Wednesday, November 14, 2012

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.









Tuesday, October 30, 2012

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. 



Tuesday, September 25, 2012

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

Saturday, July 14, 2012

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).

Friday, July 13, 2012

Live from Paris: Learning through Research workshop


It's been far too long since I've written here, as counting the number of Science Videos of the Month missing will attest. But with some projects out of the way, I will have more time to devote here.

I am writing this from Paris, France, where I am attending the "Learning through Research" workshop, hosted by the Center for Research and Interdisciplinarity (CRI). The 3 day workshop has an extraordinary cast of individuals ranging from the 20 year old creator of UnCollege, on to Nobel Laureate, all with a mission in common: to re-think the way science is taught and conducted to make both more democratic, accessible and innovative. Titles of the sessions include: Innovative science teaching, Promoting innovation, Citizen science, Quick talks for emerging innovations, Scientific games, Building innovative tools for science & education, Empowering communities, and Creative learning.

I'll be writing about my experience here in the days to come. In the meantime, you should be able to follow the workshop live at this site: http://www.nightscience.org/#!live-the-event!

Saturday, May 12, 2012

My 20 minutes of fame at NerdNiteDC: Loving your inner germs

I'll be presenting tonight at NerdNiteDC at the DC9 club. It's a night of music, drinks and science. I will be presenting a fun and informal 20 minute talk about why we should love the good nerd germs and not give all of our undivided attention at the bad boys of the microbial world, using Molly Ringwald, Judd Nelson and Anthony Michael Hall in an extended metaphor all the kids are sure to get.


Sunday, February 12, 2012

A week of geeking out in DC

Things I did this week that sat well with my geek soul:

Went to the Science Club for some drinks with friends, one about to receive her PhD, another who got hers last year and is now a prof, to trade notes on life after the PhD.



Was back at the Science Club a few days after for a happy hour with the AAAS Science & Technology Policy Fellows.

Earlier that day, a few Fellows and I did a tour of NPR Headquarters. It was nerd heaven. We got a tour of the famous studios, the library, visited the NPR Music offices (where Renee Montagne happened to be passing through after a Tiny Desk recording with the Cranberries) and were shown some very cool technology being developed at NPR Labs for increasing accessibility of NPR programming to hearing- and seeing-impaired folks. Most exciting for me was being in a studio when in walks in the hosts of Alt Latino, Felix Contreras and Jasmine Garsd! I introduced myself and shook hands and yeah was totally star struck. I love Alt Latino. This week they have on Gael García Bernal as guest DJ.

Alt Latino hosts, Jasmine Garsd and Felix Contreras. Photo by Yanina Manolova/NPR


The week ended with Nerd Nite at DC9. Nerd Nite, as described on their website, is


an informal gathering at which nerds get together for nerdery of all sorts (well, mostly presentations and drinking). Nerds and non-nerds alike gather to meet, drink and learn something new.


This week's presenters spoke about sexual attraction to objects, Xenopus the wonder frog, and my favorite, the science of love, by fellow Fellow, Tania Tam. It was so much fun! And incredibly thought-provoking and informative.





Dr. Tania Tam's talk on The Science of Love.
Danger points in a romantic relationship, time on X axis, intensity on Y axis.  One line represents "companionate" relationships, the other "passionate" relationships.
                          

Monday, January 9, 2012

An un-extinction event in the Galapagos

When the word of new extinctions has become all too common, it's good to hear about when a species thought to be extinct is found to be alive.


'Extinct' Galapagos tortoise may still exist - BBC News



Well, at least the DNA says they're out there somewhere on Isabela Island.

And if they don't find the pure-breds, at least the newly identified hybrids can be used in a breeding program to bring back the Floreana Galapagos tortoise into existence and reintroduced into its native island, where it has not existed for 162 years.

Interesting how if this turns out to be true, it means that at some point the Floreana tortoise was an accidentally introduced invasive species on Isabela (and perhaps still is). In this case, turns out this may have been the salvation of the species!

Sunday, January 1, 2012

End of the Month Science Music Video: Björk - Hollow

This video, for a song Björk released only though a smartphone app called Biophilia, makes beautiful use of molecular modeling and animation.

Biomedical animator Drew Berry made the animation using models of DNA and DNA-binding and -replicating proteins.



Also make a visit to Björk's webpage to listen to her inspired message on music and nature.

Thank you Marcos for letting me know about this one!