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The 2011 Philippine Biodiversity Expedition 

May 21, 2011

When it comes to echinoderm collagen, there is always a catch

I was taught a lesson in self control the other day, while snorkeling in an area that had lots of rocks. In between the rocks were lots of crevices, and in those crevices we found some of the most magnificent of all the sea urchins. The self-control of the sea urchins (which I will talk about in a moment) inspired self-control in me with respect to scientific collecting as well.

The aforementioned magnificent urchin goes by the mellifluous name of Heterocentrotus mamillatus, and here is the creature, securely jammed into its urchin home:


That is the correct spelling of the species name. Some of my colleagues might be tempted to put an extra “m” in there to make it “mammillatus“, but that is not what the original author of the name, none other than Carl von Linné (a.k.a. Carolus Linnaeus) himself, had in mind back in 1758. The reference is to more or less the same mammalian attribute in either spelling, but there are nuances of the usage that have to be respected, and Linnaeus knew that. He was nothing if not a smart guy who knew his human anatomy. He wanted the mammalian reference in the name because when cleaned of its spines, Heterocentrotus mamillatus displays the most beautiful of smoothly domed, glassy spine tubercles that reminded him of… well, a certain mammalian attribute. Maybe he had spent too much time in the field. The big, heavy spines of Heterocentrotus sit neatly on end, one spine over each of these tubercles.  Think of balancing a baseball bat on a half-buried baseball. In the base of the spine is a neatly polished little hollow, or socket, making a finely honed ball and socket joint that any car mechanic would greatly appreciate. To think that this piece of urchin machinery, with its very fine engineering tolerances, is made basically of limestone is simply to wonder at it all the more.

At this point I feel it necessary to mention that you might have encountered these spines, minus the urchin, in various tropical places where a certain type of wind chime might be offered for sale. Turns out that when a Heterocentrotus spine is gently tapped with a hard object, such as another spine, it sounds with a gentle ring that some find pleasing to the ear.

Frankly, I am not a fan of wind chimes of any kind. The only place I have these big spines installed in my lab in San Francisco is in the form of my “Acme Echino Quake Detector”, which is a strange composite “decoration” that hangs from the ceiling with my hope that it will jangle in time to warn of the next “big one”. Otherwise, I don’t think the natural and soothing sound of any breeze that would activate a set of wind chimes needs any enhancement whatsoever, as the breeze has its own kind of auditory beauty. Humans can be strange animals sometimes.

Before people get upset, I should also chime in that Heterocentrotus spines for the “wind music” industry are not usually harvested from the living animals.  When the urchin dies, hopefully after a long and happily productive life (however that is measured by urchin standards), the spines remain so durable that they wash up in large numbers on certain beaches, where they can be picked up and employed in the noble noisy cause described above.

The genus name, Heterocentrotus, is in reference to these incredible spines, which come in two basic varieties: big and strong, and small and stubby. You can see these in the close-up below:


“Hetero” means “different”, so this urchin is named for the fact that is has two very distinct types of spines. As I’ve said before, I love it when scientific nomenclature makes sense. But if you really insist on a common name for this creature, you could call it the “slate pencil urchin”. Does that feel better? In my opinion, it shouldn’t.  There is a reason that biologists coin scientific names. How many of you out there have ever encountered a “slate pencil” in this day and age of electronic gadgetry? Would you even recognize one if it flew up your nose and did the lambada? Heck, even pencils come in mechanical form now, and not to write on slates either. And just to make matters worse, sea urchins in a completely different order, the Cidaroida, are also called “slate pencil urchins”. So much for common names.  Heterocentrotus it is. It’s really not that hard after all. If a 5-year-old can remember “Triceratops“, an adult can surely come to grips with “Heterocentrotus“.

Speaking of grips, Heterocentrotus is nearly impossible to remove from its stony home. Actually, make that fully impossible, at least without dynamite, a crowbar, or otherwise hurting the poor thing. The primary reason for this is in the spines, which are, appropriately enough, called primary spines. As I mentioned, primary spines sit on a ball and socket joint. They are held down to the urchin’s skeletal test by a ring of muscle that can be differentially contracted around the ring to point the spine in different directions. This is a handy attribute to have if you are nearly spherical, and want to point your spines at an incoming enemy, or to wedge yourself into a crevice in the rock. However, muscles are metabolically expensive to run, and sea urchins are not what you would call physiological dynamos. So there must be something else going on to keep these animals in place 24/7, safe from dislodging by waves, predators, or marauding echinodermologists.

Turns out that inside the ring of muscle is a second ring of connective tissue, which is not muscular, but composed of a connective tissue made of collagen. This tissue is ubiquitous in animals, and is usually used to connect muscles to bone, or bone to bone, amongst other uses. In the case of the sea urchins, the collagen is found in a ring just inside the muscular ring.  I’ve shown this in the diagram below (which I have modified from a couple of images in Clarke and Rowe, 1971).  In this diagram, all the spines have been removed except one primary spine, so that you can see the connection to the surface of the body, or test:


The collagen in this inner ring is rather special — it’s so-called “catch collagen”. It’s stiffness is under voluntary control by the sea urchin, probably through nerve action. When the urchin wants to move the spine, the collagen ring becomes soft and pliable, allowing the muscles to place the spine… just so… perhaps to brace against the rocky wall of a cozy reef nook or cranny. Then the urchin stiffens the collagen in the inner ring, effectively locking the spine into position. The muscles can now relax, and ta-da! A powerful brace is in place in the space with energy of zero trace. With a bunch of these spines employed in this way, the urchin simply canNOT be dislodged without breaking something — usually the spines. But in the case of Heterocentrotus, the spines are so big and so powerfully built, any prying force strong enough to make the spines move away from the rock wall usually ends up breaking the urchin’s test. And that is truly a shame, given just how beautiful this animal is.

A few other last words about catch collagen. This substance is part of a group of such tissues in echinoderms known generally as “mutable collagenous tissues”. These have been found in all the major echinoderm groups. In fact, alongside the special stereom version of calcium carbonate used to make echinoderm skeletal elements and basic 5-part symmetry in adults, I would list mutable collagenous tissue as a unifying characteristic of the phylum. In the body wall of a starfish, for example, mutable collagenous tissues can be softened to allow the animal to glide neatly over uneven surfaces, then stiffened to lock the animal into place in an infinite number of what look like the most awkward poses that would be the envy of any acrobat. Such staying power, with no energy output! In sea cucumbers, we have arguably the most extreme usage of mutable collagenous tissues. The entire body can soften to allow movements into the tiniest of holes and cracks, yet stiffen again in an instant to hold the front end of the animal up to filter feed with elevated tentacles around the mouth, or wedge the animal into a small crack.

Okay, I lied. There is one more thing I wanted to add. Turns out that there is at least one other place where similar mutable collagen can be found. This is between the pelvic bones of human females (and perhaps other mammals). One of the many hormonal changes that happen in women during child-bearing is the softening of this connective tissue to loosen the bones in the pelvic girdle, allowing them to move a bit relative to one another. With a 10-pounder in the womb, many women have been the perhaps unknowing, yet ever-so-slightly happier beneficiary of collagenous tissue softening. With all that yelling going on, most women aren’t thinking about that during the joyous occasion of childbirth, and who could blame them?

(Almost) all of this ran through my head as I looked at Heterocentrotus locked into its home, and after a few attempts to brute-force them out of there, I gave up. It felt like picking the rarest and most beautiful of flowers in the woods with a weed-whacker.


Filed under: Mooi,Philippines,Shallow Water — rmooi @ 3:24 am

May 18, 2011

Science is cool

Science + Lightning + Dry Day + Local Beverages = this time lapse photo.

Science + Lightning + Dry Day + Local Beverages = this time lapse photo by Rich Ross, Bart Shepherd and Matt Wandell

Filed under: Philippines — ejessup @ 11:52 pm

Urchins are really into rock

I’m thinking that maybe there is a career in sea urchin dentistry.

While working at Sepok Point today, I came to realize that most of the biomass in sea urchins in the Verde Island Passage is arguably in the form of Echinometra mathaei, also known as the rock boring urchin.  The concept of a boring urchin is not new to my colleagues here, who are very gracious in tolerating my windy stories about what I think are remarkable animals.  However, Echinometra really does bore — right into rock.  It does this in part by abrasion from its formidable spines, but mostly by using its teeth.  Urchins actually have five teeth, mounted in a 5-part, radial jaw that can open and close like the chuck of a drill.  This jaw apparatus is known as Aristotle’s lantern, for reasons that are obscure and part of a strange history of urchin nomenclature.  But we’ll let that go for now or this blog entry will end up being a treatise, not a nature nugget.  Suffice it to say that the mouth of the urchin is situated on the bottom surface of the globose body, and large enough to allow protrusion of the Aristotle’s lantern so that it can chew on, um… the rock.

The 5 teeth of an urchin are sharp and chisel-shaped at the tip. Although they are largely made of limestone, the teeth are hardened by “doping” this limestone with magnesium, a process known as dolomitization.  The term, incidentally, derives from an Italian mountain chain known as the Dolomites.  The mountains are very hard limestone with… high magnesium content.  Who would have thought there was a connection between sea urchin dentition and mountains in Tyrol?

Anyway… these hard little teeth can do a lot of damage to rock, especially over the lifespan of a sea urchin.  Here is the culprit, removed from his (or her — it’s hard to tell from the outside) boring life in the rock:


In spite of the hardened teeth and fierce-looking spines, these little fellows are gardeners.  Sort of.  They don’t chew straight down into the rock, but make a channel, or a groove in the stone.  This channel is enlarged as the animal grows, and as it harvests its food.  This consists of algae growing in the channel.  Bare surfaces don’t stay that way for very long in the sea.  Algae is a very quick colonizer of newly exposed surfaces, including those chewed to nakedness by busy little urchin teeth.  As the urchin chews, it removes a bit of the rock along with the algal food, thereby doing two jobs — making a protective channel in which to live, and getting nutrition from the algae growing inside this home.  Soon, the rock can look a bit like Swiss cheese:


When the algae at one end of the channel are all eaten, the urchin moves along to the other, allowing regrowth of the plant cover.  By the time the urchin gets to the end of the channel, there is enough regrowth to make it worthwhile to move slowly back to the other end again, munching the newer algae as urchin inches along.  The rock is hard, but hey, the urchin has all day.  There is some evidence to suggest that individual urchins can keep this up for decades.  In light of that supposition, it’s no wonder that a perfectly good coastline can start to look like this for much of its length:


Which brings us to the question of urchin dentistry.  Now that I think of it, maybe the idea of being an echinoid dental practitioner needs some rethinking.  Besides being very hard, sea urchin teeth are advanced along the inside of the jaw as they wear out, providing fresh tooth tip as the old tip erodes away.  Urchin teeth are very cleverly designed as long shafts of tightly packed, minute plates such that as these flake off the worn end, they leave a fresh, sharp edge.  No need for night guards or other hideous plastic dental aides to prevent wear from gnashing or grinding.

One could say that the teeth are boring, but never dull.

Along some parts of the Mabini coast, I have noticed that young Echinometra start out in less boring accommodations.  They crawl into a dead barnacle, which has become a shell of its former self:


Presumably as they outgrow this living situation, the urchins crawl out of the barnacle and start a new channel, or get into an old groove left behind by an urchin who has gone on to that great cheeserock in the sky.

I should mention that there is an urchin that does burrow straight down into the rock, making a cylindrical shaft in which it can live like Timmy stuck in a shallow well.  This urchin, Echinostrephus aciculatus, has no need for rescue from Lassie, though, as it is perfectly shaped to fit into its tiny well, with the spines sticking out ever so much:


How Echinostrephus manages to make this amazing vertical shaft, which is several times as deep as the urchin is high, is not fully understood.  Presumably they use their Aristotle’s lantern as well.  The shaft of the boring is long enough that when disturbed, for example by an urchin-hunting echinoderm biologist, the urchin quickly skootches (to use the highly scientific term) down into the hole.  The animals are nicely designed for this.  The body is slightly conical, with a narrow end pointing downwards.  This end is furnished with lots of strong tube feet that pull the urchin downward.  The spines on the bottom of the body are very short, as opposed to the ones on the more exposed top, as can be seen in this laboriously extracted captive, flipped upside down (i.e. mouth upwards):


How this stationary urchin makes it’s living is not understood either.  Some claim that it snags bits of drifting food with the long, exposed spines.  One has to question whether that is enough.  They can’t farm like the Echinometra does, because it’s too dark down there in the recesses of the bore hole.

As usual, nature leaves me with no recourse but a fascinated shrug.

Filed under: Mooi,Philippines,Shallow Water — rmooi @ 8:57 am

May 17, 2011

Steinhart arrives in Anilao

First sunset after the first day in the Philippines

First sunset after the first day in the Philippines

After a 14 hour plane flight and a 3 hour drive, Steinhart Aquarium biologists Bart Shepherd, Rich Ross and Matt Wandell arrived at Club Ocellaris and were treated to a breakfast of garlic rice, eggs and French toast. After filling our bellies, we suited up, went diving and have been on the move ever since. The first night, after a spectacular sunset,we dove on a stony coral dominated site called “Dead Palm” (apparently there used to be a dead palm tree under water). At the end of the dive we encountered something that we never imagined we would run into, never mind on the first night – Acropora sp. corals spawning. Thousands of egg/sperm bundles released into the water by branching corals filled the ocean with a peach colored ‘snowstorm’ rising towards the surface. Many screams of excitement could be heard under water. We collected some of the spawn, and after email discussions with friends from project SECORE (SExual COral REproduction – http://www.secore.org/ ), we tried to mix the gametes to harvest and settle ‘baby’ corals.  The effort was not completely successful because Acropora corals cannot self-fertilize and we couldn’t collect material from multiple corals. Regardless, the experience was worth the effort, and sets the stage for future work.

YouTube Preview Image http://www.vimeo.com/23717993

The collection of coral fragments has been moving along well, and we are getting ready to pack up the first shipment back to the Academy. We have been collecting fragments that have naturally detached from mother colonies, or harvesting small fragments from the growing edge of large colonies.  The parent colony should quickly heal and show no sign of disturbance within a week or so.

Traditionally coral fragments are collected and either glued to something (rock, a concrete disk, or a plastic plug) or left loose and stored in some kind of rack land in a holding tank. This presents a a couple of problems with water flow and water quality.  It also can cause shipping problems, as the coral either sits unsupported in the shipping bag, or is rubber banded to some Styrofoam (both of which can stress the coral and involve additional handling). Inspired by the work Ken Nedimyer is doing in Florida at the CRF (Coral Restoration Foundation – http://www.coralrestoration.org/ ), and after prototyping the system in the Philippine Coral Reef at the aquarium, we placed our coral strings about 50 meters off shore.

Coral fragments waiting for shipment to CAS

Coral fragments waiting for shipment to CAS

This system keep the fragments up in the water column with good water, flow and light until we are ready to ship them. For shipping, we simply snip the middle of the zip tie chain ( leaving the rest in place for future use) and attach the coral to another zip tie looped through some Styrofoam. This way the fragment is suspended in the shipping bag, and it will be hard for it to bump the sides or bottom, which can cause damage. The lines themselves are silicone airline tubing strung between repurposed plastic water bottles (floats) and dive weights (sinkers). Additional lines can be added to an existing float to quickly and simply extend the system. It seems to be working well and we are anxious to hear how the corals arrive at their new home in San Francisco.

Last night we spent two hours muck diving collecting cephalopods and seeing amazing and bizarre creatures, but we are out of time so that will have to be covered in a future blog as we are off to Manila for meetings and shipping.

Richard Ross, Bart Shepherd and Matt Wandell.

Filed under: Philippines — ejessup @ 5:15 pm

May 14, 2011

If it’s Tuesday, it must be Talisay!

A tight education outreach schedule has kept Meg and me hop-scotching the country ever since we arrived in the Philippines on May 8th. Earlier this week we delivered our first outreach to a combined audience of 30 university faculty and high school teachers at the University of Santo Tomas in Manila, the oldest university in Asia at 400 years old. We had expected a larger turnout, but tropical storm Bebeng wrecked havoc with roads and air flights and prevented another 40 faculty from attending the session.  Each of our sessions includes an overview of the Philippine Biodiversity Expedition, a presentation by at least one of the scientists on any preliminary findings from the field, and demonstrations of hands-on interactive lesson plans and educational activities for the classroom. They have had a pretty good time acting out the Carbon Cycle Role Play lesson plan to learn about how carbon atoms are exchanged in the environment and practice their observation skills with a scientific sketching activity.

Teachers practicing their observation skills in a sketching activity

Teachers practicing their observation skills in a sketching activity



Two days later we were at Taal Lake where we made another presentation to a group of local government officials and elementary school teachers, including the mayor of Talisay, a small municipality, or barangay, right on the lake.  Taal Lake is very interesting biologically because at one time it was connected to the ocean.  Among the endemics found in the lake that biologists, Dave Catania, Chrissy Piotrowski, Bob VanSyoc, Vanessa Knutson and Don Dumale were particularly interested in collecting is the endemic freshwater species of sea snake and sardine, whose closest relatives live in the ocean. The lake is designated as a protected area, but still faces many threats including the introduction of an invasive species of cichlid, the jaguar fish, which threatens native species in the lake. Situated on an island in the lake is Taal Volcano, looking very peaceful while we were there but it is still currently at a very active Stage 2 eruption alert.  

Taal Lake sunset

Taal Lake sunset

Friday we were at University of the Philippines in Los  Baños, whose lush, tropical campus is located at the foot of Mount Makiling, a 1090m inactive volcano located about 65 km southeast of Manila. It was an added treat to have expedition physician Matt Lewin with us to talk about the mobile snakebite kit that he has developed. Next stop was the University of Batangas where we reached nearly 70 faculty and teachers. With just four outreaches under our belts and eight more to go, we are looking forward to meeting with more of our colleagues here. Next stop, Southern Luzon State University, and then on to Calatagan.

Roberta Brett

Senior Science Content Specialist

Filed under: Brett,Philippines — rbrett @ 8:36 pm

May 13, 2011

Shallow Water field station in high gear

The Shallow Water field site was in high gear yesterday. Most CAS and Filipino researchers were in camp along with a local film crew documenting the expedition.

YouTube Preview Image

Filed under: Philippines — Brian Simison @ 4:11 pm

Photosynthetic Slugs

This is by far one of my favorite animals collected on the expedition, I did not even knew these existed!

Marionia rubra

Marionia rubra

This slug’s sequesters/hosts single celled, algae as symbionts in its cerata (the fuzzy bits on its back).  The symbiosis is a mutualism: dinoflagellates from the genus Symbiodinium get raw materials required for photosynthesis and a safe place to live with full access to sunlight inside the slug’s body.  In return the dinos donate some portion of the sugars they generate from photosynthesis to the slug, meaning that most of the slug’s food is generated inside its body!

(Explanation courtesy of Dr. Michele Weber)

Elliott Jessup
Diving Safety Officer
California Academy of Sciences

Filed under: Academy,Diving,Jessup,Philippines,Shallow Water — ejessup @ 4:15 am

May 12, 2011

Nylon Stockings and Safety Pins–Occasional Notes from the Expedition Physician

We have had an accident and illness free expedition, thus far. Nevertheless, we are well prepared with conventional and improvised methods of first aid. I have learned a lot in just a few days in the jungle. Most of my experience has been expedition travel to areas of extreme heat such as the Gobi Desert, but never the jungle. The arachnologists and botanists are super hardy. I have never sweated so much in my life. I am learning collection techniques such as aspirating insects through rubber hoses I would normally use as tourniquets or catheters. I am learning, but have not mastered the art of sifting leaf litter…

mvi_4326 mvi_4327

…I have been experimenting with women’s nylon stockings as a barrier to the leeches locals refer to as fire leeches. They are very comfortable under socks and I haven’t had a single leech attach to my legs, yet. I don’t know how durable or effective the nylons will be as I already have a run in one of them. I will go back to the store and try a different type next time we are in town. The salesman seemed to think my questions about the den numbers were a little odd.

Occasional Tip:

Safety pins can be useful for immobilizing an arm without having to remove the victim’s shirt. The techniques are slightly different for those wearing long- or short-sleeved shirts.

Method of splinting arm or shoulder using safety pins if patient has short-sleeved shirt. Try to use sturdy parts of the shirt to secure the pins (e.g. pocket seems and cuffs) to reduce the chances of tearing.

Method of splinting arm or shoulder using safety pins if patient has long-sleeved shirt. Try to use sturdy parts of the shirt to secure the pins (e.g. pocket seems and cuffs) to reduce the chances of tearing.

Method of splinting arm or shoulder using safety pins if patient has short-sleeved shirt.

Method of splinting arm or shoulder using safety pins if patient has short-sleeved shirt.

Filed under: Philippines — cgriswold @ 7:21 am

Shallow Water Team update

The Aquarium team has joined the shallow water expedition early this morning and have already made two dives. In spite of enduring a 13 hour flight that departed SFO at 11PM and arrived in Manila at 3 AM and a 2 hour drive south to the CAS field station, the aquarium team of Bart ShepherdMatt Wandell and Richard Ross were suited up and ready for their first dive in Balayan Bay only hours after arriving.

CAS Dive Safety Officer, Elliot Jessup debriefing new arrivals for their first dive
CAS Dive Safety Officer, Elliott Jessup debriefing new arrivals for their first dive.




Loading the boats


CAS videographer David McGuire preparing video equipment


Dr VanSyoc ready to go


Dito, Healy, Elliott, Terry and Beth motoring to dive sites.


Chrissy Piotrowski sampling something from the sand, probably some kind of worm


Sea Pen


Beth Moore searching for seahorses and pipefish


snowflake moray eel (Echidna nebulosa)


Very cute puffer fish


A little and big tunicate (a.k.a. urochordates or sea squirts)


this big puffy sea star (Choriaster granulatus) is about the size of a dinner plate


Dr Rich Mooi sharing one of his finds with Beth and Elliott


Dave Catania of CAS and Joseph of the Philippines National Museum processing samples from today’s dives


Terry Gosliner processing todays specimens.


The expedition is proceeding well with many new species being discovered every week,

Filed under: Philippines,Shallow Water,Simison — Brian Simison @ 3:51 am

Acusilas, a rare SE Asian orb building spider that hides in a leaf at the center of its web, Mt Makiling, Philippines

Acusilas, a rare SE Asian orb building spider that hides in a leaf at the center of its web, Mt Makiling, Philippines

Filed under: Philippines — cgriswold @ 12:45 am
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