Biotech Breakthrough: The CRISPR/Cas System

 

By John McLaughlin

In the last few years, a huge amount of excitement has grown over the CRISPR/Cas system and its use in targeted genome editing; this acronym derives from Clustered Regularly Interspaced Short Palindromic Repeats and their CRISPR-associated genes (Cas). CRISPR loci, which are found in many species of bacteria and most archae, have been collectively described as an RNA-based “immune system,” because of their ability to recognize and destroy foreign phage and plasmid DNA.

 

Although the acronym was first coined in a 2002 paper, CRISPR has only recently been exploited as a research tool. How does the system work and what is its use in the lab? There are at least three distinct types of CRISPR system. A typical “type II” CRISPR locus consists of several protein-coding Cas genes adjacent to an array of direct repeat and spacer sequences. The direct repeats are usually palindromic and conserved, in contrast to the much more variable spacers; these repeat-spacer sequences are transcribed as one unit and then processed into short CRISPR-RNAs (crRNAs).  A 2007 Science article demonstrated that a bacterial population could acquire resistance to phage infection by incorporating DNA fragments from the invading phage genome into a CRISPR locus, in the form of new spacer sequences. The newly acquired spacers are then transcribed and processed into crRNAs, associate with a trans-activating RNA (tracRNA) and Cas protein, and are eventually guided to a homologous DNA sequence to catalyze a double-stranded break.

 

The CRISPR system can be flexibly “reprogrammed” by designing custom chimeric RNAs (chiRNA), which serve the function of both crRNA and tracRNA in one molecule. By co-expressing a “designer” chiRNA with a Cas protein, a targeted and specific DNA break can be created in the genome; after providing an exogenous DNA template to help repair the break, customized knock-ins or knock-outs can be generated. Judging from the rapid technical advances made in the last few years, the system promises to be an efficient and high-throughput format for genome editing. To date, knock-outs have been created in a variety of organisms including rats, flies, and human cells.

 

CRISPR/Cas technology has attracted scientific attention as well as commercial interests. In November 2014, biologists Jennifer Doudna and Emmanuelle Charpentier were honored as co-recipients of the 2015 Breakthrough Prize in the Life Sciences, for their work in dissecting the mechanism of CRISPR’s sequence-specific DNA cleavage. According to its proponents, the possible applications of the CRISPR system seem almost limitless. CRISPR Therapeutics, a recently formed company dedicated to translating the technology into genetic disease therapies, has raised 25 million dollars from new investors. And just last month, the pharmaceutical company Novartis began collaborations with Intellia Therapeutics and Caribou Biosciences in order to pursue new therapeutics using CRISPR/Cas.

 

A technology as potentially lucrative as this one does not develop without controversy. MIT Technology Review recently reported on the competing startup companies aiming to exploit CRISPR technology, and the ensuing battles over intellectual property rights in different organisms. In fact, last year the Broad Institute and MIT were awarded a patent which covers the use of CRISPR genome-editing technology in eukaryotes. Feng Zhang, who is listed as Inventor on the patent, and his lab at MIT were the first to publish on CRISPR’s functionality in human cells.

 

In a few years, this exciting technology may be a commonplace fixture of the biology lab. Only time will tell if the CRISPR craze produces the amazing breakthroughs that scientists, and the general public, are eagerly awaiting.

Are Existing Policies Regulating Recombinant DNA Technology Adapted for Synthetic Biology?

 

By Florence Chaverneff, PhD

 

Background on Synthetic Biology

Synthetic biology is gaining increasing interest as one of the most promising new technologies of the 21st century. Its revolutionary nature, wide-ranging applications across several scientific disciplines, and the fact that it may help solve some of the world’s most pressing issues, all contribute to the justified enthusiasm for the field. As the boundaries, prospects and even nature of synthetic biology still need to be clearly outlined, the definition advanced by a high-level expert group of the European Commission, encompasses it well: “Synthetic Biology is the engineering of biology: the synthesis of complex, biologically based (or inspired) systems which display functions that do not exist in nature. This engineering perspective may be applied at all levels of the hierarchy of biological structures-from individual molecules to whole cells, tissues and organisms.”

 

In the same manner that recombinant DNA technology revolutionized biology in the 1970s, synthetic biology is breaking new grounds. However, because it requires a greater need for DNA synthesis than recombinant DNA technology, synthetic biology brings life sciences closer to engineering. It aims to make biology easy to engineer. And that is the revolutionary part. Its multi-disciplinary nature at the nexus of biology, engineering, genetics, computational biosciences and chemistry implies that synthetic biology be practiced in a global and networked fashion, posing it as the ultimate collaborative venue for scientific research.

 

Applications of Synthetic Biology

The array of what synthetic biology allows to design and produce, from biomolecules, to cells, pathways, and ultimately, to living organisms, in by itself gives an idea of the power of the technology. Synthetic biology, with its new category of tools that allow advanced DNA synthesis, conceptualization of biologically complex systems, and standardization for mass production is more approachable to a less skilled workforce in a more efficient and manageable manner than what is currently practiced in biotechnology companies.

 

Applications of synthetic biology are wide-ranging, from global health (e.g. vaccine and antibody production, regenerative medicine, development of therapies for cancer, approaches for cell therapy) to generation of biofuels, to food production. And as the field is growing, technologies are bound to evolve, giving rise to an even wider array of applications. One of the most notable and highly publicized successes of synthetic biology was published in Nature Biotechnology in 2003. The article describes a novel way of producing the anti-malarial drug artemisinin, using the bacteria E. coli as a host, in which enzyme and metabolic pathway for artemisinin production were expressed. Artemisinin synthesized in this manner can be produced at much higher yield and much lower cost than by plant extraction. These considerations are of great importance for an anti-malarial drug, destined to large populations in low income countries.  Another powerful example of the promises held by synthetic biology lies in a study published last year in Science, reporting the assembly of a synthetic yeast chromosome, heavily edited from its natural counterpart, yet functional when expressed in its organism.

 

Crafting Policies for Synthetic Biology

Despite being over a decade old, synthetic biology is still in its infancy, its full potential has yet to be realized, and a regulatory framework indispensable to any new technology that can be applied to life sciences, will have to match the field’s evolution. Some policies for synthetic biology may be adapted from existing ones that were designed to regulate recombinant DNA technology and genetic engineering. However, it is critical that new regulations, tailored to synthetic biology, which is tantamount to engineering artificial life, be established. Considerable changes in regulations should be avoided, as they might result in holding up development of the fast-evolving synthetic biology.

 

Perhaps one of the most important policy aspects to consider for synthetic biology is linked to its sheer nature. Synthetic biology permits manufacturing of whole living organisms, which, if released in the environment, could greatly affect it by interacting with ecosystems. It is therefore imperative that preventive measures be taken and that ethical oversight be installed to avoid misuse of the technology. Another policy aspect particular to synthetic biology is related to its multi-disciplinary nature: all its practitioners, not just biologists, should be educated in biosafety. Additionally, policies should allow for training of scientist, researchers and other professionals to meet the demands of the field. Several top institutions in the US have already launched graduate programs in synthetic biology, but more educational programs are required.

 

Synthetic biology research and frameworks for funding are also vital to support evolution of the field by strengthening research and development capabilities, and supporting innovation. Synthetic biology should be practiced in academic institutions and private ventures alike.  In both instances, policies should be adapted so that results from research meet demands of modern economy, by taking measures to industrialize innovation in commercially successful ways through facilitation of technology transfer and intellectual property management.

 

Finally, because synthetic biology is heavily reliant on openness and sharing and holds great potential for becoming the poster child of international scientific cooperation, national policies formulated in the US and elsewhere could serve as template for transnational policies.

 

Growing the Future

 

First Ever Biofabricate Conference a Great Success

 

By Celine Cammarata

 

Last week I had the good fortune of attending the first ever Biofabricate conference, a day-long event born of the combined genius of SynBioBeta and BioCouture. Hosted at the stylish (if somewhat creepily modern) Microsoft Research Center in Times Square, the summit brought together an illustrious group of synthetic biologists, bio-engineers, designers, architects, entrepreneurs, and more. While, as the name implied, the discussion focused on creation of materials and products through biological means, this topic turned out to be incredibly diverse – after all, what does it really mean for something to be “biofabricated”?

 

For some, biofabrication revolves around improving our communication and interaction with cells and organisms. Researchers such as Microsoft’s Andrew Phillips are developing new coding languages and platforms to program cells and other biologicals, while others continue to develop an ever-expanding suit of methods to edit genomes. Techniques to guide cell growth have led to incredible breakthroughs such as the ability to grow patient-specific replacement bones, not to mention design of made-to-order organisms at companies such as Ginkgo Bioworks.

 

For others, biofabrication is about using nature to inspire and create products and processes that, in turn, are kinder to nature – and to us. Mushrooms were a star in this realm, specifically their matrix-like mycelium that can be used to forge bricks, packaging and other materials that are entirely compostable (EcoVative is the leader in this burgeoning industry). Bacteria are also pulling their weight, helping make environmentally friendly plastics from waste and building materials without a kiln. Furthermore, bio-inspired products can open new avenues for devices that are compatible with our own bodies; Dr. Fiorenzo Omenetto’s technology to create almost anything out of silk – a fully bio-compatible and incredibly safe material – were particularly impressive.

 

Biofabrication is also explored through art and design. From growing bone and leather fineries to employing various strains of bacteria to dye textiles, work from designers who have stepped into the lab was truly multidisciplinary. Designers can also help us understand how biotechnology fits into our society, as with the playfully creative design fiction of NextNature or the exploratory architecture of Terreform1.

All these themes, more intertwined than they are disparate, share a sense of collaboration – not only among ourselves, but with nature, biology, the larger world in which humans exist. At a first glance, the work of programming cells, cultivating tissues, or using organisms to grow materials may seem to be about trying to control nature, or “play god” as the internet likes to put it. But throughout the work presented at Biofabricate it was apparent that this research and these technologies instead require acceptance of nature and the way that it works. When bacteria are dying your textiles, you have to be willing to accept their choice of patterns. When mushrooms are making your bricks, you may need to learn new architectural techniques. You can develop a programing language to talk to cells and organisms, but to do so you must learn their language. Nearly all the speakers expressed that part of the pleasure and benefit of working with biological materials and systems is that biology can often propose better solutions that we may ever think of on our own.

 

Altogether Biofabricate was a resounding success: though the conference was only publicly announced a few months in advance, registration was completely sold out and clichéd as it might sound, the gathering had a palpable energy, with every overheard snippet of conversation more interesting than the last. The barrier-breaking combination of design and biology is a winning recipe that promises many more successful gatherings to come.

Is There Really a Reproducibility Problem in the Biomedical Sciences?

 

By John McLaughlin

The ability to reproduce experimental findings is a keystone of the scientific method; it is a major part of what makes modern science such a successful social activity. In the past few years, however, there has been growing alarm over what is being called a “reproducibility crisis” in science, particularly the biomedical sciences.

 

One especially high-profile example was discussed in a Nature commentary two years ago: The biotech company Amgen, before investing resources into a new drug program, attempted to reproduce the findings of what it considered 53 “landmark” papers in the cancer biology field, and failed to do so for all but six of the publications. This raises the question, are resources being misguidedly invested into therapeutics that are based on flawed results? And more importantly, is this problem unique to pre-clinical research or is it more pervasive?

 

The replication problem is definitely receiving attention, in both the popular and scientific press. Several of the world’s most elite scientific journals, including Nature and Science, have recently published editorials calling for answers. Unsurprisingly, the proposed solutions have varied. Some are pushing for more extreme approaches, such as hiring independent, third party laboratories to reproduce the findings of a paper before it reaches publication. Other suggestions have been more modest; journals should require increased transparency regarding the description of experimental methods, and raw data should be submitted to open-access repositories where they can be scrutinized more closely.

 

The call for more rigorous standards of reproducibility is already evoking concrete responses. Last year, several organizations, including PLOS One, the Science Exchange, and Mendeley, together started the Reproducibility Initiative, which bills itself as an effort to “reward high quality reproducible research”. Here’s the basic idea: scientists confidentially submit their experiments for replication (for a fee), choosing among a network of labs with expertise in a chosen technique. If the findings are confirmed, they can boast an “Independently Validated” badge upon publication of the results. They have already received a $1.3 million grant to reproduce 50 of the “most impactful” cancer biology studies published during 2010-2012.

 

But if this practice becomes a norm, it may place further financial burdens on labs that are already struggling for funds. Are there any more modest, practical changes we can begin making in our own labs to combat this problem? Part of the solution can be improved graduate training of scientists; regarding the day-to-day use of statistics, which types of analysis are appropriate for your experiment, what sample sizes are needed and what conclusions can reasonably be drawn? Miscommunication between scientists may be a factor as well. Today’s biological science involves complicated experimental techniques, using highly complex animal and cell culture models; more intimate knowledge of the methods may be needed in order to faithfully replicate the results.

 

On the flip side, are institutional and cultural issues also playing a role? The frantic competition for academic faculty positions and grant funding may skew incentives, encouraging post-docs and PIs to cut corners and push for publication as quickly as possible, in high-tier journals. Nobel Laureate Randy Schekman called attention to this problem last year, and vowed to boycott publishing in “glamour” journals like Nature, Cell, and Science.

 

Whether or not you agree there is a replication crisis in biomedical science, it surely can’t hurt to encourage more openness, transparency, and improved training. The next generation of young scientists would benefit from making these practices a cultural norm.

 

 

 

 

Should Postdocs Jump The Academic Ship?

By Elizabeth Ohneck, PhD

 

A recent series of articles on NPR called “Science Squeeze” painted a rather abysmal picture of the current state of scientific research, from lack of funding, to job shortages for young scientists, to stories of scientists “giving up,” leaving academia for other, though not always better, ventures. The article “Too Few University Jobs for America’s Young Scientists” features interviews with a few postdocs at NYU about their current situations and their prospects for an academic future. Their responses are not altogether negative, but are far from resoundingly positive. The article also hints that PhDs may be better off pursuing careers outside of academia, a path that more and more graduate students and postdocs are beginning to take. To get a broader perspective on how the current scientific research climate is affecting the career trajectories of postdocs, I talked with several postdoctoral scientists at varying stages of their careers about their reactions to the NPR series and how the issues presented affect their outlook for the future.

 

Not all postdocs are ready to jump the proverbial ship when it comes to pursuing an academic career, despite awareness of the hurdles ahead. Dr. Randy Morgenstein, a senior postdoc an Ivy League university, pointed out the limited scope of the NPR series, which focused on only a couple specific universities and individuals whose situations were particularly dire, and felt the articles portrayed the academic environment in an overly gloomy manner without actually addressing the overarching flaws in the system. “The articles make a pity party out of 1 or 2 places or people without making me feel the system isn’t working. So overall, I think they might have presented the state of scientific research in this country in too much of doomsday state… A better approach would have been to make me feel bad for society because good scientists are unable to get grants and do research.” He acknowledges, however, the truth of difficulties in obtaining grants and the competition for an extremely limited number of faculty positions. Despite these factors, he is persistent in pursuing a career in academia. “Academic research gives you the most freedom to pursue the research you are interested in. I like that aspect of it and think it is worth the risk to pursue.” When asked how one might overcome the obstacles in funding and faculty position availability, he responded, “I think anyone becoming a PI has to be self-confident almost to the point of arrogance, and therefore think that it’s the other people who won’t be able to get grants.  I do not think I am doing anything special to overcome these difficulties. Same as everyone else, I am trying to publish the best papers that I can, hopefully on a topic that people think is worth funding in the future.”

 

What about those who have successfully made the transition from postdoc to assistant professor, who might provide hope for those postdocs still set on an academic track? Dr. Francis Alonzo III is one such scientist, having recently obtained an assistant professor position at Loyola University Chicago. He chose to pursue an academic career because of his love of science and education, and credits his success to persistence, passion, drive, and curiosity. In addition, he added, “I really just could not see myself doing anything else. Because of that, I knew what my goals were from the start and worked as hard as I needed to get there.” But he feels that the NPR series accurately portrayed the state of scientific research, and this reality of uncertain funding means securing an assistant professorship doesn’t necessarily relieve his apprehension. “I do still love engaging in the scientific process and being involved in training and educating students,” says Dr. Alonzo. “And I still get a lot of joy coming into the lab everyday. However, I am considerably more apprehensive about what the future holds. In particular because I am just gearing up to submit my first larger grants and I have no idea how my ideas will be perceived.”

 

There are, however, many postdocs struggling to find jobs, and many who are turning away from academia in hopes of finding more opportunities. Dr. Bree Szostek Barker, a junior postdoc at the University of North Carolina, originally planned to pursue an academic career, but has recently been looking into possibilities outside of academia. She feels the NPR series actually understated the severity of the problems with funding and the job outlook in academic research. “The articles’ focus on a few universities, namely Baylor and Virginia, makes it appear that this is an issue isolated to a portion of schools/institutions/researchers that overextended during good times,” she said. “Every university and the vast majority of PI’s are feeling this, with the exception of the select few who are immeasurably successful.” The lack of job security created by limited academic positions and uncertain funding resulting from the current system of the academic research sector has pushed her to explore alternative careers. But securing a job in the private sector or a job that is not research-based has turned up its own set of problems; specifically, PhDs and postdocs seem to be missing relevant experience in the eyes of recruiters for these positions. For this reason, Dr. Szostek Barker disagrees with the assertion made in “Too Few University Jobs for America’s Young Scientists” that there are abundant jobs for PhDs outside of academia. “The fact is the number of jobs seeking a PhD with no experience in their industry is low and to pretend otherwise is offensive. And the jobs that do arise are so heavily competed for that the chances of getting the position is extremely slim,” she said, adding, “Unfortunately academia doesn’t count as ‘experience’ for anything except academia.”

 

It seems that the NPR series may have portrayed academic research in too much of a doom-and-gloom state, but also didn’t delve deep enough into the overarching problems in the structure of the scientific research sector. Funding is difficult to obtain, and faculty positions are few. Yet there are success stories to be found, and there are postdocs maintaining a hopeful outlook in spite of the enormous obstacles they face. But the system in which each PI trains multiple successors is unsustainable, and so to overcome job shortages, many postdocs are looking outside of academia for careers. What is not acknowledged in this series is that these non-academic jobs may be equally as hard to come by. Altogether, the consensus is that the system is flawed. But how do we fix the system? More money alone is likely not the answer. What contributes to one’s success on the academic track? Plenty of bright, passionate, confident, motivated scientists end up leaving academia, unable to secure funding, or worn down by the fierce competition, so what factors, both personal and academic, allow some to flourish while forcing others out? And finally, how can we better prepare PhDs for jobs outside of academia? The NPR series has brought these issues to the public eye. Hopefully this exposure will drive further discussion and a search for solutions to ensure a future full of happy, fulfilled scientists and prolific, productive scientific research.

 

What Would Scottish Independence Mean for Science?

 

By Sally Burn, PhD

What do the following have in common: John Logie Baird, Alexander Graham Bell, Alexander Fleming, and James Watt? Well, apart from being scientists or engineers who have had profound effects on your daily life (by virtue of inventing the television, telephone, penicillin, and modern steam engine respectively), they are also Scottish. Scotland, if you are not familiar with it, is a small country within the United Kingdom (UK) that is home to just over five million people (or around 8% of the UK’s total 64 million inhabitants). Despite its small size, it is an incredibly well accomplished and well-funded nation in the fields of science and engineering – it is also the country that produced Dolly the sheep, the first mammal cloned from a somatic cell. According to the Scottish government’s website, Scottish research is cited by scientists from other countries more often than that of any other country, when citations are compared relative to Gross Domestic Product. I completed my MSc, PhD and first postdoc in Scotland, so I have witnessed firsthand the excellent facilities and high quality research this little powerhouse has to offer.

Scotland is an all-round great place to live and be a scientist. However, not everyone is happy. To condense down an awful lot of history, let’s just say that there was a lot of bloody fighting from medieval times through to the early 1700s during which England and Scotland tussled over who owned Scotland. In 1707 Scotland entered the union to become part of the-then Kingdom of Great Britain (the forerunner of the UK), and was governed entirely from London until 1999 when limited self-government was permitted. But this is not enough for many Scots, who now want complete independence from the UK (which also includes England, Wales, and Northern Ireland). In theory, Scotland would become an independent country, with a small population but amazing science capabilities… or would it? The majority of my Scottish or Scotland-based science contacts seem to think otherwise. They envision major drains on funding and personnel, not helped by a predicted economic nightmare. Supporters of independence, however, are confident that separation from the UK will be a positive move and that there is no reason for the existing excellence in science to falter.

Residents of Scotland will cast their vote on independence on September 18th. Scizzle asked four Scottish-based scientists how they will be voting and what independence will, in their minds, mean for Scottish science. Some respondents have chosen to remain anonymous as the subject is sensitive and they currently work in Scotland. It should also be noted that the views expressed are their own and do not reflect those of their employers.

NO TO INDEPENDENCE – Anon, Edinburgh-based postdoctoral researcher

As the Scottish referendum looms, ‘No’ campaign supporters are increasingly being labelled as being ‘negative’ or ‘scaremongerers’, tainting the ideal of Scottish independence. But what I fear the Yes campaigners are missing is that we are already living the dream – in a country recovering from financial crisis, our children still go to university without paying fees and we can all see a doctor and receive prescription drugs free of charge. Both of these benefits do not extend to the English taxpayer and I can’t help but think these benefits in Scotland are funded – at least in part – by the British taxpayer. The same goes for science – proportionally, we receive more public funding per capita than the rest of the UK.

While several prominent scientists have come out publically to state their fears for the future security of Scottish science funding in the event of a ‘Yes’ vote, the story behind closed doors is more worrying; rumours of capital grants already being denied to Scottish institutions alongside new group leaders being called in for discussions about future funding ‘issues’.

The people of Scotland are being asked to make what is for many an emotional decision. But for those of us whose families are dependent on jobs in the science and engineering sectors, the luxury of an emotional decision simply is not there. If Scotland gains independence my husband will be relocated to England. As a female postdoc with young children, I don’t fancy my chances at gaining a new position if competition increases due to fewer jobs/less funding. I used to believe it was entirely possible to ‘have it all’ – a fulfilling family life and an exciting career as a postdoc. Despite have a baby, I’m no stranger to nights in the lab because science is my passion and I’m more than willing to sacrifice sleep to the cause. But in the event of a ‘Yes’ vote, my family will most likely have to leave our home and start over again. Science is a luxury, and I’ve no doubt many of us will fall victim to a mass ‘cull’. So on September 18th, I won’t be voting ‘No thanks’, I’ll be voting ‘Please, No’.

 

NO TO INDEPENDENCE – Peter Hohenstein, Edinburgh-based principal investigator

It’s not rocket science. Good research needs three things: good people, good institutes and good money. The quality of an institute comes down to the people that work there and the amount of money they can spend. Good people will come to good institutes with good funding. So in the end it’s only about the money. And that’s where the problem is.

The numbers are not new, Scotland gets 13% of Research Council money (through being good) for 8% of the UK population. This is hundreds of millions of pounds. The Yes campaign thinks there will be a shared RC structure between Scotland and the rest of the UK (rUK), but forgets to ask the question ‘why would they?’. Why would rUK give research funding to a country that just decided to leave them, let alone more than they would be able to fund themselves? There are enough good scientists in England and Wales to spend the money on. Wellcome Trust have not made clear yet what their position on an independent Scotland will be. Other big charities neither, but again, why would they spend their money in another country? Cancer Research UK doesn’t spend its money in Belgium or Iceland, why would they spend it in Scotland if the Scots themselves decide to leave? Scottish charities will need a long time to get the same brand recognition (and thereby income) as the UK version have at the moment to fill this gap, if that ever happens (and again, also with charities Scotland wins a bigger portion of funding than based on population). Nobody knows at the moment if and when an independent Scotland could get into the EU. What does that mean for EU funding? Financially research in Scotland can only be worse off. Independence would give an extra hole in the budget of £6billion that needs to be filled somehow regardless of this, so an independent Scottish government will not be able to compensate. If Scotland eventually gets in the EU they will have to drop the ‘English students only’ tuition fee policy, giving an extra £150million gap in the science and education budget. I don’t think anybody outside the Yes campaign seriously believes an independent Scotland will be able to keep up the science funding levels. The sums simply don’t add up.

Right now the situation is made worse due the uncertainty about what is going to happen. Nobody is at the moment able to plan ahead in case there is a ‘Yes’ vote. And once it’s there, there are only 18 months to get things sorted. This is madness. The simplest grant application expects you to plan ahead longer in advance, and right now the whole of research funding in general is in limbo and would have 18 months to sort things out. I don’t see another possibility than a complete mess in the way universities and institutes will function and can be managed for several years to come for lack of planning opportunities.

Scotland will lose its attraction for good scientists to come to and stay in. 13 years ago I came to the UK, but since then I stayed in Scotland. I stayed because I love Scotland, and because I could do good science here with good funding. I don’t think an independent Scotland will have a comparable attraction to people as the UK as a whole has. Especially if a transition to an independent funding system turns out as messy as I fear – fewer good people will come to Scotland, more good people will leave Scotland. Scientists are used to following the funding streams, all over the world if needed. A large number of scientists are on temporary contracts anyhow, they’re expected to move around every few years for a big part of their career. Why would they come to or stay in Scotland if the funding is a mess and going down? Science in Scotland could all too easily slip into a negative spiral of losing good people and funding. It won’t take long to lose everything the country has worked on for three centuries, it will take much longer (if ever at all) to get it back.

As a non-Brit myself I don’t have any emotional feelings against or in favour of Scottish Independence. I would be the first to agree ‘No’ voters are for a big part driven by fear, as well as thinking ‘Yes’ voters are guilty of day-dreaming. Yes, Scotland has shown to bring forth great research and great scientists. But why would Scotland decide to risk the financial foundations of its science? John Logie Baird was a Scot, but he did his ground-breaking work on the development of the television in Hastings in the south of England. Alexander Bell was from Edinburgh, but was trained and worked in London (before moving to Canada). The Scot Alexander Fleming discovered penicillin, but it took British funding from the Medical Research Council (as well as the German Jewish refugee Ernst Chain and Australian Howard Florey working in Oxford, England) to bring out its potential. James Watt was born near the Firth of Clyde but to make his steam engine a commercial success he had to partner up with Birmingham (England)-born Matthew Boulton. Science transcends borders, funding much less so. Scots can be brilliant, but they have always worked in the context of the wider UK, and why wouldn’t they? And it goes both ways, England-born and trained Peter Higgs won the Nobel Prize for work he did (until his retirement very recently) at the University of Edinburgh.

Some might say an immigrant in Scotland like me should not voice an opinion on Scottish Independence. I think every scientist in Scotland should (especially since the universities don’t), wherever they are originally from and whatever their opinion is. In the case of a ‘Yes’ vote Scottish science might eventually catch up again, but science in the rest of the world would have steamed ahead while we are spending time, energy and money on setting up a new scientific (funding) system. Are nationalist emotions important enough to make our own lives unnecessary difficult? For me that’s not rocket science…

 

YES TO INDEPENDENCE – Keith Erskine, Edinburgh-based laboratory technician

If Scotland became independent, it would need to grow its economy and invest in industry, and obviously universities and other scientific bodies would be at the heart of this. Scotland has a good history of innovation, discovery and invention, and this would be more necessary than ever before, if we were independent.

Throughout the debates and arguments over the pros and cons of independence, both sides of the debate seem to paint a picture where the amount of money in the economy and in individual’s pockets appears to be much the same as it is now, regardless of which way the referendum goes – the main difference seems to be more about how money is spent and who decides this. Currently, and rightly in my opinion, the UK government has to put the needs of the majority of its people first and because Scotland is so much smaller than England in terms of population, many decisions which have a direct impact on Scotland and Scottish people are not being made by people whose main priority is what is best for Scotland. This would not be the case in an independent Scotland, and this could only ever be beneficial in a situation where an industry or field which was central or important for the future of the country was in need of funding or help from the government.

I actually think that the psychological boost of a new found optimism and positivity from the recreation of an independent country could inspire millions both domestically and abroad to work on the growth and development of science and technology. There would be a need to build and grow, and this would surely attract the minds and money of the world of science, to be a part of that.

All I see is new opportunity if the vote is yes, and I am excited about the possibility of being there to witness it happening. I find the thought inspiring and exciting, and I hope that it can be the legacy of my generation in the history of Scotland.

 

NO TO INDEPENDENCE – Anon, Dundee-based scientist

Scotland currently produces outstanding research and attracts a disproportionately large share of science funding. Our current membership of the UK gives us access to generous funding from UK research councils and from the EU. It also makes it easy for groups across the UK to collaborate and share skills, expensive equipment, and access world-class facilities. This is central to any developed economy, and something that Scotland should be proud of.

Why would we want to change this enviable position?

Pro-independence campaigners argue that Westminster will cut budgets. However, despite the financial crisis, funding of the life sciences has been well protected compared with many other areas. In contrast, what is promised on independence is vague. The Scottish Government has asserted that the UK research councils will continue funding Scottish research. Not only is this contradictory to the argument for leaving the UK, it seems wildly optimistic to expect the UK to continue funding a foreign country.

The lack of planning for post-independence funding is shocking. What happens if, in fact, the UK does not intend to fund research in an independent Scotland? We can’t fall back on EU funding and facilities because we won’t be part of the EU for several years at least. Even a short gap in funding would severely damage research here; researchers need money to continue their work and to eat. If the money dries up for even a matter of months, many people would need to leave to find other jobs. Once people have left, it is virtually impossible to reassemble teams and expertise that have been carefully built over decades.

Indeed, what happens if the UK does intend to fund research in an independent Scotland? Although we may continue to receive money, we would lose any political say in how the Westminster government decides science-funding policy. This would put us in a very precarious and dependent position; precisely the opposite of what independence is supposed to achieve.

Collaboration and sharing is fundamental to science. Why should we rip up the fabric of UK research and build unnecessary barriers in an unfunded, poorly planned future?

 

The Language of Scientific Discovery

 

By Asu Erden

Most of us are aware of the political controversies surrounding the human papillomavirus (HPV) vaccine. Some of us even have personal anecdotes relating to this highly charged subject. “I remember my aunt calling me to ask me about the vaccine. She was worried about what it meant for her children’s health and why her son should get an immunization aimed at preventing cervical cancer,” said Dr. Heather Marshall, a postdoctoral fellow at the Yale Department of Immunology. The confusion is all too common. As scientists, we have failed Dr. Marshall’s aunt and millions like her. In fact, the HPV vaccine has been extremely poorly marketed despite its astounding efficacy. The Centers for Disease Control (CDC) estimates that the quadrivalent vaccine offered in the US has an efficacy against genital pre-cancers and warts of nearly 100% in previously unexposed women, as well as 90% against genital warts and 75% against anal cancer in men. Despite the remarkable efficacy of the vaccine, not all parents in the US want to have their sons and daughters vaccinated. The scientific achievement that a vaccine embodies is not enough. This is one of the tragedies brought about by the failure of science communication. The HPV vaccine has been marketed towards young girls. Why has it not been made clear that both women and men should get the vaccine and that the early age of vaccination is only meant to increase vaccine efficacy? Men and women can actually be immunized up until the age of 26, after which it is assumed that you have most likely been exposed to one or more of the HPV strains that the vaccine protects against. In reality, you can still get the vaccine after this age. It will just not be as efficacious.

 

“The contribution of science is to have enlarged beyond all former bounds the evidence we must take account of before forming our opinions” wrote British biologist Sir Peter Medawar in Pluto’s Republic. In this day and age, the Internet provides readers around the world with a spate of resources – most of which not peer-reviewed – on just about anything. Unlike newspapers and books, blogs are most often not fact-checked. Just have a look at the Natural News blog and you’ll see how harmful misinformation disguised in a professional layout can be. As Dr. Marshall notes “a hundred years ago, it took weeks or months for a piece of scientific news to reach the other end of the country or the other side of the Atlantic. Fifty years ago it took a few hours or days. Twenty years ago it became one second but that sort of news still had a very narrow audience. Today you can literally reach 100 million people within a few seconds, which is really scary.” It is scary because it comes with a duty to inform that too many scientists choose to ignore out of frustration and because of the lack of any tangible benefits to their career. Dr. Schatz, professor of Immunobiology and Molecular Biophysics and Biochemistry at Yale, deplored that the connection is very tenuous between talking to students at local high schools and increasing interest and funding for scientific research. It inevitably comes down to scientists’ intrinsic motivations to go out there and share their research with the public.

 

As a graduate student at Yale and as a scientist, I find these realities challenging. I am unsure as to when I first came to realize the widening mismatch between how scientists talk to the public about their research and how they should talk about it. But this is something that every budding and established scientist is aware of. Yet we are seldom taught how to translate scientific concepts back into the vernacular. Science truly has a separate language that facilitates talking about complex concepts with peers that share the same premises. It is easy to forget that this has been taught to us and does not come naturally. I discussed this with Will Khoury-Hanold, a graduate student in my lab. His involvement with the Science in the News initiative – which trains Yale graduate students to give talks to high school students about a broad range of current scientific topics – taught him a lot in this regard. He described science as requiring a greater leap than other disciplines. “Anyone can pick up a history book and read about the elements that led to the Civil War. It’s not the same with science. […] With science, it’s about translating it back to English.” This is hard to do, and we often shy away from talking to the public. But in a world where Jenny McCarthy is hired by The View and has access to a 3 million viewer platform to spread her anti-vaccine views, scientists have to speak up and as loudly as they can to provide the public with fact-checked truths. Of course entertainers can aptly serve the cause: if you have not seen this vaccine-related video by Penn & Teller I strongly encourage you to do so. Nevertheless, the duty to inform the public about these matters should fall on scientists.

Scientists are partly responsible for the failures of science communication. Clearly, we have a tendency to revel in esoteric statements about our research and about science more generally. If you take the word “theory” for instance, its scientific meaning widely differs from its colloquial understanding. For non-scientists, a theory is something that has yet to be proven. For scientists, a theory is “a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses […] theories do not turn into facts through the accumulation of evidence. Rather, theories are the end points of science. They are understandings that develop from extensive observation, experimentation, and creative reflection,” as pointed out by the National Academy of Sciences. Our arcane vocabulary makes it seem as though understanding science were a luxury. We need to use more accessible language so that such misrepresentations of scientific truths do not happen. Is it the fault of scientists that the HPV vaccine was poorly marketed? Perhaps not directly but we should have made it clearer to journalists why the vaccine is so important and how it is significantly reducing the incidence of cervical cancer. Another infamous example is that of the alleged correlation found between the measles, mumps, and rubella (MMR) vaccine and autism. While the study published by Mr. Wakefield in 1998 has been debunked and his medical license was stripped, most people still don’t know why his results were wrong. Not only did he not comply with the clinical trial rules for his study, the putative correlation he claimed to have found was based on a confounding factor. What is that you say? That would be an example of scientific jargon but what it really means is this: the MMR vaccine usually gets administered around the age of 2, which is also the age at which most children start speaking. One of the clearer symptoms of autism is to not start speaking when you are supposed to. Thus, autism inherently gets diagnosed around the age of 2. This is what underlines the correlation Wakefield reported. The confounding factor was the age of the children. When it comes down to their kids’ health, reminding parents that “correlation is not causation” achieves little. Having the population actually exposed to that concept more generally would achieve much more.

 

As Dr. Marshall emphasized, “a lot of the time it can come down to the scientist. If you had asked me [about it] a couple of years ago, I might not have said this as easily.” As scientists we never get properly trained to know how to answer that phone call we might get from journalists who under the pressure of publication might perform less than optimal fact-checking. By not being as clear as possible we inadvertently provide ground for sensationalism. But this reflects a broader failure to communicate science to the public. We live in a world where it is acceptable not to know what a gene is or how evolution actually works. To remedy this, scientists need to make concepts they are familiar with more accessible and report their research aptly.

 

 

But the language of scientific discovery and science communication is not solely beneficial to the public. It can help scientists better share their research with people beyond the realm of their own department. A good talk fosters cross-fertilization between fields. Scientists have a tendency to narrowly focus on their thought-processes and dig a deeper and deeper hole to burrow themselves into. As a result, we lose the forest for the trees. Many graduate students, postdoctoral fellows, professors, and department chairs have encountered this somewhere along the line. Insufficient training in writing and in giving public speeches results in science talks that fail to convey their points across. The problem is that scientists are asked to give many talks and presentations. What happens most often is that they regurgitate PowerPoints they prepared for specialists in their field and use them to give talks to an unspecialized audience.

 

The challenge and art of giving a good talk is to know your audience and to aptly choose the level of detail versus abstraction that suits said audience. “We as a species – by which I mean scientists –,” added Professor Schatz “are so programmed to show the data that it takes effort not to.” That skill is not just useful when communicating science to a lay audience. It fosters collaborations and thus important breakthroughs within the field of scientific research. Professor Schatz recalled an immunology meeting organized by the Federation of American Societies for Experimental Biology he was at a few months ago. One of the speakers at that conference was Dr. Margaret Goodell who specializes in the field of stem cell research and therefore stood out as not being an immunology-related speaker. She gave such an inspiring and thought-provoking talk that immunology professors were lining up to discuss potential collaborations with her lab. This does not happen when content prevails over format. At a time when knowledge within the sciences has become so specialized, collaborations become a necessity. If as scientists we are unable to communicate our research to people outside our field – whether they are scientists or not – we prevent such collaborations from budding. It also prevents good scientists from getting grants because they are unable to write well enough about their research.

 

Most scientists get into their field with the hope to increase the spectrum of human knowledge about the world surrounding us, even if only by a little bit. And most of us thrive on the possibility of understanding something about nature that no one had understood previously and of sharing it with the rest of the world. But somewhere along the line, this humanistic ideal wanes or at least no longer suffices. “You make a scientific discovery and you can’t wait to share it with your peers” said Will. Why this does not necessarily translate into a desire to talk about your research to the public remains somewhat elusive. So to those scientists out there, I must ask: do you remember your personal statement for college and for graduate school? You meant it when you said that you wanted to save the world by increasing our understanding of worm neurobiology or by curing cancer. Don’t forget it!

Sensationalized Science

 

By Elizabeth Ohneck, PhD

 

In a recent Letter to Nature, researchers from the Scripps Research Institute announced that they had successfully engineered a bacterium that could recognize and replicate DNA containing an unnatural base pair (UBP). Their publication, entitled “A semi-synthetic organism with an expanded genetic alphabet”, demonstrated that E. coli could recognize, take up, and utilize man-made nucleotides to reproduce a plasmid containing a base pair of the synthetic nucleotides, faithfully replicating the UBP for over 20 generations (read more about it in our post about the paper).

 

The findings presented by the authors are incredibly exciting and have huge implications for future research in genetics, microbiology, and medicine. The presentation, however, is concerning. The authors refer to their strain of E. coli as “semi-synthetic.” Such a term could, for non-scientists (or even the scientist with a highly active imagination), conjure up images of some half bacterium-half robot, a sort of Frankenstein’s monster bacterium manufactured by man in the lab. What they actually have is a strain of E. coli carrying two plasmids, one that expresses an algal transporter able to import the synthetic nucleotides, and one containing the UBP. The introduction of plasmids into bacteria is a staple of biological research, and non-native proteins are regularly expressed in microorganisms from E. coli to yeast for countless research and industrial purposes. Are these microorganisms, then, also considered semi-synthetic? Referring to this E. coli strain as such actually does the findings a disservice, as part of what makes this report so exciting is that a common organism could recognize and utilize synthetic nucleotides with its own DNA replication machinery. The idea of an “expanded genetic alphabet” is also somewhat of a stretch, as the second plasmid contained a single UBP but was otherwise composed of canonical, naturally occurring A-T/G-C base pairs. This single UBP wasn’t utilized in any biological or genetic function; it was merely maintained during plasmid replication. Can we consider this UBP a true expansion of the genetic alphabet if it is not interpreted for inclusion in a bacterial function? Do the lofty terms used in the title sensationalize the story in an effort to attract an audience?

 

For trained scientists, this issue may seem minor; after all, would anyone outside of the research sector truly read or pay attention to this paper? If the research results become a news story, they might. In fact, the bigger problem is the communication of this research to the general public by the media, which further sensationalized the story. CNN even published an article entitled “New life engineered with artificial DNA.” One merely needs to glance through the comments section of the online article to understand the backlash of such a claim. Is this organism really “new life?” Is “artificial DNA” perhaps an overstatement?

 

The current climate of public attitude toward health science and genetic research is bitterly divided. Consider, for example, the well-publicized, acrimonious debates over vaccination, pharmaceuticals, and GMOs. Articles that imply scientists are “playing God” by “creating new life” only increase suspicion and inflame anti-science sentiment among groups already wary or contemptuous of health and science research. While it’s important to draw readers and sell stories, sensationalizing the science inhibits fair dialogue over the subject and detracts from the value of the scientific discovery.

 

The advancement of science needs public support – financially, politically, and even in terms of morale – which we can only gain through transparency and the communication of accurate information in the interest of educating the public. As research scientists, good communication starts with us. We have the responsibility to ensure our findings are clearly and truthfully conveyed to any audience, including among the research community. In turn, it is up to science writers and journalists to ensure the appropriate communication of scientific research to the public, in a manner intended to do more than sell stories. Science, itself, is sensational. Let’s not allow fabricated drama to take away from the excitement and wonder of scientific discovery.

DNA is made of A, C, T, G…X, and Y?

 

By Elaine To

 

In biology classes, everybody is taught that deoxyribonucleic acid (DNA, AKA the genetic information of a cell) has four and only four nucleotide bases. Adenine (A) and thymine (T) base pair together and cytosine (C) and guanine (G) base pair together. For the first time ever, researchers have expanded the genetic alphabet to include two additional bases: dNaM (X) and d5SICS (Y).

The researchers have previously shown that DNA polymerases, the enzymes responsible for replicating DNA, successfully replicate DNA containing the dNaM-d5SICS base pair. However these reactions were not carried out within living cells. The researchers decided to try this in the bacterium Escherichia coli due to the simplicity of the cells. Multiple factors had to be optimized in preparation for carrying out these reactions inside cells.

Firstly, the unnatural bases must be present inside the bacteria for DNA polymerase to use them as raw materials. Cells normally obtain A, C, T, and G from breaking down food or recycling previously used nucleotides. Both these pathways were not options for X and Y, so the researchers first tried passive diffusion across the cell membrane. Once X and Y diffused into the cell, they could then be phosphorylated by naturally occurring enzymes to their triphosphate form, which is the form that DNA polymerases recognize and use. The phosphorylation was unsuccessful.

The researchers then explored the idea of transporting the triphosphate forms (XTP and YTP) directly into the cells. Uptake of XTP and YTP by nucleotide triphosphate transporters from multiple other species was screened. The PtNTT2 transporter from the diatom Phaeodactylum tricornutum was most efficient at bringing XTP and YTP into the cells.

The next issue was the instability of XTP and YTP in the culture medium, especially when the E. coli were actively growing. Tests were first carried out on the natural triphosphate ATP. It was determined that addition of KPi to the culture medium increased ATP stability significantly and that KPi had the same effect on XTP and YTP.

And with that, the researchers were ready to generate their E. coli organism containing X and Y. They prepared two circular pieces of DNA, known as plasmids, which are easy to transport into bacteria. One plasmid contained the gene for the PtNTT2 transporter and the other contained a gene with an A-T base pair replaced by X and an analog of Y. Since YTP is the provided substrate, any newly produced plasmid will contain X and Y. This distinguishes it from the original template plasmid containing X and the Y analog.

After inserting both plasmids into the bacteria and growing them in KPi, XTP, and YTP containing medium, the plasmids were extracted from inside the cells. Analyzing the total nucleotide content with mass spectrometry showed that Y was clearly present. X was not detected, but it is known to fragment poorly and thus be difficult to detect with mass spectrometry.

To check the incorporation of XTP and YTP into the extracted plasmid, it was replicated in a PCR reaction using the natural nucleotides, YTP, and biotinylated XTP as substrates. The new product should contain biotin and thus react with streptavidin, which binds very strongly to biotin. As expected, streptavidin bound to the PCR product, confirming that the X-Y base pair is in the plasmid.

Sequencing of the plasmid shows that the nucleotide sequence is correct up until the expected location of the X-Y base pair. The sequencing reaction terminates at this location because there is no X nor Y provided in the sequencing reagents. This proves that X-Y is present in the right location in the plasmid.

In a series of landmark experiments, the researchers have shown replication of DNA containing an unnatural base pair inside living cells. The next step to be undertaken is the transcription of this DNA to mRNA and then hopefully translation into a functional protein. It is conceivable that the incorporation of X-Y into mRNA will soon transpire due to the similarity of DNA and RNA. Subsequently, work that has already been done in incorporating unnatural amino acids could be leveraged to facilitate the use of X-Y in codons that result in proteins.

The Biomedical Research Crisis

 

By Neeley Remmers, PhD

 

Call it “woman’s intuition” if you will, but all throughout my graduate career I had this persistent voice in the back of my head trying to tell me something. It started as a gentle, lulling whisper in my first year that gradually grew into full-blown fire alarm screeching in my head. What was this alarm? My own growing concern over the sustainability of biomedical science and its job market. I had been exposed, to some degree, of the decline and volatility of research jobs in industry prior to attending graduate school and knew of the ever increasing influx of graduate students entering the biomedical field despite the fact that the number of available faculty and research positions had remained constant. My concerns were fully realized when I went to a career development conference in my 4th year, right about the time I needed to start making more concrete plans as to where I wanted to take my career. The recent article published in PNAS co-authored by Bruce Alberts, Marc W. Kirschner, Shirley Tilghman, and Harold Varmus eloquently highlights some of the concerns I have myself as well as additional faults of the current system used by the biomedical field and gives insightful recommendations as to how to remedy the situation to prevent our field from imploding.

 

The authors adequately identify the root cause of the looming implosion of biomedical research – the assumption that there will be continual, rapid growth in the field creating job security for those already established and creating a job market rich with opportunity for new scientists. This assumption had been frequently used as bait to persuade me into joining the field even though the NIH budget had already begun to diminish after experiencing a decade of growth by the time I entered college. This decline in available federal funds (thanks to recent economic hardships felt everywhere) has fully opened our eyes to our current situation of having a supply of highly-qualified scientists that surpasses the number of available research positions, more specifically academic research positions. This influx of skilled scientists was the catalyst needed to synthesize a number of other problems that have recently surfaced in biomedical research that hurt everyone in the field, particularly new investigators. I won’t spend time going into detail on these additional problems highlighted by the authors, but I do want to spend a few moments touching on a subject they missed that I feel could also be adding to our current dilemma.

 

One cause of our problem outlined by the authors is there being too heavy a focus on conducting “translational research.” First, neither the authors nor I are trying to downplay the importance of translational research. After all, for a many of us, advancing medicine is the main reason we decided to enter research. However, it does seem like these days many are over-looking the importance of basic research and that you need solid, basic foundation before you can jump into translational research. By doing quality basic research first, you can gain a firm grasp on the mechanisms that dictate whichever physiological process you are studying and can be more successful in translating that knowledge into clinically relevant studies. Part of the push towards doing more translational research, though, comes from Congress and support from the general public. In this day and age, people like to see immediate results, and translational research can provide the public with results that have a more direct correlation to patient care as opposed to basic science. These results may not always be positive, but even the negative results give a better appearance to the public that something worthwhile is being done with the money they have given us. The problem here is that the general public does not understand the scientific process and the time and effort that goes into discovering new, efficient therapies; a problem easily remedied by educating the public about the research process. Once they realize how important the basic science is to translational research, we can bring some focus back towards awarding investigators who propose long-term, high-quality science rather than on those who propose short-term, translational projects.

 

Back to the article, the authors give their recommendations for how to rescue biomedical research. I will refrain from commenting too much on how we might remedy the grants review process, selecting review panels, and such as addressed by the authors as I do not have much experience or knowledge in these areas. What I can comment on is their recommendations for altering the way we train new scientists. As mentioned earlier, there has been an inflation of graduate students and post-doctoral researchers in recent years that far surpasses the number of available jobs. This is in part due to the fact that it is cheaper for senior scientists to bring students and post-docs into their labs rather than hire staff scientists and restructuring grant guidelines in terms of salaries, as outlined in the article, could certainly help this. The authors suggest that by prohibiting payment of students from grants and increasing pay of post-docs will help to reduce the numbers of incoming graduate students, promote career advancement of post-docs, and encourage hiring staff scientists all of which can be beneficial in the long-run.

 

Aside from simply limiting the number of incoming graduate students, I feel it is necessary that graduate programs start implementing career development programs into student training. In the past, one’s career path in science was pretty clear and the apprenticeship scheme used to train current graduate students worked well. However, in today’s world only about 25% of current graduate students will be able to obtain a faculty position leaving the other 75% of current graduate students to find employment elsewhere rendering the apprenticeship scheme no longer a valid training model. Instead, we need to increase efforts to introduce students early on to the many other career options available to them in science by giving them opportunities to meet with professionals in these areas. Students can then begin to make valuable connections to establish relationships with a secondary mentor that can help them get into the fields of patents, policy, scientific writing, etc.

 

Change in the structure of the biomedical science enterprise is desperately needed to prevent it from collapsing. The reality is that the model currently in use may have worked well in the past but is severely out-of-date for today’s economy. Serious changes are warranted in order to get back to the days of exciting scientific discovery rather than living in the days of scientific survival.