Le cadavre exquis boira le vin nouveau

I'm currently reading "Fooled by Randomness" by N.Talib, and I'm really enjoying a chapter dedicated on randomness in humanities... So let me start with two quotes:

" 'Reality is part of the dialectic of consciousness' says Derrida; however, according to Scuglia[1] , it is not so much reality that is part of the dialectic of consciousness, but rather the absurdity, and hence the futility, of reality."

"Sound is the change in the specific condition of segregation of the material parts, and in the negation of this condition; merely an abstract or an ideal ideality, as it were, of that specification [...]"

Very exciting. Now you have to guess: one of the two quotes is from Hegel, and the other one has been generated from a computer using the Postmodernism generator, created by Andrew C. Bulhak using the Dada Engine. (you can find the whole article I've created here, and if you want to make your own paper just click here).
Now, it's all fun, and if you know some philosophy you've probably guessed right (Hegel is the second one, also because it's very unlikely that he've quoted Derrida which was born 101 years after his death...). The point is, with another random combination (without Derrida being quoted) could someone have fooled you? To be honest I'm not a philosopher nor a postmodernist and I'll be concerned if you fool me with a scientific paper on spatial analysis rather than this (it would be nice to actually have a positivist generator to see how it would work...). I simply don't care much, but actually Alan Sokal, a physicist  of New York University, tried to submit a paper on Social Text by randomly creating (not with a computer this time) meaningless sentences... Well you can read his accepted and published paper here....Later in the same year, Sokal explains his point in another paper, (this time generated non-randomly I think):

"For some years I've been troubled by an apparent decline in the standards of intellectual rigor in certain precincts of the American academic humanities [...]. I decided to try a modest (though admittedly uncontrolled) experiment: Would a leading North American journal of cultural studies -- whose editorial collective includes such luminaries as Fredric Jameson and Andrew Ross -- publish an article liberally salted with nonsense if (a) it sounded good and (b) it flattered the editors' ideological preconceptions?"


and then states:

"Social Text's acceptance of my article exemplifies the intellectual arrogance of Theory -- meaning postmodernist literarytheory -- carried to its logical extreme. No wonder they didn't bother to consult a physicist. If all is discourse and ``text,'' then knowledge of the real world is superfluous; even physics becomes just another branch of Cultural Studies. If, moreover, all is rhetoric and ``language games,'' then internal logical consistency is superfluous too: a patina of theoretical sophistication serves equally well. Incomprehensibility becomes a virtue; allusions, metaphors and puns substitute for evidence and logic. My own article is, if anything, an extremely modest example of this well-established genre." (bold mine)

Scary, but perhaps true also in some archaeology and anthropology? While asking this question I've just read on Carl Lipo's blog how the executive committee of the  American Anthropological Association  are proposing to rephrase  their mission statement removing the word "science" (see here).

UPDATES: Simulpast, STDM and paper

Lot's of things happened the last few weeks so I need to update you on couple of things...
I've been in Barcelona last week and spent a wonderful time with the folks of the Spanish Research Council, where they allowed me to present two papers related to my PhD. They are just going to start a very exciting project called simulpast from early next year:
I quote from their website:

"The aim of the project is to develop an innovative and interdisciplinary methodological framework to model and simulate ancient societies and their relationship with environmental transformations. The propject will include 11 Research Groups of 7 different Institutions with more than 60 researchers from several fields (archaeology, anthropology, computer science, environmental studies, physics, mathematics and sociology). The leader institution is the IMF-CSIC in Barcelona."

I've never heard of any archaeological project centred on computational modelling having such broad range of case studies. This is a great opportunity and I'm really looking forward on the project outcomes. And I guess this can also be a great leap forward in terms of terms of standardisation and communicability of models. Good Luck and Thanks for the Tapas!!!

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In the mean time I'm keeping myself (and Mark Lake) busy, as we are working for a paper which will go deeper on some of the topics we've explored for the CECD conference this September. We'll mainly focus on cultural transmission models of fitness-enhancing traits (2 and n-traits) with frequency dependency of the fitness and different types of Carrying Capacity (shared and independent) looking at short term dynamics and long term equilibrium of adoption rate and trait diversity. Stay tuned for more info!!!

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The last but not the least! I'm quite excited, since there will be a International Symposium of Spatio-Temporal Analysis and Data Mining hosted here at UCL on July!!! This is a great chance to see many advanced techniques in spatio-temporal analysis and simulation which might give us some new perspectives in archaeology!!!

Inference From Confirming Evidence

Every once in a while I read papers in Archaeology claiming about there allegedly scientific methods failing to choose the right type of hypothesis testing for their models. While reading Taleb's "The Black Swan" I come across a very nice  psychological experiment conducted 50 years ago by Wason (1960).
The basic idea is that you have a data-set with a specific pattern, and in order to explain the underlying rule you conduct a series of experiments to test and propose a model. Of course in archaeology you cannot strictly do experiments all the time, but you can look for other data which will support or not support your model.
Now the experiment is based on a simple sequence of number, and one should simply "discover" the underlying rule. The player can propose another sequence of numbers and the experimenter will tell you whether such sequence can been generated from the same algorithm of the original data-set or not.

The sequence is:

2-4-6

Now, most people will most likely propose something like following sequence:

8-10-12

which will basically test the model increase by two. Now if the experimenter will tell you "Yes", you'll be probably quite happy about that, and probably you will write a paper for the Journal of Integer Sequences, which believe it or not, actually exists) with something lines:
"Our experiment confirmed our hypothesis of the increase by two rule". Very few will claim that this model is wrong and will be part of the scientific knowledge of your field (I'm sure that none of the editors of Journal of Integer Sequences will accept your paper, nor will fall on this trap...)
Now the big problem here is that the algorithm with which 2-4-6 has been generated was numbers in ascending order. Thus actually 5-6-7 would also have been accepted by the experimenter. However, it's vert likely that most people uses these experiments to confirm their model rather trying to falsify it. Testing 5-6-7 would have allowed a re-evaluation of the originally proposed rule and might have lead to the right answer.
The question now is: what sequence of number are you proposing in your archaeological research?


References:

• Taleb, N.N.,2007, The Black Swan: The Impact of the Highly Improbable, Random House, 
• Wason, P.C., 1960, On the failure to eliminate hypotheses in a conceptual task, The Quarterly Journal of Experimental Psychology, 12: 3, 129-140.

apply() function and ABM in R

I know know...I've been away again...
We (myself and Mark Lake) are presenting a paper at the CECD conference and we have still some to stuff to finish...so I'm really, really busy... I'll post asap a much more detailed post on the conference and on our paper, but before that I just wanted to share an useful link I found this morning which would have been handy a couple of month ago.
As I said, I'm writing my ABM in R this time. There are many good reasons (but also bad reasons) for this which I'm gonna write on another post (yes I keep promising...). Having said that, R is terribly slow. Yes  you can write things in C and call them inside your function, but the main reason is that it is terribly bad on looping. And an ABM involves a lot of looping. Then I realised that many people avoid using  loops in R, and instead use the series of "apply" function. These are however hard to grasp, but this blog explains it very elegantly. I wish I had read this long ago...Anyway, when you master the "apply" family, you can also play around with the mcapply() function of the multicore package which parallels the apply function through your cores, fastening alot your simulation!

London Cycle Hire Scheme and Flow Analysis

If you are living in London, you'll probably noticed all these new blue bikes of the London Cycle Hire Scheme. It's a brilliant idea as the number of fellow cyclist will increase more and more, hopefully gaining some more respect from the people sitting in those tin boxes.
Anyway. I was wondering how did they managed to calculate correctly the flow of cycles, so that  you always have some of them available in your station. The obvious guess is that there will be cycles of flows towards the city centre and from the city centre, as most people will be using these for commuting. Having said that, Oliver O'Brein of CASA has created a web-GIS which shows you the currently available number of bikes at each dock with a time-series of bike availability through the past 24 hrs at each location. He also made a video which nicely shows the inward and outward flow. Really cool. You can find more details on his blog.

Communicating (Agent-Based) Models

So, you've worked hard and finally you have a working ABM, full of features and parameters and you are super-excited and want to show everybody your latest phase space or time-series. You go to a conference or you write a paper, in any case chances are that people will misunderstand your model, or will simply take for granted it's underlying algorithm and there will be very few questions...especially if your audience is not trained....
I think that one of the biggest problem archaeological (and non) ABM must face is when your model reaches it's audience and you have a small window of time (10~30 minutes) and/or space (3000~5000 words) to communicate all the algorithms and submodels you've used.  Now even in an ideal (?) word where everybody understands Java, C++ or NetLogo (or even R in my case), few people will have the patience and the willingness to go through your raw code and try to understand how really your model works. Most people, will simply look at your conclusions, or read through the old-fashioned text-based way of communicating your model. The problem then is how you evaluate other people's model. Well the short answer at this stage is that you could but you won't. And the risk is that we lose the scientific feedback process, bringing us back to simple story-telling with perhaps some fancy dynamic illustrations....
The thing is that, I'm much convinced that greatest achievement that archaeology can gain from ABM, is not the actual bunch of codes and files, but the formalisation of submodels. We tell stories and we tend often to avoid details in the non-computational modelling process. We delineate the larger trends without tackling the smallest issues. This epistemological laziness  (as one of my supervisors would call) is however strictly prohibited in an ABM. Or to better put, you can still place lazy models, but people will discover this and criticise it..but only if your model, submodels and algorithm are well communicated.
So the communication problem is really a big issue, and the risk is to be trapped with a series of over-complicated hyper-realistic models, with very long codes that nobody will ever read and check...

I'm having a series of nice chats with Yu Fujimoto, a visiting scholar from the Faculty of Culture and Information Science at the Doshisha University in Japan. The discussions are around whether models should be communicated through UMLs (Unified Modeling Language)  or using the ODD (Overview Design Concepts, and Details) Protocols advocated by Volker Grimm or simply by series of pseudo-codes. All modes of communications are around, but not common in archaeology. One reason is that a non-trained archaeologist will struggle to understand pseudo-codes, and will definitely reject UML as something mystic and unquestionably complicated. This leaves ODD, which hopefully will take over. Ideally journals should allow the upload of the source code and also an additional appendix with the ODD description of the code, leaving aims&objectives, brief description, experiments results and discussion as the core elements of the paper. Of course, having said that, the problem of model communication in conferences remains tricky, as going through the ODD will most likely use the entire time-block and you'll hear the 5 minutes bell ringing as soon as you reach the second D....

R Plotting tips

Yes...I haven't been updating the blog for a very long while...But I'm really busy with many things right know.... Our paper for the "Cultural Evolution in Spatially Structured Populations" have been accepted so we are currently working on that, and I have also stuffs for the PhD and a couple of papers I'm working on...busy busy busy.....
I've also started writing a couple of ABM using R, which sounds crazy at first (also at second, and third) but it has some nice things which I'll write about extensively in a future post.
But for know, I just wanted to start a series of very small posts (mainly for archaeologists) of small tips, which are astonishing simple concepts which however takes a couple of hours of googling and forum foraging...
For instance, have you ever tried to plot a time series of BC or BP dates? Suppose you have a sequence of count per century as follows:

data<-c(789,100,923,444,224,192,83,45,32,21,19,22,23,42,120)

plotting this as a timeseries is very simple:

plot(data,type="l")

and then you realise that you want something meaningful on the x-axis and you write the follow

dates<-c(3500,3400,3300,3200,3100,3000,2900,2800,2700,2600,2500,2400,2300,2200,2100)

 perhaps, if you know a bit of R you'll choose the more elegant nested function

dates<-sort(seq(2100,3500,100),decreasing=TRUE)

In any case you'll try to plot this as follow:

plot(x=dates,y=data,type="l")

and you'll find out that R ignored the ordering of the vector dates, and it even reversed your time-series.

My practical solution was to use negative values on the plot, and then delete the "-" with gimp or something (yes I should really be ashamed of myself).
Well for the small portion of people who had the same problem and here's the solution

plot(x=dates,y=data,type="l",xlim=c(max(dates),min(dates)))

Basically you can tell to the plot function that the range of values for the x axis is from the greatest value (the oldest date in our case, thus the largest number) to the smallest value. R will simply then read the values of dates in the correct order and plot the TS in the way it should look like.
Easy.