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By now we have all heard about the importance of the microbial life that lives inside of us. Yet one of the questions that researchers still face is, how similar is one person’s gut microbiota to another’s? Finding patterns is an important research goal.
When gut microbiota research first began to gather steam in 2011, a group of scientists introduced the idea of ‘enterotypes’ – well-balanced gut bacterial states. Their data indicated that the different species of bacteria present in people’s guts did not show a random representation or a continuum; instead, species composition fell into three robust patterns that showed up in subjects from four different countries.
In a similar vein, a research group at UCLA recently introduced the idea of two ‘metabotypes’ based on the kinds of metabolites produced by gut bacteria. According to Braun, no matter what species are present in the gut, there are only two output options: “People’s microbial communities make one mode of products or a different mode of products.” Meaning, there are just two categories of metabolic activity: metabotype one and metabotype two. Enterotypes and metabotypes are still debated categories, but they open the door to an important upcoming topic in gut microbiota research: patient stratification.
Stratifying the Patient
Think about a cliff that you might encounter while hiking. To most of us, it just looks like a big wall of rock. But to a geologist, it has different layers that tell a story. Similarly, as research increases knowledge of gut microbiota composition and function, clinicians will be able to take a notoriously messy diagnostic category like ‘allergy’ and break it down into subgroups able to respond to different treatments.
I’ve heard from several scientists and practicing clinicians that gut microbiota is a potential way to stratify healthy people into categories, and also to stratify patients within an existing category. Obesity, for example, is still a poorly-understood condition from a clinical standpoint. Karine Clément, a Parisian physician and professor who has spent much of her career investigating obesity says, “It’s very heterogeneous, and this is why also I thought that studying the gut microbiota was interesting because…it’s a way maybe to stratify better patient groups. And over time, if you have individuals with a low bacterial gene amount, and low diversity, maybe it’s important to find this group and find accurate treatment for them.”
Your gut enterotype might not be something to add to your OKCupid profile just yet. But stay tuned for ways to better define yourself, and opt for better health, through intestinal investigation.
Kristina Campbell, the “Intestinal Gardener”, writes for the Gut Microbiota for Health Experts Exchange.
by Sarah Boon,
Our long observation of the natural world has yielded many interesting secrets, enhancing our scientific knowledge and leading to changes in policy and legislation. For example, measurements of CO2 concentrations at Mauna Loa since 1958 have shown a steady increase in atmospheric carbon dioxide concentrations, while satellite images of Arctic regions since 1979 have confirmed the decline in Arctic sea ice extent. The Global Land Ice Monitoring from Space (GLIMS) project – which just released its latest book last month – has been monitoring global glacier change since 1998, documenting the exposure of gravel valleys long buried by glaciers.
What all these records have in common, however, is that they only go back so far. If a scientist wants to move beyond the time frame of the instrumental record – and believe me, they do! – they have to bridge the gap by exploiting new data sources.
There are data rescue projects, like the Nimbus project. It aims to restore 1960s data from a long-forgotten weather satellite used originally to monitor clouds, and extend the record of sea ice extent for both the Arctic and Antarctic.
Other traditional science-oriented approaches include paleo-records like ice cores and tree rings, sediment cores from lakes and the ocean bed, and corals. Each of these so-called ‘proxy’ records can provide information on past climates, hydrology, vegetation, and more.
A key non-scientific data source, however, is historical records. Scientists are teaming up with historians to move data collection out of the STEM realm and into the STEAM (science, technology, engineering, arts and math) world. Yes, that’s right – science and history, working together to answer science questions.
This isn’t so odd in the field of archaeology, where researchers routinely work with historians to gain a better understanding of the context in which archaeological finds exist. Recently the BBC aired a show on the Quest for Bannockburn, in which archaeologists Neil Oliver and Tony Pollard search for the site of the famous battle between England’s Edward II and Scotland’s Robert the Bruce. Throughout their search, they refer repeatedly to historical accounts of the battle itself, and to other historical records from the time period. Closer to home, the recent Parks Canada search for the Franklin ship, Erebus, was directed by recorded Inuit history, which pinpointed the area in which the ship was found.
The environmental sciences have also benefited from historical records. Early explorers often took detailed natural history measurements during their travels, such as weather observations in the Antarctic. Companies like the Hudson Bay Company (HBC) recorded the number of animal pelts traded by First Nations groups.
The HBC data were used in 1942 by researchers from Oxford University to reconstruct lynx population cycles. In 1983, researchers used 17th century tax records from Scandinavia to document the expansion of local glaciers during the Little Ice Age: formerly prosperous farmers saw declines in revenues as glaciers advanced and ruined their farmlands. More recently, researchers at the University of Sunderland, UK, used ice observations in 200 year old log books from British whaling ships to show that Arctic sea ice used to have a much greater in extent than it does now. The Mountain Legacy Project, housed at the University of Victoria, uses photographs taken in Canada’s mountains by land surveyors from 1861 – 1953 to examine landscape change over time. Researchers have even coined the field of historical ecology, using historical sources to guide modern ecosystem restoration efforts.
Using these data can be tricky, as they weren’t collected with science in mind. If these limitations are made clear from the outset, however, the data remain highly useful, and represent the ingenuity and creative spirit that’s attributable to both sciences and humanities alike.
What observations are you recording today that might be used by scientists of the future?
Sarah Boon has straddled the worlds of freelance writing/editing and academic science for the past 15 years. She blogs at Watershed Moments [http://snowhydro1.wordpress.com] about the environment, science communication & policy, women in science and academic culture.
Tagged with: Antarctic • archaeology • Arctic • climate • corals • Erebus • Franklin ship • GLIMS • Global Land Ice Monitoring from Space • HBC • historical ecology • historical record • history • Hudson Bay Company • hydrology • ice cores • Inuit • John Franklin • lakes • lynx population reconstruction • Mauna Loa • Mountain Legacy Project • Neil Oliver • Nimbus project • oceans • Quest for Bannockburn • Sarah Boon • science • sea ice • sediment cores • STEAM • STEM • Tony Pollard • tree rings
Modern life without language is impossible to comprehend, or rather, just impossible. Language and speech are central to how we convey information and emotion, form bonds, conduct business, and organize ourselves into productive societies. To communicate ideas, facts, and feelings – and understand what others mean when they speak – is a hallmark of humanity.
On the surface, spoken language seems basic and intrinsic. After all, speech is one of the things we learn earliest in life. But deep within the brain’s folds, spoken language is surprisingly complex, and for linguists is a place of great unknown.
Even in our über-tech age, generating and interpreting language is something humans do better than computers. We’re better than machines at understanding nuance, context, and humour. And even the most powerful computers can’t handle one job at which some humans excel: a mash-up of multitasking known as simultaneous interpretation.
Simultaneous interpreters listen to speech in one language, process it, understand it, and translate it – in real time – into another language. They typically translate from an acquired language into their mother tongue, always under the time crunch of instantly required results.
Recently, this Mosaic Science story on simultaneous interpreters caught my eye. Today, it seems almost quaint to find real humans processing language, in a one-to-one speaker-to-translator ratio, in real time. Some situations, however, demand it. The United Nations is probably the best-known example, but simultaneous interpreters for spoken or sign language can be found at conferences, interviews, and even theatrical productions.
Neurologically speaking, the job is tough. Speaking while listening and having two languages active at once are extreme feats of multitasking. Simultaneous interpretation is spontaneous, unpredictable, and demands attention to tone, body language, facial expressions, and word order, which differs across languages. At the UN, where the stakes are high and correct understanding is key, simultaneous interpreting can be so draining that interpreters typically work only 20-minute shifts before taking a break.
The Mosaic story explains how the human ability to speak and translate language comes down to well-synced executive function. Like other highly complex abilities, language goes beyond one focused area of the brain. Broca’s area is only part of the story. Rather, language involves fast, precise networking between multiple areas, and the grace is in the coordination.
Researchers are exploring a new idea — that maybe our most sophisticated abilities is less about specific brain regions and more about how evolutionarily basic regions interact.
Support for this idea comes from fMRI studies, which show that the caudate nucleus, a coordination centre deep in the brain’s core, is active during language production. The caudate rallies different regions of the brain into exquisitely choreographed abilities, like learning, memory, decision-making, and planning.
What does the caudate nucleus look like in someone who’s a super-user of this synchrony centre? Here’s an interesting experiment: one group at the University of Geneva used fMRI scans to look inside the brains of 50 multilingual students while they listened to a sentence, repeated that sentence, and then were asked to translate the sentence into another language and speak it aloud.
Nineteen of these students spent the next year being trained as simultaneous interpreters, while the remainder did not. One year after the initial tests, the trainee group’s brains had changed, but not how you might expect: their caudate nuclei were less active during the third (translation) task. In other words, they became more efficient controllers and mental multi-taskers.
Something similar has been observed among elite chess players: the more experienced the player, the smaller their caudate nucleus. Since the caudate is involved in controlling so many things, this leads to some interesting questions. It opens the door to new ways of training our brains to be more efficient processors. And maybe there’s even a way to do that without having to become adept at this.
Allison MacLachlan (@a_maclachlan) earned her M.Sc. in science writing from MIT in 2011. She lives in Toronto, works in book publishing at Owlkids, and enjoys writing about health, biology and psychology.
On November 12th, almost a half-million of us sat glued to our screens watching scientists watch the space voyager Rosetta gently drop the lander, Philae, onto a comet.
After Philae landed we all held our breath for nearly a half hour, waiting for Philae’s confirmation to travel the 500-million kilometres back to earth telling us that she* had landed and everything was well and good.
As someone on Twitter commented during that 28-minute wait, “Never has the speed of light felt so slow.”
Now I don’t know about the rest of you, but wow. That just about did me in.
However, let’s go back a minute so I can reiterate a point: We spent hours watching scientists watching screens.
Here, in a world of sound bites and instant answers; a world where newscasters breathlessly deliver even the most mundane news, and headlines shout to grab our attention; a world where life is over-stimulating by design, hundreds of thousands of us settled in to quietly watch and wait in silence.
And that is the first lesson of Philae.
Lesson #1 – Science is Slow Work
Poaching an egg takes 3 minutes no matter how many chefs or dollars you throw at it. Much of science is the same way. It takes the time it takes. Cells divide in a day. Drosophila reproduce in a week. Ecosystems recover over decades. Climate trends show themselves over centuries.
Rosetta left Earth 10 years ago. Of course those scientists have been busy during the interim. Rosetta has, after all, been gathering data all that time. But to set something in motion knowing it’s going to take a decade before its culminating event occurs requires setting aside any dreams of instant gratification.
To do the work of science means committing to the long haul.
Lesson #2 — Eureka Is Just the Beginning
“This morning, we hit a milestone, an important milestone of this mission. But this mission isn’t just about arriving at a comet. It’s about studying the comet. It’s about placing a lander on a comet, but again, the mission does not end there. The science continues…” — ESA’s Laurence O’Rourke on Rosetta’s arrival at the comet (August 2014)
Science doesn’t end when a problem is solved, a discovery is made, or an answer is found. Each of those big moments creates a new jumping off point for inquiry and discovery.
Lesson #3 – Slow Science Requires Long Political Will
At a cost of 1.3 billion euros ($1.8B CDN), the success of the Rosetta Mission hinged on the foresight, political commitment and cooperation of ESA’s twenty member nations.
These nations span political and ideological boundaries. For each nation, membership and financial support to ESA have successfully transcended decades of election cycles and political shifts at home.
This kind of commitment to the long view, despite shifts in political winds, is necessary if science is going to progress within a country. When good science is devalued and defunded over political ideology we all lose.
How do you get political commitment?
Lesson #4 – Engage the People
I am certain that outside of scientific circles, most people were unaware of the Rosetta mission until the day of Philae’s landing. But then ESA kicked in with a publicity blitz and an imaginative social media presence that enamoured the public.
In a refreshing departure from the often dry commentary supplied by agency representatives or the talking-points chatter of mainstream media, the Tweets from and between Rosetta and Philae gave such personality to the space vehicles that it was hard to remember that they were composed by ESA staff.
This kind of delightful, but informative, engagement is powerful. By the time the landing was over, Philae had 390,000 followers on Twitter and we were in love with the little lander.
However, getting this kind of buy-in from the public requires something else – something we don’t have here in Canada.
Lesson #5 – Allow Free and Open Communications
This tweet says it all.
Lesson #6 – Slow Science Requires Optimism
Sometimes life gives you lemons …or in this case, a shadow on your solar panels:
In science, this kind of thing happens. Results don’t come out as expected. Studies fall apart. Batteries or, worse, carefully bred study animals die, setting work back decades. And when that happens scientists who are in it for the long haul have to embrace a good deal of optimism.
“It has been a huge success, the whole team is delighted … We still hope that at a later stage of the mission, perhaps when we are nearer to the Sun, that we might have enough solar illumination to wake up the lander and re-establish communication.” — Stephan Ulamec, lander manager at the DLR German Aerospace Agency.
Thank you Philae. Sleep well.
* Philae’s social media team considers Philae to be a “he” but to me the lander’s personality felt like a she. Given the circumstances, I’d like to think we can both be right.
Kimberly Moynahan writes on the natural sciences and reflects on that uneasy space in the Venn diagram where humans and wildlife overlap, both physically and emotionally. Her work can be found on her blog, Endless Forms Most Beautiful.
by Ron Miksha
The marriage of Stephen Hawking and Jane Wilde – as told through the ex-wife’s memoir – has become the stuff of a Hollywood tragic-romance. I have not read her memoir but have read excerpts and reviews of it. The Jane Wilde Hawking Jones book, Travelling to Infinity – My Life with Stephen, was written a few years after their divorce (the Hawkings had been together for nearly 30 years). The Theory of Everything, the Hollywood adaptation, is a very loose interpretation of her story of their time together. The film makes a compelling and fascinating account, but it is an extraordinarily unfaithful rendering. The screenplay adapters knew what they were doing in their rewrite – they were presenting a story that should fill theatre seats. It is intended as entertainment, of course.
As entertainment, the movie works well. The viewer is quickly engaged in the awkward charm and cerebral wit of young Stephen Hawking (Eddie Redmayne) and the quiet poise and dignity of his wife Jane (Felicity Jones). The film begins with Hawking’s arrival at Cambridge, the first signs of his progressive motor neuron disease, his PhD defence, and his meeting of Jane. (They were introduced through Jane’s sister, but the movie has us believe that Hawking spied her at a party and pursued her through some quirky schemes.) The movie trails through Jane’s incredible efforts to build a semblance of a family life for their children while simultaneously dealing with her husband’s unimaginably challenging progressive paralysis, her own infidelity, and Hawking’s growing fame. The film shows their parting and a final reconciliation. Although they were married nearly 30 years and their children became adults, the ending scenes present the children as grammar-school kids, for obvious emotional effect.
The movie does a good job documenting the progression of Hawking’s motor neuron disease, which has been described as a variant of ALS. (It is a variant only because it has been slowly progressive – all of his symptoms fall well within this broad-spectrum disorder.) Hawking was diagnosed at age 21 and the disease has slowly paralyzed him – albeit at a rate one-tenth the “normal” progression of the illness. It took 20 years for his disability to mimic the presentation found within 2 years in a typical ALS patient. The movie does an exceptionally stirring job of showing the difficulties family, friends, and spouses endure as they try to maintain normal lives while caring for profoundly ill loved ones.
But the movie should not be taken as a serious factual representation of the life of the Hawkings. For example, as Jane is unzipping her boyfriend’s tent, Stephen is far away, having his trachea neatly incised by a surgeon. Although the juxtaposed symbolism is startling and brilliant as it equates young Jane’s affair with the slitting of her husband’s throat, things didn’t happen quite that way. For pursuers of fact, I would point you towards Stephen Hawking: A Brief History of Mine. This more accurate account shows us that Jane is not so young – it is a mature 42-year-old Jane Hawking who made the life-saving decision for her husband’s continued ventilation. The tracheotomy came months later. And, according to Jane’s memoir, she stayed faithful to Stephen – the camping scene is entirely contrived theatre.
A few more overt fabrications in the movie:
- A friend asks Stephen about his sex life. Hawking’s actor smirks and responds. The scene is shear invention – Hawking, according to Jane’s memoir, never spoke openly about sex, “which for him was as taboo a subject as his illness.”
- The movie shows Hawking’s friends breaking the news about the diagnosis to Jane. In the film, the Hawkings were depicted as a couple – in reality, she heard about his ALS by chance and they were not even dating yet.
- A game of croquet figures large in the movie – it symbolizes Hawking’s frustration with his illness and Jane’s loyalty. The game never happened.
- In the movie, Hawking coughs and chokes at a formal concert and is whisked away in an ambulance – reality was not as dramatic. During a stop in Geneva, his friends were concerned about his persistent cough. They called a doctor. He was admitted to a hospital. The tracheotomy came after Hawking had recovered and had been on a ventilator for months.
The family friend. The movie leads the viewer to believe that Jane’s friend, Johnathan Jones, was the family’s sole helper for years. This is not true. A series of Hawking’s grad students lived with the family and helped with his care – one even travelled to California and lived with the family there for a year. The family friend did not. Further, the movie shows Hawking suffering the indignity of his wife’s boyfriend lifting Stephen from the toilet, implying this was how life worked in the Hawking household. It didn’t work that way, but it creates great theatre.
- To simplify things, many of Hawking’s colleagues are merged into a single person. This was most artfully executed in “Brian,” portrayed as Hawking’s close friend and confidant, the gentleman who tries to rescue Stephen Hawking from despair. In real life, no such person existed.
The voice. In the movie, Jane remarks that Hawking’s new voice is “American” – this drew laughter from the audience, but in reality, she never said it. Instead, Jane thought the voice sounded like a cyborg from the British television series, Doctor Who.
I think that Physics actually receives a reasonable treatment from this Hollywood flick, although the New York Times reviewer calls it vastly over-simplified. Of course it is – this is a mass-consumption movie, not a Feynman lecture. At one point, Jane spews one of Hawking’s theories at a dinner table. This theatrical device describes the science in layman’s terms and helps the audience grasp an outline of the scientist’s work. But this movie is not a science movie, and its makers do not portend as much. For the real physics, Errol Morris’s documentary A Brief History of Time will not disappoint you.
In the film, I felt that Stephen Hawking’s religious beliefs are intentionally muddled. In what I assume is an attempt to appease a largely religious American audience, Hawking’s well-known and frequently stated atheism is toned down and his wife’s religiosity (which is genuine) was amplified. Hawking was shown making allowances for God in the universe and, near the movie’s end, Hawking is asked directly about the role of a deity (and his own beliefs) – the film’s answer is a very indirect and highly qualified retreat from Stephen Hawking’s often stated principles. But perhaps vague innuendo about religion is the best way to satisfy those who may attend this show. To be direct, the producers could have used this quote from Hawking: “There is no god. No one created the universe and no one directs our fate.” You can see Hawking make this statement and its context at this link. It is not presented as a muddled triviality.
Although this Mountain Mystery blog is usually about Earth Science topics, I have written at length about this new movie for two reasons. First, I saw the film last night at a first-screening event here in Calgary. My tickets were provided through the distributor, E-One Entertainment and were sent to me by the Canadian Science Writers Association, of which I am a member. So, with gratitude for the E-One advance screening tickets (the movies opens here on Friday) and with thanks to the CSWA, I felt I would blog this bit about the film. But there is a second reason for blogging about The Theory of Everything. And it is personal.
Like Stephen Hawking, I have a variant of motor neuron disease. I sensed something was amiss for most of my life. But I was nearly 40 when I finally began to tumble and fall. (The first time resulted in a broken arm; a series of lesser mishaps soon followed.) It took a year of clumsy movement, slow walking, and weakness before I approached a physician. Another year passed before a neurologist reluctantly told me that I probably had ALS. We would monitor the disease monthly and see how it progressed. All of the tests (mostly electrified wires that made me jump like a dead frog) pointed to motor neuron disease, but progression has been incredibly slow. What I have is certainly not typical ALS, nor is Hawking’s disease typical ALS. It is best described as a motor neuron disorder (of which there are many flavours). It took years, but I recently surrendered my outdoor ambulations to a wheelchair, curtailed my travels, reduced my work. Fatigue is chronic. Everything I do takes more energy and frustration than you can imagine. Both of my feet have pronounced foot-drop which requires me to lift my legs high when I try to walk, lest I trip on my toes and plant my face into our wooden floor. My left hand hangs limp and its fingers no longer coordinate their movements very well. My right arm does not rise above my head. But like Stephen Hawking in his younger days, I also have a dedicated wife who spends her free time doing things I should be able to do and who tirelessly works to make my life easier and more comfortable.
Unlike Stephen Hawking, I am not profoundly disabled. Nor am I profoundly intelligent. We are all different people, aren’t we? Most of us have some debilitation – often unseen emotional or mental challenges, sometimes unseen medical problems, sometimes severe disabilities that startle others unexpectedly. We all travel the same road, all bound to the same destiny. With that in mind, the movie – The Theory of Everything – is less remarkable than it might seem. It is a movie about all of us. It is worth watching, not as a documentary about a scientist and his wife, but as a glimpse into the reality of life and the suffering that every one of us endures.
Ron Miksha is a science writer based in Calgary. Ron has worked as a radio broadcaster, a beekeeper, and he is a geophysicist. His book Bad Beekeeping highlights his 10 years of caring for a thousand colonies of bees; The Mountain Mystery explains how we came to know the origin of mountains. This review appeared originally in Ron’ blog.