ph.D. advisor found an op-ed once by a guy saying that if he ate a plant engineered with a human gene and ate it, it’s cannibalism. That’s a little ridiculous…after all, humans share quite a bit of DNA with plants (so that salad you had for lunch…you may be 50% cannibal), and at the molecular level, we’re all pretty similar, made of all the same stuff. We’re all breathing in and incorporating atoms of people and diseases long gone and forgotten by history…does that make us all cannibals?

it is difficult to trust a large company (I’m uncomfortable having Google know everything about me at some level), but Monsanto does, ultimately want to help farmers and they recently acquired a company that models climate/climate change to help farmers grow food in what will be an increasingly changing climate. That’s not the move of a company that doesn’t think about the future and leaving the Earth a better place (of course, they’ll make money doing it, but profit isn’t inherently evil…it just can be). I know a few scientists that work at Monsanto and I would consider working for them myself (not that they have reason to hire me— especially after I’ve been a bit harsh on them here..after all I think too much and ask too many questions). I am not an expert in everything Monsanto does (in fact, a lot of it is kind of under wraps, trade secret…which also probably doesn’t help themselves), nor farming. I am a plant scientist studying plant development

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PiPC4: Leverage.

This is part 4 of plants in popular culture! In this one, I’m going to talk about several episodes of the show which center on plants and the biotech industry. There is more information in the included links, but see also my friend Johnna’s New Under The Sun blog for a good primer on GM technology.

‘Leverage’ is one of a genre of shows with a Robin Hood theme (I can imagine why that’s appealing these days); con artists become good guys to steal from the rich & powerful and help those without means get justice (that isn’t attainable through usual channels for various reasons). If you haven’t watched it, it’s a really fun show. They have a light touch, some tense and involved plots, and I am a huge shipper for Pardison or Harker (the couple of Parker & Hardison— if someone as weird as Parker can learn to love, maybe there’s hope for me too).

I recently powered through the series on Netflix and was struck by not only one, but two, episodes where they con two different large plant biotech firms (or people working at them, more accurately).

There’s a lot of opinion out there about Genetically modified organisms (GMOs) and whether they’re safe or not. Like any technology, GM is neutral. It is how it’s used on a case-by-case basis that determines whether it’s actually bad or not. There are some real upsides to GM plants. But of course we have to be circumspect in our use of them. They aren’t silver bullets that will solve all the world’s problems. But there are some uses that are indeed completely worthwhile; if a GM crop increases the nutritional value of a crop or it uses up less space/input to grow the same amount, or it’s a super-biofuel source those are good things for the world.

In S3:E3 of the show, the Leverage crew take down Wakefield Inc., a plant biotech firm with an impressive security system. And a firm that’s on shaky financial footing. Biotech is expensive. Or more specifically they take down a scientist and the colluding head of security that are trying to save the company in a rather radical way; the scientist has stored away a strain of the fungus Ug99 (a very real plant pathogen that is devastating to non-resistant wheat, which is currently most wheat grown in Africa/Asia). The scientist has spent billions developing a strain of wheat that can resist the deadly Ug99 strain that no one else has (such a strain of wheat does apparently exist). And then she was going to just release the pathogen and sell the Wakefield resistant wheat to farmers who wanted to protect their crop. A plant pathogen is potentially a devastating weapon.

Is the Ug99 strain the intellectual property of the company? Or should it be widely shared so many minds can work on finding a solution? My personal answer is that when it’s something that potentially devastating, sharing is the better policy; but it does mean potential competition from other companies as they race for a solution (this happens to some degree now; there are several very large plant biotech/Ag firms producing seeds and pesticides to sell to farmers).

I don’t think they ever explicitly bring up GMO technology; the resistant wheat could have been bred with traditional genetics (itself a form of genetic modification) assuming a naturally occurring resistance gene could be found (which may not exist in every case).

In S4:E5 the Leverage crew takes on Verd Agriculture, a pretty clear stand in for Monsanto. They’ve stolen an “open source” potato developed by a small farmer with a possibly flimsy claim that she has used Verd seeds in the development of the potato. So how can they keep us out of there? Modern agriculture owes a lot to small farmers selecting desirable traits over time and slowly bringing them together. The scientific revolution has brought a new twist on old methods that traditional breeding can’t hold a candle to.

Modern genetics began in the 19th century with Gregor Mendel and his observing the physical appearance (the phenotype) of traits that vary in pea plants (like round vs. wrinkled seeds or short vs. tall plants) and showing that they’re inherited in very specific patterns– particularly when tracking multiple traits at one time. Nearly a century later, the double helix of DNA was proposed and it’s mechanisms of coding information deciphered. Note: I just related a huge part of the history of science in a few brief sentences. The obvious connection between the DNA sequence (and the specific organization of the 4 bases that make up DNA into genes– the genotype) and the phenotype that scientists almost take for granted now did not exist. In fact, the genotype-phenotype question is still a very open one when it comes to what are known as complex traits (where more than one gene contributes to that particular trait). And even more recently thrown into the mix is the field of epigenetics; that can also affect how genes are expressed and therefore physical traits. There is a lot of complexity in biology to say the least.

Modern high throughput technologies, more basic knowledge than ever about how plants work, and knowing what genes underlie specific traits are being applied to the world’s food supply. For many plants (ones that have a level of genetic/DNA sequence information in a database), there are detectable genetic markers (a specific DNA sequence or even a single DNA base pair) that associate with specific traits can be probed in an individual seed (like overall biomass, for instance). Seeds with the most desirable combination of markers/traits can now be selected without even having to grow the plant (though in a lot of cases, combining traits is a long term experimental process involving growing thousands of plants and tossing out most of them)! The other big tool that modern molecular biologists have is the ability to find a gene that will confer a trait (e.g. herbivore resistance, like the Bt toxin that targets specific species of butterflies/moths that eat crop plants) to a plant via genetic modification; in this case it means inserting a gene into the genome; usually a random process, but there are some new technologies that enable plant scientists to target where that genetic modification lands. Of course, these new technologies are resource intensive and on a commercial scale, only the giant companies like Monsanto can viably do them (in fact, I think the seed genotyping technology is proprietary to Monsanto).

All of the above is by way of saying that a small farmer breeding a super-potato is a little far fetched, though not impossible if it’s a very well funded small farmer with a lab. So called bio-hacking is happening now– there was a funded kickstarter to create a visible light producing tree to replace street lamps (that I just don’t think will ever work), for instance. If a super-plant is created through natural breeding, is it any less engineered than a GMO? Another thing the corrupt CEO of Verd talks about is being able to distribute the super-potato globally. It’s true that a large company can distribute things a lot more widely than a single farmer ever could; even if she just gave it away as she did after the Leverage team steal it back (sprouting is a key trait in this episode as they only rescued a small part of the tuber; see my post on Tomacco for more on this).

So are big biotech seed companies evil? One reason companies make good targets is that they’re big and feed into a much larger industrialized system where we get a lot of our food here in the US. And of course size means that there are things that can fall through the cracks and lapses might occur (any organization has these problems). There are also instances where companies meet the minimal legal standard to operate/release a product, which can be insufficient in some cases (it might be legal, but from a human perspective or environmental one, it’s plainly insufficient). Companies that have intellectual property like Monsanto also really lock down their information and aren’t very transparent about their products. In Monsanto’s case, they are opening up a bit more with generalities of their technology and starting to talk to the end users of their products (not the farmers who buy their seeds, but to the people who end up eating the food those farmers produce). That is good to see. Another question to keep in mind is whether or not the issue is biotech specific or just a feature of agriculture generally; agriculture is disruptive, no matter what. The same is true of intellectual property issues; a lot of those are not biotech specific, but are broader problems with the patent system.

As for product safety, Monsanto knows that if they put out a truly dangerous product, they’re in a lot of trouble. I would hope any company would realize this and want to provide a service that helps consumers, employees, the company itself, and shareholders all without destroying the planet. But then I am an idealist. Nathanael Johnson on Grist did a fantastic series about GMO technology that is worth taking a look at if you’d like to know more about them. It’s not all good or all bad; it’s messy and complicated. GM can do some real good in the world, but is not a panacea– I think even a big biotech firm would admit that. Use the right tool for the right situation, which won’t always be the GMO (even if that runs counter to a company’s interest; science ideally provides robust answers to questions…it’s not always an answer you or a company will like, however).

In the end, ‘Leverage’ (which has a lot more food/plant centered episodes too) gets a few things right, but is best understood as getting back at ‘The Man’ and helping the little guy, which of course is really satisfying for most of us. No one likes a bully or feeling crushed under the enormous weight of a company, Government or other large institution. There is risk to any new technology, but just doing without it is also not the best option either. Mindfulness is becoming all the rage these days and in my opinion, mindful use of any technology makes good sense.

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PiPC2: Tomacco.

Tomacco.

‘The Simpsons’ is one of my favorite shows. And it brings me to the second in my series on plants in popular culture. See my first post in the series here (spoiler alert).

In the episode from Season 11 ‘E-I-E-I-(annoyed grunt)’, Homer creates a plant that’s a hybrid between tobacco and tomato.

In addition to the plant-centered theme, this episode is also great because it’s the one where Homer sees a movie with Zorro in it and attempts to emulate Zorro by challenging people around town to duels after slapping them with a white glove. After the first incident at the movie theater where Homer defends Marge’s honor, he takes a ketchup bottle and squeezes out a red ‘H’ on Marge’s dress as Zorro would make a ‘Z’ with is sword.

After a lot of glove slapping, Homer is finally taken up on his offer to duel by a Southern Colonel who’s in town. The Colonel chooses ‘pistols at dawn’ as the dueling method. Homer goes home despondent and talks to his family about it. Through some very funny dialog, The Simpsons escape the Colonel who is camped out on their front lawn and flee town, apparently never to return.

Now before getting to Tomacco, there are some interesting things set up early on in this episode. There’s ketchup and southern culture (also associated with tobacco) in the form of dueling and the Colonel (I know dueling is not specific to The South)- a foreshadowing of what’s to come. There’s also a set up of what is basically horribly processed food at the beginning of the episode- Buzz cola (advertised by WWII soldiers on D-Day…), milk duds soaked in movie theater butter (someone must have tried this in real life…), and ketchup.

So The Simpsons take up residence on Grandpa Simpson’s old farm to lay low. Despite the rustic home, Homer decides he’s going to become a farmer and the family sort of enthusiastically follows despite raccoons- er, cats with rabies- on top of it all.

Seeds to grow things are essential to a farmer and so Homer goes to the local farm shop to get some farm equipment and seeds- and Gummi bears where the initial implication is that he’s going to plant them in the soil to see what they grow into. The fact that Homer initially gets a handful of Gummi Bears to potentially plant is also a statement about how most of us are pretty divorced from where our food actually comes from. This is also another example of a processed food in the episode.

The locals tell him he won’t grow anything at ‘The ol’ Simpson place’, but Homer wants to prove them wrong despite apparent high soil pH.

Back on the farm and a month after planting…nothing is growing. By comparison, the neighboring farm has corn literally grown up to elephant eye height. Desperate, Homer calls his friend Lenny at the nuclear power plant to ship him some plutonium (yes, that’s radioactive) to use as a soil supplement, to grow large plants- overnight (I love the way cartoons show radioactivity with things glowing visibly- in reality, you don’t see the deadly kind of radiation).

Giant plants don’t grow (not even invisible ones- not a reasonable hypothesis, Homer, but keep trying) but Lisa discovers a tiny seedling buried underneath the soil. And the family discovers a whole bunch of seedlings growing underneath a layer of soil. What are they? Did the Gummi bears magically become seeds and sprout? One thing is for sure, you’d likely get one, maybe two depending on your population size of seeds started with that would turn out to have a similar set of mutations and thus create the same kind of plant.

When the plantlets bear fruit some time later- they look exactly like tomatoes- this happens:

Bart: Bleh!  Tastes like cigarette butts.

Marge:[takes the half-eaten “tomato”] That’s odd.  The outside looks like a tomato, but the inside is brown.

Lisa: Maybe the tomato seeds crossbred with the tobacco seeds.

Homer: Oh, great, I’ve got a field full of mutants.

Bart: Gimmie.  I want more.  [grabs back the tomato and eats it]

Lisa: I thought you said it tasted terrible.

Bart: It does.  [grinds out the remains of the first tomato] But it’s smooth and mild.  [grabs another] And refreshingly addictive.

Homer: Addictive, eh?

Homer calls this new ‘mutant’ Tomacco and sells it on the side of the road to passers by (as Ralph Wiggum takes a bite- “It tastes like Grandma”). Marge is trying to sell home-made mincemeat pies (where she got the ingredients for it is not explained), but doesn’t have any takers because the addictive tomacco is so, well, addictive. This series of scenes suggests we as a society are addicted to our modern food products (read: sugar) that are the result of science and reject the home made, the local, the healthier. While science is partly responsible for this, there are also societal reasons for it as well. Although it is a little ironic that Homer is essentially a small scale farmer in this episode.

Tomacco is so successful that Laramie, the cigarette company, comes and makes an offer for it of $150 million which The Simpsons decline demanding 100 times that amount which gets them kicked out of the Laramie limo. Back on the farm, there are other problems; namely neighboring farm animals have gotten into the field and nearly eaten all of the tomacco crop! And they’re addicted to it too. In the end, the last tomacco plant is destroyed, and the Simpsons return to 742 Evergreen Terrace and resolve their issues with the dueller- with a mince meat pie (Of course, they do have a duel first).

What’s the reality of the science behind this episode (hint: not much, but it’s still fun)?

Based on This analysis of the family that tomatoes and tobacco are in (commonly called the nightshade family), they are distantly related; sharing a relative some 25 million ago. Given that the definition of a species is typically ‘a population that can interbreed’, tobacco (Nicotiana tobacum) and tomato (Solanum lycopersicum) likely can’t pollinate one another, despite still having similarly structured genomes (diploid chromosome number = 24 in each). However, one person did graft a tomato shoot onto a tobacco root stock and created a tomato like fruit that had tobacco in it- or nicotine, suggesting that nicotine is being produced and transported from the tobacco root into the tomato shoot system.

As for Lisa’s assertion that tomato and tobacco seeds must have gotten mixed together and the plutonium radiation must have brought them together- it does not work that way. Radiation can definitely mutate DNA. The Sci-fi writer, Neal Stephenson, told a story (sorry, I don’t remember where) about when he was a kid where his Boy Scout troop grew maize seeds exposed to the core of a nuclear power plant to see who could grow the weirdest plant. Radiation that your body is exposed to can cause single nucleotides to change (may or may not be consequential) to inducing a so called ‘double-stranded break’ which is what it sounds like; a chromosome (a double helix of DNA millions to billions of nucleotides long) breaks in two (or more) segments and the cell’s repair machinery can’t always fix that kind of damage correctly (which end goes together with which end?). Higher radiation usually means more damage done (radiation has effects on cells besides on DNA too).

As for the assertion that the tomacco plants are ‘mutants’, well, yes they are. But in science, a mutant is defined in less pejorative terms. We all have different DNA in our bodies and so we could all be considered mutants in some way. Individual genes have different versions called alleles that float around in a population (that’s how natural selection works- it needs variety to select and at the base of physical variation is gene variability). Geneticists talk about ‘The wild-type’ that can be defined as the most common allele of a gene in a population and anything different is considered ‘mutant’. Alternatively, it’s not necessary to designate a ‘normal’ and a ‘mutant’ and just give the frequencies of an allele within a population. Basic researchers also use a reference called a wild type too that we compare intentionally made mutants (often meaning complete loss-of-function of the gene of interest) and expose both to a condition to see if the mutant responds differently from the wild-type. This is how we often figure out what a gene’s particular function is within an organism (yes, it’s more complicated than this, but it’s the basic idea).

After treating with plutonium, there’s a whole field of tomacco plants all of a sudden. In reality, as noted above, radiation wouldn’t affect each seed the same way so it’s unlikely to produce a combination more than once or twice that will result in the tomacco plant. Now it is possible that tomacco is vegetatively apomictic- sending out roots (called ‘runners’) that pop up elsewhere and become new shoot systems (though clones of the original). Potatoes can do this, as can many grasses and aspen trees. Or Homer made cuttings of one plant that regenerated into whole tomacco plants. Some plants can be propagated that way as well.

It really is true that alkaline soils (or basic soil, pH>7) make it hard to grow most plants. It’s what would be called ‘marginal’ farmland until it can be rectified (which may involve growing other plants to remediate the soil).

Although The Simpsons is one of the smartest shows on television (employing many former scientists, mathematicians, etc.) they are there to tell good stories and be funny. Not necessarily get science right. The larger issues this episode brings up, that foods heavily modified by humans may be inherently bad for us. However, the story is more complicated than that. Humans have been selecting traits and modifying plants ever since we started agriculture. We can now extract sugar and put it into forms like Gummi bears or butter soaked milk duds that our ancestors couldn’t have dreamed of, and that may be highly addicting- the sugar craving that many of us struggle with. However, genetic modification (either traditional or modern) is not necessarily all bad as increasing production of agriculture will be necessary to feed the world.

It is largely not how we modify the plants themselves, but how we process them after harvest that’s the issue. Laramie could be a stand in for Monsanto- wanting a new plant technology to sell to farmers, but Monsanto isn’t all evil- far from it. They want to make plants that require less input of resources and increase yield- to soften the footprint that agriculture has (and they are still that crop- whatever it is- Monsanto is not in the business of producing combination species like tomacco as far as I know- even a desirable one). Now any institution as big as a Monsanto will have things that are problematic which can happen when making money is as important as fulfilling a scientific mission. I don’t think it’s worth Monsanto’s time to try to create GM crops that are smaller in scale than soy beans, maize, cotton and rice, though I can’t divine what Monsanto’s next projects are…they are rather secretive about what they work on.

2% of the US population are farmers. That leaves 98% of us that are mostly clueless about how or food is grown, where exactly it comes from (solanacious species of plants are distributed all over the world with the highest diversity in South America which is where potatoes, tomatoes, peppers, and tobacco originate). Do we plant Gummi bears? I hope most people know that we don’t. But a larger point of this episode is that when we’re cut off from where our food comes from, we’re also ignorant of agricultural and environmental issues in growing it, the footprint it has, and whether a few large companies really do run the show in producing things that aren’t the healthiest of products.

Connecting to what nature produces, where food comes from, how it’s farmed, what problems farmers face, what is seasonal (even if you still buy it year round), what environmental impact that crop has, and avoiding overly processed foods all has a lot of potential upside for individuals’ health and well being. Studies show that connecting with nature is good for the human mind.

This turned into a long post! Thanks for reading if you made it this far. Time for some Milk Duds soaked in butter…

Ever on and on.

Patent.

Supreme Court

The supreme court ruled on the Myriad genetics case this week and they unanimously held that genes from nature are not patentable. That’s the right decision.

The Justices in their decision demonstrated some pretty bad science illiteracy, however. Thinking the term cDNA means ‘composite DNA’ and not what it actually is: complementary DNA for instance. And Justice Scalia wrote a concurring opinion stating that he couldn’t affirm his knowledge or belief in the basic molecular biology underpinning the case even though he agreed with the ruling. These are 9 smart people with smart people working for them. And yet they demonstrated scientific illiteracy about some of the most basic of biology.

And they’re not the only ones. I have trouble conveying what I do for a living to friends as well. they’re not biologists. They don’t have the concerns of a scientist. they have their own careers to focus on. That said, I wish there was a standard knowledge base that nearly everyone had (this is true of more than just biology- I think everyone should know the order of the planets and that they go around the sun, which planets have moons, and how long the Earth takes to go around the sun as well as why we have seasons here on Earth).

So here are the molecular biology concepts I wish that everyone knew:

  • A gene is a specific sequence of DNA on a chromosome (and genes can have many variations, or alleles, which are the raw material of natural selection and account for the different humans that exist, and the different organisms in nature).
  • A chromosome can contain thousands of individual genes.
  • Genes have DNA near them that determine whether they are switched on or off depending on contexts.
  • When a gene is switched on, or expressed as we biologists say, they become messenger RNA (mRNA) that is single stranded, as opposed to the iconic double helix of DNA (the mRNA sequence is based on what biologists call the ‘coding strand’ of DNA).
  • mRNA, after some processing, can be translated (read) into a protein which do all of the activities to build and maintain a cell.
  • Some viruses, that have an RNA genome, such as HIV, have a gene called reverse transcriptase that makes a DNA copy from an RNA template. this is a complementary DNA, or cDNA. In the case of a virus, this allows the viral genome to be integrated into the host genome, to be awakened later.
  • Reverse transcriptase has been isolated in many forms and can be used to make a DNA copy of a fully processed mRNA molecule. That is what Myriad made. In molecular biology research, making cDNA allows for easy quantification of gene expression level.

I’m probably not the greatest communicator of science, but these are the things I would like everyone to know. These ideas of basic genetics are the keys to the rest of modern biology.

Ever on and on.

Surreal.

Down the rabbit hole

I’ve been reminded lately that science is largely done for fun by the people who choose to do it for a living. Lawrence Krauss talks about taking joy in science, something I didn’t do very well at all throughout my Ph.D. or my postdoc. Being serious all the time was my demeanor a lot, actually. I’m that person who gets told ‘you’re so serious’ all the time. I ceased to see the fun part of science which really can be thought of as going down the rabbit hole like Alice to Wonderland. Though the original ‘Through the Looking Glass’ wrold is a dark place, there’s also some whimsical and interesting things- it’s an adventure and involves risk, stepping out your door can be a dangerous business. Assuming your’e open to what’s out there.

Openness to possibility is key to scientific progress. Though the House Science Committee Chair seems to disagree with this notion and thinks science is about what are perceived priorities that will immediately enrich our economy. While some things are fairly obvious to fund and invest in, how do you account for getting the World Wide Web out of CERN? That’s a happy accident that permits me to transmit this to readers. All because of a large scale science experiment discovering fundamental (likely useless) structures of the universe. Lasers were similar. Electromagnets. Who knew that specific and certain plants produce compounds that work as medicines (maybe intuitive as people have done this for thousands of years, but there’s likely a lot to be discovered out there still). A lot of discoveries come out of stydying the ecosystems and identifying what’s there. how it interacts with everything else and no immediate economic benefit from that until it’s discovered. The initial discovery of microbes was useless too.

Play

Science is full of stories where basic discoveries are made all at once by several people at once because they’re ready to be made due to the studies of previous generations. Charles Darwin and Alfred Wallace discovered the process of natural selection and they were simply observing the nature and there was no practical application in mind, though it turns out that evolution is quite important in unifying all life on Earth and means we can use things learned in one living system to others. And even transfer genes between organisms via recombinant DNA technology.

Scientists need to have a sense of play. This example of studying cicada wings is a good recent example of just how something seemingly pointless to fund research into, but turns out could lead to some very useful things for people. Wonder is essential.

Taking things seriously all the time can lead to burn out. I’ve written about it before. In fact, that’s a big theme in a lot of this blog; I am writing to hopefully help other scientists avoid the mental doldrums I found myself in and am now, after many years, climbing out of.

Leap

The funding for scientific research is probably the worst it’s ever been. This is forcing young scientists, postdocs and graduate students particularly, to consider alternatives. Science is hard for a lot of us to let go, another theme of this blog. Where do we leap to? I recently met Kat Alexander, someone who quit her Ph.D. program and her story resonates with me, even though I haven’t done that yet. It would seem to be gut wrenching. Many of us have truly been pursuing science since we were little kids. And now, it’s a little hard to talk to advisors about alternate paths. And for me, it’s hard to know when to make a clean break in terms of my research. Rep. Smith’s proposal would make it even harder to get traction in the scientific world.

Fake-it

I was recently in Washington, DC for a friends‘ wedding and went to the National Gallery’s ‘Fake It’ exhibit. It examined the history of photography and how from the beginning, photographers were manipulating images in all sorts of ways. Sometimes for artistic purposes, sometimes to highlight societal issues, and sometimes to fake real events. All before we had Photoshop software. Studying the photographs, it was sometimes very hard to tell what was manipulated. The surface belies what is actually there. It’s similar with scientific grant proposals. Many sound ridiculous on the surface (why would anyone even care about that!?), but are actually quite profound. Even grants that are designed to find disease treatments sound a little esoteric in some way.

Scientists push the boundaries of knowledge, like the peripheral vision of an eye where things are just seen. Stars seen with peripheral vision often disappear when you look right at them. This is due to how the different light perceiving cells in the eye optimally see dim light at the periphery and bright, color vision in the middle. The goal of science is to bring those seemingly hidden stars to full light, so everyone can see the world as it is. And when those dim stars are fully illuminated, science is moving onto the next frontier, the new periphery.

Rep. Smith doesn’t seem to understand that. If NSF grants are submitted to Congress for review after they’re approved in the grant review process, it won’t just be social sciences that are defunded. I am guessing that Rep. Smith is not a believer in climate change- so why would we fund research into it if he had his way? Similar with Evolution. I know not all Republicans hold those positions, but many in Congress seem to- it’s not hard to find examples of anti-science Republicans.

There are more than enough real scientific problems to solve and novel systems to explore them. Funding could increase somewhat so we can make even more discoveries, have more accidental applications come from it and enrich people’s lives. I want to spread what scientists learn about the world and educate the public. It’s F$%^ing amazing that we landed the Curiosity Rover on Mars, as one example. Humans like stories and what scientists do is tell the story of nature and document just how they uncovered those things, and give credit to those whose work theirs is based upon. Scientists are starting to get better at telling their stories in engaging ways and disseminating research that was funded by the tax payer back to that tax payer, but much more needs to be done.

It is extremely competitive, no grant is a shoe in today. Between the competition, the lack of jobs- private sector and academic in STEM (arts too) fields- it is no wonder that many scientists want an alternative, or are getting anxious about their present. The current system hasn’t really trained us for alternatives, partly by design and partly because scientists tend to be very focused individuals who have been set on pursuing science from an early age. The social science grants Rep. Smith objects to probably do have real relevance, it just isn’t obvious on the surface.

There are certainly reforms to the science funding system and the academic system that would be welcome. This just isn’t one of them. Try again.

Ever on and on.

Creationism.

I’m going to tackle this topic even though I know it is polarizing. 


I read a column in The Chronicle of Higher Education today asking to scientists who support the theory of evolution to be kinder to creationists- and at least to not treat them like their idiots. Some of them clearly are not; you can present them the evidence for evolution and a creationist will just say ‘I think there is a different set of facts’ (no, there aren’t, but I’m not here to convince anyone- I think it’s futile to do so, people have to be convinced on their own, make their own discoveries). 

The thing I get confused about with creationism is that it seems like such a limited view of what God created with the universe (or even more than one universe, possibly). 

A scientist’s job, through the empirical method, describes nature as well as they possibly can. Through that study, the evidence suggests that the universe is very old, 13,700,000,000 years old. That there are atoms made up of quarks and a whole host of other sub-atomic particles that are not obvious to the naked eye and zoom around at nearly the speed of light- 299,792,458 meters/second. These small particles and fields they represent make up everything in the universe. Life on Earth is ~2,000,000,000 years old, the Earth, 4,600,000,000 years old. The oceans formed, continents moved! Volcanoes erupted in massive and destructive explosions! Life has had myriad forms and dynamics over its history and we humans are a current incarnation of the mechanism of evolution, in a deeply philosophical sense, we are a way for the universe to know itself. Our brains have 83,000,000,000 neurons that form even more synaptic connections. Our bodies interact with microbes and other parts of the natural world- like plants!- that enables us to live and function on this Earth (all have DNA too- a rather elegant molecule for data storage). As humans, we’ve progressed far enough to be able to send the Voyager spacecraft to the edge of the solar system- 11,000,000,000 miles away! And there’s a ton we just don’t know or understand even still. Nature is complicated and doesn’t yield secrets easily. The fact that our brains have comprehended as much as we have is impressive. 

This astounding complexity would make me say, if I were religious, ‘Dear God, you created something incredible!!!! Far beyond what’s written down in The Good Book!’. I am assuming that God, all-powerful, wouldn’t allow us to know things we aren’t allowed to know, of course.  

The numbers and mechanisms of the universe create a hugely richer picture of the universe than a 6,000 year old Earth with everything intact all of a sudden. The logistics of Noah’s Ark boggle the mind if you consider the millions of species of animals out there (including the insects?). did he also take on all the plants of the world (250,000 flowering species alone- most wouldn’t survive a flooded Earth)?

Is the more epic universe that science has painted a more uncertain place? Probably so. But therein lies the mystery and the frontiers of exploration. Living with uncertainty is hard (believe me, read previous posts here, uncertainty is quite difficult), but none of it means you can’t still be a very decent person and do your part to make the world a better place. 

None of it precludes believing in a God it seems to me; It just deepens what God actually did in creating the universe. Staring at the night sky as a kid was one of the most inspiring things ever to me. And to realize that it’s more ancient and grander than I even knew then, well, that’s amazing! The part of the universe we’re aware of constitutes ~4% of what’s out there…96% is other stuff we have no idea about yet. 

So to the extent that I’m spiritual, the evidence of science suggests God did so much more than what’s enumerated in The Bible- a book that gives some good guidance on how to behave in the world, not a manual for how the world goes, to paraphrase Galileo. 

I can get how the Renaissance Catholic Church would feel threatened by any view that wasn’t what they said was ‘how things are’, but in 2012 in a democratic society, it seems like there’s something else going on that makes creationists reject modern science (and in my mind, not give God his/her full due). And I must underscore, accepting a bigger vision of the universe in no way means you can no longer be religious, or a believer, or destroy one’s faith. 

I’m sure people smarter and more articulate than I am have made a similar argument as I’ve outlined here, but I’m writing it again myself to get it out of my head- it’s something I think about fairly often. 

My goal is not to convince anyone. I do think there needs to be a respectful voice in articulating our points of view and reasonable people can disagree. I do see how scientists (I feel this way too sometimes too) get frustrated when a whole community (like creationists) rejects what is overwhelming evidence that evolution happens; many scientists went out exploring nature and came back with natural selection as a mechanism for life to evolve. Evolution has had practical impact on all of our lives as well; from our crops we eat (selectively bred) to vaccines and antibiotics that kill harmful microbes, but spare us (by targeting things specific to the bacteria, not us- reflecting vast differences in DNA/cellular make up). Scientists don’t come upon mechanisms of how nature works easily and we fight it out amongst ourselves until a theory emerges that stands up to most challenges (and even then, it continues to be challenged and refined). So to have our hard work rejected is hard to take, especially when it seems to a lot of us that we’ve uncovered some new piece of creation, that deepens our understanding of nature- making God, if you’re religious- all the more impressive. 

So scientists often see limits to creationist thinking (it’s all in that one book?); whereas scientists went directly to the primary source- nature itself. 

Scientists also tend to reject absolutist thinking. Science is a process, not an absolute way of knowing things, but a way to be more certain. We stare into the void often enough and get rejected by our methods of trying to understand what’s going on so often that we realize anything we say comes with some level of uncertainty. Which makes scientific theories all the more impressive; Gravity, evolution, cell theory, The standard model, relativity, have all been vetted so thoroughly that scientists have accepted their veracity and continue to use them as a basis for experiments. 

That doesn’t mean that scientists can be mean to creationists and belittle them (that will convince no one to come to accept evolution), but does explain why scientists have a hard time understanding a Creationist point of view- an absolute view oftentimes. When presented with evidence counter to a hypothesis we hold to be true, scientists do something remarkable; we change our minds- often slowly, but we do.