Trial and terror (2)

Let’s hope at least one student picks out my proposed subject for his Bachelor dissertation… I just heard that the various research groups together handed in over 500 topics! I can’t really imagine how they will distribute these subjects to the students: each description is about half a printed page, so they need to print a 250 page catalogue! It’s totally insane, if you ask me… Sure, students need to be able to choose, but where’s the point in offering a choice between way too many subjects to even look at, let alone to read… It makes no sense at all. Educational Committee: do your job and cut the number of subjects to two per supervisor! That’ll leave the truly interesting subjects easier to notice Anyway, in the meantime, I designed my experiments, and once I get the equipment I’m ready to start testing the feasibility.

Trial and terror

If someone would like to get rid of an old, even coarse-resolution digital (whether or not SLR) camera, no matter in what condition as long as it’s still capable of taking pictures, I’m interested! That is, only at bottom prices, because it’s meant to be demolished by me to replace the hotmirror inside, to experiment with high quality ground or kite based NIR pictures. I’d reward you additionally by personally sending you the nicest resulting pictures in full resolution :-p

School playtime

Who said school playtime is exclusively for children? Think again – especially when a hobby is half your job.
As a teaching assistant, I needed to come up with some research topics for students with their Bachelor dissertation… Deadline: tomorrow! And as always with me: the first 10% of a task takes 90% of the time, and vice versa. I’ve got a serious problem with getting started, and so I keep on delaying everything until the deadline. Just by chatting about photography last night in a cafe, I suddenly had a great flash of inspiration: a feasibility study on in situ NIR photography (near-infrared photography) of intertidal seaweeds, to quantify stress (in casu: salinity and drought stress) based on changing photosynthetic pigment concentrations (well in this case, specifically chlorophyll). The general idea is old wine: I’ve been using NIR reflection with (marine) vegetation for a long time now, but always based on satellite imagery. However, a huge disadvantage of satellite imagery still is the coarse spatial resolution: it is useless when it comes to studying intertidal areas (at least with affordable imagery). So the new bottle (to me, at least), is an ordinary digital compact camera, provided with a NIR-pass filter (NPF) mounted on a filter adapter.
The school playtime really is to determine the feasibility of the feasibility study So again, long live Google, I came across some brilliant stuff! For a start, IR photography has widely been used in art, so photographic art blogs are a major source of information (see the high reflection, and hence the white color, on a gray scale, of the vegetation? This is what I want to study in seaweeds). Also, already the first hit in Google returned a personal website of a remote sensing specialist as an interesting starting point in the scientific field.
I also found out that I have the odds a bit against me, as my Canon Powershot A640 seems to be one of the types with a very strong internal IR cut filter, virtually unreachably placed just before the otherwise very IR sensitive sensor. I need to verify this tonight by aiming a remote control in action to my camera and determining whether or not I can see a light from the remote control in a dark room. I’ll also go and ask for the opinion of some professional photographers in a photo shop. Anyway, expect a more detailed technical post on how this turns out later on, as I think this may prove valuable information to others as well. It’s just exciting: playing with some fancy tools in a “scientific” context If this yields good results, I might start using it more often :-p

Talking about photography, in the end I did bring my camera to my desk to photograph some nice sunsets, but now I cursed myself because of the missed opportunity to photograph some amazing scenes of the quay at home in the fog last night, and some pictures of the snow at the waterside this morning… damn…

Maiken

Just found this great sailing blog by Fredrik Fransson and Håkan Larsson (listed under “links” as their blog has been inactive since their arrival) – no, not by simply randomly surfing the internet during working hours
I was browsing to the NASA’s OceanColor Web in search for information about their “.out” file type to import processed MODIS satellite imagery in a GIS (for those who care, apparently it’s just the same as HDF, or at least it works just fine with Idrisi’s HDF-Eos import tool). It’s been a long time since I last visited the OceanColor homepage, so I don’t know how long this particular topic has been online, but satellite imagery of a South Pacific volcano eruption was highlighted for general interest. A rarely seen phenomenon was mentioned in the caption: the plume of ash and pumice carried downstream at the sea surface. Already very well visible from space, and completely otherworldly when seen from a lonesome yacht in the pacific, as showed by the link to this blog. The post with the pictures ultimately received 259 comments!
However rare, this kind of experience is exactly what makes wandering the seas on a sailing yacht worth it. Seeing things that you wouldn’t if you’d stay at home or walk on the trails (or, in this case, take the crowded ferry lines from point a to point b in a fast, straight line). I’m sure there is plenty of other interesting stuff and pictures on their blog (for instance, swimming with the whales), of course I haven’t read it all yet, but I will. But for now, it is an excellent bit of publicity for those planning a sailing holiday. A bit more elaborate than my previous sailing experiences (see “unjealousing” and “blue“).

Scientific leisure diving

From: coral-list-bounces@coral.aoml.noaa.gov on behalf of Nathan T. Schwarck
Sent: Fri 1/26/2007 7:19 PM
To: coral-list@coral.aoml.noaa.gov
Subject: [Coral-List] American Academy of Underwater Sciences AnnualSymposium Invitation

All persons interested in underwater sciences or scientific diving are
invited to attend the American Academy of Underwater Sciences Annual
Symposium. This year’s symposium is hosted by the University of Miami’s
Rosenstiel School of Marine and Atmospheric Science in Miami, Florida; March
5-10, 2007. Scientists, Dive Safety Officers, students and diving
technicians are invited to contribute and present papers or posters
describing recent research, underwater research diving techniques and
technological developments related to scientific diving.

Hmm… This is typically the sort of symposium that people attend who always find an excuse to get paid for diving under the guise of science. Er… like me. But I won’t go; I seriously don’t think the international scientific diving community would appreciate my way of “scientific diving”, you know, like getting 24 cages of 20kg each up and down all the time on my own, or diving alone with someone snorkeling at the surface for “surface security”, or getting arrested for not having a diving flag marking the boat (that was cool! My first time taken into custody!). I’m actually quite lucky I’m a marine scientist in Belgium: the expensive “Scientific Diver Certificate” is not required here, but it is elsewhere, and it is almost always required to attend an international expedition. However, the reality of low-cost field research in the middle of nowhere differs enormously from the neat scientific missions organized by wealthy laboratories or research initiatives… And sadly, there’s no session on low-budget scientific diving in the symposium…
Anyway, if I get to dive again in Oman in the framework of a monitoring contract, I’m sure decent logistics and support in the field will also be assured, to the relief of certain people staying at home

Okay, enough cowboy-talk, to reassure you: I don’t do this kind of “rodeo-diving” deeper than 5m anyway, so there’s no need to worry.

Horse manure or not – remember to publish!

At least, that’s what my professor always says, referring to the wealth of papers published by our lab in the past, as opposed to the present lack of continuity in publications, caused by certain new, rather unproductive people (ahum). So although what he said had nothing to do with my blog, I decided to have a new start here, too – I must say other people urged me to do so as well. Well, a new year, a new blogger engine, a new start, sounds good I suppose…
Actually I’ve had thoughts about reorganizing my blog by splitting it into one related to my work as a would-be marine scientist, and one related to leisure and stuff. But on second thoughts apparently I haven’t always time (or interest) to maintain one blog, let alone two, and in any case it sometimes is a thin line between work and non-work, so let me stick to this one – just don’t expect me to publish every day… On the other hand, two blogs would have been an exciting opportunity to architect open-source, global partnerships as to implement integrated paradigms. In the longer run, I could even productize global applications and incentivize next-generation interactive functionalities. (This bullshit generator really IS brilliant!)

It’s actually not only a new start for my blog, I also started writing my first international scientific paper, since I’m about to finalize the remote sensing analyses and I was getting a bit tired of the (however righteous) insinuations made by my professor.

Pauly, K. et al. (2007, hopefully) High resolution superspectral satellite imagery: a new low-cost tool to map benthic macroalgal communities? Journal of Phycology xx (x), xxxx-xxxx.

Thinking of a proper journal was actually a tough call: papers focusing on the actual use of satellite sensors to map different kinds of seaweeds can be counted using only one hand (well, that’s exactly why I did it). It is far from top-quality research: people who saw my self-made “GPS-located video transects to ground-truth the image” will acknowledge that, so I can forget every journal with an impact factor above 3. On the other hand, I still want it to have an impact factor higher than 1 and preferably higher than 2… Then considering the scope, there wasn’t much choice left. Just to give you an idea: the impact factor of Nature and Science is above 30, meaning my work is at least 10 times more irrelevant than the general news-catching science. (Moreover, if this gets accepted after all, I WILL productize my open-source, low cost applications!) The writing should take no more than two months, the review process might take up to six or more. Every single word needs to be scrutinized… And to say that I had a complete scientific paper on informatics ready-made in just about 2 seconds…

Next projects: implementing remote sensing in phylogeny (*this is not bullshit*), and a long-term study of the impacts of the fertilizer plant in Oman, provided I’ll get the monitoring contract (there’s a good chance, but in Oman nothing is sure until it is established). A few months ago, I was criticized for my ecological research in general an my remote sensing research in particular because it puts me too far away from what the rest of the group does, and when I proposed the former project I was criticized because phylogenetic research would blur the “red line” troughout my PhD thesis. So about the last remark, for once and for all: “The ecology of macroalgal communities in the Arabian Seas, including the introduction of remote sensing as a new tool in phycological research.” How about that?!

Oh, by the way, can someone remind me to bring my camera to the lab? The sunsets are magnificent lately, and I have a keen interest in photographing sunsets!

A la recherche du temps perdu

Wow… I guess my blog has never been out for so long before… A whole month has gone by, a whole month during which I couldn’t find a minute of spare time to post something, although so much has happened I’m starting to wonder how I could ever catch up. I guess I’ll start by illustrating my previous posts with some pictures and then I’ll add further stories when I get to them by association of thoughts
In short, the last two weeks in Oman have been wonderful, interesting and fun, regardless the lack of comfort and hygiene (and even of sanitary water whatsoever during the last four days), Tom’s severe viral illness which made us visit a local Baghdad-like hospital and my day of food-caused cholera and typhus (a.k.a. traveller’s sickness). The latter can be easily overcome in a nice and clean western house, but being in a village with a temporary lack of water kind of obliged me to break my 500m sprinting record eacht time to the nearest 50cm high bush in the desert, if you see what I mean. Anyway, as I said, apart from that the last two weeks have been wonderful, interesting and fun!

What has been far less fun: my Stereo-II (satellite earth observation) project proposal got turned down… Since this was the only option for me to obtain independent funding and more adequate supervisors for my preferred PhD subject, I actually can’t see what to do in the future right now… I still know what to do during the current academic year: I have to supervise an MSc dissertation and I can work on at least three publications resulting from all the previous sampling campaigns, but I can only hope time will tell what to do after that. I’ve considered lots of options, varying from working as a marine ecologist in a commercial environmental impact assessment in Oman to starting something completely different, but of course it’s a way too early to make decisions. Let’s say I’ve got about 6 months to talk to some people and to explore various alternative routes.
To be continued… next season?

Eureka!

has finally managed to get their archive right – meaning all files have names, and guess what, all files even have the correct name! So I was finally able to download the missing satellite image of my research site acquired during winter, essential to develop a seasonal study. 5 months after date, but of course better late than never, as I was already starting to fear the image was lost in the chaos of their database… So instead of presenting the Ministry of Environment in Oman and the congress in Italy some nice finished results, I’ll have to stick to a preliminary exploration and complete the study after returning from Oman… Fair enough.

While the former organization is doing their utter best to mess up cherished datasets, automated real-time end products of processed data continue to find their way to the average man-with-the-moustache on the internet. By far the coolest example, especially in these thunderstorm-forsaken days, is this lightning detection tool. As I’m writing this, 4 major thunderstorms in and around Belgium are mercilessly barraging Earth and its inhabitants. Muhahahaha Another impressive example of live statistics are the worldometers. While you read this sentence, somewhere in the world 14 people die and 7000 metric tons of anthropogenic CO2 are released into the atmosphere… And lightning has hit the Earth almost 2500 times

The sky is not the limit

My satellite remote sensing research goes hand in hand with two huge developments in geography – a very exciting coincidence. First of all, remote sensing has left the strictly geographical field, and where remote sensing studies were carried out solely by geographical experts and focused mainly on technical aspects in the past (even when the subject was strictly biological), a wealth of remote sensing studies now relies heavily on biologists (or archaeologists or whatever) for data interpretation. Secondly, remote sensing software and GIS is getting widely available and straightforward to use. One of the leading examples today is Google Earth, incorporating several GIS layers and satellite imagery of different resolutions to offer a continuously browsable digital globe. I think we’re merely starting to see the potential of such freeware.

Look at this one: where molecular-phylogenetic studies created merely trees of life in the past, potentially linked with a database of sample localities whether or not plotted separately on a 2D map, Bill Piel now developed a tool allowing to plot phylogenetic trees on a Google Earth’s 3D globe, based on uploading a simple text file linking the studied specimens with their occurrence site. Think of the possibilities this creates! Not only will it allow for visually establishing hypotheses of geographical forcing mechanisms in evolution (vicariance, etc.), but this could potentially allow to include a 4th dimension: if the tree nodes can be dated, several globe layers could be added like an onion, showing the position of continents at several evolutionary nodes, thus helping to prove biogeographic hypotheses!

I’m sending in the mob, again…

: You had submitted an abstract for the 4th Wokshop when it was still scheduled for February 2006. We would like to request again your confirmation whether this abstract is still valid for consideration for the new workshop date 19-21 September.
In order to consider your abstract for the presentation planning, please confirm until the 26th July at latest the validity of the abstract. Additionally, could you please let us know which abstract is the correct one, as we received two versions: number 260005 or number 260116 – the titles are different but the text is the same.

Me: [bolds added to make my point here]
There seems to be some misunderstanding: in e-correspondance with B.H. on May 2 I already stated my submission was still valid. She added that she would just notify the conference team to keep the submitted abstract and I shouldn’t submit a new one.
As for the ambiguity between the abstracts 260005 and 260116 as you state, I recall only submitting one abstract, and I can only find one definite file on my computer; can I review these abstracts on the internet or could you show me the difference in titles?
One more thing: I’m still lacking some datasets, acquired in March. I found imagery of one of my research sites (Sur, Gulf of Oman) in the archive, but wrongly named SE_Australia (all of the three images of this site are named like this – fairly surprising, since “SE_Australia” is nowhere mentioned in my proposal or request). I found this by browsing all images in the archive potentially matching the acquisition dates I was looking for, since some have no names at all. However, I was still not able to locate the imagery of Mirbat (Dhofar, Arabian Sea, Oman) in the archive. I tried to access the released ftp server as adviced on May 3 through e-mail with B.H. several times, but didn’t succeed to gain access. Could you advice on this please?

: We are delighted to notify you that your submission (260005 ) for the upcoming 4th workshop from 19-21 September has been accepted as poster presentation.

So no word about the two titles anymore. There’s a good thing about that: they seem to have the ability to solve problems, created by themselves, on their own after all. But still no word about the missing imagery… What did I say about answering the goddamn question before? And of course my abstract is merely accepted as a poster presentation: without the lacking image I couldn’t fill 45 minutes to talk in the plenary session anyway (although I could fill 1,5 hour talking about the problems to aquire a f***** image in the first place)!

*Weary sigh*