Plants, zombies, and science

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I recently returned from a 2 week trip to Cuba, mainly dedicated to visit family. Brought back loads of pictures and many impressions and ideas. I was disconnected from the internet world for the duration, except three brief checks of my email and two status updates on Facebook.  As both DH and myself are news junkies, I expected serious withdrawal symptoms, but we adapted quickly to a blissful state of ignorance about issues such as the fiscal cliff. I have not been as relaxed in a long time.

Back to the real world, I conducted a phone conversation about joining the bioinformatics research program I mentioned in my previous entry. The conversation, one day after my arrival, stretched the abilities of my brain cells to almost a breaking point, but I am happy to report that I am on the list for their next workshop. Sluggishly, my mind has started to remember all the great insights I had during the ASCB conference. And emails from colleagues sharing articles and insights about science education are nudging the process along.

Enter Plants versus zombies (PvZ).

During my Gamification MOOC experience, we were directed to explore Plants versus zombies as a well-designed game with elements guaranteeing success (levels of increasing complexity, enough challenge to keep it interesting but not so hard to provoke frustration and defeat, funky badges etc). I scoffed at the idea of actually trying the game- I looked at the screenshots, read the lecture notes, and moved forward.

Then came the trip and the tablet. I decided not to bring along the Apple of my eyes, my sleek MacBook Pro, and invested in an Asus Nexus 7 tablet to cover the basics (I love it, btw). I loaded it with ebooks and music, and as I had a 14 year old nephew to meet, I asked my son to put some games on it. That’s how PvZ made it into my life.

During the first leg of the travel, my son showed me how to play the game. Within hours, I was hooked. During the coming days, I, previously so condescending of the million of Angry Bird addicts of the world, spent hours strategizing about the kind of mushroom or pea shooter to choose.  And in-between, I could see why this game was used in the gamification course as an example of a well-designed game.

My nephew already had it on his cell phone, by the way.

Back to my world of science education, I keep asking myself: how to make science courses, in particular those introductory biology courses that most instructors fear, in such a way that students would find as absorbing and challenging as a game like PvZ? Is it possible to make it so interesting but without trivializing it completely?

If anybody knows the answer, please let me know.

I got a boss to fight. Be back soon…

ASCB 2012: perspective from the education side part 2

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a picture showing an abacus

An abacus- as relevant to today’s math as some of the classical genetics experiments to bioinformatics

My itinerary of the ASCB conference was guided by the Education string, which spread across Sunday and Monday. There were talks and symposia for K-12, undergrad, and graduate education. The main poster session was on Monday.

By the way- the website for the Meeting is extremely well organized, with links to abstracts, program pages, videos, and other goodies.

Among the most memorable talks from an undergrad perspective was David Botstein’s “Integrated introductory science curriculum for undergraduates at Princeton.”  He started with the observation that education of biologists have become less quantitative over the past years (decades?), and many biologists lack the math and computer science background very much needed for current biological research. (The importance of physics was a recurring theme in the meeting, illustrated by the variety of high level microscopy techniques).  To address that, Princeton developed an Integrated science curriculum. Basically, it covers a variety of fundamental topics in biology, math, physics, chemistry, and computer science; which should provide undergrads with a solid foundation to embark on any scientific discipline. One of the golden nuggets I took from his talk was the “Just in time principle,” meaning only teach what is needed at the moment to avoid student confusion. He did mention how difficult was to develop the curriculum to make it so streamlined. The other was the importance to teach only “fundamental,” not “traditional” topics, and as example mentioned some of the classic molecular biology experiments from the 1950s.  And one that really hit home was the comment ‘it is crazy to teach statistics without computers.” In fact, I have taught some statistics without computers- but quickly incorporated programs as it felt, in fact, that it did not make sense to show students how statistics is done in the real world.

Now I want to make it clear that he did not deem useless to teach the history of science experiments in general, but in the case of this particular compressed curriculum.

Another beauty of this curriculum is that computer programming is taught from day 1, including Java and Mathlab. These are very useful tools, and students feel empowered; not to mention that those tools help them to find internships or even jobs.

The next presentation was from Stanford, “Beyond the cookbook: a rigorous, research-based lab course for all.” The Bio44 lab course by Tim Stearns and his team used p53 as an attractive target for student research: to identify mutant alleles of p53 in tumors and figure out what is wrong with them. The presentation started with their goal: to offer a lab course with real experiments, leading edge tools, and modern technology. The techniques used were quite impressive for a student lab: from bioinformatics to western blots including GFP tagging. And the student evaluations made the audience chuckle- some students expressed their frustration at the amount of troubleshooting and repetition that had to be done for success- something scientists are very familiar with.

A common theme of both presentations was the amount of resources and funding needed for such programs and courses. Throughout the education string of the conference it was evident that without generous funding by (among others) the Howard Hughes Institute, NSF, or the Bill and Melinda Gates Foundation, many educational innovations could not have happened.

However, there are options open to less privileged institutions….coming in part 3.

ASCB 2012: perspective from the education side part 1


A poster imitating the Hinger Games at ASCB2012

I was reading The hunger games during the conference, so this poster made me chuckle.

I confess this is my first American Society of Cell Biology meeting, and very probably the last also. It was not my kind of meeting even when I was involved with Cell Biology research: it was just too broad, too “basic;” and more specialized meetings were preferred- cancer, immunology, etc.
My plan this year was to aim at an education conference or a science conference with a strong educational angle (ASM CUE comes to my mind)- am still hoping for it! But it just happened that one of my collaborators at Carnegie-Mellon University’s OLI project,  Anya Goodman, was presenting there, and she proposed a poster about our preliminary data. Thanks to her diligence the abstract was submitted in time, and got accepted. The meeting being in San Francisco, I was able (and happy) to attend.
As anybody attending a research conference knows, a lot of prep work and planning helps getting things done. My goals were to learn about any major cell biology paradigm changes but mainly to connect with other educators involved in science and particularly biology education. In fact, I was pleasantly surprised to see a whole education string.
Another aspect that surprised me was the openness to non-scientists. The keynote address was open to the general public (upon registration), and the speakers: Secretary of Energy Steven Chu and Apple and Genentech chairman Arthur Levinson tailored their talks to appeal to both scientists and non-scientists, a difficult feat in which the former was more successful. Chu combined overarching visions with witty humor, explanations of scientific findings with inspirational advice, and achieved a general feeling of elation of having somebody so accomplished and smart in our Administration. I just discovered his talk has been uploaded to youtube.
On the other hand, Levinson’s talk went deeper and was more technical; and while his presentation was exciting to those in the cancer field, it sounded a bit too promotional of their new product. Which is understandable. But maybe not the most appropriate for a keynote speech.
There was a whole corner dedicated to educational resources, of which I snapped up many (and they are still in my to-be-sorted pile), but what was encouraging was the number of books, pamphlets, and talks dedicated to grad students and postdocs who may be considering education as a career path. That this included mainly teaching institutions (even community colleges) is in indication of the reality check of scientific organizations.  In fact, I was very pleased to see at any of the education-related events many students, not only professors.

In the next part (parts?) I will address some of the most memorable talks/presentations I attended.

Training in thinking

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Picture of brain model

Brain model: somehow seemed fitting for a biology and thinking discussion

I intended this blog posting to be more specific and researched, but life is happening at high speed around me and if I want to make it professional…well it will not get written.

Last week, on the first day of class of an anatomy and physiology course (intended for pre-nursing students), we dedicated some time to a biomolecules review. I use it as a group approach: divide students in groups, assign each group a type of biomolecules: lipids, proteins etc, and ask them to look up 4 pieces of information: chemical composition, simplified diagram of structure, cellular localization, and function. After 15-20 minutes they input the info to a big table on the whiteboard, and then we discuss as a class- or should I say: I go over the table expanding and clarifying issues.

This is something I have done many times and I am familiar with the types of challenges and misconceptions that come up. So I was surprised to see one I had never seen before: for cellular localization of monosaccharides (simple sugars), particularly glucose, the group wrote mitochondria. I blinked.

In case you are not a biologist: this is a connection that at the same time makes and does not make sense. I asked the student how did they get the idea, and he said they figured out that simple sugars are cellular fuels, and that in another section of the book it said that the energy collected from glucose is harvested in the mitochondria. Ergo, glucose is present in mitochondria.

Indeed, those two pieces of information are correct separately. However, glucose does not really make it to the mitochondria (not as part of that particular process, at least): it is degraded outside the mitochondria in another process, and one of the intermediate products is the one that enters the mitochondria. Moreover, simple sugars do not tend to be associated to a specific place in the cell- as fuel molecules, they are usually taken up or released and used quickly. There is a dynamic nature to where simple sugars are present (usually briefly), and this is part of the whole idea of localization. Some cellular components have set places, others move around. A seemingly simple question suddenly acquired multiple layers of complexity that are not easy to convey in a short time frame.

On a side note: I was observing what students were doing to find the information. A few of them were thumbing through the paper textbook. Many had the book as an ebook on their laptops or tablets, and were doing word search. A large proportion of the students were doing google searches on their smartphones.

I see this a lot- students put together pieces of isolated information to arrive to a conclusion. The pieces sometimes sound similarly or seem to be related, and often students jump to the conclusion that they are related, or one derives from the other. And that scares and frustrates me.

I think that as a science educator, I am not alone feeling often helpless when faced by the lack of critical thinking skills in student populations. Honestly, I do not know or remember how I acquired my critical thinking skills. I know I have them, but I do not recall anybody explaining them to me. And very often, when foraying into educational sites I find myself confused by the ed lingo.

After that class, I had a long chat with an instructional technology and education expert, and we talked about critical thinking and the Socratic method. I will write more about some specific ideas she gave me about how to make memorization more engaging, or how to prod students through questions to arrive to conclusions.

Still thinking about this, suddenly an image came back to me from a distant past. I am in third year of college: it is our Biochemistry I class at the Faculty of Biology of the University of Havana. We are a relatively small group now: maybe 50 students. Two years of relentless Calculus, Physics, and Chemistry have withered (weeded out, as some professors bluntly say) our group from their original 150.

picture of Faculty of Biology, University of Havana, Cuba

Faculty of Biology, University of Havana, Cuba

Professor Joaquin Diaz Brito is walking us through gkycolysis and Krebs cycle. This is pre-Powerpoint time, and this is Biochemistry, so he is writing each step with the corresponding structures on the blackboard, and we are taking notes. Hours pass as we grind through each and every reaction, enzyme, inhibitors, activators. We get to the end of it and we see the circle on the board, and the reactions starting from glucose, winding down all the way to carbon dioxide and water. We sit back with a sigh of relief. It makes sense. We get it.

Joaquin turns around, his eyes twinkling.

“Now think about this- what happens if the reactions go backward?”

We look. The static drawing on the board starts spinning, as suddenly we see the arrows going on reverse. It is a magical moment that I clearly remember after decades, when metabolism became alive in front of my eyes.

We groan. And we love it. We love Joaquin for the magic of the cell, suddenly revealed.

I need to know how to do this for my students.

Gracias, profe. You just gave me some ideas.

(while writing this, I turned to the internet. I unearthed some article references and links, but the one that warmed my heart was this one, reporting on Prof. Joaquin Diaz Brito’s teaching achievements. )

Indications of a bright future through science

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Indications of a bright future through science.

Searching for information

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So you have an idea of what you want to study-explore-research. You think that it passes the “So what” test. Now you have to look for information.

picture showing apples

In search for the apple of knowledge

What you do?

I am sure most of you (and even me!) will google up the word. Very probably you (and I) will use Wikipedia as a starting point. Nothing wrong with it…as long as it is the starting point.

Here are some more strategies:

  • database search: there are plenty of databases, one of the most used being Pubmed (Entrez) but there is Library of Congress and many others. If in doubt talk to the librarians. They will help you not only to choose databases, but also to establish searches based on keywords or other criteria.
  • Crawling the story of the paper: most topics will have a few labs that are known and prestigious regarding the topic, and you want to identify them quickly. Then you start the detective work backwards and laterally. Backwards means going backward in time with the papers. Chances are that the description of the methodology or model used in all papers is tucked away in a paper 20 years ago. Laterally means looking for other people involved in this research via collaborations, sharing resources etc. Even if the sharing is purely methodological, it is always worth to know what people do with the same system using a certain model.
  • Be aware of controversies and rivalries. This is harder to spot if you are outside the field, but look for any statement regarding differing opinions or experiments that cannot be repeated. You may find a completely different view of the topic.
  • High impact journals are usually the most respected source of knowledge. However do not underestimate the information coming from other sources. Besides controversies, there may be sheer practical reasons for scientists not to travel to a certain prestigious conference or publishing in a certain paper, such as…money.
  • 21st century tools: explore the social media. See if any of the main scientists related to the topic has a blog or is on Twitter. If so, be sure to follow them and make intelligent comments on their postings. Who knows, maybe they will notice you and share some of their nuggets of wisdom (or inside information).
  • San Diego is a great place for biosciences. Every week there is probably a world-renown expert giving a seminar somewhere in La Jolla. Many of them are open to the public, some require registration but not fees, and some may require something to pay. You can have the chance to actually see and listen to the main expert in your topic, how cool is that! Ok how do you know about the seminars? There are some aggregator sites such as Biocom, and San Diego Biotech network, the latter actually has a long list of other networking groups in the region. You may need to visit your favorite institutions’ websites for seminar schedules.
  • San Diego is also a great conference place. Many big name events happen in the Convention Center. And many events require volunteers. Or offer discounted registration for students. So look up the conference schedules and see if you can volunteer to any of those! Once inside, you can probably use some of your time to wander around and maybe corral your favorite scientist.
  • AAAS is a great organization, and their conferences are usually very affordable for students.

While you can obviously find lots of information from paper articles, there may be changes happening in relationship to your topic. Exciting preliminary results, several results heralding a paradigm change, new emerging technologies…that information is priceless to have a good sense of what is going on in the filed. Therefore I encourage you to think out of the box regarding the search for knowledge. The closer you are to the source, the more recent and probably relevant the information.

Good luck in your quest!

So what?

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Next week my students are presenting the outline of their research project. Most of them have an idea of project, some rather focused, others less, but the point in this course (Molecular Biology) is to address the molecular level of their topic. As I write the instructions of the outline, the questions that reverberates in my mind is “so what?”

I remember that question clearly from my grad student and especially post doc years. It was something along the lines: your presentation should say “what,then what, and so what.” Meaning, you will present the problem-issue-background of your plan, then you will explain what is that you will do about it, and what is its significance. The “so what” part was indeed the most critical: what is the impact, usefulness, advantage, or importance of your plan?

Here is an expanded version of this advice, directed to research proposals.

While it is always better to have a narrowly focused research topic, being too broad right now is not a big problem. There will be time to develop a focus on something, and the different courses give students the chance to look at their topic from different angles. For this course it is the molecular angle, which is not difficult once you correlate a characteristic with a function, which immediately connects with function.

Of course there is a need to keep our eyes on the big picture too. Because otherwise we lose the “so what” test. The study of a particular function of a particular molecule is not done just because it is fun. There should be a rationale for it. Sometimes the rationale is an immediate application, which is nice. But sometimes it is about clarifying an issue that is controversial, or explaining a phenomenon that is unclear. But remember, to convince your audience you need to pass the test. And while today your audience is that of your classmates, next time it may be a future supervisor or a hiring committee. So it is good to be prepared!

And here is a video I was going to show during my research presentation, but ran out of time. It is about a Ph.D. thesis, but I guess it is not that different for Masters. Enjoy!


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