Fun with Tilt-Shifting

This is totally off subject, but I found a site that allows you to modify your jpegs to simulate tilt-shift photography. If you’ve never heard of this, it’s the process of simulating a narrow depth of field and saturating the color to produce an image that looks like a miniature. It works best on scenery that contains many small elements like vehicles or buildings photographed from above. This is going to change the way I take pictures!

Nice Port from Castle Hill:

Nice from Castle Hill:

Nice shoreline from Castle Hill:

Port of Fontvielle, Monte Carlo, from Monaco-ville:

Monte Carlo from Palace Square:

Inland Menton:

Menton:

Academia.edu loosens up

Academia.edu is addressing issues of apparent bias:

I had a bit of correspondence with Richard Price at Academia.edu who assures me that the concerns about some scientists not being eligible to join is not valid. Here are some parts of our correspondence, which I have rearranged to make it more coherent, and added some comments in square brackets:

“We do encourage researchers in government labs to sign up. They can add their government lab as a university. Los Alamos National Laboratory is on Academia.edu at http://lanl.academia.edu/…We are going to make it clearer on the registration form that other institutions are welcomed too…Anyone is welcome to join as an independent researcher. Currently they have to type in ‘Independent Researcher’ into the University box on the sign up form.”

He also made it clear that they are revising their forms to make these provisions clearer.

Bill Silvert – Posted to Ecolog

I’ll check in with them soon to see if any changes have been implemeted.

Academia.edu and online professional isolationism

I recently discovered Academia.edu, an online social network that “helps academics answer the question ‘Who’s researching what?’”. I’ve blogged about how scientists are behind the online social networking curve before, and numbers back up my observations, so I was interested to see if this network might help. I don’t think it does.

Let’s start with the name. The name and mission don’t match, implying non-academic research doesn’t count. It’s clear the creators haven’t thought of federal and other government scientists, not to mention non-government organizations, and consulting firms that publish. I say that because the structure of the network is based on placing yourself within Universities and then Departments. You can be a faculty, post-doc, graduate student, or other. So where do I fit?

The best I can do is enter “United States Environmental Protection Agency” as a university. The department is less clear. For better or worse, this is where I fit in the Agency: Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Ecological Exposure Research Division, Ecosystem Research Branch. And yes, each level has a manager. If the agency is analagous to a university, then ORD is analagous to a college, and thus not included in the site’s hierarchy. But is the lab or division analagous to a department? I’ve gone with the lab as a department. Better would be to change “University” to the more general “Institution”, and add levels of organization to the hierarchy. “Faculty” could be changed to “Primary Investigator”.

Online social networks are only useful if people you want to connect with are also part. This represents a fundamental problem for such sites, i.e. many people will join only after a critical threshold of apparent usefulness is reached, but you can’t get there unless people join. Moreover, people use networks for different purposes, confusing their utility. I, for example, reserve Facebook for friends and family, and use LinkedIn for professional contacts, whereas some use Facebook for business contacts, and other just collect “friends” as a hobby. The problem with LinkedIn for me as a scientist has been the relatively low number of scientist-members, hence the critical-threshold problem for colleagues who see little use for it or other online social networks. This is supremely ironic  because the internet’s primitive ancestor, the Arpanet, was created by researchers for researchers.

Academia.com might appear to be a solution, especially if many scientists join, but there is a cost. The site serves to preserve academic isolationism. If the apparent target audience joins and uses this social network to the exclusion of others, academics will have successfully created a virtual ivory tower. To be sure, no single online social network serves all purposes. Indeed, it will be many years, if ever, before competition among online social networks shakes out. After all, MySpace, once king among kids, appears to be seriously faltering. What then should one do? We have a few choices: join nothing, join everything, or join selectively. If teh internets scares you, by all means join nothing. But neither can anyone be expected to join everything. So the logical course of action is to experiment with a few selected networks and see what develops. Indeed, site development is a dynamic process occurring between site administrators and the membership, so you can influence the process by participating. Joining only one, especially academia.com, will only serve to isolate you and scientists in general. In an age where science is highly relevant to our daily lives, yet where funding is not keeping pace, and scientific illiteracy abounds, online isolationism is the last thing the scientific community needs.

I advocate for LinkedIn because of its features, because certain critical thresholds have already be crossed namely popularity among non-scientific professionals, and because we need to engage this community. Therefore we’d be better served by adding scientific functionality to existing networks, through the creation of scientifically oriented widgets for example, than building new networks.

WordPress does not allow the Research Blogging widget

I tried adding the Research Blogging widget to this blog by pasting the html code generated by ResearchBlogging.org into the text widget, but the code just kept disappearing every time I hit ’save’. It turns out that wordpress is very skittish about the html it will allow, fearing java script hacks.

ResearchBlogging.org said:

I believe the reason is that WordPress.com prohibits outside advertisements. Since our widget uses the iFrame HTML code frequently used for ads (and indeed we do plan on using it to serve small ads to support our service), it’s not allowed on WordPress.com

Solution: Add the RSS feed.

WordPress media wierdness

I’m having problems with WordPress’ management of files, so my resumes will be not be available.  I’ll try to fix it as soon as possible.

Promising preliminary results

Perhaps my favorite step in the scientific process is exploring new data to see what you have. Depending on how risky a study is, the first exploration of results can be suspenseful. Did the pilot work?  Is that experimental method sound? I just got the first sets of data in from a project that aims to develop new methods for spatial analysis of source areas for water-borne materials in watersheds. The methods are experimental, so I knew there was risk going in.

The techniques to be developed are tools for spatially quantifying sources of materials causing downstream exposure, and terrestrial drivers of material contribution to rivers. Applied to desirable water quality parameters, resource shed analysis can assess sources of directional flow-related ecosystem services. Further, with resource sheds, source area identification is possible for water quality parameters measured at the mouth, rather than having to take multiple samples in different areas of the watershed, making the technique highly efficient. Extending the analysis beyond individual case studies, changes in spatial patterns of material contribution to surface water runoff could be evaluated over time. Seasonal patterns may exist. Resource shed analysis applied over extended time periods could assess how changes in land cover alter patterns of material loading.

Here, I am trying to see if there are areas that consistently and highly influence material loading. My scientific objective is to map the spatial distribution of the correlation between individual watershed cell contribution to total discharge, and material load exiting at the river mouth. I’m using resource sheds generated with the Distributed Large Basin Runoff model. This model divides watersheds into 1km^2 cells. The resource shed, or source area, for water exiting the river mouth is physically confined to the watershed, but because precipitation and cell drainage characteristics vary spatially, different areas of the watershed will contribute more or less to total discharge over time. Hence, if an area is a consistent source for material loading, I hypothesize, then that area will contribute more to discharge (be a more important part of the resource shed) when material loads are high. So, if it works, we should expect to see spatially coherent areas of correlation, including perhaps “hotspots” of high correlation. If it doesn’t work, then correlations should be uniformly low, or randomly distributed.

To initially explore this I’m using time-series water quality and contaminant data from the Heidelberg University National Center for Water Quality Research. They have continuous or extensive data sets, some sampled daily, of nutrients and pesticides collected from the mouths of several watersheds that drain into Lake Erie (Cuyahoga, Maumee, Sandusky) for which I have resource sheds. Spearman correlation between a cell’s contribution (determined by the resource shed) and material load (determined by the water quality data) over the course of a month (June 2008) in the Maumee River watershed were calculated. Each correlation was based on 30 points (one for each day of the month). Since the watershed has 17,000 cells, this process had to be automated.

The inital exploration shows that the method is sound. Illustrated below are the spatial distribution of spearman rank correlations of cell contribution and material load at the mouth for suspended solids, Total Phosphorus (TP), Total Kjeldahl Nitrogen (TKN), Chloride, soluble Reactive Phosphorus (SRP), and Nitrate-Nitrite, during June 2008. Correlations are non-randomly distributed, and differ between water quality parameters. Sub-basins are clearly visible. Total phosphorus and nitrogen are not independent of suspended solids, and so have similar patterns. SRP and nitrate-nitrite have a pattern somewhat opposite of suspended solids, e.g. compare the central and southern basins. There are some areas of very low or negative correlation consistent across several parameters.

All of this is very encouraging so I’ll be pressing on.

More on resource sheds:

Video of source areas through time

Intro to resource sheds

Selecting the right journal

Question: When does a paper get rejected?

Answer: When it’s reviewed as “interesting”, “thoughtful”, “provocative”, “original”, and “creative.”…but wrong for the journal.

I just got a manuscript accepted -on the third journal attempt. Now that it’s finally coming out, I can relax, look forward to the proofs, and ask…why did this take so damn long? In this case it boils down to finding the right venue for the material, and perhaps, requesting the right reviewers. The problem is that there’s no magic formula for deciding where to submit a manuscript. As an author, you have to weigh shooting for the best journal possible vs. the delay of being rejected and submitting to another journal. You have to consider the manuscript’s generality. You have to decide on your target audience. And of course we all want the most prestigious journal possible, or at least one with a good impact  factor (oh just admit it, we all think about that). This paper, “Development of resource shed delineation in aquatic ecosystems” was a bit problematic because it didn’t fit neatly into one subject. Or as I wrote in the first cover letter:

Our multi-disciplinary approach expands an ecological concept by using hydrology and oceanography. Hence our intended target audience is larger than that of a journal specialized in a single discipline (e.g. hydrology, limnology, or ecology). Moreover, due to numerous potential applications to ecological issues of high management priority, we intend to target a wide audience of applied ecologists and managers.

I figured Ecological Applications might be an appropriate venue, since it is “concerned broadly with the applications of ecological science to environmental problems.” They didn’t agree and sent it back without review. Okay, how about Limnology and Oceanography? I’ve published there twice as first author. They sent it out for review, and the comments weren’t bad. The manuscript could be shortened, okay…clarify this and that…right. No real problems that couldn’t be addressed in a re-write, but rejected. Looking closer I fixed on this comment: “Analysis/Interpretation – This seems ok, but I am not a modeler or a physical limnologist.” And there it is, I recommended the wrong reviewers.

To be fair, I probably tried to do too much in a single manuscript. You know, the usual: apply a concept from one discipline to another, introduce a new approach, argue for its use based on historical development of the field, present results, interpret them, and suggest a host of applications. I had also recommended reviewers that were more on the ecological and basic-science side. So trying again this time with Environmental Science and Technology I scaled the thing back and importantly, suggested reviewers more on the applied-science side. And, following a re-write, was finally successful.

BTW, this is the manuscript I wrote about concerning supplemental material. Ironically, in the re-write I reduced the scope in order to better focus the paper, eliminating supplementary material altogether. With the publication of this paper, and vetting of our application of the concept of resource shed in the peer-reviewed literature, we are now free to work on atlases of resource sheds in Lake Erie and Lake Ontario.

Art of the disclaimer

About a year or so ago, we EPA scientists learned that, from now on, all our scientific products had to have a disclaimer. This included papers, posters, presentations…even abstracts. The suggested text was, if I can remember correctly,  ”Disclaimer: Although reviewed and approved by EPA, this document does not necessarily reflect the policies or represent the official views of the Agency.” That’s a 23-word sentence. If you’re not familiar with the importance of word counts, most scientific documents have word limits, especially abstracts. So having to include 23 words is  a lot, especially when you only have 200 words to play with. But notice I said “suggested”. There’s no official disclaimer. So the question is, what’s the shortest disclaimer I can write?

“The views expressed are those of the author and do not necessarily reflect the views and policies of the Agency” =20 words, suggested by internal reviewer.

“Although this work was reviewed by USEPA and approved for publication, official Agency policy is not established herein” – 18 words.

“No Agency positions are established in this expression of the author’s views” – 12 words.

“Although reviewed and approved, this publication does not establish EPA policy”  - 11 words.

“This publication does not establish USEPA policy” – 7 words

“No agency policies are herein established” – 6 words

Some light shed on UK academic visitation

An explanation of the deportations provided by Highland Statistics Ltd.

The problem is that Prof Anderson is a non EU resident coming into the UK/EU for commercial work. And that is not allowed. Same rules apply in the US.

- Alain, Highland Statistics, Ltd., posted to Ecolog

More advice:

It depends on the country, but the general rule is that if you are getting any sort of remuneration, even an honorarium, you may need a business visa, or someone may decide you need a business visa once you get to immigration. Business visas are now frequently required by many countries if you are attending a scientific conference, even if you are not receiving anything. 

SO you can either research the situation and hope you get it right and get the visa in time (the U.S. is notoriously fickle and slow) or come in as a tourist and answer accordingly.  

There may be UNESCO guidelines on receiving support for conferences and on visas, but if so, no one seems to be following them.

- David Duffy, posted to Ecolog

 

Cartoonists with Ph.D.s are not welcome in the UK either

Concerning the UK deportation of scientists, apprently this happens to cartoonists with Ph.Ds too (see Oct 26).