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Advice on Big Data Experiments and Analysis, Part I: Planning

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.

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In defence of model organisms

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?

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12th genome of Christmas: The platypus

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.

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11th genome of Christmas: Us

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.

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10th genome of Christmas: The laboratory mouse

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.

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9th genome of Christmas: Medaka and friends

My ninth genome of Christmas is a bit of an indulgence: the gentlemanly, diminutive Medaka fish, or Japanese rice paddy fish.

When Mendel’s laws were rediscovered in the 1900s, many scientists turned to local species they could keep easily to explore this brave, new world of genetics. In America, Thomas Hunt chose the fruit fly. Scientists in Germany explored the guppy and Ginuea pigs. In England, crop plants were the focus of early genetics. In Japan, researchers turned to the tiny Medaka fish, a common addition to many of the ornamental ponds maintained in Japanese gardens.

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Cyanobacteria: the greatest chemists in the world

You might think that the best chemists on earth are humans, living perhaps in Cambridge, Heidelberg, Paris, Tokyo or Shenzhen, beavering away in laboratories filled with glassware, extraction hoods and other human-made things. But then you would be discounting a multitude of bacteria that have cracked all sorts of chemistry problems over the course of their long evolution, and that still harbour secrets about how they manipulate molecules. One inventive clade of bacteria, the cyanobacteria, quite literally changed the world, and built the foundations of modern life.

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6th genome of Christmas: the deadly Plasmodium… plant?

If humans have an arch enemy, it might well be the tiny, blood-borne parasite Plasmodium falciparum. This nasty beast causes most of the malaria in sub-Saharan Africa and, together with its cousins, in many tropical zones throughout the world. It kills huge numbers of children every year, and constantly cycles through the bloodstreams of its many survivors. It has been with us since our explosive migration out of east Africa, and in fact many genetic diseases (including sickle-cell aneamia and thalassemias) are tolerated by human populations because they confer an advantage against this nasty parasite.

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5th genome of Christmas: The Fly

The humble fruit fly – Drosophila melanogaster, to be specific – has played a central role in the history of genetics and molecular biology and continues to be important in research.

Championed by the legendary Thomas Morgan at the start of the 20th Century, Drosophila provided a practical foundation for genetics – long before the discovery of DNA as vehicle for passing down heritable information through generations. Morgan and colleagues developed the concepts of ‘gene’ and ‘linkage’, and so we have ‘Morgans’ (and more commonly, centi-Morgans, cM) as the basic units of genetic maps.

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