Science blog

29 November 2013

From base pairs to bedside...

Katie Howe and Allan Sudlow report on their experiences from the EMBL Genomics, Medicine and Society conference.

The first draft of a complete human genome was published in 2001. It took 13 years to complete and cost a massive $2.7bn. Since then the cost of genome sequencing has plummeted. 12 years on it is now possible to sequence a human genome for less than $1000.

In light of these rapid advances, the EMBL Genomics, Medicine and Society conference brought together a diverse audience to explore how new genomic technologies may benefit public health and to discuss some of the challenges for the future. The conference was part of EMBL’s Science and Society conference series, which aims to consider how advances in biology impact on society. Our TalkScience events have explored social and ethical consequences of genetic technologies in the past, whether it be genetic testing kits sold to the public, or pre-implantation genetic testing in fertility clinics.

During the conference we heard about the wide range of projects that aim to enhance our understanding of genome function and help us pinpoint the genetic mutations that lead to particular diseases. Examples include the 1000 Genomes Project and the International Cancer Genome Consortium. Recently, David Cameron committed £100m for sequencing the genomes of 100,000 people in the UK. These projects generate huge quantities of valuable genomic information but this presents serious problems for data storage and management. Professor Eric Green, Director of the National Human Genome Research Institute, noted that, “We are no longer data limited. We are analysis limited”.

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The Human Genome (Shutterstock)

In the British Library’s Science team we are interested in the generation, storage and re-use of scientific information and data, so were particularly keen to hear Dr Paul Flicek’s presentation on “genomics as an information science”. Paul observed that if the price of a Ferrari had fallen at the same rate as genome sequencing it would now cost less than a dollar! He noted that nowadays, a major cost associated with genome sequencing is the storage and management of genomic information and this is set to become the dominant cost as the price of the sequencing itself drops further. Paul reminded us that in order to fulfil the promise of genomic research treating disease, ambitious plans to sequence the genomes of huge numbers of individuals must be accompanied by major investment in the infrastructure to support data management and advanced data analysis.

The shrinking cost of genome sequencing has also led to a thriving industry in direct-to-consumer (DTC) genetic testing. For $100, personal genome companies such as 23andme and Navigenics offer members of the public the opportunity to have their DNA tested and uncover their predisposition to certain genetic conditions, which may then inform their healthcare options. Just this week, the United States Food and Drug Administration (FDA) issued a warning to 23andme to cease the marketing of their personal DNA spit kit due to concerns over the “public health consequences of inaccurate results” from their service. But others have argued that consumers have the right to their own genetic information, and the emphasis should be on educating doctors and patients about how to interpret the results rather than banning these tests. This story illustrates the controversy surrounding genomic medicine.

While personalised genomic medicine holds enormous potential for public health, conference speaker Professor Tim Caulfield warned that the benefits of DTC genetic testing are often amplified in promotional material. Tim’s opinion was that getting enough exercise, eating healthily and not smoking will have greater health benefits than many of the unproven personalised genomic approaches that are being marketed.

Whilst in Heidelberg, we also found some time to explore some of the local sights. We visited the ancient Heidelberg castle and the “student prison”. But the highlight for us was the German Apothecary Museum - a veritable treasure trove of historical scientific equipment. We spotted a 19th century Bunsen Burner - very topical since the iconic burner was invented by Robert Bunsen and his colleague Peter Desaga at Heidelberg University in 1851.

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German Apothecary Museum (Photo: Allan Sudlow)

We left Heidelberg thinking that although genomic technologies are undoubtedly a source of great promise, they also present many ethical, social and legal issues. There remains a huge challenge in translating recent advances in genomics into tangible healthcare solutions.

Katie Howe and Allan Sudlow

22 November 2013

Decision making in the twilight of uncertainty

Johanna Kieniewicz writes on her impressions from the Living With Environmental Change partnership’s annual assembly.

At the Living With Environmental Change partnership’s annual assembly, Defra’s Chief Science Adviser, Dr. Ian Boyd, presented a stark statistic: in a recent Defra focus group, two thirds of the participants reported that they distrusted scientists. Although we didn’t discover the context for this revelation, many of us walked away from the meeting thinking about how we could do better. How can we ensure more policy-relevant science? How can we communicate it better? And how can we reassure the general public that uncertainty in science is perfectly normal and is not a reason for distrust?

At this same meeting, I was delighted to present on the Science Team’s Envia project. Envia is a tool to improve the discovery and access of environmental information, and it fits the aims of this meeting nicely: that is, to provide researchers, policymakers and practitioners with the evidence and tools they need to make sound decisions in an uncertain world. With a general theme of ‘decision making in the twilight of uncertainty’, the LWEC Assembly brought together a wide range of academics, representatives from research councils and government bodies such as Defra and the Environment Agency, to discuss challenges pertaining to uncertainty and how they might be overcome. Perhaps most importantly, how can we best equip our decision makers with the evidence they need to make sound decisions pertaining to climate change, bovine tuberculosis, or our energy future—when the repercussions of actions taken in any of these areas are far from certain?

 

Dave Rafaelli presenting at LWEC 2013
Dave Rafaelli (U. York) presenting at LWEC 2013

So, while we at the British Library would like to think that we are doing our part around developing an evidence base that is suitable for use by researchers and practitioners alike, we recognise this is one small part of a much bigger picture. Ultimately, this information must be drawn together, synthesised in a way that enables policymakers to make sound decisions based on all the available evidence. And areas of uncertainty should be laid out clearly. Boyd emphasised the importance of scientists presenting balanced arguments, where all evidence is laid bare.  Although we, as scientists (who are also citizens), might personally advocate a particular solution, when communicating in a professional context we must remain unbiased. To be clear, there needs to be the appropriate weighting given to evidence – if 95% of the evidence points one way, we wouldn’t expect the small proportion of contrary evidence to be given the same level of attention. In order for the public to trust scientists, they need to know that we aren’t reading the evidence to see only what we would like to see in it.

With presentations looking at how individual research projects are dealing with uncertainty, including perspectives from the social sciences, here are a few nuggets of wisdom that I thought it would be useful to pass on:

  • Scientists should always be honest about what they don’t know. The sources of uncertainty in their models should be explicit — and they need to communicate those limitations with humility. While it might be tempting to give policymakers ‘simple’ answers, scientists must keep the complexity intact. Politicians are accustomed to weighing up complex situations and multiple sources of data. When it comes to making potentially irreversible decisions pertaining to the environment, giving policymakers the whole story is essential both to sound decision-making and establishing trust.
  • Uncertainty isn’t a completely foreign concept to most people. We all live in an uncertain world, and have to make decisions based on our best guesses. From choosing whether or not to bring an umbrella with us when we leave the house, to playing card games, to getting a mortgage on a property, uncertainty is not something that those who claim to be distrustful of scientists are actually unfamiliar with!
  • There are things to be learned from other fields, particularly the humanities and social sciences who are thinking about uncertainty in both psychological and philosophical terms. Moreover, economics is a field that that policymakers are often more comfortable with than science, yet it is also rife with uncertainty. Although it can be argued that the studious ignoring of economic uncertainties led to the financial crisis, there are lessons to be learned from that as well.
  • There is a huge need for research that straddles disciplinary boundaries. Several speakers pointed out the necessity for social science perspectives on global change issues, alongside the scientific. There is also a need for research that is ‘fit for purpose’ when it comes to policy implementation. However, the speakers pointed out, this research isn’t necessarily considered ‘groundbreaking’; it does not lead to Nature papers —and thus is not the sort of research most ambitious academics are interested in pursuing.

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 The audience at the LWEC Assembly took these messages to heart. We in the Science Team at the Library will be thinking about how some of these ideas can be reflected in what we do. And hopefully we aren’t doing too badly. Our Envia pilot project is already improving the way in which flooding researchers and practitioners can find information that is relevant to their work. DataCite, for which we are the UK lead, enables and encourages the citation and sharing of research data. On the biomedical front, we recognise that even when a paper is openly available, that does not mean it is accessible (from the perspective of intelligibility). Our recently launched Access to Understanding science writing competition encourages early career researchers to summarise academic articles in an engaging and accessible manner. And our upcoming Beautiful Science exhibition will be looking at the visualisation of scientific data, encouraging audiences to consider how science is communicated visually. So while we can’t crack the uncertainty in climate models, we would like to think that we are helping researchers and practitioners get the evidence they need for their work and communicate more effectively to policymakers in an uncertain world.

 

If you are interested in looking into this in a bit more detail, here are a few useful resources for you!

A video of the LWEC Assembly will be posted on the ESKTN TV Youtube Channel

Sense about Science GuideMaking Sense of Uncertainty: Why Uncertainty is a part of science.

David Spiegelhalter’s Understanding Uncertainty website. He also wrote this excellent piece in Nature about interpreting scientific claims

Royal Society meeting proceedings on Handling Uncertainty in Science

Making Science Count in Government – a much debated (also see comments section) piece by Ian Boyd, published in E-Life

15 November 2013

Explaining Focal Osteoporosis to My Gran

As the BL Science Team and Europe PubMed Central launch the second year of Access to Understanding, a plain English science writing competition, Allan Sudlow reflects on the challenges of explaining science to a broad audience.

Scientific journal articles are written by scientists to be read by other scientists. Those scientists are usually experts on the topic they are reading about. Thus, journal articles tend to be written in a highly technical style, laden with acronyms and jargon, and this ‘compressed’ language is used to squeeze in as many facts as possible, within a given word count. There is a huge amount of assumed knowledge needed to even begin to understand what is being said. Scientists fall into writing in this way as it’s the most efficient way of communicating with their peers. But what about others who are interested in the latest research findings but aren’t part of this scientific community?

Access to Understanding is a science writing competition aimed at early career scientists organised by the Science Team at the British Library, in collaboration with Europe PubMed Central. Competition entrants choose from a selection of free-to-access articles in this online biomedical literature resource, and describe the science in 800 words or less. They need to explain, in plain English, the reason why the research was done, what the scientists found, and why those findings are important. This is challenging.

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Source: Shutterstock Copyright: Ivelin Radkov

Entries need to be self-explanatory and represent the science accurately. Entrants are encouraged to be informative but not patronising, and engaging without over-selling the importance of the research findings. Knowing your audience is key but this, in itself, is not easy when that audience can be anyone who is interested enough to read the summary. The advice we have provided to competition entrants aims to address some of these challenges by setting out specifics in the context of the competition, giving helpful writing tips, and highlighting the views of the judges of the 2013 competition.

So, why would any jobbing scientist want to enter the Access to Understanding competition in the first place?   Well, I predicted the number of entries last year as 50. We received just under 400. This was a fantastic response and it was interesting to hear some of the motivations that the entrants had for taking on this difficult challenge. For some, it was recognising the importance of communicating cutting-edge science beyond their own community, for others it was developing their writing skills in this context. Some scientists saw this as a way to showcase these skills to a broader audience, and have since gone on to pursue their interests in this domain, entering further science writing competitions and seeking employment in roles that require an ability to write about science for a broad audience.

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Source: Shutterstock Copyright: Sebastian Kaulitzki

To me, the challenges and the motivations for entering a competition like Access to Understanding, are summed up by the slightly obscure title of this blog post. Before you lambast me, I recognise that many grandmothers may be scientific or clinical research experts, though not mine! Last year’s competition entrants and judges agreed that being able to explain a complex piece of science to a relative who as has no knowledge of the subject, and keep them interested, is a great test of your ability to communicate science effectively. So if you have heard of ‘osteoporosis’ but aren’t sure what factors influence how and why it happens, find out more by reading about it and other scientific findings, beautifully explained, in the shortlisted entries from 2013.

Good luck to all this year’s entrants to Access to Understanding. We will be reading and evaluating your entries with critical interest, and admiration!

13 November 2013

Science-writing competition

Access to Understanding is a prestigious, international science-writing competition aimed at PhD students and early career post-doctoral researchers, developed by Europe PubMed Central and The British Library.

The winner will receive an iPad and have their entry published in eLife. Read on for more…

Access to Understanding 2014 flyer

For more information: http://EuropePMC.org/ScienceWritingCompetition
Questions: Engagement@EuropePMC.org

Access to Understanding is supported by the Europe PubMed Central Funders Group.

08 November 2013

Why not cite data?

Rachael Kotarski, our Content Expert for scientific datasets, explains why citing data as well as the article is the way forward.

In a previous post, Lee-Ann Coleman looked at citations in science, asking what should be cited, and what a citation means. The answers to these questions are not necessarily simple, but one response we have been hearing (and that we support), is that data needs to be cited.

Citing data not only gives credit to those who created or gathered it, but can also give some kudos to the repository that looks after it. Despite the fact that data is also key to verifying and validating research, it is not yet standard practice to cite it when writing a paper. And even if it is cited, it is rarely done in a way that allows you to identify and access that data.

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Citation should connect the literature to its data foundations. Image source: Shutterstock.

As part of the Opportunities for Data Exchange (ODE) project, we investigated data citation and the ways in which data centres, publishers, libraries and researchers can encourage better data citation.

What does ‘better data citation’ look like and how do we encourage it to happen? We examined three aspects of current practice in order to answer this question:

  • How data is cited?
  • What data is cited?
  • Where is data cited within the article?

How to cite
A data citation needs to contain enough information to find and verify the data that was used, as well as give credit to those who spent considerable time/money/effort generating or collecting the data. The DataCite recommended data citation is just one example of how to include details that support these aims (and it’s pretty simple!):

Creator (publication year): Title. Publisher. Identifier.

What to cite
Data are not necessarily fixed, stable or homogenous objects, so citing them can be considerably more complicated than for articles. It is important for testing reproducibility that regardless of subsequent changes to the data or subsets of it, they are cited as used. Aspects such as the version used or date downloaded should also be encapsulated in the citation, where necessary. Linking users via an identifier (such as a DOI as used by DataCite) to the location of that exact version or subset of the data is also important. An example of citing a specific wave of data from GESIS demonstrates this:

Förster, Peter; Brähler, Elmar; Stöbel-Richter, Yve; Berth Hendrik (2012): Saxonian longitudinal study – wave 24, 2010. GESIS Data Archive, Cologne. ZA6242 Data file version 1.0.0, doi: 10.4232/1.11322

Where to cite in the article
Where you cite data in the article may depend on the form of the data being cited. For example, data obtained via colleagues but not widely available may be best mentioned in acknowledgements, and data identified by accession numbers could be cited inline in the body of the article. But the interviewees who participated in the ODE study largely advocated citation of datasets in the full reference list, to promote tracking and credit. In order to do this, data needs a full, stable citation, which also depends on reliable, long-term storage and management of the data. Of course publisher requirements play an important role. But that’s a post for another day!

These are the three ‘simple’ steps to better citation of data, but there are still cultural and behavioural barriers to sharing data. In the ODE report we concluded that the whole community - researchers, publishers, libraries and data centres - all have a role in promoting and encouraging data citation.

ODE

The recent Out of Cite, Out of Mind report has since updated and greatly extended the ODE work, with an excellent set of first principles for data citation:

CODATA-ICSTI Task Group on Data Citation Standards and Practices (2013) Out of Cite, Out of Mind: The Current State of Practice, Policy, and Technology for the Citation of Data. Data Science Journal vol. 12 p. CIDCR1-CIDCR75 doi: 10.2481/dsj.OSOM13-043

I recommend it – and encourage anyone thinking about citing their data (or anyone else’s) to stop thinking and start doing it.

 

01 November 2013

So You Want to be a Scientist?

Call yourself a scientist? Well, before 1833 that would have been a bit tricky. The word didn’t exist. Allan Sudlow delves into the Library’s science collections to discover the origin of this appellation.

As Sydney Ross sets out at the start of his 1962 essay “Scientist: The Story of a Word”:

“..the need for a new word is socially determined, right at the start, and any subsequent changes of denotation, as well as the cluster of connotations surrounding it, are also in response to demands from society.”

Annals of Science, 18 (2), p65-85 (1962).

Ross noted that the designation scientist came with a social shift in the nineteenth century away from the aspirations of established giants of the field, such as Humphrey Davy and Michael Faraday. Both owed their reputations and livelihoods to science but largely eschewed profit in preference to the pursuit of scientific research for enlightenment and public benefit. According to Ross, Faraday never referred to himself as a scientist, describing himself as an experimental philosopher to the end of his career. Ross argues that the implied professional specialism meant that the word scientist made a business of science, presenting the role as another alternative profession to physician, lawyer or clergyman.

General consensus (including the Oxford English Dictionary online entry) is that the term scientist was first used in print in 1834 in an anonymous review of Mary Somerville's On the Connexion of the Physical Sciences in the Quarterly Review.

The Rev. William Whewell, polymath and philosopher, was the author of this somewhat jocular review. He restated his thoughts on this coinage more formally a few years later:

 “As we cannot use physician for a cultivator of physics, I have called him a physicist. We need very much a name to describe a cultivator of science in general. I should incline to call him a Scientist. Thus we might say, that as an Artist is a Musician, Painter, or Poet, a Scientist is a Mathematician, Physicist or Naturalist.”

Preface to The Philosophy of the Inductive Sciences (1840).

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William Whewell by J. Rylands, albumen carte-de-visite, 1860s, NPG Ax18390, under CC BY-NC-ND 3.0

In this same piece, Whewell draws comparisons to derivations for others' roles including Journalist and Tobacconist, and a joke about the clergy:

“I may notice another example of the necessity of avoiding ambiguous words. A philosopher who makes method his study, would naturally be termed a Methodist; but unluckily this word is already appropriated to a religious sect.”

Debate over the word was still raging in the early part of the twentieth century, as correspondence in the letters section of a 1924 edition of Nature reveals:

“Let me therefore plead with you, Sir, who have done so much to raise the standard of the scientific literature, and with all others have striven to show that scientific and linguistic precision are not incompatible, to give us a lead in this matter. If you will not have “scientist”, at least provide us with some other single word.  Norman R. Campbell”

And the response…

“Hitherto the word “scientist” has not been used in the columns of Nature to designate a man of science or scientific worker….We, have therefore invited a number of authorities on good English, including distinguished men of science, to favour us with their opinions on the desirability, or otherwise, of adopting the word “scientist”. Editor, Nature”

Nature Vol 114 p788 (1924).

Reflecting the norms of the time, the implication here is that all scientists and people in comparable professions are men.

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Source: Natural History Museum Library, London; under CC BY-NC 3.0

Whewell was a great wordsmith and renowned for coining a host of new terms relating to science. He came up with the term scientist at a meeting of the British Association for the Advancement of Science in Cambridge in 1833. When I took a look at the report of the meeting, I was delighted and saddened to see that among the signatures of those attending, “S.T. Coleridge, Grove, Highgate”; an entry written just over a year before Coleridge’s death.

An interesting reflection on the times when clergymen such as Whewell drew comparisons between the Arts and Sciences to define the word scientist, in the company of poets, philosophers, artists and other persons of learning.

So what does it mean to be a called a scientist today? The OED online definition of a scientist is:

“A person with expert knowledge of a science; a person using scientific methods”

Can I call myself a scientist? For several years, I was a neuroscientist/cell biologist and then involved in science funding, policy and strategy. My current role at the Library still involves both aspects of the above description, though my job title does not include the word “scientist”. Personally, I don’t mind how I am described in this professional context; I’d rather be known for what I do.