A NARROW conveyor belt runs between a lorry and a set of pallets stacked ten-high with shoebox-sized containers. Inside each of them is a clutch of mice ready for dispatch to some distant laboratory, along with enough food and water-laden gel to sustain them on their journey. Most of the containers have five occupants; some special bloodlines, for example those that have been bred to be diabetic, and thus pee more, travel in smaller numbers. “Feels like the first time”, by Foreigner, may be playing unobtrusively in the background, but the loading of the lorry is utterly routine. All told, 3m mice a year ride this conveyor belt.

Plenty of other creatures do their bit for science, from yeast to flatworms to zebra fish to marmosets and, unhappily, chimpanzees. But mice and rats make up the overwhelming majority of the vertebrates used in research. And they cannot be just any old rodents. Lab mice mostly come from specific strains that have been deliberately inbred, with siblings mated to each other generation after generation until the whole bloodline is genetically very much of a muchness. Once your lab is used to working with a particular strain, you will tend to keep coming back to it—or, perhaps, to variants of it that have a specific set of genes “knocked out” or rewritten. When you need more mice, you will send off for some as similar as possible to the ones you already have. And for a great many labs, the rodents that they get delivered will have passed through this loading bay. The Jackson Laboratory, in Bar Harbor, Maine, is one of the world’s biggest suppliers of laboratory mice.

Both in academia and among pharma companies life without mice from JAX, as everyone here calls it, or one of its competitors is inconceivable. But the mouse’s position as the researcher’s best friend is not without problems. More than 80% of the candidate drugs that make it into clinical trials because they worked in mice do not go on to work well in humans. What’s worse, it has recently become clear that attempts by one lab to go back and replicate mouse studies carried out by another fail much more often than one would wish. Despite the best efforts of JAX and its ilk, the world’s lab mice are both mimicking the biology of sick humans with insufficient fidelity and responding to experiments with insufficient uniformity.

A lot of the poor reproducibility—and thus, presumably, many of the unhelpful results—rests on details of the way that researchers keep their animals, or run their experiments. However reliably uniform the mice are when they are shipped off from JAX, if they do not get handled in the same ways later on they will not produce the same results. Aspects of the care and feeding of mice that were previously seen as insignificant are turning out to matter a lot.

But there is a deeper problem, too. The mice used to model a particular human disease often offer only the roughest sketch of the malady the researchers are trying to address. And in many cases the inbred nature of lab mice makes them a poor guide to what will go on in a broader, more genetically diverse population. The underpinnings of life have complexities that the sought-after simplicities of the laboratory mouse have not come close to cracking. So JAX is using new genetic technologies, cunning statistics and mouse-breeding projects of unprecedented ambition to crack further.

Earth-born companions

Mice are small, cheap to rear and don’t mind living crammed together, whether in a lab enclosure or under a barn floor. They’re quick: quick to reach sexual maturity and quick to gestate (you can get a new generation every three weeks). Quick to die, as well; a lifespan of two years or so makes studies of a whole life, or of multiple generations, quite easy.

On top of all these natural advantages, when modern biology laboratories started looking for a workhorse in the early 20th century the mouse had something extra going for it. For decades European and Japanese mouse “fanciers” had been breeding animals with interesting behaviours or particular coat colours. Mouse genetics was not a science, but it was a well-practised art. When Clarence Cook Little, who founded the Jackson Laboratory, started looking into the causes of cancer in humans in the 1900s, appropriately-bred mice were the obvious way forward.

Once scientists took their murine turn, the benefits of continuing down that road were self-reinforcing; the more they learned to do with mice, the more they wanted to do. At JAX and elsewhere mice were used to study cancer, immunology, diet, neuropathology and more. In the 1970s biotechnology opened up new possibilities—putting in specific human genes to make them better models for specific diseases, knocking out particular genes to try and work out what purpose they serve. JAX was at the forefront of the technology, doing on a large scale what individual labs would struggle to do on their own.

Lab mice became a commodity, one that scientists ordered in from afar and that they defined by their bloodlines and genes. But not all mice are equal, even if their genomes are. If you do an experiment on a set of mice that are littermates and on another set raised apart, they will respond differently. If, as some labs do, you use only males for experiments, you may get different results from those in co-ed labs.

Trouble with reproducing laboratory results is not confined to mouse studies, or even to biology. Journals are, in general, not interested in negative results, so the scientific literature lacks mention of failure. Scientists are unwittingly biased toward results consistent with their hopes and expectations, and may suffer from perverse incentives. Take those failed clinical trials: testing a drug on humans and finding out it doesn’t work costs a lot of money. But being the person who kills a promising drug that colleagues have been working on for years, on the basis of some borderline results in mice, takes a lot of character. A fundamental problem in irreproducible research is that crucial details about how experiments are done are often omitted from published papers. Sometimes this is sloppiness—not noting down things that are known to make a difference. But sometimes it is nescience—not noting down things that everyone has assumed will not make a difference but which, in fact, do. Mouse studies are currently confronting a number of areas where such unknowns have been rife.

Nature’s social union

A study published in 2014 showed that mice in pain studies experienced extreme levels of stress if the researchers handling them were men, but not if they were women—a difference no one had thought to look for, or report. In 2016 a furious debate erupted about how studies might be affected by the lab mouse’s microbiome, the bacteria that live in and on it. These microscopic fellow travellers differ among strains of mice, or among otherwise identical mice bred in different places, or even in the same mouse from one season to the next. Science is just now figuring out how much difference these bugs make to human health; it should come as no surprise that microbiomes influence mouse studies as well.

At JAX they take bacteria seriously. Near the lorry in the loading bay sit racks of mouse chow waiting to be sterilised in a nearby autoclave—in essence, an oven big enough for a couple of cars. Everything the mice will be exposed to from the moment they are born until a researcher pops open the box they travel in will be similarly sterilised.

Bacteria are not the only intruders the lab wants kept out. The mousetraps in the hallway are there to forestall incomers, not escapees; the joke goes that local mice have heard how cushy things are inside. The air that flushes through the little transparent apartments housing one male and two females in rigidly controlled polygamy is impeccably filtered.

The technicians who wander around removing newly weaned pups and replenishing food and water are dressed head to toe in cleanroom suits, hands gloved and feet bootied, peering out through visors. Tubes coming from their headgear reveal that their air supply is filtered, too. Music—at the moment, the breathy intro to Jethro Tull’s “Cross-Eyed Mary”—is piped in constantly to stop the mice from being spooked by any loud noises. The soft-rock playlist balances what is perceived to be calming to the mice and what the technicians can bear to hear all day long. Think dentist’s office.

Some of the mice being so carefully and protectively raised are good for a range of work. The lab’s biggest seller is C57BL/6, or “Black Six”, a long-established inbred strain also available elsewhere, which is by far the world’s most popular lab mouse. Others are bred, or engineered, to show specific symptoms or syndromes. You can buy a mouse that is given to something like depression, or to something like Alzheimer’s disease, or that just sits around like a couch potato, growing unhealthier by the day. Some mice can model more than one thing. A red-eyed albino called SJL has a susceptibility to nervous-system inflammation which makes it a good model for multiple-sclerosis research; it has also been used as a model for calming down violence, because males are particularly aggressive. Some mice—unsurprisingly, given the in-breeding—have weak spots. Black Six is a poor tool for studying hearing because it tends to grow deaf.

Some of the less-used strains are stored not in cages but as frozen sperm and eggs. This genetic back-up system also keeps the bestselling strains straight. Inbred strains are subject to “genetic drift” as fluctuations build up in the gene pool. To ensure that every shipment of Black Six and SJL does exactly what the customers expect the lab back-crosses its strains with ancestral sperm every five generations.

And then there is the creation of new mice—mice with particular genes added, or removed, to order. There are lots of such mice already; soon there will be many, many more. In August 2016 JAX received a $28m grant for the latest part of a grand international project to produce some 20,000 new strains of Black Six, each with one of the 20,000 genes in the mouse genome removed, and see what ails them. It seemed a gargantuan project ten years ago; now, thanks to new genome-editing techniques, especially one called CRISPR-Cas9, its later stages border on the routine.

Indeed, CRISPR may usher in the era of true designer mice. If you want a beastie that’s particularly wee, sleekit, cowering and timorous, for example, you could ask for mutations in the Ghrhr gene, which can govern size; Foxq1, which makes coats shiny; and Lypd1 and Atcay—mutations that provide, respectively, a fearful nature and general skittishness.

Poetically satisfying though such polygenic high-jinks might be, in general mouse research has tended to go a gene at a time: “That’s what we can do easily,” says Nadia Rosenthal, JAX’s scientific director. And for some diseases, such as muscular dystrophy or cystic fibrosis, a single gene is all it takes to capture pretty much everything, since the disease is caused by a single-gene mutation in humans. But the role genes play in most diseases is a lot more complex. Trying to understand them, and thus model them, on a gene-by-gene basis quickly gets researchers into what Dr Rosenthal calls “unfeasibly tricky genetics”.

Tricky as it may be, though, somehow this work has to get done if the research is to provide both an understanding of the underlying mechanisms and new ways of intervening. And getting that sort of understanding means embracing what labs like JAX have largely tried to dispose of: genetic diversity. Only with diverse populations can you pick up the subtle relations between genes which influence the most common and debilitating conditions.

This was the idea behind Collaborative Cross, an effort begun at JAX in 2004 and since developed by a community of researchers spread all around the world. (The outcomes of research carried out at JAX are not patented: every new model or bloodline created here is open-source.) The ambitious project started with a “founding population” of five standard laboratory strains and three more-or-less wild ones that, between them, contained all the genetic diversity that the mice known to science have to offer. From these the researchers produced hundreds of new inbred lines. Within each line diversity is very low, but between them it is high. “Outcrossing” these lines with each other produces more diverse populations in a controlled way, with detailed knowledge of the progenitor lines allowing the new combinations of genes to be tracked. Lots of diversity, lots of replicability: the best of both worlds.

Working with mice that differ, albeit in very well understood ways, allows you to see which of the differences matter, and thus trace the complex ways that different genes work together—or fail to. “You can come to profound insights about genetic interactions, which is very hard to do if you put one mutation in one mouse, and another, and a third, and look at three mice to try to figure out if those things are related,” says Dr Rosenthal. “This way you let the genetics tell you how things are related by simply allowing the population to reveal the important genetic components.”

Man’s dominion

“Simply” may not strike all researchers as the right word. The power of this new technique comes with significant costs: you have to do more experiments and master more demanding statistics. To help other researchers make the leap to the new techniques, researchers at JAX and elsewhere are working on new software to do the statistical heavy lifting. This has its risks. Researchers relying on computer programs to do statistical tests they do not fully understand has proved to be a problem in a wide range of recent research.

If the research is harder, though, the results may be correspondingly more rewarding. And CRISPR makes them easy to build on. Sarah Stephenson came to JAX from Australia to use its Collaborative Cross mice in research on Parkinson’s. Having traced the network of genes involved she might go on to use CRISPR to see what actually happens when some or all of those genes are changed or deleted. There is a good chance that some of them will model particular aspects of Parkinson’s better than anything available now. Other researchers will then be able to use those mice to look for therapies and drugs.

The sound of “Start me up” now echoes around the loading bay; the lorry has departed. Soon this production facility will move 32km away from JAX proper, establishing itself in a recently vacated Lowe’s hardware store (the staff refer to the new digs as “J-Lowe’s”). The care and feeding of the mice there will be more automated, which will reduce their stress levels. Their exposure to bacteria and pathogens will fall yet further.