Attending several large conferences every year, I know what Andre at Youtube is talking about:
This has even a name – Powerpoint Karaoke, yea, yea.
Craving comes from the insula
You may renember the homunculus – a projection of body functions on brain areas. There is an interesting clinical extension stemming from 69 stroke patients of which 15 immediately, easily and permanently quit smoking. One patient said that his “body forgot the urge to smoke”. Sure, this analysis may still be somewhat confounded by the fact that certainly more areas are usually destroyed – but there are interesting approaches that could be followed up, the authors speculate about influencing sensory airway representation, neurotransmitter therapy and monitoring of smoking cessation programs. So stroke may help to quit smoking but I think there are better ways to do that. Seems that Science won this race with Nature. Yea, yea.
Addendum
Don’t miss the follow up.
More -omics
Genomeweb Daily News has a short -omics story
describing the 2-year-old project as one that will “have more immediate impact on medicine and medical practices than the Human Genome Project,†the University of Alberta said researchers have catalogued “2,500 metabolites, 1,200 drugs, and 3,500 food components that can be found in the human body.â€
Here is the the Human Metabolome Database by Genome Alberta that reports slightly different figures on the intro page (attn HMDB is not identical to the Human Mitochondrial Database!)
The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database currently contains more than 2100 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (>1 mM) or relatively rare (<1 nM). Additionally, approximately 5500 protein (and DNA) sequences are linked to these metabolite entries.
The NAR Jan issue has the accompanying paper:
Metabolomics is a newly emerging field of ‘omics’ research concerned with the high-throughput identification, quantification and characterization of the small molecule metabolites in the metabolome.
Biomedical journal search – a small gift
Pubmed often leads you to dead ends – journal citations without a link to the journals’ home. Google helps sometimes but is always time consuming. As a little gift for you, I have written a small bookmarklet that will scan the Regensburg library files – just left click on the
link below and move it to your browser toolbar. With just a mouse click you can then locate the journals homepage.
Addendum
Another approach – the LibraryLookup Bookmarklet Generator.
(Re)programming adult into pluripotent cells
Last August I found an interesting paper in Cell that could mark a scientific breakthrough. In a step down approach the authors were able to reduce a mix of 24 transcription factors to 4 that were still able to induce a mouse embryonic stem cell signature (by using a fusion cassette of ß-galactosidase and neomycin resistance into Fbx15 gene).
The magic cocktail consisted of Oct3/4 and Sox2 (both embryonic stem cell core factors that directly target Fbx15), c-My (does global histone acetylation) and Klf4 (represses p53 directly).
My first question is if this cocktail reprogramms differentiated cells or if it just selects rare progenitors otherwise hidden under more fibroblast cells. My second question is if these are fully reprogrammed cells – or if the Fbx15 signature is somewhat misleading. My third question: Is this effect mouse specific?
I have now checked ISI if any paper is already citing this work – it seems that we need more patience. Yea, yea.
Offline blogging
Usually I write emails to my blog server but there are more professional solutions: Sun Weblog Publisher (R) and Microsoft Live Writer (R). Quite nice tools but insert unnecessary tags, yea, yea.
Beam me up, Scotty, ….
Mirror neurons
I found an interesting extension of my self blog at Edge
Five and a half years ago, Edge published a notable essay by neuroscientist V.S. Ramachandran, entitled MIRROR NEURONS and imitation learning as the driving force behind “the great leap forward” …
And, one year ago, we published a related essay, Mirror Neurons and the Brain in a Vat [1.10.06], which further developed this set of ideas …
Here, for the Edge 10th Anniversary Essay, we are pleased to present a new work, “The Neurology of Self-Awareness”, in which “Rama” explores the concept of the self, tying in the ideas of researchers such as Horace Barlow, Nick Humphrey, David Premack and Marvin Minsky (among others), who have suggested that consciousness may have evolved primarily in a social context.
Ramachandran shows an interesting development – by chance quite similar what I am currently reading from Alfred Adler and his scholar Rudolf Dreikurs: children (and adults) want to be accepted as individuals and want to be at the same time part of a group. Martin Buber comes to my mind “Der Mensch wird erst am Du zum Ich”. Yea, yea.
Don’t miss the NYPL digital gallery for a more detailed view of mirror neurons.
DNA data travel across Europe
heise.de reports that a top German politician wants to apply the Prüm contract also to the EU. The Prüm contract signed in May 2006 by Germany, France, Luxembourg, Netherlands, Austria and Spain regulates anti terror measurements and cross border prosecution of crimes. Mainstay of these activities are databases that allow the exchange of DNA and fingerprint data. Within the first 6 weeks of activity (as by November 2006) they report 1500 German hits in Austrian records (8 million inhabitants) and 1400 Austrian hits in German records (82 million inhabitants) if I understand that correctly. What does this now mean to have a German or a British or Swiss passport? For a respectable citizen and for a desperado?
Addendum
5-2-07 update U.S.
6-3-07 update Germany
Allein im vergangenen Jahr nahmen die deutschen Polizeibehörden laut einer BKA-Statistik 72.280 Verdächtigen den genetischen Fingerabdruck ab, “immer häufiger auch bei eher geringfügigen Straftaten”, kritisiert Datenschützer Weichert.
Banned DNA tests
The Korea Herald writes – as noticed by Hsien Hsien Lei
The government yesterday released a set of new regulations to ban or restrict genetic tests in 20 categories amid ethical concerns over DNA tests … According to the new guidelines, DNA labs will be banned from conducting tests in 14 categories including body mass, intelligence, strength, propensity for violence, longevity, mental health, diabetes, blood pressure and asthma.
Although I do not believe that genetic testing for “asthma genes” will make any sense without the context of scientific studies, I think that such regulations are overdue – at least when genetic testing does not provide any benefit but may pose harm. If you have asthma or not, is a clinical question – and the answer will be an appropriate treatment or not. If you ever will get asthma is a question that nobody can answer. Even if genetic prediction will be ever possible, there is still no preventive measurement (at least by Jan 18, 2006, 16:14:23) . Yea, yea.
déjà-vu
ZEIT online has an interesting article about ddéjà-vu – a rare syndrome. Some psychiatrists believe that déjà -vu episodes are the result of a faulty memory that brings up a similar episode. Others believe that there is nothing at all – just electric loops of a petite mals that can also be triggered by electric stimulation of the gyrus parahippocampus. ZEIT online also cites a study of Alan Brown that adds evidence for some kind of implantable memory.
I have frequently déjà-vus when reading the scientific literature (sometimes I even believe in groundhog days). One of my teachers in Marburg always said that “study of the scientific literature prevents from new discoveries”. Yea, yea.
Playing with your browser
Some blog authors are nuts about protecting their web site from copying files. There are many ways to protect your site – but only one really good (publish nothing). I often see small javascripts that disable the ability to right-click where javascript.about.com has a much simpler solution:
<body oncontextmenu=”return false;”>
Please try a right click now…
If you are fooled by a web author in such a way, what could you do? tech-recipes has the answer: Of course, we can use javascript to turn it back on.
When visiting the offending website, type the following into the URL bar of your browser:
javascript:void(document.oncontextmenu=null)
Happy browsing, yea, yea.
Serendipity
What is serendipity? Probably an artifical word used by Hugh Walpole 1754 in a letter he wrote to his friend Horace Mann
the effect by which one accidentally discovers something fortunate, especially while looking for something else entirely
Some examples www.scienceiq.com/Facts/
Ambroise Pare learned otherwise when, after running out of oil during the siege on Turin, he found his untreated soldiers recovering better than the treated ones. Another example is Louis Pasteur. He left a culture of chicken cholera microbes in his lab … Rontgen’s chance observation of a green glow in the corner of his laboratory led to the discovery of X-rays. … Finding a way to make rubber impervious to temperature changes became an obsession to Charles Goodyear. One day, in 1844, after countless unsuccessful trials, he dropped a mixture of rubber and sulfur on a hot stove. …Vulcanization was born…. Kekule proposed the cyclical structure of the benzene ring after dreaming.
Anf course the famous text by Arthur Kornberg, Stanford Medicine 1995 “Of serendipity and science” (that seems to vanished from the internet).
Photoshopped
How to recognize photoshopped pictures? This will be a routine task for future editorial process (BTW I already recognized a faked gel gel picture where the edges and density of the bands looked somewhat artifical). However, with the ever increasing technical capacities we probably need non-destroyable, watermarked pictures from professional scanning and digitizing equipment.
In the meantime, check Wikipedia and the links there. I believe that the majority of the faked pictures could have been detected by splitting up color channels and looking at non-continous transitions of hue (“Farbton”), saturation (“Sättigung”) and brightness (“Helligkeit”) or grey value. This will even work with scanned figures although I would recommed to check original computer files (that may always be electronically stamped by previous publishers). Don´t miss the website of the mp3 developers).
Addendum
Here is another examples how to recognize photoshop spoof:
set the hue to a low setting, the saturation to a higher setting, and mess with the light and look for blotches of color that don’t follow the rest of the image
22-2-07: The JBC has now adopted an explicit policy
“No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The groupings of images from different parts of the same gel, or from different gels, fields or exposures must be made explicit by the arrangement of the figure (e.g. using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if and as long as they do not obscure or eliminate any information present in the original. Nonlinear adjustments (e.g. changes to gamma settings) must be disclosed in the figure legend.
11-9-07 Hamin Farid has developed tools to detect digital tampering.
I am the guy with the hammer, and everything is a nail
We could think in more general terms about this quote from an interesting benchmarking paper. (I renember a DFG referee saying that I am no expert for the applied study. Vice versa we all see studies where everything is treated with a hammer.)
With a lot of data on my desk, however, I am more interested in the technical conclusions of the paper and feel quite comfortable with their opinion that commercial RDBMSs are not always the best choice. These RDBMSs include more and more features, and missing features are included in add-on packages from third party vendors. With these ever increasing features also useless overhead is being increased with penalty for performance.
A redesign for special databases like those used in genetic epidemiology and bioinformatics therefore seems to be invitable. Some may have already noticed my preference for SQLite, HDF-5, NetCDF.
- Do we really need client-server mode?
- We may ask if not 90% of all tasks can be done in presorted arrays (or materialized views).
- Why can`t processes run completely in virtual memory without disk I/O?
- Is there any chance to compile to machine code for better performance?
- Why not ordering task for priority with those having minimum latency being the first in the row?
Yea, yea.