Hello, I’m an #ActualLivingScientist (AMA)

I’ve seen a lot of calls recently for scientists to do some outreach and explain to the general public what they do for a living, how science works, etc.

A major effort came in February after David Steen, PhD (@AlongsideWild), tweeted that “most Americans can’t name a living scientist.” With some help from Mary Roblyer (@darthmom7), the hashtag #actuallivingscientist took off on Twitter, with scientists introducing themselves and their work.

So…hi!  I want to do something similar here, as well as open the floor up for questions.

My Science Career

I have a Bachelor’s in Zoology from a small, four-year liberal arts university, with emphasis on genetics and animal behavior.  I received an honors diploma for my independent study research on developmental genetics of C. elegans, a tiny hermaphroditic roundworm.  (I also had to sit an exam, but that’s less exciting.)  I also did internships at zoos, doing animal care work as well as observational research on various animal behavior.

After graduation I worked as a zookeeper and then at an animal shelter for a few years.

I currently work at a medical school in the research department.  I am a research assistant in a lab that investigates how to grow new blood vessels in hearts with heart disease, using stem cells created in the lab.  I have been listed as an author on several papers we have published in research journals.

wp_20160810_10_35_35_pro
I also make cool designs with my pipette tips when I bored at work.

Ask Me Anything

As part of my outreach, I’d like to invite my readers to ask me anything they are curious about regarding science.  Some topics might include:

  • Daily tasks of my job
  • Current experiments in the field of stem cell therapy for heart disease
  • Where my funding comes from
  • Clarification of any terminology I’ve used in this post
  • How scientific papers get published
  • Science in science fiction
  • How science intersects with my religion
  • My opinions of current science topics in the news
  • What kind of music I listen to in the lab

For personal and professional reasons, I can’t give too many details about my current work.  But I will do my best to answer all your questions as fully as possibly.

Basically, if you ask a sincere, polite question, you will get a sincere, polite answer.  Leave your question in the comments below, and I’ll respond to you there.  If your question is really good, I might even make a whole post about it. 🙂

The questions don’t even have to be about biology; I have plenty of scientist friends in other disciplines I can appeal to.  Though, if you have a very specific question like How much Force power can Yoda output?, I’d encourage you to try submitting it to What If?  because I don’t have time to watch The Empire Strikes Back repeatedly to check the X-wing’s rate of ascent.

Some previous posts I’ve written about science:

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Hidden Figures

I am unavailable to march today, but one of my sorority sisters is attending the Women’s March in DC and offered to make a sign listing the names of those of us there in spirit, and I asked her to include my own.  In the meanwhile, I’m going to give a shout out to a movie featuring some other awesome women: Hidden Figures.

Image result for hidden figures

This biopic follows three African-American women at NASA during the space race of the 60s. Though some of it is a bit dramatized, it is all based on real life. I saw it opening weekend and loved it…and apparently so did a lot of other people.  In its opening weekend it actually beat Rogue One (which had already been out a few weeks, but was playing in nearly twice as many theaters) at the box office, and held on to the #1 spot over MLK Jr. weekend, too.  It’s a great movie for anyone to enjoy, but I would really encourage all young women especially to see it.

On to the science!

Katherine Goble (Taraji P. Henson) is a brilliant mathematician working as a “computer” at Langley Research Center and is assigned to the Space Task Group to help with the calculations for the launch and landing of Alan Shepard and John Glenn.  In Glenn’s case, putting a man into orbit around the Earth has never been done, so there isn’t a mathematical model for the situation.  Rather than looking at it as an “applied math” situation from a physics perspective, Goble finds a purely mathematical model that simply fits the numbers.

My favorite quote from her: “So, yes, they let women do some things at NASA, Mr. Johnson, and it’s not because we wear skirts.  It’s because we wear glasses.”  I think I related to her most of all the women.

Mary Jackson (Janelle Monáe) is an aspiring engineer, attempting to take night classes at a white high school. She is supported in this by her Polish-Jewish boss, but her husband (Aldis Hodge) is more hesitant.  I liked how the movie showed the struggle for civil rights not as one united movement pushing forward to a single goal, but going in fits and starts, with many different foci, sometimes at odds within the movement (white women especially don’t appear as allies here).  When Mary doesn’t want their young kids to see the news about a firebombing of a bus, her husband replies, “Everybody needs to see this.”  It was a powerful moment for me, thinking about present day events: videos captured on phones and uploaded, violence against innocent people that can no longer be hidden.  If we want to change the world, we have to face it first.

Dorothy Vaughan (Octavia Spencer) watches as men install the IBM that may put her whole staff of computers out of a job.  So she learns FORTRAN from a library book and starts working with the machine.  But she doesn’t stop there…she teaches her entire staff of African-American women how to program as well, ensuring that the whole group is kept on to work with the IBM.  Now that’s “leaning in.”

So the science part is great.  But the movie also shows these women as not just scientists, but leaders in their community as well.  They are moral women; we see them going to church, raising children, and participating in positive relationships with good men.  They support each other in their struggles and ambitions.

I was so impressed with the marketing for this movie.  It did a great job focusing on the three leading women in advertisements, so much so that I was surprised by the appearance of several white or male actors during the movie because I hadn’t even realized they were going to be in it.  I think this shows that a movie featuring black women can perform well, and hopefully Hollywood will taken this lesson from Hidden Figures and give us more.

One last note: the movie also shows astronaut John Glenn in a very good light, a point of pride for us in Ohio.  He unfortunately didn’t get to see it before he passed away last year, but it was a wonderful tribute to him.  (They also just renamed the Columbus airport for him recently.)

So if you are looking for sometime to do this weekend that will both entertain you and make you think about how far we have come–and how far we have to go–I highly recommend checking out a showing of Hidden Figures.  And I think I may go learn FORTRAN now. ~_^

Black History Month: Henrietta Lacks, HeLa cells, and informed consent

February in the US is Black History Month.  In my mind, there are kind of two parts to this.  The first is celebrating the many accomplishments of African-Americans, from MLK Jr. and Harriet Tubman to these awesome women in STEM.  I also loved these photos floating around on Facebook:

The second part is remembering the many injustices and struggles that African-Americans have undergone during our country’s history.  In the face of these wrongs, we as a culture can:

  • bring them to light
  • try to right the wrongs as much as possible
  • take steps to make sure they don’t happen again in the future

That brings me to the story of Henrietta Lacks, told so compellingly in the 2010 book The Immortal Life of Henrietta Lacks by Rebecca Skloot (which I wrote about briefly here).

In 1951, Lacks presented at Johns Hopkins Hospital with cervical cancer; as a poor, African-American woman and mother of five, in that time and place her medical treatment options were limited, and she soon succumbed to the disease.  During her treatment at Johns Hopkins, samples of her tumor cells were removed without her knowledge or permission, which was a common practice at the time.

These cells were cultured in vitro (basically, grown in dishes in a special nutrient broth) in the lab of Dr. George Gey.  The researchers soon discovered that, unlike previous attempts to culture human cells, Lacks’ cells did not die off after dividing a few times.  They kept growing and dividing; they were the first human immortal cell line and were subsequently named HeLa cells.

HeLa cells grew so well, in fact, that they began contaminating other cell lines.  Researchers began looking into the genome (genetic data) of Lacks’ cells and tracked down her family, who were stunned to learn that a piece of their mother, who passed away soon after giving her tumor sample in 1951, was somehow still alive in scientific labs all over the world.

Can you imagine what that revelation must have been like for the Lacks family?  Especially since their inadequate public science education barely prepared them to understand concepts like “cells” and “culture” and “genome.”

Still, the Lacks family is justly proud of Henrietta’s contribution to science.  HeLa cells have been used in a huge number of important experiments, including Jonas Salk’s development of the polio vaccine.

HeLa cover
The cover features a famous picture of Henrietta Lacks.  Notice the subtle bolding of “He La”

The Immortal Life of Henrietta Lacks, as well as numerous journalistic articles (and blog posts), have done a great deal to bring the story of Henrietta and HeLa cells to light.  But this fame is a double-edged sword: the privacy of the Lacks family has been irrevocably compromised.  Their family history has been thrust into the national spotlight, and, since the DNA of HeLa cells has now been sequenced, even pieces of their genetic code have been analyzed.

The Lacks family does now have some say in how HeLa cells can be used.  In 2013, the family reached an agreement with the National Institute of Health (NIH) to give family members an advisory role regarding which researchers can access the HeLa genetic data.  (These researchers must also acknowledge the contribution of Henrietta and the Lacks family in their publications.)  

But they have never seen, and likely never will see, any of the money that derives from the multitude of discoveries and nearly 11,000 patents relating to HeLa cells.  Though financial compensation has never been their goal, and from a practical standpoint it would be nigh impossible at this point, it hardly seems fair that others will continue to profit from use of their ancestor’s cells while they do not.  

Clearly the only way to really fix this situation involves a time machine.  (Sadly, all the sci-fi stories I read tell me that time travel causes more problems than it solves.)  

But seriously, if the Lacks family is now satisfied, let’s look forward: how can we prevent a case like Henrietta Lacks’ in the future?

Informed consent has been a standard in medical ethics for decades now.  Researchers must ask permission from their subjects before doing any human research.  (At least, they do if they want federal funding and to be published in reputable journals.)  The federal government is currently revising these regulations, referred to as the Common Rule.  

Rebecca Skloot and others favor the inclusion of a requirement for “broad consent,” so that even anonymous, “non-identifiable” samples require some general consent before experimental use.  (To be fair, samples today are coded so much better than simply using patients’ initials like “HeLa.”  But it is still technically possible to re-identify some samples through genetics, etc.)

Critics argue that this will just result in more paperwork, bogging down science while throwing another paper at patients to be signed without real understanding.  I am a practical person, but I refuse to build science, no matter how great, on the backs of the uneducated and disenfranchised.  While another case like Henrietta Lacks’ is unlikely, public education about tissue research is critical to our ability to continue to do great science while respecting human dignity.

Henrietta Lacks is still changing the face of science today in many ways, whether it’s regarding cancer treatment or medical ethics.  I encourage you to read more at the links throughout this post, and I encourage respectful discussion in the comments.

Bad Biology in Marie Lu’s Champion

*SPOILERS* ahead for Legend, Prodigy, and especially Champion by Marie Lu.

 

As I’ve been reading popular YA dystopian series, I’ve noticed a common motif: plagues.  The Matched, Maze Runner, and Legend series all have a plot element (generally in the 3rd book) involving some kind of terrible disease that main characters are trying to stop.  This element is used for societal and ethical commentary, because these plagues were engineered and unleashed by people. However, using a disease as a plot device opens the door to biological science fiction, which is something I really enjoy…when it’s done well.

Sorry, Eureka, that's not how you pipette. Nope.
Sorry, Eureka, that’s not how you pipette. Nope.

Now, I really enjoyed Champion, the finale of the Legend trilogy, but its biology is utter crap.

The first two books, Legend and Prodigy, don’t really go into biological details, and that’s fine.  We know that Day’s brother Eden is being used as a bioweapon against the Colonies, having been infected with a virus by the Republic government.  June, who as one of the Republic’s elite has had regular vaccinations against the plague viruses, also came down sick with something as she and Day were escaping to the Colonies.

The science starts to take a turn for the worse in Champion.  First, the Colonies threaten to halt the peace process unless the Republic provides the cure for the viral plague spreading through their territory; the Republic government assumes it’s Eden’s plague and requests to study him to develop the cure.  Herein lies our first problem: who in their right mind would attack a NEIGHBORING COUNTRY with a weaponized virus without first having the cure, or at least retaining samples to study?  It’s no good if you win the war, only to kill your own population when the virus makes its way back to you, which it inevitably will if it’s as extremely contagious as you designed it to be.

This is merely a flaw of logic; it can be waved away by supposing that the Republic is a thoroughly incompetent government.  Almost exactly ¾ of the way through Champion, we reach flaws in biology.

Scientists tell June that they haven’t been able to develop a cure from Eden’s blood, because the virus attacking the Colonies is a mutated form.  The cure they are trying to develop consists of “cure particles” which attach to an infected cell and keep it from lysing (breaking) open and dying.  But the mutated virus paradigm somehow changes the way the cure particles interact with the cells, and the ones made from Eden’s blood can’t attach to the cells infected with the mutated virus…

This explanation takes at least two pages, where plenty of scientific jargon is thrown around, and none of it makes any sense.  I am not even clear on whether the “tubes” are initially part of the cure particles or the cell itself.

Viruses do work by attacking a cell, then commandeering its machinery to produce more copies of itself, then lysing the cell open to let the new copies of the virus spread.  But treating a virus typically doesn’t mean stopping the cells themselves from lysing, but rather encouraging the immune system to attack the virus itself more effectively.

Most of what we do to treat viruses relies on the principle of antigens and antibodies in the immune system.  When our body recognizes virus invaders (“antigens”), it creates specific antibodies to attach to them, which prevents them from entering cells and also helps direct other aspects of the immune system to destroy them.

This wikipedia schematic shows how antibodies bind to specific antigens with a "lock and key" model
This wikipedia schematic shows how antibodies bind to specific antigens with a “lock and key” model

The idea that Eden and June’s blood could hold the key to treatment of the virus follows this principle.  In the current Ebola epidemic, we have seen survivor Dr. Kent Brantly’s blood used to successfully treat one other patient, and is now being tried for two others, including the Dallas nurse who contracted the disease on American soil.  His blood serum has antibodies against the virus, which when transfused into another patient will help effectively tag the virus for the patient’s immune system to destroy.

So, the book’s “cure particles” seem similar to antibodies, but it has confused their target, which is the viral particles themselves, not the cells they infect.  (I still have no idea what the “tubes” are meant to be.)  Unless the setting is meant to be in an alternate universe (no indication of this in the books), antigens and antibodies would still work the same in future North America as they do now, and I doubt the knowledge regarding them would have been lost in ~100 years.

So to take that concept further, it also makes no sense that Eden and June would have to go through all kinds of harrowing tests, including taking bone marrow (?!), when all that’s needed is the antibodies in their blood.

The supposed mutation of the virus is another issue.  We find out that Eden is not Patient 0 for the Colonies’ current virus after all; the virus is actually a combination of Eden’s and the one that June had while crossing the border.  (Shouldn’t June’s vaccinations have protected her?  Was she only vaccinated against viruses prevalent in LA?  Or are the vaccinations a sham to keep the populace calm?)

Viruses mutate naturally all the time; that’s why the components of flu vaccines change from year to year.  (However, there’s no reason to think Ebola will mutate specifically to become airborne.) I don’t know how likely it is for two random viruses to combine together naturally.  It can and does happen with similar strains of viruses, like two types of influenza; it’s called “antigenic shift” and is thought to be responsible for several flu outbreaks, including the H1N1 outbreak of 2009.  But we have no way of knowing if Eden and June’s viruses are at all similar.  So the scientist’s assertion that the Colonies tampered with the virus to create the new mutated strain could make sense.

Except…there’s no scientific way that I know of to prove it.  Splicing DNA or RNA together generally doesn’t leave any kind of fingerprint, certainly not a “marker” that could be “labeled” in a cell.  Perhaps if the Colonies’ scientists added extra “foreign” DNA or RNA not found in either virus?  But the Republic scientists would have had to sequence the whole viral DNA to find it, analyze what every gene does, then develop a way to tag the foreign ones.  And I can’t think of a reason for the Colonies to do that anyway.

Lastly, where are the original researchers that did the bioweapon research on Eden?  They should be involved in making the cure, since they oversaw the development of the virus.  Instead, we have random doctors at the hospital working on Eden and Tess, and a “lab tech” explaining the science to June.  Perhaps all the lead researchers have been executed, or Day refused to let them around his brother to avoid trauma.  But for such an important project, with the future of the country literally at stake, it seems the people with the most expertise should have been called in.

http://xkcd.com/683/
http://xkcd.com/683/

All these scientific inaccuracies cannot be fully explained away by the story; the fault lies with the author.  I truly wish Marie Lu had biologists critique these pages, or even better, left them out entirely, and not just because it would have slightly increased my enjoyment of the book.  With the current Ebola outbreak and inane controversies over vaccination, it’s important for people, especially young adults, to be scientifically literate about virology and immunology.  While the bad science probably doesn’t do any harm, Champion could have been used to educate young people about how viruses work, and how we try to fight them.   A sad missed opportunity in an otherwise great book.


I am not an epidemiologist/virologist/immunologist, but I do have a degree in zoology and work in medical research.  If you think any of my science in this post is wrong, or if you have any better explanation of the virology as presented in the book, I would love to be corrected and learn more.  Also, I’ve only read this series once and I don’t own it, so please correct me on any details from the books that may be relevant.

Some rational words about Ebola

I am scared of a lot of things.  Tornadoes.  Spiders. Venomous anything.  I am also scared of Ebola.  Terrified, really.  I am more scared of Ebola than pretty much any other disease, including things I might actually have a slight chance of getting, like breast cancer or AIDS.  I blame my sixth grade science teacher, who described the movie Outbreak to us in class one day.

Now, of course, this is totally irrational.  As a scientist I realize this.  So, let’s all calm down and talk about some facts.  Since my epidemiological knowledge is limited to some undergrad courses in biology and the mechanics of the game Pandemic, we’ll turn to the experts.

Tara C. Smith is a microbiologist/epidemiologist at Kent State University, which is just a short car trip away for me here in Northeast Ohio, and she also writes about infectious diseases for media, books, etc.  She has written a very nice piece describing why we in the US should not be panicking about the possibility of an Ebola outbreak here, because a lot of public “knowledge” about Ebola is exaggerated or incomplete.  Please read it, and take some deep calming breaths with me:

Everything you know about Ebola is wrong


Also, here are my suggestions for naming the diseases in Pandemic:

Yes, those are petri dishes to hold the game pieces
Yes, those are petri dishes to hold the game pieces

 

Yellow: AIDS (Ebola, yellow fever)

Blue: Spanish Influenza (Bubonic plague, Swine flu)

Black: Leprosy

Red: Bird flu (SARS)

Purple: ??