Archive for September, 2007

Creeks Running North, Hawks Flying South

30 September 2007

Wtf?  The best bloggers make me want to chuck my notebook into a ravine.  Good thing that here in the valley ravines are hard to come by.  I suppose I could lob my laptop into the arboretum’s purported Putah “creek.”

So, go read Helen’s “Storm” and “Breakin’ the Law” and Chris’ “Hills Ferry


When Animal Memes Attack!

29 September 2007

The last time I got tagged with a meme…well Decimating Birds: Episode V is coming any day now. I swear.

Now Brian has tagged me with the “Cool Animal Meme” that’s been racing around the interwebs like a Chinchilla on crystal meth. So…here it goes (I’ve broken things down by vert and invert so I could squeeze a bit more in):

An Interesting Animal I Had


Interesting is certainly one way to describe Clyde. He has acres of personality and makes some of the strangest noises I’ve ever heard come from a dog. Here are three videos of Clyde interacting with a log in Tomales Bay (which he liked), a hawk feather, and a snake skin shed (both of which he did not like).


A couple of springs ago I brought in a mantis egg case from the garden and put in on our window sill. I watched it carefully for a couple of weeks then promptly forgot about it. A couple of months later, while enjoying a cup of coffee, I glanced over at the sill and saw this:

I set most of the hatchlings free, but kept one which survived until about Christmas. My manticulture experiments this year didn’t fare so well, I accidentally left the container open and the mantis fled. Oh, well there’s always next year…

An Interesting Animal I Ate

Okay, this is going to sound weird. Bobcat.  Let me explain (not that it will help)…

When I was a kid my dad hit a bobcat on the way home. Always one to seize an opportunity, my father threw the cat in in the back of the pickup with the idea of salvaging the pelt (which is still around some place). We also got a fair amount of venison this way. My dad also cooked up some of the bobcat meat because, you know, why not?

I don’t remember what it tasted like, but my dad sent me to my mom’s house with a little tupperware of cooked bobcat meat. This of course, totally freaked out my mother (which was surely my father’s intention) but my mom’s pot dealing/gourmet chef landlord raved “It tastes like filet mignon!”


I’m a bit ashamed to admit that I’ve never intentionally eaten a terrestrial arthropod. We did have an “invertabrate dinner” at the end of my invertebrate biology course but all of the goodies were of the marine and/or molluscan persuasion. I can’t say I’m terribly fond of land snail, but fried conch is delicious.

Probably the tastiest invertebrate eats I’ve had was in El Rocío, Andalucía. After rolling into the dusty Spanish town we parked next to a hitching post and walked down the dirt roads till we found a little tapas bar, complete with horses hitched outside. We ordered up a round chipirones: whole baby squid with garlic and lemon. You had to pick the tiny beaks out of your teeth. Washed down with a cold bottle of Alhambra..yum!

With the prospect of doing field work in Southern China, I imagine my interesting animals I have eaten list is set to grow considerably.

An Interesting Animal In The Museum


Photo by Sam and/or Sophie from here.

This one’s easy. This juvenile blue whale from the Göteburg Naturhistoriska Museum is surely the most pimped out whale mount on the planet. I tweaked the photo a bit to try to expose the interior a little better, here is how the museum website describes it:

The great blue whale which was preparated in 1865, is exhibited beside its own skeleton and other whales and seals in “Valsalen”. This 15 meter long baby whale is the only stuffed blue whale in the world! Its jaws can be opened, and once a year you can inspect its inside with its wooden floor, flowered tapestry and mahogany benches.

I guess we had good timing because when we visited the whale was open and we climbed on inside, Jonah-style. Being inside a large animal is rather surreal, but I have to say, with the handsome wooden benches and the upholstered walls, the inside of a whale is far cozier than either the Bible or Pinocchio would have you believe.


Explorit’s giant cave cockroaches (Blaberus giganteus) are pretty fun to share with kids and especially parents. They are much more lively than the hissing cockroaches (though I like them too). They secrete a mild vinegary chemical predator deterrent and are freaking huge.

An Interesting Thing I Did With Or To An Animal

My first ever field biology project at eight or nine, was to tie colored thread to the wrists of toads to try and track their movement and figure out how many individuals were living in our yard. I have no recollection of the results although I do remember recapturing several.


I’ve done some interesting things to the cave roaches. They have wings but they can’t really fly. However, they can flutter their wings to glide to the ground when tossed in the air. They can also use them to flip back over when they are put on their back. I know, it seems mean, but think about what most people do to cockroaches.

An Interesting Animal In Its Natural Habitat

Well, I don’t really remember this, but when my parents were first bringing me home from the hospital it was a rainy, bleak day. On the way home they spotted a sodden Golden Eagle walking alongside the road. In true hippie fashion they promptly gave me an ‘indian name’: ‘Walking Eagle.’ Here’s the tattoo I have that commemorates that moment:




A few years ago, when I was working as an intern at Fossil Butte National Monument in Wyoming I had my most memorable Eagle encounter. I was prospecting for Eocene mammal fossils in the Wasatch Formation. As I came over the crest of Cundick Ridge I came face to beak with an Eagle roosting on a rock. I was probably several meters away but it felt like I could have reached out and touched it.

My heart skipped a beat as I stood there awestruck and paralyzed in the presence of this gigantic bird.  After what felt like minutes, but must have been a split second, the eagle casually leapt off the rock into empty space, unfurled its wings, beat them twice and sailed off. It was out of sight in a few moments, replaced by a few stray fluffs of down slowly tumbling down the cliff.


Again, it’s tough to pick just one.  Finding adult ant lions with kids this spring was pretty awesome.  And lately I’ve become obsessed with scorpion hunting.  Most recently I got a big kick out of seeing an octopus while exploring tidepools in Cambria.  None of the photos turned out really well but this was the best of the lot (its the brownish thing center left).

In that eerie way that often happens with exciting animal encounters, I somehow anticipated the whole thing.  As I watched hermit crabs and bat stars I had this ‘octopodial’ feeling. But I certainly didn’t expect to see one of these cryptic masters of disguise, even though I knew that they were probably around.

I was leaning over to examine a chunk of blueschist or something, when I heard a  sudden squirt and turned to see a fist-sized cephalopod inching away.  It morphed from a deep red, to brown, to almost black then back to brown.  I got a short video, you can hear the excitement in my annoying nasal drone:

I still wish I had picked it up, damn it.

Okay, I spent waay too much time on this.  It seems like everyone and their mom has already picked up this meme.  But I’d be nice to see what Carel has to say after he gets back from his blogging vacation.

Oh yeah and Jessica of the brand new blog Inorganics should give it a shot, although I’m predicting some overlap!

Can You Hear Me Now?

27 September 2007

Sure, this Miocene whale ibone looks sick, but the reception’s crap.

The ice cream truck trolls down the street promising sweet frozen treats with doppler distorted midified Scott Joplin, as my neighbor hums along. The message is the medium, compressed and rarefied.

When our fishapod ancestors first flopped out onto land, they were up against some serious obstacles. One might think that breathing would have presented the greatest difficulty. But, in fact, our lobe-finned predecessors were probably quite comfortable with air breathing, much as modern lungfish are today.

But life on land poses significant impediments to even the most gifted aquatic air breathers. Air is approximately 800 times less dense than water–our ancestors must have felt freaking fat awriggling on the shore. Then there is the dessication issue. Chapped and clumsy, the earliest tetrapods must have seen dry land as a nice place to visit but not an ideal home.

[hopefully you are forgiving all of the rampant anthropomorphizing so far…much more follows]

The low density of air also makes it a piss-poor conductor of sound waves. The speed of sound in water is almost 1500 meters per second, compared to a sluggish 344 meters per second in air. Fish have a sophisticated sensory organ that is highly sensitive to compression waves (i.e. sound) among other things. However, this lateral line system is entirely useless on land and has been lost in most living tetrapods (but retained in some amphibians).

Early vertebrates also exapted their vestibular organs (used to determine position and orientation in the water) to detect acoustic waves. Many fish have small bony structures in their skulls, otoliths(click that link, it’s rad) that are sensitive to sound vibrations in the water. Some fish even use their swim bladder to aid in hearing. As the waves move from the liquid water/fish medium into the gassy bladder they refract up toward the brain. The swim bladder itself turns out to be an exapted lung!

All of these structures are great for hearing sound in the water, but all are probably worthless for detecting the subtle vibrations of our ethereal atmosphere. Dry land must have been a world of eerie silence for the first terrestrial vertebrates.

But, as might be suspected, tetrapods got to solving this problem right quick. Well, assuming you take a few tens of millions of years to be quick.

The challenge is catching aerial vibrations and funneling them down into that same vestibular bony labyrinth that was co-opted by early swimming vertebrates. As noted, air isn’t very dense, so you need some delicate tissue in order to do this.

When Bell designed his and telephone, he faced precisely the same challenge. Morse had already worked out how to translate a physical signal into an electrical one. But a tapping finger is considerably more palpable than a whispered, or even shouted, word.

Following the lead of others, Bell first experimented with a vibrating reed that used a magnet to translate physical vibrations into electrical impulses. After some modest success, he ultimately hitched his reed to a thin membrane which was much more sensitive to the subtle vibrations of the human voice (think kazoo).

Incidentally, the Italian emigrant Antonio Meucci did precisely the same thing when designing a remote communication device, the “telettrofono” for his invalid wife about twenty years before Bell.

The most recent claimant to the title of first membrane-based telecommunication device predates Bell and Meucci by only about 260 million years. Writing in a recent PLOS (open access snap!) paper, entitled “Impedance-Matching Hearing in Palezoic Reptiles: Evidence of Advanced Sensory Perception at an Early Stage of Amniote Evolution” Johannes Müller and Linda Tsuji document the earliest reported organism with what we might call an “aerial ear.”

Middle ear reconstruction of Macroleter poezicus. Figure 3 from Müller and Tsuji 2007.

For what it’s worth, Macroleter is a non-pareiasaurian parareptile from the Permian Mezen River Basin of Russia. Along with some its fellow bomb ass parareptilian cousins, Macroleter appears to have constructed one of the first ‘tympanic’ ear by stretching a skin membrane (pink above) across the back end of the skull. The vibrations detected by this ear were piped into the skull via the stapes (yellow above) which might be viewed as analogous to Bells vibrating reed by the generous reader.

Interestingly, the authors relate this specialized hearing structure to other adaptations related to a “dim-light” (i.e. nocturnal) lifestyle, most notably an enlarged eye socket. Even more intriguingly, they suggest that these adaptations may be related to survival of terrestrial organisms across the Permo-Triassic extinction event.

While Macroleter and co. may have been among the first to develop the tympanic ear, they were hardly the only ones.


We’re exapting all the way to the tangled bank.


Müller, J. and L Tsuji; 2007. Impedance-Matching Hearing in Paleozoic Reptiles: Evidence of Advanced Sensory Perception at an Early Stage of Amniote Evolution. PLoS ONE 2(9): e889 doi:10.1371/journal.pone.0000889

Wikipedia Invention of the Telephone:

Are You Gonna Eat That?

26 September 2007

Oh precious, darling little Science Daily, what would we do without you?

Is There Any Validity To The So-called 5-second Rule?

I hate to (ahem) spoil it for you, but the answer is…no. Puff reporting you say? Nonsense! Check this masterful line of science writing:

Retrieving food outdoors is also generally safe, says Chambliss, as long as it doesn’t fall on potential reservoirs of infection such as piles of animal poop.

Oh, fuck it. Manzanita berries are good, I’m totally going for it.

berry dung

Next up…”Does Tossing Salt Over Your Shoulder Really Ward Off Bad Juju?”

I’ve Been Imprisoned on the Moon

19 September 2007

Speaking of psychedelic, Silver freaking Apples are playing Davis tonight! WTF? I don’t quite know what to expect, but you can be damn sure I’ll be there, drinking out of the magic urn no less. Tour info at pitchfork, info about tonight’s show from KDVS 90.3 FM.

Hope to see you there!

In The Eyes of the Aye-ayes

18 September 2007

Or, “Officer. Of course my pupils are dilated. I’m nocturnal…hey, check out all those colors….”

Aye-Aye trip

Painting by Joseph Wolf (c. 1863), crudely distorted by me.
Original at Wikimedia Commons.

According to Malagasy lore, when an Aye-aye (Daubentonia madagascariensis) fingers you with his hyper-elongate middle digit your number’s up. You know, kind of a reverse E.T. effect. This is but one of several compelling reasons not to take hallucinogens in Madagascar1

No doubt about it, Aye-ayes are trippy critters even without any entheogenic assistance. Early naturalists originally thought this strange arboreal animal was some kind of effed up nocturnal squirrel, given its rodent-like incisors and long bushy tail. Today, it’s regarded as an exceptionally primitive primate primate (zing), one that diverged from our own lineage some fifty-odd million years ago. In fact despite it’s otherworldly appearance, the lifestyle of Daubentonia may not be far removed from that of our early primate ancestors2.

Aye-ayes do most of their foraging at night, employing a unique acoustic strategy to find prey. Like Larry Craig in a airport bathroom, they use an elaborate repertoire of finger taps to search for insect larva tunneling through rotten wood (sound clip here). When a tasty, wriggly morsel is detected, the primate then uses it sharp incisors to peel away the bark and then fishes out the grub with its hypertrophied middle finger.

In spite of this specialized tool kit, Aye-ayes also dine on a wide range of other invertebrate prey and fruit, even raiding human food crops. This latter habit, along with the whole harbinger of death thing, has lead to a rocky relationship between Aye-ayes and the human inhabitants of Madagascar. The Aye-aye is now critically endangered due to direct persecution and even more so due to habitat loss and degradation. It’s not at all certain that Daubentonia madagascariensis won’t go the suffer the same fate as it’s larger cousin Daubentonia robusta, the Giant Aye-aye which went extinct in the early 20th century.

Aye-ayes have been in the news lately, thanks to a new study from Perry et al. appearing in the Journal of Molecular Biology and Evolution. This study looks at the genes involved in the production of opsins, the proteins used to by vertebrates to absorb light in the retina. Opsins come in two varieties. Rhodopsin (shown below) is used by the rods as a general light detector and is important in night vision. Photopsins (or iodopsins) are used by the cones for color vision.


Computer model of Rhodopsin, an important vision protein.

The new study found no evidence of degradation in the color sensitive opsin genes in the Aye-aye. This is somewhat surprising because night light levels are so low that color vision shouldn’t be possible. The genes that control color vision should be of little value to a nocturnal primate and would be expected to accumulate mutations overtime without selective correction.

Even more surprising, these genes appear to have undergone “purifying selection.” In other words, they aren’t just strangely conserved anachronisms, but are in fact actively evolving under some selective pressure. This suggests the opsins play some important functional role in the Aye-aye.

As per usual, the press release (and hence most news reports) herald this as a totally unexpected and shocking discovery. And, as per usual, this isn’t strictly the case. In fact, in a way, the new study confirms predictions made 10 years ago by Nei et al. in the, wait for it…Journal of Molecular Biology and Evolution.

In a fascinating paper entitled “Color Vision of Ancestral Organisms of Higher Primates” (pdf) Nei et al. looked at the opsin genes in a wide range of primates as well as in four ‘outgroup’ vertebrates very distantly related to primates (goat, chicken, anole and gecko). Toward the end the paper, the authors note that,

Recent studies of opsin genes indicate that the blue and red/green genes of primates have coexisted in the genome for more than 500 Myr and, thus, the red/green gene did not become extinct during the long nocturnal stage of mammalian evolution. (Nei et al. 1997)

Hm. Then things get even weirder. The authors then discuss a study of blind cave fish that found their color vision genes to be highly conserved and even undergoing purifying selection (e.g. actively evolving). They go on to postulate that opsins may play an important role in controlling biological clocks (Bora? nudge nudge) and therefore could be vital even in organisms without color vision or even eyes3.

Multifunction in biology, especially in complex organs, is truly interesting as it hints at exaptive shortcuts up “mount improbable.” Mammals probably evolved from organisms with decent color vision, but most living mammals apparently don’t see color well. The most notable exception is primates and it was always supposed that primates had to ‘reinvent’ color vision as they transitioned from nocturnal insectivores or generalist feeders to diurnal fruit and leaf eaters.

Nei et al. hint at a possible backdoor route, with early primates retaining much of the genetic “instructions” for color vision because they were serving an additional important function in setting biorhythms. When the lifestyle changes that favored color vision rolled around, primates would have ‘simply’ had to deploy the opsin genes back into their color detecting role. All of this is entirely speculative of course, but damn fun!

In their new study on Aye-aye opsins, Perry et al. take a different tack interpreting the apparently functional genes as an indication of something like night-time color vision!

We speculate that dichromatic nocturnal primates may be able to perceive color while foraging under moonlight conditions, and suggest that behavioral and ecological comparisons among dichromatic and monochromatic nocturnal primates will help to elucidate the specific activities for which color vision perception is advantageous. (Perry et al. 2007)

Of course, the two hypothesis aren’t necessarily contradictory, opsins may provide some night-time visual function and a biorhythmical one. We clearly have much, much more work to do in working out the patterns of visual evolution in our primate brothers and sisters and mammals at large. Of course, if we lose the Aye-aye first we’ll be losing an important witness to this history, and more importantly we’ll lose a fascinating creature that deserves to be preserved.


Nei, M., J. Zhang and S. Yokoyama; 1997. Color Vision of Ancestral Organisms of Higher Primates. Mol. Biol. Evol. 14(6):611-618

Perry, G. H., R. D. Martin and B. C. Verelli; 2007. Signatures of Functional Constraint at Aye-aye Opsin Genes: The Potential of Adaptive Color Vision in a Nocturnal Primate. Mol. Biol. Evol. 24(9):1963-1970


1Fine, since you asked here are some others:

  • experiencing an overwhelming urge to hug an Alluaudia.
  • trying to swim to Mozambique to prove a biogeographical point.
  • freaky-ass midnight lemur calls.

2For those keeping score at home, there are a number of interesting purported Aye-aye analogs in the fossil record. One of these was the plesiadapid and close primate relative Chiromyoides. Even more Aye-aye like were the Apatamyidae who had sharp incisors and elongate digits and almost assuredly pursued a lifestyle quite similar to Daubentonia. I’m fortunate enough to have done my own small part to add to the record of the apatamyids by finding a few probable apatamyid teeth when I worked as an intern at Fossil Butte National Monument.

Perhaps most amazingly there were even Aye-ayeish dinosaurs! Scansoriopteryx from late Jurassic china was an arboreal feathered-dinosaur with elongate fingers. It’s tempting to imagine the precursors (or should I say prevolancers?) of bats and pterosaurs using their elongate fingers to fish out grubs before exapting them it the frames for flying membranes, but I’m not aware of any fossil evidence to support this.

3Another organ that plays a major role in biorhythms and circadian cycles also had an optical origin. The pineal gland, which produces melatonin and regulates our internal clocks as well as some aspects of puberty is found deep within the human brain. It probably began however as a photoreceptor near the top of the skulls of ancient ancestors. In fact, in some modern organisms the pineal ‘eye’ remains near the roof of the skull and may actually be light sensitive.

The pineal gland is also supposed to play a role in transcendental meditation, according to various new agers and was regarded by Descartes as the seat of the soul. It’s also been (controversially) tied to LSD function in the brain and some have even suggested that it produces our brain’s own DMT analog. Oh, yeah…full circle baby…

Hey! Who Let the Crinoids in?

16 September 2007

Boneyard #5 is up at The Ethical Palaeontologist (oh, fine. I plugged that extra vowel in). I think this is the first one to include inverts: Crinoids and [spit take] Hyoliths courtesy of Catalogue of Organisms! Sweet.

I failed to get off my rear and submit a proper post, but Julia snuck in my derivative collection of dinosaur dittys from a couple of weeks back. Thanks Julia!

I’ll see everyone here for round 6 or 7 in October! And in the meanwhile, keep your ears peeled for an upcoming post on the evolution of tympanic ears.