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[23 Dec 12: 13:20]
Inbox zero! I don't even remember the last time I could say that!

[06 Aug 12: 14:21]
Phew! Done with nine 20min oral exams, three more to go. To be continued tomorrow...

[14 Oct 11: 11:45]
Just received an email from a computer science student - with an AOL email address?

[03 Jul 11: 22:26]
Google citation alerts suck: I just found out by accident I rolled over h-index of 13 and 500 citations http://blogarchive.brembs.net/citations.php

[21 May 11: 18:14]
6.15pm: Does god have Alzheimer? No #rapture in Europe...

[01 May 11: 11:31]
w00t! Just been invited to present at OKCon 2011! #OKCon2011


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Blogging on Peer-Reviewed ResearchWow am I out of the loop! Last I heard about the origins of life (abiogenesis) was in high school when we were discussing Manfred Eigen's Hypercycle. It all seemed really theoretical at the time and very remote from any real chemistry. And now I come across this fantastic video on PZ Myers' Pharyngula:



So basically, micelles can form the containers in which some early form of PCR might have been going on at places with convection such as hydrothermal vents. Brilliant and very plausible. I love to learn about stuff like this! These ten minutes were worth more than a whole lecture. Fantastic!
:-)

This is the work of Howard Hughes investigator Jack Szostak. Here are some links to some of his recent paprs:
Template-directed synthesis of a genetic polymer in a model protocell (Nature)
An Expanded Set of Amino Acid Analogs for the Ribosomal Translation of Unnatural Peptides ( PLoS One)
Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template (PNAS)
Selection and evolution of enzymes from a partially randomized non-catalytic scaffold (Nature)
Structural Insights into the Evolution of a Non-Biological Protein: Importance of Surface Residues in Protein Fold Optimization ( PLoS One)
Functional information and the emergence of biocomplexity (PNAS)
Posted on Monday 16 June 2008 - 16:28:56 comment: 1
abiogenesis   evolution   chemistry   video   

This one comes via Pharyngula. PZ Myers managed to write the entire syllabus for a course that involved creationism/intelligent design:

A magic man done it.

Yup, that's it. You can close your mouths and start clapping now. Apparently, PZ has the line from this video:



I think it's absolutely hilarious and should be THE tagline for anyone arguing with someone promoting ID/creationism as a science subject in school.
Posted on Monday 16 June 2008 - 15:16:28 comment: 0
evolution   creationism   intelligent design   video   fun   

I'm sitting in the Arlanda airport of Stockholm, Sweden right now, waiting for my flight back to Berlin. I interviewed for a professorship in neurophysiology at the University of Uppsala. Everybody there told me they liked what I had to say. However, the committee will only recommend their choice to the faculty and the final decision is not expected before august/september. You'll find out if I move to Uppsala
Posted on Sunday 15 June 2008 - 11:39:19 comment: 0
interview   Uppsala   

Originally, it was planned to release our latest video on the Drosophila flight simulator with an article I wrote for the website of BBC radio show "The Naked Scientists". However, I now was invited to contribute to the neuroscience carnival "Encephalon" and the article is not quite ready for publication, yet (but very soon, check here). So I decided to go ahead and load the video onto YouTube for the carnival and for your viewing pleasure:


Intro by Apocalyptica.
Posted on Sunday 08 June 2008 - 23:05:30 comment: 0
Drosophila   flight simulator   video   fun   flight   science   

Blogging on Peer-Reviewed ResearchI had the priviledge to meet Randolph Nesse ("Why we get sick", his blog) here in Berlin at a dinner with visiting blogger Bora. He now sent me one of his articles on Evolutionary Medicine: "The great opportunity: Evolutionary applications to medicine and public health" It's open access so you can go and download it without subscription. What is evolutionary medicine? From the article: "At the core of evolutionary medicine is recognition that diseases need both proximate explanations of bodily mechanisms and evolutionary explanations of why natural selection has left the body vulnerable to disease." The article is about how much medical research and education would have to gain from a more evolutionary perspective in their approach to disease. Here are some more quotes from the text:
An evolutionary perspective fundamentally challenges the prevalent but fundamentally incorrect metaphor of the body as a machine designed by an engineer. Bodies are vulnerable to disease – and remarkably resilient – precisely because they are not machines built from a plan. They are, instead, bundles of compromises shaped by natural selection in small increments to maximize reproduction, not health. Understanding the body as a product of natural selection, not design, offers new research questions and a framework for making medical education more coherent.
I also liked this one:
Universities talk a lot about promoting interdisciplinary work precisely because their structures so efficiently prevent it. However, disciplines exist for good reasons. There is too much to know. Trying to synthesize work from diverse areas is frustrating, especially if the goal is general understanding, not some fine point. Also, going beyond your specialty means you will inevitably get some things wrong. It is easier to maintain quality by keeping to a narrow focus.
The authors argue, and I think successfully, that without the evolutionary perspective, medicine is only using half of biology. Obviously, one important aspect is genetics. The authors reinforce the notion that many if not most genes which are associated with a certain disease are not defective in any way:
Many physicians think of genes that cause disease as abnormalities in an otherwise ‘normal’ genome. This is a nonevolutionary view on two counts. First, it tacitly views the genome as a product of design with a blueprint that defines ‘normal.’ The genome is, instead, a collection of those genes that have tended to increase reproductive success (or hitchhiked on the success of other genes) while interacting with each other and the environment to construct a functional organism. Second, while some DNA sequences can be accurately described as ‘damaged’, it is increasingly clear that many medically relevant genetic variations are helpful or harmful only in interaction with particular aspects of environments.
I really like this argument and I also think that it constitutes a very profound insight which changes the way in which diseases are perceived. There is one really small instance where I would argue differently, though:
Taking out [...] a gene and looking to see what goes wrong can generate hypotheses about how an organ or gene is useful. Often, no abnormality is observed. Of course, this does not mean that the gene is useless, only that its effects are covered by redundant systems, that its benefits are manifest only in special situations, or that the benefit is just too small to be observed in a laboratory setting.
Redundancy is something that is very hard to achieve in evolution. If one gene is functional, the redundant gene is not needed and will accumulate mutations. I would argue that degeneracy is a much better explanation for many failures to find a phenotype associated with a specific gene knock-out.
Besides the interesting and important insights into evolutionary medicine in general, the article also offers a few fascinating factoids such as:
Nearly 10% of Staphylococcus aureus are now resistant even to methicillin; infections
caused by this resistant organism now cause 18 650 deaths per year, more than the 12 500 caused by AIDS (Klevens et al. 2007). The economic burden of antibiotic resistance is estimated at about $80 billion annually in the USA.

In all, I found it to be a very interesting and enlightening article which will help me explain why what I'm doing is not only fun, interesting and beautiful, but may also one day be useful. mistrust.png
Posted on Wednesday 04 June 2008 - 11:14:27 comment: 0
evolutionary medicine   Nesse   evolution   

Now here's a must-read for anyone interested in entering a science career. The journal "Ethics in Science and Environmental Politics" has just published a special issue called "The use and misuse of bibliometric indices in evaluating scholarly performance". The title says it all and if you think that some unknown math nerds have gotten together to publish their new bibliometric formulae, you are sorely mistaken. Big shots in the science industry such as Nature Editor-in-Chief Philip Campbell and some other people you might know join the author list. I still haven't read all of the papers, but already now I can quote some instant classics: Philip Campbell:
Our own internal research demonstrates how a high journal impact factor can be the skewed result of many citations of a few papers rather than the average level of the majority, reducing its value as an objective measure of an individual paper. [...] The majority of our papers received fewer than 20 citations. [per year] [...] the numbers quoted in calculating the impact factor are highly questionable. Try as we might, my colleagues and I cannot reconcile our own counts of citable items in Nature, several other Nature journals and indeed Science, with those used by ISI. [...] the judgement of ‘better’ is best kept independent of the impact factor. [...] for a sure assessment of an individual, there is truly no substitute for reading the papers themselves, regardless of the journal in which they appear.
William Cheung:
young scientists may even develop bad writing habits (e.g. exaggerating implications of findings, over-simplifying analyses and conclusions, ignoring caveats) if an excessive desire to publish in high-impact journals skews their scientific judgement or publication ethics. [...] The use of publication counts and number of citations to assess academic performance do affect the publishing strategy of young scientists. Particularly, at the stage of being a post-doc, to compete for the limited number of junior faculty or equivalent research positions, one would try to maximize the number of publications and their impacts in a short time-horizon
Peter Lawrence:
It has always been crucial for research scientists to publish their work. There have always been 3 purposes: first, to disseminate new information so that others can learn from it; second, so that other scientists may repeat the studies, or build on them with additional observations or experiments; and only third, so that the support, financial or otherwise, for the scientist can be justified to interested parties. This third reason used to be subsidiary, but no longer; publication has become the main goal because it is the scientist’s lifeline (Lawrence 2003). This enormous change in emphasis has damaged the practice of science, has transformed the motivation of researchers, changed the way results are presented and reduced the accuracy and accessibility of the scientific literature. [...] Since scientists are now assessed, not so much by the validity, interest or quality of the work itself, but by the impact factor of the journal (Steele et al. 2006), many, if not most scientists, spend too much time and effort thinking and worrying about publication strategy. [...] Politics enervates science. [...] I predict that ‘citation-fishing and citation-bartering’ will become common practice [...] scientists will claim superiority over others if they have more citations, and this will be endorsed by bean counters everywhere [...] There are other consequences of the use of numerical measures: given that meeting them rewards aggressive, acquisitive and exploitative behaviour (Lawrence 2002, Lawrence 2003, Montgomerie & Birkhead 2005), their use will select for scientists with these characteristics. [...] grant applications do not describe what you will actually do but are in reality an ingenuity and knowledge test in which honesty is little valued; they amount to an attempt to demonstrate that one knows what one is doing and can divine what the outcomes of experiments will be and assess what might be risky to reveal.
Todd & Ladle:
Our paper supports Lawrence’s (2007, p. R583) view that impact factors and citations are ‘dodgy evaluation criteria’, and we strongly advise against a system that wholly relies upon them to evaluate a scientist’s contribution.
Definitely one of the most insightful articles is The Siege of Science. If all of this doesn't whet your appetite to go and read all of them, I don't know what possibly could. The total of the articles just reinforces my point of view: we need to get rid of journals. Period. All of them. One single, peer-reviewed, open-access database for primary scientific literature. Have journals publish reviews or such. A single open-access scientific database provides everyone with the most important asessment resource: the scientific papers to read and study. If any additional metrics are required, then one can sort articles according to downloads, citations, comments, ratings, editor's choice, media coverage, trackbacks, links or whatever else strikes your fancy. Of course, on every paper you can click on any author and get all their papers with all the meta-data. On top of all that, no more ISI, PubMed or any other indices to search for papers: they're all searchable in full text in one place.
Posted on Tuesday 03 June 2008 - 17:29:09 comment: 0
bibliometrics   science publishing   citations   citation metrics   impact factor   citation statistics   

I finally had some time to upload the videos I have from our various gymnastics shows we did. Have fun!


Link: sevenload.com

Link: sevenload.com

Link: sevenload.com

Link: sevenload.com

Posted on Monday 26 May 2008 - 15:46:26 comment: 3
gymnastics   pommel horse   high bar   show   video   fun   

Just got back late last night from a brief stint to the Austrian Alps (Hintertux) for a final snowboarding trip this season. I haven't been boarding since 2002 when I took the opportunity to watch some competitions of the Olympics in Salt Lake City, Utah and went snowboardng there. Obviously, I was more than a little itching to go!
The weather was perfect and the snow fantastic so it was a formidable trip. Now, of course, I'm sore as hell, but that's what you get for not going down the hills for 6 years! smallgrin.png
Here's a picture of what our resort looked like the past 4 days, taken with my Palm Treo:

hintertux08_thumb.jpg
Posted on Wednesday 14 May 2008 - 17:29:26 comment: 1
sports   snowboarding   Hintertux   

Blogging on Peer-Reviewed ResearchProbably the most important common denominator of evolutionary theory and neuroscience is degeneracy. The degeneracy found in gene networks and the degeneracy found in the organization of brains. See e.g. 2001 PNAS article by nobel laureate Gerald Edelman. In it he writes:
[Degeneracy] is both necessary for, and an inevitable outcome of, natural selection.
In other words: if there were no evolution, there would be no degeneracy.
Therefore, creationists will have to explain why there is degeneracy if there is no evolution.

In the latest issue of ScienceExpress, there is an absolutely fantastic study by Tagkopoulos et al. from Princeton showing how evolution leads to gene-networks which are both anticipatory and degenerate. From the abstract:
We show that in silico biochemical networks, evolving randomly under precisely defined complex habitats, capture the dynamical, multi-dimensional structure of diverse environments by forming internal models that allow prediction of environmental change. We provide evidence for such anticipatory behavior by revealing striking correlations of Escherichia coli transcriptional responses to temperature and oxygen perturbations — precisely mirroring the co-variation of these parameters upon transitions between the outside world and the mammalian gastrointestinal-tract.
It is interesting to note that in the article, the authors confuse degeneracy with "redundancy" which, of course, it a very different thing. Notwithstanding, their meticulously designed simulations and experiments have elucidated how amazingly intricate and complex comparatively simple organisms can become if you allow them to evolve and that degeneracy is both a prerequisite and an outcome of evolution.

This paper joins one in Nature I already reported about. It also shows how the complex, degenerate properties of gene networks underscoring the importance of the ubiquitous concept of degeneracy.
Together, these two papers have the potential to develop into two of the most important papers in all of biology. They are required reading for everyone with an interest in evolution.

To close the loop to neuroscience: the degeneracy which is displayed in evolved gene networks is reflected in the evolved organization of brains. Different network configurations can produce the same behavioral output (Prinz et al. Nature Neuroscience, 2004). This degeneracy in the brain also leads to something not explicitly shown in gene-networks (AFAIK): the same neuronal network can produce different behaviors even under identical external circumstances (our own study on spontaneous behavior and Briggman et al, Science, 2005). It has been known for quite some time now that spontaneous behavioral variability has enormous fitness benefits and is affected in a variety of psychiatric disorders. This is now not so surprising any more. It's all starting to make perfect sense now.
Posted on Friday 09 May 2008 - 12:40:53 comment: 4294967281
evolution   creationism   robustness   degeneracy   neuroscience   

The journal "Epidemiology" has a series of great articles on why we need to get rid of Thomson Scientific's Impact Factor. I've reported about this ridiculously influencial number before and how irrational, stupid and detrimental to science it is (1, 2, 3). Here the links to the great Epidemiology articles (via Coturnix):
I think there's more than enough evidence that the Thomson Scientific impact factor is a pernicious invention that needs to be eradicated and replaced by a multivariate measure consisting of post-publication reviews, ratings, access statistics, citations, media coverage, link-counts, etc.

To say it with the authors at Epidemiology:
in its present format, the impact factor should be killed off, and the sooner the better.

Having a collection of impact measures will only be sensibly feasible in a large, decentralized databank in which all peer-reviewed scientific primary literature is collected, cross-referenced and stored. Of course, the algorithms for any such metric need to be transparent. The data is all there, the technology is around. Now we only need to get the word out and bring the majority of scientists behind us. If scientists are as rational as they claim, they have no choice but to follow their rationality and get on with the program

If this is so, why do we still have journals? One of the authors has the answer:

The irresistible fascination with (and picturesque uses of) a construct so scientifically weak as BIF are simple reminders that scientists are embedded in and embody culture. We are vain and contradictory human beings too [...].
Posted on Friday 09 May 2008 - 10:30:34 comment: 1
Thomson Scientific   impact factor   citation statistics   citation metrics   journal ranking   

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