New blog launched through SciLogs

Last week I finally launched my blog Science Extracted through SciLogs. I am so excited to be part of this network of science bloggers who have such diverse interests and perspectives. There will sometimes be overlap in what I post here and on Science Extracted but I will generally try to post unique things on each site so follow me on both! I see Bench and Beyond as a way to try out new ideas and formats and perhaps be a bit more personal.



Without further ado, here is my latest post on Science Extracted:



This week in science 100 years ago: an unexpected mystery

Shiraz on a shoestring! First installment: Doohickey 2013 California red blend

Last night I was in the mood for wine. I should clarify that I am always am in the mood for wine but concerns for health and work productivity temper my hobby to a couple nights a week. But on this particular evening I saw an older couple enjoying a bottle of white at the thai restaurant my husband and I were at.

I am very susceptible to temptation when I see two people drinking wine. It seems so intimate and shared compared to drinking separate beers. It is also more aspirational: the promise of being transformed to a more decadent and romantic life with the pop of the cork.

So when we got home it was the same old decision, should we open a "good" bottle (in the $10-$20 range) or stick with good ol' 3 buck chuck? With 30 meer months away my standard of living has increased non-commensurately with my postdoc salary. 3 buck chuck (then 2 bucks) was fine in my early 20's but now, I crave complexity. 

I recognize that life is even harder for postdocs trying to raise a family, as opposed to a 14 lb. mutt, but living on a postdoc salary does make things tricky for someone with sommelier tastes. While decent wines can be found in the $10-20 range, too often my husband and I crack open a bottle on Friday only to be overcome with the alcohol after-taste or underwhelmed with watery-ness. 

Thus, the regular feature: Shiraz on a Shoestring. Last night's wine was a proprietary red blend from "Doohickey" made from California grapes, 2013 vintage. Selling for around $14, it has a pleasing deep red color. It's nice nose accurately predicts an oaky and vanilla-filled beginning with mouthfuls of blackberry. It is consistently strong at the start and finish without any alcohol after-taste. I would highly recommend and just in time for the weekend!

Reader Request: Where have all the honeybees gone?

Spring is in the air, and so too are the bees. But spring is also a reminder that the US and Europe are still experiencing a mysterious phenomenon where more bee hives than usual are not surviving the winter. This topic was a reader request and as I am infinitely grateful to my blog readers, I tried to get on it as soon as possible and was excited to see that there have been new developments in the last months.

Starting in 2006, beekeepers noticed a drastic increase in the failure of bee colonies. The phenomenon came to be known as colony collapse disorder (CCD) where adult bees were simply disappearing, leaving behind hives with a queen and often enough, honey stores.

Honey aside, honeybees play an incredibly large role in pollinating commercial crops, including almonds and many fruit, worth $15 billion in the US (1). At its peak in the 2007-2008 season, 35% of colonies collapsed. Though CCD has been on the decline in recent years, with 23% of colonies collapsing last year, scientists and farmers alike are still concerned in what causes CCD and how to prevent it.

Leading theories include neonicotinoid pesticide use, the parasitic mite Varroa destructor, the parasitic fungi Nosema, and decreased nutritional diversity and availability.

Nosema and parasitic mites were both implicated early on in the investigation, but there are cases of CCD without any infection and conversely, healthy colonies that are infected.

Pesticide use has long been a suspect. Last year a study from Harvard found that clothianidin and imidacloprid led to loss of six of 12 colonies (2). However many in the science blogosphere – as well as the company that makes imidacloprid – have criticized the amount of pesticide tested, the sample size, and the statistical analysis.

Several other studies have found that bees exposed to these pesticides were more susceptible to Nosema infection due to immune suppression (3,4). Neonicotinoid exposure also impaired olfactory learning and memory (5). Amid mounting studies, the European Union banned neonicotinoids in 2013. The US has been slower to change regulation but the Environmental Protection Agency (EPA) said earlier this month that it was unlikely to approve new neonicotinoid pesticide use as it continues to assess pesticide safety for bees.

At the same time, a study published in March by researchers at the EPA, the US Department of Agriculture (USDA), and University of Maryland found that only field doses at the extreme end had a significant effect on colony survival in the three-year study (6). They conclude pesticide use is “unlikely a sole cause of colony declines.”

Thus, despite intermittent news stories suggesting otherwise, no one factor has been able to account for CCD. The USDA, who is leading the federal response, says it is likely a combination of two or more of these factors.

Last month researchers in Australia published a study showing how stress from a variety of sources can rapidly lead to collapse in the colony. They attached tiny radio trackers to bees to examine their foraging behavior (side note: they literally glued them to the bee’s chest). They induced bees to start foraging at a younger age (precocious foraging) by creating colonies with younger demographics (7).

Younger forager bees were less successful at bringing back food and were more likely to die while trying to forage. The consequent decreased food supply led the remaining bees in the hive to start foraging at an even younger age.

Stresses such as starvation and disease are known to cause precocious foraging in bee populations. The researchers used their data to model bee population dynamics under chronic stress and showed that precocious foraging led to a positive feedback loop w

here progressively younger bees were even less successful, leading to a rapid decline in the colony.

While previous models have only been able to account for a slow decline, the researchers say they are the first to “display dynamics of colony population collapse that are similar to field reports.”

“The failure of a honey bee colony is a breakdown of a society…Understanding why and how colonies fail therefore requires more than analyzing how individual bees react to stressors,” said the researchers.

A review published in Science last Month agrees with this assessment saying that while chronic exposure to multiple stressors is driving CCD, “the precise combination apparently differs from place to place.”  (8).

They go on to say “Although the causes of pollinator decline may be complex and subject to disagreement, solutions need not be; taking steps to reduce or remove any of these stresses is likely to benefit pollinator health,” The authors call for growing more bee-friendly flowers and decreasing dietary stress as well as decreased use of pesticides.

References:

1. “Vanishing Bees.” National Defense Resources Council. <http://www.nrdc.org/wildlife/animals/bees.asp> Retrieved April 13^th, 2015.

2. Lu, C. Warchol, K.M., Callahan, R.A. (2014). Sub-lethal exposure to neonicotinoids impaired honey bees winterization before proceeding to colony collapse disorder. Bulletin of Insectology 67 (1): 125-130.

3. Pettis, Jeffery S., Johnson, J., Dively, G., et al. (2012). Pesticide exposure in honey bees results in increased levels of the gut pathogen Nosema. Naturwissenschaften 99 (2): 153–8.

4. Di Prisco, G., Cavaliere, V., Annoscia, D., et al. (2013). Neonicotinoid clothianidin adversely affects insect immunity and promotes replication of a viral pathogen in honey bees. PNAS 110(46):18466–18471, doi:10.1073/pnas.1314923110.

5. Williamson, S.M., Wright, G.A. (2013). "Exposure to multiple cholinergic pesticides impairs olfactory learning and memory in honeybees". J of Experimental Biology 216 (10): 1799–807.

6. Dively G.P., Embrey M.S., Kamel A., Hawthorne D.J., Pettis J.S. (2015) Assessment of Chronic Sublethal Effects of Imidacloprid on Honey Bee Colony Health. PLoS ONE 10(3): e0118748. doi:10.1371/journal.pone.0118748.

7. Perry, C., Sovik, E., Myerscough, M.R., Barron, A.B. 2015. Rapid behavioral maturation accelerates failure of stressed honey bee colonies. PNAS 112(11): 3427–3432, doi: 10.1073/pnas.1422089112.

8. Goulson D, Nicholls E, Botías C, Rotheray EL. (2015). Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science. 2015 Mar 27;347(6229):1255957. doi: 10.1126/science.1255957.

A rainy forecast for science in the US on a rainy afternoon - but with suggestions from top scientists on how to fix the forecast

I remember getting hints of the tough times scientists were having even before starting graduate school just before the Great Recession. Early on to mid-way through graduate school professors would try to ameliorate our worries that “this was a good time to be in school” because “things would get better by the time we graduated.” Then of course came the 2013 sequestration and by the end of graduate school I wasn’t hearing any more optimism.

Now, in my postdoc, there is nearly constant talk about the worry to find a job, the salary for postdocs who are often trying to raise a family, talk of a longstanding professor not having their grant renewed and another faculty member having to leave the department and start again somewhere else.

So much so that it is easy to become immune to the negative climate and accept that this is the way things are with funding rates in the teens, versus 30% in the early 2000s. After all, there is nothing that can be done, right? Also, let’s not get too down on ourselves as PhD graduates still have lower unemployment rates than the general population.

But then my PhD advisor sent me an article published in PNAS, written by four of the top scientists in the US including Dr. Bruce Alberts who was awarded the National Medal of Science last year. In the article they lay out the “systemic flaws” in the “US biomedical research ecosystem” and their proposals for slowly fixing the system.  

They explain that after WWII, America adopted the belief that research would expand indefinitely. What followed was a drastic increase in the size of universities and continual increase in the budget of the National Institute of Health (NIH), the major funding agency for research, up until the 1990s. But as funding slowed, there is an unprecedented amount of demand for grants due also to an increased workforce and increased costs of doing research.

The funding system:

The current funding system for science is generally a lengthy process where professors apply for research money (and increasingly their own salary – the authors point out) through grant agencies, which can be governmental or private. The proposed projects, as well as the previous publication record of the professor are evaluated. But the system rewards only those projects that will most likely succeed and produce results quickly (otherwise those grants are not renewed) and those that have a clear benefit to science.

But as many have pointed out, including the authors of the article, many scientific advances have come from basic scientific endeavors without any foreseeable translational benefit. The current system stands in the way of developing new approaches or paradigms.

Of course it makes sense that the National Institute of Health has an impetus to fund those studies that will likely improve the health of Americans. The alternative governmental source, the National Science Foundation, however only has $7 billion instead of the over $30 billion budget of the NIH.

Yesterday I attended a talk and was impressed by a pioneering technique to get crystallographic data on very small protein crystals using existing technology. Later the researcher said that he would not have been able to develop this method if he had been at a traditional research institution – he is at Janelia Farms, which is a Howard Hughes Medical Institute (HHMI) research campus where researchers are fully funded without having to apply for research grants and are highly encouraged to take on risky projects. But HHMI investigators are a vast minority of researchers. 

He echoed the same sentiments as those of Alberts, et al.: that the time-consuming process of applying for grants not only takes time away from scientific reflection but also can be a drain on excitement and motivation – in some ways, the most important resource scientists have. He has observed colleagues very excited about a new idea. But by the time that idea got NIH funding two years later, their enthusiasm was attenuated.

The pressure to publish:

Because high-impact publications are the gateway to getting more funding, the authors claim that the current hypercompetitive environment encourages researchers to both rush to publish their results, sometimes cutting corners, and also to exaggerate their findings and the significance of their work. They suggest that this has contributed to an upward trend in the inability to replicate published results.

I have personally observed that the inability to reproduce results has led to a lot of wasted time, money, and morale. If the results of an experiment differ from those published and accepted in the field, the first instinct is to check all the numerous variables, including methodology, reagents, and the experimenter themselves (especially if the researcher in question is a student).

Their solution is to de-emphasize the importance of publications in analyzing the merit of scientists. Rather funding agencies should also examine the quality of the researcher’s work and their overall contribution to the science field; have they contributed to a new break-through or paradigm shift?

The ever-increasing PhD workforce:

Scientists have been trying to call attention to the unsustainability of the increasing workforce for years. But science currently operates on a pyramidal scheme where low-paid graduate students and postdocs carry out the brunt of science with the hope of one day having a lab of their own. Thus each lab produces many more trainees (sometimes dozens) than can possibly replace that single professorial position. As a result, the number of PhD graduates is increasing while the number of academic positions is relatively stagnate. It used to be the private and governmental sector could absorb some of these graduates but now those markets are also becoming saturated.

They suggest, as have others, that the only viable option is to de-incentivize the over-reliance on students and postdocs by limiting the amount of research funds that can be used to pay their salaries and limiting the number of years postdocs could be paid from federal funds. Instead, they would be paid through training grants and personal fellowships: forcing universities to accept less graduate students. Additionally many have called for an increase in the salary of students and postdocs so that researchers would see staff scientists as a more viable option. A result of this is that laboratories would hire less people and lab sizes would shrink, but Alberts, et al. makes the argument that since staff scientists are more permanent, productivity would not decrease.

In addition, it would seem to me that professors would have more time to mentor the students and postdocs they do have.

Importantly the authors point out that increasing the NIH budget, while helpful, is not a permanent solution as this simply drives growth in institutions that will quickly eat up any new resources. Rather they call for gradual policy changes in how science is funded that will take effect over ten years.

As it takes a long time to change the direction of a bulky ship such as the science enterprise, I can only hope that there will be more communication between scientists and policy makers and more action in government. As these recommendations appear to be bipartisan there is no reason not to act now.

Beyond the Bench: Poetry Edition

In college I took a poetry writing class for fun. I really enjoyed the writing and editing process though now I can't bring myself to read my poems about smoking Pall Malls and rebelling against gender norms. During an office visit my wonderful professor recommended that I use my unique background in science as inspiration in my poems. But I was not really in a place scientifically and as a fledging poet to fully realize her vision. But what I took away from her suggestion was the possibility to merge my two interests – how science and poetry are not inherently polar opposites.

I have heard, mainly in abstract terms, how art and poetry can change the way one thinks and approaches science. As someone who enjoys painting and writing, I also unfortunately struggle to imagine how this is done practically – I think about science and then when I need a break, I paint. Sometimes I paint about science and technology but I have not found a way, consciously at least, to bring art into science (aside from some nice Illustrator images for presentations).

And so I have come to highly respect and appreciate those who can merge the two worlds and by doing so, enrich both. In that vein, I will be posting about some poets who were also scientists (or scientists who were also poets) or who brought scientific themes to their poetry.

Margaret Cavendish Lucas was a philosopher, writer, and scientist of the seventeenth century. In 1667 she sparked a debate by asking to attend a session of the Royal Society of London and was eventually allowed to attend to see Robert Boyle demonstrate several experiments. She wrote about topics such as the scientific method and how the matter that makes up humans, rather than a divine God, enabled us to think. Below is one of her more famous poems.

Of Many Worlds in This World

Just like as in a nest of boxes round,
Degrees of sizes in each box are found.
So, in this world, may many others be
Thinner and less, and less still by degree:
Although they are not subject to our sense,
A world may be no bigger than two-pence.
Nature is curious, and such works may shape,
Which our dull senses easily escape:
For creatures, small as atoms, may be there,
If every one a creature's figure bear.
If atoms four, a world can make, then see
What several worlds might in an ear-ring be:
For millions of those atoms may be in
The head of one small, little, single pin.
And if thus small, then ladies may well wear
A world of worlds, as pendants in each ear.

Her writing strikes me as straightforward for the time – less than 50 years after Shakespeare was producing the works that would perplex middle and high schoolers for centuries. The poem encapsulates the excitement of scientific discovery. Things at the cellular level may be just as exciting as the planets and space, which seems to capture the imagination of the general public much more. With the line: “A world may be no bigger than a two-pence,” I envision a bustling cellular city in the vein of London circa the industrial revolution: people pushing their wares on carts along axon tracks, the protein patrolmen monitoring the streets for people in the wrong place, and the occasional bacterial thief that threatens to disturb the whole society.

The last lines, “ladies may well wear a world of worlds, as pendants in each ear” evoke the aristocracy to which Cavendish belonged. And just as we may be blind to the cellular and atomic worlds underlying our being, aristocrats were blind to the troubles as well as essentiality of the working class. The line “our dull senses easily escape” could be a critique of her class and the dullness of being a woman in a time when women had no access to science. Though I could be misinterpreting it through my modern lens, “Nature is curious,” suggests that it is in human nature, which also encompasses women, to be fascinated by the world around them.

Genetic factors associated with autism also linked to higher intelligence

From “Rain Man” to the BBC’s “Sherlock Holmes”, popular culture portrays autistic people as having astounding abilities in areas of memory and deduction while lacking basic social skills.  While most people with autism spectrum disorder (ASD) are intellectually impaired, research supports the idea that they can have increased cognition in non-verbal areas.

But a study published yesterday by researchers from University of Edinburgh was the first to find a link between genetic factors for autism and higher intelligence in people without the condition.

ASD  is a developmental disability that causes behavioral, learning, and social communication disabilities. One out of 68 children are reported to have ASD in the U.S. according to the Centers for Disease Control and Prevention.

Up till now it was impossible to rule out that cognitive defects seen in autistic individuals were simply did not come from the environment, driven by the social and communication challenges of autism.

At this point, it is helpful to have a brief refresher on genetics: Our genes encode the information that tells our cells what to do. While everyone has the same genes, we have slightly different versions, or alleles, of the genes that help make us different from each other. These versions are passed on to our children.

Sometimes a single rare mutation can cause disease, such as in Cystic Fibrosis. But often it is more complex with mutations in different genes working together or with the environment to cause disease.

This more complicated version is the case for ASD. Last year it was shown that many gene alleles that are risk factors for autism are actually common in the general population but a combination are needed to cause autism.

The researchers wanted to see if these common risk alleles for autism were linked to cognition. They examined nearly 10,000 adults in the general population (i.e. without autism) and tested their cognitive performance on four tests as well as analyzing their DNA for alleles known to be associated with ASD.

They found a positive correlation between the presence of ASD risk-alleles and general cognitive performance. Specifically, those with the ASD-associated alleles did better on tests for verbal fluency, logical memory, and vocabulary.

The researchers suggest this finding will give insight into why some autistic people display incredible intelligence in certain areas and help understanding of how genetic factors for autism change brain function.

Clarke, J-K., et al. (2015). Common polygenic risk for autism spectrum disorder (ASD) is associated with cognitive ability in the general population. Molecular Psychiatry. doi: 10.1038/mp.2015.12