Category Archives: Philosophy

Philosophy, Software

Infinite stupidity?

This is a new Edge conversation with Mark D Pagel.

A tiny number of ideas can go a long way, as we’ve seen. And the Internet makes that more and more likely. What’s happening is that we might, in fact, be at a time in our history where we’re being domesticated by these great big societal things, such as Facebook and the Internet. We’re being domesticated by them, because fewer and fewer and fewer of us have to be innovators to get by. Continue reading Infinite stupidity? →

 

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Philosophy

The lying Dutchman

Another series of faked studies are reported by washingtonpost

“Many of Stapel’s students graduated without having ever run an experiment, the report says. Stapel told them that their time was better spent analyzing data and writing. The commission writes that Stapel was ’lord of the data’ in his collaborations. It says colleagues or students who asked to see raw data were given excuses or even threatened and insulted.”

 

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Philosophy

Make hypotheses!

The main challenge for bioinformatics is certainly not to stop at the description of all these nice networks and pathways but to develop hypotheses that add to our understanding (and that may be tested further). So, I am a little bit late to say that I liked the presentation of Sascha Sauer ( MPG Berlin ) at a meeting Paris at May 31, 2011 on genomic epidemiology using the title “Make hypotheses”. Continue reading Make hypotheses! →

 

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Genetics, Philosophy

Too much to read too little time

I didn’t find so much time to update the blog during the past few months – there are too many attractions out there, and so many interesting things to do. The never ending problem is that there is too much to read and too little time. This is, however, what also other people find, for example genomeweb.com

Pedro Beltrao at the Public Rambling blog says there never seems to be enough time to keep up with all the literature researchers keep churning out. In 2009, 848,865 papers were added to PubMed, he says — that’s something like 1.6 papers per minute. While there’s definitely no scarcity of outlets to publish, is anyone even paying attention?

Or the Latest Everything blog

From a half-forgotten Einstein quote to the complete works of J. S. Bach, everything is instantly available. But what can we really do with it all? A HALF-CENTURY ago Marshall McLuhan wrote: “We are today as far into the electric age as the Elizabethans had advanced into the typographical and mechanical age. And we are experiencing the same confusions and indecisions which they had felt when living simultaneously in two contrasted forms of society and experience.”

who republishes theNew Scientist article (04 April 2011) pp. 1-3 in Surfing the data flood: Continue reading Too much to read too little time →

 

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Philosophy

Science is an emergent system too

From Edge / NY Times

We often try to understand problems by taking apart and studying their constituent parts. But emergent problems can’t be understood this way. Emergent systems are ones in which many different elements interact. The pattern of interaction then produces a new element that is greater than the sum of the parts, which then exercises a top-down influence on the constituent elements. Continue reading Science is an emergent system too →

 

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Genetics, Noteworthy, Philosophy

LIMIT TO 5! What about a maximum of 5 papers per year per scientist?

Undoubtly, there is an avalanche of poor research – as the Chronicle wrote last June, “we must stop the avalanche of low-quality research”

the amount of redundant, inconsequential, and outright poor research has swelled in recent decades, filling countless pages in journals and monographs. Consider this tally from Science two decades ago: Only 45 percent of the articles published in the 4,500 top scientific journals were cited within the first five years after publication. In recent years, the figure seems to have dropped further

Also Genomeweb writes

Pedro Beltrao at the Public Rambling blog says there never seems to be enough time to keep up with all the literature researchers keep churning out. In 2009, 848,865 papers were added to PubMed, he says — that’s something like 1.6 papers per minute.

Continuing a discussion Continue reading LIMIT TO 5! What about a maximum of 5 papers per year per scientist? →

 

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Philosophy

Gambling with the planet

Found at project-syndicate.org, a piece by Joseph E. Stiglitz (Professor at Columbia University and a Nobel laureate in Economics):

In the end, those gambling in Las Vegas lose more than they gain. As a society, we are gambling – with our big banks, with our nuclear power facilities, with our planet. As in Las Vegas, the lucky few – the bankers that put our economy at risk and the owners of energy companies that put our planet at risk – may walk off with a mint. But on average and almost certainly, we as a society, like all gamblers, will lose.
That, unfortunately, is a lesson of Japan’s disaster that we continue to ignore at our peril.

 

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Genetics, Philosophy, Theology

The DNA window at the King’s College Chapel at the Strand

Here is another take home item of the recent EMGS 2011 meeting at the King’s College. Located in the apse there are 5 topics as originally conceived by Gilbert Scott: Christ in the carpenter’s shop, Christ and the lawyers, Christ healing the sick, Christ teaching the people and The Cruxification. While that may all be appropriate for today’s Sunday Continue reading The DNA window at the King’s College Chapel at the Strand →

 

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Philosophy, Theology

4 tons of CO2

I flew this night to San Francisco, having a chance to read some magazines in flight, including an interview of Stefan Klein with Peter Singer in ZEIT MAGAZIN yesterday. The interview has been done by Skype as Singer says “it is immoral to travel without serious reasons” – a classical Utilitarian perspective that does however not even stop him arguing Continue reading 4 tons of CO2 →

 

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Philosophy

Papers 2 – disappointing

I have long been waiting for upgrading Papers 1.9 as it is getting so slow with 10,000+ PDFs; there are notorious bugs that were never fixed (just delete an entry and see what happens). With the big hype around Papers 2, I hoped that all these problems would be cured while I also urgently need OCR, annotation and citation management.
When reading at the new support forum at http://support.mekentosj.com/discussions/problems/3118-papers-2-going-back-to-papers-1 of all the glitches introduced instead, it is probably time to say good bye now to Mekentosj.

 

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Philosophy, Video

Plagiarism or sloppy citation?

We have an interesting discussion here in Germany, how many sloppy citations are being allowed in a dissertation. Does plagiarism only start with central text passages? We all have signed a form like

Ich versichere, dass ich die Arbeit ohne fremde Hilfe und ohne Benutzung anderer als der angegebenen Quellen angefertigt habe und dass die Arbeit in gleicher oder ähnlicher Form noch keiner anderen Prüfungsbehörde vorgelegen hat und von dieser als Teil einer Prüfungsleistung angenommen wurde. Alle Ausführungen, die wörtlich oder sinngemäß übernommen wurden, sind als solche gekennzeichnet.

which is rather clear: “I used only the cited references and nothing else.” Continue reading Plagiarism or sloppy citation? →

 

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Philosophy

We are not suggesting that peer review is infallible

Nature medicine recently acknowledged our work as science bloggers by admitting

We are not suggesting, however, that peer review is infallible. Nonetheless, as editors, we hope that anyone accepting an invitation to review a manuscript considers that commitment as being of comparable importance to the other responsibilities of a busy researcher. And although we know that more pressing issues can take precedence over reviewing a manuscript, we still expect that the same level of integrity and objective, critical analysis will be applied to the assessment of the manuscript under review as is applied to the referee’s own work.

In German we say “blauäugig” which translates to “wonderful naive”. There are so many examples of non-integrity and non-objectivity of published research where the peer review failed to a large extent – many examples here and at other sites like retractionwatch or badscience. All these papers by Friedhelm Herrmann, Marion Brach and Roland Mertelsmann with the most recent examples by Carsten Carlberg (“It’s all her fault, and probably today is the worst day of her life when the world sees what she has done”“) and Silvia Bulfone Paus (“it was Elena and Vadim and the journal editors should have caught us“)

With the pervasiveness of the Internet, and the speed of communication it permits, commentary and criticism of research findings can occur almost immediately after their online publi­ cation. This medium should be actively embraced by the research community as a dynamic forum.

There is not even a trackback possibility for that Nature medicine editorial – the whole blogger’s laudatio thing reeks of hypocrisy.

 

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Joke, Philosophy

On the impossibility of being expert

The BMJ christmas edition has again some nice papers – with a theoretical account on denialism and the next paper on the impossibility of being expert. This looks like the best joke there, sorry Tony, probably unintended.

Since Alvin Toffler coined the phrase “information overload” in 1970, the growth of scientific and medical information has been inexorable. There are now 25 400 journals in science, technology, and medicine, and their number is increasing by 3.5% a year; in 2009, they published 1.5 million articles. PubMed now cites more than 20 million papers.

Yea, yea.

 

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Allergy, Philosophy, Software

Keep secret

There is a new Edge Special Event about the Hillis’s question “WHO GETS TO KEEP SECRETS?”

The question of secrecy in the information age is clearly a deep social (and mathematical) problem, and well worth paying attention to.
When does my right to privacy trump your need for security?; Should a democratic government be allowed to practice secret diplomacy? Would we rather live in a world with guaranteed privacy or a world in which there are no secrets? If the answer is somewhere in between, how do we draw the line?

With all the wikileaks hype over the last year, the Edge essay is la perfect supplement to our last paper about anonymity in genetics – check out BMC Ethics “Caught you: Threats to confidentiality due to the public release of large-scale genetic data sets“.
What we didn’t mention in this paper are more complicated statistics like stochastic record linkage – more on that in RJournal 2/2010, p.61 ff

 

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