You call this science???

I have not written much in the past months, being focused on work and writing some articles on simulations of uman societies. However, the news I found on PLOS: Ghostwriting: The Dirty Little Secret of Medical Publishing That Just Got Bigger have prompted my reaction.

An article written by PLOS editors has described in detail the practice of ghostwriting "scientific" papers by specialized companies hired by pharmaceutical giants. Of course - favourable to the pharmaceuticals. Then the papers were "given" - readymade - to "researchers".

If you are an editor, author, reviewer, or reader of medical journals, or if you depend on your doctor or health care provider getting unbiased information from medical journals, then the 1,500 documents now hosted on the PLoS Medicine Web site should make you very concerned and angry. Because, quite simply, the story told in these documents amounts to one of the most compelling expositions ever seen of the systematic manipulation and abuse of scholarly publishing by the pharmaceutical industry and its commercial partners in their attempt to influence the health care decisions of physicians and the general public.

[...]

It's time to get serious about tackling ghostwriting. As has been shown in the documents released after the Vioxx scandal [7], this practice can result in lasting injury and even deaths as a result of prescribers and patients being misinformed about risks. Without action, the practice will undoubtedly continue. How did we get to the point that falsifying the medical literature is acceptable? How did an industry whose products have contributed to astounding advances in global health over the past several decades come to accept such practices as the norm? Whatever the reasons, as the pipeline for new drugs dries up and companies increasingly scramble for an ever-diminishing proportion of the market in “me-too” drugs, the medical publishing and pharmaceutical industries and the medical academic community have become locked into a cycle of mutual dependency, in which truth and a lack of bias have come to be seen as optional extras. Medical journal editors need to decide whether they want to roll over and just join the marketing departments of pharmaceutical companies. Authors who put their names to such papers need to consider whether doing so is more important than having a medical literature that can be believed in. Politicians need to consider the harm done by an environment that incites companies into insane races for profit rather than for medical need. And companies need to consider whether the arms race they have started will in the end benefit anyone. After all, even drug company employees get sick; do they trust ghost authors?

Instant infamy - plus criminal charges for the involved - this is what comes to my mind...

Interesting links

This time for almost purely informational:

I have stumbled upon a few very interesting links. The first is to a set of Richard Feynman physics lectures captured on video, and restored, paid for and put on the WEB by Bill Gates. At last some of the money I paid for Windows went back to something useful and good.
http://research.microsoft.com/apps/tools/tuva/index.htm

The second link is to a book caled Physics for Future Presidents. Its WEB site is
http://nortonbooks.typepad.com/physics_for_future_presid/
I dare not to comment on capabilities of presidents of the US, France or Zimbabwe. But I daresay the book should be translated into Polish ASAP.

The third link is to a set of symposiums on astrophysics at London Imperial College http://www3.imperial.ac.uk/astrophysics. The one that caught my attention was a debate on Dark Energy. I hope to live to see the issue resolved. And I do expect that twenty years from now we might look at the current period with some dismay. Or not?

Decision making efficiency

I have been studying opinion formation for some time now, with a few papers published or to be published. Generally, my outlook on the capacities of human species to make rational - no, OPTIMAL - decisions is rather bleak.

Hunting through papers written on the subject I found one written by Amé, J.-M.; Halloy, J.; Rivault, C.; Detrain, C. & Deneubourg, J. L. Collegial decision making based on social amplification leads to optimal group formation, Proceedings of National Academy of Sciences, 2006, 103, 5835-5840.

And there is hope! we have founs at least one species capable of:

This experimental and theoretical study of shelter selection by cockroach groups demonstrates that choices can emerge through nonlinear interaction dynamics between equal individuals without perfect knowledge or leadership. We identify a simple mechanism whereby a decision is taken on the move with limited information and signaling and without comparison of available opportunities. This mechanism leads to optimal mean benefit for group individuals.

So, the old SF joke about cockroach surviving after we demolish the world with atmo bombs has a good, scientific basis. They are, collectively, smarter. Because I can not recall many examples when humans could take a good decision through interaction dynamics between equal individuals without perfect knowledge or leadership. A decision that would be taken on the move with limited information and signaling and without comparison of available opportunities. And turned out to be an optimal one.

Scare the public!!!

It seems that one of the duties of so called "science journalism" is to scare the general public witless. It is not so difficult, bearing in mind that the public is generally witless to start with, but let's focus on scaring them then.

Example?
What would you think when reading the following title: Caesarean delivery can alter DNA ? Monster mutants caused by cesarean birth? Permanent changes of DNA? ... Horror...

Yet this is the modern world: the title of the original publication is much less interesting: Epigenetic modulation at birth – altered DNA-methylation in white blood cells after Caesarean section
by T Schlinzig, S Johansson, A Gunnar, TJ Ekström and M Norman.
This does not sound so scary, does it?
And what you find in the abstract is

Aim: Delivery by C-section (CS) has been associated with increased risk for allergy, diabetes and leukaemia. Whereas the underlying cause is unknown, epigenetic change of the genome has been suggested as a candidate molecular mechanism for perinatal contributions to later disease risk. We hypothesized that mode of delivery affects epigenetic activity in newborn infants.

Methods: A total of 37 newborn infants were included. Spontaneous vaginal delivery (VD) occurred in 21, and 16 infants were delivered by elective CS. Blood was sampled from the umbilical cord and 3–5 days after birth. DNA-methylation was analyzed in leucocytes.

Results: Infants born by CS exhibited higher DNA-methylation in leucocytes compared with that of those born by VD (p < 0.001). After VD, newborn infants exhibited stable levels of DNA-methylation, as evidenced by comparing cord blood values with those 3–5 days after birth (p = 0.55). On postnatal days 3–5, DNA-methylation had decreased in the CS group (p = 0.01) and was no longer significantly different from that of VD (p = 0.10).

Conclusion: DNA-methylation is higher in infants delivered by CS than in infants vaginally born. Although currently unknown how gene expression is affected, or whether epigenetic differences related to mode of delivery are long-lasting, our findings open a new area of clinical research with potentially important public health implications.

Seems the effect is temporary, causes unknown and effects unknown as well. OK - I have nothing against the continued research, the topic may be important - but should Karolinska Institute really be involved in scaring everyone?

Or is it just my imagination that DNA is a dirty word? I remember the protesters holding up placards with "we do not want DNA in our tomatoes". Is this the time to ban DNA from our children as well?

Where do wars come from?

I have found - by a curious accident - a very interesting article by Samuel Bowles:
Did Warfare Among Ancestral Hunter-Gatherers Affect the Evolution of Human Social Behaviors?, Science, 2009, 324, 1293-1298,

Abstract:

Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist.

In the light of Jared Diamond getting sued for writing about social strife in New Guinea by the very people who have told him the stories of the violence in the first place it is very risky direction of research. According to "politically correct" explanations wars are charactersictic only for white, aggressive and doministic western civilization. Savages are, by definition, noble. Fortunately for Bowles his work is based on field research done by others, so the chances of beinf sued for putting some tribe "in bad light" are slim. But who knows...

Seriously - what I have found important was a careful combination of theory/model and observations. As it should be in science.

SkyNet?

As the new terminator movie approaches the notion of people building Skynet Artificial Intelligence seems a dark prospect. Yet there is something that looks just like it...

At http://www.intelligencerealm.com/aisystem we might find an attempt to build AI in the free multiple client mode, using home computers a la SETI.

The aim:

This project uses Internet-connected computers in order to leverage the computing power of many machines. You can participate by downloading and running a free program on your computer. You will need to download the BOINC client manager from the BOINC web site. If you have any issues with the BOINC software please address them to their network of volunteers on the help page. We will post the source code on SourceForge.net project site. We expect to launch new versions often so please bear with us. Building a neural network simulator requires much more than raw computing power and each released version will incrementally increase the system's features.

How they do it?

Results
To date we have simulated 709,358,333,333 neurons. The human brain has an estimated 100 billion neurons.
Computing Information
The neural network simulator is an application that simulates neurons. Each downloaded work unit generates 500,000 biophysical neurons. Because the simulator is in an initial phase and we have very few cellular models implemented, we can only use it to test for simulations capacity. We have completed the first phase of the project, to simulate over 100 billion neurons. The second largest brain simulation has been done on a cluster of 27 machines, with 100 billion neurons simulated over a period of 50 days. While it was a very interesting experiment which pushed the frontier further on it was a partial simulation only, in the sense that many of the required components were not implemented due to hardware constraints.

The neurons were created, simulated and then destroyed in memory, without any data being stored. Based on their results the estimate for full brain simulations was calculated to be the year 2016; we would like to prove otherwise. From a practical point of view it didn't advance the knowledge further on and that's why we would like to continue along this line of thought and bridge these results with some practical data. The problem of storage and computing power is esential for large scale brain simulations because without them we can't plan and estimate these requirements. Without planning there is also no clear understanding as to what is needed in order to do that. As we advance with the simulation and more and more neurons get simulated, we should be able to make increasingly precise estimations on storage, number of computers required, duration, bandwidth and other factors. Regardless of the fact that at this stage our simulation is not precise and it lacks in many aspects, this is what we want to achieve with your help.

There is also the added benefit that once we will publish these results and the public at large would see that the capacity to simulate the entire brain is considerably higher than previously thought, a large stumbling block will be removed from the path of artificial intelligence.

Is this dangerous? Well, the FAQ confirm the danger

If the system will eventually be smarter than you, its creator, wouldn't that pose a risk?
It sure does. We understand the negative and positive implications of building an Artificial Intelligence system. That's why we have already restricted access and we will implement multiple levels of control and monitoring.

Nice. Fine. OK.

But... If the system turns out truly alien, and truly smarter than us - then what kind of security will be sufficient? Especially as the beast runs not in some enclosed laboratory, but in the wilderness of world wide network.

What worries me particularly is how the system will get the information:

Knowledge Acquisition:
The knowledge acquisition module is used for retrieving and defining the information that will form the future memories of the system. We are using a robot (i.e. web bot) to extract information from the Internet.

Hmmm... if the system learns about the RWOT (Real World Out There) from the Internet, it is going to be very, very confused.

The only hope is that the project shall fail.

Peer review in practice

It is worse than I thought.
submission date: March 6th
sent to referees: March 24 (why wait almost three weeks?)
on April 14h reminders sent to referees, because they have not responded.

My own average as a referee - so far - was less than one week for reviews (including those where I had to do totally new calculations to prove authors wrong). But I am an amateur.

Judging by some recent publications titled "Are we training pitbulls for peer review" (or something like this) there is a growing worry about the cornerstone of scientific credibility - the belief that the published work IS checked and may be safely used by others.

We'll soon become much like pop artists: publish (rubbish) or perish. And science will become a beuty contest for funding. Dark future.

Amateur Scientist - the story continues

After the first step of publishing in a little known open access electronic journal I have sent some work to a leading physics paper - without any affiliation.

The paper is under review - but I am glad to announce that the lack of affiliation has not been any problem for the Editors.

So, I guess that I shall wait now for the Referees' opinions.

Publish or perish?

It turns out that - not really. At least at Lublin Technical University. In December, the Dean of the University has run a survey about worls published in the last three years by the researchers. And quite a few have published -- nothing!

Yes, I can imagine someone working in recluse on some grand work (Fermat's Theorem, for example), not publishing anything for 20 years. But even the famous story of Andrew Wiles shows that he had recveived recognition for work before the proof of FLT. In most cases, even if soemone is writing a huge monograph on some subject (which can take more than three years), it is possible to publish small fragments, if only to check the opinions of others or the interest in the work...

But in Poland one can be a scientist without doing science.

First step

The first step in the direction described a few days ago has been done. Journal of Artificial Societies and Social Simulation vol. 12, no. 1, 2009 has published a forum article Modelling Opinion Formation with Physics Tools: Call for Closer Link with Reality, without any reference to my affiliation (none) or credentials other than the text itself.

Of course, it is not an original research paper, but a review and discussion one, so the criteria are lighter. And JASSS is a specialized, electronic-version only journal, not on the higherst top of the citation index. But at least one myth is busted: it is possible for an outsider to comment and be heard within academic world proper.

Hooray for the amateurs.

Amateur scientist

Writing Country of Blindfolded I gradually came to the idea of re-creating amateur science as a honourable pasttime, jjust as fascinating as flower arrangement, speed racing or computer games. Of course it is not for everyone (I mean speed racing).

Following some posts and letters I have decided to check if the idea is doable. It is not the same thing to post some papers on the arXiv, where there is no peer review as to decide to publish in a proper journal. To run the gauntlet with no proper affiliation attached to the author's name.

So, for the past few months, my evenings were filled with working on a couple of papers - this is the reason for the lack of posts here. The first part of the experiment comes near the end, the second should be finished in a few months.

We shall see, if indeed it is possible, with enough persistance, to enter the ivory tower via kitchen entrance.

Science of magic

... or to be more exact, of conjuring. Very interesting window on the capabilities and mis-capabilities of human brain.

Two recent articles:
Macknik, S.; Randi, J.; Robbins, A.; Thompson, J. & Martinez-Conde, S. Attention and awareness in stage magic: turning tricks into research Nature Reviews Neuroscience, 2008, 9, 871,

Kuhn, G.; Amlani, A. A. & Rensink, R. A. Towards a science of magic Trends in Cognitive Sciences, Elsevier, 2008, 12, 349

There are also reviews in december issues of NewScientist and Scientific Amarican, but the access to these is restricted.

An excellent tool

During the Christmas free time I have discovered a great tool: a personal wiki application that allows to gather snippets (and more) of information from many sources.
The application is called wikidPad,and is available from sourceforge: http://wikidpad.sourceforge.net/ .

To quote the description:

wikidPad is a real-time wiki
wikidPad is not a web server, or application server, or groupware solution. wikidPad is a standalone notepad like application, albeit notepad on steroids. wikidPad is like an IDE for your thoughts.


IDE for your thoughts
Software developers have grown accustomed to certain features from their integrated development environment that make their jobs easier. Features like auto-completion, outline views, incremental search, easy source code navigation. IDE's that provide these features can greatly increase developer productivity. wikidPad attempts to utilize some of these features to address the problem of personal information management.

Personal Information Management
How do you manage all of the random bits of information in your personal and professional life? Word documents, text files, Microsoft Outlook folders/notes. If you're an expert user maybe you have a weblog, or a personal database, or possibly an outlining application. Where do you track your wifes favorite food, your bosses kids names, your personal todo list, the name of the movie you just read a review of, the name of the book a friend recommended. wikidPad was created to address this issue of personal information management. It provides a place to manage the massive amounts of information you have stuffed in your head, on stickies, or on your computer.

A great help in organising my notes and thoughts. Highly recommended!