BONUS PROJECTS' BLOGS
Below are the most recent entries in the BONUS projects' blogs. To read the entries of your favorite project, select it from the list on the left.
09.01.2018 08:12It’s not a time to be picky, and sprat knows it better (The view of a data scientist - BONUS BIO-C3 & BONUS INSPIRE)
Sprat and herring eat the same food, but should they compete, then the sprat will more likely win. That is because sprat is less picky about what it eats, and also more successful in finding its meal than herring. And the competition is tough, since food is limiting for both species these days in the Baltic Sea.
These were very shortly the main findings of the BONUS INSPIRE clupeid feeding survey in the summer of 2015, where >1500 fish were caught and cut open, to have a close look at what they had eaten.
09.01.2018 00:02EU competition seeks eco-tech innovations for a cleaner Baltic Sea! (BONUS RETURN)
29.11.2017 15:05Theoretical vs. empirical/applied approach (BONUS BALTICAPP - Race Against Eutrophication Blog)
It has become apparent for me recently that there is a great dividing between theoretical and empirical/applied approaches in science. Particularly in economics this dividing seems to be very strict. This was made clear to me when I started an Advanced Econometrics course in PhD program for Economics this fall. We were told that this course is purely theoretical and if there are anyone interested more in applied side of things they may consider hard if the course is too difficult for them. We were told that particularly PhD students in so called applied sciences should probably dismiss. I decided to not to dismiss and it was a good call since so far studies have been going well, although I’m definitely an applied researcher and as such not a “real” researcher, as it was made clear to us.
Ever since I’ve been thinking about this division and classification of the researchers. In my opinion theoretical and applied sides are both rather important. It is clear that there has to be solid theory behind an applied work. But it appears equally clear that good theory is worth of nothing if there is no empirical evidence to support the theory or if there is no application for the theory. In addition, new ideas for theory development may originate form surprising empirical findings. Also, applied work may show that the theory does not hold in practice. Therefore, it seems that there is justification for both sides and those can actually benefit from each other.
Thus, it seems rather counterintuitive that theoretical researchers don’t give much appreciation for applied researchers. In econometrics and statistics this might have something to do with the fact that the methods are often applied in a bad manner and important theoretical aspects are ignored. If theoretical researcher reads such empirical paper that is published in a journal, it is understandable that the theoretical researcher becomes upset and feels that his/hers work is not understood.
In many cases and in many papers statistics are done wrong. The problem might be that statistical and econometrics courses are typically either strictly theoretical or strictly applied. Then we learn advanced theoretical things in one course and some examples and some coding on another course. The problem is that the connection between theory and the empirical application might be left incomplete, to say at least. For example, in our Advanced Econometrics course we struggle mostly with the proofs of the theorems. We have learned how to derive distributions of the test statistics and to show the asymptotic consistency of the parameter. But how to apply these learnings with the real data? In the other hand, I took another course that was purely applied. There we were given some data and some codes and examples, but the theory behind the examples was not discussed at all. A good course would really combine these two worlds, because clearly those are not separate.
I don’t how is the situation in other fields, but at least in Economics I see an opportunity for improvement in how theoretical and applied sides of science should be thought. This would narrow the gap between the field work and work that is done in theory labs. It would probably decrease the hatred between the deputies of the sides. Also the books should entertain the theoretical justifications and empirical applications to really show the students/researchers how the theory is applied correctly to real data.Best regards, Matti Sihvonen
27.11.2017 11:07New COCOA publication (Sources & Sinks: A Tale of Coastal Biogeochemistry - BONUS COCOA)
Myself and co-workers measured the removal of riverine nitrate via the processes denitrification and anammox in the sandy and muddy sediments of the oligotrophic Öre Estuary at the Swedish coast of the Quark Strait, Northern Baltic Sea. Estuaries are generally assumed to be sinks of the land-derived, riverine load of nutrients and organic matter and thus hotspots of the "coastal filter". We found that the Öre Estuary gradually removes most of the riverine nitrate long after peak loading, after temporary "trapping" in phytoplankton biomass. Read the full story here:
Hellemann D, Tallberg P, Bartl I, Voss M, Hietanen S (2017) Denitrification in an oligotrophic estuary: a delayed sink for riverine nitrate. Marine Ecology Progress Series 583:63-80. http://www.int-res.com/articles/meps_oa/m583p063.pdf
06.11.2017 20:55New Dr. in COCOA! (Sources & Sinks: A Tale of Coastal Biogeochemistry - BONUS COCOA)
....and hence is from now on Dr. Bartl!
During her PhD, supervised by Maren Voss, Ines sailed both stormy and calm waters of the southern and northern Baltic Sea and spent hours, days and nights in cold rooms, spiking water samples from the benthic boundary layer with nitrogen tracer, followed by filtering, filtering and...filtering.
21.09.2017 19:28New COCOA publications out! (Sources & Sinks: A Tale of Coastal Biogeochemistry - BONUS COCOA)
and co-authors investigated the erodibility potential of coastal sediments and identified
regulating key factors of sediment resuspension. The study took place at the South-Western
Finnish Archipelago coast, which offers a divers habitat of different sediment
types. Measurements were done with a core based erosion device (EROMES) at the
Tväminne Zoological Station. The full
study and all interesting outcomes can be found here:
Pilditch AC, Harris R, Hietanen S, Pettersson H, Norkko A (2017) Sediment
properties, biota, and local habitat structure explain variation in the
erodibility of coastal sediments. Limnology and Oceanography, doi:10.1002/lno.10622.
and co-authors estimated the filter function of Baltic Sea coastal sediments for
the elements nitrogen (N) and phosphorus (P), i.e. they calculated how much N and
P is permanently removed from the coastal Baltic water column via benthic denitrification
and burial, respectively. For this, they compiled and analyzed published removal
rates of N and P from around the Baltic Sea coastline and could, for instance, identify
key environmental factors for the regulation of N and P in the coastal filter. For more on this and the main outcome (no spoiler here) please look at:
Asmala E, Carstensen J, Conley DJ, Slomp CP, Stadmark J, Voss M (2017) Efficiency of the coastal filter: Nitrogen and phosphorus removal in the Baltic Sea. Limnology and Oceanography.doi:10.1002/lno.10644
Excellent Baltic Sea must-reads for the long autumn evenings!
01.08.2017 22:23Equipment explained: part IV - the HAPS corer (Sources & Sinks: A Tale of Coastal Biogeochemistry - BONUS COCOA)
This post might as well be entitled “Ode to HAPS”. For one thing, the HAPS corer is by far my favorite sediment sampler, clearly deserving of being sung about. For another thing, it already has been (cruise internally) sung about, showing that not only I have a personal affection for it, but that it is popular among several COCOA people (aka the HAPS gang).
So what is this HAPS sampler and what is so special about it?
The HAPS is a sediment corer for coarse sediments, i.e. sands. The tricky parts with sand sediments are that they are quite hard and sturdy, and that they have big pores, which impose only weak cohesive forces onto the pore water. This can result in water actually flowing through the pore space of sand (advective pore water flow), which has everyone experienced who ever saw a wave washing up a beach…and then disappearing into the sand under the own feet.
Pore water flow has huge implications for organic matter turnover, sediment biogeochemistry, and general elemental cycling- however, in terms of sampling, it means particularly one thing: how not to lose the pore water during core retrieval, if it´s so mobile? (In more plain words: pore water flow in sand is scientifically and ecologically really cool stuff, but it does add a challenging element to undisturbed sampling of sand sediments).
Luckily, there is the HAPS!
We wondered for years, what its name stands for (maybe “happy and prosperous sampling”?!), until getting the answer from the inventors themselves (Kanneworff & Nicolaisen 1973): apparently, “haps” is a Danish exclamation used when something is grasped very quickly. And that´s exactly what the HAPS does: after coring, a tight top lid keeps the sediment in the core, and during core retrieval, a super sharp, quick and tight shovel cuts immediately under the sediment core, so that pore waters are kept where they belong- in the sediment. However, never forget to use the core lid, otherwise also the super quick shovel does not help in holding any sample (*learned from experience*).
This sounds like basic sediment coring theory. Yet, the difference of the HAPS to e.g. the GEMAX corer is its weight, its stability and the speed of its closing mechanism.
Like the GEMAX (Equipment explained: part II - the GEMAX / GEMINI corer), HAPS is basically a gravity corer, i.e. it cuts into the sediment based on its own weight. But even if GEMAX does feel heavy when loading it onto the ship, it is too light to be able to cut into sand sediment. Plus, sands are usually located in high energy environments (too turbulent for finer particles to settle), where samplers need to be heavy to go down the water column and onto the sediment surface without being drifted away. The net weight of a HAPS corer is ~ 100 kg, which can be added up by additional 60 kg of lead weights, and a square bottom frame supports high stability at the sea floor. It is made out of stainless steel, including the core barrel and the closing shovel, which are both sharpened for uncompromising sediment penetration. If the weight of a fully loaded sampler should still be too light to penetrate the sediment, it can be equipped with a powerful vibrator unit. Insider tip: don´t drive it for too long, you might anchor yourself in the seafloor.
Undisturbed samples are easily to be seen in the clear water phase on top of the sediment, which during our sampling at the Finnish coast sometimes also included Saduria sp., having been surprised by the quick sampling (Killing in the name of).
Well, HAPS got its name for a reason.
20.07.2017 12:00EAERE 2017 (BONUS BALTICAPP - Race Against Eutrophication Blog)
In this blog I will tell about the EAERE conference held in Athens. First I must emphasize that it was really hot out there. I have never experienced such a hot temperatures (35-45 degrees) in my life before. Luckily the air conditioning worked just well in the conference places and all the other facilities were also very well handled. Overall the conference was a good and learning experience. I witnessed some great presentations and speeches. I guess that the best presentations (among those I saw) focused on micro-econometric data analysis and intertemporal optimization. I guess that it was particularly beneficial to see the overall level and current trends in environmental economics. It appears that macro models and everything related to climate change is now cool. Also behavioral and network economics appear to be very hot fields right now. My subject of interest, namely empirical agricultural production analysis and agri-environmental modelling seems rather uninteresting subject currently, to say at least. But that’s ok, I keep calm and continue working with my PhD anyway. At least I am still excited about it (now that I’m working with the second paper)!
There was also one very good plenary speech, which handled multiple layers of uncertainty, including model selection uncertainty. I found this particularly interesting, of course, because I have been struggling with uncertainty (regarding particularly model selection) issues for so long time now. I actually started to loose my interest in structural uncertainty entirely. But now it seems that it might actually be the key to get my first paper published. I got this idea that perhaps I should reframe the problem so that the focus is, again, shifted to these structural uncertainty issues within the optimization problem. It would be absolutely perfect if I could find a way to formulate the profit maximization problem analytically so that the parametric and model selection uncertainty would be taken into account explicitly. This, however, might be very challenging and perhaps beyond my abilities, given the time limits at least. But in any case, I should stress the structural uncertainty, because it appears to be generally interesting topic after all; for a moment I thought I was the last person on earth interested in it.
My presentation in the conference went just fine. Needless to say I was very nervous about it. The audience wasn’t large, which was just fine. One reason for the lack of audience, among the fact that nobody is generally interest in empirically bio-economic modelling in the context of agriculture (or fertilizers (!)), might have been that it was a last parallel session before the dinner and the busses started to leave just after the session. I guess most of the people went to hotel to rest and get ready for the evening. Anyway, I got some comments for some Chinese senior researcher, which was very nice, although I couldn’t understand her comments at the moment, because of the very challenging accent. However, after reprocessing the echoes in my ears for a while I understood what she said. Anyway, the comments were very trivial and I’m a little bit upset that I couldn’t respond to those at the moment, but better luck next time perhaps. I also was a discussant for a one presentation in our session. I think it went well and the situation resolved rather nicely in the end. The dinner, by the way, was great and we had very good time. Even the head master of the Greek bank was there to give his speech, which was super funny (the speech I mean).
I must say that I didn’t seize the opportunity to network with foreign people at all, which was a little bit unfortunate. The thing is that there was such a huge amount of Finnish environmental economists there that most of the time we just chatted with each other in some isolated corner. And during the dinner we also had Finnish tables. Luckily some German researches shared a table with us in the end. Thus, some international communications did take place, but not much. Anyway, it was a very nice event and all. I really hope that I could participate the next one also (which will be held in Gothenburg), but it will be much more unlikely because it will be a world conference so the competition will be much tougher. I know for a fact that the second paper will be much more interesting in terms of environmental economics than the first one, but will it be enough, remains to be seen. It would be nice to see the Gothenburg because it is capital if Scandinavian Heavy Metal!
Thus, Rock on and see you next month!
Bets regards: Matti Sihvonen
05.07.2017 15:03How can Sweden bridge the gap between innovation and commercialisation in the Baltics? (BONUS RETURN)
04.07.2017 21:57An affair of the heart (Sources & Sinks: A Tale of Coastal Biogeochemistry - BONUS COCOA)
And here it comes: my drawing turned out to be dominated by hearts. Hearts around N2. In relationship with a gas? Well, that does solve the problem of “plus avec” invitations via “take a breath of air”, but of course there was also a deeper meaning in using the symbols. Take a look at the drawing / bar-scribble, for better understanding re-coloured:
The 30 sec explanatory
talk went somewhere along the lines of....
“The Baltic Sea in northern Europe has too
many nutrients, mostly nitrate, which leads to algae blooms (--> green scribble) and oxygen
deficiency, so the sea is in bad ecological condition (--> sad smiley). The only way to remove
nitrogen from an aquatic ecosystem is via denitrification and anammox, which
results in N2 that goes into the air (--> that´s good *at least in a
eutrophic system* --> HEARTS). Estuaries are recognized as potential
hot spots of nitrogen removal and these are the 3 estuaries I looked at.“ FULL
STOP and a deep breath.
Don´t put me down on scientific spotless accuracy, but nevertheless, my piece of art & speech was convincing enough to score second place. Now I am proud owner of a new coffee cup.
The conference was rounded up by a hike in the national park Bic at the St. Lawrence Stream on World Ocean Day, strengthening our attachment to the biggest estuary of the world.
Thanks UQAR for organizing such an interesting symposium!
29.06.2017 12:36Engaging cities and municipalities to clean up the Baltic Sea (BONUS RETURN)
26.06.2017 20:10Most of the Baltic zooplankton is specialized on small food (The view of a data scientist - BONUS BIO-C3 & BONUS INSPIRE)
22.06.2017 16:09Keep calm and listening the Kocinka (Storm in a teacup - water is everywhere BONUS SOILS2SEA)
Hi to all very busy people,
swiming aginst main stream of life in neverending haste, I want to invite you to relax on the Kocinka side.
It takes ONLY one minute...
Pictures from last field trip - June 2017:
20.06.2017 10:45BONUS RETURN kicks off (BONUS RETURN)
A new EU funded project aimed at turning waste into profit officially kicked off in Sweden with a conference on 19th and 20th June at Sånga Säby. Members from Sweden, Finland and Poland, gathered in the north of Stockholm to set strategies for the three-year long project.
05.06.2017 09:26Upsides and downsides, mostly downsides.. (BONUS BALTICAPP - Race Against Eutrophication Blog)
We had a very interesting PhD course on econometrics in Bergen Norway. We were introduced to modern methods of empirical data analysis including instrumental variables, differences-in-differences and regression discontinuity. The topics of the examples were from environmental and resource economics and included themes such as relationships between conflicts and resource discoveries, price shocks and civil conflicts, the political resource curses and environmental speed limits in Oslo. The course took three days. During the visit in Bergen we also got an opportunity to explore the beautiful city (or village). The surrounding mountains were particularly impressive. It also became apparent that the Bergen is a rather rainy place; there is approx. 300 rainy days a year, we were told. It also became clear that Norway is a very expensive country. The oil money seems to increase the prices beyond the level that at least we Finnish people would consider reasonable. The get the points from the course we have to hand in a home assignment by the end of the September. In this assignment we are asked to get some data related to our PhD research and to explore the data via some method introduced in the course. Then we are asked to write a paper about the data, method applied and the results. Thus, if data are good, one could expand this home assignment to a real paper. This is of course what I am planning to do if I get good data. Therefore the quest for data is now one of the priorities during the summer. I was thinking about data regarding some policy or regional shift. Thus, for example, data could be about an effect of a subsidy policy on different agricultural regions. Then I could apply regression discontinuity method for the data analysis.
We also had another PhD course, namely a project management course. However, although the lecturer was very good and inspirational person, I did not found the course very useful. I took it mostly as a language improving exercise than anything else since I have no interests in project management or managing in general. Of course it is useful to be able to manage ones own work but I don’t think that getting a course on that is very useful. Anyway, I’m sure that some participants did found the course useful and we did have some delightful conversations during the course.
There was also a third PhD course, namely Economic Growth and Natural Resources. We had to hand in some home assignments and then there was an exam. This was very interesting course because the topic was in the field of macroeconomics, which I am not familiar with. Therefore it was good introduction to the unexamined territory. Macroeconomics is good for environmental economist because most of the macroeconomic analysis is dynamic. Therefore I might take another macro course in September, which focuses on dynamic optimisation methods. I think it might be particularly useful for me.
It has also become clear that to publish a paper is rather hard task. We got a refusal from a first journal because “the article did not fit the scope of the journal”. The refusal, however, might have been a fortunate thing because the journal, namely the Environmental modelling and software, was probably not a good journal for the article because in the first paper we did not model any environmental aspects. The first paper discussed simply agricultural system consisting of nitrogen and phosphorus yield responses and the development of soil phosphorus. Therefore the scope of the article is clearly agriculture and not environment, although those two scopes are quite related. Only after the refusal I started to understand that the scope of the journal is rather important thing. I started to examine the potential journals for our paper. During this examination I realised that our paper is kind of a weird mixture of data analysis and optimisation. Therefore it might be difficult to find a journal that would consider the paper a good fit for the scope. Anyway, I did submit the paper for another journal and I am now waiting for a refusal or some other answer. I just hope that it will be accepted to some journal since the second paper is a direct extension for the first paper.
The refusal also reminded me of the saying of Hannu Vartiainen after the first Microeconomic lecture: “the PhD work consists of upsides and downsides, mostly downsides”. It certainly is so that the work has been mostly downsides and there have been times when I have considered calling my model a setback-model because there have been so many setbacks down the road.
The second, and actually the most important priority during this summer, is to get a second paper ready. I have been working on it now rather intensively and I think it is coming together quite nicely. So far the analysis has been theoretical, which is a nice change from a mainly empirical and numerical analysis carried out in previous paper. However, the next step is to include leaching functions for nitrogen and phosphorus into the numerical analysis. Therefore the scope is wider in this paper since it will discuss agricultural and environmental aspects via bio-economic modelling. As such the second paper will most likely be easier to sell to journal (compared to the first paper). But, it remains to be seen.
Meanwhile, we still wait for the summer to start here in Finland.
See you next time,
Best regards: Matti Sihvonen
18.05.2017 10:42Full of the joys of spring and springs (Storm in a teacup - water is everywhere BONUS SOILS2SEA)
In the fieldwork the most important is ... smile, thermos and Occupational Health and Safety :)
15.05.2017 16:20BONUS BaltCoast Summer School 2017: Call for applications is now open! (BONUS BALTCOAST blog)
This is the 2nd Summer School organized by BONUS BaltCoast project and after a successful run in 2016 at Klaipeda University (Lithuania) it will take place now in Latvia, coordinated by University of Latvia.
06.05.2017 11:01Equipment explained- part III: the t-brush (Sources & Sinks: A Tale of Coastal Biogeochemistry - BONUS COCOA)
Last time in EE II you learned all about soft sediment coring with a GEMINI/GEMAX corer. Muddy soft sediments are generally sticky, often stinky, and sampling them will most likely make you look like a little piglet that enjoyed a decent roll in its favorite pit. That´s why we wrap us in orange rubber and simply accept the mud stains on everything uncovered, such as… the face.
A bucket full of black mud from the seafloor. Everything not in the bucket can be found on Anni and me, though the picture shows a rather clean state of us (pictures: Ines Bartl, IOW).
But what about the core sleeves that hold our samples, what degree of mud stain is acceptable there?
Very simple: none.
One of the most crucial points in getting reliable data are undisturbed and uncontaminated samples. When working with sediment, a fast track to destroy your sample directly onboard is to get sediments from deeper layers onto the top surface and the water overlying the surface, mixing totally different element compositions and concentrations.
This points a big finger to constant cleaning: fingers, top lids, sub sampling gear and the core sleeves. And with a sleeve diameter of 8-9 cm which tool would be better suited for that job than a t(oilet) brush?Clean core sleeves thanks to lots of water and a t(oilet) brush (picture: Franziska Thoms, IOW).
totally serious about this: a toilet brush is one of the essential key tools in
And so romantic in the sunset (picture: Franziska Thoms, IOW).