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

10Mar/09Off

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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12Feb/09Off

Darwin Day Linkfest – My Favorites

Though we are nearing the end of the "official" Darwin Day celebration, considering Charles Darwin's 200th birthday and the 150th anniversary of the publication of The Origin of Species, 2009 is sure to be the Year of Darwin. In fact, a slew of events will be filling the entire month of February and there are bound to be internets full of evolutionary goodness throughout the year.

The entries for the Blog for Darwin "blog swarm" are only just beginning to roll in. In this post, you will find my favorite Darwinian entries.

First and foremost, I would like to ask you all to read my own post, Darwin and the Heart of Evolution, which recounts a simplified evolutionary history in the development of our cherished organ - the heart.

On to the link love!

  • The Beagle Project Blog gives their own rundown of the best Darwin posts, here, here, and here.
  • The Digital Cuttlefish sings us the single most amazing science song ever written. It is pure beautiful poetry. Everyone should read it and hang the lyrics upon their wall.
  • Richard Wiseman Blog brings us an amazing afterimage optical illusion of Darwin himself  - a great alternative to the ubiquitous and similar Jesus illusion.
  • Observations of a Nerd explains why she is not a "Darwinist" (and why no one should be, really). As I like to say, Evolutionary Theory is to Darwinism as the blue whale is to Pakicetus.
  • If I ever gave Valentine's Day a second thought, I would most certainly give this Valentine's Day Card to my wife (hat tip to The Oyster's Garter). Thankfully my wife views the wretched holiday in the same light as I do.
  • FYI: Science! tells a great tale of teaching evolution in high school biology classrooms.
  • The Southern Fried Scientist and WhySharksMatter over at Southern Fried Science, and Kevin Zelnio of The Other 95% and Deep Sea News have begun a massive undertaking, celebrating both Darwin's birthday and the Origin's publication in November: They are growing beards from scratch between now and November for "The Great Darwin Beard Challenge". Now that's some dedication!
  • Life Science Tools of the Trade gives an incredibly entertaining look at Darwin's methods of specimen collection. In Darwin's own words (describing a rare and now critically endangered fox), "He was so intently absorbed in watching the work of the officers, that I was able, by quietly walking up behind, to knock him on the head with my geological hammer."
  • It's Alive!! speaks of Darwin's ecological villainy. It's in the same vein as the previous link - you just have to read it - short and very funny. Excerpt: "Darwin did eat a bunch of endangered turtles, lizards, birds and other animals during his voyage. It’s one of 10 fun facts about Darwin. Hah! Take that vegans."
  • Mike of 10,000 Birds gives a beautiful rundown on why birders should love Darwin.

Those are all the posts I've managed to read through thus far. I am certain that many new and wonderful posts will arise over the coming days, my favorite of which I will continue to add to this post.  Cheers! And have a Happy Darwin Day!

3Feb/09Off

Carnival of Evolution #8 (Part Two)

Welcome back to the Carnival of Evolution - the place where the sideshow freaks of nature, the genetic mutants of the Tree of Life, run the show. Yes - we are all mutants, each of us with our own mutant powers, whether that be gripping plastic electronic mice with opposable thumbs or using specialized spiny penises to scrape the competing life juice of our competitors from the orifice of our beloved (sorry - I've been reading Dr. Tatiana's Sex Advice for All Creation - about the evolution of sex in the animal kingdom).

To what do we owe our gratitude for such wondrous gifts? Why, nothing more than the variable nature of inheritance and a competition for survival and reproduction.

As mentioned in the previous edition of the carnival, posted here just a few short days ago, a whole new slew of evolutionary links appeared in our BlogCarnival.com submission basket upon submission of edition #8.  Thus, in a special unprecedented issue, I now bring you PART TWO of this month's Carnival of Evolution #8.  We have some new faces appearing in this issue, intermingled with familiar acclaimed contributors of editions past.

A quick administrative note to future contributors: don't even think of submitting a post entitled "Teaching Intelligent Design." You will be summarily rejected.

An example of the type of detritus not likely to make it into a blog carnival devoted to the wonders of natural selection includes articles attempting to claim that the amazing complexity of some biological phenomenon is too great to have happened naturally.

via Wikipedia

A sperm's journey through, as Peter Buckland of Forms Most Beautiful puts it,  "potentially hostile vaginal territory" is indeed an utterly astonishing and deadly adventure. But what about wasted sperm, unimplanted blastocysts, and the developmental disorders that plague human reproduction? Ahh, that’s okay…Apparently God still did it.

"Oh yeah? How do you know?" I hear my opponent whine. Well, I don't know. Anyone who has studied or considered the philosophy of science understands that nothing is absolutely knowable. Thankfully, Kuhn and Popper showed us that that's okay - pragmatism works just fine.

The thing about evolution - it has an almost unfathomable mountains of evidence backing it. One simple yet always entertaining type of evidence that can be used to ease folks into an evolutionary understanding is that of human vestigial traits. The List Universe gives us one of the better rundowns of the top ten vestigial evidences of human evolution that I've seen.

But the arguments will continue to spew forth. Luckily The Evolving Mind is there as the Clever Criticisms of Evolution arise – criticisms that aren’t so clever that he can’t refute them - in this fourth part of a series.

The Splendid (Ranongga) White-eye (GrrlScientist)

The Splendid (Ranongga) White-eye (GrrlScientist)

So what else can we do to spread the knowledge? The Mississippi Atheists give us a great post on "how to defend science education in your state" – Stand strong my fellow southern and proud while also intelligent and scientific brethren (and sistren?). The South will rise again (or eventually for the first time)! Author's note: I'm a native Arkansan and Texan.

What if you are someone that is fascinated by evolution, but does not necessarily understand the science behind it or how to read all those weird pictures with the branches? One start would be to take a stroll over to Life Before Death to get a layperson's crash course in how to interpret evolutionary trees.

Of course, once you understand evolution, you can use that thinking to do all sorts of other wacky things - such as compare the language of motorists and their vehicles with chimps and the evolution of language, as The Physics of Chi and the Evolution of Man has done in a very entertaining post. (e.g. In car language, a horn means "Watch out" or "Aahh" or "Hello" or "MOVE!", while yelling out the window generally means "I'm angry for some reason, but I can't tell you why because I'm driving." Chimps have all this and more - minus the driving)

Orius

Or you can muse on how the “second brain” in our belly is actually the first one we evolved, as expounded upon at Doomsday Labs.

Or as Seeds Aside tells us - you can go out and discover new pieces of the evolutionary puzzle, such as the curious tale (and first report) of an insect pollination relationship between a TRUE bug (hemipteran) and a plant.

Or perhaps you may find that the “Great Speciators,” the white-eyes (a bird), apparently do evolve faster than any other avian group on earth - a tale brought to us by the prolific GrrlScientist of Living the Scientific Life.

Alternatively, you could host a debate on "Who was more important: Darwin or Lincoln?" as the Smithsonian's Surprising Science has done ( I was certainly surprised at that one - a better question: "Who would win in a deathmatch: Darwin or Lincoln?").

And finally, if one is feeling particularly ambitious you could attempt to plan an entire year in which you only did things related to Darwin - The Year of Charles Darwin Ultimate Tour (Part 1) - also at Surprising Science.

There are just oh so many things to do with evolutionary knowledge...

With that, the two-part Carnival of Evolution #8 concludes. Join us again in one month as the Carnival of Evolution #9 makes its appearance at Moneduloides. Use this handy form for submissions. We are seeking new hosts, so please volunteer if you have

the will.  Let's make this carnival last!!

For other great reading, check out the Carnival of the Blue #21 (dedicated to the Ocean) at The Oyster's Garter and the Circus of the Spineless #35 (dedicated to invertebrates) at The Other 95%.

20Jan/09Off

Adaptation of the Week – Timber Rattlesnake Camouflage

Image by John White

Image by John White

I've decided to start a weekly series highlighting interesting, strange, or just plain cool evolutionary adaptations. If any of you have suggestions for adaptations that you find particularly interesting, I would be happy to include them.

I'm gonna start off with a species that is dear to my heart, the Timber Rattlesnake (Crotalus horridus). Back in my college days, before moving on to molecular and developmental biology, I was an HHMI undergraduate fellow privileged to spend a summer working under Dr. Steven Beaupre radio-tracking timber rattlesnakes in the Ozark Mountains of Northwest Arkansas.

During the summer, I had about a dozen snakes "assigned" to me. These snakes lived in a large expanse of fairly remote wilderness and it was my job to find each of them on every other day using radio-telemetry, after which I would record a bunch of data on them. One of the most interesting things about the Timber Rattlesnake I learned is that they have largely de-evolved their need or use of their rattle. Granted, this is not really true and most herpetologists and evolutionary biologists would rightly throw a fit for me phrasing it as such; I am using the term de-evolve very loosely. If you pick up one of these snakes and throw it in a bucket (to take it to the lab for example), they will most certainly rattle as if the world is coming to an end.

Watch your step!

Watch your step!

Nevertheless, in the wild these snakes are incredibly loathe to make any noise whatsoever, which is quite different from my experiences with diamondbacks in Texas. Diamondbacks that I have found typically want you to know immediately that you are getting close and should get the Hell back. However, I routinely tracked these Timbers and would sit a mere 5-6 feet away from them while taking down their info. By and large, they were content to stare at me tasting my air. The few times they felt threatened, they simply unraveled themselves and slithered away. In fact, in one of the most frightening events of my life (shortened version of the story here), a particular snake's signal bounced strangely leading me to accidentally kick it. Not only did it not strike me (which would have certainly lead to my death under the circumstances), it never rattled. It simply stood erect on its coil, feinting, and doing a great job of looking incredibly terrifying (in response to which my lungs released a bloody-murder scream that I don't believe I can ever replicate).

Can you hear me now?  Good.

"Can you hear me now? Good."

The point of all this is that the Timber has taken a different route to self-defense: near-perfect camouflage. More often than not, I would track a snake and know that I was standing withing 10 feet of it yet spend an extra fifteen minutes just trying to see it, even though it was often coiled among the leaves in the open.  Many people in the Ozark Mountains can live their entire lives living among Timbers and yet never actually see one in the wild.

Obviously the animal kingdom is filled with myriad examples of camouflage even more amazing than the relatively simple colorations of the Timber Rattlesnake. However, I find the example of the Timber interesting largely because of the public perception of how a rattlesnake should behave (this includes their mild disposition as well as their camouflage).

18Dec/08Off

Carnival of Evolution – Call for Submissions

Carnival of Evolution #8

Carnival of Evolution #8

I will be hosting the next biweekly installment of the Carnival of Evolution #8 (a blog carnival devoted to...well...you can figure it out) here at biochemicalsoul.

You can submit your own articles that either directly or indirectly deal with Evolution by using this handy form.

If you would also like to host, check out the CoE mothership site for hosting details.