Science Wednesday

Time for science in the time of pandemic

Of the challenges that face us during this pandemic, balancing a full time job with young children at home has to be right up there on the difficult list. Listening to my friends and colleagues, bravely managing that tight-rope act, I looked for something I could do to help.  I remembered an idea that arose out of frustration over the thin science in our sons’ elementary curriculum – Science Wednesday.  We did small scale science projects at home on Wednesdays, after school.  Little experiments and kitchen sink inquiries designed to spark my sons’ interest and get them thinking about the natural world around them. I dug through an old hard drive and, miraculously found the ideas and notes for it, recorded way back.

The Zoom session

With the help of my friend, Beth Wilbur, we put together a rough plan. We’d invite the children of our friends, colleagues, and family to join us, once a week (on Wednesday mornings) for a live Zoom session.  During that time, we’d review their results from the previous week and introduce the next activity to come. We’d begin with the experiments I’d used in the past, since I knew they were do-able and didn’t require fancy tools. As a test, Beth and I ran the experiments ourselves, taking notes on potential problems and photos to document our results. We came up with a template for a “Grown-up Guide” (for the parents), which included a list of required items, an outline of the plan, and a few guidance photos for each experiment.

Once we were confident we had two, easy-to-reproduce experiments, we started outreach. Very quickly, our “class” size numbered over ten – enough to get started. It was gratifying to hear the parents’ response to the idea – a bit of excitement, mixed in with a large portion of relief.

The group consisted of ages ranging from 5 to 13. Quite the spread and quite the challenge. After the first two sessions (“Water Transport in Celery” and “The Naked Egg”), it became clear that, if we aimed for the 8-10 year olds, the older kids would figure out their own extensions and adaptations, while the younger kids were happy to come along for the ride.

Two weeks into things, with 20 kids signed up, I decided to reach out to my biology-teacher friends. After all, they could do a much better job than I ever could and they’d have even more creative ideas. My request came right at the time most of them were trying to figure out how to teach their own classes online, so I kept the ask to just one session and I’d manage all the technology, handouts, and communication. Biology educators are the most generous souls and this was no exception. Soon we had a group of some of the best high school, AP, and college biology teachers in the country thinking about at-home experiments the kids could try. Here’s our star-studded line-up:

• Nancy Monson, Opposable Thumbs (How your hand works)
• Eric J. Simon, Amazing Red Cabbage Juice (pH)
• Peggy O’Neill Skinner, Seed Germination (A closer look at beans)
• Diane Sweeney, The Blubber Glove (Hot or Not?)
• Brad Williamson, Marine Microfossils (from Iowa!)
• Carol Williamson, Pollinators in Your Backyard
• Alyssa Wood, Penny Dirt (Copper oxide and malachite)

The kids were terrific and their results impressive. With each experiment, they caught onto the question and came up with their own answers, often extending their effort to include artful drawings, short video clips of their observations, and added investigations into something new that occurred to them. For example, a few of the kids planted the seedlings they sprouted on damp paper towels and then proceeded to watch them grow over weeks. They brought new tools to the table – digital thermometers, ziplock bags, flashlights, new ways to label, and methods to align a small magnifying glass to their iPhones in order to get a better look at the microfossils. Click on the photo gallery below to see these young scientists at work!

 

Working without your thumb

Digital thermometers to confirm precise temperature

A flash light to reveal the insides of a “naked” egg

Ziplock bags to hold the blubber

Magnifying glass taped to a camera lens for finding microfossils

Marine microfossils discovered

Labeling each experimental condition with the object in question

Using a window for labeling and light

Measuring water transport in celery

Pennies tallied

Alyssa’s diagram of penny dirt

Modeling the human hand

 

Eric J. Simon

The educators were pretty darned creative too.  Not only did they devise fabulous inquiry ideas, but they experimented themselves and found refinements or adaptations that saved time-pressed parents from extra trips to the grocery store. Their educator superpowers were on prime display and each week I’d be impressed all over again by a new innovation or a creative way to inspire enthusiasm from a Zoom window.  Carol Williamson encouraged the kids to hold up their pollinator grid to the camera if they had something they wanted to share. Peggy Skinner suggested taping their seed germination bags to the wall, at eye-level, so that they could easily

Alyssa Wood

check in on progress each day. Eric Simon drew acid-base analogies that brought home the concept of pH. Brad Williamson tickled their imagination by showing the original site of the marine microfossils samples we sent to them by mail – in Iowa!  Alyssa Wood brought home the concept of penny dirt (aka copper oxide) and brilliant blue malachite by showing photos of the statue of liberty and wearing a lady

Peggy O’Neill Skinner

liberty head dress during the Zoom session. Nancy Monson upped their investment in the question of opposable thumbs by showing delightful photos of chimpanzees, pandas, and possums. Carol Williamson urged the kids to explore gardens, playgrounds and nearby parks looking for pollinators and then document what they found.

We decided to end the sessions with the arrival of summer – always better to leave them wanting more, right? A few good lesson emerged from all of this:

• Keep the live sessions short and punchy (attention spans and enough Zoom already…)
• It was helpful to begin each session the same way, with a familiar patter, and a map with red stars to indicate where in the world the students lived (Luca lives in Sweden!)
• Activities with an end-product seem to foster creative flourishes (those models of the human hand!)
• It’s helpful to have a few experiments that continue, beyond a week (e.g. germinating seeds) to give the students headroom for more exploration
• Even though the plan here was to give parents a break, most of the parents stayed nearby during the Zoom sessions and got involved in the investigations themselves, which only added richness
• Flexibility was key – you can’t get your hands on dried beans? No problem, try pumpkin or sunflower seeds!  No white vinegar in the house? Cider vinegar will work!
• It took kids awhile to warm up to speaking in the Zoom sessions, but by the end, they all wanted to share and many of them brought other, related items to show to the teachers and to each other

And can I just say again how fabulously creative these teachers are?  I’ve had the good fortune to work with biology educators for my entire professional career and they never cease to amaze me.

Thanks, everyone.  That was fun.

Meet Homo naledi

Homo naledi skull replica.

Sixty biologists in a New Orleans hotel conference room with a paleoanthropologist, a replica of an early hominin skull, and a revised story of our human ancestry?  Does it get any better than that?

John Hawks at BLC 13

Last week, Dr. John Hawks (University of Wisconsin-Madison) gave the keynote address at the 13th annual Biology Leadership Conference in New Orleans, LA. Hawks is part of the team that, in 2013, discovered the bones of a previously unidentified hominin species in a South African cave. The name of the new species, Homo naledi, refers to the Rising Star cave where the bones were found (“naledi” means “star” in the local Sethoso language).

Among his other academic qualifications, Hawks is a mighty good storyteller. He held us spellbound with the Rising Star story… It started in 2013 with two local cavers who, under the guidance of Lee Berger (from the University of Witwatersrand and the principal investigator on the Rising Star project), were systematically exploring caves in an area know as the “Cradle of Humankind“, a UNESCO World heritage site about 30 miles northwest of Johannesburg, South Africa. Deep underground, they found a narrow opening (7.5 inches wide) that led to the chamber where the bones were found. They snapped a few pictures, took them to Berger, who immediately recognized the importance of the find when he could see a skull and a mandible that were clearly hominin.

We know that living apes, chimpanzees and humans are close relatives to each other, with nearly identical genomes, but we humans are even more closely related to Australopithecus and other extinct human ancestors. Researchers know that the evolutionary lineage leading to humans diverged from the other apes somewhere around 6 or 7 million years ago. The species in that diverged group are collectively referred to as hominins, a group consisting of modern humans, extinct human species, and our immediate ancestors.

The path to the chamber. (source: National Geographic)

Looking at that photo of a clearly hominin specimen and listening to the cavers’ description of where they found it, Lee was faced with the difficult question of how to get in there and, even more of a challenge, how to get the bones out? Getting to the spot requires a 150-foot initial descent, a “superman crawl” through a 10″ high tunnel (so named because you have to navigate it with one arm up in order to squeeze through), then a steep climb up a stone wall (called the Dragon’s Back), followed by a descent through a 7.5 inch wide, 40 foot-long vertical chute into the chamber – and all done in the absence of natural light, without a safety harness (there’s no room!).

Underground astronauts (source: National Geographic)

Berger knew that he would need a very special team to pull this off. So, in October 2013, he posted a request on Facebook, calling for experienced paleontologist/archeologists with caving experience who were not claustrophobic, who could drop everything and come to South Africa for a few months, and who were small enough to fit through a 7.5 inch tunnel. Quite the list of specific job requirements! He received 57 applicants – all qualified – and from there, he picked six. The so-called “underground astronauts” pictured here. All women. All experienced professionals. And all able to wriggle their way through that narrow chute.

On the strength of their find, the scientists reached out to the National Geographic Society and the expedition was on. By November, a 60-person camp was set up and running by the Rising Star Cave.

Photo by Elen Feuerriegel.

And down they went. What is it like to work inside this cave? Hawks described cramped and claustrophobic conditions, razor-sharp rocks, dust, darkness, and a tangled mass of cables and cords with which the team has wired the site. Have a look at this National Geographic video to get a feel for getting into the chamber. The careful removal of 100’s of bones must be done while documenting their found-placement, all the while gingerly maneuvering so as not to disturb the site. The expedition’s National Geographic blog site gives a feeling for the work with stories aplenty recounting their day-to-day challenges and showcasing the teams impressive problem solving. I’m particularly fond of this award-winning photo, taken by Elen Feuerriegel (one of the astronauts) showing the scanning set up inside the cave. Before excavating, each area is carefully scanned to create a 3D-rendered image for reference. In this photo, Lindsay Eaves monitors the scanner on a laptop, while precariously perched in a fissure while her colleague, Becca Peixotto, operates the scanner, off-camera to the right.

Over the course of the first 20 days the astronauts pulled up 1200 specimens from 15 individual skeletons – painstakingly, carefully, piece by piece.  To put this into perspective, finding one complete skeleton of a previously unidentified hominin would be miraculous; to find 15 is simply unheard of. Before the Rising Star expedition, the only early hominins we had were Lucy (40% of an Australopithicus skeleton), Turkana boy and one skeleton of Australopithicus sediba (also found by Lee Berger) – that was it. The skeletal record of human ancestry. With this first find (and they’re still digging) they have one complete skeleton (except for two small bones) and multiple copies of most all of the bones. They have 107 foot elements, 190 teeth, 150 wrist and hand elements, skulls, mandibles, limb bones.  What’s more, they appear to have remains from a variety of individuals – male, female, toddlers, adolescents, and older individuals (old = 35 years).

So what have they learned about the specimens so far?  From the remains the scientists can estimate that an adult H.naledi was about four and a half feet tall, roughly 80 – 110 lbs in weight. There are aspects of H. naledi that are very human-like. For instance, they have human-sized teeth, human-proportioned limbs and arched feet (making it possible to be a good long distance walker), and human-like wrist anatomy. But they also have many important ape-like qualities like curved fingers for grasping, shoulders built for overhead reach and climbing, a flared pelvis, and most notably very small skulls (an H. naledi brain would be one-third the size of a modern human brain) with a forward-sloping face.

Artist’s rendering of Homo naledi (source: National Geographic)

Who is this creature? Could these fossil remains actually be a variety of species whose bones were jumbled up together in the same cave? The team quickly dismissed that idea since the various copies of any single bone were all the same. These specimens all have what Hawks refers to as a ‘mosaic of features’ from Australopithicus and Homid. In the same way that A. sediba (Berger’s earlier find) does. But here’s the thing – both naledi and sediba are mosaics, but they are different mosaics. Each has a different combination of australopith-like traits and human-like traits.

Where does H. naledi fall in the phylogeny? Is this an early human ancestor? Or could this be the last of a more primitive creature who was living among more modern humans? Maybe there is more diversity to the homo family tree than scientists thought?  Maybe there are other fossils out there, with still other variations, that would even further complicate our family tree?

What makes this puzzle even more challenging is they have not yet been able to date the H.naledi remains. Are they 3 million years old or 30,000 years old? Typically paleoanthropologists position their finds in time by dating the surrounding rock or by dating faunal remains found with the specimens. In this case, there are no other faunal remains and the bones were found lying on the sediment surface, not embedded in rock. Not only that, the sediment can’t be dated because all the sediment in the cave came from the cave – there are no markers. Hawks explained that they might be able to obtain age estimations from dental enamel. They’ve also earmarked some of the bones for destruction in order to perform radiocarbon dating on them. Within a few months, Hawks says, they will have that data.

The Rising Star team has been extremely open with their findings. Scientists from all over the world have been invited to examine the fossils, their first article was published in the open access journal eLife, and the 3D printing files for 96 fossil specimens are openly shared on Morphosource, allowing anyone with access to a 3D printer to create their own H. Naledi fossil. The October issue of the National Geographic magazine is a great place to read the whole story and delight in the images.

Hawks closed his wonderful talk with a question for us to consider…what interpretation can we make of the placement of these bones?  Why were they all together like this, without any other faunal remains, far beneath the earth’s surface, in a single cave chamber? Hawks assured us that they were not washed there by water. There are no marks on the bones that would indicate they were dragged there by an animal to be eaten. There is no debris in the cave that might suggest the creatures were living there. There are no other remains from other creatures. Could this be a burial chamber? Maybe living H. naledi took their dead to the cave’s opening and dropped them in? Was there a ritual involved, which would imply a culture and social behavior not typically associated with such a small-sized brain?

Clearly much remains to be discovered in the Rising Star cave. More bones to be found, timelines to be established, and meaning to be made. It was that very spirit of discovery and “not-knowingness” that struck me the most in Dr. Hawk’s talk. I lost track of how many times he said “We just don’t know…” during the 90 minutes he spent with us and what could be more inspiring than that?  Even more exciting, it appears that we don’t even know what we thought we knew.

A Closer Look at a Caffeine Story

Coffea canephora. Bali – Indonesia – July 2007 – Guy Sabattier

Like many people around the world, I begin my every morning with a rather large cup of coffee. Caffeine – found in coffee, tea, mate, and chocolate – is the most widely consumed psychoactive substance in the world. So it was with great interest that I greeted the news, published in Science on Thursday last week, that an international team of scientists has sequenced the genome of the coffee plant, Coffea canephora.

Molecular structure of caffeine.

Getting inside the coffee plant’s genome provides a biochemical view into the mechanism for creating caffeine (start with xanthosine, shave a bit off here, add a bit there and – voila – caffeine).  But here’s the really interesting part – the coffee plant and the cacao plant produce caffeine in different ways. In other words, the biochemical pathway for producing this important molecule evolved more than once. Different evolutionary paths to the same end point. Biologists call this phenomenon convergent evolution. The independent evolution of similar features in different lineages (think wings in birds and bats, the camera eye in vertebrates and octopuses, the ability to glide in flying squirrels and sugar gliders). When this happens, it’s a good indication that the evolved adaptation is pretty useful. And, indeed, caffeine is a very useful molecule for these plants – it helps to ward off enemies, to attract pollinators (and keep them coming back for more), makes the soil immediately surrounding the plant inhospitable to competing plants, and it deters leaf-eating pests. For the rest of us, it provides that much-needed kick-in-the-pants each morning.

As excited as I was about this story, I was quite taken with the way different news groups elected to cover it:

Here’s the New York Times article:

Here’s the Washington Post article:

Washington Post.

And here is Fox News coverage:

Fox News.

The thrust of the WaPo and Fox coverage is on the “mutation”, the possibilities for manipulation, and the slightly shadow-ey (the “quirk”) scariness of what might come next – genetically modified coffee??

It’s startling to see how few of the primary news channels covered what was most interesting about this finding. Namely, the intensely interesting evolution story and the way genomic tools help scientists solve problems and understand the mechanisms of life.  Only Carl Zimmer, that noteworthy NYT Science journalist, included a clear and helpful description of the evolution element in his story. Sidebar: note the illustration choices in the three articles – the cup of coffee, the barista’s product. The New York Times at least shows the coffee beans but not a one of them show the actual plant, let alone the plant in its environment.  How we report the news – the headline, the image, the story – these are all vital ingredients that help shape public perception and our attitudes toward science.

 

 

What Happened to the Passenger Pigeon?

Passenger Pigeons. Photo by Todd McGrain

I just picked up Joel Greenberg’s A Feathered River Across the Sky:  The Passenger Pigeon’s Flight to Extinction.  What a terrific read.  I had no idea how abundant this bird was – apparently, the most numerous bird species in North America (and possibly the world) in the 1800’s.  Get this:  In 1813 John Audubon saw a flock that took three days to pass overhead! Witnesses frequently described the birds in quasi-Biblical terms. In their wake, passenger pigeons often left behind ravaged fields, broken limbs (too many of them roosting on one branch), and feet-thick coatings of their droppings.  According to Lake County, Illinois records, “they flew in flocks that darkened the sun.” A single nesting ground in Wisconsin was reported to cover 850 square miles. Such abundance meant for happy hunting. You see where this is going….  By the turn of the century, the species was extinct. There was a captive pair at the Cincinnati zoo – the female of which (the last living member of the species) died in 1914. The publication of Greenberg’s book is timed with the 100 year anniversary.

Greenberg tells the story well. He puts the extinction in its cultural context and writes with great insight about the bird’s natural history (Greenberg is a naturalist and the author of the bird blog, Birdzilla).  The short answer as to why the passenger pigeon went extinct is that it tasted good and was easy to kill.  Of course, Americans got better and better at killing the birds with efficient methods and when you combined that with destruction of the bird’s natural habitat through the logging industry…

One element I loved about the story is the way that, long after the species was extinct, people kept reporting sightings of them and coming up with crazy explanations to explain their reduced numbers – they were in the southwest desert, they migrated to South America, they had all drowned in the Pacific Ocean, or they were hanging out offshore (just out of sight).  As Greenberg suggests, maybe the human role in the pigeon’s extinction was just too much to own (sound familiar?)

The actual pigeon specimen being used for its DNA. Photo by Brian Royal.

Today there is a plan afoot to bring back a genetic recreation of the bird:  The Great Passenger Pigeon Comeback. George Church (of the Human Genome Project) is working on this with Stewart Brand‘s (of the Whole Earth Catalog and The WELL fame) foundation Revive & Restore.  Love the combo.  They plan to take passenger pigeon genes from the toe pads of museum specimens ( pictured at the right) and combine them with genes from the band-tailed pigeon.

If reading the book is more than you want to take on, there is a fabulous New Yorker article by Jonathan Rosen that excerpts the story extremely well. And if you want to make the passenger pigeon a part of your travel plans in 2014, there is a memorial to the passenger pigeon at the Grange Insurance Audubon Center in Columbus, Ohio.

Tiny Conspiracies

The Bassler Lab

Bonnie Bassler

We’ve just concluded the ninth annual Biology Leadership Conference (BLC) in South Carolina and what a weekend it was! Our keynote speaker,  Dr. Bonnie Bassler , gave the meeting a rip-roaring start with a research talk about her lab’s work with bacteria, figuring out how they talk to each other, and, as an outgrowth of that work, gaining insight into the evolution of  multicellularity.

Bacteria, Earth’s earliest lifeforms, are single-celled organisms, covered with a membrane, and filled with cytoplasm that includes only one piece of DNA.  Compared with humans and other mammals, they have very little genetic information (only a couple of thousand genes) with which to work.  Their lives appear to be fairly mundane – they grow, divide and replicate.

As humans, our relationship, with bacteria is pretty interesting.  Humans, like all organisms, are made up of cells – roughly a trillion cells that make up one human body.  It turns out that you have 10 times more bacteria cells than human cells on and inside of you (there are roughly 40,000 species of bacteria in the gut alone!).  In other words, you are really 90% bacteria.  And if you look at the gene pool, those proportions become even more astounding. We know that there are 20k genes in the human being.  Well, if you tally up all of that bacterial genetic material, you have 100x more bacterial genes, than human genes, in and on you.  So, doing the math – you are only 1% human.

Bacteria R Us, illustration by Bryan Christie

But all of those bacteria are not just passive riders in and on your human form, they are very busy creatures.  They provide an amazing repertoire of functions that you can’t do on your own – food digestion, educating your immune system, and vitamin production.  They also cover you in an invisible film – a sort of body armor.

But we don’t hear much about all of those positive contributions. When we hear news about bacteria, it’s mostly bad news  – lyme disease, toxic shock, or food poisoning – the myriad ways that bacteria make us sick.

Hawaiian Bobtail Squid

Dr. Bassler started as a postdoctoral fellow in the lab of Dr. Mike Silverman (from the Agoroun Institute, now retired), who had been working on a special kind of bacteria, Vibrio fischeri, that live in a mutally beneficial relatonship with a marine organism – the Hawaiian bobtail squid (pictured at left).  This squid has a pristine, one-to-one symbiotic relationship with the bacterium Vibrio fischeri.  The squid provides a safe and comfortable home, the bacteria provide light.

Here’s the story from the squid’s point of view:  during the day, the squid buries itself in sand to avoid being eaten by predators. Good strategy. In this video you can see the squid’s camoflauge behavior. It comes out at night to hunt, but of course, it’s difficult to hunt in the dark.  Fortunately, the bobtail squid has a specialized light organ, two glowing lobes, located on the underside of its body, loaded with (10 to the 12th cells per ml) bioluminescent bacteria.   The squid’s ink sac works like a shutter, controlling the amount of light shining down, into the dark water below.  The light organ and ink sac are controlled by  a light organ on the squid’s topside, so that the bacterial light precisely matches the light coming from the stars and moon above. In effect, the squid counter-illuminates itself to avoid predation, while hunting.  Together, the squid and its bacteria are the stealth bomber of the ocean.

Vibrio fisheri

From the bacteria’s point of view, the light organ is a safe haven,  loaded with nutrients.  The bacteria and the squid, as a pair, manage to avoid wasting valuable resources by only turning on the light when appropriate – that is, only at night, and only when there are enough bacteria around to make it worthwhile.  The light is turned on by a sort of chemostat – the bacteria make and release a small pheromone (called an autoinducer).  As they grow and divide, they sense the level of the autoinducer.  A particular autoinducer level is the cue to turn on the light.  In the morning, the squid pumps out most of the bacteria from its light organ – and the process resets itself.

The biochemical key to this beautiful process is this autoinducer.  As the bacteria grow and divide, the molecule builds up precisely in proportion to the number of bacteria present.  The bacteria use the autoinducer as a communication proxy – initiating a response (turning on the light), based on the detection of that chemical’s level. In effect, the bacteria are using the level of the autoinducer as a method for counting their number – or quorum sensing.  It’s as if the bacteria vote chemically –  and then turn on the group behavior.

The enzyme that makes the autoinducer freely moves in and out of the bacterial cell.  The receptor that detects the molecule’s presence sits on the cell surface (like a hormone receptor). When the molecule reaches a certain concentration, it binds to the receptor on many bacterial cells, in the typical lock and key manner, and that binding action turns on the bioluminescence. Like a light switch.

Endosymbiosis

And here’s the interesting connection to the evolution of multicellularity.  According to the endosymbiotic theory, early ancestors of eukaryotic cells engulfed and incorporated other prokaryotic cells.  Eventually, the engulfed cell formed a relationship with its engulfer and became a cell living within another cell – an endosymbiont.  In the same way, we can look at quorum sensing as an early version of development in complex, multicellular organisms.  Turning on the light among hundreds of bioluminescent bacteria is similar to turning on hundreds of genes in a multicellular organism at a particular time.  These luminescing bacteria perform their action in synchrony – behaving just like multicellular organisms when they do.

So what all are these bacteria doing with quorum sensing? Turns out, there’s a wide range of these autoinducer chemicals that participate in various bacterial group functions. To mention just two examples: such a chemical in  P. aeruginosa is involved with production of virulence factors and biofilms and such a chemical in E. carotovora is involved with  antibiotic production.

Quorum sensing helps bacteria to strategically time their invasions. When you think about it, it makes no sense from the bacterium’s point of view to kill the organism it has invaded. The better idea is to dribble out molecules and give the host a chance to mount an immune response so that the host and the bacteria can continue their relationship.  For the bacteria, it is much better to wait, count itself, and then, when the numbers are right, mount a group assault and infect the host in such a way that both the host and the bacteria survive.

Bacterial community: biofilm on your teeth.

But it’s not as simple as one species of bacteria living in or on one host. Like all other organisms, bacteria live in complex communities, surrounded by many other bacterial species.  Take for example, that thick film you feel on your teeth in the morning?  There are roughly  600 species of bacteria at work, creating that lovely film for you each day. Imagine the “noise” with 600 bacterial species, sending out their biochemical signals. So, if bacteria live in these complex communities, surrounded with all of that biochemical noise, how do they take a census?

To answer that question, the Bassler lab went looking for genes.  In the process, they found that there were really two signals.  Two chemical signals (autoinducers 1 and 2) tell the Vibrio fisheri bacteria to produce light.  But why two?  Why is it useful to have two circuits to provide one line of information?  To get to the bottom of that question, the Bassler lab made bacterial mutants with only one system, then collected their bacterial chemical output and applied it to bacteria with both systems. Using this method, they figured out that the second system was turned on by every species’ autoinducer chemical.  In other words, one system allows bacteria to detect “self” and talk with their kin while the second system detects “other” and allows for interspecies communication.

The gene involved in interspecies communication  is luxS and all of bacteria studied by Bassler’s lab have this gene.  When the researchers collected the molecule produced by the luxS gene, purified it, and determined its structure, they found that every bacterial species made the exact same molecule.  In effect, the chemical encoded by the luxS gene provides a common chemical  “language”. The bacteria are, in a sense, “bilingual”.  They can talk to each other, within their species, and they can talk across species. “Am I alone?”  “Am I in a group?”  “Am I winning or am I losing?”

The film on your teeth, mentioned earlier, is a complex, architected community.  Bonnie speculates that there is most likely a vast chemical lexicon among bacteria yet to be discovered. Imagine the possibilities if we could devise methods to interfere with these bacterial conversations! Take antibiotic-resistant bacterial pathogens, for example. Rather than search for newer and stronger antibiotics to kill these resistant bacteria, perhaps we could modify their behavior and limit their virulence by interrupting their conversations?  And by interrupting the signal, perhaps we could buy time for the host’s immune system to get rid of the bacteria on its own.  Chemical interference could be aimed at  the autoinducer 1 signal, for a targeted approach, or the autoinducer 2 signal for a broad spectrum approach.

What method might be taken to interfere with the bacteria’s signal?  One approach would be to search for an antagonist to block signal reception – a way to interfere with the shape of the lock/key fit of the signal chemical and its membrane-bound receptor.  Turns out, there are libraries of thousands of molecules, created by chemists, that can be screened in search of molecules for this purpose.  And here’s the really sweet part about the bioluminescent bacteria: They give a no-nonsense indication of each chemical candidate’s success – does the light go on or not?  Robots in the Bassler lab screen scads of these chemicals – up to a million molecules in ten days –  testing them with their bacterial communities. Of course, they devise methods to make certain that the tested molecules aren’t acting like bleach and just killing the bacteria.  As a result of this work, they’ve now narrowed it down to 12 molecule candidates that interfere with the receptor.  Initial experiments with these candidates and a virulent bacterium that kills mice looks very encouraging. The chemicals interfere with the bacterial conversation sufficiently to prevent the mouse from succumbing to the bacterial infection.  Of course, there are many miles yet to go before these methods might be available to apply to human bacterial diseases – the molecules must be tested, refined, made deliverable in human systems, etc.  But the important thing is – it works.

If you’d like to hear more from Bonnie, you can view her 2009 TED talk or this wonderful video of Bonnie, in her lab, talking about the nature of science and the work in her lab.  Thank you, Bonnie, for such an inspirational talk!

CSA Farm Share

Dover Farm

This year, our family decided to join a community farm.  We did a little research and decided to buy a share in The Dover Farm, a small-scale CSA (community supported agriculture) operation, just 5 miles from our home.  The produce is pesticide free, polyculture, and the farm is ecologically sound and sustainable.  Our single share entitles us for a weekly pick up, starting the first week of June and running through early October.  A way for us to buy local, seasonal, ultra fresh, and directly from the farmer.

In addition to the greenhouses (where they sprout the seeds in March, this being New England and all), they have some lovely acreage and a population of chickens (which I’m guessing help with fertilization, as well as providing fresh eggs).

This week's bounty

Each week, new bounty awaits us when we arrive for our scheduled Tuesday afternoon pick-up.  Today we came home with a bulging (recyclable) bag of lettuce, spinach, curly kale, rainbow chard, bok choi, red komatsuna (a type of bok choy, I learned), kohlrabi (stay tuned), spring onions, and sugar snap peas.  Yum.  One of the (many) things I like about being a member of this Farm is that you are exposed to veggies and fruit that you might not normally buy or eat. Take kohlrabi, for instance.  I honestly have no idea what to do with it and, in fact, they remind me a bit of little green alien guys in the movie, Toy Story, who are stuck in the vending machine (“The Claw!”).  But never fear, The Dover Farm blog to the rescue!!  There’s a really sweet recipe there for Asian Kohlrabi Slaw – along with a great stir fry idea for all of that bok choy.  Each week, a new adventure!

Handheld Wireless Microscope

My hair - as seen through the lens of a handheld, wireless microscope

That’s my hair.  Up close and personal.  As viewed through the lens of a handheld, wireless digital microscope.  That image of my hair was sent wirelessly from the microscope (as I held it to my head), across the room, to my waiting iPhone, and uploaded to my computer to be placed in this blog post.

Sweet.

So, here’s how it works… I downloaded the free Airmicro app from iTunes onto my iPhone and configured the wireless settings.  You could also upload the images to your laptop or desktop computer, of course. The microscope, called aProScope, is small and light (very portable).  It has a built-in light source and you can purchase interchangeable lenses (10x, 30x, 50x, 100x, 400x).  The device can be used in “touch view” mode (touch the specimen you want to examine) or “distance view”, giving you a half inch distance between the microscope cone and the specimen.  In distance view, you can mount the microscope on a stand, giving you a great way to project dissections up on a computer screen (and record them) or as a document reader.

The company’s website has a number of interesting looking activities, labs and lesson plans but if you really want to hear the full scoop on teaching with this tool, you should be in touch with Sheri Wischusen (Louisiana State University) who has been putting it through its paces.

Here are a few other images I grabbed with the Proscope – any guesses on what they are?

Watson and Crick Model

During our recent family trip to London, I managed a stealth visit to the Science Museum, located just behind the Natural History Museum in South Kensington.  I had heard that the Science Museum housed the original model that molecular biologists, James Watson and Francis Crick, created in 1953 to depict the structure of DNA.  The.  Original.

So while the rest of my family explored the Natural History Museum, I dashed over (both museums are free admission – what a concept).  I spotted a helpful looking museum guide and breathlessly asked him where I might find the Watson/Crick model.  He broke into a big smile and delightedly offered to walk me to it (he must not get the request very often).  Sure enough – there it was – in a glass case. Humbly displayed with other 19th and 20th century innovations.

I was struck by two things when looking at this remarkable piece of science history.  First, how BIG it was.  This was no small-scale, desk-top model – they were really trying to make a statement with this thing.  Second, that it was made up of odd sorts of materials – clamps and wire and shapes cut of of sheet metal.  It was as if they just looked around the lab to see what they had on hand and said, “right!  let’s use this!”  I loved it.  Have a look:

and another...

Watson and Crick DNA Model

And another view...

London’s Natural History Museum

Diplodocus in the Central Hall in the Natural History Museum of London

Our family just returned from a trip to the UK, which included five days in London. Despite the snow and ice, we had a wonderful time exploring the city.  Lots of long walks, great meals (yes, you can find good and reasonably priced food in London!), and fabulous museums. Because they are publicly funded, many of the museums in the city are free – the Tate, the British Museum, the Victoria and Albert and the Natural History Museum. Home to a vast life and earth science collection, the Natural History Museum, which opened its doors in 1881, has an impressive history that includes original notebooks, journals, manuscripts and specimen collections from notable scientific figures –  including Charles Darwin.

The Cocoon

In addition to its magnificent collections of fossils, dinosaur bones, taxidermied creatures, this venerable institution has a fabulous new wing called the Darwin Centre.  I was very taken with the design of the Centre and its state-of-the art use of technology.  The Centre is housed within a giant, eight-story cocoon.  You begin your visit with a ride on a glass elevator to the 7th floor and work your way down a guided ramp.  As you walk through the cocoon, you encounter displays of specimens, interactive exhibits, plant and insect collections, interspersed with video projections on the cocoon walls which explain and guide you through.  Periodically, you come upon a window that allows you to peer into a working laboratory within the center of the cocoon.  Literally, a window on the hidden world of scientific research, revealing the scientists at work.  At different times, various scientists are there to answer your questions or explain the work that’s going on in the lab.

I was particularly taken with the climate change wall and the  table-top animated touch screen exhibits which invite you to use your hands to drag images, make selections, move items around as you explore the given concept. There was a particularly effective one on DNA testing and a delightful exploration of miscroscopy where you work to identify a mystery specimen.

When you visit the cocoon you have the option to extend and enrich your experience by way of a program they call NaturePlus.

NaturePlus Station

As you enter the cocoon, you pick up a free NaturePlus Card, with a unique bar code and number.  At most of the exhibit stations, you can scan your card and collect highlights (particular images, favorite activities, or memorable facts) for later consumption. Back at home, you register on the Natural History Museum’s web site, create your own personalized web page with your NaturePlus Card number and all of your selected museum content becomes available to you.  Such a clever way to deal with the problem of “information overload” we encounter at most museums – saving (and personalizing!) stuff for later.

The Gulf Oil Spill On Your Desktop

Like most of us, I’ve been watching the latest developments from the Gulf of Mexico with growing alarm.  Like a blight, like a creature bent on destruction, the black slick is growing, moving ever closer to the fragile Gulf coast, threatening every living creature in its path.  The thing about oil spills (and bacteria, and galaxies, and mitochondria, and black holes) is that their scale is just too difficult to visualize. Our failure to really grasp the enormity, the complexity of the thing means that we fail to grasp its impact.

But with this oil spill we have a few, new visualization tools.  And they’re not just in the hands of the experts – they are on our own computers and cell phones.  Just this week, video was released of the actual source of the Gulf oil – spewing out of a broken well, nearly a mile below the ocean’s surface.  Let me say that again.  Video from a mile underwater.  Whoa.  Representative Edward Markey (Chair of the Committee on Energy Independence and Global Warming) has posted a live feed of the spill (spill cam) on his web site. In addition to that we have amazing photographs, artfully portraying the scope and scale of the disaster.  NASA satellite images, readily downloadable with a click give you a clear view of the spill – and you can watch it play out over time.  Google Earth has now made NASA’s MODIS imagery available as a downloadable overlay for Google Earth. But to really give you a personal sense of scale – use Google Earth’s “Places of Interest” layer to look at the spill in situ, as it changes over time, and then place it over your own region of the globe.  And here’s a nice one – “ifitwasmyhome“, where you can instantly overlay the spill on a map anywhere.  See how far the slick stretches over landmarks that you know.