Sunday, April 25, 2010

What are you? Zooplankton? Hahahahahahahaha.

After a whole month of preparations, it finally happened: the procession of species. It started a little bit late for us, since I had a race in the morning. But thanks to cell phones, we could join the parade half way through. Kobe was really excited and waiting for the first sign of the parade and the rest of the lab.

Here are some random pictures of the different species and musicians bringing life music. Our lab was interviewed by CTV, and we were definitely the most coordinated group. Everybody asked us what we were, and after the answer invariable bursted out laughing; but we made quite the impression, and we will participate again next year.

The parade ended in a park, with some entertainment for the kids (although a cannon was probably not the most appropriate play instrument in this hippie crowd ;-)

And this is the gang: me, Quinn, Amanda, Kyle, Ingrid, Lies, Cian, Britt, Kobe. A big thanks to all of you, since I literally did nothing for this except providing Lies' time and expertise.

The parade also made the local news!

For all the pictures, see the Picasa web album:

2010-Species parade KW

Friday, April 23, 2010

Field trip Carolinian forests

In September, Marina will join our lab. She will study spatial patterns and metacommunity dynamics in Carolinian forest understory plants, and Andrew MacDougall is her co-advisor (since obviously I know nothing about plants). Today we visited 2 forest fragments, just to get an idea on the spatial (and temporal) scales of heterogeneity, and to get an idea of the practical considerations that drive the development of a research program.

The first set of pictures are some overviews of the different landscapes.

Here are some pictures of the field ecologists in action (guess I am missing on all these pictures ;-)

And here are some close-ups of the various understory plants.

We finished our trip with a visit to Andrew's new field site. He planted 45 ha (?) with native plants for a large-scale field experiment. Sadly enough, we have a very dry spring, and almost no germination. They predict rain for the weekend, but will it be enough? Sadly, this was a disappointing end of an informative and fun field trip.

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Now we just have to wait what questions Marina will choose to explore for her PhD. (And you can see all the pictures in high resolution in the lab picasa site.)

2010-04 Field visit Carolinian forests

Wednesday, April 21, 2010

Embracing the digital article

This is one of the best texts I have seen on the whole tablet reading experience, "Embracing the digital book" by Craig Mod. Not only very informative and well-argued, but also beautifully designed, which is of course the whole point of his article/journal.

But why do I mention this in this lab blog? Just imagine the possibilities if there would be a similar platform for scientific articles, that implements his ideas on "the network (or, e-reader 'social' features)":

So consider this: 10,000 of us reading the same Kindle book, each of us highlighting and taking notes. Would the aggregate of this not be illuminating? If I want to publicly share my notes with fellow Kindle or iBooks readers, shouldn’t there be a system in place to do this?
Show me the overlap of 10,000 readers' highlighted passages in a digital book. This is our ‘Cliff Notes.’ We don’t need Derek Sivers' brilliant summaries[14]anymore (sorry Derek!) — we’re collectively summarizing for each other as we read and mark our digital copies.
Show me a heat map of passages — ‘hottest’ to ‘coldest’. Which chapters in this Obama biography should I absolutely not miss?(FIG 7)
Let Stefan Sagmeister publicly share the passages he’s highlighted in the new Murakami Haruki novel. This is something I want to see. And I bet you do, too

 Replace "(Kindle) book", "novel", "biography" with scientific article, and all the authors with scientists you admire, and you have indeed the perfect tool to stay on top of the current literature, even outside your field of expertise.

His Fig. 7 illustrates the power of this approach, by automatically generating a crowd-sourced one page summary of an article with all the important sections highlighted or extracted:

You currently have several tools that implement some of these ideas:

  • Faculty of 1000 (expert opinion on recent literature)
  • Plos One (collect user notes on articles)
  • Zotero (annotate your research sources and share this with collaborators)
However, this also illustrates the problem: different implementations, platforms, philosophies. So I guess I will have to wait another 10 years before I will see something like this implemented?

Wednesday, April 14, 2010

The latest Birdfish

The Churchill Northern Studies Centre has hosted researchers from the Cottenie lab for the past couple years. This year we were invited to contribute a short write-up on our summer 2009 field season. You can read the article here:

Also, be sure to check out the CNSC's website for a preview of their new facility! The staff and volunteers at the CNSC are very supportive and a terrific resource for anyone doing science in the north. You can read their blog here:

Tuesday, April 13, 2010

Hypotheses or data first? Update 2

Since we seem to be on a roll on the what should come first in science, this Nature article actually presents a much better written and argued case in favour of combining the strengths of both approaches (maybe scientists should do what they are good at, science, and leave the writing to, journalists with a PhD?). Some of the costs for doing these genome studies: US$1 billion. How does that stack up to other funding, I have no idea, but this is a big number.

The one aspect that she does not address, and that strikes me as the most crucial aspect, is that mutations seem not to be the main driver! The "poster child of gene mutations", IDH1, appears in 0.3% (1 out of 335) of colorectal, 12% of a type of brain cancer, and 8% of a type of leukaemia cancer. So does this mean that in more than 90% of the cases there is another cause for these cancers? Or what am I missing here, because from that perspective, this seems to be a huge waste of time and effort indeed!

Saturday, April 10, 2010

More costumes

How many do you need to make a costume? Apparently more than 5. However, based on this last evening, we now have a full design, including the know-how on how to make it. So the next time we meet, we should have 6 full Daphnia costumes for the parade. 

4 degrees to work with papier mache, your quality education at work

To illustrate that this is part of the rostrum, all you dirty minds 

Britt's rad sewing skills

While the rest is chugging the alcohol
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Friday, April 9, 2010

This is why we do this ...

research or science or playing or fun or exploration or whatever you want to call it.

Some background: Amanda, Ingrid, and Erin performed a very novel experiment in Churchill last summer (see their blog for more fun stuff). Amanda processed all the samples and is in the process of analyzing the data. Because of the design, it gets complicated very quickly, and so Amanda is honing her R-skills to visualize the results before we go p-value hunting. In the figure above you see the different sampling dates (the 5 big boxes), and the boxplots show dissimilarities between experimental pools, freshwater pools where we added salt to, with control saline pools (uneven numbers) and control freshwater pools (even numbers).

Now the fun stuff:

  • On the first sampling date which was before the salt manipulation, no difference between the even and uneven comparisons, so far so good
  • On the second and third sampling date, some clear differences between the dissimilarities with the salt and freshwater control pools: even numbers less dissimilar than the uneven numbers, so far so good
  • But it is in the completely different direction BAM! Adding salt makes them more dissimilar to the saline control pools. 
  • This is consistent for all experimental treatments, and for 2 full weeks, so very likely not a spurious result.
  • And then it disappears in the last 2 sampling periods
So the questions we have to answer:
  • why in all pools, even some that were not manipulated?
  • why does the effect disappear later on?
  • what is the mechanism?
  • and why opposite to our predictions?
This is what makes science so cool, completely unexpected results. Hopefully we will be able to tell you what the answer is in the not so near future. More to come.

Thursday, April 8, 2010

Hypotheses or data first - Update

We discussed these two articles mentioned in a previous post in our Community Ecology class, and this is the summary of the very interesting discussion between the students, the TAs, and Tom and I:

  • It is not one or the other (which is actually acknowledges by using the "first" in the title)
  • The scientific method is cyclical and depends on data, hypotheses, predictions, increased information, or is cyclical as is illustrated by Tom
  • But I added (which was not supported by the majority of the students, or Tom ;-) that the start of the scientific method is data, or the description of a natural phenomenon
  • I also tried to argue that the "hypotheses first" in its extreme is related to religion, since religion is essentially a hypothesis (causal mechanism) without data to support it, but at this point I was way outside my zone of expertise

Wednesday, April 7, 2010

"The future of math is statistics"?

As a biology/ecology teacher and scientist, I can only hope that this will catch on:

Although he does not provide good reasons why teaching statistics as a way into mathematics would be superior to the old way (somebody must have done research on this, right?), it makes intuitive sense to me. He also does not provide a outline on how to strengthen our innate abilities to think in terms of probabilities that would avoid the way stats is often taught at the university and seems to bludgeon any interest in statistics.

The following presentation provides a more reasoned and balanced view on restructuring the mathematics curriculum:

If I can combine both suggestions (as the big compromiser that I am), probabilities/stats sound like a good way to start exploring the diversity in math topics, but that suggestion is also self-serving, because I need students that are comfortable with stats more than with math (although these two things are related).

Tuesday, April 6, 2010

Hypotheses or data first?

The recent nature issue had an interesting point-counterpoint series of 2 articles as a reflection on 10 years of the human genome project. The first article argues that hypotheses should come first because little progress has been made in the last 10 years as a result of the abundance of data from these different genome projects. The second article argues the exact opposite, that this data-driven approach has resulted in a series of break-troughs that could not have been possible with a hypothesis-driven approach.
This discussion is today still very relevant, even in our department because it mimics some of the interactions and discussion points between I.B. scientists in the science complex and in the Biodiversity institute. Here are some of my thoughts on these two articles and this discussion:
- of course data come first, hypotheses do not develop in a vacuum. All these modern tools are just an extension of old-school natural history, something that we do not include enough in our university education, I think.
- but the money quote is actually in the second article
Without comprehensive cancer genome data sets it will be difficult to distinguish signal from noise.
This implicitly says that hypotheses are necessary, because how can you get comprehensive (genome) data sets, how will define "signal"? Golub thus actually acknowledges that there is no such thing as useful data-driven research!
- The problem in both articles is that because of the nature of an opinion article, they do not use references to back up their claims, so that makes evaluating these opinions more difficult.

Saturday, April 3, 2010

Another option for a Daphnia costume, instead of chicken wire. Some of positives for this option:
- Lies can make one in a full 10 minutes
- you can see the balloons, aka the eggs a lot easier
- spine is also more obvious

Things we (royal we, thus mainly Lies) still has to figure out: arms and the head
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