# Category Archives: Uncategorized

## People always change

72 days from reading this, more than half of the cells in your body will be completely different cells than the cells in your body today.

Don’t ever let someone tell you “people never change.”

People are always changing. Sitting there, reading this, you—the mass of writhing, wiggling, cooperating, and competing cells that constitute your corporeal self—are changing. You are in flux. Millions of your cells have just died, and millions have just been born!

In talks, and on this blog, and in my papers, I often discuss this personal turnover because it leads to interesting biological questions. But I always paint this picture in the light of specific tissues. A recent conversation had me wondering—what about the entire body? What percent of our total cell number are different after a day? A week? A month?

Time for some more back of the envelope calculations!

Let’s say that 25 trillion (25 with 12 zeros after it, 25,000,000,000,000!) out of the 30 trillion of the cells in your body are red blood cells, as estimated by Sender et al. (2016). These red blood cells have an average lifetime—marking the time they are born until they are eventually recycled—of 120 days.  This turnover is a continuous process that keeps our blood fresh and functional each day.

So, every day, about $\frac{1}{120}$ of the $84\%$ of our cells are renewed, or $\frac{1}{120} \times \frac{84}{100} = 0.007$ , i.e. at least $0.7\%$ of our total cells are renewed daily! I stress at least because this estimate just includes the turnover of our red blood cells… our skin, our intestinal epithelium, and many other tissues that account for the 5 trillion cells that we didn’t include in the above calculation are continually renewed as well.

How long until half of the 30 trillion cells in your body are different from today? Again, just thinking about red blood cells, we need to calculate how long 15 trillion of these cells take to be recycled. 15 trillion is $\frac{15}{25} = 0.6 = 60\%$ of the total 25 trillion blood cells, and if the full batch of blood cells is renewed every $120$ days, this means that $60\%$ of the blood cells will be renewed in $0.6 \times 120 = 72$ days!

## A biological calendar

I recently read a bit of Why Evolution is True by Jerry Coyne and stumbled upon a fun fact I needed to dig into.

Hundreds of millions of years ago, there were corals, just like today. And, just like today, they grew by depositing a ring of calcium carbonate onto their outer skeleton every day*—similar to the growth patterns in the trunk of a tree. When you look at these growth patterns in living corals, taking into account changes of deposition with seasons, you can see annual growth patterns and, as one might expect, about 365 daily rings per year. When you look at fossil corals from 400 million years ago you see over 400 daily rings per year!

Scientists have long predicted that the rotation of the Earth must be slowing down due to tidal friction—the motion of the tides have been dampening our angular momentum (it’s stolen by the moon!). Not by much, about 1 second gets added to the day every 50,000 years. But, over millions and millions of years, these seconds add up. 600 million years ago, a day was 21 hours long, and over 410 of these days elapsed before the Earth could complete its annual journey around our sun. In 1963 Prof. John W. Wells used a biological calendar—fossilized corals—to corroborate astronomical predictions about our lengthening days.

Anyway, it was the perfect storm of fun facts. The days are getting longer, coral living 400 million years ago experienced over 400 days a year, and we can see this in a biological record.

P.S. Modern corals are still keeping a record. Using “coral chronometers” we have a record of variations in temperature, cloudiness, and even nuclear activity (some bands in corals coinciding with nuclear tests are radioactive). Maybe 400 million years from now somebody (something?) will find corals from today and see the impact of the human era. At least 400 million years from now the postdoc doing this research will have ~27 hours in a day to write up the results.

* I also just read Jurassic Park, hence the Mr. DNA adaptation.

## 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:

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.

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

Watching the ships roll by in New Orleans.

Meeting some new friends in Atlanta.

And some old friends.

Watching the dolphins, Savannah, GA

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.

## 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.

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.

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.

## My writing process

Alright y’all (can I say y’all now? I’ve lived in Florida for almost 4 years…), I’ve been tagged in a writing process blog hop thing by master blogger extraordinaire Dr. Amanda Niehaus. Bio below…

Amanda Niehaus (PhD) is a writer and scientist based in Brisbane, Australia. Her work spans the academic, nonfiction and fiction worlds – and she’s doing her best to integrate the 3. Amanda has been published in Peppermint Magazine, on pillows at the 2013 Brisbane Writers’ Festival, and you can find her online at Easy Peasy Organic (http://www.easypeasyorganic.com), Minimal Worries (http://www.minimalworries.com) and Staying Alive (http://www.easypeasyscience.com) as well as on Twitter as @EasyPeasyOrganc.

I met Amanda at the Evolution and Cancer conference in San Fransisco this last summer. Before knowing about her blogging expertise I let the beans spill that I was thinking about starting a blog (I had a lot of fun putting together a video about some research, I enjoy teaching and sharing the things we learn about our world through science, etc etc) and she told me to run with it. So here we are! Thanks Amanda.

Before I get to the meat of the post on writing, let me just say this: I don’t consider myself a writer. Which is silly, because I just wrote that (typed that?), doesn’t that make me a writer? I don’t know. I don’t consider myself a swimmer, but I like going to the beach and jumping in the ocean. It’s good exercise and it’s enjoyable. Just like this blog, and this post. Although, today I spent all day writing up some results from my research and now I’m writing about writing, so maybe it’s time I reevaluate myself. Thanks again, Amanda.

1) What am I working on?

Right now I’m taking a quick break from writing my first first-author paper to write this post. It’s really exciting and nerve-racking, and it’s embarrassing how slow the words come off my fingers. But it’s getting easier every day.

My research is on the evolution that takes place within multicellular organisms as they age. How mutations can accumulate in the little pools of stem cells that are constantly dividing to maintain your body. I think it’s a wonderful story and I can’t wait to share it with others.
2) How does my work differ from others of its genre?

Well, my science work is novel research. As for my blog, I don’t know. I honestly didn’t purposefully read any blogs before starting this one. I still don’t. I should start reading blogs! I don’t even know what my genre is.
3) Why do I write what I do?

I’m the type of person who goes to look something up on Wikipedia and, an hour later, finds 16 tabs open because I clicked every link along the way. I guess I just think a lot of things are cool and I want to learn about them. And I like telling people about these things. I like to tell stories.

This blog is my outlet to tell those stories (if they won’t fit on twitter and I’m not teaching for a while so I can’t bug my students.)

Where I’m writing from right now. Front porch and a homebrew, Gainesville, FL.

4) How does your writing process work?

So far this blog has been a perfect storm of  daydreaming and procrastination. I’ll typically learn about something, like the Voyager mission, or think about something, like the concept of a species, or want to share something, like pictures of spiders or eclipses, and if the feeling is perfect (just got to a coffee shop, but can’t bring myself to do actual work yet) I’ll start typing.

And thus, just like 99% of all the species that have existed on Earth, my writing process blog post lineage comes to an end. I’m glad that Amanda had a fitness greater than 1 on her post, so she has lineages which can still carry on her story. All of the folks I asked to continue my post lineage couldn’t. Do you want to write a blog post about your writing process? Feel free to continue off of this one!

## What’s in a species?

Take two biologists, sit them down, give them a few beers each, and then ask them to define the word “species”. Chances are you’re in for a colorful discussion. “Species” is one of those concepts that made perfect sense in high school, got fuzzy in college, and is something biology graduate students like to debate on the weekends.

Person A: It’s easy, right? If two organisms can create viable offspring, they are part of the same species.

Person B: Well, what about hybrids? You know, like when a horse and a donkey (clearly different species) mate and produce viable mules.

Person A: Well, mules are (usually) sterile, so that doesn’t count.

Person B: Ok, how about the viable and fertile offspring produced when Canids mate, like dogs and wolves or coyotes and wolves?

Person A: But those are recently diverged groups, I’d argue that they were actually subspecies of the same species (since they can produce viable fertile offspring, they’d be a subspecies by definition).

Person B: Alright Linnaeus, now you’re rewriting taxonomy. So you’re saying that as long as two organisms can produce fertile offspring, they’re members of the same species?

Person A: Right, but we can still define them into separate sub-species.

Person B: What about when organisms from two different genera produce viable offspring, like Fatshedera lizei ?

Person A: Are the offspring fertile?

Person B: Well their are some reports that…

Person A: That’s a plant anyway, the rules are different for plants.

Person B: Wait, what are the rules for “species” in asexual organisms, especially when genetic code can be passed on by horizontal gene transfer? And what about cancer as a speciation event? You know, the idea that a tumor has a separate genome from its host so it should be thought of as a different species.

Person A: No way, man. Cancers are formed from and completely dependent on their host. It’s just an extension of a single organism.

Person B: Not necessarily! The Tasmanian Devil facial tumors are spread between hosts by contact. Why shouldn’t we consider those cells a unique pathogen, no different than a virus spread between hosts? And how should we classify that ‘organism’?

Person A: Are viruses even considered alive?

Person A+B: …I think I need another drink.

Yes, I’ve had similar conversations over the years as a biology graduate student. I was reminded of the species debate after reading about the “out of Africa” concept and human speciation, and whether or not we interbred with members of other hominid groups (and, what that means for the definition of our species).