Thursday, October 26, 2006

Descriptive vs Explanatory Laws

[William Robin Thompson] was most concerned that entomologists should understand that mathematical "laws" merely expressed natural processes, they did not govern them. The distinction he made between a law as description versus law as explanation was similar to that made by Karl Pearson in The Grammer of Science.But where Pearson regarded such laws as having predictive value in physics, Thompson denied it could ever do that in biology. This was not just because mathematics were too simple in comparison with nature. Mathematics no matter how intricate, could never help biologists to understand causal relations, because natural events were made up of unique causes which were necessarily unpredictable:
"The tremendous multiplicity of factors acting on the real world has not merely the complexity of an elaborate mathematical equation, which is theoretically but not practically manageable; but implies a genuine unpredictability because the actual combination of factors has never been observed to operate and until it has, we cannot really be sure what its effect will be. Much less can we see this effects in its causes."



pg 140
Modelling Nature

Wednesday, October 25, 2006

a few key words and their definitions on the web

Monte Carlo methods: are a widely used class of computational algorithms for simulating the behavior of various physical and mathematical systems. They are distinguished from other simulation methods (such as molecular dynamics) by being stochastic, that is nondeterministic in some manner - usually by using random numbers (or more often pseudo-random numbers) - as opposed to deterministic algorithms. Because of the repetition of algorithms and the large number of calculations involved, Monte Carlo is a method suited to calculation using a computer, utilizing many techniques of computer simulation.

and another defintion -
A computer-driven model that simulates a sufficiently large number of potential interest rate paths to value a security on the basis of performance along a composite of these paths. Monte Carlo is considered the most sensitive measure of valuing interest rate-sensitive debt instruments based on historical interest rate environments and their probability of repeating. Monte Carlo has become the standard for evaluating mortgage-backed and asset-backed securities.


Markov Chain: A stochastic process with a finite number of states in which the probability of occurrence of a future state is conditional only upon the current state; past states are inconsequential. In meteorology, Markov chains have been used to describe a raindrop size distribution in which the state at time step n + 1 is determined only by collisions between pairs of drops comprising the size distribution at time step n. (from here)
Also see wiki - there are good links at the bottom. The Markov Chain Monte Carlo mentioned at the bottom is used by Kingston, Maier and Lambert(2006)

Friday, October 20, 2006

new book release and In the pipeline

Coming soon:

  1. I am waiting for two of the books from below to be delivered by the document delevery. I would be commenting about the three of them soon.
  2. There is bound to be some discussion of Monte Carlo Analysis
  3. Then either i would have written all i want about Sensitivity analysis in my formal work or you'll be hearing about that too.

In the meanwhile there is released a new book Steps Towards an Evolutionary Physics, (Preface written by Ecological Modelling editor Sven Erik Jorgensen). It appears to be taking the same stream as Lotka's work but in energy transfer; and not in demography or population dynamics. All this before reading the book - I am not sure if I am getting to read this book in a hurry. Since it does not talk about population estimation my interest in it is rather limited.

Monday, October 16, 2006

Sunday, October 15, 2006

On the position of ANN models in population ecology

Black boxes: If models that are not designed to reflect the actual processes in the under-lying systems are called black boxes. Then, in that respect ANN are indeed black boxes. ??check

Models or Laws: Model is a relation or a set of relations that relate the various components of a system. There are two ways to reach a model
- one is to study the physical and chemical processes and then use mathematical statements to express these processes. The mathematical statements would be called models; and
- two is by studying various components and finding the statistical relationships between them. The statistical relationships would be called models.

could both the methods be called empirical?

in any case, from kingsland's book pg. 100 Thompson's hypothesis is presented
If ecological interaction were found to display an underlying regularity, and if this regularity could be described mathematically, then mathematics might serve as a theoretical basis for population ecology.


Also, the book mentions on pg 85 that the term laws (and may i add models, as well) has been used in more than one way -
Specifically, Pearl used the term 'the law of population growth' for the logistic curve to possess universal applicability. Where as, Lotka used the same term
to mean an empirical relation between events having no apparent connection to principles of a more general nature. By this criteria, any other equation fitting the observations would be qualified equally as a law.

Lotka perceived that an empirical law of this sort imposed limits in two ways. First, because the fundamental principles underlying the curve were unknown (MARK1), the exact form of the equation had to be determined anew for each examples. Second, it was not possible to extrapolate much beyond the observed events, because unknown factors might come into play outside the observed range and cause departure from the law

Talking about the logistic curve as the law of population growth - the value lay not in universality or predicting but
in the fact that it could be so easily derived from first principles, and that its constants r and K were biologically meaningful. The equation represented in other words an argument about the population which could be useful as tool of research.- MARK2

Lotka finds use of such a law in this way
"An empirical formula is therefore not so much the solution of a problem as the challenge to such solution. It is a point of interrogation, an animated question mark."
This is later (Pg 87) explained as -
by looking at how a population departs from the law, one may get a more realistic idea of the actual mechanism underlying the population growth... Knowing how a population deviates from the law tells one how to refine the initial assumptions to get more accurate understanding of how populations behave.


By reading MARK1 and MARK2 above, what I am trying to do is see if there is a fundamental similarity between the logistic curve and ANN model as population law. If so, then we know exactly where to place the ANN models in the study called population ecology or population dynamics of phytoplankton [Note to self - there needs to be a discussion on exactly which term would I be using]. And, thus how far can the results be extrapolated.

My current hypothesis (??) is -
By developing a series of empirical models and using those empirical models to
- evaluate the technique (the model is objectively evaluated by having a large percentage of testing data)
- study how the relationship varies (by performing Sensitivity analysis on model that have been found to be good approximation using objective measures)

the next things -
1) look at what exactly is Thompson above is talking about.
2) See exactly what assumption and limitation are associated with the SA techniques that I have used.
3) A very brief discussion on which term (phytoplankton, blue-green algae, any other) would be used and why.

Friday, October 13, 2006

Research Interests

Since I am looking for a job, I would like to work, or rather continue working but at a larger scale in the area that I am already working in, Population ecology.

I am looking at the population dynamics of phytoplankton in an estuary in Victoria, using bio-physical time series. I have tried to understand the short time scale dynamics, varying from the order of hours to days. I have used an iterative non-linear statistical modelling tool which in other words is called feed-forward neural network. (neural networks have been given the bad name of being a black box, however I think it has got more to do with they way they are used).

Using partial-derivative sensitivity analysis (I have come across at least one paper which gets upset with this terminology) I have tried to evaluate the strength of the relation between each of the bio-physical parameter and chlorophyll. (chlorophyll is used an indicator of phytoplankton population.) And to see how the relationships change as the time interval between chlorophyll and bio-physical parameters is increased.

Now what I would like to do further is

  1. Study non-linear time-series and see how does chaos (which appears in weather time series and water flows) appear in ecological time-series.
  2. Study oceanography, my approach to my project was as a mathematician. I have, hopefully, learned some decent amount of biology in the process. However, I am sure there are quite a few things out there – so, I would like to do a short course in oceanography. (Note: I did NOT say I wanted to do a short course in chaotic time series analysis)
  3. Study Bayesian: Bayesian is used to quantify uncertainty. It is being used to make ecological models more accessible to decision makers who can use them as decision support systems.