interactive learning

Open Students platform - Students speak out for Open Access to research findings

Hello together,

this blog post comes in two versions, short and long. If you are not sure what Open Access (OA) means, take a look at Wikipedia's description here: http://en.wikipedia.org/wiki/Open_access .

SHORT: Students now have their own Open Access platform, Open Students
www.openstudents.org .

LONG:
Those of you who have already written longer scientific texts (e.g. assignments, bachelor, master or PhD theses, or research papers) will have experienced situations in which some particularly relevant piece of information seemed to be hidden in an article you did not have at hand.

What you would normally do in such situations is to check whether Google Scholar ( http://scholar.google.com ) or some other search engine can locate the paper for you, which is often the case, especially for articles published during the last decade. The problems start when you want to access the full text version - fewer and fewer university libraries can afford the high subscription fees publishers charge for providing access to the full text (this publishing model is generally called subscription-based, or toll-access), and even if your university is among the lucky ones, this does not mean you get access to the article while off campus, even if non-paper versions exist.

In many cases, the publisher will provide an option to buy electronic versions of the article (for typically some dozens of Euros or equivalent), and document delivery companies provide similar services (usually scanned versions) for older articles. Both options are rarely compatible with a student's financial budget, though.

In developing countries, libraries and students generally have further constraints, especially in terms of budget, but some initiatives exist to reduce that burden somehow. For example, Access to Global Online Research in Agriculture (AGORA; www.aginternetwork.org), Health InterNetwork Access to Research Initiative (HINARI; www.who.int/hinari/) and Online Access to Research in the Environment (OARE; www.oaresciences.org/) provide free online access to the contents of many peer-reviewed scientific journals to most of the poorest countries of the world. A more comprehensive list of such initiatives is available via www.ifpri.org/library/devresources.asp .

Technically, there is no need to restrict free online access to developing countries, and so publishers like www.plos.org, www.biomedcentral.com or www.copernicus.org provide free access to all of the articles in journals they publish (a strategy called "Gold" Open Access), while others don't do that but allow authors to self-archive the final versions of their manuscripts (either the accepted drafts or the copy-edited final published articles) on their personal or institutional websites (a strategy labeled "Green" Open Access). To find out about the self-archiving policy of a particular journal, check http://romeo.eprints.org/ ; for detailed accounts of almost anything Open Access, see Peter Suber's blog at www.earlham.edu/~peters/fos/fosblog.html .

Recently, a number of funding agencies (e.g. www.nih.gov) have issued policies demanding that publications resulting from the research that they fund must be made freely available to the public (i.e. via either Green or Gold OA). The reasoning behind this is (somewhat abbreviated; there have recently been a number of conferences organized on this topic) that the funder who had financed the research already has a low incentive to pay extra money to a third party (the publisher) for reading the results, especially since all the essential aspects of scientific publishing are normally done for free by researchers - those who had received the grant write an article, while other researchers in the field (their peers) review it.

This gets us back to the students' perspective: If students have the possibility to access any scientific article or - via tools like the BioText Search Engine (http://biosearch.berkeley.edu) - their figures or other supplementary information, they stand good chances to learn more effectively than the traditional way. It is thus natural that students will enjoy and profit from Open Access to research findings, and that's precisely the message I perceive behind the creation of the new web platform www.openstudents.org . In my eyes, this is an important additional step towards a collaborative global society, especially since many experienced researchers still hesitate to embrace the OA concept, mainly for reasons of tradition.

Further such steps to more interactive ways of studying will certainly include collaborative platforms like www.wikimedia.org or www.opensource.org and online lectures like MIT's OpenCourseWare (http://ocw.mit.edu/OcwWeb/web/courses/courses/index.htm) or those collected by the World Lecture Project (www.world-lecture-project.org ; a WAYS partner). New ways of planning, funding, conducting, reporting, discussing and explaining scientific research (e.g. www.biogeosciences.net or www.pbs.org/wgbh/nova/sciencenow/) or running a campus (www.thescholarship.com ; another WAYS partner) will also be part of this excitingly developing story, as will many things currently not or not widely known.

Finally, a nice way of interacting between and beyond students are, of course, blogs like this one, and the option to comment on them.

Daniel Mietchen

On how to treat fundamental questions

Consider the following: Put a handfull of distinguished scientists from different fields together, let them talk about a topic in which they share a fundamental interest, and record the session. What outcome would you expect?

Such an experiment was run last August by the people at www.edge.org under the theme "Life: What a concept!", with the participation of Freeman Dyson, J. Craig Venter, George Church, Robert Shapiro, Dimitar Sasselov and Seth Lloyd.

The transcripts of the session have recently been put on the web at
http://www.edge.org/documents/life/Life.pdf , which I read while commuting to and from the lab this week. I found it very stimulating to follow these guys venture around many scales in space and time, and I recommend that experience to you.

Assuming that most of you will think to have good reasons to shy away from reading the 168-page pdf or watching the corresponding videos (http://www.edge.org/documents/life/life_index.html), I have compiled a list of quotes from the transcript which is about 98% shorter. The order of the quotes as presented here is not chronological but should be logical to the extent permitted by the downsampling.

It is perhaps noteworthy that some of the experiments described in here were published yesterday (http://www.sciencemag.org/cgi/content/abstract/1151721).

--------
Life: What a concept!
--------
SHAPIRO :
The idea is that this is inherent in the laws of chemistry and physics. One doesn't need a freak set of perhaps a hundred consecutive reactions that will be needed to make an RNA, and life becomes a probable thing that can be generated through the action of the laws of chemistry and physics, provided certain conditions are met. You must have the energy. It's good to have some container or compartment, because if your products just diffuse away from each other and get lost and cease to react with one another you'll eventually extinguish the cycle. You need a compartment, you need a source of energy, you need to couple the energy to the chemistry involved, and you need a sufficiently rich chemistry to allow for this network of pathways to establish itself. Having been given this, you can then start to get evolution.

---
LLOYD:
if I produce chemical A, and chemical B, I put them together, then that produces chemical C in abundance. Or if chemical A and chemical B are there and chemical D is also there, then chemical C is not produced.

Now you can see the relationship of these kinds of reactions to logic, right — if A and B, then C — if A and B and D, then not C. I'm simplifying chemistry, of course, because there there are temporal dynamics as well. But those dynamics' ifthen statements, the digital statements that lie at the bottom of computation, are an intrinsic part of chemistry.

---
SHAPIRO: They have decided that one of the eight dimensions of string theory — one of the alternative universes that are now postulated by the anthropic people, are much more habitable than this. Life has a difficult job getting started. I admit this is one extreme view of life, but it's one that makes life, as Stuart Kauffman put it, something that the universe has in a sense expected, and what one does with that fact, I leave to you.

I'm not a theologian, I'm an agnostic, which says that I really do not know what's going on. But that at least in the origin of life we have a problem that can be solved not too difficultly in a laboratory, by getting the right set of molecules, by getting an appropriate source of energy — okay, we cheat a little bit, we use a beaker as the container rather than some membrane, which is perhaps more difficult to achieve than is commonly understood, and we just try to see what happens.

---
SHAPIRO:
At one point I went and spoke to the now, unfortunately, late Stanley Miller, and asked him about the circumstances of his famous Miller-Urey experiment — the one with the electric lightning and amino acids were formed — and he handed me a biographical piece he himself had written to something called the Transactions of the Copernican Society or something like that, and he described how in building his apparatus he was concerned with questions of safety, because if you take a flask and you mix it with methane and hydrogen and ammonia, the most likely result is BOOM, with flying glass in all directions, which is definitely not publishable.

[...]
On the other hand, if you believe that life could start with good molecules, given enough energy, then the universe may be rich with start-ups, and then there may be some series of levels that you have to go through, higher and higher, in order to get life more and more advanced.

---
LLOYD:
There's a digital nature to the universe, and quantum mechanics makes this happen.

---
SHAPIRO:
Entropy is like a business. It doesn't matter if one subsidiary of the business loses money as long as the others show enough profit to offset it. What you need is a larger system, the environment, and part of it absorbs energy and gets organized, and in payment for that, the rest of the environment gets disorganized, usually by going up a little bit in temperature, which is the common denominator of entropy. If you convert other kinds of energy to heat, you can pay for a lot of organization.

---
LLOYD:
So why does complex behavior arise? Well, the universe is computing at its most microscopic scales. Two electrons, two bits of information, every time they collide, those bits flip. It's just these natural interaction and information processing that we use when we build quantum computers. Now I claim — and I can claim this because this is a mathematical theorem, which is different from just mere observational evidence — that when you have something that is computing and you program it at random, just tossing IN little random bits of programming, that it necessarily generates complex behavior.

---
SHAPIRO:
[planets similar to] Earth are subject to a sort of tension because the inside, which is pure iron, is very electron-rich, while the outside, due to continual escape of hydrogen into space because water gets broken up by radiation, is electron-poor, so that at various places on the Earth there will be interfaces where electron-rich molecules are interfaced with electron-poor molecules. These are then prominent sites for the origin of life. Everyone can have his own favorite site. Some argue for the interiors of volcanoes, some argue for vents, some argue for the monolayer of the space of the ocean.

---
SASSELOV:
It turns out that plate tectonics, as understood from Earth, is a process which has been going on theoretically much more easily on a slightly bigger planet. In fact if you do the theory, as best as you can today, the Earth is at the margin of what is viable in terms of plate tectonics. Probably some of you may know that plate tectonics is a very important aspect of the viability of a planet in terms of surface conditions, because it's a good thermostat, it keeps the climate more or less stable over long periods of time, and also allows you to have easy access to the large reservoir of chemicals and gasses in the mantle of the planet.

---
DYSON: "One of the laws of physics which is absolutely crucial [...] is the fact that objects bound together by gravity have negative specific heat."

---
VENTER: What role does gravity play in the larger — in the super Earths?

SASSELOV: It's actually a positive role. In the sense that if you take the general amount of out-gassing, fluxes, which interchange between the mantle and the atmosphere of the Earth, the Earth's gravity is very close to marginal [...] in retaining a sufficient atmosphere, and hence making this thermostat being viable, and really providing you with stable conditions over at least a billion years. So having more gravity is actually better.

---
SASSELOV (on planetary preconditions for life):
"stability over long periods of time, but sufficiently low or moderate temperatures. (Stars are very stable over billions of years, but they all have very high temperatures, all throughout.) And basically the overall thermodynamic window that Morowitz is talking about, which allows complex chemistry. That's actually much broader than simply having water."

---
SASSELOV:
Then the question is, how much do we know about planetary systems? Up until 12 years ago, essentially we knew only of one: the solar system. That situation is very similar to what we have with life. We only have one example. And that's bad from many points of view, and we — 'we' meaning astronomers — learned it the hard way, because it turned out that what we had theorized about planets was very solar system-centric, and we missed a lot of things that we should not have missed, but that always happens when you have only one example of something.

---
SHAPIRO: Which is the closest known super Earth?

SASSELOV: The closest known is called — in fact there are two of them: Gliese 581c and d, and both of them are super Earths, and are just 20 light years away. Wilhelm Gliese was a German astronomer (1915-1993).

CHURCH: When will they arrive here?

SASSELOV: Next week.

---
SHAPIRO: There was a wonderful paper written by Chris Chyba and Carol Cleland about three years ago about definitions of life, and how even defining what definition is can get you into philosophical doo-doo. And it's best to look for phenomena that by their properties we would be happy to classify as alive, and to not worry too much about definition.

---
VENTER: So two base pair change in a genome could be sufficient to create a new species out of 1.5 billion.

DYSON: Yes.

VENTER: I'm not sure everybody will buy that definition... So that makes you a very different species than George.

DYSON: The real problem is the lawyers. You have the endangered species act; that means you have to make a legal definition of the species.

CHURCH: That's true. We're all endangered.

---
VENTER:
We just started asking very simple questions for example — if one species needed 1,800 genes and the other needed 550, are there species that can get by with less? Can you define a minimal genetic operating system for life? Could we define life at a genetic level? Obviously extremely naive questions but the view of biochemistry and genomics by the scientific community was very limited as well. For example when we published the
Haemophilus influenzae genome a well known biochemist at Stanford University said we obviously assembled it wrong because it didn't have a complete TCA cycle. And everybody knew that every organism had a complete glycolytic pathway and a complete TCA cycle. And Haemophilus only has half of one.

SHAPIRO: Therefore it's not an organism.

VENTER: No, therefore they assumed we made a mistake in the sequencing and the assembly. Now we see every repertoire under the sun, for example the third organism that we sequenced was the first Achaea that we did with Carl Woese, it was methanococcus jannaschii, which has neither a TCA cycle nor glycolysis. It makes all its cellular energy by methanogenesis, going from CO2 to methane, using hydrogen as its energy source. CO2 is its carbon source for all the carbon in the cell.

---
SHAPIRO:
biologists [...] only would recognize as life something that could be cultured by them and
then published. Albert Sangiorgi once said that a drug is something that, injected into an animal, produces a paper. A microorganism is something which when put in one of its favorite culture media leads to a paper. Nowadays you might say it leads to a DNA sequence, which would be a different argument.

VENTER: But eventually a paper.

---
SHAPIRO :
I was publishing papers like this and I got the reputation, or the nickname in the laboratory of the prebiotic chemist, of 'Dr. No'. If someone wanted a paper murdered, send it to me as a referee. And so on. At some point, someone said, Shapiro, you've got to be positive somewhere. So how did life start?

CfP: 9th International Conference on Intelligent Tutoring Systems, Montreal, Canada

ITS'2008 - CALL FOR PAPERS

9th International Conference on Intelligent Tutoring Systems
June 23-27, 2008 Montreal, Canada

http://gdac.dinfo.uqam.ca/its2008/

******** Important Announcement *********************

NEW deadline extended until January 24, 12h PM (midnight) Easter time

******** REVISED Dates *********************

January 24th, 2008 : Paper & Poster submission.

January 24th, 2008 : Workshop & tutorial proposal due.

March 7th, 2008 : Notification of acceptance (full papers & posters).

=== April 1st, 2008 : Young Researchers Track submission. ===

April 6th, 2008 : Copyright form submission (full papers & posters).

April 6th, 2008 : Final camera-ready manuscript (full papers & posters).

April 16th, 2008 : Author registration deadline .

April 20th to May 8th : Workshop, Demonstrations and tutorial deadlines.

**** Theme: Intelligent Tutoring Systems: Past and Future *********

The 9th International Conference on Intelligent Tutoring Systems provides a
leading international forum for the dissemination of original results in the
design, implementation, and evaluation of intelligent tutoring systems and
related areas. The conference will draw researchers from a broad spectrum of
disciplines ranging from artificial intelligence and cognitive sciences to
pedagogy and educational psychology. The conference explores the real world
impact of intelligent tutoring systems (ITSs) on an increasingly global
scale.

Improved authoring tools and learning object standards enable fielding
systems and curricula in real world settings on an unprecedented scale.
Researchers deploy ITSs in ever larger studies, and increasingly use data
from real students, tasks, and settings to guide new research. With high
volumes of student interaction data, data mining and machine learning,
tutoring systems can learn from experience and improve their teaching
performance.

Increasing number of realistic evaluation studies also broaden researchers'
knowledge about the educational contexts for which ITSs are best suited. At
the same time, researchers explore how to expand and improve student-tutor
communication, for example, how to achieve more flexible and responsive
discourse with students, help students integrate Web resources into
learning, use mobile technologies and games to enhance student motivation
and learning, and address multicultural perspectives.

ITS'2008 will be supported by a strong international program committee that
will ensure full and effective refereeing of all submitted papers.

********** Topics of ************

Original papers related to the design, implementation and evaluation of
intelligent tutoring systems are solicited. Topics include, but are not
limited to, the followings:

- Adaptive Hypermedia
- Evaluation of Instructional Systems
- Learning Environments
- Affect and Models of Emotion
- Human Factors and Interface Design
- Machine Learning in ITS
- Agent-based Tutoring Systems
- Instructional Design
- Narratives in Learning
- Natural Language and Discourse
- Architectures
- Instructor Networking
- Pedagogical Agent
- Assessment
- Intelligent Agents
- Pedagogical Planning
- Authoring Systems
- Intelligent Web-Based Learning
- Situated Learning
- Case-Based Reasoning Systems
- Intelligent Multimedia Systems
- Speech and Dialogue Systems
- Cognitive Modeling
- Internet Environments
- Student Modeling
- Collaborative Learning
- Knowledge Acquisition
- Virtual Reality
- Digital Learning Games
- Knowledge Construction
- Web-based Training Systems
- Distributed Learning Environments
- Knowledge Representation
- Wireless and Mobile Learning
- Electronic Commerce and Learning
- Learning Companions

********** Contacts and Paper Submission ******************

Roger Nkambou (co-chair), University of Quebec at Montreal, Canada -
nkambou.roger@uqam.ca Susanne Lajoie (co-chair), McGill, Canada -
lajoie@mcgill.ca

Conference website: http://gdac.dinfo.uqam.ca/its2008

Proceedings of the conference will be published by Springer Verlag in its
Lecture Notes in Computer Science series.