My spot, your spot.

I grew up on an island with seven million other people. Let’s just say it was difficult to find a spot to call your own. One day, as a youngin’ exploring the world on my bike, I broke off a path that ran along Sunrise highway and continued on down a hiking trail that snaked along a waterway in the local state park. I eventually came to a small clearing, sat down, and heard the weirdest thing. Nobody. No cars, no lawnmowers, no people. Just the birds and the chipmunks and the occasional splash of a fish.

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I felt as if I had stumbled on secret treasure. I spent a lot of time at this spot over my formative years, reading and thinking and being alone with my little patch of Long Island wilderness.

Before I left town for college I carved a “V” into the tree next to the water and said goodbye. While at college, I decided to major in biology, a decision shaped by my time out in the woods watching nature. I even wrote an essay about this spot for my freshmen writing class.

That biology major took on a life of its own, turning into an adventure through states, labs, and disciplines, and eventually resulting in a PhD from a zoology department and a dissertation on cancer and aging.
Last weekend Begum and I were visiting my parents and we decided to go for a quick hike before the ferry back to CT. A rush of memories came back, and I ran along this trail explaining my spot to her. She eventually found the V for me.

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Both of these images are from June 2017

It was the first time in over a decade that I set foot in this clearing. Needless to say, it was a powerful experience, and it sparked a bout of retrospection that, thankfully, I have been happy to ride.
I said a thank you, and another goodbye, and we ran to catch our ferry.

This summer, I hope you go out and explore, and find your own spot.

Spider Sunday is back! Kind of.

Spider Sund… err… Monday is back!

Back when we lived in Florida, stumbling on cool spiders was easy. Just open your door, take a few steps, and BOOM, golden orb-weaver (not to be confused with a yellow garden spider) taking care of your wasp problem. Or role out of bed to discover your new roommate, a Carolina Wolf, is on the prowl for mice (I presume). Maybe she’ll even bring along her closest 100 kin.

But New England, with its “seasons,” is a different story*. So, imagine my surprise and delight when Begum and I were hiking around Farm River State Park and saw this little fella scurry across the path:

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At Farm River State Park, CT. Picture taken with Galaxy s7. 

After some quick searches, I outsourced my initial guess to the amazing sciencesphere of twitter:

@HereBeSpiders11 with the save! Looks like this is a type of ground spider (we did find it on the ground), specifically it looks like a male Sergiolus capulatusThanks!

Some suspect that the awesome pattern may be an adaptation to mimic the velvet ant (which is actually a wingless wasp), known for their extremely painful stings!

Looking forward to what we find on our next hike.

*Actually, maybe it is not such a different story. Looks like we will just have to be more attentive on our next hike!

Roadtrippin’ with my favorite ally

Begüm gave me a GoPro camera as a gift for submitting my dissertation (because I live such an #extreme life). We put it to good use and made a timelapse of our travels from Florida to New England! I think it came out pretty cool, check it out:

There is no audio—I recommend choosing your own song. On a related note, we had our playlist on shuffle and “New York State of Mind” by Billy Joel came on right when we reached the Verrazano bridge. It was a pretty powerful homecoming moment for this Long Island kid. And then it started raining pizza and bagels (ok, I made that part up.)

Our route:

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Gainesville, FL –> New Orleans, LA –> Atlanta, GA –> Savannah, GA –> Raleigh, NC –> Philadelphia, PA –> Long Island, NY –> New Haven, CT –> Boston, MA

 

Many many thanks to our friends Scott, Dorian, Kevin, and Rich and Amber who hosted us along our journey. During graduate school we always daydreamed about taking a roadtrip after we finished up, and you really made it possible for us.

Begüm is the family photographer, so I don’t have many images to share. But, here are a few scenes from the road.

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All packed up saying goodbye to our little apartment and our little garden.

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Watching the ships roll by in New Orleans.

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Meeting some new friends in Atlanta.

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And some old friends.

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Watching the dolphins, Savannah, GA

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Becky helping us unpack, Long Island, NY

 

We hope to fill out that map with more trips in the near future! Next up: Cannataros head West (Geneseo, Niagara Falls, maybe some Canada adventures).

p.s. Dear Upstate NY friends: We are willing to trade delicious homebrew in exchange for lodging.

Want to find life on Mars? There’s a catch…

There has been a lot of talk recently about “getting our ass to Mars” (to phrase it as Dr. Buzz Aldrin has on social media). Whether it’s Elon Musk talking about the new SpaceX plan to colonize Mars (first passengers might be taking off by 2024, start saving!), the record low global sea ice levels here on Earth, or just the results of recent elections (Fig. 1) — people have been thinking about extraterrestrial adventures.

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Figure 1: Google Trends for “I dont want to live on this planet anymore” searches. November 8th 2016 was election day in the USA.

This gives me a good excuse to share one of the most interesting challenges we face when finding a landing spot on the Red Planet.

Surely, when sending a Rover to Mars in search of life, like we will in the year 2020, we would want to send it to the place that is the most likely to harbor life (or has the ingredients necessary for life according to our understanding of what life requires here on Earth). Right? This is probably true for when we want to send humans there as well— the more similar to Earth, the higher our chances of survival. But, there is a catch.

The site we think would be the most likely to harbor life would also be the most likely to be infected with life from Earth­— life that could outcompete the local Martians and lead to a planet-wide extinction. We (or, our microbes) could be the classic Hollywood alien invaders who annihilate local life in the search for resources.

Now, someone who has never read this blog or sat through a microbiology class might think “Hey, easy solution, just sanitize things before takeoff! Plus, the harsh conditions of space travel will get rid of any pesky stowaways.” Not so easy.

Firstly, let’s pretend for a moment that our bodies are not harboring a complete ecosystem of microbial life, and that somehow we can guarantee that humans and their waste never contact the surface of Mars. Still, microscopic life is everywhere on Earth. And I mean everywherelike 800 meters below the ice in an Antarctic subterranean lake everywhere. I think it is safe to say that some of this life will contaminate anything we send to Mars. In fact, 65 species of bacteria were found stowed away on the 2012 Mars Curiosity Rover.

Secondly, some microbial Earthlings are extreme. And I mean extreme— like proliferating at 403,627 × Earth’s gravity extreme. Like living in a liquid asphalt desert extreme. And yes, like living outside in space for 1 and a half years extreme.

So, the possibility of microbial stowaways surviving to mars is real.

And, of course, NASA knows this. In fact, they have a whole Office of Planetary Protection devoted to, among other things, “Avoiding the biological contamination of explored environments that may obscure our ability to find life elsewhere – if it exists; …”. The United Nations knows this as well. The Treaty on Principles Governing the Activities of States in the Exploration and Use of Outer Space, including the Moon and Other Celestial Bodies includes:

States Parties to the Treaty shall pursue studies of outer space, including the moon and other celestial bodies, and conduct exploration of them so as to avoid their harmful contamination and also adverse changes in the environment of the Earth resulting from the introduction of extraterrestrial matter and, where necessary, shall adopt appropriate measures for this purpose.

The possibility of contaminating planets that may harbor life presents a real ethical dilemma for robotic and human colonists. Should we search out life on a planet surface and also risk infecting the planet with Earthling microbes? Should we colonize another planet if it means we may destroy the local inhabitants? I’m not going to try and answer those questions here, but feel free to leave thoughts here or tweet them to me.

What are you?

If we’ve ever talked shop, or you’ve seen some of my slides, you know I like talking about what constitutes “you.” Especially as it pertains to the ever-changing, continually in flux, nature of our cells.

Which is why my friend Anthony knew I would enjoy this video (thanks for forwarding it along!) I particularly enjoy their discourse on our non-static essence. Don’t let anyone ever tell you that “people never change!” I could talk about this for hours, and I’ve devoted much of my research to the subject, but I’ll let the videos take it away– they do a really beautiful job.

What are you?

 

I also really enjoyed their Ship of Theseus explanation!

 

When you are done chewing on that, I hope you will check these out–

You are two.

 

 

Genetic Engineering Will Change Everything Forever – CRISPR.

 

It’s an exciting time to be a biologist!

Things I learned the hard way (in graduate school)

Dear friends,

It has been a while, I know. My tweets, posts, and overall online ponderings have dwindled this last year. But a lot has happened! I finished up my Ph.D. research, wrote up and successfully defended my dissertation, graduated from the University of Florida, and started as a postdoc at Yale University.

 

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Featured: my wife, Begüm, UF Ph.D. grad ’15, aerospace engineering.

 

Now that we are (almost) all moved and the work/life balance is settling into somewhat normalcy I have had some time to reflect on my graduate school experience. I was thinking about writing a post on “what I wish I learned sooner” or “what I would tell myself 6 years ago”, but after giving it some thought I realized that I wouldn’t change anything about my path through grad school. Every lesson that I learned “the hard way” was a necessary struggle. Nevertheless, I’d like to share some of the lessons I learned the hard way, and maybe if you are reading this as a first year graduate student you can keep them in mind as you forge your own path and learn your own lessons.  So, off the top of my head, things I learned the hard way, in no particular order:

  • Treat grad school like a 9-5 job.

    When I first got to graduate school the postdoc in our lab suggested I treat graduate school like a 9-5 job. As in, have the discipline to go work every workday, even if you do not have any obvious obligations. It was easy to not do this, since my advisor didn’t set any rules about being in the lab, my work didn’t revolve around keeping lab animals happy, and I only taught a few days a week. Plus, I just moved to Florida and was living in a small city with 50,000 other young adults…

    Grad school is a lot of work. Before you know it there will be a bunch of obligations to tend to, many of which are completely new. Teaching, grading, your own classes and homework and exams, and, hopefully, your own batch of new research. Not to mention the little things nobody talks about, like spending an entire week trying to figure out how to use a program to make one figure that you never even use.

    All I’m saying is that you will thank yourself later if you build work habits and discipline early, even if you do not have any established research yet. (Thanks for the advice, April!)

    That all being said, make sure you figure out when it is appropriate to close your email, turn off your phone, unplug from the internet, and take care of your mental and physical wellbeing.

  • Find where you work best.

    The lab wasn’t always the best place to do work. Maybe your labmates are doing intensive noisy work. Maybe people are holding office hours. Maybe the building is old and heavily used and in Florida and it fills up with cockroaches after 4pm. I went through many phases in grad school with ideas about where I worked best. In the beginning, it was the library, in the middle it was a coffee shop, and at the end it was in the lab and at home (and at the VERY end it was everywhere, all the time). And, if you have a mental block, it might be best to get up and go for a long walk and change your environment.

  • Comment your code.

    I know this is the first thing you learn as a new coder/programmer. I know the (good) code shared on stackexchange is beautifully commented. I know it is SO obvious that this is the best practice. But, it is easy to get lazy. Especially when you don’t think anyone else will ever see that particular batch of code.

    I didn’t know how easy it is to completely forget what I just did two weeks ago. Maybe you are meeting with your advisor, and she suggests trying to do X,Y, and Z, and you say “Great idea! I actually did that two weeks ago!” and then you go to pull up your code (if you can find it, that’s another lesson I learned the hard way) and it looks like someone else wrote it.

    Trust me, even if you are writing one line of code to do something fairly trivial, add a comment saying what you are doing, why you are doing it, and how it works (in English)… and how it fits in with the rest. Maybe it’ll take an extra minute that feels wasted, but it is better than actually wasting 15 minutes at some later point trying to decipher your mess. You will thank yourself when a reviewer comments on results you generated 8 months ago and you need to rerun everything! On that note, I found using github extremely useful during the latter part of my Ph.D. work. Especially when I had multiple projects going on at the same time and I needed to jump between them and remember exactly where I left off.

  • Create figures directly from your code.

    Perhaps you have no formal training when it comes to coding. Perhaps you learned everything in a nice GUI and you can save figures by clicking “Save Figure As…” (I learned in RStudio). Perhaps you have gone years coding and generating results and saving them to random folders throughout your computer and it has never been a problem. You finally submit the first chapter of your dissertation for peer-review, and:

    “Please resubmit Figure 2 at 600 DPI.” Ok, no problem, you think: where is the code I used to generate the original figure 8 months ago? Where did I even save the original PDF?!

    Better way: directly save your figures within your code. This is fairly simple in R, and I do something like this:

 

>#####

>#Alright, time to make that neat figure from the data generated from the code immediately above (descriptive comments throughout!)

>#Mouse, tumorigenesis incidence, things I can Ctrl+F here

>#####

>plot.count <- 0    #initialize some counter

 

>plot.count <- plot.count+1    #this counter goes up 1 time every time you run the code to generate a new figure in the same folder. This way, you can try a bunch of dimensions/font sizes/etc. in a row and pick which looks the best

>png(height=12,width=8,unit=”in”,res=300, file=paste(“C:/Users/Vincent/Desktop/aging/evo_tradeoff_figures/”,”mouse_combined_wline_exitseminar”,plot.count,”.png”,sep=””))  #making a png image, and now we know the exact dimensions, resolution, and where it was saved. Note that the counter is within the (descriptive) filename.

> #CODE TO OUTPUT THE PLOTS GOES HERE.

>dev.off()   #Turn off the “I’m outputting images to a file now” signal.

There, now you can look back to your code and see how the figure was made, where it was saved, and easily redo it!

 

  • Do not use powerpoint to create (manuscript) figures.

    Powerpoint is great. Over the last few years I have become a powerpoint whizkid. I love it. But, I’ve come to realize that it isn’t the ideal choice when making (professional) figures. It IS great for a quick and dirty manipulation of something for a presentation. It is great because it is easy. But, when you are stitching a bunch of images together, over a background, with a specific DPI requirement, and dozens of layers, you might need something a little less easy. That’s where GIMP (GNU Image Manipulation Program) came into play. It took some getting used to, but trust me, it’s worth it. (Just like learning LaTeX over Word.)

    https://www.gimp.org/

  • Set up alerts to find new papers.

    Whether it is a specific journal’s Table of Contents or something like Google Scholar Alerts, do yourself a favor and set up some automated email service that alerts you to new papers in your field and interests. Even if you just take note of authors and titles and abstracts, it’ll keep you at the edge of your field, and you never know who you will meet at a conference!

  • Join listservs

    The messages I received through Evoldir alerted me to numerous conferences and postdoc opportunities. Worth deleting a dozen or so messages every morning.

  • Join Twitter (maintain a semi-professional social media presence)

    I once heard someone describe their persona on twitter akin to if they were at a beer and wine social at a conference. Professional, but also fun and somewhat personal. Through Twitter I have shared my interests, met many researchers in my field, and have had my research (e.g. slides at a conference) sent out to tens of thousands of people. It’s great! Plus, you never know, maybe your university will even pick up on your story and want to share it with the world.

 

 

  • Give talks!!

    My graduate career has been punctuated by the talks I’ve given. Nothing helps you solidify your thoughts and results like having to announce them to a group of colleagues. Invite the meanest, most critical, and intimidating professors you can think of, because they will probably have the best feedback. Invite mathematicians if you describe math. If you have the opportunity to present in an informal setting, then share new half-baked ideas with colleagues. I can’t stress this enough, sharing your work with the field is one of the most challenging and rewarding parts of graduate school.

 

If you went through this journey and want to share some things you learned the hard way, let me know! I’ll update if I think of anything else.

Fun Fact about your diet…

Spoiler alert: I usually start my seminars by talking about how we are all in a continual flux of our constituent cells. Don’t tell me that “people never change”… yes, they do, in fact every day a huge chunk of every person dies and is reborn. For instance, perhaps 84% of our cells are red blood cells, and each one of those cells only lives about 100-120 days (meaning that 2.4 million new cells need to be produced every second)! Not only that, our entire intestinal epithelium is completely renewed every few days, and we lose (and gain) about a Billion (Carl Sagan emphasis added here) cells in our small intestine every 20 minutes.  Woah.  OK, … so what happens to the cells that “leave” our intestines? They enter the part of the gut where the “food” goes. So, do we eat them? Do we eat our own cells? Are we constantly, every day, digesting ourselves?

Yes.

According to the Food and Nutrition Encyclopedia, every day 25% of the protein in our diet comes from digesting our own intestinal cells! Think about that. Today, perhaps one fourth of the protein in your diet came from digesting your own flesh!

And then I can start talking about my research.