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Humor, Medicine and Literature, Research, Science

Can science journals have beautiful prose?

Can science journals have beautiful prose?

5331998702_2e6ab9e5e8_zScientific journals are not known for being scintillating or inspiring reading. But could they be? A recent article in Nature elaborated on an online discussion started by Stephen Heard, an ecologist at the University of New Brunswick.

In a guest post on the Tree of Life science blog, Heard argued that snappier, livelier writing could attract and retain more readers. “Style and beauty are not incompatible with scientific writing,” he wrote. Papers could appeal to undergraduates, science writers, politicians, and the public.

But is a journal really an appropriate outlet for such writing? Blogs and commentaries might be better mediums for creativity and literary flair, as research articles often must adhere to a more rigid format and provide detailed descriptions of materials, methods and results. Participants in the online discussion have pointed out that clarity and order have a beauty in themselves, the inexorable logic on display in the progression from hypothesis to data to results. Others worried that stylishness would make science research less accessible to non-native speakers of English. Some mentioned (and critiqued) the conventional idea that whimsy and humor cover up flawed science and detract from clarity. And many others praised the idea of incorporating pleasure along with function.

In the original piece, Heard suggested three reasons scientists don’t write beautifully more often:

It could be that writing beautifully in scientific papers is a bad idea, and we know it. Perhaps readers don’t respect scientists who resist the conventional turgidity of our writing form. I don’t think this is true, although I’m aware of no formal analysis.

Or it could be that beauty is a good idea, but well-meaning reviewers and editors squash it. In my paper I argue that beauty (like humour) can recruit readers to a paper and retain them as they read; but that reviewers and editors tend to resist its use. But again, there’s no formal analysis, so I was forced to make both halves of that argument via anecdote.

Or it could be we just don’t have a culture of appreciating, and working to produce, beauty in our writing. I think this is most of the explanation: it’s not that we are opposed to beauty as much as it doesn’t occur to us that scientific writing could aspire to it.

He sees three ways this could change: scientists can add some whimsy to their own writing, leave it in others’ writing when editing, and praise it when they see it. He exclaims:

Wouldn’t it be great if there was an award for the best scientific writing of the year? I don’t mean the best science – we have plenty of awards for that – but the best writing to appear in our primary literature. Such awards exist for lay science writing; if one existed for technical writing I’d be thrilled to make nominations and I’d volunteer to judge.

Heard keeps his own science blog, Scientist Sees Squirrel.

Photo by Ashley Campbell

Events, Science

Nobel laureate Randy Schekman on the importance of scientists clearly communicating about their work

Nobel laureate Randy Schekman on the importance of scientists clearly communicating about their work

colorful brains - 560

I consider myself a professional nerd (my background is in chemistry and neuroscience) and have attended many academic talks during my life. I’ll be honest: I’ve spaced out during quite a few talks that were outside of my area of expertise.

Earlier this week, I attended a talk on campus by 2013 Nobel laureate and Stanford alumnus Randy Schekman, PhD. The subject of his talk – how cells expel a special kind of vesicle – was way out of my comfort zone. (I’m more neuroscientist than chemist.) But Schekman didn’t lose me as an audience member.

After Schekman finished speaking about his research, he was asked to comment about the role of teaching in his life. His answer, during which he explained that one of his responsibilities at UC Berkeley is to teach is an undergraduate seminar, explains my engagement during his talk.

“I’ve learned when you teach undergraduates – people who are smart but uninitiated – you have to make yourself understood,” Schekman said.

It is obviously this effort, this desire to succeed at communicating the complexities of what happens in his lab and his field to undergraduates and experts alike, that makes Schekman an accessible speaker.

And Schekman made clear that making yourself understood has benefits beyond connecting with your audience. As he told the audience, every now and then he teaches an outstanding student who challenges him, forcing him to think more deeply about subjects he thought he knew well.

Schekman spoke at the Medical Grand Rounds and was this year’s Rubenstein lecturer. Founded by friends of Edward Rubenstein, MD, the lectureship was created to honor Rubenstein’s commitment to the intersection of education with the clinical sciences.

Kimberlee D’Ardenne is a writing intern in the medical school’s Office of Communication and Public Affairs.

Previously: Hawkeye Pierce (i.e. Alan Alda) teaches scientists how to better communicate about their work, A call to fix the “crisis of communication” in science, Stanford’s Thomas Südhof wins 2013 Nobel Prize in Medicine and Challenging scientists to better communicate their ideas to the public
Photo by Joan M. Mas

Imaging, Neuroscience, Research, Science, Stanford News

New insights into how the brain stays bright

New insights into how the brain stays bright

Neon brainAxel Brunger, PhD, professor and chair of Stanford’s Department of Molecular and Cellular Physioogy , and a team composed of several Stanford colleagues and UCSF scientists including Yifan Cheng, PhD, have moved neuroscience a step forward with a close-up inspection of a brain-wide nano-recycling operation.

A healthy adult brain accounts for about 2 percent of a healthy person’s weight, and it consumes about 20 percent of all the energy that person’s body uses. That’s a lot of sugar getting burned up in your head, and here’s why: Incessant chit-chat throughout the brain’s staggeringly complex circuitry. A single nerve cell (of the brain’s estimated 100 billion) may communicate directly with as many as a million others, with the median in the vicinity of 10,000.

To transmit signals to one another, nerve cells release specialized chemicals called neurotransmitters into small gaps called synapses that separate one nerve cell in a circuit from the next. The firing patterns of our synapses underwrite our consciousness, emotions and behavior. The simple act of tasting a doughnut requires millions of simultaneous and precise synaptic firing events throughout the brain and, in turn, precisely coordinated timing of neurotransmitter release.

You’d better believe these chemicals don’t just ooze out of nerve cells at random. Prior to their release, they’re sequestered within membrane-bound packets, or vesicles, inside the cells. Every time a nerve cell transmits a signal to the next one – which can be more than 100 times a second – hundreds of tiny chemical-packed vesicles approach the edge of the first nerve cell and fuse with its outer membrane, like a small bubble merging with a larger one surrounding it. At just the right time, numerous vesicles’ stored contents spill out into the synapse, to be quickly taken up by receptors dotting the nearby edge of the nerve cell on the synapse’s far side, where, like little electronic ones and zeroes in a computer circuit, they may either trigger or impede the firing of an impulse along that next nerve cell.

Each instance of bubble-like fusion – and this happens not only in neurotransmitter release but in hormone secretion and other processes throughout the body – is carefully managed by a complex of interconnecting proteins, collectively known as the SNARE complex. The molecular equivalent of a clamp, the SNARE complex guides the vesicle ever nearer to the nerve-cell’s surface and then, at just the right moment, squishes it up against the cell’s outer membrane. The vesicle bursts, spilling its contents into the synapse.

Myriad repetitions of this process typify the average day in the life of the average nerve cell. This requires not only a ton of energy (which I guess is where the doughnut comes in) but ultra-efficient recycling. The entire SNARE complex must be constantly disassembled, then reassembled. In a new study in Nature, Brunger and his associates snagged a set of near-atomic-scale snapshots of the SNARE complex as well as the molecular machinery that recycles its components, allowing them to make sophisticated guesses about how the whole thing works. (See the Howard Hughes Medical Institute’s news release on the study here.)

This has been a long time coming. In fact, Brunger’s lab first determined the molecular structure of the SNARE complex, via X-ray crystallography, in 1998. The careful decades-long process of tracking down the SNARE complex’s components and their interactions won Stanford neuroscientist Tom Sudhof, MD, the 2013 Nobel Prize in Medicine. But despite its immense importance, you probably haven’t heard much about it. Studies of molecular structures are in general opaque to lay readers, complicated systems such as the SNARE complex all the more so. The popular press pays attention to the awarding of the Nobel, but seldom to the long, towering staircase of incremental discoveries that was climbed to earn it.

Previously: Revealed: The likely role of Parkinson’s protein in the healthy brain, Step by step, Sudhof stalked the devil in the details, snagged a Nobel and But is it news? How the Nobel prize transformed “noteworthy” into “newsworthy”
Photo by Carolyn Speranza

Aging, Ethics, Medicine and Society, Research, Science, Stanford News

Golden years? Researcher explores longevity research and the companies banking on its success

Golden years? Researcher explores longevity research and the companies banking on its success

Elderly Japanese woman for Scott blog postAlthough I haven’t had a birthday yet this year, the transition to writing 2015 on all my checks (whoops, did I just date myself there? ahem) has made me feel older. Coincidentally, I’ve also been working on an article for an upcoming issue of Stanford Medicine magazine about aging and longevity. So, yeah. I’ve been thinking a lot about the passage of time.

That’s why I was really interested to learn that Stanford bioethicist Christopher Scott, PhD, teamed up with Nature Biotechnology senior editor Laura DeFrancesco to c0-author a feature article examining the commercialization of longevity research. The article layers research advances with the rise and fall (and rise again) of companies and organizations that have tossed their hats into the anti-aging ring since the 1990s. With it, Scott and DeFrancesco paint a picture of a dynamic field on the brink of something big. As Scott explained in an email to me:

Aging research, as we knew it in the 1990s and 2000’s, is being abandoned in favor of something much more ambitious. The central features of longevity research include an embrace of big data, a pivot away from studies hoping to find aging genes, a recognition that aging is best thought of a collection of diseases, not just one disease.

I’m fascinated by how quickly this new direction has taken off, especially since classic aging research yielded so little, and became saddled with hype. Longevity research has that same feel to it, and from an ethics and policy perspective one question is whether the promise of healthy lifespans will outrun the reality of the science.

And there’s the rub. As Scott points out, it’s not enough to just live long. No one wants a prolonged, but unhealthy, old age. We need to live long and well. The concept that gained ground is “healthspan” rather than “lifespan.” And from Google’s Calico to Craig Venter’s Human Longevity, Inc , there are a lot of bright minds (and plenty of $) focused on this problem. But there’s a lot at stake.

As Scott explained:

These are highly consequential decisions (funding research, creating new companies, establishing new scientific disciplines), technological inventions, and social changes that are being pursued on the tacit assumption that such decisions, inventions, and changes do lead to a healthier, longer life and the promise of a better future. In ethics, I think these assumptions are largely unexplored and unacknowledged.

The article is a fascinating cross-section of a rapidly growing field, but, as Scott points out, there are still many questions that scientists haven’t addressed. It’s well worth the time to read, whether you’re a writer on a deadline or just a person trying to figure out how to gracefully change that “4” into a “5” on …all your paperwork.

Previously: Exploring the value of longevity with bioethicist Ezekiel Emanuel , Tick tock goes the clock – is aging the biggest illness of all? and Researchers aim to extend how long – and how well – we live
Photo by Maya Stone

Behavioral Science, Research, Science

Hormone similarity helps bird couples stay together

Hormone similarity helps bird couples stay together

GreatTit002My husband and I — total opposites. He’s neat, I’m messy. He’s early, I’m late. He dislikes socializing, I love to go out with friends. He digs meat and potatoes, I’m a veggie. And I could go on.

So if we were a type of European songbird called the great tit, I’m afraid we wouldn’t be together. Great tits choose mates quite similar to each other, with a recent study from the Netherlands Institute of Ecology showing they even have similar hormone levels. And those levels converge the longer the birds are together.

Researchers, who presented at the 2015 annual meeting of the Society for Integrative and Comparitive Biology, measured the levels of corticosterone, a stress hormone, in breeding pairs of great tits. Pairs with similar levels of hormones were also more likely to have more healthy babies. “For at least three years, the pairs that stay together increase their similarities year after year after year,” ecologist Jenny Ouyang, PhD, said in a release.

Pairs with dissimilar levels were more likely to “divorce” or break-up, a costly move in the avian world when being without a mate reduces your chances to reproduce. Some researchers have speculated that coordinating the feeding of the babies might lead the partners to have more similar hormone levels. But the exact mechanism remains unknown.

Thankfully, my husband and I can talk, hopefully avoiding the need to compare our hormone levels, which I’d bet are quite different, and growing more so every day.

Previously: “Love hormone” may mediate wider range of relationships than previously thought, Stress hormones moonlight as immune-system traffic cops and My couple’s match: Applying for medical residency as a duo
Photo by Shirley Clarke

Genetics, Research, Science, Stanford News

Show-off! Protein upstages DNA by ordering amino-acid add-ons

Show-off! Protein upstages DNA by ordering amino-acid add-ons

Show-offEvery living cell is a metropolis in which the vast bulk of work is performed by phenomenally productive laborers called proteins. Proteins work so hard – and the work that must be done in a cell changes so rapidly – that turnover in the labor force is immense. To maintain the brisk pace of life inside a cell, new proteins must constantly be assembled.

The machines responsible for that assembly are called ribosomes – as many as 10 million of them within a single mammalian cell, each capable of stapling together up to 200 amino acids (the building blocks of proteins) per second. The resulting amino-acid strings immediately fold themselves into characteristic structures reflecting their precise composition.

There are about 20 different varieties of amino acids, so the number of possible combinations a ribosome can make, in theory, is mind-boggling. But a ribosome doesn’t just piece together whatever protein suits its passing fancy. It carefully heeds instructions stored on lengthy strands of DNA inside the cell’s nucleus, in a massive library known as the genome: a gigantic set of genes (the recipes for proteins), written in a ribosome-readable chemical code. But genes never leave the nucleus, and ribosomes never enter it.

Bridging that physical gap is a substance called messenger RNA, chemically similar to DNA but physically far more flexible and athletic. Like couriers carrying copies of a royal edict, messenger RNA molecules constantly exit the nucleus, where they were produced as portable copies of one gene or another. They head for the watery suburbs of the cell where protein construction takes place. And there, they find a ribosome, climb in, are fed through the ribosome’s molecular machinery, and get spit out like spent ticker tape once the ribosome has finished reading the recipe and assembling the specified protein product.

Under ordinary circumstances, ribosomes faithfully follow genetic instructions. But with all that whirling and whirring, sometimes things go wrong: The mRNA molecule or the ribosome is defective or, for some other reason, the protein-in-the-making is faulty.

Misspelled or misfolded proteins can wreak havoc. Happily, cells have “quality control” teams that can pick apart poorly produced proteins, tear up malfunctioning messenger RNA and retire rotten ribosomes.

In exploring that process, Stanford biochemist Onn Brandman, PhD, and colleagues at the University of California and University of Utah may have turned molecular-biological dogma on its head. In a new study in Science, Brandman and his associates report that they’ve identified a member of the quality-control squad, a protein called rqc2, that gloms onto stalled ribosomes – and then does something no protein has ever previously been shown to do: call out for the delivery of two particular amino acids, which get attached in random sequences to the aberrant protein under construction.

“Our results defy textbook science, showing for the first time that the building blocks of a protein, amino acids, can be assembled without the standard blueprints,” Brandman told me. “In the case we observed, neither DNA nor messenger RNA but a protein directs that a pair of amino acids be randomly added, in small stretches, to the ends of proteins that have stalled mid-synthesis. The function of these ‘tails’  isn’t known. But in yeast, elevated levels are correlated with proteotoxic stress, a condition that in humans may be involved in disorders such as Alzheimer’s, Parkinson’s and Huntington’s disease.”

Previously: Key to naked mole rat longevity may be related to their body’s ability to make proteins accurately and Night of the living dead gene: Pseudogene wakes up, puts chill on inflammation
Photo by Iain Farrell

Infectious Disease, otolaryngology, Public Health, Research, Science, Stanford News

New version of popular antibiotic eliminates side effect of deafness

New version of popular antibiotic eliminates side effect of deafness

About five years before he died, my father was prescribed gentamycin, one of the most commonly used class of antibiotics called aminoglycosides, for a heart infection of unknown origins. The antibiotic successfully cured him of the life-threatening infection, but it also left him with a life-changing side effect, one with the strange-sounding name of oscillopsia.

Oscillopsia is a balance disorder that creates the illusion of an unstable visual world in its patients that can be quite disabling. For my father, it messed with his tennis game in the remaining years of his life and forced him to sit on the couch when he would rather have been running around with his grandchildren. But he was lucky. In addition to balance disorders, side effects from these cheap and extremely effective antibiotics that have been used for decades worldwide, include high rates of deafness and kidney damage.

ChengNow, Stanford researchers led by otolaryngologoist Alan Cheng, MD, (pictured at left) and Tony Ricci, PhD, have made a modified version of these drugs that successfully treats infections without the side effects of deafness and kidney damage. In a press release on the study, which was published Friday in the Journal of Clinical Investigation, I wrote about a boy (whose story is also told in this Stanford-produced video) who lost his hearing from these antibiotic treatments during his battle with cancer:

On Christmas Eve, 2002, Bryce Faber was diagnosed with a deadly cancer called neuroblastoma. The 2-year-old’s treatment, which, in addition to surgery, included massive amounts of radiation followed by even more massive amounts of antibiotics, no doubt saved his life. But those same mega-doses of antibiotics, while staving off infections in his immunosuppressed body, caused a permanent side effect: deafness.

“All I remember is coming out of treatment not being able to hear anything,” said Bryce, now a healthy 14-year-old living in Arizona. “I asked my mom, ‘Why have all the people stopped talking?’ He was 90 percent deaf.

These are extremely important life-saving drugs, Ricci, a basic scientist and expert on the biophysics of the inner ear, told me. But they could be so much better if patients didn’t have to risk their toxic side effects. So far, the new versions of the drug that he and colleagues developed have only been tested in mice, but the hope is to conduct clinical trials as soon as is safely possible. “If we can eventually prevent people from going deaf from taking these antibiotics, in my mind, we will have been successful,” Ricci said. “Our goal is to replace the existing aminoglycosides with ones that aren’t toxic.”

The new drugs have not yet been tested as to whether they still cause balance disorders. That’s on the docket for the future. But my article describing this wedding of basic science with clinical treatment is a hopeful reminder of the importance of modern-day scientists to public health.

Previously: Listen to this: Research upends understanding of how humans perceive sound; Stanford developed probe aids study of hearing and Studying the inner ear and advancing research in developmental biology

Research, Science, Stanford News

Some of Stanford Medicine’s biggest developments from the last year

Some of Stanford Medicine's biggest developments from the last year

DiehnWhen pondering what were the biggest medical stories out of Stanford Medicine this year, we turned to some very reliable sources: our office’s team of talented science writers, who regularly talk with and write about the work of the school’s researchers. What did these wordsmiths pick as some of the most important developments? In no particular order:

  • a study showing that the DNA of peanut-allergic kids changes with immune therapy
  • researchers’ tracking of a mysterious polio-like illness in kids
  • the development of a blood test that could provide rapid, accurate method of detecting solid cancers
  • a study showing that an infusion of young blood recharges the brains of old mice
  • the invention of a nanotech microchip to diagnose type-1 diabetes
  • an analysis showing that a gene variant puts women more at risk of Alzheimer’s disease than men
  • the development of a noninvasive way to detect heart-transplant rejection weeks or months earlier than previously possible
  • a study showing that breast cancer patients with bilateral mastectomy don’t have better survival rates
  • the discovery of brain abnormalities in patients with ME/chronic fatigue syndrome
  • the development of a technique for measuring insulin levels in fruit flies, giving researchers a powerful new way to study diabetes

Photo, of radiation oncologist Maximilian Diehn, MD, PhD (who shared senior authorship of a paper describing how a blood sample could one day be enough to diagnose many types of solid cancers), by Norbert von der Groeben

Infectious Disease, Research, Science, Stanford News

Science Friday-style podcast explains work toward a universal flu vaccine

Science Friday-style podcast explains work toward a universal flu vaccine

I had the pleasure of teaching a class this fall to a group of mostly chemistry and chemical engineering graduate students, helping them improve their skills communicating about their science with the public. For her assignment, graduate student Julie Fogarty recorded this Science Friday-style segment on work taking place in the lab of chemical biologist and bioengineer James Swartz, PhD. Swartz and colleagues are trying to develop a universal flu vaccine that would eliminate the need to get a new vaccine each year – something all of us would probably appreciate. (Here I’m thinking about my colleague Michelle Brandt, who recently suffered the woes of not finding time to get her kids vaccinated.)

Julie’s brother Skyped in for his role as Science Friday host extraordinaire Ira Flatow in this segment, while Julie played the enthusiastic and articulate guest. It’s often difficult to explain complex science in audio format, but Julie does a fantastic job explaining the work in way that is very visual. I love her description of the flu virus as a little mushroom.

(A previous blog entry featured another student, Rhiannon Thomas-Tran, who produced a great video about her work.)

Previously: Working to create a universal flu vaccine, Graduate student explains pain research in two-minute video and How one mom learned the importance of the flu shot – the hard way

Genetics, Neuroscience, Research, Science, Stanford News

Yeast advance understanding of Parkinson’s disease, says Stanford study

Yeast advance understanding of Parkinson's disease, says Stanford study

It’s amazing to me that the tiny, one-celled yeast can be such a powerful research tool. Now geneticist Aaron Gitler, PhD, has shown that the diminutive organism can even help advance the understanding of Parkinson’s disease and aid in identifying new genes involved in the disorder and new pathways and potential drug targets. He published his findings today in Neuron and told me in an email:

Parkinson’s disease is associated with many genetic and environmental susceptibility factors. Two of the newest Parkinson’s disease genes, EIF4G1 and VPS35, encode proteins involved in protein translation (the act of making protein from RNA messages) and protein sorting (shuttling proteins to the correct locations inside the cell), respectively. We used unbiased yeast genetic screens to unexpectedly discover a strong genetic interaction between these two genes, suggesting that the proteins they encode work together.

The proteins, EIF4G1 and VPS35, have changed very little from yeast to humans. Gitler and his colleagues showed that VPS35 interacts functionally with another protein implicated in Parkinson’s disease, alpha-synuclein, in yeast, round worms and even laboratory mice. As Gitler described:

Together, our findings connect three seemingly distinct Parkinson’s disease genes and provide a path forward for understanding how these genes might contribute to the disease and for identifying therapeutic interventions. More generally, our approach underscores the power of simple model systems for interrogating even complex human diseases.

Previously: Researchers pinpoint genetic suspects in ALS and In Stanford/Gladstone study, yeast genetics further ALS research

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