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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)
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 |

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

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 |
Link: sevenload.com
Link: sevenload.com
Link: sevenload.com
Link: sevenload.com
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!

Here's a picture of what our resort looked like the past 4 days, taken with my Palm Treo:
[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 |
- Epidemiologists (of All People) Should Question Journal Impact Factors
- Impact Factor: Good Reasons for Concern
- How Come Scientists Uncritically Adopt and Embody Thomson's Bibliographic Impact Factor?
- Rise and Fall of the Thomson Impact Factor
- The Impact Factor Follies
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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