PR vs. Nature vs. NASA vs. new life forms

The press echo was huge. Catched me by surprise as well. Sounds interesting. A bacteria that can go without phosphor.

Turns out this is only half of the story. Many scientists critizised the paper and the main point of the paper seems to be not well proven. The bacteria most likely used phosphor during the experiments. The used soil was simply contaminated.

But: Nobody knows for sure as long as there are no reproductions.

Derek Lowe writes an excellent article about it: http://pipeline.corante.com/archives/2010/12/02/life_with_arsenic_whod_have_thought.php

And Rosie Redfield sums it up:

If this data was presented by a PhD student at their committee meeting, I'd send them back to the bench to do more cleanup and controls.

http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html

The original paper:
Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.) PMID: 21127214

Egon about failing to aquire a grant

Hum... That's really funny somehow... :D
http://chem-bla-ics.blogspot.com/2010/11/more-fails-aka-no-vr-grant-awarded.html

On the other hand it's really sad to see that (imho) top scientists with the right attitude (getting things done, open access to data and methods and a great vision for the future) don't get funded. And the reason seems to be something completely different. Arg. @Egon: Happens, but in the long run this one won't matter at all. I guess they just did this to make us laugh.

ACS versus LeadScope - a sad summary

How big companies can easily kill smaller companies. There is something wrong in the legal system I guess:

http://depth-first.com/articles/2010/11/04/acs-versus-leadscope-leadscope-tells-its-story-in-court-document/

Cancer and the modern world

Cancer is really the pest of modern times. Often people tend to believe that the amount of cancer cases has increased. And - of course - in former times there was much less cancer.

True.

But only because people died earlier. Subsequently not many cancer types would occur at those ages. Despite that even the old greek described melanoma.

The other interesting thing is: If people become older. Their peers will be more likely die of cancer. That causes imho a huge bias in the perception of cancer.

Derek Lowe writes about it in detail:
http://pipeline.corante.com/archives/2010/10/20/is_cancer_a_disease_of_the_modern_world.php

Statistics and the validity of medical literature

http://pipeline.corante.com/archives/2010/10/19/trusting_the_medical_literature.php

Rebattle of anti blogger argumentation by Egon

http://chem-bla-ics.blogspot.com/2010/10/royce-murray-and-caveat-emptor.html

Mendeley CiteULike and a bit of controversy

Some thoughts about Mendeley and CiteULike:

http://blindscientist.genedrift.org/2010/09/17/a-short-list-of-things-i-dont-like-about-mendeley

http://scienceoftheinvisible.blogspot.com/2010/09/long-list-of-things-i-dont-like-about.html

http://chem-bla-ics.blogspot.com/2010/09/list-of-things-i-miss-in-citeulike.html

Cool papers August 10

My picks:
Nature Reviews drug discovery: Gene and drug matrix for personalized cancer therapy
http://www.nature.com/nrd/journal/v9/n8/full/nrd3181-c1.html

Nature BT: Can HIV be cured by Stem cell therapy?
http://www.nature.com/nbt/journal/v28/n8/full/nbt0810-807.html#/ref1


Nature Reviews Cancer: The evolutionary dynamics of cancer prevention:
http://www.nature.com/nrc/journal/v10/n8/full/nrc2892.htm

Colleagues from my grad school in PLoS CB: Alexander Skupin, Helmut Kettenmann, Martin Falcke

about Calcium Signals Driven by Single Channel Noise
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000870

Nature BT:  Microarrays in the clinic:
http://www.nature.com/nbt/journal/v28/n8/full/nbt0810-810.html

Interesting papers:
TIBS about a VDAC (Voltage dependent anion channel between mitrochondria and cytosol) and the validity of 3D structures
http://dx.doi.org/10.1016/j.tibs.2010.03.005


Zhiping Weng scores benchmarks again - protein protein docking benchmark version 4.0 in Proteins
http://onlinelibrary.wiley.com/doi/10.1002/prot.22830/abstract

Nice read about enchancing docking by using known templates that match. Especially the evaluation is cool: Proteins: Docking by structural similarity at protein-protein interfaces
http://onlinelibrary.wiley.com/doi/10.1002/prot.22812/pdf

PLoS Medicine tells us that having friends is healthy. I do not like the generalized sentences at the beginning (10% of britains feel lonely and stuff like that) without any references. But the rest is telling.
Social Relationships and Mortality Risk: A Meta-analytic Reviewhttp://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000316

Nature SMB about how they internally fight plagiarism:
http://www.nature.com/nsmb/journal/v17/n8/full/nsmb0810-917.html

Genome Biology wants better genome annotations: Genomic information infrastructure after the delugehttp://genomebiology.com/2010/11/7/402

Nature Biotechnology about a sad success. Gaining 3 months on average.
Industry makes strides in melanoma.
http://www.nature.com/nbt/journal/v28/n8/full/nbt0810-763.html

Nature expresses concerns about a Enzyme activity chip:
http://www.nature.com/news/2010/100728/full/466540b.html

Nature - finally - direct to consumer DNA tests will be regulated: http://www.nature.com/nature/journal/v466/n7308/full/466797a.html

Nature about really cheap shots by republicans on science funds (alhtough it's funny to read):
http://www.nature.com/nature/journal/v466/n7308/full/466797b.html

Nature reviews two book reviews about Leadership:
http://www.nature.com/nature/journal/v466/n7308/full/466819a.html

Nature News: Citizen science: Folding at home becomes gaming and thinking at home:
http://www.nature.com/news/2010/100804/full/466685a.html


Bioinformatics: Over-optimism in bioinformatics. A really cool study how over-optimism biases papers:
http://bioinformatics.oxfordjournals.org/cgi/content/full/26/16/1990

Nature about kill'em all (mosquitos):
http://www.nature.com/news/2010/100721/full/466432a.html

RNA - not waste - again:
http://www.nature.com/nature/journal/v466/n7306/full/nature09190.html

WTF? ACS Chemical information and modeling reviews Word perfect.
http://pubs.acs.org/doi/full/10.1021/ci100291b

ACS CINFM: Comparing ligand binding pockets usind C alphas alone:
http://pubs.acs.org/doi/abs/10.1021/ci100210c

Nature Reviews Cancer: It's nicer with Dicer - miRNA levels are lowered in human caners - but why? http://www.nature.com/nrc/journal/v10/n8/full/nrc2910.html

Science about Do We Have the Energy for the Next Transition?
http://www.sciencemag.org/cgi/content/full/329/5993/780?rss=1

Cool papers July 10

Nature says: Happy birthday human genome :) with this special:
http://www.nature.com/news/specials/humangenome/index.html

PLoS CB tells us about the history of Bioinformatics aka Computational Biology aka Biological Mathematics aka...
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000809

Interesting NGS + RNA Expression profiling setup:
Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencinghttp://nar.oxfordjournals.org/cgi/content/full/38/12/3999

Nature Genetics explores GWAS and the limits of what SNPs can tell:
On beyond GWAS:
http://www.nature.com/ng/journal/v42/n7/full/ng0710-551.html
Common SNPs explain a large proportion of the heritability for human height:
http://www.nature.com/ng/journal/v42/n7/full/ng.608.html


A novel GWAS analysis package based on Random Forrests 
Bioinformatics: On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data:
http://bioinformatics.oxfordjournals.org/cgi/content/full/26/14/1752

Future of publication - no real conclusion from Nature. Interesting: arxiv.org is mentioned, but busted because it is used "only" as preprint server and not as discussion platform.
Nature: When blogs make sense
http://www.nature.com/nature/journal/v466/n7302/full/466008a.html

Nature Reviews Cancer: Envisioning the future of early anticancer drug development:  http://www.nature.com/nrc/journal/v10/n7/full/nrc2870.html

Nature Reviews Genetics: Next-generation genomics: an integrative approach
http://www.nature.com/nrg/journal/v11/n7/full/nrg2795.html

Protein superposition reloaded - this time especially for variation. Hmm. I do not see any comparison with other methods:
BMC Bioinformatics: Robust probabilistic superposition and comparison of protein structures
http://www.biomedcentral.com/1471-2105/11/363

BMC Bioinformatics: Knowledge-based annotation of small molecule binding sites in proteins
http://www.biomedcentral.com/1471-2105/11/365

Nature Reviews Drug Discovery: Integrating molecular diagnostics into anticancer drug discoveryhttp://www.nature.com/nrd/journal/v9/n7/abs/nrd3135.html

Science: Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:
 http://www.sciencemag.org/cgi/content/full/329/5987/75?rss=1

Science Traveler's guide: Summer trips featuring some german places (Martin Gropius Bau in Berlin is really cool):
http://www.sciencemag.org/cgi/content/full/329/5987/34-a?rss=1

Epigenetics takes the centerstage again. Not sure what this means:
http://www.sciencemag.org/cgi/content/full/329/5987/27?rss=1

The Seductive Allure of Behavioral Epigeneticshttp://www.sciencemag.org/cgi/content/full/329/5987/24?rss=1

Cool papers June 10

Personal Highlights:

Nature Reviews Genetics:Next-generation genomics: an integrative approach
http://www.nature.com/nrg/journal/v11/n7/full/nrg2795.html

Nature Reviews Cancer: Envisioning the future of early anticancer drug development
http://www.nature.com/nrc/journal/v10/n7/full/nrc2870.html

Nature Reviews Drug Discovery: Virtual screening: an endless staircase?
http://www.nature.com/nrd/journal/v9/n4/abs/nrd3139.html



Cool papers:

 
Letter to the editor: About pharmaceutical companies and their ways to make more money
http://www.sciencemag.org/cgi/content/full/328/5984/1354-a


Book review: The power of checklists
http://www.sciencemag.org/cgi/content/full/328/5984/1357-a 


Cloud computing for comparative genomics
http://www.biomedcentral.com/1471-2105/11/259


GPU computing for systems biology
http://bib.oxfordjournals.org/cgi/content/short/11/3/323?rss=1

BLOGS
Whenever I am feeling down I write a Nature article
http://www.hcs.harvard.edu/~hsp/index.php?id=143_Nature 

People: Daniel Branton, Ph.D. and Jonathan Rothberg, Ph.D. (serial life sciences entrepreneur)
http://www.nature.com/nrd/journal/v9/n6/full/nrd3200.html

Q&A: Cancer cell metabolism - all you need to know
http://www.nature.com/nature/journal/v465/n7298/full/465562a.html

GPUs for RNA Microarray association studies
http://www.biomedcentral.com/1471-2105/11/329


Insights into Mentorship
http://www.nature.com/nature/journal/v465/n7298/full/nature09040.html

Maybe a cool method to deliver cancer drugs better to where they are needed
http://www.nature.com/nrd/journal/v9/n6/full/nrd3191.html
http://www.sciencemag.org/cgi/content/full/328/5981/1031

California vs. Nature (does it mimic USA vs. BP. vs UK? .. no). From the comments: "Fuck Nature - PLoS yea!". ok.
http://pipeline.corante.com/archives/2010/06/15/california_vs_nature.php

Pay people for compliance. Happens everywhere. Let's extend it to medicine.
http://pipeline.corante.com/archives/2010/06/15/paying_people_to_take_their_medications.php


Another method and webserver for RNA structural comparison called FRASS. Cool. They also take into account my LaJolla method. And the best: LaJolla does score very well.
http://www.biomedcentral.com/1471-2105/11/327

Self-Injurious Behavior in Adolescents. Interesting article from PLoS Medicine:
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000240
also interesting: Secondary prevention of suicide:
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000271
and - old people also kill themselves:
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000254

Journals vs. Pandemics vs. Hysteria vs. Reality. Critical Assessment in PLoS Medicine:
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000282

Venter scores again: Starring the synthetic bacteria man!
http://www.sciencemag.org/cgi/content/full/328/5981/958?

History vs. Archeology is exciting - more about the forgotten Paris zodiac Napoleon lended from Egypt:
http://www.nature.com/nature/journal/v465/n7298/full/465551a.html

Empowerment is key - a book review - I can't put it betterhttp://www.nature.com/nature/journal/v465/n7298/full/465550a.html

Protein crystallization - not an easy business - featuring an enhancement from Robert Fischett
http://www.nature.com/nature/journal/v465/n7299/full/465824a.html

Barabási about patterns of human behaviour. Cool. A book reveiw. Also interesting in the context of surveillance and such.
http://www.nature.com/nature/journal/v465/n7299/full/465692a.html

That's funny. Nature misspelling names. Happens I guess :)
http://www.nature.com/nature/journal/v465/n7300/full/nature09167.html
 
Really telling life: Obituary: Martin Gardner. Check out his books and this article:


http://www.nature.com/nature/journal/v465/n7300/full/465884a.html

Scientific metrics, IF, H factor and much more explained:
http://www.nature.com/news/2010/100616/full/465864a.html

Screening for cancer IS cool (not me - it's Lancet):
http://www.nature.com/nrc/journal/v10/n6/full/nrc2866.html

A primer to metastasis of cancer cells:
http://www.nature.com/nrc/journal/v10/n6/full/nrc2859.html

Nature about The role of mentorship in protégé performance

shown in the field of Mathematics:
http://www.nature.com/nature/journal/v465/n7298/abs/nature09040.html

MicroRNA processing without Dicer in Genome Biology:
http://genomebiology.com/2010/11/6/123
and also in Nature Reviews:
Small RNAs: Dispensable Dicer
http://www.nature.com/nrm/journal/v11/n7/full/nrm2932.html

Modularity of nucleotide binding pockets in proteins:
http://nar.oxfordjournals.org/cgi/content/short/38/11/3809?rss=1

Protein protein interaction IS complex indeed:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000821

Mutations in Drosophila - happening more often than one might think.
Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000924


That's what I want to read: NGS + a cool analysis:
Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000991


Maybe something for the newly founded German Academy of Sciences?
Nature: The right kind of elitismhttp://www.nature.com/nature/journal/v465/n7301/full/465986a.html


Cancer drugs hurt. And more long term research is needed.
Science: Childhood's Cures Haunted by Adulthood's 'Late Effects'

http://www.sciencemag.org/cgi/content/full/328/5985/1474?rss=1

Simply the future: Integrating stuff. Reminds me a little bit of the early beginnings of Computers. At the beginning they were small (in terms of transistors) and stupid. Now they are.. Hmm. Still stupid, but mankind has managed to make them superlarge and really powerful calculators that can be used for a range of things. The hope is that mankind can make abstractions on many levels to make sense out of the celullar machinery for the better.
Nature Reviews Genetics: From The Editors
http://www.nature.com/nrg/journal/v11/n7/full/nrg2826.html


Cool section in Nature (Article series):
Nature: Applications of Next Generation Sequencing
http://www.nature.com/nrg/series/nextgeneration/index.html

Detecting methylation can be powerful for many things. For instance diagnostics of cancer types and such. And there seems to be a new cool method available that can boost research there:
Nature Reviews Genetics: Technology: DNA methylation while you sequence
http://www.nature.com/nrg/journal/v11/n7/full/nrg2817.html

Interesting: There is a correlation between CpG content and mutation rate. But correlations can be tricky. 
Nature Review Genetics: Mutation: It's the CpG content that counts

http://www.nature.com/nrg/journal/v11/n7/full/nrg2820.html


Neandertal strikes. And keeps us busy most probably:
Nature Reviews Genetics: Genomics: Technical feat gives clues to human origins

http://www.nature.com/nrg/journal/v11/n7/full/nrg2821.html

Interesting. Knock out half of the genes on a diploid genome and get half of the protein content. But not always.
Nature Reviews Genetics: Functional genomics: One gene or two?http://www.nature.com/nrg/journal/v11/n7/full/nrg2816.html

Quotes

Fortunately, one of my most valuable career experiences was to learn early on not to be timid about trying new methods about which I knew little
http://www.nature.com/nrd/journal/v9/n6/full/nrd3200.html
Daniel Branton, Ph.D. Emeritus Professor of Biology, Harvard University, Boston, Massachusetts, USA.

Myon Robot of the Humboldt University and this Dr. "I do not publish papers" Hild

Now to something completely different. Nothing about Bioinformatics or Systems Biology - but about: artificial intelligence and robotics.

Once upon a time I had the opportunity to write my Studienarbeit (roughly a Bachelor's degree in the old german degree system) with Manfred Hild (Dr. Hild).

Manfred is mathematician and was ever interested in non linear systems and recurrent neural nets. Meaning (buzz words:) artificial intelligence and robotics. Additionally, he is able to solder and build real electronic stuff (something many computer scientists cannot do at all). Yea. At my time Manfred built strange small walking robots that learnt by themselves how to crawl using recurrent neural nets. Or talking robots that developed their own language. Really really cool stuff. But also really compelling and interesting for me.

Well. I followed a different path and ended up with Bioformatics and Systems Biology (not that bad though :) ).

During the last 7 years Manfred worked hard to build up an independent research group at the HU (Humboldt University) called "Labor für Neurorobotik" (http://www.neurorobotik.de). And he was really successful as it seems.

More interestingly, Manfred - as scientist - almost completely ignores the publication machinery. He just does a good job. This is truly something to learn from.

During the last weeks the group was able to catch great media coverage on their most recent project: The Myon robot. Check out that video and feel inspired: http://video.golem.de/wissenschaft/3289/making-of-myon.html

Blogs recommendations

This post is some kind of work in progress. I will add more blogs over the next week, months, years and update them frequently. Stay tuned.

Which blogs do you find in the following? Mainly blogs from individuals in the field of biology, genetics, bioinformatics, systems biology, drug design.

Roughly bioinformatics / computational chemistry:
http://blog.openhelix.eu/
http://chem-bla-ics.blogspot.com/
http://blog.rguha.net/
http://rosettadesigngroup.com/blog
http://depth-first.com/

Roughly biology /genetics:
http://pipeline.corante.com/

A good method to brainstorm and develop ideas and still stay focused

I am following the BioJava Hackathlon 2010 via some blogs, and Andreas introduced a cool method to think about things: http://creatingminds.org/tools/post_up.htm IMHO a nice way to make brainstorming and developing ideas more focused :)

There are blogs... and there are really cool blogs :)

This one writes only about really strange (or funny) stuff that got peer reviewed... Check it out :)

http://blogs.discovermagazine.com/discoblog/