Boing Boing » biotech

Of coral and common sense: Why it's important to test our theories

Maggie Koerth-Baker — Thu, 27 Dec 2012 16:46:28 +0000

Pseudopterosins are a family of naturally occurring chemicals with the power to reduce inflammation, skin irritation, and pain. In other words, they make a great additive in skin cream. If you want skin that less red, pseudopterosins can help. Want a lotion that soothes your face after a particularly vigorous round of exfoliation? Call on pseudopterosins.

Pseudopterosins come from a coral called Pseudopterogorgia elisabethae. That's it in the photo above. For years, researchers and pharmaceutical companies thought they were sustainably harvesting P. elisabethae because, instead of simply gathering any of the coral they could find, they merely pruned it — leaving plenty of the creature to grow back.

But, it turns out that this is a really good example of a frustrating problem — what seems sustainable is not always actually sustainable. Doing the right thing, environmentally speaking, isn't as intuitive as we'd like it to be. (Also, pruning an animal isn't like pruning a plant.) At Deep Sea News, Dr. M explains:

After prunings in 2002 and 2005 and before the annual spawning, Christopher Page and Howard Lasker examined 24 pruned corals and 20 unpruned corals. What the researchers found is that although colonies appeared healthy pruned corals produced less eggs. ... Why would pruned corals produce less eggs and sperm? When organisms are injured more energy is diverted away from reproduction and toward repair. Interestingly, this pruning may actually also creating artificial selection. If workers are targeting larger and fuller corals to prune, then smaller less thick corals will be reproducing more and eventually become more dominant.

This is why science is important. Because, frequently, "common sense" isn't really all that sensical.

Read the full story

Silicon Valley, meet Genome Valley

Maggie Koerth-Baker — Tue, 04 Dec 2012 20:14:35 +0000

More than 100 biomedical and life science companies are clustered in Genome Valley, a research park in Hyderabad, India. (Via Joanne Manaster)

Guerrilla Grafters covertly add fruit-tree branches to ornamental trees

Cory Doctorow — Tue, 25 Sep 2012 14:09:12 +0000

The Guerrilla Grafters are a group of rogue artists who roam San Francisco, covertly grafting fruit-tree branches onto ornamental trees to create a municipal free lunch. John Robb calls it "resilient disobedience."

How can you improve the productivity of your community even if the officials are against it?
One way is through resilient disobedience. For example, there’s a group of gardeners in San Francisco that are spreading organic graffiti across the city. How? By grafting branches from fruit trees onto ornamental trees that have been planted along sidewalks and in parks.
They are using a very simple tongue in groove splice that’s held together with annotated electrical tape. Good luck to them.

Personal Biochar Kilns, Portable Factories, DiY Septic Tank Cleaning, and Guerrilla Grafting (via Warren Ellis)

Genetically modified mosquitoes proposed for anti-dengue fight in Key West

Xeni Jardin — Tue, 24 Jul 2012 17:05:28 +0000

British biotechnology company Oxitec Ltd is trying to convince the locals in Key West to use genetically modified mosquitoes in their fight to eradicate dengue fever in the area. What could possibly go wrong?

NYT series on genetically-targeted cancer treatments

Xeni Jardin — Mon, 09 Jul 2012 21:25:13 +0000

When you have been diagnosed with cancer, as I have, you quickly grow accustomed to "friendly cancer spam." Friends, relatives, and well-meaning acquaintances routinely forward you a gazillion identical links to whatever this week's hot cancer news headline may be.

So it was for me with this New York Times story on Lukas Wartman, a leukemia doctor and researcher at Washington University who developed leukemia. As he faced death last Fall, his cancer genome was sequenced by his colleagues.

What was revealed then led to a treatment plan that targeted the specifics of his genetic makeup. And so far, according to Gina Kolata's report, that experimental treatment plan has been an amazing success. Snip:

Dr. Ley’s team tried a type of analysis that they had never done before. They fully sequenced the genes of both his cancer cells and healthy cells for comparison, and at the same time analyzed his RNA, a close chemical cousin to DNA, for clues to what his genes were doing.
The researchers on the project put other work aside for weeks, running one of the university’s 26 sequencing machines and supercomputer around the clock. And they found a culprit — a normal gene that was in overdrive, churning out huge amounts of a protein that appeared to be spurring the cancer’s growth.
Even better, there was a promising new drug that might shut down the malfunctioning gene — a drug that had been tested and approved only for advanced kidney cancer. Dr. Wartman became the first person ever to take it for leukemia.
And now, against all odds, his cancer is in remission and has been since last fall. While no one can say that Dr. Wartman is cured, after facing certain death last fall, he is alive and doing well.

Suffice it to say that this stuff is relevant to my interests. It is routine for breast cancer patients like me to receive genetic screening for the BRCA mutation, and sometimes a few additional known genetic factors. But there is so much that we do not know, and a growing sense that this infinite array of genetic unknowns could lead to more saved lives, and better quality of life for those of us who have been diagnosed with the disease.

I know I'm not alone in feeling like the treatment I am receiving now will one day be perceived as blunt and barbaric, when genetically-targeted therapies like the ones outlined in these stories become the norm. Those of us undergoing the brutal routine of chemo, radiation, and surgery to keep cancer at bay long for the day when more precise technologies can stop the disease without so much collateral damage.

And then, there is the greater hope that maybe one day all of this will lead to the other "c-word."

A cure.

Read the full article: "In Treatment for Leukemia, Glimpses of the Future."

Part two in the series: "A New Treatment’s Tantalizing Promise Brings Heartbreaking Ups and Downs"

And part three: "A Game Changer in Revealing a Cancer’s Prognosis."

There is a related item in the Economist. Here is the referenced study in the journal Nature from researchers at Washington University.

(image: Shutterstock)

Babies driving robot wheelchairs (super cute video)

Xeni Jardin — Fri, 27 Apr 2012 21:22:25 +0000

[Video Link]

Here's an amazing feel-good video with which to end your week, via the National Science Foundation. The really awesome footage starts around a minute and a half in.

"James C. (Cole) Galloway, associate professor of physical therapy, and Sunil Agrawal, professor of mechanical engineering -- have outfitted kid-size robots to provide mobility to children who are unable to fully explore the world on their own."

The robotic assistance devices are designed to help infants whose mobility and independence is limited by conditions such as autism, spina bifida, muscular dystrophy, Down syndrome, and cerebral palsy.

I understand that these will be among the many exhibits on display at the USA Science Fest at the Washington, DC Convention Center on Sat., April 28th. Babies probably not included.

Vat-grown bio-fashion

Cory Doctorow — Sun, 11 Jul 2010 08:17:37 +0000

Robbo sez, "In the age of 3D printing and growing new body parts in a lab - the fashion industry steps forth and joins the fray - using bacteria to grow clothing. As described in a post on the ecouterre.com site: 'designer Suzanne Lee has crafted fashion items that look both cool and unsettling. No doubt we'll all soon be wearing clothing we can print out or grow - purchasing designs online and then heading down to the kitchen to try things on. Biodegradable? Possibly. Could also be used to thicken gravy.'

Biocouture (Thanks, Robbo)

Biomanufacturing replaces coal-fired brick kilns with room-temp bacteria and sand

Cory Doctorow — Mon, 17 May 2010 01:35:04 +0000

The coal-fired baking of bricks generates more CO2 annually than the entire aviation industry. A biomanufacturing process aims to change that, replacing fire with a mixture of non-pathogenic bacteria and sand. It's cheap, and the inventor, Professor Ginger Dosier, says it produces better and more sustainable bricks.

There are over 1.3 trillion bricks manufactured each year worldwide, and over 10% are made by hand in coal-fired ovens. On average, the baking process emits 1.4 pounds of carbon per brick - more than the world's entire aviation fleet. In countries like India and China, outdated coal-fired brick kilns consume more energy, emit more carbon, and produce great quantities of particulate air pollution. Dosier's process replaces baking with simple mixing, and because it is low-tech (apart from the production of the bacterial activate), can be done onsite in localities without modern infrastructure. The process uses no heat at all:mixing sand and non-pathogenic bacteria (sporosar) and putting the mixture into molds. The bacteria induce calcite precipitation in the sand and yield bricks with sandstone-like properties. If biomanufactured bricks replaced each new brick on the planet, it would save nearly 800 million tons of CO2 annually.

Biomanufactured Brick: Bricks Without Clay or Carbon (via Beyond the Beyond)

Previously:

ACLU prevails: US Fed Judge invalidates gene patent

Cory Doctorow — Mon, 29 Mar 2010 16:17:12 +0000

United States District Court Judge Robert W. Sweet has invalidated Myriad Genetics's infamous "breast cancer patent" -- a patent on genetic mutations that cause breast cancer, which Myriad has exercised in the form of a high lab-fee for analysis on samples (Myriad threatens to sue any independent lab that performs the analysis).

The suit was brought by the ACLU and the Public Patent Foundation, who argued that US Patent and Trademark Office was wrong to grant patents on genes, as these are not patentable subject matter. The judge agreed, saying that gene patents are patents on a "law of nature" and called the isolation of genes and filing patents on them "a lawyer's trick that circumvents the prohibition on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result."

Which sounds to me like a precedent against all patents that rely on isolated genes. Of course, this isn't over: the pharma/biotech stalwarts interviewed in the linked NYT piece are talking appeal, and I'm sure they'll try to go all the way to the Supreme Court.

I think that the problem here is in the untested idea that imparting exclusive rights to the genome will incentivize more research than allowing anyone to build on discoveries in the genome. It's clear that some exclusive rights provide an incentive so some people to do work. But these exclusive rights also scare off people who have good ideas but are worried about being bankrupted by someone who beat them to the patent.

Combined with that is the natural abhorrence many of us feel at the thought that genes might be patented. Genes aren't a good subject for propertization. Your genes aren't even yours -- you didn't create them. Your parents didn't really create them, either. You're your genes' steward, as are we all, and so many of us have a strong intuition that when someone else claims to own something from our genome, they're being ridiculous, or evil, or both.

Myriad Genetics, the company that holds the patents with the University of Utah Research Foundation, asked the court to dismiss the case, claiming that the work of isolating the DNA from the body transforms it and makes it patentable. Such patents, it said, have been granted for decades; the Supreme Court upheld patents on living organisms in 1980. In fact, many in the patent field had predicted the courts would throw out the suit.
Judge Sweet, however, ruled that the patents were "improperly granted" because they involved a "law of nature." He said that many critics of gene patents considered the idea that isolating a gene made it patentable "a 'lawyer's trick' that circumvents the prohibition on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result."
The case could have far-reaching implications. About 20 percent of human genes have been patented, and multibillion-dollar industries have been built atop the intellectual property rights that the patents grant.

ACLU Challenges Patents On Breast Cancer Genes: BRCA

Judge Invalidates Human Gene Patent

(Thanks, Gimpy!)

(Image: Dna rendering, a Creative Commons Attribution (2.0) image from ynse's photostream)

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