Brittany Wenger, 17, Wins Google Science Fair Grand Prize For Breast Cancer Diagnosis App

The Grand Prize winner of the science fair, for good reason, was a 17-year-old from Lakewood Ranch, Florida. Combining the fields of biology and computer science, Wenger wrote an app that helps doctors diagnose breast cancer, according to the description of her project on Google.

The type of computer program, called a “neural network,” was designed by Wenger to mimic the human brain: Give it a massive amount of information (in this case, 7.6 million trials), and the artificial “brain” will learn to detect complex patterns and make diagnostic calls on breast cancer. Her program used data from “fine needle aspirates,” a minimally invasive procedure that, unfortunately, is often one of the least precise diagnosis processes, according to Fox News. But Wenger is helping change that, as her program correctly identifies 99 percent of malignant tumors.

via Brittany Wenger, 17, Wins Google Science Fair Grand Prize For Breast Cancer Diagnosis App.

Very amazing and inspiring science projects from teenagers. See Brittany’s winning project here.

Synthetic Biology Incubator Launches

Yes, an incubator! Just for synthetic biology! It’s being hosted at Singularity University in Silicon Valley. Does anyone need any more convincing that there is a huge future in synthetic biology, through big leaps in both innovation and technology? The way we work with biology is changing, evolving, from observation to invention.

Looks like the incubator is providing resources, mentoring, and stipends for their chosen startups. Hopefully it will be like what tech incubators such as Y Combinator have done for computer startups – no doubt that many will fail or have to change their business plans and project ideas, but at the very least, there will be increased coverage and education about what synthetic biology is capable of.

“Teeming with ambitious ideas and some pretty futuristic potential, synthetic biology is an emerging multidisciplinary field in which the principles of genetic engineering are coupled with genome design software to capitalize on the plummeting cost of DNA analysis and synthesis. The approach is to construct artificial biological systems in a similar way that computer chips are made. The result is a broad array of potential technologies that could lead to a radical transformation across a variety of sectors, including medicine.”

There’s a great video at the end of the article that gives an intro to synthetic biology, too.

Source: http://singularityhub.com/2012/05/29/inaugural-synthetic-biology-incubator-synbio-launches-at-singularity-university/

Dan Barber’s Culinary Crusade – WSJ.com

“Butchering and eating animals may not be called kindness, but eating soy burgers that rely on pesticides and fertilizers precipitates destruction too. You don’t have to eat meat, but you should have the good judgment to relinquish the high horse. There is no such thing as guilt-free eating.”

WSJ Soapbox piece on food, sustainability, local diets, and the environment by Dan Barber, chef at Blue Hill at the Stone Barns Center for Food and Agriculture. He discusses his opinions on what is best for humans to eat – best for us in a way that is healthy, and best for the earth in a way that is sustainable and logical – based on nutrient cycles, tracing the energy flow, and the inputs and outputs unique to different areas and their soils, as well as culture and our biological needs. Interesting ideas on “ecological intelligence” and an argument against vegetarianism (it’s always good to hear the reasoning behind both sides!).

“What I don’t like about sustainable foodies—and I’m considered one of them—is that we carry an air of preachiness about food. (No one wants to be told what to eat, whether it’s by your mother or by a group of holier-than-thou chefs.) But true sustainability is about more than just deciding to cook with local ingredients or not allowing your child to have corn syrup. It’s about cuisine that’s evolved out of what the land is telling you it wants to grow. As one farmer said to me, Food systems don’t last; cuisine does.”

Source: Dan Barber’s Culinary Crusade – WSJ.com

Genome Compiler is released!

Genome Compiler‘s first public release just came out, as announced by Omri Drory, the founder and CEO of Genome Compiler. It’s a software tool for designing and debugging synthetic DNA, and ordering it, too! Haven’t played around with it yet but I’m excited to (update later after I try it out). Everyone is starting to make big, visible steps towards making synthetic biology more accessible, modular, and highly functional. Hopefully this will lead to many more awesome developments.

Tuna carry Fukushima radiation to California

A study released today by scientists Daniel Madigan and Nicholas Fisher cite findings from 15 bluefin tuna caught off of San Diego — 10 times more radioactive cesium than fish from previous years. These fish likely migrated from the waters near Japan, where bluefin tuna are known to spawn, the same area that was affected by the Fukushima nuclear reactor meltdown last year, which released radioactive materials into the water. The idea itself is already enough to fuel some worries, as fish is well-known for transmitting toxins in the water to the humans who like to eat them (think of all of the seafood watch mercury scares). However, the levels are just below the Japanese government’s safety limits, and probably don’t pose any threat to humans, though the scientists do not make any advising comment either way. The fact that the fish were found all the way across the ocean with traces from the nuclear reaction is a large cause of concern, though.

New Scientist article by Sara Reardon

The levels might not be high enough to harm you if you tucked into a tuna sandwich, but some tuna are still carrying radioactive caesium from the leak at the Fukushima Daiichi plant last March. Researchers hope that similarly low levels of radiation in turtles, sea birds and sharks will allow the migration patterns of little-studied species to be tracked.

Daniel Madigan, a marine biologist at Stanford University in California, was already studying how Pacific bluefin tuna (Thunnus orientalis) migrate across the Pacific Ocean when the Japanese tsunami put a new twist on his experiment.

The leak at the Fukushima Daiichi reactor released caesium isotopes into the Pacific, and fish can pick up the radioactive material from the water they swim in and from the food they eat.

Juvenile tuna can take between one and four months to swim the 9000 kilometres from Japan to California. The researchers measured caesium isotopes in young tuna caught off the coast of San Diego, and found detectable levels of caesium-134 in 15 fish. The isotope could not be detected in fish that were caught before 2011.

Because caesium-134 has a half-life of two years, Madigan expects that researchers will be able to find it in the long-lived fish for some time to come. Tuna migration patterns are well known, he says, but the radiation may be useful in tracking other species such as salmon sharks (Lamna ditropis). If these sharks behave as researchers suspect they do, the migratory males would carry Fukushima radiation, but the stationary females would not.

——

My first reaction: think beyond bluefin tuna to basic ecology and food chains — there are probably a bunch of marine species that have absorbed the radiation, that are being eaten by larger fish and organisms, which are then eaten by larger ones, and so on. Who knows how high the levels are in the smaller fish that get eaten by the tuna? Don’t we eat some of those species, too? Also, from a bioaccumulation standpoint, cesium gets magnified in biological organisms, meaning that the predator can contain higher concentrations than the prey. Not only this, but many of them are probably migratory, just like Pacific bluefin tuna.

Although, add in these quotes from the authors as mentioned in a Washington Post article about the finding:

“Much will depend on the concentration in the prey fish, which in turn is ultimately dependent on the water concentration. If concentrations in water will eventually decline, as we would expect, due to dilution and dispersion, then concentrations in living organisms will eventually decline as well.” – Nicholas Fisher

“However, certain small fish around Japan showed very high levels after the accident. If certain larger predators happen to feed on these prey, higher levels than we observed may be possible.” – Daniel Madigan

An NPR article dismisses the hype around fear of food, and states that the cesium levels found are not any more cause for panic than the already-existent levels of radiation in seafood from past nuclear testing and naturally occurring radiation:

“So the question is, how much more radiation did these particular tuna fish contain? The answer is: A trivial amount. In fact, radiation from the cesium is 30 times less than the radiation that’s already in the fish naturally in the form of potassium-40, according to the research paper. And the natural polonium-210 packs a radiation dose 200 times larger than the dose from the cesium.”

Confused? This is definitely a problem that I run into often with scientific journalism, coloring the results when communicating scientific findings. If you’re not sure what to believe, the solid solution is always to go straight back to the source and make a decision yourself. Even then, be wary, because authors have their own bias about why they’re conducting their research and what they say with their findings, despite the emphasis on just relaying the facts and making sound conclusions from those. It’s always going to be like this on some level, as we are human and all have our own opinions.

Thankfully, the authors of the study made their article open access (open source scientific knowledge, something to be discussed later), and you can read it in its entirety here.

Fig. 1A of the article shows the migration pattern of the bluefin and yellowfin tuna, as well as uptake and decay patterns of cesium from the water over the growth period.

I don’t think there’s a huge need for panic and re-evaluation of the bluefin tuna stock and how you choose or buy your sushi, based on this study. As argued in the NPR article, the authors themselves say:

“Total radiocesium concentrations of post-Fukushima PBFT [Pacific bluefin tuna] were approximately thirty times less than concentrations of naturally occurring 40K [potassium-40] in post-Fukushima PBFT and YFT [yellowfin tuna] and pre-Fukushima PBFT. […] Thus, even though 2011 PBFT showed a 10-fold increase in radiocesium concentrations, 134Cs [cesium-134] and 137Cs [cesium-137] would still likely provide low doses of radioactivity relative to naturally occurring radionuclides, particularly 210Po [potassium-210] and 40K.”

But, again, we should be conscious of the ecological footprint from the data, and the methods used in this study demonstrate how capable we are of detecting radioactive substances in seafood and marine organisms — especially ones that migrate long distances and are affected by growth and radioactive decay rates. The levels (“<<1% of total radiocesium released into Japanese waters”), while small, is “a conservative estimate based on one species”. The authors suggest further studies on turtles, sharks, and seabirds that feed and live near the affected areas, that are also migratory:

“However, the presence of Fukushima-derived radiocesium in all 2011 PBFT individuals reported here suggests that study of other HMS [highly migratory species] is warranted. Our results demonstrate that Fukushima-derived radionuclides in animal tissues can serve as tracers of both migration origin (presence or absence of 134Cs) and potentially, timing (using 134Cs:137Cs ratios) in mobile marine mammals, providing valuable complementary movement data to extensive tagging programs in the Pacific.”

If anything, further data would help us understand how radioactive materials move throughout the ecosystem, and the rate at which they are transported, disappear, or are magnified. The study outlines a detailed way to track this using cesium-134 levels and cesium-134:cesium-137 ratios.

Urnatur

‘In Swedish, urnatur means “ancient nature.” It also is the name of a wooded retreat in southern Sweden, hand built by forester Håkan Strotz and his wife, biologist and designer Ulrika Krynitz. While he embraces the offerings of nature, she is drawn to modern design; the result is a transcendental landscape and lifestyle that is best experienced than explained.’

http://www.urnatur.se/

Beautiful beautiful beautiful. This place also has an “air castle”…treehouse. As in…I should live here.