Jabberwocky Ecology

Some meandering thoughts on the difference between EcologicalData.org and DataONE

In the comments of my post on the Ecological Data Wiki Jarrett Byrnes asked an excellent question:

Very cool. I’m curious, how do you think this will compare/contrast/fight with the Data One project – https://www.dataone.org/ – or is this a different beast altogether?

As I started to answer it I realized that my thoughts on the matter were better served by a full post, both because they are a bit lengthy and because I don’t actually know much about DataONE and would love to have some of their folks come by, correct my mistaken impressions, and just chat about this stuff in general.

To begin with I should say that I’m still trying to figure this out myself, both because I’m still figuring out exactly what DataONE is going to be, and because EcologicalData is still evolving. I think that both projects goals could be largely defined as “Organizing Ecology’s Data,” but that’s a pretty difficult task, involving a lot of components and a lot of different ways to tackle them. So, my general perspective is that the more folks we have trying the merrier. I suspect there will be plenty of room for multiple related projects, but I’d be just as happy (even happier probably) if we could eventually find a single centralized location for handling all of this. All I want is solution to the challenge.

But, to get to the question at hand, here are the differences I see based on my current understanding of DataONE:

1. Approach. There are currently two major paradigms for organizing large amounts of information. The first is to figure out a way to tell computers how to do it for us (e.g., Google), the second is to crowdsource it’s development and curation (e.g., Wikipedia). DataONE is taking the computer based approach. It’s heavy on metadata, ontologies, etc. The goal is to manage the complexities of ecological data by providing the computer with very detailed descriptions of the data that it can understand. We’re taking the human approach, keeping things simple and trying to leverage the collective knowledge and effort of the field. As part of this difference in approach I suspect that EcologicalData will be much more interactive and community driven (the goal is for the community to actually run the site, just like Wikipedia) whereas DataONE will tend to be more centralized and hierarchical. I honestly couldn’t tell you which will turn out better (perhaps the two approaches will each turn out to be better for different things) but I’m really glad that we’re trying both at the same time to figure out what will work and where their relative strengths might be.

2. Actually serving data. DataONE will do this; we won’t. This is part of the difference in approach. If the computer can handle all of the thinking with respect to the data then you want it to do that and just spit out what you want. Centralizing the distribution of heterogeneous data is a really complicated task and I’m excited the folks at DataONE are tackling the challenge.

a. One of the other challenges for serving data is that is that you have to get all of the folks who “own” the data to let you provide it. This is one of the reasons I came up with the Data Wiki idea. By serving as a portal it helps circumvent the challenges of getting all of the individual stake holders to agree to participate.

b. We do provide a tool for data acquisition, the EcoData Retriever, that likewise focuses on circumventing the need to negotiate with data providers by allowing each individual investigator to automatically download the data from the source. But, this just sets up each dataset independently, whereas I’m presuming that DataONE will let you just run one big query of all the data (which I’m totally looking forward to by the way) [1].

3. Focus. The primary motivation behind the Data Wiki goes beyond identifying datasets and really focuses on how you should use them. Having worked with other folks’ data for a number of years I can say that the biggest challenging (for me anyway) is actually figuring out all of the details of when and how the dataset should be used. This isn’t just a question of reading metadata either. It’s a question of integrating thoughts and approaches from across the literature. What I would like to see develop on the Data Wiki pages is the development of concise descriptions for how to go about using these datasets in the best way possible.  This is a very difficult task to automate and one where I think a crowdsourced solution is likely the most effective. We haven’t done a great job of this yet, but Allen Hurlbert and I have some plans to develop a couple of good examples early in the fall to help demonstrate the idea.

4. We’re open for business. Ha ha, eat our dust DataONE. But seriously, we’ve taken a super simple approach which means we can get up and running quickly. DataONE is doing something much more complicated and so things may take some time to roll out. I’m hoping to get a better idea of what their time lines look like at ESA. I’m sure their tools will be well worth the wait.

5. Oh, and their budget is a little over $2,000,000/year, which is just slightly larger than our budget of around $5,000/year.

So, there is my lengthy and meandering response to Jarrett’s question. I’m looking forward to chatting with DataONE folks at ESA to find out more about what they are up to, and I’d love to have them stop by here to chat and clear up my presumably numerous misconceptions.


[1] Though we do have some ideas for managing something somewhat similar, so stay tuned for EcoData Retriever 2.0. Hopefully coming to an internet near you sometime this spring.

Navigating ESA

Next week is the annual meeting of the Ecological Society of America. If you’ve ever been to ESA, then you know it’s….big, often between 3000-5000 ecologists (which I thought was big until I heard about some of the biomedical conferences which have the attendance of a small city). It seems like most of those people are giving talks or posters. Obviously it’s impossible to see everything, and frankly with talks spread out across 20-odd different rooms which are usually spread out across the far corners of the convention center plus various hotels, it’s probably not possible to see even a fraction of the things you’re interested in. If you try to do the ESA blitzkrieg (and most young graduate students will try at least once), you are guaranteeing an overwhelming, lonely, and futile experience. So, how do you navigate this beast and keep your sanity? I have two recommendations:

1)      Pick a strategy. Some years I choose to focus on a specific concept or research area to learn a lot about a breaking area of ecology in a short period of time (like the year a majority of what I saw had the word ‘metacommunity’ in the title). Some years I choose breadth because I want to have a better feeling for where the field in general is going or to look for interesting new ideas (one year I saw talks that spanned from theory to empirical and from physiology to ecosystems – ah that was a fun year). The point is, decide what you want to get out of ESA before you go because once you get there, there’s a lot going on.

2)       Find a conference buddy (or buddies). You can’t see everything, but if you coordinate with a friend then you can hear about twice as much as you can see. It helps with processing talks and keeping them from just blending together. It also has the added benefit of giving you someone to talk to regularly and keeping you from feeling like just another faceless cog in the giant ESA machine.  Ethan and I often use this strategy, especially when there is more than one really interesting talk at the same time. Then we get together afterwards and swap stories. Just a piece of advice: make sure your conference buddy either has a good memory or takes good notes. I’m not pointing fingers or anything, but there’s nothing more frustrating than giving a detailed rendition of the talk you saw, asking about the talk they saw that you really want to know about, and getting, “It was really good. Uh, my notes here say they did something with a neutral model and the results were really compelling. The paper’s coming out soon. “

Distributed Ecology [Blogrolling]

I’ve been waiting for a while now for Ted Hart’s blog to get up enough steam to send folks over there, and since in the last two weeks he’s had three posts, revamped the mission of the blog, and engaged in the ongoing conversation about Lindenmayer & Likens, it seems like that time has arrived.

The blog is called Distributed Ecology because, as Ted describes,

I chose distributed ecology as a title because I like the idea of ecological thought like distributed computing. Lots of us scientists like little nodes around the web thinking and processing ideas into something great.

Sounds like what I’m hoping to see (and am increasingly witnessing) from the ecology blogs. So, head on over, check it out, click on the RSS button, and welcome Ted to the ecology blogging community.

The war over academic publishing has officially begun


The last week has been an interesting one for academic publishing. First a 24 year old programmer name Aaron Swartz was arrested for allegedly breaking into MIT’s network and downloading 5 million articles from JSTOR. Given his background it has been surmised that he planned on making the documents publicly available. He faces up to 35 years in federal prison.

In response to the arrest Gregory Maxwell, a “technologist” and hobbyist scientist uploaded nearly 20,000 JSTOR [1] articles from the Philosophical Transactions of the Royal Society to The Pirate Bay, a bittorrent file sharing site infamous for facilitating the illegal sharing of music and movies. As explanation for the upload Maxwell posted a scathing, and generally trenchant, critique of the current academic publishing system that I am going to reproduce here in it’s entirety so that those uncomfortable with [2], or blocked from, visiting The Pirate Bay can read it [3]. In it he notes that since all of the articles he posted were published prior to 1923 they are all in the public domain.

This archive contains 18,592 scientific publications totaling
33GiB, all from Philosophical Transactions of the Royal Society
and which should be  available to everyone at no cost, but most
have previously only been made available at high prices through
paywall gatekeepers like JSTOR.

Limited access to the  documents here is typically sold for $19
USD per article, though some of the older ones are available as
cheaply as $8. Purchasing access to this collection one article
at a time would cost hundreds of thousands of dollars.

Also included is the basic factual metadata allowing you to
locate works by title, author, or publication date, and a
checksum file to allow you to check for corruption.

I've had these files for a long time, but I've been afraid that if I
published them I would be subject to unjust legal harassment by those who
profit from controlling access to these works.

I now feel that I've been making the wrong decision.

On July 19th 2011, Aaron Swartz was criminally charged by the US Attorney
General's office for, effectively, downloading too many academic papers
from JSTOR.

Academic publishing is an odd system - the authors are not paid for their
writing, nor are the peer reviewers (they're just more unpaid academics),
and in some fields even the journal editors are unpaid. Sometimes the
authors must even pay the publishers.

And yet scientific publications are some of the most outrageously
expensive pieces of literature you can buy. In the past, the high access
fees supported the costly mechanical reproduction of niche paper journals,
but online distribution has mostly made this function obsolete.

As far as I can tell, the money paid for access today serves little
significant purpose except to perpetuate dead business models. The
"publish or perish" pressure in academia gives the authors an impossibly
weak negotiating position, and the existing system has enormous inertia.

Those with the most power to change the system--the long-tenured luminary
scholars whose works give legitimacy and prestige to the journals, rather
than the other way around--are the least impacted by its failures. They
are supported by institutions who invisibly provide access to all of the
resources they need. And as the journals depend on them, they may ask
for alterations to the standard contract without risking their career on
the loss of a publication offer. Many don't even realize the extent to
which academic work is inaccessible to the general public, nor do they
realize what sort of work is being done outside universities that would
benefit by it.

Large publishers are now able to purchase the political clout needed
to abuse the narrow commercial scope of copyright protection, extending
it to completely inapplicable areas: slavish reproductions of historic
documents and art, for example, and exploiting the labors of unpaid
scientists. They're even able to make the taxpayers pay for their
attacks on free society by pursuing criminal prosecution (copyright has
classically been a civil matter) and by burdening public institutions
with outrageous subscription fees.

Copyright is a legal fiction representing a narrow compromise: we give
up some of our natural right to exchange information in exchange for
creating an economic incentive to author, so that we may all enjoy more
works. When publishers abuse the system to prop up their existence,
when they misrepresent the extent of copyright coverage, when they use
threats of frivolous litigation to suppress the dissemination of publicly
owned works, they are stealing from everyone else.

Several years ago I came into possession, through rather boring and
lawful means, of a large collection of JSTOR documents.

These particular documents are the historic back archives of the
Philosophical Transactions of the Royal Society - a prestigious scientific
journal with a history extending back to the 1600s.

The portion of the collection included in this archive, ones published
prior to 1923 and therefore obviously in the public domain, total some
18,592 papers and 33 gigabytes of data.

The documents are part of the shared heritage of all mankind,
and are rightfully in the public domain, but they are not available
freely. Instead the articles are available at $19 each--for one month's
viewing, by one person, on one computer. It's a steal. From you.

When I received these documents I had grand plans of uploading them to
Wikipedia's sister site for reference works, Wikisource - where they
could be tightly interlinked with Wikipedia, providing interesting
historical context to the encyclopedia articles. For example, Uranus
was discovered in 1781 by William Herschel; why not take a look at
the paper where he originally disclosed his discovery? (Or one of the
several follow on publications about its satellites, or the dozens of
other papers he authored?)

But I soon found the reality of the situation to be less than appealing:
publishing the documents freely was likely to bring frivolous litigation
from the publishers.

As in many other cases, I could expect them to claim that their slavish
reproduction - scanning the documents - created a new copyright
interest. Or that distributing the documents complete with the trivial
watermarks they added constituted unlawful copying of that mark. They
might even pursue strawman criminal charges claiming that whoever obtained
the files must have violated some kind of anti-hacking laws.

In my discreet inquiry, I was unable to find anyone willing to cover
the potentially unbounded legal costs I risked, even though the only
unlawful action here is the fraudulent misuse of copyright by JSTOR and
the Royal Society to withhold access from the public to that which is
legally and morally everyone's property.

In the meantime, and to great fanfare as part of their 350th anniversary,
the RSOL opened up "free" access to their historic archives - but "free"
only meant "with many odious terms", and access was limited to about
100 articles.

All too often journals, galleries, and museums are becoming not
disseminators of knowledge - as their lofty mission statements
suggest - but censors of knowledge, because censoring is the one thing
they do better than the Internet does. Stewardship and curation are
valuable functions, but their value is negative when there is only one
steward and one curator, whose judgment reigns supreme as the final word
on what everyone else sees and knows. If their recommendations have value
they can be heeded without the coercive abuse of copyright to silence

The liberal dissemination of knowledge is essential to scientific
inquiry. More than in any other area, the application of restrictive
copyright is inappropriate for academic works: there is no sticky question
of how to pay authors or reviewers, as the publishers are already not
paying them. And unlike 'mere' works of entertainment, liberal access
to scientific work impacts the well-being of all mankind. Our continued
survival may even depend on it.

If I can remove even one dollar of ill-gained income from a poisonous
industry which acts to suppress scientific and historic understanding,
then whatever personal cost I suffer will be justified ΓΓé¼ΓÇ¥it will be one
less dollar spent in the war against knowledge. One less dollar spent
lobbying for laws that make downloading too many scientific papers
a crime.

I had considered releasing this collection anonymously, but others pointed
out that the obviously overzealous prosecutors of Aaron Swartz would
probably accuse him of it and add it to their growing list of ridiculous
charges. This didn't sit well with my conscience, and I generally believe
that anything worth doing is worth attaching your name to.

I'm interested in hearing about any enjoyable discoveries or even useful
applications which come of this archive.

- ----
Greg Maxwell - July 20th 2011
gmaxwell@gmail.com  Bitcoin: 14csFEJHk3SYbkBmajyJ3ktpsd2TmwDEBb

These stories have been covered widely and the discussion has been heavy on Twitter and in the blogosphere. The important part of this discussion for academic publishing is that it has brought many of the absurdities of the current academic publishing system into the public eye, and a lot of people are shocked and unhappy [4]. This is all happening at the same time that Britain is finally standing up to the big publishing companies as their profits [5] and business models increasingly hamper rather than benefit the scientific process, and serious questions are raised about whether we should be publishing in peer-reviewed journals at all. I suspect that we will look back on 2011 as the tipping point year when academic publishing changed forever.


[1] In an interview with Wired Campus JSTOR claimed that these aren’t technically their articles because even though JSTOR did digitize these files, and each file includes an indication of JSTORs involvement, the files lack JSTOR’s cover page, so it’s not really their files, it’s the Royal Society’s files. Which first made me think “Wow, that’s about the lamest duck and cover excuse I’ve ever heard” and then “Hey, so if I just delete the cover page off a JSTOR file then apparently they surrender all claim to it. Nice!”

[2] In addition to questionable legality of the site some of the advertising there isn’t exactly workplace appropriate.

[3] I think that given the context he would be fine with us reprinting the entire statement. I’ve done some very minor cleaning up of some junk codes for readability. The original is available here.

[4] But also conflicted about the behavior of the individuals in question.

[5] ~$120 million/year for Wiley and ~$1 billion/year for Reed Elsevier (source LibraryJournal.com).

A Plea for Pluralism

As you may have seen earlier either on Jabberwocky, EEB and Flow, or over at Oikos‘ new blog, the most recent piece about how some branch of ecology is ruining ecology has caused some discussion in the blogosphere. Everytime one of these comes out, I tell myself I’m going to write a blog post but then I think, “that’s just one cranky person,” and i get distracted doing science that is killing ecology (Given the plethora of opinions about what is ruining our field, odds are you too are killing ecology, regardless of what type of science you do). But as these opinion pieces keep emerging, I have increasingly come to feel that these debates on the ‘best’ approach reflect a very limited view of the scientific endeavor.  Every approach (field ecology, microcosms, theory, meta-analysis, macroecology, insert your favorite approach that I’ve missed here) is fundamentally limited in its scope, focus, and ability to divine answers from nature, yet has unique strengths in what it allows us to do. Theory is abstracted from nature, but can also provide a concrete set of expectations and processes for empiricists to work with. Microcosms, while similarly critiqued for their abstraction from reality, can also give the clearest indication about whether ideas and theories work (or don’t) under the most ideal scenarios. Field ecology (particularly experimental manipulation) has been considered the gold standard for its ability to show cause and effect in ‘real’ ecosystems, but it is also messy, expensive, time-consuming (I say this thinking of my own field site, perhaps yours is less so) and in a natural setting it is impossible to have control over all of the important (and potentially confounding) variables. Macroecology and meta-analysis allow us to step back from individual systems and taxa to ask whether patterns and processes are general across nature, general within certain subsets of systems, or unpredictably important (and unimportant). However they lack the ability to manipulate nature directly to tease out cause and effect more definitively. Because all approaches have limitations, the exclusive use of any one approach is guaranteed to give us a limited and possibly flawed view of reality. In the scientific utopia that lives in my head, these different approaches to addressing scientific questions live together harmoniously, results from one approach generate questions best addressed with another approach and the cumulative evidence from all approaches give us a more complete understanding of nature. When I read opinion pieces that advocate for a particular approach above all others, I worry that this utopia only exists in my head. After all, those opinion pieces never seem to be balanced by a counter argument  for plurality. But then sometimes I read things – often on the internet – and I think: it may be in my head, but maybe my head is not the only one that dream resides in.

Bridging, not building, divides in ecology [Things you should read]

There is an excellent post over at EEB & Flow on the empirical divide,inspired by an editorial by David Lindenmayer and Gene Likens in the most recent ESA Bulletin, titled “Losing the Culture of Ecology”. It was great to see some thoughtful and data driven consideration of the idea that we should choose to emphasize one broad area of ecology over another. I really like their conclusion that these “divides” are really driven by other things:

The tensions between “indoor ecology” and field ecology have been conflated with changes in the philosophy of modern ecology, in the difficulties of obtaining funding and publishing as a modern ecologist, and some degree of thinking the “grass is always greener” in the other field. In fact, the empirical divide may not be as wide as is often suggested.

This post motivated some discussion in the comments, and on Twitter,




And a nice follow up post by Jeremy Fox at the Oikos blog.

It’s all pretty short and well worth the read.

The Ecological Data Wiki

Here at Weecology we’re really into open science and that’s why we’re excited to announce our first serious attempt to facilitate open science beyond the confines of our own research – The Ecological Data Wiki.

The idea behind this project is simple. There is a large and rapidly increasing amount of ecology related data available thanks to initiatives sponsoring the collection of large-scale data and efforts to increase the publication of already collected datasets. As a result, progress in ecology is increasingly limited by the speed at which we can find and use existing data. The Ecological Data Wiki is intended to serve as a central source for identifying datasets that are useful to the study of ecology and quickly figuring out the best ways to use them. The idea is to use the knowlege and effort of the entire ecological community to compile this information rather than relying on each scientist to contribute information for their own studies. Just think of it as the Wikipedia of ecology data.

We’re just getting things off the ground, but we’d love it if you’d come by, take a look around, and if you think you can be of help sign up, learn how to get started, and contribute. We’re currently in private beta, but you can generally expect to have an account activated within about 24 hours.

Let us know what you think about the site and any suggestions you have in the comments. If you’d like to chat about the wiki (or anything else) in person, Ethan will be presenting on this during the Wednesday poster session at ESA.

Michael Nielsen on the importance and value of Open Science

We are pretty excited about what modern technology can do for science and in particular the potential for increasingly rapid sharing of, and collaboration on, data and ideas. It’s the big picture that explains why we like to blog, tweet, publish data and code, and we’ve benefited greatly from others who do the same. So, when we saw this great talk by Michael Nielsen about Open Science, we just had to share.

(via, appropriately enough, @gvwilson and @TEDxWaterloo on Twitter)

Why computer labs should never be controlled by individual colleges/departments

Some time ago in academia we realized that it didn’t make sense for individual scientists or even entire departments to maintain their own high performance computing resources. Use of these resources by an individual is intensive, but sporadic, and maintenance of the resources is expensive [1] so the universities soon realized they were better off having centralized high performance computing centers so that computing resources were available when needed and the averaging effects of having large numbers of individuals using the same computers meant that the machines didn’t spend much time sitting idle. This was obviously a smart decision.

So, why haven’t universities been smart enough to centralize an even more valuable computational resource, their computer labs?

As any student of Software Carpentry will tell you, it is far more important to be able to program well than it is to have access to a really large high performance computing center. This means that the most important computational resource a university has is the classes that teach their students how to program, and the computer labs on which they rely.

At my university [2] all of the computer labs on campus are controlled by either individual departments or individual colleges. This means that if you want to teach a class in one of them you can’t request it as a room through the normal scheduling process, you have to ask the cognizant university fiefdom for permission. This wouldn’t be a huge issue, except that in my experience the answer is typically a resounding no. And it’s not a “no, where really sorry but the classroom is booked solid with our own classes,” it’s “no, that computer lab is ours, good luck” [3].

And this means that we end up wasting a lot of expensive university resources. For example, last year I taught in a computer lab “owned” by another college [4]. I taught in the second class slot of a four slot afternoon. In the slot before my class there was a class that used the room about four times during the semester (out of 48 class periods). There were no classes in the other two afternoon slots [5]. That means that classes were being taught in the lab only 27% of the time or 2% of the time if I hadn’t been granted an exception to use the lab [6].

Since computing skills are increasingly critical to many areas of science (and everything else for that matter) this territoriality with respect to computer labs means that they proliferate across campus. The departments/colleges of Computer Science, Engineering, Social Sciences, Natural Resources and Biology [7] all end up creating and maintaining their own computer labs, and those labs end up sitting empty (or being used by students to send email) most of the time. This is horrifyingly inefficient in an era where funds for higher education are increasingly hard to come by and where technology turns over at an ever increasing rate. Which [8] brings me to the title of this post. The solution to this problem is for universities to stop allowing computer labs to be controlled by individual colleges/departments in exactly the same way that most classrooms are not controlled by colleges/departments. Most universities have a central unit that schedules classrooms and classes are fit into the available spaces. There is of course a highly justified bias to putting classes in the buildings of the cognizant department, but large classes in particular may very well not be in the department’s building. It works this way because if it didn’t then the university would be wasting huge amounts of space having one or more lecture halls in every department, even if they were only needed a few hours a week. The same issue applies to computer labs, only they are also packed full of expensive electronics. So please universities, for the love of all that is good and right and simply fiscally sound in the world, start treating computer labs like what they are: really valuable and expensive classrooms.


[1] Think of a single scientist who keeps 10 expensive computers, only uses them a total of 1-2 months per year, but when he does the 10 computers aren’t really enough so he has to wait a long time to finish the analysis.

[2] And I think the point I’m about to make is generally true; at least it has been at several other universities I’ve worked over the years.

[3] Or in some cases something more like “Frak you. You fraking biologists have no fraking right to teach anyone a fraking thing about fraking computers.” Needless to say, the individual in question wasn’t actually saying frak, but this is a family blog.

[4] As a result of a personal favor done for one administrator by another administrator.

[5] I know because I took advantage of this to hold my office hours in the computer lab following class.

[6] To be fair it should be noted that this and other computer labs are often used by students for doing homework (along with other less educationally oriented activities) when classes are not using the rooms, but in this case the classroom was a small part of a much larger lab and since I never witnessed the non-classroom portion of the lab being filled to capacity, the argument stands.

[7] etc., etc., etc.

[8] finally…

Postdoc position in Jim Brown’s group studying the major patterns of biodiversity

There is a new postdoctoral research position available in Jim Brown’s lab at the University of New Mexico to study some of the major patterns of biodiversity. We know a bit about the research and it’s going to be an awesome project with a bunch of incredibly bright people involved. Jim’s lab is also one of the most intellectually stimulating and supportive environments that you could possibly work in. Seriously, if you are even remotely qualified then you should apply for this position. We’re both thinking about applying and we already have faculty positions :). Here’s the full ad:

The Department of Biology at the University of New Mexico is seeking applications for a post-doc position in ecology/biodiversity. The post doc will be expected to play a major role in a multi-investigator, multi- institutional project supported by a four-year NSF Macrosystems Ecology grant. The research will focus on metabolic processes underlying the major patterns of biodiversity, especially in pervasive temperature dependence and requires a demonstrated working knowledge of theory, mathematical and computer
modeling skills.

Applicants must have a Ph.D. in ecology or a related discipline.

Review begins with the first applications and continues until the position is filled. Applicants must submit a cover letter and a curriculum vitae along with at least three phone numbers of references, three letters of recommendation and PDF’s of relevant preprints and publications to be sent directly to ecohire@unm.edu attn: James Brown. Application materials must be received by July 25, 2011, for best consideration.

Questions related to this posting may be directed to Dr. James Brown at ecohire@unm.edu or to Katherine Thannisch at kthannis@unm.edu.

The University of New Mexico is an Equal Opportunity/Affirmative Action Employer and Educator. Women and underrepresented minorities are encouraged to apply.

How far we have come in communicating and discussing science

When I started graduate school (a little over a decade ago):

  1. Online literature searching was just becoming common
  2. You had to mail your manuscripts to the journals in triplicate
  3. Responses to published articles (when they happened) took a year or more. Mostly people just talked about problems they saw (or thought they saw) with people in neighboring offices.


  1. A paper is published
  2. Within hours a member of our group posts it to the “Papers of the week” page on our wiki [1]
  3.  A few hours later another member of our group posts a comment saying “Hey, there’s something about this that doesn’t make sense to me” and then a day later posts again to say that they are pretty convinced that something doesn’t add up [2]
  4. A few days/weeks [3] later I’m traveling and on the train ride from the airport to my hotel I take out my phone, open up twitter, and see a tweet, that is pointing to a blog post, that purports to show proof that the paper is wrong


Now, I still haven’t read the paper, and so I have no idea who’s right or what’s wrong [4]. And of course this sort of thing has been discussed extensively in relationship to #arseniclife. But there was something about the fact that it was happening in ecology, in an area of research that I was professionally interested in, that really brought home to me how far we’ve come in last decade [5].


[1] I think – “I really should read that”

[2] I put it on my To Do list to read the paper once I get back from an upcoming trip and, since I’m apparently already out of touch at the tender age of 34, think – “If there’s really something there we’ll have to think about righting a response” (It never occurs to me to do anything other than write up something formal and send it to the journal)

[3] Who can keep track really

[4] Which is why I haven’t actually linked any of this to the paper/posts/tweets in question. This post is really about the process, not the science.

[5] And then just to drive the point fully home, after I dropped off my stuff I picked up my phone, hit the Nearby button on Yelp, found great Chinese food a quarter of a mile away, had the GPS walk me there, came back, enjoyed a video call with my daughter, and then fired up WordPress to post about my day. Before bed I’m going to go for a quick trip in my flying car.

You don’t become great by trying to be great

xkcd comic 896

xkcd does it again. Just plain awesome.