Science in several languages

There are different versions of this old joke (the one with "butterfly" is the most common), but as this one is about science, and foreign languages is another love of mine, I thought I'd post this one.

What caused the meth epidemic? The answer was hidden in a graph.

Source: Derrick Quenzer, Steve Suo/The Oregonian. Y-axis indicates magnitude of increase, 1 = starting value, 2  = doubling, 3 = tripling.

Reporter Steve Suo of The Oregonian was investigating the dramatic worsening of the meth epidemic, asking, what caused the dramatic rise of methamphetamine abuse in the western United States?

The answer came from the graph above. Suo gathered extensive amounts of data from numerous sources and compiled what he found. He noted a rise and decline of various meth abuse indicators over time. One surprising aspect of the pattern is that it occurred in different states across the western US, and the patterns seemed synchronized. Further investigation revealed the rises were positively correlated with the purity of meth on the streets, and the decline of purity was negatively impacted with increased regulation of the raw materials of meth (see shaded boxes in graph).

Thus, the numbers clearly indicated that with proper regulatory intervention, the meth epidemic can be controlled. Too bad these regulations get in the way of fat profits for companies that sell cold medication, or else we would have wiped out the meth epidemic ages ago.

For a fantastic piece of investigative journalism, watch Frontline and The Oregonian's story on "the unnecessary epidemic". The facts, the numbers, and the stories will shock you. One thing that struck me is how much the graphs, the math and the numbers speak to policy formulation, and how much they are ignored in the face of large profits for a few.

http://www.pbs.org/wgbh/pages/frontline/meth/

It's been a while...Monthly Science Music Video is back.

Some Budding Yeast I Used to Grow (Gotye Parody)

Roaming planets in fiction and reality

When I saw Lars von Trier's Melancholia last year, I was deeply moved my the haunting metaphoric approach to the devastation that is depression. As a scientist, I felt the need to apply suspension of disbelief to appreciate the movie for its artistry and emotional truth, assuming that something like a rogue planet drifting without a star system didn't exist in real life. Boy was I wrong. Scientists have known for some years now that such orphan planets, roaming the universe with no star to orbit around, do exist. And the artist conception of the latest starless planet discovered, CFBDSIR2149, looks eerily like the planet of doom in the movie (illustration of CFBDSIR2149 below).

ESO / L. Calcada / P. Delorme / Nick Risinger (skysurvey.org) / R. Saito / VVV Consortium

Check out this little film explaining the latest rogue planet discovery, followed by a trailer for the film Melancholia.

My chromosomes and me

The diagram to the left is a pictorial representation of 22 of my 23 chromosomes as provided by the personal genomics company 23andMe, which I sent samples of my DNA (mailing a tube full of spit) for analysis. The colors represent the likely geographic origins of my DNA, green blocks representing African origins, orange blocks representing Asian origins, and blue blocks representing European origins. In my case, the DNA of Asian origin most likely is Amerindian, a population whose genetic features is most like East Asian populations.

My family immigrated from Ecuador to the US when I was little. And I remember distinctly when the US Census form first came to our home in the space where we were asked to choose race we checked off "Other" and filled in "mestizo". We grew up thinking of ourselves as mestizo rather than belonging to any of the races listed as options in the form. Mestizos being people of both European and Amerindian ancestry, it was a conjecture apparent from one quick look at my family. The results of this DNA analysis done by 23andMe confirm this long held assertion of ours.

The genetic map I show here is only one type of data provided by 23andMe. The results provided to me online also tell me what traits I am likely to have based on my genetics. The company accurately predicted, for example, that I most likely have dark brown eyes and wavy hair. They predicted my blood type, and suggest I am only mildly lactose tolerant. What's interesting about the latter result is that lactose tolerance is a trait primarily determined by genetics, but the environment can have a role in influencing it (for example, by the nature of bacteria living in my intestines). The prediction is pretty good, as I can tolerate a glass of milk OK, but more than that gets me belly upset.

Since the genetic information gleaned from my DNA can be so useful in telling me about traits I know of or suspected, what can it tell me about traits I don't know about, in particular, medically relevant traits, such as propensity towards certain diseases or disorders, or responses to drugs? Though the results to such things are presented and clearly explained, they are always presented "assuming [my] European ethnicity". The company makes a call based on the sources of DNA in my genome (shown in the above diagram) and says I'm European. This is important because versions of genes that determine traits don't usually do it in isolation, they do it in the genomic context in which they exist. Meaning that one version of a gene X for trait A in one genome may cause trait B in another. This is due to combinations of different gene versions that can interact to determine what the trait.

Knowing that the nature of our genomes is tied to the ethnicity we belong to, and that this can affect interpretations of genetic data, how relevant is it to my data that I am Hispanic? Hispanics (or Latinos) run a whole spectrum of genomic signatures, from nearly 100% European, to nearly 100% Amerindian, to nearly 100% African, and the vast majority of populations are in between. So it seems that being Hispanic does not lend itself to increasing the predictive power of genetic signatures. In fact, it may be completely irrelevant, in contrast to more homogenous populations, such as, for example Ashkenazi Jews, Japanese, or Zulus.

Figure from the Bustamante lab website, showing the principal components underlying genetic variation in Latin American populations. Note that genetic variation constitutes a range determined by three sources of genetic variation: African, Native American (or Amerindian) and European.

Given that most health standards in the United States are based on a white population with DNA largely originating in Europe, how can health guidelines and recommendations be refined by personal genomics so they more accurately reflect our individual biologies? At the moment, it seems we have inadequate information or understanding of how to best use genetic information to make health decisions, some of which will vary depending on our genetic backgrounds, some of which will be more influenced by environmental conditions. Can a slightly lactose tolerant person like me, for example, improve lactose tolerance with a certain diet? Or would it be best for me to ignore the "got milk" campaign altogether and forgo milk in my diet? The role of ethnicity, genetics and health is one I hope to see explored in the years to come at scientific conferences and in research publications.

This post is part of the Diversity in Science Blog Carnival #18: Latino / Hispanic Health: Science and Advocacy. 

Science music video - Darwin Deez - dna

It's been a long long time since this blog has been active. Time to reactivate it with a science music video. Will be writing more soon.

Darwin Deez - dna

Learning through Research workshop: Day 1

This conference has been amazing! Though I have been taking much notes, the rest of my time has been spent talking to such an interesting and enthusiastic collection of people here while I have the chance, so not much time to updating the blog promptly. Here is the summary of Day 1. I have long detailed notes which I would be very happy to share with anyone. If you want those, just email me at mdvinces at gmail.com.

SUMMARY of today’s session:

Opening remarks - by François Taddei, Frédéric Dardel, Claudie Haignere, Ariel Lindner

Lee Hartwell – Teaching the teachers in a new information era 

Having received a Nobel Prize for his work on cell cycle checkpoints, Lee has been an early advocate for personalized medicine and at Arizona State University is pioneering science teacher training. Three steps for teaching science to non-science majors (whether students or teachers of students):

            INTEREST -> MOTIVATON ->SKILLS

Too often traditional education focuses on the Skills part, at the cost of Interest and Motivation, which in the end undermines acquisition of Skills.

Nathalie Kuldell– Teaching and Learning with imperfect learning machines: Using synthetic biology for teaching students and teaching teacher.  

Nathalie has been using Synthetic Biology to engage students in biological engineering, and now is using the same techniques, through the online BioBuilder.org platform, for teaching teachers. The platform has three main elements: 1. Online content, including explanatory animations. 2. Activities for both the lab and the classroom. 3. A space for sharing data, results, practices, ideas.

This approach brings the exciting engineering aspects of hands-on design and building into biology education.

Stephen Friend – Democratization of biomedicine.

 

Expertise in medicine has been the closely guarded domain of the medical experts. But the time is now for democratizing biomedicine, empowering patients to control how their data is used, empowering physicians and drug companies with unparalleled power or personal patient data, and moving medicine into a commons space where real advances in predictive medicine can be accomplished. Stephen is founder and president of Sage Bionetworks, which aims at providing the necessary commons for biomedical information.

François Taddei – From individual questioning to collective exploration – the education revolution. 

Education is today a conservative affair done much as it has been done for hundreds of years. While technology progresses ever more rapidly, education has fallen behind, to the detriment of societies where more people are left out of understanding and engagement of science. Goal is to reform university education so it is open source and accessible to more people and not limited to elite campuses, hand in hand with opensource software and hardware movements, and to allow learning by playing. Some of this is being done at the CRI already, but ultimately want to establish a model for Open FIESTA (Faculty for Innovation in Education, Science, Technology and Arts).