Patients who contribute their data to research are primarily motivated by a desire to help others with the same plight, through the development of better treatments or even a cure. Out of respect for these individuals, and to uphold the fundamental tenets of the scientific process, I’d like the clinical trials community to shift its default position on data sharing and reuse to align to data availability on publication, similar to the life science community. This will enable more robust, rigorous research, create new opportunities for discovery and build trust between patients and scientists.
I have tweeted prolifically about the UK Referendum on membership in the European Union, strongly supporting the REMAIN (staying in the EU) campaign. In response to requests for a more substantial explanation of my position, I present here a short version and a long version of my views.
This is the third and final post in a series in which I share some lessons learned about how to plan, manage, analyse and deliver a ‘big biodata’ project successfully.
Now that you have the results of your carefully planned, meticulously managed and diligently analysed experiment, it’s time to decide on what to publish, and where.
Continue reading “Publishing Big Data Science”
This is the second of three blog posts about planning, managing and delivering a ‘big biodata’ project. Here, I share some of my experience and lessons learned in management and analysis – because you can’t have one without the other. Continue reading “Managing and Analysing Big Data – Part II”
Biology has changed a lot over the past decade, driven by ever-cheaper data gathering technologies: genomics, transcriptomics, proteomics, metabolomics and imaging of all sorts. After a few years of gleeful abandon in the data generation department, analysis has come to the fore, demanding a whole new outlook and on-going collaboration between scientists, statisticians, engineers and others who bring to the table a very broad range of skills and experience.
I have written about the rise of human as a first-class model organism, and am an enthusiastic user of this outbred, large vertebrate, which can walk right into pre-funded phenotyping centres (hospitals). However, some scientists are (somewhat flippantly) predicting ‘the demise of all non-human model organisms’ completely, only conceding the necessity for using mouse in impossible-in-human verification experiments. Although such positions tend to be put forward in jest, their underlying argument resonates: given our obsession on human health, and how much we can do humans – with broad outbred genetics, iPSC cell lines and organoids – why should we bother with other systems?
In 1799 George Shaw, the head of the Natural History Museum in London, received a bizarre pelt from a Captain in Australia: a duck bill attached to what felt like mole skin. Shaw examined the specimen and wrote up a description of it in a scientific journal, but he couldn’t help confessing that it was “impossible not to entertain some doubts as to the genuine nature of the animal, and to surmise that there might have been practised some arts of deception in its structure.” Hoaxes were rife at the time, with Chinese traders stitching together parts of different animals – part bird, part mammal – to make artful concoctions that would trick European visitors. Georgian London was becoming rather skeptical of these increasingly fantastical pieces of taxidermy.
Ever since the discovery of DNA as the molecule responsible for genetics, in particular when it became clear that the ordering of the chemical components in this polymer was the information that DNA stored, scientists have dreamt about determining the full sequence of the human genome. For Francis Crick, who co-discovered the structure of DNA (along with James Watson, using data from Rosalind Franklin) this would be the final step towards unifying life and chemistry: demystifying the remarkable process that leads to us and all other living creatures. Back in 1953 this was a fantasy, but slowly and steadily over the ensuing decades it became a reality.
After human, the most studied animal, by a long margin, is mouse. Or, more strictly, the laboratory mouse, which is a rather curious creation of the last 200 years of breeding and science.
Laboratory mice originate mainly from circus mice and pet “fancy” mice kept by wealthy American and European ladies in the 18th century. Many of these mice had their roots in Japan and China, where their ancestors would have been kept by rich households. Unsurprisingly, the selection of which mice to breed over the centuries came down to habituation to humans and coat colour rather than scientific principles.