Author of this article:

Professor David Hume FSB, FMedSci, FRSE is the Director of The Roslin Institute

What does the future of animal production hold? David Hume looks forward.

We need to plan for increased production of animal products.

Major funders such as the Gates Foundationand CGIAR have recognised that livestock are the major route out of poverty for the poorest farmers.

And there is increasing recognition thatprotein malnutrition has long-term effects on development of cognitive ability. Vegetarianism is not an option; there is evidence of subclinical malnutrition on vegetarian diets even in Western countries, and in developing countries high quality vegetable protein sources are no more available than animal protein.

The challenge will be to meet this demand for animal products whilst at the same time reducing the overall environmental impact.

Selection game

Everything that we eat is a genetically-selected organism that would not exist in its current form but for human intervention. Much of what we eat is already genetically-modified in that the mutations that produced desirable traits were artifically induced using radiation or chemicals prior to selection. The fact that everything we eat is a product of human intervention is as true for animals as it is for plants, even though intensive selection of animal breeds is a relatively modern phenomenon.

There have been massive increases in productivity in the livestock sector in the past 40 years. These gains have been achieved through a combination of genetic improvement and better husbandry, nutrition and disease control. The dairy, swine and poultry sectors are highly structured with a small number of international companies controlling large proportions of breeding and production. In contrast, the sheep, goat and beef cattle sectors are less highly structured and for these species together with others (e.g. buffalo, deer, llama, alpaca, camel) there remains considerable scope for improvements in productivity.

Furthermore, compared  to land-based agriculture, we are at early stage in fish domestication, and substantial productivity and feed efficiency gains are clearly possible.

Improved efficiency of animals will involve continued selection, based upon genome-wide selection and high density genetic markers. Advances in systems biology, and knowledge from analysis of genotype-phenotype relationships will make such selection more predictive. In all major livestock,cloning of productive animals is available and already cost-effective, although the legal and ethical issues in Europe have yet to be resolved.

Nevertheless, it is very unlikely that existing genetic variation in animals will continue to generate the rate of gain in size or offspring number, for example, obtained in the past. A different kind of genetically-modified animal will be required.

Transgenesis [genetic engineering] to produce desired traits is possible and could provide clear benefits to the consumer in terms of cost, health, animal welfare and environment if regulatory requirements were based upon science rather than assertion. The first vanguard of genetically-modified animals, the Aquabounty salmon, has almost made its way through the regulatory hurdles in the US. As in plants, the immediate need is to protect against catastrophic pathogens such as avian influenza or African swine fever.

An alternative to transgenesis is the new genome editing technologies, which produce precise genetic changes without any residual insertion of foreign genetic material. One can reasonably argue that genome editing is identical to natural or induced random mutations in molecular terms and is considerably less likely to produce unforeseen consequences than the shotgun approach of selective breeding. 

Bet the future farm

The future of livestock farming will undoubtedly involve further intensification. A greater understanding of the underlying mechanisms regulating behaviour in animals is essential to fully address the welfare issues associated with this change.

There is also a pressing need for the development of objective measures of stress in animals. There are ethical and economic arguments for improving the environments in which animals are kept rather than selecting genotypes. However, it is worth remembering that selection for behaviours such as docility and herdability has already occurred, and was essential to the domestication of animals. 

What will constrain future advances in livestock production is investment. Large animal research is expensive. Over the past 20 years, there has been systematic underinvestment in the sector by governments all over the world, and expertise and infrastructure has declined. International development agencies and funders have placed disproportionate emphasis on crop research. 

Livestock improvement is not a sector that can be left to industry. The applications of genomic selection require accurate performance measurements on very large numbers of animals. The profit margins for farming livestock at the individual farmer (or animal) level are small.  Even in the poultry and pig breeding industries, where there is consolidation of the sector, the global players are dwarves compared to pharmaceutical or seed companies.

Sustainable gains in productivity of livestock can be achieved within the next 20 years. But they will only be achieved if governments recognise that the required research is “public good”, and re-enter and re-engage with the livestock research sector with substantial investment.

Add your comment.

About David Hume

Professor David Hume FSB, FMedSci, FRSE is the Director of The Roslin Institute, which is linked in the minds of many with a famous sheep. Since it joined the University of Edinburgh in 2008, and moved to a new research building in 2011, it has grown to well over 450 staff and students, and can make a reasonable claim to be the world’s leading animal sciences research institute.

Hume is an Australian but has worked all over the world. His main area of interest is the molecular basis of disease resistance and susceptibility with a particular focus on the function of specialised cells of the immune system in infection, inflammatory disease and cancer.

Geoff Mulgan 

Predictive tools will move from being of marginal interest to part of mainstream culture.

Prediction is now much more an art than a science. Economic forecasting has been shown to be little more accurate than guesswork. Political forecasting is just as suspect: as the political scientist Philip Tetlock showed, experts are terrible at predicting what will actually happen.[1] Worse, many professional futurists continue to repeat old predictions (like the end of work and long-tenure jobs, university campuses and live theatre) even when they've been proven to be wrong.

But my prediction is that  predictive tools will move from being of marginal interest to become part of mainstream culture and everyday life.  

The main reason is that science is increasingly entering this murky territory.  

Weather forecasting has steadily improved - even if only a few days into the future. In business, companies like Wonga have made money through superior algorithms for predicting risk and credit-worthiness (the ethics of the loans that result are of course another matter). When you walk into a GP's surgery the PARR (patients at risk of re-entering hospital) system may be  assessing your chances of entering hospital. In criminal justice the Level of Service Inventory-Revised (LSI-R) has been  used for a long time, and  shown to be fairly accurate.  Kaggle runs regular competitions for programmers to develop algorithms which can demonstrate better predictions, for example of school results or health.  

In many fields, prediction won't be easy: genetic tests, for example, have been much less useful for predicting disease risks than many expected. But there's no doubting the direction of travel. 

Rigour is also being brought to more intuitive kinds of prediction: for example, observing three minutes of a marital row to predict whether the marriage will survive, or the first few seconds of a job interview, or a short stretch of a tutor teaching a class to predict their overall scores. 

As predictive models become more mainstream it's possible that our thinking about prediction will change. In the film Minority Report it's presented as a modern version of astrology - if you gaze into the scientific crystal ball you can know for certain what will happen. Instead the opposite is likely. People will become much more aware of probabilities, and therefore more immunised against the idea that the future is knowable. We'll all become more Bayesian - able to understand that the world around us is probabilistic rather than deterministic. That will help us to be better decision-makers. If for example you're given a prediction of your risk of entering hospital in the next two years you may decide to radically change your lifestyle.  

Indeed the greatest value from these models lies less in prediction itself but rather in changing our awareness that  we can change how the dice fall. The paradox is that where the science fiction of predictive tools tended to diminish the space for human agency, the science may end up expanding it. 

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posted by Michael Spitz

by @Spitz

The press has recently gone wild celebrating what seems like a fantasy wunderkind tale, that of a teenager from Maryland who on his own initiative developed a non-invasive, five minute test for pancreatic, ovarian, and lung cancer that is 168 times faster, 26,000 times less expensive, and over 400 times more sensitive than current diagnostic assays.

Before you call BS on this seemingly unbelievable story, check out Mr. Jack Andraka’s TED Talk. In his own words you’ll discover how Jack was deeply moved by the passing of a close family friend from pancreatic cancer, a personal tragedy that motivated him to find a way to simplify and improve diagnostics for the devastating disease. Using his “go-to” source for information, Google, Jack keyword searched his way into medical history.

What makes this story even timelier and poignant is how it represents the perfect storm of digital health:

The empowered e-Patient and e-Caregiver

Although Jack was powerless to assist his family friend while he was alive, the spirit of sympathy, connectedness, and wanting to help spurred Jack’s quest for earlier diagnosis, driving him to overcome every barrier until an effective solution was discovered, saving future patients.

The Internet as open data source

As Jack mentions near the close of his TED Talk, the Web empowers billions of people throughout the world with a treasure trove of instantaneously accessible global information, enabling eager amateurs and seasoned professionals alike to dive into data and change the course of science and innovation.

Digital channels as connection conduits

Not only did Jack use the Web to choose the right mesothelin biomarker and creatively meld it with a nanotube testing mechanism, but he personally emailed two hundred scientists with his grant proposal, finally finding a single insightful researcher willing to take a risk on this precocious teen.

Paradigm shift from outside the entrenched system

Much like Thomas Kuhn theorized, scientific change and novel invention usually comes from a state of crisis, introduced by an outsider with little bias and loaded with fresh perspectives. In this sense, who better than a teenager armed with nothing but a computer, his imagination, and tireless determination?

Jack’s story is inspirational to all digital health users, entrepreneurs, and advocates who celebrate the amazing opportunities that lie at the unique convergence of health, communications, and technology. After all, if a Googling teenager can change the face of cancer detection, imagine what an entire generation of wired mavericks can do?

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For our September 2012 health survey, we explored how U.S. adults are using the internet and digital technology as tools related to health and healthcare. Among our findings:

81% of U.S. adults use the internet and 59% say they have looked online for health information in the past year. 35% of U.S. adults say they have gone online specifically to try to figure out what medical condition they or someone else might have. 

39% of online health seekers say they looked for information related to their own situation. Another 39% say they looked for information related to someone else’s health or medical situation. An additional 15% of these internet users say they were looking both on their own and someone else’s behalf.

Seven in ten (69%) U.S. adults track a health indicator for themselves or a loved one and many say this activity has changed their overall approach to health, according to a new survey by the Pew Research Center’s Internet & American Life Project. In all:

• 60% of U.S. adults say they track their weight, diet, or exercise routine.
• 33% of U.S. adults track health indicators or symptoms, like blood pressure, blood sugar, headaches, or sleep patterns.
• 12% of U.S. adults track health indicators or symptoms for a loved one.

Fore more information on the reports and data associated with these findings, please see: 2012 Health Survey Data.

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Using knowledge to create knowledge is the major concept of the emerging knowledge society. This way, knowledge becomes sustainable and a tool to realize the millennium goals. But to achieve this in the most effective way, we will have to make inventories of knowledge.

ICMCC (International Council on Medical & Care Compunetics) is an international foundation operating as the knowledge centre for medical and care compunetics (COMPUting & Networking, its EThICs and Social/societal implications), making information on medicine and care available to patients using compunetics as well as distributing information on the use of compunetics in medicine and care to patients and professionals.

Knowledge is derived from the synthesis between information and experience. ICMCC is becoming the global guiding platform in bringing information and experience related to medical and care compunetics together, thus creating the necessary inventories of knowledge. As we are aiming at both the patient/citizen and the professional we also target and facilitate the shifting relationship between the two.-Read more

Humetrix iBlueButton app won the ONC's Blue Button Mashup Challenge.

posted by:By: Jonah Comstock 

The Office of the National Coordinator for Health Information Technology (ONC) is working to promote more patient engagement and access with their own records. One avenue of this work is with the Meaningful Use Stage 2 guidelines, but the office is also working with data holders and app developers to encourage the development of a patient health data ecosystem through an update and an expansion of the Blue Button program that’s being called Blue Button Plus, the ONC announced in a recent webinar, hosted by the National eHealth Collaborative.

“There’s a lot of democratization of information. Back and forth and sharing and co-creation of knowledge, and some of that has to be spilling over into health,” Lygeia Ricciardi, acting director of the Office of Consumer eHealth, said. “ONC in this context views itself not as the leader of this movement, but as a catalyst, pulling together the various forces moving in this direction in synergistic ways.”

HIPAA already requires that consumers have access to their own records if they request them, but under Meaningful Use Stage 1, they might only be able to access them through an online viewing portal. Stage 2, which will roll out for the earliest EHR adopters at the start of 2013, has a stricter requirement that patients be able to view, download, and transmit their data.

This paves the way, Ricciardi said, for the implementation of Blue Button Plus, which could possibly be a requirement in Stage 3 (the Stage 3 guidelines, which will go into effect in 2016 at the earliest, are not yet set.) Named after the original blue button that was implemented on the VA website starting in 2010, ONC uses the term “Blue Button” to refer to the act of patients downloading their own health records, something that should only become more feasible as providers switch over to EHRs. The ONC advocates that patients have access to their health records to make it easier to keep track of medications, to switch doctors or insurers, or to get care when they’re away from home. Also, when patients have access to their own records, they can spot errors and call to have them corrected.

Data holders that are themselves part of the government — like Medicare and Medicaid, Veterans Affairs, and the military — are implementing Blue Button Plus directly. But the ONC wants to encourage private data holders, such as hospitals, doctors, and private insurers, to make their data available in the same way. Toward that end, it has launched Blue Button Pledge, a partnership which has signed on 450 partners that are either data holders or organizations with a lot of public influence to get the word out about the initiative.

Blue Button Plus, which has previously been referred to as the Automate Blue Button Initiative, will not only make a patient’s health data accessible, it will make it accessible in a mobile and flexible way. Through Blue Button Pledge, the ONC will encourage data holders to format patient data in a consistent way. Whereas right now Blue Button data can only be accessed as an unformatted ASCII text block, Blue Button Plus will be in a data format that third party apps can shape into easy-to-use graphical interfaces, according to ONC. In addition, Blue Button Plus will be designed so consumers can give a third-party app access to their medical records and have it be continually updated, without their needing to sign in every time or manually download their records over and over.

To demonstrate some ways in which Blue Button Plus could be helpful, the ONC launched aBlue Button Mashup Challenge on Challenge.gov, asking app developers to integrate patient health records with some other source of information. Some of the winning apps allowed users to view their medication history on a timeline alongside doctor visits and conditions, or to see all of their medications with a list of side effects and counter-indications. ONC also launched a design challenge to make the Blue Button readout look, in Presidential Innovation Fellow Ryan Panchadsaram’s words “less like a cash register receipt.”

Although support has been wide-ranging, the participants in the ONC webinar acknowledged that it would take effort to change patient and provider attitudes sufficiently to make patient engagement the norm.

“We recognize there may be barriers,” said ONC policy analyst Erin Poetter. “Patients may worry about being viewed as a difficult patient. Doctors might not be accustomed to patients asking a lot of questions or to having their authority challenged. It’s really going to require a shift for both parties.”

But Dr. Henry Wei, a Presidential Innovation Fellow, said it will ultimately be up to patients to demand the rights to their own information.

“You have to ask your data holder to ‘Give us our Blue Button!’” he said. “It’s not evil, it’s just inertia. Get out there. Make yourself known.”

The participants acknowledged that large personal health record movements, like Google Health, had failed in the recent past. But HHS Innovator in Residence Pierce Graham-Jones said what Blue Button Plus is trying to put into place is exactly what was missing in 2011: ubiquitous patient access to digitized records.

“The past was a very manual world of entry, the future is going to be a world of automation,” he said.

Graham-Jones said a number of data holders are already designing Blue Button Plus features, and that some would be on display at the HIMSS conference in March.

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Jeremy Hunt, the health secretary. Photograph: Jonathan Brady/PA

About Author

Profile

Randeep Ramesh is social affairs editor for the Guardian. He was the paper's south Asia correspondent for six years and a leader writer for the paper, specialising in globalisation. He was a City news editor and worked on the home news desk. He has won Scoop of the Year and What the Papers Say Investigation of the Year for work on parliamentary lobbying scandals

Genomics England will aim to attract private investment in life sciences, but campaigners raise patient privacy concerns

The health secretary is launching a new government organisation to oversee the creation of a genomic revolution in healthcare that will attract big business investment, but which will raise concerns over patient privacy in the NHS.

Using the NHS's 65th birthday to push for a new "personalised" medical service, Jeremy Hunt will launch Genomics England, a state-owned entity led by Sir John Chisholm, a former chair of the medical research council who made millions from the sell-off of the government defence firm QinetiQ.

With the health service reeling from a series of regulatory scandals over patient care, the government has chosen an opportune moment to make the case for Genomics England, which will aim to attract investment from companies interested in building a new life sciences industry alongside the NHS by offering them cash from a ringfenced partnership fund, currently valued at £300m.

In May the prime minister announced that £10m from this fund would be used to match the Chinese billionaire Li Ka-shing's £20m donation to Oxford University's big data healthcare centre, which plans to analyse NHS patient records, DNA sequencing and clinical trials in an effort to improve detection and treatment of a range of conditions.

Hunt will tell a hand-picked audience at a London hospital that "by 2015 the aim is to put the UK at the forefront of the genome revolution worldwide, with whole-genome sequencing linked to patient diagnosis, treatment and care".

However, critics say the commercial push combined with a plan to create a DNA databank – to match those in countries such as the US and Japan – plus a subtle relaxing of patient privacy rights should be a matter of public concern. They point out that DNA differs from other sensitive health data in that it can be used as a tool to identify and track individuals and their relatives.

Campaigners say that a series of changes to the NHS will allow patients, who do not opt out of the system, to be cold-called by their GP on behalf of private companies to ask whether they would take part in clinical studies.

From this year there will be a default assumption that patients can be contacted to take part in clinical trials. With the government enforcing a rule to share medical data, pharmaceutical firms would be able to identify patients for drug trials because their case history and genetic makeup suggests they are susceptible to particular diseases.

Responding to a series of requests under the Freedom of Information Act, the Department of Health admitted that the NHS could contact patients about trials run by "academic institutes, third sector and commercial companies", a right enshrined in the new health service constitution.

The pharmaceutical industry argues that the change is necessary because of the need to cut costs in drug development, which traditionally has involved testing new treatments on groups that are representative of the general population rather than patients who have been specially selected.

Edward Hockings, a bioethicist from the pressure group Ethics andGenetics, who made the FoI requests, said: "We are moving closer to the American system in which pharmaceutical companies can buy patient data and target people with aggressive marketing."

He said he was concerned about why the government had not been clearer about its intentions and the risks involved. "The benefits of doing this will not accrue to the people whose data it is, but to private companies," he said.

"At no point have the government sought to ask the public what they think about selling intimate, personal medical information, commercialising genetic data held on a central database or making NHS users available for clinical trials."

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Registration   closed 

[BC]2 CONFERENCE SCHEDULE

Thursday, 4. July 2013
8:00		Arrival & Registration
9:00		Welcome Notes: Ed Constable, Vice Rector Research, University of Basel Manolis Dermitzakis, Program Chair [BC]2 2013, SIB & University of Geneva
9:30		Opening Keynote Lecture: Human Genome Variation and Personalized Medicine, Stylianos Antonarakis, University of Geneva.
10:30		Coffee Break & Poster Session
		Session I (Chair: Niko Beerenwinkel)
11:00		Whole-Genome Sequence Based Association Studies of Complex Traits: the UK10K Project, Nicole Soranzo, Sanger Institute, UK.
11:30		New Methods for the Analysis of Human Population Genomic Data Adam Siepel, Cornell University, Ithaca NY, USA.
12:00		Rare Variants: Abundant and Deleterious, yet only Marginally Important for Disease Daniel Wegmann, University of Fribourg, Switzerland.
12:30		Lunch Break & Poster Session
		Session II (Chair: Jacqui Beckmann)
14:00		Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links Sven Bergmann, Université de Lausanne & SIB, Switzerland.
14:30		Genomics of Regulatory Variation Kerrin Small, King's College London,UK.
15:00		Trans-eQTL Mapping in over 8'000 Samples Reveals Genetic Variants that Define Hallmarks of Disease Lude Franke, University of Groningen, The Netherlands.
15:30		Coffee Break & Poster Session
		Session III (Chair: Ioannis Xenarios)
16:00		Transcriptome Sequencing Uncovers Functional Variation in the Human Genome Tuuli Lappalainen, Stanford University, USA.
16:30		Genetic Variability and the Proteome, Ruedi Aebersold, ETH Zürich, Switzerland.
17:00		Discovering Basel ...
Friday, 5. July 2011
8:30		Arrival & Registration
		Session IV (Chair: Sven Bergmann)
9:00		Human Germ Line and Somatic Mutation Rates: Evolution, Biology and Statistical Genetics Shamil Sunyaev, Harvard University, USA.
9:30		Epigenome Mapping at Allelic Resolution to Interrogate Genomic Basis of Human Disease Tomi Pastinen, McGill University, Montreal, Canada.
10:00		Interpreting Patterns of DNA Methylation on a Genome-wide Scale Michael Stadler, FMI & SIB, Basel, Switzerland.
10:30		Coffee Break & Poster Session
		Session V (Chair: Alexandre Reymond)
11:00		Novel method identified SNPs in the imprinted gene KCNK9 exhibiting parent-of origin effect on BMIZoltan Kutalik, CHUV-UNIL & SIB, Lausanne, Switzerland.
11:30		Human Genome Diversity and the Personal Drug Response Profile Urs A. Meyer, University of Basel, Switzerland.
12:00		Clinical Bioinformatics: a Paradigm Change in Medicine,Jaques Beckmann, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
12:30		Lunch Break & Poster Session
		Session VI (Chair: Ron Appel)
14:00		SIB - best poster award winner
		SIB - best graduate paper award winner
		SIB - young Bioinformatician award winner
15:00		Closing Keynote Lecture: Challenges of Rapid Population Growth to Modeling Human Genetic Variation Andrew Clark, Cornell University, Ithaca NY, USA.
16:00		Closing remarks Manolis Dermitzakis, Program Chair [BC]2 2013, SIB & University of GenevaTorsten Schwede, [BC]2  Series Chair, Biozentrum University of Basel & SIB
ca. 16:30		End of Conference & Departure