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The 2011 Philippine Biodiversity Expedition 

June 1, 2011

Jet Lag: Timing is as important (or more so) than medications

Jet Lag

Jet lag is a problem affecting the majority of people traveling rapidly or non-stop through multiple time zones. The more time zones traversed, the more likely one is to experience jet lag and the longer it takes to recover. East-West and West-East travel cause symptoms much more than North-South and South North travel because the problem is related to time zones more than distance flown.

My experience is that the conventional “1 day of recovery per time zone traveled (over two time zones),” is pretty good. Unfortunately, many people have back-logged professional obligations and are missed by family who want and need attention. At this time of year, there are graduations and grandparents’ days at schools. Consequently, in addition to spouses and kids, there are important guests from out of town to host and entertain. Jet lag can be minimized with some good planning, a little luck and, sometimes, with supplements such as melatonin, zolpidem (aka Ambien). Other medications such as modafinil (aka Provigil) are in the late stages of clinical trials and show promise for treating jet lag. Unlike melatonin and zolpidem, modafinil is used to aid in alertness rather than as an agent to improve the timing and quality of sleep. BTW–I have no financial interest or relationships with the manufacturers of these drugs!

There is no one recipe to combat jet-lag and people taking medications for conditions such as diabetes and hypertension. During air travel, a diabetic person should take his or her daily dose of insulin and eat according to local time (departure schedule). For a diabetic person traveling east-bound over multiple time zones, the day is effectively shortened. On arrival, the person should eat and administer insulin according to local time, but reduce the insulin dose by 1/3.  For travel west-bound, the day will lengthen and a second dose of insulin may administered with guidance from a glucose monitoring device.

Airlines such as Philippine Airlines (PAL) do a good job scheduling their flights from San Francisco to Manila and Manila to San Francisco. From Manila, flights generally leave at night and arrive at night, in San Francisco. My flight from Manila left at 10:30 PM and arrived in San Francisco at 10:30 PM.The evening meal was served almost immediately and I was able to sleep for virtually the entire first half of the flight.

Briefly, my strategy for combating jet lag on my return from the Philippines was a follows:

1. On the day of departure, I spent as much time outside as I could

2. I packed a meal so that I could eat as soon as I got on the plane and go straight to sleep. PAL uses the same strategy, so I had an entrée before my entrée.

3. I slept for six straight hours (thank you, zolpidem) on the plane and then stayed awake for the remaining flight time and until I got home (about 9 hours awake time).

4. Went to sleep as soon as I got home and woke up about 0630 and felt pretty darn good the next day—again, maximizing exposure to sunlight even coated with SPF 100+.

5. The main point is to try to get on the schedule of your destination as soon as possible. If it is not possible, then it is quite reasonable to consider pharmacological interventions.

6. Everyone is different. When I tried melatonin to help with circadian disturbances during medical school I slept beautifully, but with horrendous nightmares (e.g. I couldn’t save my drowning parrot and, another time, dreamed I was walking across the Golden Gate Bridge on a windy day and the side rails had been removed. A lesser nightmare was a visit from an angry Pope John Paul asserting that I was making crank calls to the Vatican.I felt guilty even though I didn’t do it…and I’m Jewish).

Pharmacological Interventions:

Melatonin:Melatonin is a popular food supplement that is among the best studied interventions for circadian disturbances, including jet lag. It is not regulated the way most drugs are, since the FDA considers it to be a food supplement. Thus, formulations may vary in content, consistency, absorption and quality. I have to admit, I have not been a fan of melatonin, but need to reconsider my early prejudice now that more systematic and methodologically sound studies are being carried out. To date, the results of clinical trials are all over the place. In part, this is because flight attendants are often used as subjects and they have very complex, disordered sleep patterns. I do find it interesting that the doses used, typically 0.5mg to 5mg, result in serum concentrations orders of magnitude higher than those produced by anyone’s body.There are no data to suggest combining melatonin with prescribed medications such as zolpidem improves either one’s effects. Well described side-effects include hangovers or lethargy the next day, nightmares, confusion, headaches, but the percentages of people exhibiting these adverse reactions—while well-described– is also not well quantified…People taking blood thinners such as warfarin and those with seizure disorders should be very cautious about using melatonin.

Zolpidem (e.g. Ambien) and other sedative-hypnotic agents like lorazepam, temazepam and alprazolam (e.g. Ativan, Restoril and Xanax, respectively):

Disruption of sleep is a major factor in the unpleasantness and general morbidity associated with jet lag. A lot attention has been given to the use of sedative-hypnotics for the induction and maintenance of sleep. Each of the medications listed above has a different half-life and utility depending on the types of disordered sleep encountered by different people. Briefly, zolpidem has a short half-life, but works quickly (~30 minutes) and it often used to help initiate sleep. If getting to sleep is harder than maintaining it, a medication such as zolpidem or alprazolam might be most effective in ameliorating symptoms of sleep disruption. A longer acting medication such as temazepam should be considered for those with more difficulty maintaining sleep.

Adverse Effects

As with all medications the intended, salutary, effects need to be balanced with the risks. For example, alprazolam interacts with a lot of other medications, such as warfarin.

In addition, ALL benzodiazepines (generally your drugs with the suffixes, “-pam” and “lam”, but including Librium) are verboten in pregnancy, “Class D” (Dangerous). Women of child-bearing age who have any chance of being pregnant should not take these drugs. Benzodiazepines act on the same basic receptors as alcohol and cause the same general types of birth defects as seen with fetal alcohol syndrome (FAS).Nevertheless, if an isolated dose or doses are taken prior to the discovery of pregnancy, it is not cause for panic. Like alcohol, the dose and chronicity make the poison—just stop and talk to your physician about any further evaluation or testing that might be warranted.As with pregnancy, all benzodiazepines are considered Dangerous in lactation. Nursing mothers should not take these medications.

Adverse effects from benzodiazepines include those described during pregnancy and also include amnesia, grogginess, interactions with other medications and severe withdrawal syndromes and addiction, such that people occasionally die from withdrawal seizures. The potential for abuse of these medications is fairly high. If you have had problems with substance abuse/addiction, including with alcohol, these medications should probably be studiously avoided for elective use.That being said, the short-term benefits of having a good night of sleep cannot be underestimated—in the absence of addiction issues and the use of medications with adverse interactions with these drugs.

Zolpidem (Ambien) is considered to be fairly safe in pregnancy (“Class B”…presumed safe based on animal studies) and is generally accepted to be safe during lactation for the children of nursing mothers. I generally favor this specific medication for lactating or pregnant/potentially pregnant women.Relatively common side effects include amnesia (e.g. not remembering any of the words played in last night’s unfinished Scrabble game), confusion, nausea and erratic behavior. If you made out with the passenger next to you and don’t remember it having happened when he/she asked for your number (erratic + amnesia)…this is not the medication for you. The former happened to me and the latter to a friend. That is the absolute truth.

Pharmacological interventions you can expect to see approved by the FDA in the near future:

Modafinil (e.g. Provigil). This is an interesting drug approved for use in narcolepsy and in shift-work sleep disorder. It is generally taken 1 hour prior to starting a shift. Jet lag and shift-work sleep disorders have a lot in common with respect to disrupted sleep and overall circadian disturbance.Most recently, Phase III clinical trials have been completed and published with seemingly good results.

Interestingly, sildenafil citrate (aka “Viagra”) has been shown to enhance adaptation to changing light schedules…in hamsters.In this study, out of Argentina, a dose of 3.5 mg/kg (or about 245 mg for a 70 kg male) was injected into the hamsters to achieve this effect.  I didn’t read the study all that carefully but didn’t see any comments other than those about circadian re-entrainment and I was left to ponder, “Were they breeding like rabbits?” Viagra for humans with erectile dysfunction is generally given in increments of 25, 50 and 100mg and I imagine that at hamster doses it would cause significant nasal congestion and a blistering headache. I think this one is a long way away from approval for use in jet lag.


Don’t get prescriptions that are likely to last any longer than you actually need (a five or six day supply)

Don’t drive when tired or having taken any of these medications in the past 6 hours

Don’t mix with alcohol

Don’t accept medications from friends…we recently saw the case of a patient who was given doses of his friend’s “sleeping pills,” that turned out to be methadone and a fatal overdose, at that. Plan ahead and get a proper prescription.

If you are taking medications for which blood levels are measured (e.g. warfarin, lithium, carbamezapine, digoxin) then there is a good chance they interact with alprazolam and other medications or foods in an unsafe way.Others that commonly interact with food or drugs include anti-cholesterol drugs in the –statin class (grapefruit juice inhibits the enzyme that breaks down the drug with potentially fatal consequences) and MAOI and mixed-MAOI inhibitors.

Avoiding caffeine and alcohol: Generally not recommended, yet no systematic study of these “self-medications” has ever been undertaken. I don’t recommend them, but more than that would be confusing fact with opinion.

This is so far from a complete list of admonitions that you really need to talk to your doctor.

Be Positive!

1. You will not be more tired than usual for the rest of your life.

2. Thoughtful planning of sleep and wake times during travel can shorten the duration of symptoms from jet lag.

3. Being happy to be home and seeing your family, friends and colleagues is probably the best remedy.

I won’t remember having written this, tomorrow, but feel free to correspond. I welcome any comments, suggestions and useful criticisms. I will do my best to respond promptly. SAFE TRAVELS!

Filed under: Academy,Philippines — mlewin @ 5:22 pm

May 27, 2011

Taal Tails – May 12, 2011

The initial timing was unfortunate, a storm kept the Hearst Expedition divers out of the sea for two days, but as the storm abated and the nearshore water became clearer, several of us made a trip to Lake Taal, an hour and a half north of Club Ocellaris, the base of operations for the expedition’s shallow water marine component. Compensation for not diving those two additional days was a glimpse at a truly unique place.


For the purpose at hand, the timing couldn’t have been better. A stage 2 alert had virtually shut down the local tourist industry, which exists to take people to and from the island in the Lake and show them around on horseback. What is this alert? You see, the island in Lake Taal is an active volcano, with the most recent eruption having ended in 1977. The alert was issued and remains in effect because monitors recorded several seismic events early on, a rise in magma level, and an increase of noxious emissions.

Why visit an active volcano? Well, the surrounding lake has a very interesting history. Lake Taal is the third largest lake in the Philippines in terms of surface area and possibly the deepest (approaching 200 meters). The surface of Lake Taal lies at an elevation of less than 30 meters which means that a significant part of the lake water lies below sea level. Lake Taal used to be broadly open to the ocean, but volcanic activity approximately 250 years ago closed it off, and over time, runoff from the surrounding mountains has lowered the salinity to a point where it is essentially freshwater. Many of the Lake’s native fishes are derived from marine species that have adapted to freshwater, including the Lake’s most famous inhabitant, the world’s only freshwater sardine, the Tawilis (Sardinellla tawilis), an endemic species found nowhere else.

The logistics for our half-day excursion proved more challenging due to the presence of an ABS-CBN news team doing a documentary on the Hearst Philippine Expedition tentatively due to air in September. Upon arriving at the Talisay Yacht Club, we began unloading our gear and obtained gasoline for the electroshocker. Representatives from the Bureau of Fisheries and Aquatic Resources (BFAR) and PUSOD (a non-profit Philippine environmental organization) were present along with the TV crew. While we discussed our plan, the Invertebrate Zoology team made a small shore collection. With our gear finally loaded on two bangkas, we set off for Volcano Island.


Lake Taal is home to extensive aquaculture operations with thousands of floating cages for raising tiapia and milkfish. The heaviest concentration of cages lies in the northern and western parts of the lake. It was in this region we made our first stop, at a particular place where Philippine scientists reported netting two or three kinds of gobies new to science. These are species not yet named in the scientific literature. En route to this first stop, the bangka carrying our invertebrate zoologists experienced engine trouble and put to shore. In a wonderful turn of events, there were two pipefishes in the water next to the boat that they were able to collect. This was one of our targets for this trip. The operable bangka went to pick-up the Invertebrate Zoology team and bring them to the first site. The second boat joined us later, after repairs were made. It was time to begin our search in earnest.


Our primary tool for this hunt was an electroshocker. This is a device primarily used by fisheries biologists to capture fishes for tagging and/or data gathering. It is essentially a sophisticated power supply using two electrodes to create an electric field in the water, stunning fish that can then be netted. Our unit consists of a small gasoline generator to power the electronics box both of which are mounted on a pack frame. Everything checked out fine, but each time we started to fish, the unit registered an overload. Our backup plan called for dipnets and a small seine. While executing this “plan B,” we noticed areas of hot water in excess of 50 deg. C. that had seeped up through the sand plus plenty of sulphurous odors. It then occurred to me that this might provide an explanation for why the electroshocker failed to work. Volcanic activity increased the amount of dissolved minerals in the lake water near Volcano Island increasing the conductivity to a point where the unit could only register an overload. Subsequent inquiry not only confirmed this but also revealed that the entire lake has high conductivity.


Regarding the specimens we did manage to collect, no conclusions could ever be drawn from a sample that small, but there are some highlights. We did collect seven gobies, of which three are common and the remaining four, very small. We will probably seek the help of specialists to determine what they are or if they might be new to science. The three freshwater pipefishes are of particular interest to Dr. Healy Hamilton and the researchers in her lab at the California Academy of Sciences who are working on a molecular phylogeny of the seahorse / pipefish family Syngnathidae. Probably the most significant aspect of our visit to Lake Taal concerns the jaguar fish, an aggressive, fish-eating, Central American Cichlid, introduced a little over 15 years ago. Since then, this invasive species has increased to the point where it is now ranks fourth in number of individuals caught per year. We were able to provide limited anecdotal evidence of just how pervasive the jaguar fish has become. We also observed first hand, it’s tolerance for poor water quality, a definite competitive advantage. Finally, for our mini-expedition to Volcano Island, a delicious lunch was provided by Ipat Luna of PUSOD, and even though we weren’t able to collect the famous freshwater sardine, the Tawilis, we were able to taste it.

We presented our findings during a meeting at the town hall in Talisay. In attendance were representatives from PUSOD and BFAR as well as mayors from several municipalities around the lake. The good news is that the Philippine government approved a comprehensive management plan for Lake Taal that has strong local support. Implementation and enforcement of the plan’s provisions are the next critical steps.


-Dave Catania

Filed under: Academy,Catania,Philippines,Shallow Water,Terrestrial — admin @ 2:50 pm

Like…totally tubular!

Most of the critters I’m working with during this expedition are so tiny that you need a microscope to examine them…sometimes even just to locate them!   There are lots of exceptions, however, and one of them involves a very cool critter called a chaetopterid worm that I encountered the other day. Since it was fairly big and impressive (colleagues actually stopped by to gawk at it in awe) and because these are such creepy-cool worms, I thought I’d share.
While working in a sandy seagrass area the other day, I dug up a large parchment (which is sand stuck together with mucus) tube about an inch in diameter that was sticking up out of the sandy sea bottom.
Typically this type of tube houses a fanworm (a sabellid) with delicate fan-shaped radioles stretched into a sort of funnel-shaped plume like this:
In sabellid fanworms each radiole has tiny hair-like structures called cirri used to filter small particles of food from the water to be carried to the mouth.   So considering the tube’s appearance, I was expecting a nice fat fanworm to emerge as I eagerly cut into my tube back at the lab, kind of like I was unwrapping some sort of creepy worm shaped gift.  This tube, however, was shaped more like a “U” buried under the sand and so I suspected that it might house something a bit different. And it did…a very large chaetopterid worm!
Chaetopterids are very specialized polychaetes (marine bristleworms) that live their lives confined in tubes. These worms have 3 distinct body regions: the head/anterior region is large and equipped with bristles and a set of palps used for sensory.  The middle of the body is made up of the darkened gut and highly modified lobes that pump back and forth like big flaps to provide a steady water current used in feeding.
The tail/posterior region is more “normal-worm-looking”, meaning long with foot appendages called parapodia carrying bristles on either side of the body.


These worms feed using mucus nets which they string across the inside of their tubes to trap food particles by pumping water through their tubes to filter food onto the net.   Once it’s full of food they eat the whole deal and then proceed to make a new net. Other critters, such as smaller worms and crabs, often live alongside chaetopterids in their tubes as commensal animals which score free food scraps and shelter while living there.

Another cool thing about these worms is that even though they live rather clandestine lives hidden in tubes, they produce bioluminescence (they emit light!). What in the world they are doing with this light-producing capability?  Well, we don’t know for certain.  Studies have shown that when a chaetopterid is disturbed, it shoots a wave of glowing particles from its tube.  One idea is that this light surge alerts prospective predators that “I don’t taste particularly good”, or maybe the light bursts are used to freak out and evict some of the free-loading critters out their tubes if it starts getting too crowded in there.

Many polychaetes and other invertebrates emit light when disturbed, either for warning/predator avoidance or for communication with potential mates.   The yellow bands shown here on a nereid “pileworm” may be bioluminescent areas of the body used for signaling.
Polychaete worm behavior and physiology is as extremely diverse as their morphology.  For such “sleeper” creatures that are unfamiliar to most regular folks, polychaete worms actually have alot going on!

Filed under: Academy,Diving,Philippines,Piotrowski,Shallow Water,Uncategorized — cpiotrowski @ 4:39 am

May 26, 2011

Transition from Land to Sea.

Night prospecting in clear waters

I had a fantastic two + weeks with the Terrestrial Team. They summited Mt. Banahaw as I moved to Anilao to join the Academy’s aquatic biology research team. The snorkling and diving here is unbelievable. The forested slopes of Mt. Banahaw are treacherous and, for the most part, without trails. Travel is by foot and machete. The leech burden was too small to continue my experiments with nylons. Plus, they are too hot to wear in this climate. The botany team collected more than 300 samples on Mt. Banahaw, while the entomology/arachnology team collected more specimens than I could count.

It was hot and muggy on the mountain and I couldn’t help but think about our patients at the VA Medical Center up the street from the Academy. I’ve heard many of their stories while at work there and I still can’t imagine what it must have been like to live in the jungle with, baseline, dangerous conditions and in fear of illness or injury from combat.

Illness (most commonly, diarrhea and febrile illnesses such as malaria) and injury are common during expedition travel, even in ideal conditions. To date, from a medical standpoint, we have been lucky about major trauma in the field. The worst injury, thus far (and for the entire expedition, I hope) occurred when a porter caught a machete by the blade.  The injury occurred late in the afternoon, far from camp (about 2 hours hike). By the time we got back it was dark.  During exploration of the wound and irrigation with more than a liter of sterile saline, my headlamp and the other lights were attracting insects to the surgical field. It was an anxiety provoking injury for both him and me. He could not feel three fingers (thumb, index and middle) when pricked with a sharp needle, compared to brisk hand withdrawal when his ring and little fingers were pricked with the same pin.  I couldn’t find any obvious nerve injury on exploration of the wound.  I suspect he had spasms of the underlying muscles or the nerve was struck, but not cut. He did well, with return of normal sensation within 24 hours and no infection after 4 days.

Additionally, during a deep dive, one of our crew was envenomed by a large lion fish. The pain was excruciating and the currents strong. It was about 3 hours to get to shore and by the time he arrived at camp, the pain had spread from his lower leg to his knee and hip. The venoms in the family are protein-based and effectively treated by immersion in warm water (not more than 115 degrees Fahrenheit). The heat denatures the proteins and decreases the pain.  At least three barbs penetrated his wet suit and he reported losing some power in his right foot because of the pain. In the conditions he was working, this type of impediment can create dangers much greater than the painful injury, itself.  Lion fish have invaded (i.e. been introduced by humans) to the warmer waters skirting the U.S. and Caribbean. Thus, lion fish stings are becoming significantly more common in areas outside their native waters. They are voracious predators and poorly controlled because their natural enemies are not present in their new habitats.

We saw a similar thing in the forests of Mt. Banahaw in the form of cane toads…an invasive species from the America with a voracious appetite for endemic species and it has few predators here to keep their populations in check. They are not dangerous to humans like the lion fish, but are a distressing sight in the rain forest knowing they are potentially permanent residents.  At a dive site near Anilao nicknamed “Basura” (Trash), divers found incredible quantities of trash intermingled with the corals and fish life. Included among these discarded objects were a headless Ken doll and a green, stuffed Tele-Tubby.  Every piece of garbage reminds me that our children might not have the same privileges we have had on this visit to the beautiful and hospitable Philippines–Save Our Planet!

Finally, with respect to this part of my commentary I want to raise awareness of several disturbing events that occurred during May: First, a park ranger from the Mt. Makiling preserve was murdered after reporting illegal squatters and poachers in the forest. This occurred in broad daylight, in front of the courthouse in Los Banos. The work of conservation is highly political and is in direct conflict with lucrative, illegal practices such as poaching. On the slopes of Mt. Banahaw, Dr. Darin Penneys and I came upon a loaded civet (endangered cat) trap in the forest. Later in the week, when the birds and mammals team joined the Botany/Entomology crew on the mountain, mist nets used to catch, tag and release flying animals were stolen.

The work and logistics of field work are hard enough without these additional complications. On this expedition, the typical day starts at sunrise (~0600) and often ends well after midnight because data have to be processed. The incredible volume of information that needs to be recorded, transferred to computers and stored with accuracy is a labor intensive activity taking place each night after field work is completed for the day. Keeping up takes significant mental and physical discipline as any delays in data transfer processing increases the risk of error and confusion, later. Also, procrastination would result in an unmanageable volume of work. The Cal Academy crew and our colleagues from the University of the Philippines are true professionals: They get this job done every night no matter how tired they are from the exertion of the day’s work. It is a simple concept, but far from easy!

I’ve attached photographs–in no special order, yet–taken by members of the terrestrial team now hunkered down in Isarog because of the typhoon. The majority of these were taken by Nataliya Polydouri, a graduate student from U.C. Berkeley after I drowned my camera during a river crossing.

I’ve been away from the forest for almost a week and already it feels like a long time ago. The ocean life in Anilao is magnificent, but I miss the forest and my botany and invertebrate (scientist) friends, already. I can hardly wait to see my family and share my experiences with them. Similarly, I can hardly wait to revisit the Philippines. I have more than 20 expeditions under my belt and I’ve never seen worked with such a fascinatingly diverse group of scientists in one place as extraordinary as this one.

Briefly:  I have received several inquiries about whether the application of insect repellent should precede or follow the application of sunscreen. Traditional teaching is that insect repellents (e.g. DEET-based products) should be applied after sunscreen. The evidence for this is unclear from the literature as I interpret it. Both insect repellent and sunscreen require multiple applications during the day and both seem to have the intended effect when they are applied diligently. In my experience:  Complete coverage by clothes is the most effective way to keep the sun and pests away from skin.

Please send your questions and comments to me, here, and/or to the Center for Exploration and Travel Health at the California Academy of Sciences (CETH). I will try to answer them, promptly.  To learn more: http://research.calacademy.org/ieth or contact me at mlewin@calacademy.org

Filed under: Academy,Philippines,Web — mlewin @ 10:17 am

May 13, 2011

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 11, 2011

Expedition Video

Gala video

Here is the expedition video that was shown at the Academy’s Big Bang Gala on May 5th, 2011.

Watch now.

Filed under: Academy,Philippines — admin @ 1:49 pm

May 8, 2011

Rubble with a Cause

While other Shallow Water researchers are busily gathering sea urchins, sieving sediment for sand dollars, spotting vibrant and cryptic miniature sea slugs, stalking elusive reef fish, and gardening the reef to harvest symbiotic barnacles, I….as odd as this is going to sound….am collecting rocks.

A tub of.....rocks???

A tub of.....rocks???

Not just any rocks, mind you….. specifically coral rubble rocks. Coral rubble consists of fragments of hermatypic (reef-forming) coral which, over time and during storms, have broken from the reef and rest on the seafloor, providing habitat and surface area for the settlement of new recruits.  I collect these coral rubble fragments in search of polychaete worms.

When diving on a coral reef, several fairly obvious species of polychaetes can be observed. Polychaetes are a highly diverse (about 10,000 known species) group of segmented marine “bristle worms” distantly related to earthworms and which occur in all habitats of all marine ecosystems.  Polychaete worms vary in size from a couple of millimeters up to 2 meters in length.  These organisms serve as an important food source for birds, fish and other invertebrates, function in symbiotic relationships with various other reef organisms, and may even bio-engineer reef environments.

Examples of polychaetes you may have encountered in photos or on reefs include the “Christmas tree worms” and “feather duster worms”. These two types of sedentary polychaetes can be easily observed living in tubes deeply buried within large sections of live coral.  Many other polychaetes are free-living and do not form permanent tubes.

Spirobranchus gaymardi, "christmas tree worms", on coral
Spirobranchus gigantea complex cf. gaymardi, “christmas tree worms”, on live coral
Sabellastarte indica "feather-duster worm"

Sabellastarte indica, "feather-duster worm"

We are strongly against destructive sampling activities that would adversely affect the reef, so I don’t collect these worms burrowed in live coral. Many of these are common species, anyhow, and are quite well-studied (although others may benefit from taxonomic revision or DNA comparisons with other populations).

However…let me tell you….the really interesting stuff is in the rocks! As I dive, I typically head for the “dead” looking section of the reef.  You know, the area you might pass over accidentally on your way to the cool-looking colorful stuff but would certainly not intentionally photograph because it’s all basically one greyish color and has little interesting macro-fauna living associated with it.
This is my hunting grounds.

Searching for worms under coral rubble

Searching for worms under coral rubble

I carefully turn over all the most interesting-looking rocks and coral rubble in the immediate area. Sometimes I get lucky and there might be an obvious larger animal sheltering under the rubble, using it for cover from daylight as it waits to forage at night. Other times, there may be a nice fat worm tube stuck to the underside of the rubble…that one’s a keeper.

Most of the time, though, I just select a few rocks that I think look particularly promising, bag them up in whirlpacks and add them to my collecting bag. My rock collection helps keep me stay neutrally buoyant as my tank grows lighter at the end of the dive, but if I go overboard on collecting heavy stuff our Dive Safety Officer, Elliot Jessup, is often around with a lift bag (similar to an orange partly-deflated balloon) to help me slowly transport my rubble to the surface.

Using a lift bag makes carrying rubble easy

Using a lift bag makes carrying rubble easy

Collecting rubble may seem like sort of a weird activity, and perhaps folks don’t get quite as worked up about admiring my catch of rocks at the end of a dive as they might, say, a cool new fish. However, after the rubble sits in the tub next to my microscope for a few hours, it becomes apparent that these chunks of rubble abound with tiny yet fascinating cryptic organisms. In most cases, animals that live within rubble remain hidden for part or all of their lives, and thus are less likely to have been studied yet by humans. We can learn a great deal about the true biodiversity of a coral reef from closely examining its rubble communities.

Each batch of rubble and all animals from it is labeled with data

Each batch of rubble and all animals from it is labeled with data

Small organisms use the crevices and spaces within rubble rocks for a hard surface to attach to or for a refuge that is safely hidden from large predators. Miniature food webs occur within a chunk of rubble.  Algae is fed upon by grazers, who may in turn be fed upon by small predators.  Many organisms live within rubble crevices for much of their reproductive lives, releasing gametes or buds into the water column from these safe confines during their reproductive periods (more about this in a future posting).

Syllidae, a small but striking worm from the rubble

Syllidae, a small but striking worm from the rubble

Eunice, another resident of rubble

Eunice, another resident of rubble

Communities of organisms inhabiting coral rubble have been used in scientific studies for measuring diversity, productivity, and general reef health. Some organisms living in these communities assist in the breakdown of the rubble itself, permitting the release of calcium carbonate into the water for use in building new reef structure.

Dorvilleidae, another worm from rubble

Dorvilleidae, another worm from rubble

For me, examining coral rubble is an excellent way to sample for the small and cryptic “sleeper” critters  (such as polychaete worms) which live hidden lives buried deep within the reef ecosystem, quietly providing critical services to the community.

Once I have my samples, I can return the rubble back to the seafloor to be colonized again.

Filed under: Academy,Diving,Philippines,Piotrowski,Shallow Water — cpiotrowski @ 4:16 pm

Got the tools and they know how to use em’

Scientific Diving involves an extensive toolbox, some that might be familiar to the technical, commercial, or recreational diver, and some that are completely unique to science underwater.  One of the biggest challenges scientific divers run into is task loading.  The scientific diver is operating life support equipment while monitoring time, depth, and decompression status as they complete the scientific tasks underwater.  This can involve everything from running transect tape, laying line, working in quadrats, operating video and photo equipment, collecting, sampling, and recording all of this information accurately!

Proper education is a must and includes a minimum of 100 hrs of advanced training in areas such as physics, physiology, decompression, nitrox diving, navigation, site survey, collection, diver rescue techniques, CPR, 1st Aid, AED use, O2 Administration and more.  After scientific diver authorization the training doesn’t stop – underwater researchers are always learning new techniques and increasing their efficiency underwater with the proper tools for the job.  The following are  a few of the tools we are using on the 2011 Philippine Biodiversity Expedition:

Bob Van Syoc takes a clipping

EMT Shears double as a required cutting device and a collection tool used for taking small clips of corals without remove more than what’s needed.  “Whirl-pak” bags are used for storing specimens individually in salt water until they are preserved for future study, all the collections are then stored in a mesh collecting bag with a rigid opening and clipped to the diver with a double ended bolt snap.

Divers Notebook, Pockets, Backup lights, SMB, and Lift Bag

Underwater notebooks are a great addition to a research divers toolkit, enabling date recording and communication without the limited space of a slate which must be erased after each use. Auxiliary pockets can be useful storing smaller items that the diver might not want to clip to one of the d-rings on the backplate/wing/harness configuration. Surface Marker Buoys (aka Safety Sausages) are a must for ocean diving, they can not only be a life saver if caught in a current or diving with heavy boat traffic, but can also be used for live-boating to identify the divers location. LED lights are useful during night dives and during the day to make up for lost light associated with depth – very helpful when searching for the next new species!

Piotrowski and Jessup bring live-rock to the surface using lift bags.

Lift bags are used carefully for bringing samples such as live-rock to the surface.

Jessup using canister light to look for barnacles

The hip-mounted canister light provides considerably more lumens than the standard dive light, and allows for hands free operation.  These lights from Hollis Gear are 16 watts and provide up to 5 hours of burn time with a lithium battery. Also worn in this shot is a Datamask by Oceanic – this mask was designed for military use and provides the diver with a heads up display showing depth, dive time, decompression status, and tank pressure (via transmitter) all in the bottom right corner of the mask.  This one is new for me. I have to say I was quite skeptical at first, but after testing the mask extensively I’ve found a new tool that definitely improves a scientific dive!

Placing the camera

Underwater photo and video equipment can play a key role for the scientific research diver allowing them to document the worksite, specific species, and can even be used as shown leaving a weighted tripod at the bottom of the water column to record animal behavior without divers disturbing the habitat. Underwater housing and cameras can range from a few hundred dollars to tens of thousands for production quality media. With recent improvements in dSLR technology a research diver can capture both high resolution photos as well as high definition video all with a single mid-range priced camera.

With 140 safe dives under our belt and 28 new species discovered, the first two weeks of 2011 Philippine Biodiversity Expedition have been very successful for the shallow water team. Stay tuned for more posts from the rest of the team!

Elliott Jessup
Diving Safety Officer
California Academy of Sciences

Filed under: Academy,Diving,Jessup,Philippines — ejessup @ 3:41 am

May 5, 2011

Planetarium Dome Images

I work in the Science Vizualization Studio and the specimens I’m collecting on this trip are the videos and photography we shoot This footage will not only be used for current events like the Academy’s Gala on May 5th and our live webcast on May 19th, but also for future exhibits and planetarium productions.

For the dome we use a specialized camera system, which incorporates the use of fisheye lenses. The result are videos and timelapse sequences which have a field of view of 180 degrees; round and immersive, perfect for the dome.

And we are not the only ones loving our camera setup…

Filed under: Academy,Outreach,Philippines — admin @ 5:24 pm

Collecting critters and images

Photo: Sea Stewards

“All clear?” “All clear. Diver in!” Mati, our Filipino dive guide”confirms and I roll off the narrow V of the canoe hull of the wooden trimaran called Pangkas. Barely missing the bamboo outrigger I’m handed my video camera and dip down to avoid the biologists who follow. As the bubbles clear the scene beneath the boat opens, exposing one of the great wonders of the world, a coral reef so diverse in shape, and texture and color it is like staring at a canvas by Gauguin.  It is hard to determine which part to process and appreciate first, the colors or the brush strokes, the shadows or the subtleties.

The bright tropical light paints shimmering stripes across the reef
crest bringing into highlight the barrel sponges and large porites
coral heads that project like sentinel towers.  Parrotfish, wrasses
and damselfish provide a dynamic pulse against the backdrop.  It is

The California Academy of Sciences Research team settles down and each
expert scours the bottom for new nudibranchs, barnacles, octocorals
and fish to study and describe.

<i>Photo: Sea Stewards</i>

Face down, each scientist enters their own world, processing and
excluding all of the distractions and narrowing their focus down to
their organisms of expertise.  Bob Van Syoc aka Barnacle Bob points at
a tiny pock mark on the lace fan of a seafan.  An underwater thumbs up
and a new species is trimmed away from the host.

<i>Photo: Sea Stewards</i>

So small they look like flaws in the garment of the lace, this
barnacle may live only with this species of sea fan.  Dr. Terry
Gossliner, our expedition leader has found nine new species of
nudibranchs, a brightly colored marine snail.  Some of these
shell-less marine snails are so small they are almost impossible to
see among the soft corals and coral rubble. These people see things we don’t.

<i>Photo: Sea Stewards</i>

My job is the big picture. Through the viewfinder I try to convey the
fragile and irreplaceable beauty of the ocean, and the threats that
face it.  The angle is wide, the corals and fish and worms are all
there, but so are the plastic and people and the human impacts on the
reef.  Tim Horn and I have been working hard to shoot the wildlife and
expedition for the Big Bang Gala video to be premiered at the
California Academy of Sciences May 5.  Now we are onto shooting full
dome vistas of this intriguing country of islands.

Expeditions like this one are strenuous and incredibly fatiguing.  The
planning alone is exhausting, encompassing an entire team who do not
get to venture into the wild. We owe it to them and our Philippine
colleagues to work every minute we are here. The shallow water team
whom Im diving with is hitting the water 3-4 times per day, and
spending the wee hours cataloging, describing and preserving the

Well past midnight Tim and I are downloading images, performing a
quick render and edit and staying up watching the high definition
video crawl through the wire at a nudibranch’s pace back to the
Academy for the final edit.

For the Gala, our work is nearly complete and I’m excited to see the
final cut of the video, and learn the audience’s response when they
see it for the first time Thursday night.
Until then, its back in the water.

<i>Photo: Sea Stewards</i>

Filed under: Academy,Philippines — dmcguire @ 9:57 am
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