Save us from the microbes: Superantibiotics

Warnings about an impending post-antibiotic apocalypse have, over the last five years, grown increasingly stark, with estimates placing the annual number of mortalities from antibiotic-resistant bacterial infections at 700,000 worldwide, a number that could rise to 10m in the next three decades.

Many scientists are pinning their hopes on “superantibiotics”, essentially re-engineering existing drugs to overcome microbial resistance and make them thousands of times more potent.

But this also has it’s pitfalls and problems. Want to know more? Find out about it here.

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Reality check: Applying for the Dream Job : Part 2

antlionpit

PART II

Dear reader,

Thanks for continuing on from Part I. Here, I add a human component to Part I, reacting to the criticisms, advice, and to-do list for my career by actually considering that I have growing family, a desire for work-life balance, and  goals in life additional to being a tenure track faculty.

The crux of Part I was that I need to publish more, apply broadly, jump start my career, and move around a lot to land that perfect (or at least good enough) tenure track job. Let’s unpack the implications of this from a more holistic point of view than I had in Part I.

  1. I’m not complaining nor am I surprised by the prescriptions. I had a good sense for all these challenges when I started graduate school and that sense was strengthened when I took the postdoc. Publish or perish is not a new revelation, and the peripatetic postdoc life is well known. The rules have always been clear (mostly, see below), and I’ve intuited the holes in my CV for some time now.
  2. However, I do take umbrage at the implication that, to succeed in academia in the future, the majority of us will have to take a post-postdoc, assistant professorship as a stepping stone. The argument goes, that there are so many people on the market now, to be competitive, you have to have run a lab already. In other words, we’re in danger of another level being added to the process. Postdocs used to be quite rare—they were fellowships that exceptional people took before becoming faculty (I think E.O. Wilson is a good example). But now the postdoc is a standard step in the pyramid process. Is the post-postdoc about to become normalized too? Perhaps, and maybe 20 years from now, it’ll be expected. But I am disheartened by the idea of having to take a sub-optimal (for me!) faculty job to eventually land in a better (for me!) faculty position. **
  3. At some stage, how much can one move? How many postdocs does one accept? Moreover, I have a spouse, and have already moved them for my work once. How many times can I ask them to move to a new place, make new friends, find new jobs? And my family is growing. How many times can I move my kids, especially as they approach those challenging middle school years during the post-postdoc I’m now supposed to be considering to jump start my career?
  4. Finally, I am trying to optimize more than just my faculty job aspirations. I want to move to a place where my spouse can find good work, where we can build a good community, where my kids can go to good schools, and where we don’t have to spend more than half of our income on housing and school. I want a broader quality of life to go along with that tenure track job (which brings some good quality, I agree). Am I willing to hang on for a post-postdoc and spend 3-6 years in a sub-optimal place (again, per my specific parameters) in the hopes of perhaps getting a better faculty position perhaps in a better place?

If you’re paying attention to tone, you’ll have intuited by now that the answer is bordering on no. I’m not really willing to apply broadly and move a lot to land that final job. Publishing more is the only thing that I will reasonably do to make myself more competitive. So, I will do that, and keep applying. Frankly, I am not confident that anything will come of it. My postdoc has gone on too long already and extending it another year won’t really patch the holes in my CV. So, I may be coming to the end of the line.

At some level, dear reader, you’re thinking to yourself: “Sounds about right. Objectively, you’re not good enough. You haven’t published enough, and you aren’t willing to move enough or sacrifice enough to become a tenured faculty at your dream school. There’s no judgement in that statement. It’s just how the game is played, and the game demands more.”

To which I say—fair. I’ve suspected this for some time. I decided long ago that I am going stay in the game, while playing it at the level of work-life balance that I am happy with, until the game tells me it’s time to get out. I’ve done that, and now—empirically, i.e., no interviews—my playtime seems to be coming to an end. So, I’ll pack up my good memories, friendships with great people, and large set of transferable skills and take my PhD out into the real world. I’ll have some sadness in doing that, but no sense of failure (a topic for whole other set of blog posts) and no regrets.

 

** PS. I wrote this piece and then let it sit for a while. In the intervening time between when I wrote it and when it was published, I talked to a number of folks and realized that perhaps the post-post-doc, temporary assistant professorship isn’t really all that new. Lots of people move around at the pre-tenure stage apparently, so it seems that this is an obscure rule I just didn’t know about. I still take umbrage, but my surprise is lessened. Now you know too.

The Mars Conundrum: How do we explore the Red Planet without contaminating it?

“The search for life on Mars is paired with plenty of strong warnings about how we must sterilize our spacecraft to avoid contaminating our neighbor planet. How will we know what’s native Martian if we unintentionally seed the place with Earth organisms? A popular analogy points out that Europeans unknowingly brought smallpox to the New World, and they took home syphilis. Similarly, it is argued, our robotic explorations could contaminate Mars with terrestrial microorganisms.

As an astrobiologist who researches the environments of early Mars, I suggest these arguments are misleading. The current danger of contamination via unmanned robots is actually quite low. But contamination will become unavoidable once astronauts get thereNASA, other agencies and the private sector hope to send human missions to Mars by the 2030s.”

Want to know more? Read about it here.

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Watching a new species evolve

Biologist who study experimental evolution will tell you that they get to see species evolve all the time. However, for the first time, scientists have been able to see the evolution of a completely new species, in the wild, in real-time. And it’s not something rapidly evolving like bacteria.

It’s a new species of Darwin’s finch, endemic to a small island in the Galápagos, Daphne Major. And it evolved in just two generations.

Read about this awesome study, and gather fodder for that argument that “evolution isn’t true” that you might be having over your Thanksgiving weekend, here!

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The long game against an anti-science, anti-education government

I like this post over at Small Pond Science so much, I’m not going to comment much about it. Go read it, it’s really good:

“Like you, I’m exhausted from the political assault on science and education in the United States. But please, stay with me for this little bit, at least when you can find the energy.

….

I think we should keep doing the four things that I identified before inauguration, which are things that are part of our basic job description anyway:

  • Keep up research
  • Teach critical thinking
  • Advocate publicly for evidence-based decision making
  • Build diverse and inclusive academic communities”

Seriously, stop what you’re doing and go read it now.

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The dinosaur you’re eating for Thanksgiving dinner

I giggle a little every time people ask about the dinosaur extinction (on the inside because giggling in peoples’ faces is rude (so I’ve been told… repeatedly)). Dinosaurs, in the strictest sense, are not extinct. They are walking and flying around us everyday.

And this week, they are sitting in the middle of the table.

But, in all fairness, I should mention that this is an ongoing debate. Not whether or not Thanksgiving is going to be delicious (that should be settled soon), but whether dinosaurs still walk amongst us (and will soon be in your belly).

HAPPY THANKSGIVING! ENJOY YOUR DINOSAUR!

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When This Sea Slug Eats, It Prefers the Turducken of the Sea

I’ve been trying to figure out how to write about this for a few weeks. There is a new type of predation, practiced by sea slugs called “kleptopredation”.

These psychedelic slugs eat hyrdroids, and will pop polyps off the hydroid as one might pick flowers off a stalk. But a new paper suggests that sea slugs prefer to eat hydroids that have just caught plankton.

Think of it like a bear. You (a human) just caught some salmon while fishing in Alaska (I hear it’s the thing to do there). And said bear sees this and waits for you to eat your fish before swooping in to eat you both. It’s two meals for the price of one. A little human-salmon combo meal.

These sea slugs are doing the same thing. So as you head home for Thanksgiving, potentially to eat a turducken, think about how you might be practicing some kleptopredation your self. And if you want to know more, read about it here.

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Reality check: Applying for the Dream Job: Part 1

antlion

This post is from a good friend of mine. They are on the job market and I asked them to write what it’s like to currently be on the market. The answer is: bleak. So they agreed to write an anonymous post describing their experience and offering advice to those of us currently out there pursuing the dream tenure-tracked job:  

Dear reader,

I imagine you’re a graduate student or a postdoc aiming for a tenure-track academic job. Here, I present a case study of that endeavor, from my own experience on the job market. I present it anonymously because that feels like the best approach. I want to offer general advice, not just draw focus to my specific situation. Names spark a search for idiosyncracies and contingencies, whereas I hope you are able to see some generality and applicability to your own path. In that way, perhaps you can glean some wisdom from this, even if I’m not sure what it is.

I’m going to do this in two parts. In Part I, I will describe my situation, factually, from the point of view of someone whose sole goal is to get a tenure track job. Who am I? What have I done? Why haven’t I succeeded yet? What do I need to do to succeed?

In Part II (next week), I will consider my situation as a human being, discussing family goals, work-life balance goals, and non-academic desires and ambitions.

None of these are ground shaking revelations, and I don’t know if I have any answers, but it never hurts to have one more case study out there in the ether. If this helps one person better understand their career and life, then I’ve succeeded.

PART I

My academic history

  • Field: evolution, ecology, genetics
  • Current employment: Post-doc since early 2013
  • Publications: >20 total, 2 first author glossy papers (e.g., Nature, Science, PNAS etc.), 1 first author high-impact review paper (e.g., TREE, AREES, etc.), several first author field specific papers (e.g. Ecology, Evolution, etc.), several papers with undergraduate advisees as first authors. My H-index is between 6 and 10.
  • Grants: NSF GRFP, NSF DDIG, co-author of a full NSF grant during my postdoc.
  • Teaching: Instructor of record during my postdoc, plenty of TAing in graduate school
  • Future projects: Solid (admittedly not spectacular) project ideas in model eco-evo-gen systems with strong potential for grant funding, student involvement, and new research trajectories
  • Toolkits: Ecological genomics, field work, lab work, organismal biology, museum experience, multivariate multi-level statistical expertise, outreach
  • Pedigree: Top 10 EEB program for undergrad, graduate school, and postdoc, with nationally recognized letter writers. Pedigree shouldn’t matter in an ideal world, but to the extent that it does in reality, mine is objectively excellent.

Application History

I got my PhD in early 2013, and a I published 1st author glossy paper from my graduate work in time for the 2014 job season. Since then, I’ve applied to ~ 7 jobs per season at a mix of R1s and SLACs, for a total of 26 applications. Overall, I’ve gotten zero interviews (phone, skype, or in person), hearing only that I made one long-short list (though I wouldn’t necessarily have heard about others, depending on grapevines at each school).

Real talk

I’ve had a number of conversations with friends and colleagues about my job search, and I’ve come to a stark realization, which my graduate advisor put most bluntly: “My CV is not as strong as I think it is”. That is, I’ve never really been competitive enough at any one time during my postdoc to land a choice tenure track job. Here’s why.

  • Early in my postdoc, I didn’t have my graduate work published.
  • In the middle of my postdoc, I didn’t have enough first-author postdoc papers, and my graduate papers, including that glossy, were getting old.
  • By year 5 in my postdoc, I finally had that 1st author, glossy postdoc paper, but too little too late.
  • During my entire career, I haven’t done enough to distinguish myself from my advisors.
    1. My graduate system was too similar to my advisor’s: I’ve actually had people confuse my work for theirs.
    2. My postdoc position was initially a hired position on a pre-existing grant, rather than a system I developed and funded.
    3. It is unclear how much of the second grant that I did co-author during my postdoc are my ideas versus my postdoc advisor’s, as the work is an extension of our previous work together.
    4. I may have a massively multivariate dataset from my postdoc that will churn out papers for years, but my publication record hasn’t proved that I can write those papers on my own.
  • Though the strong letters from my advisors address these concerns and promote my intangibles and other skills, the letters will not stand out because every advisor writes a glowing letter for their student.

In short, I’ve gotten stale, and I don’t have enough publications or independence to compete with the younger postdocs who have their own system and a higher rate of publication. My graduate advisor, at least, was thus not completely surprised that I haven’t gotten any interviews.

What have I done wrong and what do I need to do?

  • Publish or perish: I haven’t published enough. This is clear and not surprising. My h-index is decent and growing, but currently not competitive. More importantly, perhaps, my rate of publication is too low, despite the high profile, complex papers and datasets I have produced. Before the 2018 job season, I need to get two or three more 1st author manuscripts at least in review.
  • Numbers game: I haven’t applied broadly enough. Successful tenure-track job procurement requires an appreciable amount of luck (as discussed by Jeremy Yoder). Even with a strong CV and research program, many other factors need to line up just right to get an interview: who is on the committee, what are the final parameters of the job search, who is in the applicant pool, how many are in the applicant pool, what are the diversity goals, etc. Thus, one has to apply very broadly to increase the chances of success during a low probability process. Again, perhaps not surprising, and I need to be applying to 40 jobs per year, not 7.
  • Jump start: I took too long to get papers out as a postdoc. My main projects had long gestation times—2.5 to 3 years of data collection, plus a year in review for my big paper. I should have focused on taking other datasets to publication in the meantime, but did not. Thus, for a 5-year postdoc, I haven’t produced enough. One bit of advice I received recently was to take any sub-optimal (per my parameters) tenure track job and use that to jump-start my career (see point 2: Numbers Game and applying broadly). In that way, my productivity clock could restart, and if I was productive during the 3-4 years of being an assistant professor, then I’d be competitive again for my preferred jobs.
  • Move around: The jump-start, sub-optimal assistant professorship would make me competitive enough to land the choice faculty job at the close-to-perfect university for me. Apparently, plenty of people move several years into a professorship, as they are way more competitive than any postdoc who will not have shown yet that they can successfully run a lab. Maybe instead of looking for the “right” position, I need to look for the “right now” position, without the intention to stay where I land forever.

Conclusion

To paraphrase Cersei Lannister, in the game of academia, you publish early, apply broadly, jump-start your productivity clock if you need to, and move around a lot, or you die.

In Part II, I consider the implications of these rules for me.

 

Mail-Order CRISPR Kits Allow Absolutely Anyone to Hack DNA

CRISPR has become so pervasive, that while I was at a party this weekend in Berlin I had three different people ask me if I’m working on CRISPR (for the record, I’m not).

But now you can! Seriously, DIY CRISPR kits are now available for purchase online. Read about one journalist’s journey trying to figure out if she was successful in her gene editing endeavors.

But equally hilarious are the posts I’ve seen on facebook of scientist considering buying the kit for the cheap lab equipment (optional mini-centrifuge for 125… that normally costs a few thousand dollars…).

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How The Black Death Caused Medieval Women To Shrink

The Black Death (the OG “plague”) killed a large proportion of the population of Europe in the 14th century (30%!). But even after it had run it’s course it left long lasting and interesting effects on the population left behind.

People were on average healthier after the Black Death passed through. And for some reason, women were smaller. What’s interesting is these two factors might be correlated.

What does being healthier have to do with being shorter? Read about it here!

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