Royal Lessons for Scientific Discovery

rdeyes-2This Summer I had the chance to travel to Isle Royale (‘Royal Island’) in Lake Superior for what was a trip that would challenge me in more ways than one.  Our group, comprising 3 adults and 5 boys, drove up to Copper Harbor in the Michigan Upper Peninsula and then made the four hour ferry crossing to the Isle Royale National Park.   We spent the next 6 days hiking across the island, covering a total of 50 miles with backpacks and tents weighing us down every step of the way.

The sights were fantastic, the weather tremendous and the sheer thrill of being unreachable by text, email or phone thoroughly satisfying to say the least.  But, like any adventure of this nature, there was an element of fear that accompanied the trip.  What if anyone got hurt on the island?  How would we handle losing all our food if critters raided our camp during the night?  Might someone get seriously sick on the ferry crossing?  Had we brought enough food to keep us healthy while not overloading our back packs with unnecessary weight that would hinder our progress?  What if our portable water filters got clogged up? Continue reading “Royal Lessons for Scientific Discovery”

Because Timing Is Everything….

Camp Indian Trails Morning Flag CeremonyTiming is everything! I learned that the hard way just two weeks ago when I took my son to scout camp and thought I would try to capture the traditional American flag ceremony for posterity. I set up my camera for a panoramic shot and scanned the crowd.  Feeling very pleased with myself, I got home that evening ready to show my family the great camera skills I had honed over the Summer months. To my horror, I noticed that half of the scout troop was saluting the flag while the other half were standing to attention! I had got the timing horribly wrong (although the picture is still fun to look at in a strange sort of way).

Timing is everything in science as well.  As a technical services scientist at Promega I have sung the ‘timing’ tune to many a biologist. No more so than in the study of apoptosis where Caspases activate each other in a choreographed cascade of molecular triggers that all have their place and time in a domino sequence of enzymatic cleavage events. I frequently talk to researchers about that ‘sweet spot’ of activity when any given Caspase is busily cleaving a peptide moiety off of the next Caspase in the sequence. Finding that sweet spot is anything but trivial and often requires a considerable amount of patience during the optimization phase of experimentation.

Promega has developed a comprehensive suite of systems (see here) designed to help get the timing right for the cell and compound combinations you might be working with.  The end result is that you have experiments that are timed so as to give you reliable information about what is really happening in your cells.

Grays On the Move: Whale Watching in San Diego

As a boy, one of my favorite childhood books was without a doubt, Herman Melville’s Moby Dick. For those not familiar with the story, it tells of the obsessive quest of one Captain Ahab to kill a white whale in revenge for an attack that left him with a severed leg. The story is told by the character Ishamel who accompanies Ahab and provides the reader with a front row seat on the doomed saga of Ahab and his crew. After reading the book, I set myself the task of learning more about whales and how we can do more to protect the lives of these magnificent ‘leviathans of the deep’. My parents bought me Jacques Cousteau’s Whales one Christmas. From that moment on, my heart and mind were transfixed. This year I was privileged to see Gray whales for the first time, following their migratory path down the west coast of the United States. Together with a handful of other excited tourists, I went on a 3 hour cruise outside of San Diego bay, organized by the Scripps Institute Birch Aquarium. Below are several of the many pictures I took on that memorable day.

All Aboard Skipper!
All Aboard Skipper!

Continue reading “Grays On the Move: Whale Watching in San Diego”

The Makings Of A Cerebral Music Decoder

A Review Of Daniel Levitin’s This Is Your Brain On Music

ISBN: 978-0-452-28852-2

Physicist Emerson Pugh once quipped, “if the human brain were so simple that we could understand it, we would be so simple that we couldn’t” [1]. In his book This Is Your Brain On Music neuroscientist Daniel Levitin notes how the number of ways that brain neurons can connect is so vast that we will never fully comprehend all the thought processes that we are capable of.

In recent years, mapping techniques have revealed a lot about the functional regions of the brain. Wernicke’s area is responsible for language processing, the motor cortex for physical movement and frontal lobes for generating personalities. Both encephalography and MRI have given us key spatial-temporal data about brain function in these regions. But we also find that activities such as listening to music contravene such a simplistic compartmentalization.

In fact the perception of pitch, tempo, the emotions invoked by a piece of music and the lyrics of a song all use different parts of the brain albeit simultaneously. Levitin repeatedly emphasizes the multi-faceted aspects of the music ‘experience’ noting how a, “precision choreography of neurochemical release and uptake” leads to our appreciation of music. The brain is thus a massively parallel device, capable of carrying out several different tasks at once.

Continue reading “The Makings Of A Cerebral Music Decoder”

Where Mycologists Go To Church On Sundays

When it comes to academic triumphs and laudatory honors it can be said that mycologist Paul Stamets has his fair share. Stamets has authored six books on mushrooms, holds over twenty patents, is a winner of the Collective Heritage Institute’s Bioneers Award. Today he also runs a facility that boasts twenty four laminar flow benches across four laboratories processing between 10-20 thousand kilos of mycelia each week. He has close to a thousand mycelium cultures growing at any given time and is renowned across the world for his view of fungi as the ‘grand molecular dissemblers of nature’. And so it was that the Biopharmaceutical Technology Center was pleased to host a lecture by Stamets almost two years ago with the promissory title: How Mushrooms Can Save the World. Continue reading “Where Mycologists Go To Church On Sundays”

Rob Mies: Lessons From A Real Life ‘Bat Man’

On a blustery, frigidly cold day in mid-April, a small gathering of cub scouts from one of several local packs congregated outside the Lussier Heritage Center on the southern end of Madison for the annual bat festival. They had braved the elements to see these furry creatures, perhaps for the first time in their lives, and to put aside the myth that they are little more than Transylvanian-born vampiric vermin. The cub scouts had come to hear the experts talk. And there could have been no better person for the job of getting the education process started than conservationist Rob Mies- indisputably the star of this year’s bat show.

Continue reading “Rob Mies: Lessons From A Real Life ‘Bat Man’”

The Living Microarray: The ‘Coming Of Age’ Of Transcription Profiling

American artist Andrew Leicester has made a bit of a name for himself at Iowa State University by incorporating his art into the architectural design of the University’s Molecular Biology Building. Leicester’s much heralded G-Nome Project represents his attempt to evince the benefits and threats of genetic engineering to society, through sculpture and mosaic (1). I chanced upon Leicester’s art five years ago as an instructor at a Promega/Corning collaborative workshop in Iowa on the applicability of microarrays in transcription profiling. The workshop aimed to bring Promega’s cDNA synthesis chemistries and Corning’s cutting-edge UltraGAPS slide technologies to the attention of a small group of ebullient young scientists with a broad spectrum of research backgrounds. The floor of the atrium right outside our teaching room showcased Leicester’s ‘Novel Agents’ mosaic, incorporating a super-genetic monster as a warning of the potential perils of genetic manipulation.

Microarray results from the Iowa workshop gave us only endpoint data for the experimental conditions we were studying.

Fortunately for us, the ever-prolific genomics era seems not to have spawned the terrors that Leicester depicted in his art (at least nothing as singularly destructive as a super-genetic monster). To be sure, genetic research is playing its role in the development of novel pharmaceuticals for today’s most challenging diseases.  One can be similarly upbeat about the world of transcription profiling. Microarrays have come a long way since the days of self printing on a slide for single time point analysis.  Continue reading “The Living Microarray: The ‘Coming Of Age’ Of Transcription Profiling”

Metal Eaters Propel The Demise Of The Titanic

Shipwreck porthole.

Oceanographer Robert Ballard’s literary showpiece The Discovery Of The Titanic today sits on a shelf in my bedroom collecting dust.  Gone are the days when it was heavily leafed through by relatives and close friends mesmerized as they were by the glossy pictures and personal accounts of disaster contained within its covers.  I had dismissed from mind images of the Titanic’s Captain Edward Smith and Marconi wireless operators Jack Phillips and Harold Bride that accompany the chilling story of the fateful night.  I had forgotten about Ballard’s detailed chronicling of the turbulent expeditions that led to the eventual finding of the Titanic more than 70 years later.  And I had put aside my fascination for the flagship submersible Argo that in 1985 had scoured the Atlantic at 13,000 feet below sea level until it finally met up with the eerie wreck of the luxury liner.   But my interest in the book has recently been revived by the molecular characterization of a fastidious strain of bacteria that is “speeding up the decay of the historic wreck” (1).

When Ballard wrote his book over 25 years ago, biologists had already advanced the idea that micro-organisms were breaking down the iron cladding of the Titanic.  His description of some of the first shuddersome glimpses of the ship’s contours give us an inkling of what was known at the time:

“As we rose in slow motion up the ghostly wall of the port bow, our running lights reflected off the still-unbroken glass of portholes in a way that made me think of cats’ eyes gleaming in the dark.  In places, the rust about them formed eyelashes, sometimes tears.  As though the Titanic were weeping over her fate.  Near the upper railing- still largely intact- reddish –brown stalactites of rust hung down as much as several feet, looking like long needle-like icicles.  This phenomenon, the result of iron-eating bacteria, was well known, but never had they been seen on such a massive scale.  I subsequently dubbed them “rusticles”-  a name which seems to have stuck” (2).

Now a joint effort from scientists in Spain and Canada has uncovered the DNA signature of one of a handful of bacterial agents that lie at the heart of the rusticle phenomenon. By removing stalactite pieces from the hull of the Titanic and performing a battery of elucidative phenotypic and chemotaxonomic tests, Christina Sanchez-Porro and others have homed in on the true identity of one salt-loving microbial wreck heister called Halomonas titanicae (3).

H.titanicae, dubbed BH1, is part of a larger family of bacteria that until now had never been observed so deep below the ocean surface.  It uses iron as an inorganic source of energy, oxidizing it and leaving rust behind as a waste product.  For many of the 27 bacterial strains now known to live in the rusticles, the deep sea conditions are not sufficiently acidic for growth (2).  They get around this by manufacturing a more favorable dwelling of “highly viscous slime” that encapsulates them away from seawater and gives them an acidic habitat in which to flourish (2).   But bacteria are not the only organisms feasting on the spoils of this particular maritime tragedy.  Wood-borers have all but decimated much of the exquisite woodwork in the ship’s interior although the high density teak wood found in many of the railings, staircases and roof trims has proven to be remarkably unyielding to these voracious assailants (2).      

Opinions differ over whether the havoc that bacteria such as BH1 are wreaking should be left to continue unabated (1)   Ontario Science Center biologist Bhavleen Kaur believes that the bacterial goings-on aboard the Titanic could be used to help us better understand and halt the breakdown of other manmade sea structures such as offshore oil rigs and gas pipelines (1,4,5).  Microbial ‘iron munching’ might even find application in recycling and disposal workflows (5).  Some heritage devotees are less than happy about such proposals preferring instead to promote efforts to halt H.titanicae in its tracks and preserve the wreck for posterity.

Bollard Titanic Book

While perhaps desirable, going head-to-head with nature’s forces seems impracticable given the sheer speed at which the wreck is succumbing to bacterial breakdown.  Canadian civil engineer Henrietta Mann posited that twenty years from now there may be little more than a “rust stain on the bottom of the Atlantic” marking the location where the Titanic’s shadowy grave once lay (4,5).  It is a sobering thought that such a fate should befall what was once a 50,000 ton steel leviathan of a ship (5).  Extensive video footage and photographs may soon become the only means we have by which to remember the Titanic’s “very human story” (4,5).

Further Reading

  1. Rachel Kaufman (2010) New Bacteria Found On Titanic; Eats Metal, National Geographic News, December 10th, 2010, See
  2. Robert Ballard (1984) The Discovery Of The Titanic: Exploring The Greatest Of All Lost Ships, Madison Press Books, Toronto, ON, p.116, p.208
  3. Sánchez-Porro C, Kaur B, Mann H, & Ventosa A (2010). Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic. International journal of systematic and evolutionary microbiology, 60 (Pt 12), 2768-74 PMID: 20061494
  4. Graham Smith (2011) First it was an iceberg, now it’s bacteria: Rust-eating species ‘will destroy wreck of Titanic within 20 years’, Daily Mail, 12th January, 2011, See
  5. Rosella Lorenzi (2010) Titanic Being Eaten By Destructive Bacteria, Discovery News, 7th December, 2010, See

Running A Victory Lap For Promega’s Bioluminescence Technologies

Helping scientists design experiments and interpret data is what we do best at Promega Technical Services. This may mean spending time at the bench attempting to reproduce anomalous results or forming a team, perhaps with members of other departments, to brainstorm seemingly intractable experimental road blocks.  Still, for many of us nothing surpasses the experience of meeting these same scientists face to face whether it be on their home turf or at a booth during a tradeshow. PCArticle Continue reading “Running A Victory Lap For Promega’s Bioluminescence Technologies”

Getting Our Hands Into Some Good Ol’ Home Science

static_detection-simple_electroscopeFor many, this time of year brings with it the opportunity to enjoy a bit of holiday fun with kids. In fact just recently I had the chance to spend a day doing several home science activities with my four- and seven-year old boys. All were simple to set up using commonly found household items in a way that was both instructive and rewarding. Continue reading “Getting Our Hands Into Some Good Ol’ Home Science”