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

26Jun/09Off

Echinodermata For The Win!!

I'm back!!!

Oh...you 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.

4May/09Off

Blog Update & Carnival of Evolution #11 – Oh, For the Love of Science!

Well, as some of you have no doubt noticed, I have been rather absent from the internets as of late. On top of a heavy load of scientific experiments on my plate, I'm also spending almost every waking minute trying to get my house ready to sell for my impending move to Pittsburgh (which includes painting every square inch inside and out - and let me just say that painting exterior trim sucks!).

Thus I have had zero time to even read new interesting science literature, much less write about it.  That being said, I have had time to keep my camera on hand as I piddle around the house. Considering that Spring is out in full force here, I have quite a few really good shots I will be showing you all soon.

In the meantime, you should definitely check out the Carnival of Evolution #11, which is now live over at Oh, For the Love of Science!, care of the wonderful writer, Allie. Take a stroll with her through the Museum of Natural History as she ponders the ontogeny and phylogeny of life and the implications thereof, all the while pointing you to some of the best evolution writing from the past month.

Be sure to submit your own writings next month to the Carnival of Evolution #12, which will be hosted by the so-famous-he's-infamous Kevin Zelnio at Deep-Sea News.

Use this form to submit your posts for next month's edition.

*image source: Alex Wild / Live Science via The Primate Diaries.

5Mar/09Off

Biochemical Sole

In honor of the flatfishes...

In honor of the flatfishes...

The above image arrived in my email inbox last night from the preeminent coral reef expert and blogger extraordinaire Rick MacPherson of Malaria, Bedbugs, Sea Lice & Sunsets.

The subject line simply read "I'm just sayin..."

The pun came from his recent Carnival of the Blue #22 in which he wrote of my post on Flatfish Eyes & Recapitulation Theory :

More Weird Fish Eyes
If you still need some additional fish weirdness, Carnival of the Blue first-timer (hopefully long-timer) Daniel Brown of Biochemical Soul dredges-up memories of 9AM Developmental Biology class as he explores the evolution of flatfish eyes. This post has it all... some ontogeny, some phylogeny, some eyeball migration. Perhaps with the right encouragement we can get Daniel to focus exclusively on the ocean and change his blog title to Biochemical Sole?

Rick's wit never ceases...

Go check him out to see what I mean.

I'm actually finding myself craving fish now.

20Feb/09Off

Pseudonymous No More – The Big “Reveal”

I've decided - it's time for me to come out of my pseudonymous virtual closet.

Earlier this year I attended the ScienceOnline09 conference - a conference attended by over 200 science bloggers, educators, journalists, and researchers.

One of the sessions concerned online identity and posed the question "should individual bloggers keep their online identity anonymous or pseudonymous, or should they consider it as an extension of their professional life, writing under their true identity?" Of course, each individual is different and there can be many real and valid reasons for not broadcasting one's true identity. Many people write about controversial subjects (particularly those writing on the incompatibilities or intersections of science and religion). Others simply write on topics that may conflict with their professional positions or institutional missions.

After much thought, I've decided that I do not see any of these reasons as applying to me or my writings. After the conference, Andrew, the Southern Fried Scientist, wrote an excellent piece concerning his own identity, essentially making the same arguments and coming to the same conclusion that I do here. I'll start by quoting Andrew, as I could not have said it better (it's hard to say anything better than he can say it):

"Two sessions that got me thinking about the direction of my own blog were centered around transitions in your blog as your career progresses and whether or not to maintain anonymity (and how one goes about doing that). For me, I’m using this blog as a tool to create a track record of public outreach and education, and to voice my opinions on various marine, mycological, and mundane issues. Since I’m using it as a mechanism for career building, I see no reason to be anonymous (in this case that would actually be counter-productive)."

I see this blog in very much the same light (minus the ocean and fungi). I do not write about the details of my current scientific research (that is, as a government researcher I make sure that there are no conflicts of interest between this blog and my job). I rarely talk about religion or controversial subjects these days (I have a few much older posts that delve into the subject and aren't particularly controversial, but I now try to strictly avoid it).

In fact, I think the goals of this blog and of my writings have evolved to become a critical aspect of both my professional and personal life: namely the goal of bringing the grandeur of nature and science to the masses. Most of my writings are of the general science and biology variety (such as my Adaptations of the Week), often written with the laypublic in mind.

I initially took the handle "Irradiatus" during the beginning days of widespread internet use (mid-nineties) - and I've used it ever since. I don't even recall where it came from. When I started this blog (or a version thereof under a different name many years ago), it was nothing but a mental release - just a fun, inane, ranting, and completely unread by anyone exercise in self-expression. Thus, I stuck to my handle out of habit and ease.

But no more.

Thus, I now announce that my real name is Daniel D. Brown (my name is too common to not include my middle initial).

*Cue psychologist wife: "you sound like a narcissistic crazy person." I'm not. I just thought it was a funny announcement.

I am currently a post-doctoral researcher at the National Institute of Environmental Health Sciences (studying brain development), and sometimes an Adjunct Assistant Professor of Biology at Elon University. I received my Ph.D. studying the genetics of heart development in the lab of Dr. Frank Conlon at the University of North Carolina at Chapel Hill.

I have updated my "About" page if you want more information. If you link or refer to me, I don't really care which name you use. I will still be posting under my handle (much as Andrew maintains his "Southern Fried Scientist" identity), but that's mainly because my real name is lame and common. Of course, most of my regular readers know my real name already, and most of you probably could care less who I really am anyway.

9Feb/09Off

Tooting my Own Digital Horn – The Oyster’s Garter

I recently offered to put in a design for a new blog banner for the extraordinarily nerdy and equally awesome ocean blogger, Miriam, of The Oyster's Garter.

She didn't hate my design, which now adorns her digital abode.

If you haven't been to The Oyster's Garter, or if you find yourself thinking "what the hell is an oyster's garter?" then I highly recommend you stroll through your nearest tube over to her place to figure it out for yourself. I particularly enjoyed her recent poetic, lyrical edition of the Carnival of the Blue #21.

The Oysters Garter

The Oyster's Garter