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


Medical Research on Animal Models – Where Do You Stand?

Our self-aware cousins

Our self-aware cousins

This weekend I heard an incredibly interesting story on NPR's This American Life titled "Almost Human Resources" (Act 3). The story was all about the issues surrounding chimpanzees in the human world surpassing their usefulness and how we should care for them. Apparently this now includes retirement homes with TVs.

This story, along with a recent tangential debate over at Southern Fried Science and PETA's "sea kittens" campaign, sent my mind down a familiar path - one that anyone working in biology inevitably travels from time to time: the ethics of animal research for science.

There have been myriad writings, books, movies, discussions, and laws surrounding the practice of using animals for research. I'm sure most of us in the science world have come to very similar conclusions on the subject, though we may vary widely in the details.

Nonetheless, I'm very interested to hear where YOU, my readers and my fellow scientist peers, currently stand on the subject. I would like this post to be interactive.

First, I'd like to give my own thoughts.

In general, I view all living things as uber-complex organic robots (humans included). All life is amazing, precious, and beautiful - from bacteria to humans - but I still see us all as robots, running our nearly unfathomable genetic programs, developmental processes, and higher-level emergent programs of conscious and sub-conscious thought.

Mirror Test

Mirror Test

At the same time, I feel - for no rational reason really - that consciousness and self-awareness inherently grant those that harbor them the right to live relatively free from human induced suffering. This is a feeling. We all feel it, at least for humans. We feel the immorality of conducting experiments on other human beings (though this was not always the case). Why? Because it's...just...wrong.

It's for this reason that I'm completely opposed to any medical research on chimpanzees or any great apes. There is no doubt that our great ape cousins share many if not most of our own emotional and sensory perceptions, as well as similar intellectual abilities (similar in type - not necessarily degree). For all intents and purposes, I see them as people. Not human people. Not anthropomorphized animals. But sentient to semi-sentient beings.

It's hard to measure degrees of self-awareness and know whether another creature has it. But the classic mirror test is one simple way to find when the answer is a clear yes. As of right now, great apes, dolphins, elephants, and at least one bird species, the magpie, have passed the test and shown that they have some understanding of "self."

If a creature can have any understanding of what is being done to "them," I am completely against it. Recently Orac at Respectful Insolence posted on the discontinuation of using dogs for teaching surgery techniques. He caught some flak from a few commenters for showing an emotional relief that dog use was being halted - at least partially because he loves dogs. As if any decisions on the use of other beings for our own benefit could be arrived at using only reason!

No - we as humans place some inherent value on consciousness, on self-awareness. Dogs may or may not be "self-aware" as defined by behavioral scientists. They can't pass the mirror test, but anyone who has had a dog knows that they clearly experience something akin to guilt, and a whole host of emotions similar to those of our own (I'm being careful here not to anthropomorphize). They know when they have done something wrong.

As any behavioral biologist, psychologist, or cognitive neuroscientist knows, there is no clear dividing line between conscious being and automaton. What about rhesus monkeys and the other more "primitive" primates? I personally feel that much monkey research - particularly those studies on the cutting edge of such diseases as A.I.D.S. - are critical right now. However, I also know that I could never be one to perform such studies. There is a mental hypocrisy here in my own mind. I would feel wrong performing primate research. But I support it to a limited extent.

But for some animals, it seems clear when they are well beyond that gray fuzzy line. Xenopus frogs, as far as any observation or measurement can tell, are much too dumb to have any sort of self-awareness. The same can be said of mice or rats. They simply do not have the cognitive capacity - the hardware - to generate emergent properties like self-awareness as we know it. It seems more than clear to science, I believe, that these creatures are fuzzy automatons. I have performed studies (using incredibly regulated and humane methods) using these creatures, and I have no qualms about it, so long as the use of animal models are absolutely critical to the study at hand. Hundreds of thousands of lives have been saved or vastly improved by such studies. Few people alive today (in America at least) can imagine what the state of human health would be without mice and rat studies.

And just to go one level further "down" the evolutionary ladder, consider fish.

Fish are NOT "sea kittens." We understand at least at a basic level what overall types of brain structures and neural pathways are required for higher cognition. Fish do not have these structures. They are insanely complex, from a genetic standpoint. They are beautiful. They are unimaginably important to the ecosystems of the earth. But they are still slimy scaly robotic automatons incapable of "suffering" in any human sense.

And invertebrates? Well, they're clearly organic machines. Would any of you really argue otherwise?

However, with all of the above being said, I often think about how barbaric people were only a generation ago (or sometimes less), and I wonder which of my beliefs will be considered equally barbaric by the next generation. As Richard Dawkins mused in "The God Delusion," perhaps animal rights is the issue upon which our generation will be judged to have sinned. Perhaps our ancestors will cringe at our actions (while praising the 500 year lifespans our research has given them - kidding).

What do you think? Take these polls and leave your comments below.

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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.



Doctrine: the Antithesis of Evolution and All Science

Dr. Jim West has implicitly claimed that because evolutionists often defend the theory of evolution so passionately and vociferously (or as he puts it, with "religious zeal"), then that must mean that evolution is "doctrine" [1. in this argument, I am only referring to the common usage of doctrine meaning "dogmatic system of beliefs" as opposed to the more innocuous "codified system of teachings". Of course evolution is a codified system of teachings. But it is a system that inherently acknowledges its own fallibility and tenuous nature]. (his post title: If It’s Not A Doctrine, Why Are People So Defensive?).

I hear this argument all the time, in multiple variations - claiming that because we defend evolution passionately, that means that evolution is "dogmatic" or "religious."

This is specious logic at best. I originally responded to his post in his own comment section, and I reproduce my thoughts here:

1) Just because someone is vociferous and passionate with any sort of claim, defense, proclamation, or simple statement, that does not have any bearing on its “religiosity”. Calling a passionate response “religious zeal” is simply an attempt to obfuscate the language and warp the debate.

2) Equating the passionate nature of a subject’s defense with anything concerning the nature of that subject is simple fallacious logic (i.e. what the hell does passion of a response have to do with whether or not it is doctrine?)

I will agree with the philosophical premise that ALL scientific knowledge is predicated on the prime assumption that sense relates to reality. Thankfully, simple pragmatism allows us to build science from the fact that it seems to work.

However, neither science nor evolution can be considered “doctrine” for the simple inherent acknowedgement within the scientific epistomology that it will always be possible that the prime assumption might be false. This is why science “fact” isn’t based on provability, but by falsifiability. Even the falsification of any scientific hypothesis is always considered inherently tentative. You cannot call something doctrine if that doctrine implicitly acknowledges its own fallibility.

(note: obviously in this argument, I am only referring to the common usage of doctrine meaning “dogmatic system of beliefs” as opposed to the more innocuous “codified system of teachings”. Of course evolution is a codified system of teachings. But it is a system that inherently acknowledges its own fallibility and tenuous nature.)

(Update: he has deleted my comments multiple times - maybe the word "hell" offended him? Or perhaps he couldn't argue?

Update 2: now they are online - apparently he doesn't like people to use pseudonyms. I guess I could have made up a name, but oh well - My name is easy enough to find.)


Giant Animal Smasher to Search for the Elusive “Darwin Particle”

High-energy squirrels about to release the "Darwin Particle"

Thanks to PZ Myers at Pharyngula for finding this one.  I post it here for the simple fact that this is side-splittingly hilarious! Go get your giggles on.


Malwin dismissed critics who claimed that smashing animals together at high speeds was cruel to the animals. He said, "The animals won't be feeling anything. The collision will vaporize the squirrels in a fraction of a second.  Their brains won't be able to transmit pain at those speeds, so it'll be painless for them."

Scientists currently rely on computer simulations to smash biological units, but simulations can only do so much, and without the visceral enjoyment of seeing two squirrels collide at thousands of miles an hour.


Carnival of the Godless #98

C. L. Hanson over at Letters From a Broad: The Adventures of a Friendly Ex-Mormon Atheist Mom Living in France Switzerland (I love that title) has composed the 98th biweekly edition of Carnival of the Godless, a blog carnival containing a myriad links to thoughts on atheism or tangentially related topics. This edition is particularly well done, and contains hours worth of edifying reading and links to make your brain cells hurt.

Graciously included in this latest edition is my own previous post, Hope in the Black Void of the Unknowable, in which I muse on whether we really want every human on earth to see the Universe and ourselves as science sees us, namely "no more than blips of energy in an inconsequential cosmic blink."

Check it out, and if you have your own musings on issues relating to an absence of God, go to Carnival of the Godless and find out which blog is hosting the latest edition and submit your stuff to them.