Biochemical Soul Musings on Nature, Science, Evolution, Biology, and Education


Echinodermata For The Win!!

I'm back!!! never realized I was gone?

Ah well, that's ok, because I AM back - back from a stressful few months of wondering where I would end up, how I would feed my babies (i.e. cats) and their baby-momma (my wife - yeah that does sound rather gross), and several dozen unknowns also thrown into the mix.

And after all the trials and tribulations, I can now state with certainty that I got the one job in my new future hometown (Pittsburgh) that I wanted more than anything: a post-doc in the lab of Dr. Veronica Hinman at Carnegie Mellon University.

What will I be doing you ask?

Well, I will be doing none other than studying the evolution of gene regulatory networks (GRNs). Specifically, I'll be looking at GRNs in the context of development using the wonderful sea critters in the phylum Echinodermata. For those of you not in the know, the "spiny-skinned" echinoderms are the asteroids (starfish/sea stars), ophiuroids (brittle stars), echinoids (sea urchins), holothuroids (sea cucumbers), and crinoids (feather stars, sea lillies and such).

Click for larger! Or Click HERE for super high resolution posters.

That's right folks - I am now at least an honorary marine biologist! ... kind of.  I don't know if the real marine biologists would ever deign to allow me such a title, but I can call myself whatever I want.

Many of you may know this already, but the process by which a single fertilized cell becomes a complex organism is an insanely intricate one. DNA is often called a "blueprint" for life, however in reality it's more like a cooking recipe informing each cell which ingredient to add and when, where, and how to add it - all codified into a multi-layered genetic computer program with kernels, plug-ins, sub-circuits, and all sorts of other technobabbly organic craziness.

This is where the "Gene Regulatory Network" comes in - the GRN is that central biological software controlling and allowing life itself. Not only will I be studying the structure of these networks in echinoderm development, I'll be looking at the evolutionary context of the echinoderm networks in relation to each other to suss out how they work and which parts of the networks are conserved (or not) between these amazing creatures that diverged from each other about 500 million years ago.

I'll initially be working on the "endomesoderm" network in the sea star, Asterina miniata. Down the line I'll also be contributing to the development of the sea cucumber as a new model for studying "evodevo".

In celebration, I spent a fair bit of time getting back to my art roots creating the above cladogram in the sand of the Echinoderm phylum (which you can get a poster of here if you're into echinoderms. I rendered it out in pretty high resolution, so you will definitely be getting a high quality poster. I'm pretty proud of it as it took quite a bit of work in the Blender program).

I spent a while trying to find time-lapses or animations of starfish development online, to no avail. Thus I spent a week of much needed downtime to create this computer animation: (note - you can also watch it in High Definition on youtube)

NOTE: The details of the actual metamorphosis of the rudiment into the juvenile are not accurate - it's quite hard to animate these types of changes - and to be honest I haven't actually seen these creatures in the flesh. But it's good enough to get a good idea of how the whole developmental process occurs in this type of sea star.

Anyway, I'm sure I will have much much more to say about the evolution and development of echinoderms in the future so I'll leave it at that for now.

Hopefully, I can at least be an honorary member of the cool kids club, the marine biologists: Kevin, Eric, Andrew, David, Miriam, Christie, Rick, Mark, Jason, Chris, and all the others I'm surely missing.

Comments (11) Trackbacks (1)
  1. Great Post, I always look forward to your updates.

  2. As I said on my blog… OMG YOU’RE ALIVE!!! YAY!!! I think we all were worried those beard-eating evil creatures might have developed a taste for human flesh and you had disappeared into the night.

    BUT you only get to be a part of the club when you spell my name right 😛

  3. Welcome back! That’s a pretty sweet picture. Want to make one of sharks?

  4. Congratulations on the job!

    Sounds great with the GRNs. I really would like to do evolutionary GRN modeling…

  5. Welcome back. The poster looks great.

    However, as a marine educator, I am not actually in the biologist’s club house, but rather in the little outbuilding around back. You are welcome to come visit, no beard required.

  6. welcome to the maritime mafia

  7. I’m not in the cool kids club? :(
    C’mon, I spent my whole life as the nerdy marine bio kid!

  8. Does this mean you can grow your beard again now that you have a job!

    Congrats though! I was in PB last year (not peanut butter, pittsburgh…) and thought it was a’ight. When’s the move?

    oh, and tell your wifey to call me back! :)

  9. Welcome back and congratulations on landing the awesome job!
    The poster and animation look great.
    Was the animation done in Blender as well? Course now I’m going through my rusty animation skills to reverse engineer it…
    Morph targets? Anyway it was done, Great job.

    Better bone up on the DSN Nautical terms now that your a marine biologist!