Monthly Archives: April 2013

Grad Student’s Worst Nightmare

Grad student’s worst nightmare:

Apparently this happened to a Rutgers student.  You can read the full story here.

When I read it, my stomach got a knot in it.  I remember as a grad student and post-doc having nightmares about losing data.  I backed stuff up often- on Zip discs, later CDs or DVDs, external hard drives, servers, lab computers, email attachments, etc.  It’s kind of odd how academic labs vary dramatically in their data back-up approaches.  Some are totally DIY and up to the student.  Others are standardized- with university back up servers and such.

Now that I’m in industry and data is literally the work-product I’m responsible for producing, there are rigid and advanced protocols for backing EVERYTHING up.  From computer files to actual lab notebooks.  My entire hard drive is backed up in almost real time.  On days I’ve forgotten my laptop at home, I get a loaner from IT, log in, and I have access to my exact hard drive on a server- I don’t even miss a beat.  Old-school lab notebooks (for which there is no replacement and are still used despite existence of computers) are routinely collected and scanned so there are digital backups.  The company has onsite servers and backup servers.  They also have two different offsite servers for backing up the back ups.

When I posted the above image and story on Facebook, I was regaled with stories of lost/destroyed/damaged computers.  Unzipped backpacks seem to be common.  As are spills (root beer and nail polish remover amongst them).  I also got comments like, “I’m backing up right now…”

I feel horribly for that student.  However, I’m really hoping his raw data is backed up elsewhere and he’s just hoping to not have to reanalyze it or remake/rewrite figures/chapters of his thesis.  I know when I was working on my thesis I saved it on my hard drive and on a flash drive every single day- so I had every change each day.  There were also less frequent back ups to an external hard drive and the various chapters I emailed to myself or my advisor.

Another grad student (or any researcher) nightmare:

Imagine going to your animal facility and finding this?  Source.

Imagine going to your animal facility and finding this? Source.

NYU Langone Medical Center was heavily damaged by SuperStorm Sandy- you can read about it here, here, and here.  While the news was filled with images and stories of medical staff evacuating patients, researchers everywhere were also wondering about the research labs.  Precious samples, genetically engineered mouse colonies, years of work, all in peril.

NYU’s entire animal facility, located in the basement, was flooded by the storm.  Almost all of their colonies were destroyed.  Years and years of work were destroyed along with them.  In addition to the lost colonies, without power, everything else in the labs that were not flooded was also in jeopardy- since the back up generators were swamped.

A friend and researcher on the Upper East side made room in the lab freezers for trash bags full of materials from colleagues at NYU.  Students, techs, and post-docs had basically run into the damaged buildings to dump armloads of samples (cell lines, cloning vectors, strains of bacteria and yeast, etc) from thawing freezers, clearing their bench tops with a sweep of the arm into garbage bags in the hopes of salvaging years of their lives spent constructing all of them.

Another friend who is a sales rep reported that a client (an industrial lab) busted out the walls of their building to load -80 freezers onto flat beds and move them out of lower Manhattan when it became clear how bad the flooding would be.  Holes in the building would do less damage than losing those samples.

I cannot imagine the sense of loss these researchers must have felt (or still be feeling), having years of their life’s work destroyed.  I cannot image being a 4th year grad student and being instantly back to square one- 4 years of work undone.

These are the things my nightmares are made of.  My heart breaks for colleagues living those nightmares.


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Cool science fair idea/ DIY experiment: Dancing Oobleck

Saw this on IFLS, shared from Housing a Forest.  I totally want to try it!

An oobleck is a non-Newtonian fluid, meaning that in some cases it acts like a liquid and in others a solid.  You can make it at home with water and cornstarch!  See instructions and great pictures on Housing a Forest.

See it dance!

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How to calm a baby and/or a baby mouse

Saw this article in The New York Times: “In Parents’ Embrace, Infants’ Heart Rate Drops

As I mom, I can attest to the fact that there have been numerous occasions where my children were crying- either in their bed, on the floor, or in the arms of another person- and the moment I took them into my arms, the crying ceased.  It’s often insulting to the person who has been holding them, but that is what they’ve done.

I’ve written before about research showing just how calming a mom can be for children of all ages- even just that mom’s voice, here.

It’s always oddly fascinating to me when research proves what we’ve always known/felt/believed to be true.

Turns out that human babies, and lots of other mammalian babies, respond similarly to being carried by their mother (or perhaps caregiver in the case of humans), by calming down.

Mother Mouse rescuing her pup from a cup.

Image from Esposito et al of the ‘behavioral task of maternal rescue’ wherein Mother Mouse rescues her pups from a cup.  This is similar to humans rescuing an infant from under the coffee table or a toddler from the monkey bars at the park.

A recent paper by Esposito et al entitled “Infant Calming Responses during Maternal Carrying in Humans and Mice” published in Current Biology looked at the responses of babies (of the human and murine variety) as well as dissecting what signals actually contribute to those responses (in the murine babies).

By monitoring babies movements, crying, and heart rates (electrocardiograms) the researchers found that within seconds of being carried (not just held, but picked up and moved around) by their moms, infants’ heart rates declined, their movements slowed, and their crying diminished.  Compared to an infant laying alone in a crib, just holding the infant while the mother was seated did elicit some calming effects, but not as strongly as carrying the infant.  (I’m pretty certain that further study would show this is primarily responsible for many a parent pacing up and down the aisles of an airplane to placate a cranky baby)

The same happens to mice, and since we can do experiments on mice that we can’t on babies, researchers looked further into the murine response to see how it worked.

Turns out, mice babies cry too (Ultrasonic Vocalizations, USVs).  Just like humans, when a mouse mom carries her pup, it calms down.  In a mouse, that means the pup stops crying/making USVs, adopts a compact posture (drawing up its hind legs and being still), and its heart rate drops.  The researchers used several different techniques to figure out what cues were causing these behaviors and figured out that it was a combination of actually feeling the mother grasping its skin and proprioception (basically sensing that it is being carried).

It’s fascinating to me how behaviors and responses are shared between species. It also reminds me how primal newborns are.

However, the paper had one CRITICAL flaw.  MAJOR.  As in I don’t know how the reviewers and editor missed it.

See here:

A scientific understanding of this physiological infant response could prevent parents from overreacting to infant crying. Such understanding would be beneficial to parents by reducing frustration, because unsoothable crying is a major risk factor for child abuse [26]. Source.

To this I say, “HAHAHAHA!  Are any of you even parents?!  At 3 am when you haven’t gotten any sleep and your kid just WILL NOT SHUT UP- does the knowledge that “the identified effects of carrying on parasympathetic activation and cry reduction were significant and robust” make one damn bit of difference?!*  I think not.

If I had been the reviewer, I might have responded, “If you want those two sentences in the paper, you gotta include a figure on whether that knowledge actually mattered to any parent in the dead of night with a colicky infant.”



*I’m only partly joking.  When my kids were infants and being difficult/impossible to soothe, I did remind myself that they weren’t intentionally trying to piss me off.  I suppose this understanding of what soothes them might similarly serve as a reminder that babies aren’t out to get you on a personal level at 3am by refusing to sleep and/or let you stop pacing around and/or nursing them.

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Wordless Wednesday: Imagine the possibilities

Can you imagine what the world could/would be like if this was reversed?

Source:  IFLS

Source: IFLS

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Creativity is intelligence

Saw this on IFLS and loved it.


Source:  IFLS

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Not too long ago, there was some hubbub about LEGO coming out with “girl” LEGOs.  I wrote a bit about it here.


A LEGO ad from before all toys were gendered.

Mabel has been enjoying the hand me down Mega Blocks we have for a while now.  However, she’s also recently gotten more excited about regular LEGOs.


Mabel’s first tower.

Over Christmas, we went to visit my in-laws and brought back with us all of Macs LEGOs from when he was a kid.  That renewed Macs interest in them, and since then, he’s been picking up kits when he can and works with Mabel on them.  She’s still a little young, but she enjoys building with them.

It was timely when a rep from FIRST contacted me and asked if I’d help them spread the word about their newest competition, Jr FIRST LEGO League, this one for little kids involving LEGOs.  I wrote about FIRST last year– and how crucial it is to expose kids to science.

More than 300,000 students around the globe participate in FIRST (For Inspiration and Recognition of Science and Technology)-  an educational nonprofit that uses fast-paced robotics tournaments (and other events geared towards younger kids) to get kids pumped about engineering and science! FIRST offers four programs for kids grades K through 12; each one gets more complex as students work together to design and build custom robots and solve challenges.

Before FIRST reached out to me last year, I had never heard of the program.  In the past year, I haven’t been able to get away from the program!  I’ve seen stuff on Twitter, read about local teams in the news, a recent event at the Javitz Center.

I recently participated in the Lower Hudson Valley Engineering Expo and was thrilled to get to meet some of the kids from the Ossining FIRST team.  They were all excited to talk about the program and their success.

Mac brought Mabel and Nemo to visit me while I was there (so I could nurse Nemo) and Mabel got the chance to watch the robotics teams show off their handiwork.  I was busy talking about bioengineering with middle and high school students, but Mac reported that she enjoyed watching the robots.


Local FIRST teams at the Lower Hudson Valley Engineering Expo.

FIRST sent me a little starter kit to get an idea of what the program is like and how it engages kids and their creativity.  It looks like a lot of fun- however, Mabel is still too young for it (it’s geared for K-3, ages 6-9).  So, I’ve been in touch with my local library’s LEGO League (which isn’t associated with FIRST) and plan to donate the kit.  Hopefully some of those kids will enjoy it and join a team!

The ‘instructions’ that came with the kit are really just creative jumping off points- and I can imagine it is a lot of fun.  (I want to stop imagining and actually try some of them with Mac- since, as you’ll see below, they are meant to demonstrate how creativity and problem solving differ even when two people are faced with the same challenge).

The “Built To Express” Kit was developed by LEGO Education exclusively for the Junior FIRST® LEGO® League (Jr.FLL) program and encourages Jr.FLL participants to express their thoughts and ideas on any topic by building symbolic models with LEGO bricks.

So, for instance, one challenge was:

  • Build: Imagine that you and your team are a team of scientists working on a top secret project.  Now, choose 10-15 of your bricks and build something you think you and your top secret scientist team would need in your top secret work.
  • Building time: 3 minutes.
  • Share: Share the story of your model with your team.

The other kit had more concrete challenges- where you work in pairs, both tasked with building the same thing, but working separately so you can’t see what the other is doing- you then reveal what you’ve built.  I would guess this would wind up being fun to see the differences and similarities in how each approached the challenge.

I think the various challenges would be a lot of fun to get kids building at our library’s LEGO League, or even at birthday party.

Even though Mabel is too young for JrFLL, it didn’t stop her from getting creative with the LEGOs in the kit.

lego 041513 mcphd

Can’t wait until she’s old enough to join a JrFLL team!

I’m really looking forward to Mabel getting involved in FIRST programs once she’s old enough.  They basically have competitions/programs for kids from kindergarten through high school with events and teams all over the country.  The JrFLL, for the youngest kids looks like a lot of fun (and is noncompetitive).

If you want to learn more about FIRST, check out this video or click on the embedded links above:

If you want to learn more about Jr. FIRST LEGO League in particular, check out this video or click on the links above:

And for those nerd parents reading, perhaps you’ve even come across the FIRST themed xkcd comic?

Source: xkcd

I’m guessing this type of thing is frowned upon in actual FIRST competitions! Source: xkcd

You can keep up with FIRST teams on Twitter!  FRC Teams, FIRST Comm Team, FIRST LEGO League, FIRST Tech Challenge, or with the handy hashtag #omgrobots!





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Wordless Wednesday

041613 trike mcphd

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April 17, 2013 · 3:11 pm