Your Inner Fly: Fighting dipterans share genes with you and me

Leave a comment

This is very useful for my current Molecular Biology class. Also for anybody getting introduced to Drosophila.

Why Evolution Is True

Introductory note by JAC: Matthew has produced a terrific post here, and I hope people will read it. The results of this scientific analysis are amazing and the genetic tools required to produce them are breathtaking—tools I couldn’t have imagined were possible when I was a graduate student. If I had one hope for 2014, it would be that more people would read the science posts. (Maybe you do, but just don’t comment on them!) kthxbai


by Matthew Cobb

In 2007, the genomes of 12 closely-related Drosophila species were published in Nature. This was an important moment because it enabled researchers to look beyond their traditional friend, D. melanogaster, and to study the similarities and differences between the behaviour and genes of ‘the’ fly and those of its relatives, for some species had separated only a million or so years ago, while others were much more…

View original post 1,209 more words

Dear American Gut & uBiome: You Have Some Explaining To Do.

Leave a comment

Well now I am curious…

Ex-RNA in exosomes?

Leave a comment

Ex-RNA in exosomes?

It’s fun to read about things that were part of my life and kept going. Like exosomes. My little review from 2005 still gets a lot of hits due to the current popularity of exosomes. I follow what exosome people do in their Facebook page. It was a cool project to do. Lots of ultracentrifugations. Good times. What do you think about little vesicles and exosomes? Will they be the next diagnostic breakthrough?

Frequent Players Of Video Games “See The World Differently”

Leave a comment

Frequent Players Of Video Games “See The World Differently”

This is interesting. I have been thinking for a while about engaging students who are gamers and get their feedback and ideas about online course design. On the other hand, this is obviously heavily tilted toward visual learners. Still, interesting 🙂

Cal State may turn to virtual labs | Inside Higher Ed

Leave a comment

DIY Practicum

Leave a comment


Glomerulus in the kidney.

The first time it was awkward. “Are we making the questions?” The students were not really sure what was the point of them creating the questions for a mock-practicum in the anatomy and physiology course. They got there eventually- and along the way they learned also about questions and questions- how hard it was to answer questions about minutia, and how important the wording of the questions were. I assigned them topics, so each student was responsible for their set of questions. They loosened up eventually, snapped pictures of the slides and the dissected sheep brain, laughed at how hard some of their own questions were, and if they paid attention, they did good at the real final. For the second time, they were ready and I heard some say “cool!” This time it was more sophisticated- they had hearts and kidneys and open fetal pigs, and they had to set up the microscopes with slides, and devise questions to go with them. The group moved around, they were checking their books, talking to each other, and sometimes even asking me questions. They may not know it, but I have such an admiration for this small group of women mastering not only the content of biology, but also its dynamics and its inner beauty. 

After less than one hour, we had the practice stations set up. Dissected specimens had pins attached and labeled, slides were taped to microscopes, and each student had developed a set of questions for their assigned topic. Some went overboard, others made simpler questions, but they were all engaged, comparing notes, discussing the results, communicating. Thinking. Creating. 

Yes, it is hard sometimes to be an educator. But there is this moment, when a student’s unfocused gaze suddenly sparks, and he or she says, OH, I got it now…and one can almost hear the wheels turning in their brains and the synapses firing. And THAT is priceless.

I have found that there are many occasions in the classroom when one can flip the instruction and empower students. The logistics is simple, just chunk the material or the task, and give it to individuals or small groups. Give them time to think and discuss. Be there for hints and clarification. Provide ample positive feedback. They may be suspicious in the beginning, but eventually they will embrace it. And at the end, this is the time when they come to life during class. They even forget that I am there.

And that is the sweetest thing of all!

My scary shirt and the invisible gorilla

Leave a comment


My scary tee.

“Your shirt yesterday was scary,” says Armando (not his name). “I am glad you brought a different one today.” It is a Sunday afternoon in one of California’s many State Prisons. We, a team composed by two outsiders and five inmates, have just finished a Basic Alternatives to Violence workshop in Spanish, and are going through the required post-workshop processing. The workshop went well, everybody is happy and relaxed. “What do you mean scary?” I ask. The day before I wore a black long-sleeved tee with pink girly motives, bought at a winter resort sale years ago. I needed a warm but not too thick something for skiing, and since it had become a comfy informal attire. “It had brass knuckles on it,” Armando says. “And razorblades.” The other guys nod in agreement. I frown, trying to visualize my tee. Cherries, a little bird, and high-heeled shoes come to my mind. Brass knuckles? “Oh, come on! Those are bear paws!” I remember finally. Armando shakes his head. “Those are brass knuckles,” he says with an authority I do not dare to dispute. He must know much better than I do. While this group of men has long ago renounced their violent past and seek for ways to rehabilitate themselves, there is no denial that their 25 to life sentence was for a reason.

I do not really know what a brass knuckle looks like. I google the image, and then compare it with the supposed bear paw on my shirt. They look identical. For the first time since I bought it, I start actually looking at the motives. Cherries, a high-heeled shoe, a bird. A razor. A razor blade. Brass knuckles. A cold, uncomfortable feeling settles in my stomach.


Brass knuckle

I bought the tee because of its fabric and its fit. I looked briefly at its decorations, and saw what I wanted to see- a silly collection of girly fluff: cherries, little birds, shoes. The image of brass knuckles was not familiar to me, so my mind substituted it with the nearest similar image- bear paws.

After this experience, I had searched a bit further and have discovered many websites featuring merchandise with brass knuckles on them, including women’s t-shirts.

While going to a State Prison may not seem similar to enter a classroom, there are indeed many similarities, and one involves to consider what we wear. There have been many discussions about what is preferred in a classroom: a serious formal attire or a relaxed, modern outfit. The former is sometimes appreciated by students and can elicit respect for the educator; but may be also seen as stiff and distant. The latter may help to establish a more open classroom community, but some formal students may see a jeans and sneakers-clad instructor as too lightweight. At prison, besides the rules (no blue, orange, or khaki, no jeans) it is important to avoid clothing with messages on them that may be disturbing or proselytizing, and similar care has to be taken in the classroom.

I was not aware of the menacing meaning of my supposedly harmless piece of clothing.   It was sold by a well-known apparel company, as part of a very ordinary-looking selection of winter shirts.

This is the end of my story- my shirt has been relegated now to the pile of exercise clothes, and I will be looking much more closely at any other piece of clothing with small decorations on it. Semiotics experts may discuss the importance of symbols. Other disciplines may analyze how the human brain interprets information (see the famous gorilla video or the more recent gorilla in the radiology image study).

But it still bothers me.

If you wish to know more about the organization I volunteer for, Alternatives to Violence project in California, please visit the website

Ha! Games for science.

Leave a comment

Ha! Games for science.

In my previous post, I was musing about games in science. I mentioned I had been away from the net for s couple of weeks, and I had not seen this article of The Scientist. Well I am glad I am on the right track 🙂

ASCB 2012: perspective from the education side part 3

1 Comment

painting showing an eye

Eye from one of San Francisco’s Balmy Alley murals in the Mission district. 

Still reporting from the session called “Integrated Research and Teaching and Its Benefits to Faculty and Students.” One of the talks that energized me was “The Genomics Education Partnership: An undergraduate team research experience. ” Presented by Mike Wolyniak,  who started with a cheerful comment about how his school does not have the resources of Princeton or Stanford, it shows the possibilites of collaborative research using bioinformatics. Spearheaded by the Biology Dept and Genome Center of Washington University in St. Louis, GEP enables students from a vast array of schools including big name universities, state schools, small liberal colleges, and community colleges to collaborate on large annotation projects. At a course scale, the project enables students to get acquainted with bioinformatics tools and analysis; but taken together it weaves a huge amount of data together, which are in fact publishable. The GEP website is absolutely amazing with all its resources and documents, a goldmine to anybody wishing to learn more about bioinformatics, and open to interested faculty who wish to join the project. Needless to say, I jumped on the opportunity and hope to be able to participate next year. Great timing, as I have been eager to learn more of bioinformatics.

Later that afternoon I went to the Exhibit Hall to help setting up the poster. Poster-boards stood between the rows of exhibitors, and the section dedicated to education happened to be just by some of the major microscopy companies- in fact some of the most sophisticated varieties, as we had a couple of EM companies and customizable high-end microscopes on one side, and at the end a huge mobile expo of Beckton-Dickinson’s flow cytometers. As a former microscopy person, I was all ooh and aah over some of the toys exhibited. As an educator I could not help but be saddened by how little of this is known by students. I approached some of the big boys (those who do make microscopes for classrooms) and asked about anything for education, but they shook their heads- for this conference they brought only their high end stuff.

So it was such a contrast when I saw two posters, placed coincidentally side by side, of two ways to bring microscopes to every classroom or even to every student. The poster titled: From lab to classroom: Science  with mobile phone microscopes was also featured in an article in the Conference Pressbook. It made me smile as I have seen (and encouraged) my students taking pictures through the microscope using their cell phones- a possible feat, although requiring some adjustments. This innovation, on the other hand, makes the cellphone an actual little microscope.

The poster besides it presented the epitome of elegance and simplicity – especially in contrast to the neighboring behemoths. Manu Prakash’s Foldscope is (quoting from a TED blog): “a completely functional microscope built completely by folding paper. It offers 3 optical stages, illluminating, mask holding, and it works with the standard stains and slides so it’s universal.” The Prakash lab website does not provide much information, and he stated that he did not want the poster to be photographed, as he was still in process of having the results published. I did see the Foldscope, and like everybody else, I was blown away. It is, indeed, a paper microscope, foldable, with a slot for the slide. It can also be used open, with external light, so the image gets projected on a white surface. Moving it closer or further to the surface changes the magnification. It can be adapted also for fluorescence microscopy as judged by the poster pictures. Diagnosis of diseases (mainly those caused by parasites) and education seem to be the main potential uses of this admirable invention.

I thanked Dr. Prakash for working on this kind of innovations. I love the research statements on his lab website at Stanford, especially the one dedicated to Frugal Science.

I feel encouraged by these kind of innovations, technologies that bring knowledge and possibilities within reach of every individual. I hope that within a short time, kids in the Third World will not be only hacking tablets, but also observing bugs and plants under small portable microscopes.

MOOCs and the vertical LP player

1 Comment

Vertical turntable.

I started writing this post back in October- after experiencing my first MOOC. They have been discussed all over the place now- from the NYT to the Chronicle of Higher Education and everything in-between.  By the way, those links are only examples: search and you will find. Lots. About. MOOCs.

As I started reading about the topic, a distant memory came back to me: my first visit to Sweden in the late 80s. Wide-eyed and young in my first visit to a Western country, I tried to absorb as much as I could of all the new and exciting things around me. At one of the collaborator’s home, his son (in his early 20s or younger) showed us, Third world visitors, two novelties: a small Macintosh computer where he was playing some rudimentary game, and a vertical LP player. Of those two objects, one moved forward and the other never made it. Looking back to that memory, I recall how I was much more interested in the playfulness of the first than the supposed exquisiteness of the other. Which is surprising as at that time I was much more into music and stereos than computers (personal computers did not arrive to Cuba until some years later).

Somehow this reminds me of the current MOOC madness. And no, I don’t think they are an example of a vertical LP player- I actually think MOOCs are here to stay.

If you have not heard or read about Massive Open Online Courses, well probably your best bet is to google it up. It is not my intention here to do a review of the current MOOC situation…but to comment on some of the controversies and disputes around it.

I have a good opinion about MOOCs because my first was exceptionally good. My opinion “exceptionally goo” is based in my view as an online instructor. I spend a lot of time trying to make my online courses easy to navigate, clear, fair, not too hard but not too easy, connected to real time, responsive, novel…you name it. So taking an online course that was all that and more- the professionally made and perfectly chunked lectures with doodles and little questions interrupting the text to keep our attention; the quizzes that one could not answer by word-searching or googling, the assignments that addressed real life applications with crispy grading rubrics.

Okay, n=1 is not a basis for a scientific opinion. But the truth is, I gained valuable knowledge…for free, in a rather efficient way. Not only that- the course was surrounded by a variety of forums, from a Facebook group to a LinkedIn group, connections occurring in real time between people located in different continents. If I wanted, I could have joined a bunch of meetups close to my geographical locations. It was an energizing experience.

Let’s step back for a second. A lot of people in that course were from developing countries. As somebody coming from a developing country, I know about the power of knowledge. Those online students were empowered, and their energy shone through their postings.

Going back to my original analogy of the vertical turntable versus the primitive videogame on the Mac- did I know? Could I feel the difference in destinies? I did not, I could not. But the game on the Mac, silly as it seemed, it was fun to watch. The vertical turntable was, in a way, boring. Exquisite, refined, but boring.

MOOCs are fun.

Just sayin’.

Older Entries

CUREing Ocean Plastics

STEM education exploring ocean plastic pollution

about flexible, distance and online learning (FDOL)

FDOL, an open course using COOL FISh

Main Admin Site for the WPVIP multisite

This multisite hosts public sites for and WordPress VIP


An Online Summer Book Club of Science


Teaching and learning reflections around science education

Disrupted Physician

The Physician Wellness Movement and Illegitimate Authority: The Need for Revolt and Reconstruction

The Blog of Author Tim Ferriss

Tim Ferriss's 4-Hour Workweek and Lifestyle Design Blog. Tim is an author of 5 #1 NYT/WSJ bestsellers, investor (FB, Uber, Twitter, 50+ more), and host of The Tim Ferriss Show podcast (400M+ downloads)

Here is Havana

A blog written by the gringa next door


A blog full of humorous and poignant observations.

Jung's Biology Blog

Teaching biology; bioinformatics; PSMs; academia, openteaching, openlearning


Reflexiones sobre asuntos variados, desde criminologia hasta artes ocultas.

Humanitarian Cafe

Think Outside the Box

Small Pond Science

Research, teaching, and mentorship in the sciences

Small Things Considered

Teaching and learning reflections around science education

1 Year and a 100 Books

No two people read the same book