Sunday, July 5, 2015

Theory and Practice of Reproducible Research

In the occasion of the GII Ph.D. days, I am giving a talk about Research Reproducibility and Replicability. You can find my presentation on Slideshare, as usual. Please find the reference to tools and resources inside the slides.

Tuesday, June 30, 2015

Dear Ph.D.s and Post-docs: Beware

So far I brought to their destination ten Ph.D. students. Which was their path in real life ?
One has a reasonable research carrier. Another one is trying to get into one in Saudi Arabia. Two made their step into the real life of an Engineer. Two founded a company. Two are doing a post-doc, and we will se where they will go. Other two, passed through post-docs, and still have to find their own way.
If I have to judge by my statistics, I can draw some (Bayesian) conclusions:

  • Just a few Ph.D.s can enter a research/academic carrier (between ten and twenty per cent).
  • For someone, maybe, doing a Ph.D.  was a waste of time. (But their opinion would be important)
  • Some rolled up their sleeves and are trying to make their best to get their dream (of a having an interesting job) to come true. (They can fail and need support by their former advisors, academic policies, nations' wide consciousness of the importance of their role).
  • More than four post-docs years are useless (they serve the PI, but not the postdoc). Post-docs, after a couple of years, have to come-back to reality and make plans.
  • Someone is probably lost.
I always ask myself how much responsibility I have in the worst cases, and, frankly, I do not have an answer.  I will try to do better in future.
However the problem, as highlighted by this Nature commentary,  seems to be universal, at least in many of the developed countries. Academic positions are shrinking, and, at the same time, Ph.D. students are increasing in number. And, with them, post-docs. Now, we start to see the development of these long term post-docs carriers, without hope, and I ask myself two thing: is this the best we can offer to them, and, why the hell, they do not face reality (that they will not have, in most of the cases, one position) ?
On the other side, I constantly prey for the western governments increasing their investments in research and innovation, as the real, long term, solution for exiting societal and economical crises. So far they did not, and, instead, many do the contrary. Cause and effect of the decline.

Said that, I will still continue to (moderately) enrol Ph.D. students. Ph.D. time can be great. You can see the world, meets outstanding people. Be on the edge. Hope for a better future, and that it is in your hands (and certainly it is too).

Thursday, June 25, 2015

Downscaling of climate projections and sources of uncertainties

This is (actually the second) seminar of the series of CLIMAWARE's.  The report of the first one will follow soon. The topic is: Observations and modelling of precipitation and the hydrological cycle: uncertainties and downscaling and is all about the local impacts of Climate Change.

These slides come to highlight the work of Jost von Hardenberg (GS), Elisa Palazzi (GS), Silvia Terzago and others in downscaling the projection of GCMs in order to obtain very local statistics of climate suitable to be applied, for instance, at the scale of river Adige or its main tributaries. One interesting strategy they follow is to use WRF,  i.e. a weather forecast models, to obtain such projections. We think to use their expertise to drive our hydrologic simulations in the project.

Friday, June 5, 2015

A few topics for a challenging Master thesis

It is quite a long time that I am thinking to assign some master thesis around GEOtop 3.0.

A Master Thesis could be done even on the "simple" Richards equation. In this case the idea would be implementing the nested-Newton Casulli-Zanolli's method (on unstructured grids).
Time ago I assigned a little grant on this topic, but unfortunately, the work was not completed/ The material produced, in any case, is here. (I have also some other material, in FORTRAN, anyway).  In this case, the idea would be to use Java and develop further what already made by Francesco Serafin in his thesis. 
My outstanding colleague Michael Dumbser already promised to help me to complete the precedent work, and, at that point the main work would be to translate the procedural concepts into a object-oriented framework. In any case, who does it, would place one of the first stones of GEOtop 3.0.

Just thinking loudly, once started the Richards' work (which constitutes, however,  well defined and challenging enterprise) one could think how to implement coherently different flavours of the equation, for using bimodal or other water retention curves; for extending Richards analysis to integrate also the groundwater 3D equation, or studying the coupling with the evaporation/transpiration sink.  All alternatives that are interesting either from the numerical and the physical point of view.

The original problem I had in mind when I started this post, was the more ambitious one connected with the numerics and the physics of soil freezing (see Matteo Dall'Amico Ph.D. Thesis).  Our reference paper in the topic is the 2011 Dall'Amico et al. In the thesis and in the paper we wrote the equations in  3D but solved them in 1D with a not so particularly elegant method, which the nested-Newton algorithm could surpass by far. 

Working on the cryospheric side of Richards equation open a series of opportunity and especially the collaboration with  Stephan Gruber (with Carleton we have an exchange agreement, and the candidate could also stay for a few months there). 

Actually all these topics suggest that a very basic trial could be made to envision a scheme and an infrastructure that can accomodate all of these Richards variants by minimising code rewriting. But this would be probably a theme that could be completely developed in a Ph.D. In fact all these topics' task can clearly produce journal papers, if completed, and certainly open the road to some Ph.D. carrier.

Someone can think that everything is too much challenging, and actually, it is. However, all the topics are pretty mature in my mind, and the path to the solution is pretty well designed.

Wednesday, May 27, 2015

Ecosystem Services

Everybody talks about ecosystem services (ESs). But what are they ? As part of a conversation, I already talked about, I asked to Bilal Adem Esmail and Marika Ferrari to get an informed answer. Both of them pointed my attention to the Millennium Ecosystem Assessment (2005) of which a picture is presented below. In principle, any discipline can find its place in the diagram and try to understand with whom it can profitably dialogate.

Bilal wrote of the subsequent “Cascade Model”, in which a distinction is made among structures, biophysical processes, functions and ecosystem services (as in the scheme below). This to make evident the anthropocentric nature of ESs, and their, in a sense, utilitarian nature. The cascade model, in fact, point to the benefits ESs produces and on their estimation (not excluding their economics). The  Model, besides, tries to make clear the role of Institutions and policies in the management of the feedbacks among the social  and ecological systems.

Bilal says: “Between saying and doing is half of the sea … or better there is to learn”,  learn how to concretise these holistic concepts in reality. As an example he reports what  Cowling et al. (2008) draw in their scheme below.

And here we go back to the issues discusses in the previous post. The scheme shows that the biophysical assessment is a fundamental starting point of the mainstream concept of ESs. per promuovere il mainstreaming del concetto dei SE (see the scheme below). 

If we try to specify more to the basins or hydrology management, many studies call for a paradigm shift. Pahl-Woostls (2007,2008,2011) summarise the paradigms-shifts that you can see in the table below

More in general, the community talks about  “Sustainability Transition” which, in turn, is the scope of the “Sustainability Science”. Citing Clark (2007) “Sustainability Science has emerged over the last two decades as a vibrant field of research and innovation. Today, the field has developed a core research agenda, an increasing flow of results, and a growing number of universities committed to teaching its methods and findings. Like ‘‘agricultural science’’ and ‘‘health science,’’ sustainability science is a field defined by the problems it addresses rather than by the disciplines it employs. In particular, the field seeks to facilitate what the National Research Council has called a ‘‘transition toward sustainability,’’ improving society’s capacity to use the earth in ways that simultaneously ‘‘meet the needs of a much larger but stabilizing human population, . . . sustain the life support systems of the planet, and . . . substantially reduce hunger and poverty’’

To conclude, and balance the novel you presented in the previous post, here it is a video, you will certainly enjoy.


Braat, L., and R. de Groot. 2012. The ecosystem services agenda: bridging the worlds of natural science and economics, conservation and development, and public and private policy. Ecosystem Services 1(1):4–15.

Cowling, R. M., B. Egoh, A. T. Knight, P. J. O’Farrell, B. Reyers, M. Rouget, D. J. Roux, A. Welz, and A. Wilhelm-Rechman. 2008. An operational model for mainstreaming ecosystem services for implementation. Proceedings of the National Academy of Sciences of the United States of America 105(28):9483–9488.

De Groot, R. S., R. Alkemade, L. Braat, L. Hein, and L. Willemen. 2010. Challenges in integrating the concept of ecosystem services and values in landscape planning, management and decision making. Ecological Complexity 7(3):260–272.

Millennium Ecosystem Assessment. 2005. Ecosystems and human well-being: Synthesis. Island Press, Washington, DC.

Pahl-Wostl, C., M. Craps, A. Dewulf, E. Mostert, D. Tabara, and T. Taillieu. 2007. Social learning and water resources management. Ecology and Society 12(2).

Pahl-wostl, C., E. Mostert, and D. Tàbara. 2008. The Growing Importance of Social Learning in Water Resources Management and Sustainability Science. Ecology and Society 13(1).

Pahl-Wostl, C., P. Jeffrey, N. Isendahl, and M. Brugnach. 2011. Maturing the New Water Management Paradigm: Progressing from Aspiration to Practice. Water Resources Management 25(3):837–856.

Monday, May 18, 2015

Bimodal pore size distribution and hillslope stability

This post is to highlight the work of Fabio Ciervo, a Ph.D. student of Mariolina Papa that I co-advised with Vincente Medina. His thesis had the merit to put together two nice aspects of the recent research on soils. The first came from the work of Nunzio Romano [1] and co-workers, who show consistently that many soils present a bi-modal distribution in porosity, with effects in the form of the soil-water-retention curves (SWRC), and hydraulic conductivity, once Burdine or Mualem's [2] theory is applied. The other is the novel theory of hillslope stability coming out from the joint work of Lu, Likos, and Godt (e.g. [3]).

Who wants to enjoy his thesis can find it here: Fabio Ciervo, Modeling hydrologic response of structured soil, University of Salerno, 2015.
The code, developed in Java, that solves Richards 1D equation using these bimodal SWRC can instead be found on Github.
The Thesis produced a first paper which is under review in Vadose Zone Hydrology Journal.

Some References (others in the Dissertation)

[1] -Romano, N., Nasta, P., Severino, P., and Hopmans, J.W., Using bimodal lognormal function to descrivbe soil hydraulic properties, Soil. Sci. Soc. Am. J.,  75(2), 468-480, 2011

[2] - Roth, K., Soil PhysicsInstitute of Environmental Physics, Heidelberg University,
D-69120 Heidelberg, Germany, 2012

[2] - Lu, N., and Godt, J., Hillslope hydrology and stability, Cambridge University Press, 2013