“Laughing Mantis Studio“ – http://LaughingMantis.com

Prints of my works are now available in my Redbubble store at http://LaughingMantis.redbubble.com

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.

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.

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.

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.

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 Oyster's Garter

“im a man in panties”
“Sarah Palin is a idoit”
“end of human race dna replication”
“truckpulling black widow”
“preparing for world war iii”
“i’m not even sure we exist same level of consciousness”

I have no idea how most of those came to me.

Really…

I don’t even know where to begin in summarizing this truly wonderful, enlightening, and inspiring experience. For those of you who are unaware of Science Online ’09 (at Sigma Xi in Research Triangle Park, NC), it is an annual conference (an “unconference”) devoted to the world of science blogging, writing, education, outreach, and general science enthusiasm.

Many rundowns of the conference’s events, including live-blogging of the conference, have already been written. And of course, Bora over at A Blog Around the Clock is collecting a compendium of conference related posts. Here, I thought I would just give some reflections of a few things that I personally got out of the conference.

BORA!!

First and foremost, let me just say what an amazing job Anton Zuiker, Bora Zivkovic, David Kroll, and all the other organizers have done in making this conference feel like a reunion of friends and family. I had never met any of the other participants in person, though I had chatted with several of them online. However, from day one it felt almost as if I were coming home. I know that sounds a bit hyperbolic, but one thing I’ve found in living the lab rat’s life in rural North Carolina is that it can be quite hard to find people simultaneously interested in basic science research AND in the passionate outreach and education performed by science bloggers (though I now know that you’re out there). Yet at Science Online ’09, what I saw was a community of people like me: people that love science in all it’s forms and fields, people who spend their free time outside of their day jobs talking and thinking about the most fascinating aspects of reality as seen through the empirical lens, people who LOVE their internets, their gadgets, their widgets, their feeds and aggregators, and most of all their ART (and not just the “fine” kind like that of Glendon Mellow of The Flying Trilobite).

Needless to say, it was one of the most reinvigorating and motivating conferences I’ve been to. Hopefully this newfound motivation will be apparent in the coming weeks here on this blog.

I love dinos

On day 1, I was privileged enough (largely due to the fact that I am local and was willing to be chauffeur) to experience a behind the scenes tour of the entire NC Museum of Natural Sciences, led by the intelligent and humorous Exhibit Director, Roy Campbell. Having lived in the Triangle area for eight years, I’ve visited the museum many times. It’s easily one of my favorite places in North Carolina. Never, however, had I been allowed to see the basements and backrooms, including the paleontology lab and collections. Ever since I was about 6 years old, I have been a fossil collector and paleontology enthusiast, which made the paleo lab all the more exciting for me. Two guys were inside meticulously scraping red rock away from various fossils. The picture below shows a rock 2-3 feet long encasing a creature that my brain had never before even imagined might exist: a bipedal crocodile. That’s right – as if modern crocs weren’t cool enough – there used to be little crocs walking around on two legs. I’m not even sure how to picture it – the best I can do is imagine a therapod (like a velociraptor) with a croc head. The craziest thing was that this guy had spent a year to isolate the bones in the image, and he guessed that it would take another year to finish. Talk about devotion and patience!

bipedal crocodile - that just sounds wrong!

As for the conference itself, what I took most from all of the discussions was simple inspiration to devote more time to maintaining this blog (and to reinvigorating the Carnival of Evolution). It was just so amazing to feel like a part of a true community trying to make a difference by educating and exciting the world.

As someone trying hard to break into becoming a full-time lecturer/professor at the college level, I found myself constantly hearing the discussions through the ears of a teacher. There are so many ways now to use the internet and blogging as a tool inside and outside the classroom. Of course, there was no more readily apparent example of this than the discussion moderated/hosted by the show-stoppers of the conference: MissBaker’s class, a group of “Extreme Biology” high school students. These kids were not just smart biology students. They were brilliant! And I will most certainly be studying MissBaker’s use of blogs to facilitate learning.

Some of MissBaker's students in the paleo lab of the museum.

Much of what I personally gained from the conference came from discussions during lunch / dinner / drinking at the bar. I was fortunate enough to have dinner with Kevin Zelnio (Deep Sea News), Andrew Thaler (Southern Fried Scientist), Karen James (Data Not Shown and The Beagle Project), Miriam Goldstein (The Oyster’s Garter), Mark Powell (Blogfish, Carnival of the Blue), Jason Robertshaw (Cephalopodcast) and Mike (10,000 Birds, I and the Bird). Mike mentioned a story of a recent project he and others had undertaken to fund a man in Africa to document a specific bird. After they successfully raised money for a laptop and other equipment, the man was apparently made tribal elder of his village (note I am pulling this from memory – I plan to get full details soon). So why do I find this story so interesting and useful? I recently taught “Topics in General Biology” for freshman non-majors. In this class we spend some time talking about various conservation efforts and the fact that many of the problems with conservation involve issues with providing poor local people in areas of high biodiversity with incentives to preserve their own wildlife and habitats. In areas such as Africa and South America, there is often no incentive to preserving habitat when this land can be used (for a short while) for agriculture and the like. Thus, an immediate goal for conservationists should be to find positive reinforcements and incentives for local peoples to conserve their own natural habitats.

Kevin Zelnio and Andrew Thaler in between singing sea shanties

Thanks to Mike, I now have an excellent real-world story involving a) people like you and me contributing small sums of money using b) the internet and science blogging to provide at least one man with an increased ability to c) document and spread awareness of his local wildlife and, perhaps through his new found elevated position in his community, d) spread the word about the potential positive outcomes of protecting the tribe’s environment.

Like I said, I am not personally familiar with the details of this story but I plan to put this together into a usable case study (hopefully including images if possible), since Mike has promised to provide the info. I know that there are similar projects occurring, but this one seems particularly poignant and relevant to the specific ways in which I taught my class.

As an aside, I am always looking out for interesting little biological trivia that might benefit particular subjects in the classroom. An always entertaining discussion regards that of sexual selection, which of course is filled with a myriad wacky examples throughout the animal kingdom. Thanks to Miriam, Andrew, and beer, I now have a new example that was heretofore unknown to me: a shrimp flatworm in which the females use dueling penises to get the mate. Again, this info is pulled from my then Newcastle-laden memory, so I might have the details wrong, but I fully expect Miriam to provide me with the full scoop (or anyone else who wishes to enlighten me below). There is nothing that piques the interest of non-major biology students like an entertaining story involving animal sex and strange genitalia.

In essence, it’s the new and hopefully long-lasting relationships and connections garnered from the conference for which I’m most grateful. I find it difficult to find people who share so many of my passions (that’s what I get for living in the woods), and I can’t express enough how reinforcing to my energy it’s been to hang out with so many like-minded individuals.

Thank you all (and feel free to leave a “hi” below – I’m terrible with names).

For more images from the conference: mine are HERE and others’ are HERE.

Is my soul supposed to burn like this?

I’ve had several people recently ask me about the reason for the name of this website and domain.

Let me first state that, no, I do not believe in any form of incorporeal, spiritual, immortal, or otherwise supernatural “soul.” There are many reasons that I disbelieve in a soul, but you can find a sufficient, if simple and unsophisticated, explanation of my own reasoning in this previous post.

Before I explain exactly why I call this site “biochemicalsoul,” I’d like to quote one of my favorite lines concerning the soul. These words come from Lisa Simpson – yes, that’s the yellow, animated, fictitious Lisa Simpson of Matt Groening’s creation:

“Whether or not the soul is physically real…it’s the symbol of everything fine inside us.” – Lisa Simpson

I think that quote perfectly summarizes my own usage of the word soul in my blog title. Originally, I had a website at “mychemicalsoul.com.” It was read by about five people – that’s five people that read it once, not five regular visitors. In it, I basically had compiled everything that I have produced. All my writings and rantings (most hilariously stupid and awkward – everything you can still find here pre-2008, which isn’t a far cry from what I still have going on here), all my art – ranging from sketches from junior high, to clay sculptures and wood carvings, watercolor paintings, and digital artwork and animation, and my photography. After a short while I decided “mychemicalsoul” was exceedingly lame, so I came up with the moderately less lame “biochemicalsoul.”

In essence, it was everything from my head that could be put in digital interwebbed¹,² form. Being the science/biology dork that I am, I wanted something pithy that embodied the above Lisa Simpson version of the soul and my own understanding of consciousness – namely that from a reductionist perspective, everything about who we are breaks down to complex synaptic networks and, ultimately, biochemistry.

Yeah yeah, I know – really it can be reduced to lower levels ending in quantum physics. But I couldn’t call it “neurobiochemisynapticquantumsoul.com.”

So my thoughts, interests, art, photography, and everything else in this site is about as good of a public display of my “soul” that I can put forth.

Hence: biochemicalsoul.com.

Note: I’m still migrating my art and photography, but some of it is available on the “art” tab.

Footnotes:

1. yes it is a word – look it up
2. oh, you did look it up and couldn’t find it? That’s what you get for relying on the internets

Sorry, but if you’re viewing this blog through Internet Explorer – almost NOTHING is working right.

I’m working to figure out what the heck is wrong. It seems to work fine in Firefox.