Animation—from an ancient art form to high science. Cryptic images from Paleolithic cave drawings to Shrek, the movie.

     I thought to tackle a much lighter topic than aging, cancer, toxic spills and malaria for a change of pace, especially since Christmas is getting closer and need some happier thoughts.  Today’s blog will have less to do with biology and more into a topic of great personal interest since I was 4 years old.  You may ask, “What prompted this all of a sudden?”  I’ll tell ya.  Blame it on Shrek.

     Animation, as we know today as motion picture or video, is an increasingly sophisticated art form.  It is the method of creating optical illusion of motion through a rapid display of images in two or three dimensions.  This illusion is created in our mind because of the phenomenon called “persistence of vision” in which the retina of our eye retains an afterimage for 1/25th of a second.   It is for this reason that modern films run at 24 frames per second; at 16 frames per second, the images flash and not pleasing.  We can still see motion at 10 frames per second, akin to watching someone flip a book in front you.  It is the retina that does this all on its own, not the brain as once thought; hence, the term “iconic memory “ that has been debunked by physiologists as early as 1912.  Even the concept of persistence of vision dates back to the Roman poet and philosopher, Titus Lucretius Carus (ca. 99 -55 BC), from his only known work, an epic poem called “On the Nature of the Universe.” 

     It is also a perennial surprise to me that the things we now know often have ancient beginnings.  Cave dwellers of the Upper Paleolithic era (40,000-10,000 BC) began creating images of animals in motion by superimposing multiple legs.  Without any means of making the images move, the drawing is not animation in the true sense of the word, yet they conveyed the human need to display motion in art.  Hypotheses abound on the meanings of these cave paintings, ranging from pre-historic star charts (Dr. Michael Rappenglueck, University of Munich), spiritual trances invoking the power of nature (David Lewis-Williams), imagery of past hunting successes and rituals to improve hunting success.  Considering the thousands of images painted on the walls of Lascaux alone, I think that they simply have a lot of free time and like to doodle whenever they can.  Try this on your teenagers—don’t pay the Internet and cable bills, take their mobile phone away and keep them in the house.  The artistic ones will be doodling all day, while the rest with no talent will find other mischief or sneak out to go shopping, which is sort like “hunting and gathering” the modern way.   In fact, these ancient cave dwelling artists were so good that the painting called the “The Crossed Bison” showed perspective drawings not seen in art until the Renaissance, about 15th century AD.

     In 180 AD, the Chinese invented the zoetrope.  It’s ok if you don’t know what it is.  I did not know what it meant either until I looked it up (from Greek zoe meaning life and tropos meaning turn; the “wheel of life”).   A zoetrope is a cylindrical device with vertical slits. Below the slits, inside the cylinder is a series of drawings or pictures.  When you turn the cylinder while looking though the slits, the perception of motion is created.  It must had been a hit in 180 AD, just like getting your first Polaroid  instant camera in 1948 (called the Land camera from its inventor, Edwin H. Land, who also designed the optics for the Lockheed U-2 spy plane, later shot down by the Soviets –Sorry, can’t resist the trivia).  

     Zooming on to modern times and for my fellow New York  ‘straphangers’ who may not know, there is a linear zoetrope aptly called “Masstransiscope” built in 1980 on the subway platform at Myrtle Avenue in Brooklyn.  The Masstransiscope (Sounds appropriate, doesn’t it?) consists of 228 slits set against a linear wall, behind each slit a hand painted mural is illuminated from behind.  As the train runs past the station, the riders, nicknamed straphangers for holding on to the leather straps (not leather anymore, but stainless steel now) hanging from the ceiling of the train, see  the images as a motion picture. 

     Stop-motion cinematography was developed in the 19th century and the first one was attributed to George Melies, who discovered it by accident when his camera broke down while photographing a passing bus.  By the time he restarted the film, a hearse was passing by after the bus.  Later, he discovered that his images transformed the bus into a hearse. And so began the motion picture industry, hearse notwithstanding.

     Animated films of the 20th century are a bit more complicated and involved hand drawing of each frame, the second frame slightly different from the previous ones, each drawing is traced or copied into acetate sheets called “cels,” colored and photographed one by one to create the motion picture.  The traditional cel animation was replaced in the 21st century with scanning and computer drawings, integrated with computer software.  Despite such technological advances, the art form of traditional cel animation is preserved to this day and the input of the animators remained as it was 70 years ago.  The technology has changed but the art remains blended into the new ways of creating the images.

    I fell in love with animation as a child living in a village far away from the city in the Philippine island of Luzon.  That was in the very early 60’s when television had yet to reach the village.  It was a time when a phone was a rare item and even a car passing through the village was a special event, a cause for celebration among the children who would chase the car as it sped out; must have been the same inclination that dogs have for doing the same for no reason at all.   As a 4-year old, my only recollection of that period was the movie van coming to the village every 6 months after the rainy season, a much awaited event for the young and old alike.  All the kids sit in front on the grounds of a dusty clearing at dusk, watching the driver/movie technician/marketing agent unfurl the wide screen attached to the outside of the van and get the movie projector going.  It was the only time I can remember as a kid to be in a hurry for darkness to come.

  The first 30 minutes was a promotion of Darigold powdered milk.  Back then in the village milk cames from some rare cows, water buffalos and nursing mothers.  Darigold, a brand since 1918, is a farming cooperative of over 500 dairy farmers in the United States.  Then, there was the Carnation evaporated milk promotion movie.  The company, founded in 1899 by Eldridge Amos Stuart, was famous for its for its slogan of the milk coming from “Contented Cows.”  The milk products and the contented cows were irrelevant to me; all the kids I knew hated drinking milk or had no chance to get any, anyway.  I did not even know what ‘contented’ means; thought it was something to do with bowel movement.  I was contentedly waiting for the animated cartoons of Mickey Mouse and Mighty Mouse to start.   Walt Disney’s Fantasia and Snow White and the Seven Dwarfs were just pure works of wonder to me.   Life was simpler then, or perhaps, life was always simpler for all 4 year olds anywhere on Planet Earth.

     Half a century later, animation remains an interest, though vicariously enjoyed in the guise of taking my kids to the movies.    The high tech changes in animation, though visually appealing, seemed missing something.  The only enduring animation that made its recent mark on me was Shrek, but only the first movie in 2001.  (If you have not seen it, maybe you should go out of the cave and stop making drawings on the wall !) It was a different genre all of a sudden; a bit brash, irreverent, yet reminded me of the same qualities of the old animation films.  Just like the ancient cave dwellers, each generation leaves a mark for posterity within the limits of their own technology.  Our generation is leaving so much mark that we hardly notice.  Perhaps, it is the generations a hundred years from now who will decide the defining marks of our generation.

     Shrek was an unconventional movie on its own right, but something else that struck me as unusual.  I could not pin point what it was until I watched it alone, undistracted, early in the morning while I was taking a break from writing a dreary piece on malaria.  And, there it was!  An image of not so long ago, taking me back to the old country, an image of the Philippine flag embedded within the narrative of Shrek.  I only remembered it because of the recent diplomatic flap at the US State Department when the Philippine flag was displayed incorrectly, with the side signifying the country is at war.

   To make this observation plausible, I think it is best to give a quick primer on the Philippine flag.  This tri-color flag, whose colors were influenced by the Cuban Revolution, was first raised during the proclamation of Independence from Spain by the nascent Philippine Revolutionary government in June 12, 1898.  Within the white triangle is the sun, with 8 radiating rays symbolizing the first 8 provinces that revolted against Spain, a concept similar to the Betsy Ross flag of the American Revolution with the stars representing the first 13 colonies that fought the British.   In the Philippine flag, the three stars represent the three main geographic divisions of the archipelago, the red color symbolizing the blood of the revolutionaries who signed their membership to the Katipunan, a Masonic secret society, in blood; and, the blue representing peace.   

    Among all national flags, the Philippine flag is unique because it can show a state of war by simply flying the red field on top or on the left of the observer when mounted vertically.  In times of peace, the blue side is on top.  The war flag was first flown in 1899 during the Philippine-American War, then again during World War II when American and Filipino troops fought and died side by side against the Japanese and during the EDSA Revolution that toppled the dictator, Ferdinand Marcos, from power.  The recent diplomatic issue of the United States not being familiar with the protocol by presenting the flag on its war stance during the ASEAN summit ceremony in New York City attended by President Barack Obama last September 26th  was an understandable faux pax.   

Now, take this idea with grain of salt…

     Look closely at the sun and 8 rays in the Philippine flag and then compare with the animation frame in Shrek.  The portion of the narrative was when Fiona retired into the cave to hide from the evening darkness, Shrek and Donkey was talking about the starry night by the fireside.  There were eight boulders that make up the fire pit and in one frame eight rays where radiating from the fire.  In this animation frame are both characters lying down looking at the stars, with the shadows made by the rocks framing a likeness to the Philippine flag’s emblem of the sun and 8 rays.  If you watch the previous scenes closely, variations of similar images appeared in different frames making this less of a chance imagery, but a more thoughful, conscious action.

     It could very well be just accidental and I might be simply reading too much out of this.  And, I will be the first to admit that this might very well be just a happy coincidence.  Or, I need more sleep and less coffee. 

But, consider this:

     Dreamworks SKG (the creator of Shrek), like all of the major US animated movie companies (Disney, Marvel, Hanna Barbera, Cartoon Network, Warner Brothers) all outsource their animation overseas.  Over 90% of such animation companies are located in Asia.  The Philippines is the dominant outsourcing location for 2D animation because for the last three decades the US animation industry has been using Filipino artists.  This is because of a closer understanding by Filipinos of the American mindset, the numerous pools of talent and the lower cost compared to US animators.   

     That those embedded Philippine emblems are attempts to merge the creative talent with national pride in a cryptic way seems plausible considering possible Filipino artist involvement in the creative process of Shrek’s animation. 

     This is just a hypothesis and waiting for someone to prove or disprove it.  Maybe Dreamworks can tell me later.

     Nevertheless, it is heartwarming to know that some nationalistic pride still shines out of all of this dreary work.  Who knows, maybe since the animation business is moving in the direction of India and China too, perhaps there will be more artistic, cryptic and irreverent images embedded within future movies as well.  Only Indian or Chinese descendants may likely spot them next time. 

Maybe go get your Chinese friend to check out “Kung Fu Panda” for hidden imagery.

Jonathan R. Matias

Poseidon Sciences Group

New York, NY

Additional reading:

On outsourcing and insourcing in the animation industry

The fight against cancer needs to be an asymmetric warfare; reflections on the death of a friend

A black man was killed a few days ago.  No, it’s not gang violence.  It’s neither drug related nor a party in the ‘housing projects’ gone out of hand.  It’s not an accidental shooting or from a robbery gone astray.  Nor was it even a traffic accident.  Most people would have said that he had died or simply passed away, but I say he was killed.  The word ‘dying’ seems to sound so natural, so passive, as if his death was an expected, common place event.  He was killed by something even more sinister, more insidious, more violent and even more heartbreaking.  He was killed by his own cells, his very own DNA, aberrant as it might be, but it is his own nonetheless.  He was killed by prostate cancer.  And he was my friend.  His name: Dr. Lloyd A. Williams, neurosurgeon.

I meant to write about cancer research much later on, but his death brings this subject much closer to home.  He was an unassuming man for a neurosurgeon, mild-mannered, soft-spoken, cultured and full of wonderful dreams.  On warm summer’s evenings, he would come by my home for a short visit and we would sit near the backyard fish pond watching Japanese carps swim by.   Surrounded by tall flowering night jasmines and bamboo trees, he would relax finally on those rare days when he was not working as the neurosurgeon at the two local hospitals.  We talked about science, his love of philosophy, the old books he has been collecting and his dreams of writing poetry when he can finally relax from the miseries of doing surgery 6 days a week.  He was ambitious, holding two jobs to generate enough wealth to fulfill his dreams.  An immigrant from Jamaica finally attaining the great American dream—a grand home, investment properties, a wife, a kid.  He talked about his parents and how their old dreams for him finally materializing.  I told him that there is so much coincidence here; a Jamaican immigrant living in Jamaica Estates, NY, drinking Jamaican rum.  He just laughed.  We instantly found some common interests the first time we met and I had enjoyed those rare visits year after year.  The pond was our “happy place” to unwind, feel the breeze, and settle for a spell, just enjoying a cognac or two by the side of a little campfire.

In the summer of 2009, he looked more subdued than usual.  He told me that he has inoperable late stage adenocarcinoma of the prostate that has already metastasized to the liver and pelvic bone.  I did not know what to say, but the first thing that entered my mind was how can an M.D. miss the early warning signs and let cancer get this far.  The second thought was the misery I had seen when another person I knew long ago died from metastatic lung cancer.  Then, I thought of my father-in-law who died from prostate cancer too.  The pain and suffering for both him and his family were about to come and I can’t do anything about it at all.

He was an energetic, seemingly healthy man.  The cancer was not detectable until the pain started.  Statistics say that 1 out of 6 men will get prostate cancer and African-Americans have more than twice as much probability of getting it than the rest of the male population in the United States.  I knew all of that.  I did research on prostate cancer for a few years, although in a rat model of adenocarcinoma.  I have followed the scientific literature over the years.  But, what can I do for him?

US mortality rate for prostate cancer (2003-2007) according to ethnicity. Data derived from: SEER,National Cancer Institute, NIH

There’s hardly anything out there for late stage prostate adenocarcinoma.  But, there is always hope and there is the never ending stream of scientific papers each week about cancer.  Perhaps, there might be some clue, maybe too novel as yet, that might give us some rays of hope.  So, we agreed that I will read the literature more closely and will mail him a copy of each paper that I thought would be useful.  And so started my odyssey of reading prostate cancer papers each week.   It became almost a ritual, with my secretary printing the latest articles of the week and mailing him a copy, a weekly routine that has gone on for over a year.

I had not seen him since that summer evening, though we talked on the phone.  He was fighting the cancer, traveling to different hospitals, more surgeries, more pain and more hope.   He could barely read the articles I sent him.  But, he fought this disease with such overwhelming tenacity like a gladiator in combat.  He gave a good fight.

Last Friday, October 1st, I felt the end was near.  I thought of going to his home anyway, just half a mile away from mine.  But I did not.  He died at 5:00 PM that same day.  I have the same guilty feelings that many of us lucky enough not to have cancer–yet.  They are the same emotions felt by those who survived a natural disaster or a soldier surviving a firefight in some godforsaken corner of the world while other friends did not.

Having read, scanned, and browsed all of the recent literature on prostate cancer till I was worn out seemed like a hopeless exercise in futility now.  Yes, so much is known about the biology of cancer.  Much progress has been made.  But the progress made were not big leaps forward, not even mini-jumps.  They are all micro-steps, each of those steps cost a lot, not in terms of just money, but intellectual energy because cancer researchers are among the most passionate, determined scientists I know.

To give you an idea how much has been written about it; just go search ‘prostate cancer’ at PubMed, a database comprising over 20 million citations of medical literature by the US National Library of Medicine, National Institute of Health.  From Sept. 1, 2010 till October 1, 2010 there were 400+ scientific papers on the subject in this short span of time.  The very first paper in that database was by Dr. C. E. Liesching, printed in 1894 in the British Medical Journal.  And, 768 more followed by the end of the year — 89,105 scientific papers in all from 1894 till Oct.1, 2010.  That’s just what has been indexed, not counting articles and other journals not included in PubMed.  If you think that’s a lot on just one subject, here’s another one for you.  Breast cancer papers was included in PubMed starting from the 1868 article by Dr. Thomas Bryant, also in the British Medical Journal, to a total of 219,395 papers until October 1.  Three times more papers on breasts than on prostates.  Can’t say I blame the researchers, who predominantly were mostly male.  Even if I just take an arbitrary average length of each paper as 3 pages each, this translates to 925,500 pages when you combine the two topics, almost a million pages of ideas.

Then, you may ask, “Where are we now after almost 1 million pages of print and untold billions (or trillions of dollars)?” The answer would be different for a scientist and for a lay person.  From the scientific point of view, we have made great strides in the treatments, prevention, the understanding of the mechanisms from the sub-molecular, molecular, cellular, organ and whole animal levels.  We achieved great successes in palliative care, new instrumentations to monitor the growth and development, of detection, new anticancer drugs, etc…  The list is quite long when you consider the incremental scientific advances.  For the lay person who simply wants to know if we have the means to cure or even a definitive means to prevent, then the answer would be more disappointing—we are still quite far away.  If one looks at it from a historical analogy we are still in the Renaissance Period.  Certainly we have overcome the Dark Ages and chasing fervently for answers.  We have yet to reach Enlightenment and many more, like Dr Williams, will fall victim till we do.

We have sent spaceships to the distant planets and beyond.  We have sent submersibles to the deepest depths of the oceans.  Why is the cancer problem so difficult, you may ask?  The answer is because it’s a biological phenomenon, not a physical one where all the variables are predictable and easily quantifiable. The cancer cell is a tough opponent—it mutates, it can develop resistance to drugs, it can grow faster than most normal cells, it can hide inside tissues, it can travel at will, it can lie dormant and it can make the blood vessels migrate to it to keep supplying its growing needs.  If there is an equivalent of a Superman in cells, the cancer cell is it!

I have no answers either and can only offer a philosophical view why it is this way.  The cancer cell is a cryptic enemy.  It hides in plain sight.  It blends with the environment.  And it is not a foreign body that exhibits flamboyant markers to separate it from the rest of your cells.  It is one of your own, just behaving badly by nature or by other unknown external factors that stimulated it.  In many ways, the cancer cell is parasitic, like the parasitic wasp that lay eggs on other insect larvae.  The newly hatched wasps consuming the victim till they emerged out of the victim’s body, like the monster in the movie “Alien.”  Yet, it is not quite all that either.  Cancer grows within our tissues, taking the cellular machineries of the host to propagate itself to the point that it kills the host and itself in the process.  It is also like a virus, infecting the cells, dividing to create new viruses, rupturing the cells to invade more cells.  Like cancer, the virus hides from the immune response by masking itself, pretending it is part of the body.  There are many biological analogies I can recite that explain cancer more, but always there are exceptions.  No living organisms, even plants, escape the presence of cancerous growth.  Sharks, once thought to be immune from it, is now found to also have them.  It is just that sick sharks simply get eaten by their fellow sharks so that sick animals are rarely detected.

Fighting cancer is like fighting a war in human scale, not the traditional, conventional, symmetrical one where you know who the enemy is and where they generally are.  This cancer fight is a pure asymmetric warfare, a guerilla action against the state, a conflict between two belligerents exploiting each other’s characteristic weaknesses using strategies and tactics in unconventional ways.  The enemy hides within the population of innocents, yet co-opting the innocents to do their bidding to support its own survival.  The guerilla is part of the society, just an aberrant part, with different ideologies, but looks like everyone else.  The guerilla mutates into different forms to avoid surveillance, changes tactics to adjust to situations.  The larger force trying to maintain control expends massive efforts,  materiel and fighting elements to keep the guerillas in check, catching a few out in the open, but missing many that blends well with their environment.  They lay dormant when times are bad.  They recruit new members to replace the lost ones and wait for the right time to strike back at the government’s weakest point or weakest moments.  The cycle of attrition goes on indefinitely at times, sapping the strength of the presumably stronger force little by little.  This cancer war is no different than Afghanistan, Iraq, Vietnam and others like it.

The only difference is that cancer has no ideology that we understand in human terms.  No single purpose other than the survival of its own kind.  No plans to invade other bodies outside of the confines of the single human host. No aspirations and none of the awareness that the death of the host equals its own death as well.

How do we win this war?  Certainly not through the current dogma we are following now.  The successes are incremental and easily reversed by unforeseen events, like drug resistance and mutations of the cancer cells to evade immune surveillance.  It is certainly not going to be won by drugs that simply give 4 months of life extension at best for the value of $93,000 as in Provenge.  It can only be won by asymmetric thinking, with by new ideas out of the mainstream, out- of- the- box.  But such a war against cancer has to be a determined one, fueled not by massive amounts of money directed at everything else under the sun, but a targeted approach using a new tactic never before taken.  We have enough understanding of what makes a cancer cell unique, what we are lacking is a coordinated strategy, action and purpose.  Asymmetric or not, let’s treat this like a real war, not the symbolic names politicians use.  Let’s fight it the way we won World War II, with both industry and government in synchrony to bring all its massive forces to bear on a single purpose of destroying cancer by targeted means.  It will not be won by simply nit-picking and aimless meandering in broad fronts the way we are pursuing it now.

The last sentences in Thomas Bryant’s 1896 article seem apropos:

It is true that what I have stated is not new….. If the cases I have brought forward have any influence in reminding us of what we have sometimes neglected, or in urging us to do what we cannot fail to recognize to be right, my object will have been obtained; for in our profession, as in many others, the old saying is too true, “That more error is wrought by want of thought, by far, than want of brains.”

Success in a scientific endeavor comes on the heels of the mini-successes that others had made long before.  I think we have learned so much in the last decade alone and it’s time to somehow integrate these into a more meaningful course of action.  Perhaps, in the not so distant future, we can save another Lloyd Williams from being killed by cancer in the midst of fulfilling his dreams.

Jonathan R. Matias, Chief Technology Officer

Poseidon Sciences Group, New York, NY

Additional reading

Liesching CE (1894) Br Med J., 1(1745):1241.  htttp://

Bryant T (1868) Br Med J., 2(415):608-609.

This article is dedicated to:


a neurosurgeon and a dreamer who loved science, medicine, music, philosophy and most of all, his family

The aging process and the ‘7-year Itch.’ Reflections on senescence from the summit of Mt. Colden

My blog entry seems always much longer than I had planned and this one will not be short either.  I might as well make this a tradition.

The thought of aging, as a young man, was farthest from my mind.  It was something my parents and others were going through, not me.  That mindset was a long, long time ago.  Now it’s different.   As I think about the aging process today, three things come to mind:  Mt. Colden; the 7-year itch; and an idea about aging from the past. Continue reading

The biology of being oily. Something old and something new.

      Relax.  This is not another story of the BP Deepwater Horizon oil spill in the Gulf of Mexico.  This is even more up close and personal—it’s the daily oil spill on your skin. 

      It’s the middle of the New York summer.  You sweat profusely most of the time.  Worse, your natural skin oils just oozes out of control like the Deepwater Horizon pipeline to give you that uncomfortable, shiny, unhealthy look.   Ladies, makeup just won’t hold long enough.  You’re back again to the powder room to fix the ‘paint job.’  Guys, especially those who like their heads closely shaved as if they just came out of army boot camp or just out of jail, oils just drips down your face and make your head shine like a brand new bowling ball.  If you are acne prone, then life gets even more miserable.  And it’s all because of that tiny gland, called the sebaceous gland, alongside your hair follicle that spews out natural oils, called sebum.  In the US, oily skin is a $1.2 billion dollar over-the-counter industry and about $ 2.5 billion for prescription drugs, if you have bad acne.  Part of the success of that industry is because of people like you and me, the unlucky majority of really oily folks.

      This topic is quite interesting for me for two reasons.  First, I did spend a decade and a half in the olden days doing dermatology research, especially on sebaceous glands and hair.  Second, just through serendipity, I have the answer to our oily problem.  Now that I got your attention, let me tell you a little about why you need oil and how it happens to mess up your life too (Yes, sounds like the same argument for crude oil).

Cross-section of the skin showing the sebaceous gland and hair

      There is an average of 100,000 hairs on your scalp, including fine barely visible hair and thick ones.  Then there are those non-pigmented, fine hairs on your face, arms, legs and back.  You are born with the same number of hair until you die, barring any major personal catastrophe like setting your hair on fire.   In some men and women, the hair gets thinner and less pigmented giving that balding look if one is predisposed to baldness or the thinning look that comes with age.  And, with each hair is your life time supply of oil from the sebaceous gland right next to it.  Besides that we have the much larger apocrine sweat glands in our armpits, around the nipples and the genital area that produces more sweat.  Initially odorless, the apocrine secretions become odorous depending on the mix of microorganisms present on your skin.

      Some of us have bigger glands than others; those unlucky few have overactive ones.  The sebaceous duct opens to the pores that deliver the oil outside of the skin.  It oftentimes gets clogged with oil and dead epidermal cells and then you get blackheads or whiteheads.  For many, this is already bad enough.  But, for the 85% of teenagers and the minority of young adults in this country, it can transform into full blown acne when the trapped oils cause inflammation because the acne bacteria, Proprionibacterium  acnes, starts proliferating using oil as its food source (Remarkably sounding like the oil eating marine bacteria in the Gulf) and converting the oil into irritants.  Just think of it as fresh butter off the grocery store turning rancid after you leave it out in the counter for a while.  By then you will be running to the corner drugstore to get some over the counter medication or go online for the super high tech de-plugging, skin rejuvenating, over-priced products shown on TV.

      Both men and women get acne.  The glands respond to the male hormone, testosterone, which the sebaceous cells convert to dihyrotestosterone to stimulate more oil production.  The sebaceous cells at the base of the gland starts filling up with oil.  It gets bigger and bigger as it is pushed out towards the center of the gland by new cells dividing and growing behind it.  When totally filled to capacity (sort of like an oil tanker about to run aground), the cell bursts open into the open cavity of the gland and the spilled oil gets pushed up and out of the pores.  Now you have a full blown oil spill and one that you can’t stop by capping the well.  Women produce testosterone too from the adrenal glands, from the ovary or convert estrogen to testosterone at the level of the cell where enzymes convert these precursor hormones to more active ones.   Some of us also have over active enzymes in the skin that convert more than it should or have more protein receptors than bind the hormone, transport it to the nucleus of the cell, stimulating more cells to divide and more oils to form.  This is the biological recipe for your own personal nonstop oil spill.

      You would think that since oils on our skin are such a pain, why it did not shrink throughout evolution as human beings get less and less hairy?  Who needs oil anyway?  Well, your natural oils lubricate your skin, preventing it from dehydrating and the thin coating of oil on your hair keeps it from drying up.  The chemical composition of sebum is so uniquely different from other natural oils in our body.   Why this is so remains a mystery to science, for now.  Certainly there are antimicrobial peptides, such as cathelicidin, beta defensins and histone H4, present in the sebaceous glands that can kill Staphylococcus aureus and P. acnes.  Moreover, acne is a concern probably only in the last 5,000 years, too short of a time span for evolution to allow natural selection for people with smaller glands or none at all.  Or maybe, pimples were sexy before 5,000 years ago.

      But, I think our skin oils have a higher purpose and that is to give our uniquely individual scent.  In non-mammalian primates, such as gerbils, rats and mice for example, sebaceous gland secretions are the means of communicating individual identification and sexual attraction.  Most likely early humans identify each other by their scent.  Perhaps, the sense of smell was more heightened as a means of communication before language was invented.  It still persists in our modern world only in some aboriginal cultures.  In the Desana tribe of the Amazon and the Batek Negrito of the Malay Peninsula, tribal membership is based on similarity of body odor and marriage is allowed only to a person from another tribal group with a different odor.   The Ongee of Andaman Islands, the Bororo of Brazil and the Serer Ndut of Senegal all recognize personal identity by the individual’s smell.  I remember my college Anthropology 101 seeing photographs of aborigines from Papua New Guinea during their ritual of smelling the face, armpits and chest to recognize and welcome visitors from another tribe.  Now, you can’t even dare to try that in the New York subway without getting seriously hurt or ending up in jail.

      As human beings created larger, more complex societies, the value of smell has faded from memory and is retained in social customs without true connection to the sense of smell.  An example is the Indian custom of smelling someone’s head as an affectionate greeting, a ritual dating back to thousands of years and even chronicled in ancient Indian texts as a “the greatest sign of tender love.”   That understanding in today’s society is translated to a more commercial one, looking for the smell that pleases, that creates the urge to buy, that stimulates other senses, and especially that masks other smells.  The sense of commercialism is starkly prominent in the bewildering array of perfumes in the market today. 

      Current research on smell is a sophisticated science using astounding technology that allows one to identify individual chemicals among the thousands that permeate the environment or that comes off the surfaces of plants and foods.  While most research are in the food applications of smell, the more intriguing ones are on the search for that pheromone that attracts the opposite sex, the very basic of human interactions.  The article by Saxton and his colleagues from the University of Liverpool described a steroid called androstadienone presumably from sebaceous/apocrine secretions that contribute to the smell of sweat and saliva that influence how women perceive the attractiveness of a male.  What’s interesting was that the test environment for that study was the process of ‘speed-dating,’ that strange new ritual of the modern era, so we thought,  that I am sure the Desanas, Baroros, the Ongees will find curiously familiar.

      Since we don’t need so much oil in our modern world, how do we get rid of it and acne along with it?  That has been a seemingly endless chase for solutions since the ancient Greeks and Egyptians.  Today’s armamentarium includes remedies, such as sulfur, that are as old as the first written language.  To cover all of these will bore you to death and, if you are already suffering from acne, you already know all about these anyway:     

Intra-lesional steroid,  benzoyl peroxide, antibiotics, retinoids, antiseborrheic medications, salicylic acid, alpha hydroxy acid, azelaic acid, nicotinamide, kera-tolytic soaps, combined estrogen/progestogen contraceptives,  antiandrogens, topical retinoids such as (Retin-A), adapalene (Differin), and tazarotene (Tazorac), (marketed as Roaccutane, Accutane, Amnesteem, Sotret, Claravis, Clarus), nNicotinamide, (vitamin B3), Naproxen or ibuprofen for their anti-inflammatory effects, dermabrasion,  phototherapy, deep penetrating light therapy, photodynamic therapy, surgical lancing, laser treatment, aloe vera, neem, turmeric, papaya, ananthamoola, azelaic acid (brand names Azelex, Finevin and Skinoren), heat, pantothenic acid, tea tree oil, zinc, tetracyclines, low glycemic index diet..…just to name a few.

Some are  just methods, others are purely synthetic, some are derivatives from petroleum and the rest are natural extracts of plants.  What is disconcerting these days is that what we thought was safe yesterday, is the new toxins of today.  Pregnant women particularly are so concerned when using cosmetic products these days.

The idea

      All these treatments are meant to shrink the sebaceous gland, kill the bacteria, reduce the inflammation or get rid of the oil.  The last one, getting rid of the oil, received the least serious interest since you can’t make much money by simply selling blotting paper or selling soap to disperse the oil (dispersants in the Gulf oil spill are made from soap ingredients by the way).  The commercial solution is always something that either sounds like a drug or is a drug or some esoteric formulation that combines all of these anti-acne effects for $80 bucks an ounce.

      Why not just get rid of the oil?  Seems easiest to do and least likely to involve anything that will have serious side effects.  Just like skimming the oil off the ocean surface after the BP oil spill.  It gets rid of the unsightly mess, keep the wildlife from being seriously damaged and not worry about the oil washing to the shore.  Why not do the same for your face?

Ifrenel clay powder and single use daily pack

      The idea is not unique, even for us.  We’ve thought about it for many years, but never so seriously until serendipity took over (For the etymologically challenged, the word came from the name, serendip, given by Indian sailors thousands of years ago to the island we call now as Sri Lanka because they found it purely by chanceIn those days, mariners rarely venture too far out of sight of land because they thought the  world was flat and the ship falls off beyond the horizon—unless of course when  storm blew you off course and land in Serendip by accident).  Biological ideas don’t come often.  Eureka moments are far between the ‘hurry up and wait’ mode of science.  More often it comes through an unrelated event or a side observation.  In this case, we were busy trying to develop a formulation for our barnacle, insect and shark repellent projects, looking at ways to improve the effect of this nontoxic, edible repellent.  At the time we were working with a range of materials including clay.  Also at the same time, it was a hot humid summer day, oil oozing out of my face.  I thought wistfully that maybe I should try some of these clays on myself as I have never liked the thought of using blotting paper (I did try blotting paper before just to be fair) and washing with soap just moves oil around. 

Decline in the perception of oiliness in women after single application of Ifrenel clay

      I rubbed this new clay composition on my skin, then washed it off quickly because guys usually don’t want anything on that makes them look like a girl—no offense.  Something unique happened.  The oil went away with the clay, totally absorbed and washed off.  And something else, my skin was softer, tighter, no shine and most of all, remarkably smoother—for almost the whole day!  I do have my sensitive moments too and I had been around skin care companies long enough to know that we got something really amazing.

      We eventually gave the clay a new name, Ifrenel Clay TechnologyTM, just to make it sound sexier (and French), but the composition is a proprietary mixture of clay materials found in nature.  These clays are rare, not something you will find just anywhere, except from a few mine deposits in the United States.    When one applies it to the skin only once, Ifrenel keeps the oil away for over 24 hours.  When tested on women volunteers who rated their “oil spill” from 1 to 5, with 5 being your equivalent of the Deepwater Horizon scale, the feeling of being oily went away in 10 minutes and lasted for the next 24 hours, at least.   My daughters started using Ifrenel two years ago instead of buying those brand items off  TV ads (saved me a lot of bucks). 

Reduction of acne in women after daily use of Ifrenel

      Then something else happened.  Acne went away and rarely come back, unless they forget using it.  So, off we go running another clinical trial and demonstrating that one can actually clear acne in a week.  The inflammation stopped within two days.  That’s because the acne bacteria don’t have anything to feed on and maybe taken away with the clay too.  Cystic acne can be painful to the touch, just ask anyone who has it. No longer after only two days of a single use each day because the acne bacteria is not there to convert oil into irritants.  But remember, Ifrenel is not a cure.  It just takes away your oil spill.  Acne will come back after a week if you stop clearing your oil away.

      This was a pleasant distraction from our usual marine science projects and certainly far from our malaria projects too.  Off we went to file patents for this, then launched a new company based on the technology, called Ifrenel (from I feel fresh and ‘naturele’).  It will be a hard fight to get it in the store shelves, but we will manage because we aree so confident that it works after tests in over a thousand women.  For men, you can apply it on your face and your shiny ‘bowling ball’ will have that matted, healthy look very quickly, without anyone knowing about it.

      Is this so unique just because I stumbled on it?  Without sounding like an infomercial, IfrenelTM (and its companion product called ClaynTM for just those with the oily problem without acne) is all natural clay.  It works by applying the powder on your skin when it’s dry, just before you wash it, by rubbing with your fingers (see video link below).  This also gives you that microdermabrasion workout that removes dead skin and residual cosmetic chemicals off your face.  When you wash it away, the oil goes with the clay-water mix.  Can’t apply when you skin is wet; the Ifrenel clay will absorb water and lessen the effect.  Not an easy thing to do because we are all conditioned to the soap and water routine.  This is better for you than soap so get used to it quick!  Without oil, your P acnes bacteria don’t grow, your pimples and blackhead disappear and your skin is smooth as silk all day.  No kidding.  And, your make up stays on much longer, saves you money in the long run and spare the wear and tear on your shoes going back and forth the powder room.  There are no emollients, no fancy petroleum chemicals and no silicone to make it smooth.  It’s just your fingers, your skin and Ifrenel clay.

       And how about odor?  It does even more remarkable things that I will tell you one day soon.  I might get to like dermatology research again after all these years.

      Now that this oil spill problem is solved, time to get back to more marine sciences.  Next time I will tell you about shark repellents.  Not having one at the wrong time can really mess up your day permanently.

Jonathan R. Matias

New York, NY

Poseidon Sciences Group

About Ifrenel

The science of Ifrenel      (how to use the product; must see if you want to get best benefit)

On the science of smell

Saxton TK, Lyndon A, Little AC, Roberts SC. 2008 Evidence that androstadienone, a putative human chemosignal, modulates women’s attributions of men’s attractiveness.  Hormones and Behavior. 54(5):597-601.

This Fracking problem: Chasing the solution to this controversial mining issue

      Fracking ! Sounds like a curse word, and for some people along the Marcellus Shale regions between New York and West Virginia, it already is.  Or, it may sound something like an illegal activity folks engage in somewhere in a dark back alley.  And, that also reminds me of the word “fragging” used by soldiers usually against their own senior officers, often involving a fragmentation grenade without the pin.  English is such a flexible language!

      Yesterday, there was a well attended public hearing in Pennsylvania sponsored by the EPA on the use of fracking to release natural gas from shale deposits underneath the earth’s surface.  It was a heated “debate.”  One side arguing how dangerous it is to their local environment while the industry is saying that it has been proven safe for decades.  July 22 was certainly a one ‘fracking’ day for everyone there.  It is also uncanny that it was the same day we announced a new project to develop an alternative idea to reduce the environmental impact of fracking.  Seriously, I did not even know about the public forum until I read it in Tom Zeller’s blog entry in the NY Times.  It was just serendipity.

       For those who are not familiar with the ‘fracking” business, let me give you a quick run down.

Schematic representation of the hydraulic fracturing operation

      The Marcellus Shale Formation, a geologic feature located between New York State and West Virginia, holds an estimated 262 trillion cubic feet of extractable natural gas reserves.  Although this resource has been known for a century, the Marcellus shale deposit became important in the last two decades because of the depletion of other easily accessible gas reserves, the increasing price of oil and the development of the hydraulic fracturing technology by Halliburton that made it feasible to extract natural gas.  Hydraulic fracturing or fracking for short is a process wherein fluid containing sand is pushed at high pressure through a well bore deep into the shale formation to create man-made fractures.  The hydraulic fracturing process involves injection of proppants, typically sand or ceramic beads that are lodged inside the shale to keep the fracture open. The fractured shale allows free flow of natural gas and oil into the pipeline that brings them to the surface for collection.  Over a million wells have been drilled in the Marcellus shale through hydraulic fracturing.


Bacteria that cause clogging in fracturing wells

Blame it on the bugs.    Anaerobic iron and sulfate degrading bacteria rapidly proliferate in the fracturing fluids, causing corrosion of the pipes and clogging of the proppants.  Inevitably biocides had to be included in the fracturing fluid to inhibit bacterial growth to keep the gas flowing.  However, in recent years, there has been a tremendous public concern about the environmental impact associated with hydraulic fracturing and, in particular, the possible contamination of the aquifer and nearby streams by biocides and other chemicals present in the fracturing fluid.  This triggered the frantic search for more environmentally benign options to keep anaerobic organisms from proliferating, despite the insistence of the oil industry that the technology is safe.  Considering the economic and strategic value of extracting US oil-gas reserves, an alternative technology needs to be developed as soon as possible to solve this environmental concern.  People are wary of corporations proclaiming safety and it is better for companies to solve the problem than fighting the public perception of another corporate-led environmental catastrophe. 

      Poseidon’s position on this matter?  I am neither pro nor con to fracking.  I think fracking is essential to our country’s energy independence and the continued employment of a whole lot of people during these dire economic times; the industry estimates 280,000 are employed or will be employed.  But, I also think the industry must allay the legitimate fears of the public quickly by solving the issue and finding an alternative option to improve the system.  I am sure you are thinking that sitting on the fence on this fracking problem is not a healthy thing to do.  I neither relish the ire of the Pennsylvanians nor like being at the very bottom of the list in an oil industry event (not that I have ever been on any invitation list; not yet anyway).

      What to do then?  At the risk of stopping all natural gas extraction and exploration, it is imperative that a solution be developed soon to prevent bacterial overgrowth in fracturing wells.  Because it takes only a small amount of bacteria to contaminate the well, introduction of bacteria-free fluids or other technologies proposed to date have had marginal impact on the overall problem.  A biocidal approach is still the best method.  We still need to get those Gallionella and Desulfovibrio bacteria from clogging the wells and corroding the pipes.  However, the biocidal material should be environmentally friendly and must not freely diffuse away from the bore hole.  This is where the daunting challenges lie.

      Technological advances often times are not at the same pace with the response necessary to negate environmental issues that result from catastrophic failure or unforeseen damage. The case in point is the BP Deepwater Horizon oil spill in the Gulf of Mexico.  For this reason Poseidon has embarked on an ambitious program, called the Nereus Project, to develop technologies that help ameliorate environmental problems associated with technological advances.  While developing technologies for oil spill cleanup, the Nereus Project has also been looking at alternative options that would prevent biocidal actives from leaching out to the environment from fracking fluids.

     This fracking issue is a hot topic.  Tempers are flared, businesses are at stake, livelihoods are threatened and catastrophes, both real and imagined, are all in the now time frame.  New technology development takes time and tons of money.  But, scientific advances in other fields might be applied here.  It is just a matter of looking and selecting the right ones that are available.  This time we got lucky.

Ceramic proppant coated with selenium

      On July 21, 2010, Poseidon Sciences and Selenium, Ltd. entered into a strategic partnership to develop coatings containing covalently bound selenium [Se].  Why Se and not silver or copper?  Only Se can be permanently attached to a surface and yet continue to be biologically active.  Se is approved by the FDA as a nutritional supplement as an essential nutrient and it also possesses anti-bacterial properties through the release of reactive oxygen species, such as hydrogen peroxide.  Upon contact with Se-treated surface, the reactive oxygen released by Se kills the bacteria on contact, thereby preventing biofilm formation and clogging. This killing effect is short range and does not extend far from the coated surface.  A “green technology,” Selenium’s SeLECT™ technology was originally developed within the Texas Tech University [TTU] System by Dr. Ted Reid and Dr. Julian Spallholz, co-chief scientists of Selenium, Ltd. and TTU professors.  This proprietary technology already achieved FDA 510(k) approval for two separate Class II medical devices and the first coated antimicrobial orthodontic products were introduced to the market in 2009 to prevent dental plaques.  

       When applied to industrial applications, Selenium’s patented SeLECT™ technology is marketed under the name SeGuard™. Because it is bound permanently to the coating and yet remains bioactive, Se does not have to leave the surface to exert its antimicrobial action.  Thus, leaching of SeGuard™ to the environment is prevented.  This technology will find use in the industry as a coating on proppants, sand and other materials used in hydraulic fracturing and as coatings on the iron pipes used in boreholes.  Covalently bound SeGuard™ on the surface of ceramic proppants for an example will be the next generation of non-leaching, environmentally-friendly biocidal technology. 

      If this essential nutrient for the human body is also good enough for our teeth, kills bacteria on contact and doesn’t leave the surface, what else can we ask for?

     Where to go from here?  We are still in the process of proving the concept against iron and sulfur reducing bacteria.  And, we are very optimistic since Se’s antimicrobial effect is universal.  How to make this technology work for the fracking industry will need some serious collaboration with the oil industry players and the EPA.  We do need to act faster than usual to make this happen.

     Since a vital strategic industry, people’s livelihood and the environment are at stake here, only really serious “fracking” people need apply.   

Jonathan R. Matias

Poseidon Sciences Group

New York, NY

Who is Nereus?

In Greek Mythology, Nereus was the son of the Titans—Pontus (the Sea) and Gaia (the Earth).  Always known as the “Old Man of the Sea” for his truthfulness and virtue, Nereus fathered the Nereids or sea nymphs, known for their friendly help to mariners in stormy seas.   

For further reading, please see these links:

This blog entry is derived in part from a July 22, 2010 Poseidon Sciences newsletter:

Regarding the Nereus Project:

On the selenium technology:

On the fracking problem:

Of mice and men: The ecological disasters–Deepwater Horizon and the Dust Bowl

The best laid schemes of mice and men

Go often askew

And leave us nothing but grief and pain,

For promised joy

From the Scots poem by Robert Burns, 1785, To a Mouse, on Turning Her Up in Her Nest with a Plough

For almost two decades, there has never been a spill of any sizeable magnitude in the United States.  The Exxon Valdez disaster, a heart-wrenching event way back, passed on as another historical trivia for many our younger generation.  The “Battle of the Rigs,” as I call it, during the ‘safe no-spill years,’ was not as much about oil spills, but about the eye sore that oil rigs represented near shore.  Taking the train a few weeks ago from Los Angeles to Santa Barbara brought that aesthetic concern to a more personal level.  For the very first time I gazed on the miles and miles of oil rigs dotting the Pacific horizon, against the beautiful backdrop of the ocean and the California beaches.  The environmentalists lost that battle against the expedient necessity of supplying our country’s insatiable need for oil.  And, I supposed people just got used to looking at it, the same way that a bunch of oil tankers and cargo vessels anchored out in the horizon barely get a second look.  

The prospect of oil spills was so remote during this “safe period” that the industry magazine Spill Science & Technology Bulletin, edited by my friend, Michael Champ, closed down because of not enough readership.  Also, during this period of ‘tranquility’, much of the research and development associated with oil spill response technology winded down.  Hardly any research was conducted on oil spill in general, let alone in deep ocean, even as companies ramp up to build deeper subsea oil exploration platforms.  There was either so much confidence on newfangled technologies or everyone just became so complacent because the memory of Exxon Valdez was so far into the “ancient period,” as my daughters would call those years before they were born.  (They have also a second, even worse, category called the “dinosaur years”—anytime before 1970).    Given that twenty years is quite ancient for politicians and corporate executives too and without any disasters in recent memory, there was simply no room for the “what if scenarios” of a disaster.

Even as I was writing an article early this year for Asia Pacific Coatings Journal on our subsea testing of marine coatings, oil spill was farthest from my mind.  Ironically, I wrote my concern about the Deepwater Horizon, not of any potential for an oil spill disaster of this magnitude, but on corrosion damage that may arise over the years from fouling by living things in the deep that attach to the pipelines.  The article went into print soon after the Gulf of Mexico (GoM) disaster.   Now, the Deepwater Horizon oil rig explosion yanked America back to a new reality, debunking the myth of the super safe oil platforms.   With this event, comes re-introduction of old terms (tarball, tarmats) and of new ones, to me at least (top kill, dispersants, risers, containment domes)– an array of new terms to learn before those too  pass on as another historical footnote to join the list of earth’s man-made ecological disasters. 

Surprisingly, the BP oil spill does not rank as the worst man-made ecological disasters in the United States, at least for now, although last week it surpassed the volume of the Ixtoc I Oil Spill of 1979 in the GoM.  The all-time winner so far was the ecological disaster called the Dust Bowl of 1930-1940.  Often called the Dirty Thirties, this was the period when over 500,000 Americans were left homeless and when 2.5 million Americans took the painful exodus from their homes, away from the Plains States of Kansas, Oklahoma, Texas, New Mexico and Colorado.   Compared to this, the BP oil spill seemed like a walk in the park.  The Dust Bowl was triggered by extensive farming practices in the absence of crop rotations to prevent erosion.  Combined with the start of a decade long drought, the virgin topsoil, deeply plowed by farmers for years, killed the natural grasses that held moisture.  Over 100 million acres of top soil dried up, creating dust storms that blackened the skies all the way to New York City.  Farmlands became unproductive wastelands and herds of cattle died in the fallow field.  Foreclosures followed, then hunger and famine, diseases; untold thousands likely died indirectly.  And, to make matters even worse, the Great Depression of the ‘30s sealed the fate of millions of people within that unfortunate decade.   It was all because of poor knowledge about best farming practices, lax government regulations, and unbridled greed to take as much out of the land as possible, using new mechanized technologies of agriculture.  Sounds like a familiar story, a typical recipe for all the usual disasters waiting to happen.

How did the government come to the rescue?  It was slow at first.  It was just an unbelievable event in America’s Bible Belt, almost an act of God, punishing sinners for a life badly lived.  But, common sense followed.  President Franklin Delano Roosevelt started reforms quickly.  The government began buying up cattle in designated emergency counties; those unfit for consumption were destroyed.  Those that were fit went to the Federal Surplus Relief Corporation that then supplied the meat to poor families affected by the disaster and by the Great Depression.  The cattle buying program helped scores of cattle owners avoid the foreclosures on their grazing lands.  Roosevelt ordered the planting of 200 million trees, from the Canadian to the Mexican border, as wind breakers and to hold the soil to the ground.  The government made the important step of educating the farmers on new methods of crop rotation, soil conservation, anti-erosion and terracing methods.  And, farmers were paid for every acre they were able to conserve.  This gargantuan effort by the 8th year reduced the dust bowl by 65%, just in time for the new rainfall that followed to lift the region back to productivity.

Just 80 years later, United States’ next biggest man-made disaster unfolded with all the same drama. Like the Dust Bowl, there was little planning for the ‘what if’ scenario in the Deepwater Horizon incident.  There have been a couple of major offshore oil platform spills in the US:  Santa Barbara, California (January, 1969), and the Ixtoc I Oil Spill (June, 1979) in the Gulf of Mexico.  Both were in relatively shallow water.  The Ixtoc I exploratory well disaster (at 160 ft depth) was an oil spill that lasted until March, 1980.  It was recognized as the second largest oil spill and the largest accidental marine spill in history until this 4th July when it was surpassed by Deepwater Horizon.  Robert Campbell’s June 14th chronicle of what went wrong is more accurate and more comprehensive than what I can hope to give here (see link below).  And when one compares this with the Dust Bowl, all the basic ingredients of a disaster were there in Deepwater Horizon, if one looks retrospectively as an armchair observer.  The Internet and the news media are replete with stories of who is to blame, how it happened, who is affected, what is being done to solve the issue, what animals are dying, the people suffering, businesses lost, bad weather, and the usual doom and gloom of any disastrous event in our modern times.

At least the Dust Bowl was an inspiration to two great novels by John Steinbeck, one of which won the Pulitzer Prize and both became great classic movies—Grapes of Wrath and Of Mice and Men.  I am sure after the tarballs have gone away the Deepwater Horizon will spawn some novels, although I am doubtful of great movies will come out of it.

What is there left to say?

I asked this question because everything bad has been said and hardly anything good to mention.  In Steinbeck’s novels, the disaster of his time was the backdrop to illustrate the triumph of the human spirit.  Maybe, this is the one remaining item never mentioned in the unrelenting daily coverage of the BP Oil spill drama.  And this also applies to all of the other disasters that have confronted mankind, from floods, earthquakes, landslides, wars, hurricanes and tidal waves.  We always overcome.  Short of a 10-mile wide asteroid hitting earth, mankind will make it.  We always do and we always will because, as a species, we are resilient and inventive. 

But, we have short collective memories; so little appreciation of our past mistakes.  We invent.  We create new ideas.  Our creativity oftentimes goes too far ahead of common sense.  The exhilaration of inventing and breaking new grounds do not always come hand in hand with caution. 

This oil spill will be just a bump in the road of history.  When the oil spill is collected, dispersed and degraded, we will simply write a few novels, a few action and dramatic movies, millions of pages of scientific papers and reams of new regulations.  And, after the fines have been levied, after someone goes to jail, companies get renamed  and new politicians get elected, life moves onward, heading to the next disaster, whose early warnings anticipated by a few and ignored by the many and for which we will again be thoroughly unprepared for.

But that’s us.  That’s how we are as a species.

Despite the hardships and heartaches of this current disaster, we can always have the consolation that we are survivors, that we will overcome and we will continue. And mother Earth re-adjusts.

What’s in a name?

I can’t seem to leave this topic on a banal historical note and on an idealistic, philosophical tone.  It needs something else, a little irreverence perhaps.  So, I began thinking about the name of oil rigs.  Not that I know many, actually I know of only two—Ixtoc I and Deepwater Horizon.  I can never find the origins of Ixtoc.  One website mentions it as a Mayan god protecting the harvest of maize.  In his June 15th blog, Robert Paterson cleverly juxtaposed Ixtoc to come up with Toxic.  Uncanny, but seems appropriate. 

Non-English names, especially Mayan, are definitely more exotic.  It is never easy to create the same a sense of “exoticness” with English words.  But, I thought Deepwater Horizon is sexy.   It seemed to give a deeper, mysteriously hopeful, adventurous meaning.   Deepwater Horizon, I thought would have been great name, not for an ugly oil rig, but for a submarine or an ocean going research vessel or even one of those great sailing ships.  I would have wanted to name my first, if ever, yacht like that, if I thought of it sooner.  Now, Deepwater Horizon just reminds me of another science horror movie made in 1997—Event Horizon—the story of spaceship entering the boundary of spacetime at the edge of a black hole.  In that movie, all the astronauts went mad and started murdering each other.  Seems like a good analogy for the political wrangling within the current drama of the oil spill.

Unfortunately, Deepwater Horizon will go down in history the way of Ixtox I to mean nothing more than another name for a disaster; such a waste of a sexy name.  When I chose my company name, Poseidon Sciences, most people don’t recognize it as the mighty Greek god of the seas (renamed by the Romans as Neptune), but the cruise ship that overturned after getting in the way of a monstrous rogue wave.  The only good thing is that it was only a movie—Poseidon Adventure— and not a true man-made disaster.

Jonathan R. Matias

Poseidon Sciences

New York, July 7, 2010

Robert Campbell, Reuters (June 14 2010) Special Report:  Deep water spills and short attention span.

The poem, To a Mouse, by Robert Burns.

Tara Oceans: a scientific odyssey in the tradition of HMS Beagle


The expeditions of HMS Beagle (1831-36) and Tara Oceans (2009-12). Charles Darwin and Capt Robert Fitzroy.

His Majesty’s Ship Beagle is among the most celebrated of all British warships, commissioned in 1820 as a Cherokee Class, 10-gun brig-sloop. I always thought that it was odd to name a ship after a dog,  unless of course there was an actual Mr. or Mrs. Beagle around back then who was worthy of such a recognition.  But I could not find anything about how the name was selected other than that it was named after a breed of dog.   The other warship captains must have had a fun time teasing the first captain of the Beagle.   Can anyone tell me a famous (or even not so famous) American or French ship named after a dog?   Considering how the English (and the Irish too) name their pubs– Pig & Whistle, as an example—it maybe not be altogether outside the realm of imagination for the British to choose a dog. 

Why choose the beagle for a warship’s “nom de guerre?”  That’s hardly the kind of name that instills a sense of awe, power and danger. The beagle is generally described as even tempered, merry, amiable, non-aggressive and poor guard dogs. The word beagle has many possible origins, but I like to think it came from the Gaelic word beag, meaning little.  The only reason I can find, from reading about beagles, was that the beagle, as we now know as a breed, was developed in Great Britain about the same period when the ship was commissioned.  The beagle was so well liked that it had been depicted in art and written in the popular literature long before the commissioning of the ship, as far back as the Elizabethan period.  Even in this century, the British named its Mars landing spacecraft, Beagle 2, in honor of HMS Beagle.  Or, maybe they just have yet to outgrow their fondness of beagles.  Guess who is the most popular dog in the whole wide world?  Snoopy. And, he’s a beagle, of course.  So now you know!  

I am digressing from the important topic of the day, but I can’t help but finally settle this nagging question in my mind (and yours too I’m sure). 

Now back to some science. 

In the previous blog entry on Charles Darwin, I briefly mentioned the ship.  I think it is time to at least take a moment to devote some thoughts about HMS Beagle.  After the fanfare of being the first ship of the line to cross the new London Bridge in celebration of the coronation of King George IV, the ship remained moored until later when it took part in three survey expeditions.   The Beagle itself was not a highly regarded ship of the line by its sailors who referred to it as a “coffin brig”–more likely to sink to the bottom than sail around the world. The duties of the first survey were so lonely and yet so stressful that its first commander, Lieutenant Pringle Stokes, committed suicide in Cape Horn.  On the second voyage, Stoke’s nephew, Lieutenant Robert Fitzroy was appointed captain.  In this forthcoming second voyage, Captain Fitzroy needed to avoid the same fate as his uncle by cleverly bringing in a paying passenger-naturalist who would conduct the surveys of  the land so that the ship’s officers may attend to the more important military task of ‘hydrography.”  This young man, Charles Darwin, on his way to becoming a clergyman, became that naturalist.  And the rest is history.  

HMS Beagle 

On this second voyage, initially planned as a three year survey that became five years (1831-1836), HMS Beagle circumnavigated South America and then the globe.  It was a magnificent feat of seamanship, using 22 chronometers and with only 33 seconds of error.   Though largely forgotten, HMS Beagle also had its place in world history.  It was one of the three ships that helped the British take the Falklands Islands from Argentina in 1883, eventually leading to the Falklands War between the two countries a hundred years later.  The Beagle Channel and the Beagle Islands of Tiera del Fuego, in South America’s southernmost tip, representing one of the three gateways to the Pacific, were named after this ship.  Conflicting claims to those islands also almost led to a war between Argentina and Chile in 1904.  Aptly named the Beagle Conflict, this arose because of Argentinean claims to the islands and Chile’s refusal to accede.  It took mediation by the Vatican to resolve this issue 80 years later.  Argentina accepted the papal decree of 1984 making the Beagle Islands and the Beagle Channel as territories of Chile. 

Yet, history barely remembers the Beagle and its captain.  Instead, history took note of the Beagle’s paying passenger and would-be clergyman whose ideas, formed during this voyage, became the foundation of our understanding of the diversity of life on earth. 

The tale does not end there.  One of Darwin’s most ardent detractors and one of the champions of anti-evolution crusade turned out to be none other HMS Beagle’s own Captain Fitzroy.  Their opinions of each other, though strained during the voyage, diverged dramatically long after the expedition.  It is ironic that the aspiring clergyman came up with the idea of evolution that shook the foundations of the Church teachings, while the military man, duty bound to vanquish all enemies of the Crown, became one of the Church’s most vocal champions. 

Tara Oceans 

Scientific expeditions, whether on land or at sea, always have a romantic appeal.  Expeditions meant adventure and excitement.  One can only imagine the thrill and the foreboding that Darwin felt as he embarked on this naturalists’ dream of exploration.  That same sense of adventure, despite all the sophistication and the trappings of our modern digitally enhanced world, still remains today.  

The marine ecosystem is still poorly understood; we only see bits and pieces of it.  But each ecosystem is not isolated but part of a larger system; each part impacting the whole.  Within that complexity is the diversity of life, interacting often in unique and often unfathomable ways.

Despite mankind’s technological prowess, it is not an easy task to understand this complexity.  To solve this puzzle, we do need to start at the bottom, the very basic life forms of each ecosystem and somehow integrate this into the wider knowledge of our planet’s water world.  What can be more basic that the bacteria, zooplanktons, phytoplanktons, microalgae and viruses that make up 30% of the primary biomass of the ocean and the source of 95% of the respiration of our planet.  This is what makes Tara Expeditions a unique, singular maritime adventure of our time. 

Tara Oceans is a specially designed 118 ft. aluminum schooner, sponsored by the French Center for Scientific Research (CNRS), the European Molecular Biology Laboratory (EMBL) and many other marine research institutions.  Its principal partnerships include the United Nations Environmental (UNEP) program and the International Union for Conservation of Nature (IUCN).  Its main purpose is to conduct surveys of marine ecosystems as it travels on its 3-year voyage around the world.  Tara Oceans has a 5-man crew and room for 7 scientists. Their task is to examine marine plankton and other microbial life in the oceans and near coral reefs as it travels along its 100,000-mile route.       

Tara Expeditions started in 2003 because of the vision of its patron, Agnes B, founder of one of France’s most prominent fashion brand, Agnes b.  Her dream was to understand and make a significant contribution to mitigating the effects of the warming oceans.  Since the acquisition of the schooner, Tara, that vision has already taken the ship and its research teams through 7 expeditions in the Arctic, Antarctic and the seas around Patagonia and South Georgia.  

In 2009 (coincidentally the 200th anniversary of Darwin’s birth and 150th anniversary of the publication of the Origins of Species) Tara Oceans embarked on this new 3-year odyssey to study the basic life forms that drive the diversity and productivity of our oceans.  As a moving platform, complete with sophisticated imaging and biological research facilities, Tara Oceans brings together an international team of scientists to conduct over 20 major projects.  Today, Tara Oceans is in the island of Mayotte in the Indian Ocean on a coral research project, prior to sailing to Cape Town, South Africa.  

While there is not enough room in this article to talk about all the research programs during this expedition, it might be of interest to just mention a few to give you the flavor and the sophistication of this voyage.  TANIT (TAra OceaNs ProkaryiotIc FuncTioning and Diversity) is a consortium of scientists investigating the functioning ecology and biodiversity of bacteria in the oceans.   Virus hunters from the Université de la Méditerranée (Marseille, France) shall examine the genome of the MimiVirus, the largest known virus, from the group of giant viruses, called Giruses, which infect a wide range of marine life forms.  The hunt for new ocean viruses will provide a better understanding not only of the genetic diversity but also the role these organisms play in the overall health of the oceans.  The Tara Oceans Marine Biology Imaging platform (TAOMI) integrates all of the data from the research teams as a “tool to extract functional correlations between genes, the diversity of organisms present in a given region and the physical environment.” 

How does Tara Oceans manage to attract such a wide range of scientists from the world’s premier institutions?  That I don’t know.  But, just to impress you, here is the array of acronyms of all the scientific organizations involved: 

CNRS / ENS, Paris, France; NOC, Southampton, UK; CNRS/UPMC, Paris, Roscoff, Banyuls, Villefranche-sur-Mer, France;  Stazione Zoologica, Naples, Italy ; Marine Biology Laboratory, Woods Hole, USA ;  Massachusetts Institute of Technology, Boston, USA;  University of Washington, Seattle, USA;  University of California, Santa Cruz, USA;  Flinders University, Adelaïde, Australia;  JAMSTEC, Kanagawa, Japan;  ICM-CSIC, Spain; Bigelow Laboratory, USA;  CNRS/IMM /IGS, CNRS /OOB, CNRS / UPMC, Paris, Villefranche-sur-Mer, France;  Centre Scientifique de Monaco University of Milan, Bicocca, Italy;  MNHN, Paris France;  James Cook University, Townsville, Australia;  Museum of Tropical Queensland, Townsville, Australia ; CORDIO East Africa, Mombasa, Kenya ; University of Warwick, Coventry, UK ; Nova Southeastern University, Florida, USA;  Tara Expeditions, Paris, France; University of Maine, Orono, USA;  ACRI-ST, Sofia-Antipolis, France;  LEGOS/CNRS, Toulouse, France; GIP Mercator Océan/CNRS, Ramonville St Agne, France; METEO France, Toulouse, France; Satlantic Inc., Halifax, Canada;  Hydroptic Ltd., Lisle en Dodon, France; WDC-MARE/PANGAEA®, Bremen, Germany;  IFREMER, Brest, France; University of Hawaii, USA; LOG, Wimereux, France; EMBL, Heidelberg, Germany;  University of Washington, Seattle, USA; Genoscope, Evry, France;  EBI, Cambridge, UK ; IOBIS/Cmarz/Census of Marine Life, Washington, USA. 

And, as of June 17, 2010, the newest member of the team—Poseidon Sciences

I am sure you are dying to know why we are part of this.  In my previous blog entry on Darwin, I wrote about Darwin’s 8-year passion to classify barnacles.  Unfortunately, I caught the same, perhaps nastier ‘bug’ and now on my 15th year of the same obsession.  This time, there is an urgent concern by environmentalist and the maritime industry about invasive species carried by ships on their submerged hulls.  Because Tara Oceans will sail to various oceanic environments and stop at different ports of call, it is now possible to critically examine what kinds of biological hitchhikers are present in different regions, how long they remain attached and the succession of different biofouling attachments as the ship sails through different waters.  This is an unprecedented opportunity to look at this issue, with marine biologists on board, supported by Poseidon Sciences’ marine research stations around the world.  Tara’s TAOMI system will integrate the data and enable a continuous look at the biological processes at play on a ship traversing all the oceans. 

To make this program meaningful to the maritime industry, the Tara-Poseidon program shall encourage industry participation by enabling marine coatings companies to paint 1 m2 patches on the underside of the hull to measure the performance of their coatings against fouling attachments while comparing those results with uncoated patches along the hull.  There has been a proliferation of coatings with claims of performance against fouling attachments in the absence of TBT (tributyl tin, a toxin outlawed by the International Maritime Organization of the United Nations) and copper.  This is a unique opportunity to validate the performance of such systems (copper-free and low copper) under the challenging conditions of Tara’s expeditions. 

There is one similarity between HMS Beagle and Tara Oceans.  Both ships are the tools to answer questions relevant to people of their time.  The Beagle’s mission of hydrology was crucial to maintain the British dominance of the high seas during the 19th century.  Tara Ocean’s mission, likewise among the most important of our time, 178 years later, is to understand the organisms that are crucial to support the diversity of life in our oceans and sustain the atmosphere on earth.  And, from that gained knowledge, find ways to plan for its remediation, as the founder, Ages B, had envisioned. 

As in most scientific expeditions, it is the chance of discovery that fuels the excitement.  In the case of Charles Darwin, his ideas on evolution might not have formed without the convergence of Darwin and HMS Beagle at that point in human history. 

As Tara Oceans sail through the deep blue sea–who knows.   Among us might be the next human being that could be the instrument of change in the ocean’s future. 

Welcome aboard! 

Jonathan R. Matias

Poseidon Sciences

June 28, 2010 New York, USA 

PS:  Just a little more about Captain Robert Fitzroy, the forgotten pioneer 

After the Beagle expeditions, Fitzroy made it possible for weather observation equipment to be available in every ship in English ports.  This accomplishment and his precise hydrological charts had saved countless sailors from heavy storms. The first scientific weather forecasting station was devised by Fitzroy, using the telegraph as the method to transmit data from far flung weather stations.  Despite the publication of his Weather Book in 1862, which became the inspiration for the very first daily weather forecast in the Times of London, he received little fame.  In poor health, depression from lack of recognition and losing the fight against Darwin’s evolutionary theory, Captain Fitzroy went the way of the previous captain of the Beagle.  He committed suicide in 1865.  It is only recently that the British government and the world’s atmospheric scientists recognize the pioneering work of Captain Robert Fitzroy in weather forecasting. 

The object lesson:  Be nice to the captain of Tara Oceans.  He has a lot to worry about. 

For further reading: 

About the Beagle 

The Tara Oceans scientific program 

Poseidon Sciences

The Agony and the Ecstasy: Why science writing is like learning tango and Chinese brush painting

This is an odd title and I am stuck with it.  Worse, I am compelled to explain why this is so. 

Today, I am at a loss what to choose for my next blog entry and trying to find motivation to write about scientific topics of interest to me – malaria, repellents, arsenic poisoning, the oil spill in the Gulf, etc.  Not finding the right mood for any of those, I began to read the comments left by readers of my first two blog entries.  Then it came to, the inspiration to write, but not on any of those topics.  The inspiration is to write about the subject of writing itself. 

I asked myself many questions. How come the readers liked those articles?  What makes them read them?  Is it because I write about things that have personal interest to me?  Or, could it be the writing style?

Scientific writing to me, and I started a very long time ago, reminds me of the 1961 movie “The Agony and the Ecstasy.”  For those younger folks who regard movies before 1980 as ancient classics, the movie, adapted from Irving Stone’s novel, was about the period when Michelangelo Buonarroti struggled with Pope Julius II on the subject of the painting for the Sistine Chapel at the Vatican.  The character of Michelangelo was played by Charlton Heston and that of the Pope by Rex Harrison, two of my favorite actors from the “ancient period.”

Like the painting of the Sistine Chapel, writing my first scientific paper was indeed sheer agony.  It really was because the language and style of scientific writing are too precise, too impersonal and too alien.  There was none of the flair, the colorful, expressive words that went to writing a history essay, for example.   The scientific writing I meant refers to writing for a scientific journal, where your ‘peers” review your research data and render a judgment as to whether you are either wasting their time or have really something unique, worthy of publication in their illustrious journal.  It has a language all of its own, propagated through the scientific journals by folks that also seem to be able to write exactly the same way.  It seemed to me like these people caught a virus during graduate school that stayed dormant and then get activated only when they start writing for a scientific journal.  These are the same folks, who seemed normal and talk normal most times, but suddenly “sings a different tune’, figuratively speaking, when made to write a scientific paper.

It is never the great papers that one writes as the most memorable.  It is the ones that gave you the most agony that becomes indelibly imprinted in one’s thoughts.  Like in business, the most memorable event is usually not when you made bucket loads of money, but the agony when you lost a big chunk of dough.  My first paper, which was on the embryonic development of annual fishes, was one such event.  It was based on the work that I did with Jules Markofsky while I was an intern at the Orentreich Foundation in those early days.   That was two years of work, mostly repetitive microscopy, looking at fish eggs as they develop.  It was worse than watching grass growing in your front lawn.  It was the sort of work one gives as punishment (like KP—kitchen police- duty in the army) or for someone to go through during hazing initiation rites in a fraternity. 

Then one day, after many very long months, Jules had his Eurekamoment.  The numbers began to make sense.  For years we were puzzled by the behavior of the developing eggs of the annual fish (You have to read my first blog to make sense of this one).  One month they hibernate and in other months they didn’t.  But when you line up the data chronologically according to months, then it made sense (see the graph).  During summer months, we had no hibernation or diapause in the eggs.  But in winter months, there they were.  All the animal research facilities were in light-controlled, temperature- controlled environments– so we thought.  But we were keeping fishes not in the same animal holding areas, but in our work rooms—with one window not fully covered, open to indirect sunshine. The fish must have sensed the changing photoperiod and that was the reason for the variability in the incidence of diapause.  Shorter days in winter meant higher percentage of diapause, despite incubating the eggs at constant 25 oC.

Excited, we wrote the paper, painfully and arduously.  But the writing style was just so alien to my nature.  Months of revisions go by and finally off it went to the Journal of Experimental Biology, the premier journal at the time and still is today.  Then months passed until we received the reviewer’s comments (by snail mail, internet not invented yet).  More agony.  The most memorable comment was something that goes like this (writing from my memory), “This is the worst paper I had the great misfortune of reviewing.  However, the data are so compelling that if the authors can learn how to rewrite it in proper English, the editor should consider publishing it!” That was heartbreaking.  My only consolation was that I keep telling myself that the reviewer did not know I was only 17.   Again, more agony, more months of rewrite.  A year more and it was accepted and one more year of waiting before it finally got its turn on that coveted journal.  Two years of work and two years of writing it; then followed by the sheer ecstasy of seeing one’s name in print for the very first time.  Thank God there were no online reader comments in those days.  Otherwise I would have gone the way of the first captain of HMS Beagle (You will have to read my next blog post to understand that one).   

These last two years, I had this habit of re-reading that JEZ paper.  The reviewer was right.  The paper was atrociously written and still hard to read even now.  But, he did recognize that it was a unique explanation for a unique developmental biology of a unique group of fishes.  For those masochistic few who desire to read it, please check the first referenced paper below.  Don’t blame me if you get a headache.

Ever since then, I get a little better each year.  It was an incremental improvement, less agonizing and a little more ecstasy when a paper got printed.  Yet, it was never really satisfying. 

I always say that scientific writing is like learning tango.  No one is born knowing how to dance like that; it is something one has to learn, memorize the moves while trying to avoid your partner’s toes in the process.  Then one day, it just happens, you are swinging effortlessly in precise movements in synchrony with the Latin music and you did not step on your partner’s toes, not even once.  I never learned tango right, my dance partners did not appreciate their toes getting squashed.  But I did try; so at least I can make this analogy with some personal knowledge.

I also say it is like learning Chinese brush painting.  I know because I spent half a decade learning the process, so it deserves a little prologue here to show my qualification to make that statement.  After my short adventure in the army and while in graduate school, I needed a challenge without having to carry a backpack or rifle all day long.  Jules managed to get me a meeting with a prominent Chinese painter, Master Chung-hsiang Chao, who was already 80+ at the time.  I was told that he was the only surviving son of the last court painter of Imperial China.  The rest of the families were shot when the communists entered Beijing.  I never asked him about that episode in his early life.   And after much persuasion, he agreed to take me in as a student.  I was working full time at the Foundation during the day, taking full time graduate courses on most week nights and my thesis research on weekends.  I could only come on Thursday night. 

On our first night’s trial lesson at his home/studio on the Upper East Side, I shared his dinner and we painted together.  At the end of that session an hour later he said I can come back every Thursday night.   I had to ask, reluctantly and agonizingly, how much it will cost for him to teach me.  I dreaded the answer because this nice old man sells his painting for $20,000 a piece, me being his only student and, given my position in life then, any amount would have been beyond my means.  He smiled and said $7 every Thursday night.  I was a bit confused by the offer.  He said, “$4 for your share of the cost of dinner that I will make for us and $3 for the ink and paper you use.”  And so it was, $7 for each Thursday of those five years until he went back to Taiwan to live the remainder of his years.  This experience therefore qualifies me to make this analogy. 

The annual incidence of diapause in the annual fish, N. guentheri, maintained at 25 C under ambient photoperiod in New York City.

Mountain lily growing on top of a rock, 1980, artist: JR Matias

I say it is like Chinese brush painting (and Japanese paintings too) because like scientific writing, Chinese painting is precision and pure thought.   Each brush stroke must be pre-planned; a master painter sees the entire scene of the painting about to be played out on the stretch of rice paper all in advance.    Each stroke to create a leaf of a bamboo or a lily plant is planned in his mind, the direction of the leaf, the color of the ink, the amount of ink one needs at the tip, in the middle and at the base of the brush.  In one master stroke of the brush, in a single fluid motion, like tango, he creates the bamboo leaf, starting from the dark part of the stem, to the shades of gray of the middle leaf and the dark point of the tip. There is no room for error, unlike in Western painting or pencil sketches, where one may go back to cover up or erase a misguided stroke of the brush or pen.  It is agonizing, yet it is also pure ecstasy when one does it perfectly.  I must say though that most of those 5 years was just agony, but the short moment’s perfection was ecstasy, making it all worthwhile—just like scientific writing.

But writing this and my previous blog entries are not at all like writing a scientific paper.  Here again, something changed in me.  Writing for this blog is an entirely different animal.  Here, one needs to write about a topic in science with some accuracy, yet make it enjoyable to read for the not so scientifically inclined.  It is like a different art form; a different master gene that seems to turn on my other repressed blog science writing genes that had been in hibernation for decades in my brain cells.

This writing style happened just recently.  It started when I wrote articles for our company newsletters only last year.  But, it did seem to me that this writing style seems so natural, as if I had done it before or perhaps have read something like it before.  I had to think hard where I remember such style.  This same night, as I was writing this blog entry, it dawned on me.  The year was 1978.  That was the year when I had my first rare personal meetings with Dr. Norman Orentreich, chairman of the Orentreich Foundation, where I worked by then as a research technician.  After a brief meeting about some research topics I can barely recollect now, he gave me as a gift an autographed copy of a book, The Lives of a Cell, by Dr. Lewis Thomas, his friend.  I kept that book in my bag for a few weeks, not particularly anxious to read another book on cell biology.  But, when I opened it finally on my way to work on the A train, the book that I thought was just another text book was so engrossing that I forgot about my subway stop,  ending up in the Bronx instead of Manhattan. 

The Lives of a Cell: Notes of a Biology Watcher won a National Book Award in 1974.  Lewis Thomas was a physician, poet, scientist, essayist and educator.  He was a highly regarded scientist who became the dean of Yale Medical School, NYU School of Medicine and Memorial Sloan-Kettering Institute.  Normally a book on biology would have sent a non-science reader scurrying to find something else to read or make a science person start yawning.  But this one belonged to a different class altogether.  It was science, but it was also a personal look at what science is all about, how the bits of technical information can be woven into a readable, understandable prose about the meaning of it all, integrated into a more global understanding of biology.  It was funny at times, factual, yet so insightful.  It was also a revelation to me that science need not be boring when placed in the context that can be made understandable to a non-science reader. 

But, through my years of the typical challenges of life, I forgot all about Lewis Thomas.  I did not realize until now that it was the way Lewis Thomas wrote that made that difference.  His writing was an art form on its own.  It was not the usual agony of reading a scientific paper and it also was not like reading the latest news in the NY Times either.  It was something new, for me at least.  New enough and compelling enough to miss my subway stop and arrive late for work.   And it was worth it. 

I had since lost the autographed book.  I had lent it to so many other people and lost track who got it last.  I suppose it was not really lost because I know somebody read it, enjoyed it, probably missed a train stop too and lent it to someone else who never returned it either.  It continues to live in other people.  But, I wish I had that book with me today as I write this article because I can only recall from memory his style that changed my way of writing today.

So, excuse me for turning to this entry in Wikipedia to give you a sampling of his writing style:

I have been trying to think of the earth as a kind of organism, but it is no go. I cannot think of it this way.  It is too big, too complex, with too many working parts lacking visible connections.  The other night, driving through a hilly, wooded part of southern New England, I wondered about this. If not like an organism, what is it like, what is it most like?  Then, satisfactorily for that moment, it came to me: it is most like a single cell.

                                        from:   The Lives of a Cell, Lewis Thomas, MD

I must have subconsciously followed the same path to writing.  Or, both Lewis Thomas and I had our blog writing genes turned on at the same point in our life history.  For those who love to read science and those who do science for work, I suggest you go find a copy of the Lives of a Cell.

And for those who enjoyed my style of writing about the sciences, you can thank, as I do now, Dr. Norman Orentreich and Dr. Lewis Thomas for opening up that new world for me.

Jonathan R. Matias

Poseidon Sciences

June 27, 2010, New York, NY

Reading list

Markofsky J and Matias JR (1977). Journal of Experimental Zoology, 202:49-56.

Charles Darwin’s other passion: rediscovering the origins of barnacle research

Barnacles attached on the surface of a scallop shell

This blog entry has its origins from a company newsletter I wrote in 2009 for scientists working on marine coatings. 

Darlene Brezinski, the editor of Paint & Coatings Industry magazine, liked the topic so much and asked me to take excerpts from that newsletter into the article that appeared in the magazine on the same year.  I share with you excerpts of that article here as a prologue to my next blog on HMS Beagle and Tara Oceans.

Why bother studying barnacles?  Marine biofouling is such a multi-billion dollar problem because attachments on the bottom of the ship causes drag and increased fuel consumption.  It is estimated that a supertanker from Saudi Arabia to Los Angeles port would cost an additional 1 million dollars worth of extra fuel if barnacles are present in the submerged portion of the hull.  The barnacle, Balanus amphitrite, is the most ubiquitous fouling organism that tenaciously attach to the surface.  It is perhaps one of the earliest  invasive species since it is present in practically all major ports, around the world, having been a hitchhiker on ocean going vessels for over 3,000 years.  To get them off the ship requires expensive dry docking, sand blasting. and re-painting.  Prior to the 1990’s, all marine paints contained toxins to kill barnacle larvae before they settle on the bottom of the ship.   That use has since been legislated out and the search is on for less toxic biocides and preferably nontoxic paint chemistries or repellents.  

Barnacles and an oyster attached on a submerged surface in tropical waters. Photo by Sister Avelin Mary.

So, here is the excerpt from Poseidon Marine Science News and PCI magazine.

“Having been in fish biology in my earlier years and a biomedical scientist in my middle ones, my own passion for barnacle research did not come until later after meeting Dan Rittschoff at Duke University,  Ron Price at the U.S. Naval Research Institute and Sister Avelin Mary at Sacred Heart Marine Research Centre (Tuticorin, India) in the early 1990’s.  Barnacles are not exactly the cute furry creatures one can get so passionate about.  I do have to admit that the interest was partially clouded by my capitalistic pursuits.   Like many of us in this business, we write scientific articles about the biology of the barnacle, Balanus amphitrite amphitrite Darwin, and yet did not spare any second thoughts about why Darwin’s name came to be part of it.  So, let me tell you why.

The Charles Darwin we are all familiar with is the English naturalist who wrote The Origins of Species and Natural Selection, which has since become the foundation for our understanding of evolution and the unifying explanation for the diversity of life on earth.  He wrote about his theory in 1844, then quickly shelved it inside his desk drawer, specifically instructing his wife to release it for publication only if he died unexpectedly.  Darwin was a modest man who shied away from controversies and he knew his theory will be so controversial, and even remains to be so on this 150th anniversary of writing the Origins

Charles Darwin

For 20 years, the paper remained hidden until he received a letter from a young English naturalist, Alfred Russell Wallace, then living in an island of what is now Indonesia.  In a malarial fit, Wallace remembered reading Thomas Malthus’ 1798 Essay on the Principle of Population (which coincidentally also inspired Darwin) and reached his own Eureka moment totally independently.  He quickly dispatched a letter to Darwin describing an almost identical theory of evolution.  In the typical Darwinian sense of fair play, he presented Wallace’s ideas and his own at the same time during the meeting of the prestigious Linnean Society, giving equal credit to the ideas of Wallace and the share of the controversy as well.  Yet, Darwin is credited with the theory of natural selection because his ideas were written while Wallace was yet in his teens, over 20 years before. 

Then, you may ask, what did he do for 20 years?  Besides dealing with his failing health and the tragedies in his life, he was consumed by the passion of cataloguing barnacles.  His interest in these tiny, ugly creatures began during his famous round the world voyage in HMS Beagle.  Then, at the age of 26, young Darwin was exploring the Chilean coastline looking for biological specimens when he came upon a conch shell riddled with tiny boreholes despite its thick shell.  Inside the hole was a microscopic creature, attached by its head to the shell and waving six tiny legs.  Darwin was fascinated, knowing that it is a barnacle, but without a shell. It has never been described by any naturalist before.  He was a disciplined taxonomist and organized the chaotic nomenclature of this organism, numbering over 1000 species, which were often misnamed during his time. Upon his return to England and immediately after writing his ideas on natural selection, at great expense to his health, he began his day and night obsession with barnacles that lasted for 8 years (1846-1854) cataloguing the collection from his voyage and from the hundreds more sent to him by mail from around the world . 

What drove this passion about such a mundane organism?  Perhaps a clue comes from the earlier anonymous publication of a controversial, incendiary, speculative book, Vestiges of the Natural History of Creation (later confirmed to be the work of Robert Chambers, a Scottish medical journalist).   Widely panned and mocked for its evolutionary ideas even by Darwin’s friends, the failure of the book was a great personal disappointment because Darwin expected the same response to his own ideas in his theory lying inside his desk drawer.  Even his best friend, the noted botanist Joseph Hooker wrote, “no one has the right to examine the origin of species who has not minutely described many.”  Perhaps, one reason for this obsession was indeed to “minutely observe a distinct part of the natural world and in so doing earn his right to question their origins.” 

Whatever the reason might be, Darwin started us all on a path of research towards understanding barnacle biology and the commercial opportunities that follow in its wake.  As for me, at least I have someone else to blame now for my current obsession with barnacles — Charles Robert Darwin.”

–Jonathan R. Matias,    Poseidon Sciences

Excerpted from:  Poseidon Marine Sciences News, Subsea testing

Also, read the book Darwin and the Barnacle by Rebecca Stott.  It is an engrossing story of Darwin’s passion for barnacles and the mystery of Darwin’s 20-year wait to publish his theory.

Rip Van Winkle, Hibernating Fish and Malaria Control

Annual killifish male and embryos in peat

When I think of hibernation, my first thought is my high school English literature class on Washington Irving’s tale of a Dutch settler named Rip Van Winkle.  The story’s setting is New York’s Catskills Mountains during the American Revolutionary period.  In this tale, Rip Van Winkle was a fun-loving, lazy, henpecked husband who escaped his nagging wife by running to the mountains where he encountered strange men playing nine pins.  After drinking their liquor, he fell asleep under a shady tree.  Rip returned to his village after waking up only to find out that 20 years had passed and America was a already a new republic.  Many of us would wish we can do just that when times are rough and wake up later when times are better.

Irving’s story of Rip Van Winkle was likely influenced by ancient folklores in Orkney (Scotland) where a drunken fiddler find trolls having a party, plays music with them for two hours and goes home  to find that 50 years had passed.  But there are even more older tales of a similar nature around the world, such as the German folktale of Peter Klaus, of Niamh and Oisin in Ireland, the ancient Jewish tale of Honi M’agel, the Chinese story of Ranka in 3rd century AD, the 8th century Japanese tale of Urashima Taro and the story of the Seven Sages by Diogenes Laertius of the 3rd century.  The Seven Sleepers of Ephesus tells of Christians escaping Roman persecution by sleeping in a cave to awaken after a century to a new world wherein Christianity became the new religion of the Roman Empire. 

As there are numerous variations of the hibernation theme in the literature, there are even more variations of hibernation in the natural world.  Insects do it all the time; as do seeds of plants.  Tiny invertebrates, like the tardigrade, remain in hibernation for over a hundred years in a dry state and ‘reawaken’ when exposed to water.  As long as it is hibernating, the tardigrade can withstand extremes of pressure, temperature, desiccation and low oxygen.  Artemia cysts, commonly known as brine shrimp eggs that hobbyists hatch to feed fish fry, behave like that too.  They remain hibernating in a dry state and re-animate when placed in salt water, becoming the “sea monkeys” that most of us remember as a child.   Other mammals do it too.  Female kangaroos, bears and badgers can delay the implantation of the embryo by inducing reversible developmental arrest to postpone the period of birthing until months later when food is plentiful.  Just like Rip Van Winkle, these animals escape inhospitable conditions by escaping in time.

Diapause (from the Greek dia meaning between and pauein meaning to stop), suspended animation, aestivation, hibernation and crytobiosis (hidden life) are terms that evoke images of a long, but temporary sleep.  For most organisms that are unable to physically move away, it is their only means of surviving harsh environmental conditions until the next more favorable season.  Even now, the science of suspended animation is advancing far beyond insects and arthropods.  Non-injurious suspended animation can be induced in mice for a short time by replacing the oxygen in the air it breathes with hydrogen sulfide.  The long term medical potential in human terms is delaying trauma from injury until more favorable medical interventions can be applied.

Where does fish come into this?  First, let me tell you a story of my own fascination with one unusual class of tropical fish that do exactly the same.  They are called annual killifish (from the Dutch word kill meaning small stream). They thrive only in seasonal pools that evaporate totally during the dry season.  When the rains come the following year, or even five years later, the fish population returns again to re-populate the pond.  They are not the lungfish that most of us might be familiar with.  Lungfish ‘aestivate’ in mud chambers they create before the pond dries up.  They continue breathing air through a hole on top of the moist chamber while at the same time reducing their metabolism.  Annual fish are unique because they can completely stop at three specific diapause stages of their normal embryonic development.  They escape in time by near zero metabolism and complete cessation of embryonic development.  Though not as extremophile as the tardigrade, the diapause stages of the annual killifish are more resistant than non-diapause stages to extreme conditions in their environment

My first introduction to this fish was during the 1970’s in the laboratory of Jules Markofsky, who at the time was studying the annual killifish, Nothobranchius guentheri, for aging research at the Orentreich Foundation.  Annual killifish live for about one year.  Some species even have life spans as short as 4 months.  Compare that to the guppy that can live as long as five years and the mouse or rat for about 4 years.  Back then, so little is known about the biology of the killifish that we were unable to get enough embryos to hatch synchronously to do aging research. In fact, we sought help from the Long Island Killifish Association, an esoteric and dedicated group of hobbyists that maintain such rare fish in captivity.  It was such a fascinating group that I, too, joined the Club.

Fish hobbyists know more about these unique and colorful killifish.  And, there are dozens of such specialized clubs in US and Europe.  In fact, one does not need to go to the jungle to find most of these species.  Just meet with any one of the killifish hobbyists who can share some diapause eggs.  Hobbyists continue to brave malarial mosquitoes and wild animals, even animals of the two-legged kind, to bring back live specimens from Africa and South America that are then bred in aquarium tanks.  While environmental degradation and man-made land alterations likely have doomed scores of native populations, much of the species known today exist in the aquarium hobby.

After 25 years studying diapause in N. guentheri, combined with the work of other scientists/ hobbyists, I began to have a better idea of the environmental cues that trigger the onset and termination of diapause.  The day-night cycle, temperature, humidity and maternal cues that influence the development of diapausing states in silkworm, for example, are the same in killifish—an unique example of convergent evolution. 

How about malaria?  Curiously, the geographic range of malarial mosquitoes and annual killifish in Africa and South America overlap.  George Myers, a noted ichthyologist of his time, in the 1950’s first observed reduced incidence of mosquito bites in areas populated by killifish.  Since then Richard Haas, Rudd Wildekamp, Jules Markofsky and I have proposed at various times in the last 30 years to use this fish for mosquito control.  Since most countries have a few native species of annual killifish, we can even keep the environmentalists happy since we don’t need to introduce any exotic fish to do this.  The local ones will do just as well.  All we need is to grow and distribute a lot of them around. 

The tribesmen in the sub-Sahara Africa already use annual killifish in freshwater storage containers and wells.  Hobbyists already know that ‘killies’ are larvivorous.  Yet, common anecdotal knowledge is not enough to push regulators and funding agencies to use this fish for mosquito control.  Recently, the publication in the online journal Parasites & Vectors finally verified the anecdotal evidence by methodically demonstrating the feasibility of using killifish as mosquito control agents.  In this paper, the embryos in the pre-hatching hibernating state were transported in moist peat moss and dropped in temporary ponds where they hatched, consuming all the mosquito larvae.

Although conventional larvivorous fishes have been used to rid mosquitoes in ponds as far back as the building of the Panama Canal, their use had been limited to more permanent waters.  Fish predators, like Gambusia, work great on abandoned swimming pools after hurricanes, for example.  But this fish has wrought havoc in many ecosystems because of their prolific and voracious nature.  Transporting even native conventional live fish to remote areas is a big hassle.  With only dirt roads and footpaths available to reach rain pools, mining pits and similar transient pools, transport by water trucks is just not practical. 

Now we have a transportable fish in a bag.  Instead of a water truck, a backpack is enough to carry a million diapausing killifish eggs!  Sort of like Johnny Appleseed, another American legend, bringing bags of eggs instead of bags of apple seeds. 

The idea of the ‘instant fish’ is nothing new.  It’s been tried unsuccessfully a few times as a business.  What’s new is taking this technology to a more useful purpose.

How can we transform this idea of “instant fish in a backpack” into something practical for malaria control in the future?  Stay tuned to my next blog when I get re-animated again.

— Jonathan R. Matias

Suggested reading:

Annual fish biology

mosquito control