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


Are Human-Caused Ecological Invasions Good for Evolution and Diversity?

Burmese Python in Florida

Burmese Python in Florida

Today  I read of another huge snake finding in Florida that got me thinking once again about invasive species and evolution, as did the original story from earlier this year in which I learned of the invasion. ((python image copyright Key West Magazine))

Over the past eight years, a population of Burmese pythons has been exploding in the Florida everglades. As of 2007, the population had risen from essentially none (other than the occasional recaptured pet) to an estimated 30,000 pythons (also see this report from the University of Florida).

We often hear in the news about some invasive species or another and how the state involved is seeking to exterminate or halt the invasion. Obviously, many of these invasions can have disastrous consequences on the local ecology. The pythons may endanger many threatened birds of the everglades as well as everything else small enough to fit through the giant python maw. However, as we heard in this incredibly interesting study from August, some of these invasions may actually trigger bursts of increased biodiversity.

Timber Rattlesnake in the Ozark Mountains

Timber Rattlesnake in the Ozark Mountains

To be upfront, I am not an ecologist, though I have studied ecology a fair bit during my earlier years in biology (I actually once spent a summer radio-tracking timber rattlesnakes in the Ozark Mountains). Thus, I certainly wouldn’t claim enough expertise to suggest anything about the true effects of ecological invasions.

But I do wonder about the type of world we as humans wish to create and maintain around ourselves with our increasing ecological understanding. It seems to me that the picture often painted by ecologists and conservationists is one in which every species on the planet right now becomes saved, in its current habitat and in defined “healthy” and “stable” ecosystems. Of course, none of us believes that we can save all ecosystems, or perhaps even most of them – what with the rampant destruction and fracturing of almost every habitat in every corner of the planet. Nonetheless, even if we could, is that really the goal we should be reaching for?

Do we want every current species to continue its existence in its current form? Is not extinction of some species necessary for the “progress” ((by progress I just mean change. Obviously there is no such thing as “progress” from some lower quality to a higher one when it comes to evolution – except in fitness in a given niche)) of others?

Rocky invades my porch. I couldn't resist giving him a cracker.

Rocky invades my porch. I couldn't resist giving him a cracker.

Unfortunately, the positive or negative effects of a particular invasion or ecosystem change can never be fully understood except in hindsight – and even then, our understanding of the outcome is only tenuous. So how are we to decide which species we should consider lost causes? Which are too specialized to survive long term on an inherently changing planet? Which should we support?

Granted, all of these questions rest on the assumption that our own species will be a long-lived one – long-lived on evolutionary time scales, which seems to me an extreme unlikelihood. But suspend your disbelief and imagine that our species continues to be the caretaker of this fragile little ball in space for eons to come, in some form or another. What do we wish to become of the varied ecosystems of our world? Do we wish to simply maintain the life and habitats in the still-natural parts of our lands, and allow the species to evolve within the limits of those fractured areas? Or should we allow any species to gain holds on whatever niches they can, and allow natural selection to work its magic as it has for 3.7 billion years?

We know that the vast majority of these invasions occurring in ecosystems across the planet are due to our own machinations. Ignorance and blindness to the challenges of caring long-term for enormous predatory reptiles led to the python population in Florida. Ballast water has deposited invertebrates and microorganisms in waters far flung from their original homes. So how do we decide when a particular invasion will be beneficial and in line with what nature might have done on her own anyway? How do we decide  when a particular creature has "earned" it's invasive rights?

Not as pretty as a toadstool, but hey - it's a fungus.

Not as pretty as a toadstool, but hey - it's a fungus.

I don’t claim to have even the vaguest answers to any of these questions. I welcome any of you true experts in ecology and evolution to point out any problems with these thoughts, or thoughts of your own. These questions seem largely philosophical at their base, but could conceivably have practical consequences in the far-distant to not-so-distant future. And they can ultimately only be answered by you ecologists and evolutionary biologists and the scientific knowledge you produce. The implications of these invasions and our place as both the cause and regulator of their effects simply fascinate me. Will we now become the primary constraint against which all selective pressures rest?

Or will our species die in a few century-long seconds, rendering all of the above completely moot?

Note: It turns out that the snake found this week is a red-tailed boa constrictor and not part of the python population.



Don’t Fear the Creatures

Me manly. Throw baby.

Me manly. Throw baby.

I fear nothing.

No, that is not statement of my own masculine machismo, which I generally lack. In fact, if you were to stick a fuzzy kitten or a baby before me, you would find me near-instantly reduced to fawning and cooing like a 5-year old girl. I’m not ashamed of that.

No, what I mean is that, for whatever reason – be it upbringing or genetics – I seem to lack a trait that in my experience 95% of the general public harbors. That trait is an irrational fear of some aspect of the living world.

Here is one example of this. I have talked to literally hundreds of people about this over the course of my thirty years, and without fail, nearly everyone I have ever spoken to reveal some sort of prejudicial bias against some specific branch of the animal kingdom. Usually it either is bugs in general, spiders, or snakes. For others it is raccoons, or opossoms, or rats, or any “pesky” vermin.

Often, instead of verbalizing it as fear, they will say “oh, I hate them,” or “I really don’t like them.” However, it all seems to break down to the same thing: an irrational distaste for entire groups of living creatures.

"I hate you too."

"I hate you too."

I simply cannot understand it. I mean, yes I understand intense phobias. My wife is a psychologist and I have a firm grasp on the nature of phobias. But the prevalence of this hatred and fear seems to go far beyond a massive case of societal phobia.

Considering that I seem to be alone in this (though in view of the subject of this blog in general, I’m sure many of you readers are like me), it seems to me that the main question I have is not “why do they fear?” but “why do I not fear?”

I was raised as a redneck rat-tailed child in the woods in Northeast Texas and then in the Ozark Mountains of Northwest Arkansas. I grew up surrounded with snakes, spiders, scorpions, and all manner of wildlife. But the rub of it is this: so did everyone else I ever grew up around! So did my parents, my siblings, and my friends. Yet still, all of them have some major irrational bias or another against one or more of these creatures.

So why is it you can throw a timber rattlesnake 3 feet in front of me and I’ll be like “wow! cool!”, whereas most people will scream and cry? My entire property is overrun with Northern Black Widows (see pics and video here), yet I have never had the faintest urge to call an exterminator.

I think at this point I should quickly define fear. If you stuck the same snake within striking distance of my body, you can be damn sure that fight-or-flight would kick in and I’d retreat in haste. I wouldn’t dare handle a black widow. The fight-or-flight is reflex to avoid bodily harm. The rest is rational fear, or more accurately, simple respect. This is not the fear I am talking about. I’m referring to the guttural yuk, eww, or aghhh factor that so many harbor.

So tell me, dear reader, because I honestly would like to understand – why do you fear/hate/dislike whatever part of the animal world you do?

I have thought about this a lot, and my best hypothesis is that, for me, fascination trumps fear, and even kills it. I have had an insanely passionate fascination in all things biology (and science in general) since I was 5 (as far back as I can remember). When I was young, I dissected dead things, I played with insects, and I handled king snakes. Some of my little friends did this, but even then, I remember that I seemed much more interested by those things than my friends did. So is this the simple answer? Maybe, but I’m not so sure.

If so, the question just shifts a degree to “why the hell doesn’t everyone else find the living world as fascinating as I do?”

"Be glad glass is too smooth. Be very very glad."

"Be glad glass is too smooth. Be very very glad."

I had several traumatic animal-related events as a child. When I was 9, a scorpion found its way into my pajamas while I slept. It got wedged against my calf where it stung me 8 times. My dad ran in, ripped my pants down, and stomped the scorpion that fell to the ground, while I screamed bloody murder. Still, I think scorpions are awesome. A giant black rat snake I once handled grabbed my hand and chewed it until the blood flowed (also see my related post on black rat snakes and ignorant rednecks). I’ve been stung by countless hymenoptera (hornets bees, wasps, yellow jackets). I’ve been bitten by spiders. Still, I love them all.

Is my brain simply not wired to make the kind of phobic connections that so many others have? My wife is deathly afraid of cockroaches, yet I’m sure the worst that ever happened was that she got one in her hair. Somehow I doubt that a difference in my own susceptibility to phobias or conditioning is the answer – I can’t imagine I wouldn’t develop PTSD if a truly traumatic event were to occur to me.

Am I more rational? I know that in many cases I’m much more rational than others, though I still have my own irrational quirks. However, my lack of fear also extends to other things – like death. I have thought and thought and I can honestly say there is nothing that I simply fear. There are many things that I’d rather not happen, but none that I chronically fear.

I don’t mean this to come across as arrogant at all. I have many many faults, most of which I can admit. But this seems to be a trait of mine I have observed. Those that know me – tell me if you disagree.

It just doesn’t make any sense to me to dislike, hate, or fear any type of creature. There is nothing logical about it. To me it’s like saying “I don’t like the color green.” What does that even mean? I can understand not wanting to wear green because one finds it less aesthetically pleasing or because it doesn't match one's eyes. But this is fundamentally different from not liking the color itself. I would be scared to tromp through a grizzly den, but I don’t hate or fear grizzlies in general.

Anyway, I’ve rambled enough on this. I would very much like to hear any thoughts any of you have.


The Origins of

Is it supposed to burn like this?

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 “” 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 interwebbed ((yes it is a word - look it up)), ((oh, you did look it up and couldn't find it? That's what you get for relying on the internets)) 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 “”

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.


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



Science Blogging Conference in Research Triangle Park, NC!

January 16th-18th

January 16th-18th

I had no idea such a thing existed, but thanks to Bora at A Blog Around the Clock, I am now registered for what seems like a truly enlightening and fascinating conference on science blogging.

It's called ScienceOnline09 and will be held Jan. 16-18, 2009 at the Sigma Xi Center in Research Triangle Park, NC.

To quote the ScienceOnline09 website:

This is a conference to explore new ways in communicating scientific exploration.

Our conference addresses a variety of issues and perspectives on science communication, including science literacy, the popularization of science, science in classrooms and in homes, debunking pseudoscience, using blogs as tools for presenting scientific research, writing about science, and health and medicine.

So if you live in North Carolina (or don't mind traveling), and write or blog about science, or if you are simply interested in science outreach, register for the conference online.

There are currently 37 49 people registered (you can find out who's registered here).

I hope to meet some interesting fellow bloggers soon!


Biological Databases and the Logos I Designed

I recently designed a couple of logos for Dr. J. Christopher Ellis to adorn his biological database website. I thought I'd throw him a link as well as showcase the two logos I made.

The first is for the frontpage of his site I made this using the 3D animation software, Maya 7, and Flash. Note: if you click on the logo, there are three possible animations that will occur. I know next to nothing about flash animation, but I managed to get it so that it picks one of the three events at random. As such, you may have to click several times to see all three. Yes - they are completely pointless - but I wanted to learn at least a little ActionScript. The pixelation is due to resizing to fit into this blog.

I also designed the following logo for his snoRNP database. For those of you not in the know, snoRNP stands for "small nucleolar ribonucleoprotein", which bind to snoRNAs, or "small nucleolar ribonucleic acids". Together they are involved in modifying rRNAs, or "ribosomal ribonucleic acids", which are themselves part of the structure and function of the ribosome (your protein making machines).

So for those of you involved in snoRNA research, you may find his database useful. He also has a couple of applets for finding motifs within UTRs (untranslated regions). FYI: the sites are still in early construction.

The snoRNP Database