Friday, June 20, 2014

June 20 (Day 171) - Rest day, flashback to my PhD days, future life choices

I knew last night that I would be a bit stiff this morning. Riding a road bike without any form of suspension on dirt roads is not only tough on the bike, but it really beats up the knees, wrists, and other joints as well. So, when I got a note from my PhD thesis advisor this morning saying he needed me to take some time to review a manuscript that we are going to be submitting for publication, I decided to take today as a rest day to revisit the science I left behind at NYU when I finished my PhD 3.5 years ago. My thesis advisor is actually a fairly hardcore birder himself; It has been very easy for us to stay in touch since I moved to Boston. We actually hang out and bird together in New York or Boston at least a few days each year. It was really nice to see that the project I left behind has fallen into capable hands and will eventually result in another publication on my CV. I doubt that I will return to academic science moving forward, but it was really nice to revisit my former life for at least a brief window today.

The biggest highlight of today was the Pizza Hut lunch buffet in town. The dude attending to the patrons kept trying to take my plate away. I had to growl at him like a dog when he tried this. I consumed approximately 1.5 pizzas, biked home, and fell asleep. Prior to this I did look for Willow flycatcher down the road a bit without success.

Since I know at least a few people will ask (and I don't real have much bird material today), I'll give you a not-so-quick-but-hopefully-informative overview of what I did for my PhD. I have always been interested in development. Very generally, developmental biology is the study of the events through which organisms grow and propagate themselves into subsequent generations. In more specific terms, development is the collection of genetic, cellular, and morphogenetic processes that control the specification of different cell and tissue types and the subsequent organization of these cell and tissue types into functioning and reproducing organisms. For example, there is much prenatal development between the time that an egg and a sperm unite to form a single-celled zygote and the birth of a baby 9 months later. There is subsequent and prolonged postnatal development that continues at least through the onset of the reproductive stages in this next generation. It would be impossible for any one person or laboratory to study every aspect of development, so each group of developmental biologists has its own little niche in which to study the very complex and beautiful process by which organisms take form, grow, and reproduce.

Clearly, the end goal of all of this research is to help humans in one capacity or another. However, it is difficult if not impossible to do experiments on people, so scientists instead rely on model systems to study development (and almost all other aspects of biology as well). Below is the life cycle of a human and of the model system in which I worked, the nematode C. elegans. While the body plans and the generation times are clearly very different, many of the core features of development have been conserved across evolutionary time from nematodes to humans. By studying what genes and proteins are required for the development of an organism as seemingly simple as nematode, we can actually glean quite a bit about how analogous developmental events might be regulated and executed in humans. The human genome contains about 20,000 genes. The worm genome also has about 20,000 genes, and about 35% of these are evolutionarily conserved with humans. Despite what they teach in some schools these days, you're more like a nematode than you ever realized!

Generation time ~15 years, generally 1 offspring per cycle
Personal note: humans should NOT NOT NOT chose 
to reproduce this fast!

Generation time of 2.5 days.
1 adult worm lays ~250 eggs over 3 days.
By the time the last egg is layed, the first egg has 
developed into a adult worm which itself s now laying eggs!

45 second, time lapse movie showing the ~14 hours
of embryonic development in C. elegans.
The animal hatches as a larvae after these 14 hours.
Gastrulation proper starts about at about an hour into
the clip and runs until hours 5-6.
Time stamp in top left is hours:minutes:seconds.

SO AWESOME!!! So how did I fit into this? I specifically worked on the molecular control of gastrulation in C. elegans. Embryos generally have 3 germ layers layers: endoderm, mesoderm, and ectoderm. Endoderm will become most of your internal organs. Mesoderm will generally form muscles and bones. Ectoderm will contribute to your nervous and skin systems. Nematodes don't have bones, but they do have everything else I listed above. These 3 germ layers are organized during a massive embryonic movement of cells called gastrualtion.  This organization of these germ layers is what is happening in the movie above. After they are correctly organized, the further morphogenetic articulation produces what you will recognize as a long, skinny, worm shaped body. I specifically studied what genes were required for the the very early stages of gastrulation. I explored how cells sense their physical positions relative to other cells and how they know where to move once this embryonic reorganization commences. Much of my work centered on cell polarity. This is the process by which cells asymmetrically partition function across their cell bodies. Think of it this way, a cell moving in a gastrulating embryo is moving in a given direction. Therefore, that cell must have somehow delineated or marked that axis along which it is moving; There is a vector and a polarity associated with this movement. I was able to identify a previously uncharacterized molecule that polarizes embryonic cells so that they can move in the right direction once the embryo starts reorganizing itself during gastrulation. For those that want the genetic and molecular specifics, here you go

Anyway, I write this as a bit of personal pride and also as a bit of personal practice. One thing that I think I do well is communicate seemingly complex ideas in a way that people not immediately familiar with them can grasp and find interesting. While I doubt that I will return to the laboratory, I would like somehow to be involved as an advocate for science and other forms of rational thought. I may find that the best way to do this is as a high school science teacher, I may try to get involved in science writing, or maybe, just maybe, I can get elected to Congress so that we actually have a PhD level scientist making important scientific decisions moving forward. Somebody correct me if I am wrong, but I do not think any of these people have a PhD in anything even remotely connected to science. Its absolutely terrifying! Anyway, these are just some of the things I think about as I bike what sometimes seem like endless miles around the country. I have the feeling that I will figure it all out eventually.......

Quick trivia question: We've had one president with a PhD. Who?
I'd personally like to see more......

Lastly, Queen Sonia got to do something SUPER COOL today. If you're not a baseball/sports fan this won't mean much, but if you are, the photos will require zero explanation. I'm very jealous!
HINT: there is ivy on the outfield wall!


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  2. There are 2 PhD's, 3 engineers and 3 MD's on the House Science, Space and Technology Committee.

    1. I see that Daniel Lipinski has a PhD in Political Science; who has the other PhD?

    2. This comment has been removed by the author.

    3. PhD in political science has little to no use on a science committee. The is absolutely no science involved in the study of politics. Might be the biggest misnomer in history!

      Engineers and MDs are certainly welcome and appropriate additions to the Committee, but these folks generally aren't true scientists. We need some biology, chemistry, geology, Physics PhDs to help shape policy around stem cell biology, changing ocean pH, mining and natural resource extraction, and atomic energy use. Political scientists, engineers, and MDs are general not experts in any of these areas.

    4. Calm down Dorian, I was trying to make the same point: that none of members on the committee have a PhD in the natural sciences (I just figured that the other science committee member with a PhD is Derek Kilmer with a graduate degree in Comparative Social Policy). The remark of "Anonymous" is indeed irrelevant, but I don't think there is a need to turn this into a "my field is better than yours" slugfest.

    5. I don't think my remark was irrelevant as it was in direct response to Dorian's invitation to "correct me if I am wrong". While I agree entirely that it would be beneficial to have many more individuals trained in the natural sciences serve in Congress, I think you both miss the point that anyone with a PhD understands scientific method, interpretation of research results, etc. Political Science is not politics, it is in fact a scientific discipline funded by the National Science Foundation. And, please, show me an MD who isn't well-versed in biology. Why should I believe that an intimate knowledge of the evolutionary biology of nematodes makes you any more qualified to weigh in on climate science than a man with a doctoral degree from Oxford (which clearly demonstrates his intellectual prowess) and his choice to serve on the committee (an indication of the value he places on science and technology), i.e., he's smart and he cares. These are not the people you should pick on.
      Your idea to become a high school science teacher has lot more merit, Dorian - educate the voting populace - that is sorely needed!

    6. Why do I not tell my mechanic or my dentist how they should do their jobs? Because I know NOTHING about cars or dentistry. Having a person with a degree in political science make decisions about stem cells and atomic energy does not make sense. I am not saying that a political science degree is useless, its just useless in this arena. Likewise, my biology degree is useless when it comes to urban planning; I should therefore avoid committees focused on urban development. And yes, you are correct, my biology degree isn't incredibly useful when it comes to climate science. However, a biology degree is still infinitely more useful in dealing with climate science that many other degrees. Much chemistry is common to biology and climate science, for example. The point is that in my ideal world, we'd elect loads of people with diverse fields of expertise. Right now we generally have a governing body filled with lawyer and business people who know little about anything other than making laws and money. This isn't going to cut it moving forward. I'd love to see a committee of 10 poly-sci PhDs working on campaign finance reform. This is where their expertise would be best deployed as this is their area of study. Everyone and every degree has value, it just about slotting them into the proper place.

      My PhD had nothing to do with evolutionary biology. It focused on cell biology, and it used molecular biology, genetics, and biochemistry to address specific hypotheses regarding cell polarity and morphogenesis. I can explain in molecular detail topics as diverse as chromatin organization, microRNA biogenesis and function, protein folding, synaptic function, etc etc etc. I am qualified to make decisions about policy as it relates to biology. I am not qualified to make decisions about atomic energy or the course of treatment for sick patients. Those should be left to physicists, and MDs, respectively.

    7. Agreed, basic scientists are underrepresented in congress, as are MDs. One point of defense, however: let's be clear, there are plenty of MDs conducting basic science and basic biomedical research and running their own labs. A PhD is no longer the only path into a career as a research scientist. There are medical students awarded Howard Hughes research training fellowships annually. Medical residencies are mandatorily incorporating basic science training into their curriculums and dual degrees such as the MD/PhD, after which the MD may become the primarily used degree if the student so chooses, are rapidly growing in popularity. Echoing an earlier comment, the bottom line is many if not most MDs are excellent scientists as well as clinicians. Another example, radiologists are highly trained in physics during residency, they probably ARE qualified to make decisions about atomic energy AND the course of treatment for a sick patient. Boxing MDs in as healthcare professionals who do nothing but treat sick patients is simply incorrect, so I caution overgeneralization and the definition of "scientist" as it is being used above.

    8. Very good point. I don't mean to bash MDs. You are correct that many of them do actual science in addition to their clinical work. I have no issues with MDs being on a science committee. People without ANY technical training? That's another story......

  3. Great post, Dorian! How about a Wolpert quote?

  4. Thomas Woodrow Wilson, born in Staunton, VA. Studied at Princeton & Johns Hopkins. Only American president with Ph.D.