Med and bio stories

Some of my articles on medicine, biology, and the environment

Nature, Sept 13, 2013
Next generation sequencing: The genome jigsaw
High-throughput gene sequencing is fast. But re-assembling the genomes into their original sequence is like shredding 1,000 copies of Charles Dickens’ novel A Tale of Two Cities in a woodchipper and then trying to put the text back to gether in a single book.


Nature Methods, November 2015
Nanopores: a sequencer in your backpack
Genome sequencing can now be done anywhere: in the lab, in the field, perhaps even automatically with sensors. If a sequencer is so small it fits in the palm of your hand, then sequencing everywhere and anywhere becomes a possibility. Data analysis is still necessary, though. Here, it’s all about squiggle plots. There’s software to help weave through the squiggles.


Nature June 18, 2015
Tissue engineering: Organs from the lab
Organs, and physiology in general is difficult to model. Scientists exploring new ways to get that complexity onto their lab bench, to better understand the body’s dynamics, for drug development and to propel regenerative medicine.


Cancer research – computational biology
Nature Methods, April 2016
Cancer: hunting rare somatic mutations
Hunting rare mutations that play a role in cancer is challenging. But finding them matters because they could eventually make a difference to patients. These mutations can help understand the behavior of a tumor and its behavior in an individual. And these mutations might drive the disease. But they might also just be artifacts or noise in the data. Scientists are finding ways to discover these rare mutations, which are particular needles in the haystack.


Global health
The Lancet, April 27, 2012
NIH global health fellowship reinvents itself
Training in developing countries gives medical students a feel for low-resource environments and usually focuses on infectious diseases. But change is underfoot.
Full text.


Science Now, Feb 23, 2012
The Secret of Schreckstoff
When a fish is injured, it secretes a compound that makes other fish dart away. Call it the fish version of instant messaging. Now scientists know its key ingredient.
Full text.


Nature Methods, April 2014
Cancer genomes: discerning drivers from passengers
A tumor is not born as a diseased tissue with many mutations; rather, these mutations accumulate over time. Driver mutations give a tumor a tiny growth advantage, which may be as low as an estimated 0.4%. Finding which drivers play a role in cancer might get easier now that there are data mountains from large-scale cancer genome sequencing projects. But it is still a ways to a comprehensive cancer gene variant catalog.


Cancer research – computational biology
Nature Methods, April 2016
Cancer: hunting rare somatic mutations
Hunting rare mutations that play a role in cancer is challenging. But finding them matters because they could eventually make a difference to patients. These mutations can help understand the behavior of a tumor and its behavior in an individual. And these mutations might drive the disease. But they might also just be artifacts or noise in the data. Scientists are finding ways to discover these rare mutations, which are particular needles in the haystack.


Genomics
Nature Methods, October 2016
Genomics in 3D and 4D 
Chromosomes are constantly moving around in the cell; they stretch out, they crumple up. It’s not random stretching, but regulated chromosomal gymnastics that affects to what degree genes are expressed or silenced.


Genomics – sequencing – computation
Nature Methods, May 2017
How to deduplicate PCR
PCR paranoia is understandable. When amplification leads to PCR duplicates, there are remedies.


Proteomics – High-energy physics
Nature Methods, September 2014
Structural biology: ‘seeing’ crystals the XFEL way
X-ray free electron lasers vaporize samples. After scientists put so much work into obtaining the samples, it might seem surprising to destroy the samples, which are usually proteins they have patiently coaxed into crystals, with a blam. Then again, this is is a way to measure these crystals, which allows researchers to reconstruct protein structure.


Nature Methods, February 2015
Stem cells: disease models that show and tell
Stem cells are powerful in many ways. Gene-editing is powerful. Scientists are combining these two powerful techniques to obtain better models of disease. But stem cells are finicky in the lab and without the right experimental design, no disease-in-a-dish will result.


Nature April 11, 2013
Cell Culture: A better brew
Cells are finicky. Even slight differences in media can have a large impact on them. They may be unhappy and die for unknown reasons. Scientists are exploring more rigorously what exactly their precious cells thrive on and what makes them happy. It’s science mixed with doses of superstition and alchemy.


Nature Feb. 7, 2013
Tracking metastasis and tricking cancer
Engineering approaches are letting scientists observe tumour cells to see how they detach from one spot and attach at another, and how they creep through tissue that should be too dense to let them pass. Other approaches involve scooping migrating tumour cells out of the blood and locking them in highly engineered cages to discover how they seed secondary tumours.


Science Magazine, Random Samples,February 2003, V. 299, no.5610
I’ll Trade You a Virus for Two Parasites
Mark Peppler admits that the idea for MicrobeCards came from watching his son swap hockey cards with his friends. “It reminded me of how much fun I had with baseball cards and how much information was on them,” says Peppler, an associate professor of medical microbiology and immunology at the University of Alberta in Edmonton, Canada. So he decided to create his own edition.


Nature January 16, 2014
High-security labs: Life in the danger zone
Some microbes are deadly. Working with them in a research environment takes many precautions. And scientists have to find a way to maintain instruments that cannot be removed from the lab, once they are placed under bio-containment. A new high-security lab is opening up in Frederick, Maryland, a stone’s throw from the storied US Army Medical Research Institute of Infectious Diseases (USAMRIID). The proximity is intentional.


Nature Biotechnology, July 2008
Poised to branch out
Although dendrimers have not yet taken the drug industry by storm, biomedical research and industrial applications of these tiny, highly branched molecules continue to grow. …
As with any other groundbreaking experimental treatment, progress of the first dendrimer drug, VivaGel (SPL7013), through the clinic has not been entirely smooth sailing.
Full text.


The Boston Globe, March 4, 2003
Saliva offers a mouthful of promise
Here’s a monk’s bit of advice: When the urge to spit is unrelenting, it is best to aim downward and not behind oneself to avoid accidentally besmirching one’s guardian angel. That seems quite reasonable. Looking beyond the realm of good manners, biomedical researchers are finding that this bodily secretion offers a mouthful of promising science. Last month, some of these scientists presented their newest work at the Gordon Research Conference and Symposium on Salivary Glands and Saliva in Ventura, Calif.
Full text.


New Scientist, 16 July 2008
Circumcision: To cut or not to cut?
Imagine a quick and simple surgical procedure that trials have shown could give your newborn child lifelong protection against HIV and may ward off sexually transmitted diseases and cancer too. It involves a little pain and bleeding, and occasionally goes wrong, but the risk of serious adverse effects is tiny. Would you have it done? Chances are you would. But what if you found out that other trials have called the procedure’s benefits into question, and that it involves cutting off part of your child’s penis. Now how do you feel about it?

This, in a nutshell, is the dilemma facing the parents of newborn baby boys. According to the increasingly vocal advocates of male circumcision, slicing off the foreskin is one of the most effective public-health measures ever invented and should be done routinely, like vaccination. Not so fast, say opponents. They insist that circumcision has no medical benefits.
Full text.


Marine biology – Geoengineering – Business
Scientific American.com, Oct. 7, 2002
The little plankton that could? Maybe.
No one knows whether fertilizing single-celled marine organisms is a sound way to pull more heat-trapping carbon dioxide out of the atmosphere. But that hasn’t stopped companies from developing plans to do so. Slowing global warming is a big job. But some researchers and companies say that job could be done by enlisting the help of small but fantastically numerous–and collectively mighty–marine unicellular organisms called phytoplankton.

Phytoplankton make up the chlorophyll-bearing canopy at the base of the marine food web. As part of the natural biogeophysical cycle, phytoplankton absorb atmospheric carbon dioxide, a heat-trapping gas implicated in global climate change. Some of the carbon is buried when phytoplankton die and settle to the sea bottom.

In theory–one strengthened by some experiments, including one early in 2002–fertilizing phytoplankton could accelerate this natural process, sinking carbon in gigaton quantities. Companies see opportunities. The scientific jury is out on whether such a grand-scale experiment with complex atmospheric processes would work to pull out additional carbon–and if it did, whether the cascade of subsequent effects would ultimately wreak more environmental havoc than the excess carbon would in the first place.


Die Zeit, 2/2000
Von Fischen und Frauen
Ein Abgeordneter des amerikanischen Kongresses wollte es ganz genau wissen: “Wenn diese Fische so viele Gene haben, wieso sind sie nicht klüger als wir?”, hatte er bei einer Anhörung gefragt. Die lakonische Antwort von Bob Baker, Physiologe an der New-York-Universität: “Manche von ihnen können es durchaus mit manchen von uns aufnehmen.”

“Wunderschön ist er”, schwärmt Mary Mullens an der Medical School der Universität Pennsylvania von einem Fisch, der in den führenden Labors als begehrter Modellorganismus und neuer Forschungsliebling gastiert. Der ursprünglich im indischen Ganges beheimatete Zebrafisch schwamm sogar in das Wall Street Journal, da Pharmafirmen nunmehr in ihn investieren. Denn er ist für genetische Studien ebenso geeignet wie für entwicklungsphysiologische Experimente. “Beim Zebrafisch”, so die Wissenschaftshistorikerin Evelyn Fox Keller, “passen die verfügbaren Techniken zu den aktuellen Fragen, und die Fragen passen zum Organismus: eine Konvergenz vieler Interessen und Möglichkeiten.”


The Economist, January 16, 1999
A doggie bag of drugs
In days gone by, a badly behaved pet dog would probably have been sent to obedience classes for retraining. If it continued to misbehave, a one-way trip to the vet beckoned. But a society that believes that there is (or ought to be) a pill for every ill was unlikely to put up with this state of affairs for ever.

So it is probably not surprising that America’s Food and Drug Administration (FDA), the organisation charged with making sure that drugs destined for American people are safe and effective, has just given its first formal approval for two drugs to be used to treat the behavioral problems of American dogs.