sustainable science

The energy use of the internet

daniel — Fri, 17 Oct 2008 05:34:59 -0400

In the light of limited global energy resources, we have to make up our mind on how to use them efficiently. An initial step in this process is to find out how much energy we currently spend on key elements of our global infrastructure, and how this may plausibly develop over the next few years to come.

One such attempt, relevant to online networks like WAYS, is being made in a recent paper by Jonathan G Koomey in Environmental Research Letters 3 (2008), entitled "Worldwide electricity used in data centers" (not Open Access).

Would be nice to link such considerations with those on the resource use by an individual scientist, as reported previously. Any takers?

Open Access is an important step on the way towards open science

daniel — Tue, 14 Oct 2008 06:06:35 -0400

This post is meant as a contribution to Open Access Day (OA day) which strives to raise awareness - amongst researchers, research funders, academic publishers, students, politicians and the public - of the importance of Open Access (to literature containing peer-reviewed results of scientific investigations, that is) for our global society.

One way to do this is to have people like you blog in synchronization, i.e. on four questions during OA day. To give you some inspiration on the topic, you may wish to take a look at the first such synch-blogging entry, which came from Neil Saunders, based at the University of Queensland, Australia.

I will follow Neil's formatting to address the four questions:

Why does Open Access matter to you?

OA, for me, marks a turning point within the scientific cycle, i.e. the iterative process which leads (if sufficiently funded) from a research question or idea to a hypothesis or new method that can be tested and, ultimately, to the results of those tests which then have to be communicated. This communication step is crucial, as it adds to our global knowledge foundation (often described, following Newton, as "the shoulders of giants") for new research questions or ideas that may eventually lead to things like "innovation", "insight" and "progress". If innovators-to-be, however, do not have access to the findings of their forebears (which may indeed be contemporaries), they will have to spend a lot of their time and resources by (re)inventing some aspects of the giants' shoulders before starting to work on their innovations in the first place. Open Access is a movement to lift those access barriers, and it is not only useful to researchers but it can also, for instance, help patients and their relatives to gather first-hand expert information on their specific health conditions, and it can help to inform public debates about research data with scientific implications. The full power of Open Access, however, can only be harvested if all other steps within the scientific cycle (including, e.g., notebook keeping) also become increasingly open, a goal with multiple names (of which Open Science is my favourite). This would not only reduce the considerable time lag between the obtainment of some results and their application in other circumstances but also foster the development of new citation metrics that would allow to more adequately evaluate the research accomplishments of young scientists.

How did you first become aware of it?

I had been aware of the barriers since I started reading scientific papers in the mid-1990s, as I rarely had access to much of the literature cited therein, no matter what library I went to (and I went to more than a dozen regularly at that time). I got a glimpse of a possible solution when checking out the freely available content at BioMed Central on a weekly basis some years later but this again did not cover much of my core areas of interest (Evolutionary Biophysics), nor did arxiv.org that I had discovered around the same time. So it took the Budapest Open Access Initiative to make me aware of the progress that had already been achieved or was underway by 2001, and I signed it shortly after starting to work on my PhD thesis.

Why should scientific and medical research be an open-access resource for the world?

Knowledge grows when shared. And what else is the goal of research if not growing knowledge on a global scale? Besides, I find it non-sustainable to use the limited resources that we have to constantly re-invent the wheel for reasons external to the research process.

What do you do to support Open Access, and what can others do?

As an author, I strive to publish OA (i.e. gold) but independent of whether this is possible or not, I self-archive my papers (i.e. green OA). I am neither a journal editor nor part of a publishing house but I occasionally use my blog to cover OA and related topics, particularly Open Education, and Open Science as a whole, and I link to ot he r s who do this more intensively. Finally, I am playing around with plat form s and techn olo gie s that may facilitate the transition to a more open scientific cycle, keeping a special eye on what these upcoming changes might mean to young scientists, e.g. in terms of theses and online le ctures rather than papers. Others can, of course, familiarize themselves with the issue of effectively (in both time and resources) communicating (peer-reviewed) research results via the channels that are technically possible, they can experiment with the to ol s at hand to communicate their thoughts, and they can educate even more others about these matters in more traditional ways. In fact, I think they should.

On the impact of research

daniel — Tue, 03 Jun 2008 12:32:27 -0400

Multiple approaches to measure the impact of research exist - the most common ones include citation metrics like the in-famous Journal Impact Factor or the relatively new Hirsch index, and the volume of research grants earned.

Several such measures have become important determinants of scientific careers, but a certain type of impact measures always tend to be forgotten: environmental measures. Now, in a recent contribution to the journal "Trends in Genetics" (not Open Access), biochemist Hervé Philippe takes a semi-quantitative approach to these matters. Then, he points out that scientists (even those that do not work with environmentally hazardous agents), by doing their job - research and disseminating its results to the scientific community and the public - use up natural resources (and produce waste) at a level well above the average citizen of our planet (this level has come to be known as the ecological footprint, although Philippe does not explicitly mention the concept).

This is an important article because it highlights that sustainability is not just a topic for politicians and perhaps some specialized group of scientists - no, it is a matter of concern for a biochemist, too, and indeed for anybody but in particular for scientists who are trained in the analysis of relatively complex structures. The paper is also unusual for a science article in that it contains public advice to policy makers - they should take the limitedness of natural resources into account and leave the eternal quest for economic growth, even replace it (at least temporarily) with a goal that he calls "degrowth" and which I would rephrase as "leading to a steady-state economy".

At a time when even a multinational oil company like Elf Total admits that fossil fuels are finite (English version here), it would thus seem very appropriate if scientists, science organizations and science funders would start to devote some of their current resources to investigating in detail what impact they have on the environment, and how this could be balanced, in the long run, with the actual research impact. The Ecological Footprint mentioned above was originally designed to determine the resource use of the global human society but it has since been adapted to lower-level scales, e.g. cities and industrial products, and so it should not be too difficult to get reasonably correct estimates for scientific research projects, too (especially considering that scientific research tends to be well-documented). If you know of any initiative in this direction, please post it here.

Broken Pipeline: information on funding climate in US

MCrosby — Thu, 13 Mar 2008 13:22:58 -0400

If one is considering the prospects of coming to the (or living in the) US for any type of training mechanism, it is very important to be aware of the current trends in funding. Young scientists need to think strategically about their careers and how to better make sustainable arguments on funding practices to those whom are in charge of allocating funds. You can bet that I will be one of those people advocating for this type of activity and that I will utilize the skills of understanding pitfalls (garnered from my grant writing activities) in investing in human capital for the future. This article describes what is going on with those whom are at the top of their fields and how they are seeing their lives and careers. A must read...

See: http://www.brokenpipeline.org/materials.htm

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

daniel — Thu, 31 Jan 2008 19:15:23 -0500

Hello together,

this blog 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

daniel — Fri, 25 Jan 2008 21:42:56 -0500

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?

Paper on promoting science in a developing country

daniel — Mon, 03 Dec 2007 04:43:58 -0500

The current issue of PLoS Computational Biology features a paper on how a science like computational biology can be promoted in a developing country like Cuba.
For details, see

Pons T, Montero LA, Febles JP (2007) Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country. PLoS Comput Biol 3(11): e227
doi:10.1371/journal.pcbi.0030227 (Open Access).