Tag: Misc.

I so want a few 1000 of these: Mobile Robotic Laboratory from MBARI

Thanks to Michael Ferrari for pointing me to this:: Mobile Robotic Laboratory Will Track Ocean Toxins – Popular Mechanics.  The article discusses some developments at MBARI for mobile sensor / sampler devices that could be used for various marine microbiology studies.  A few years ago I got a tour of MBARI from Alex Worden (see pics below) and got to see some of their toys but many of the developments in this article are new to me.  I can’t wait until it is possible to deploy a few hundred thousand of these and get massive amounts of data …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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ASM2013 – One of the best parts – meeting the "Young Ambassadors"

I attended the American Society for Microbiology (ASM) meeting in Denver last week.  It was a bit overwhelming as usual, with the 1000s of people there.  One surprise for me was an invitation to a after dinner party hosted by Nathan Wolfe and others from Metabiota.  I am not really a big fan of parties (as many who know me know) but this was small and even better it was mostly populated by the recipients of the ASM International Young Ambassador Award winners.  Wolfe was one of the keynote speakers at the ASM Meeting and I think he was hosting this party in part as a reception for the Young Ambassador’s.

For more on the winners see

Anyway – it was very interesting to talk to many of them.  And I even got a picture with one of them – Yu Xia from Hong Kong (we were trying to form some sort of Tree of Life with our fingers).
All societies have their good and bad parts.  Sponsoring Young Ambassadors from other countries is definitely one of the very good things ASM does.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Worth a look: PhyloFacts FAT-CAT web server: ortholog identification & function prediction

Quick post.  This seems like a potentially useful resource and tool: The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

Abstract:
The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Citizen (Funded) Science

As evidenced by the buzz around the Citizen Science session at ASM yesterday, microbial ecologists are increasingly looking for ways to engage “Citizen Scientists” to participate in large-scale projects, often by crowd-sourcing sample collection. This concept is not new; in fact, citizen scientists have been counting birds every year for over 100 years!

A recent price drop in high-throughput sequencing technology has enabled the ginormous scale of current citizen science projects. Anyone who is interested can participate by swabbing their homes or their poop! This same price drop also enables a different sort of citizen scientist. This sort of citizen scientist is not tied to any pre-existing project, but is free to imagine his own. If he can convince the right person that his project is interesting, he can fund it himself with relatively little cash.

Dan Prater is exactly this sort of citizen scientist! He was curious about the microbial succession taking place in the compost tea that he was brewing on his family’s organic farm in Indiana. So, he asked Jonathan Eisen to help him figure it out! Dan collected a time series of samples from two different batches of compost tea. He shipped the samples to UC Davis, and I prepared 16S rRNA PCR libraries from them. We went from sample collection, through a MiSeq run, to a poster at ASM (with data) in a month! <sound of my horn tooting>

If you are at ASM, you can check out this poster tomorrow, Tuesday, May 21 from 1:00-2:45pm! It’s poster #2402, entitled Phylogenetic Analysis of and Actively Aerated Compost Tea.

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note – I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad – covering all microbes – all the time – everywhere. But much of it is due to a growing interest in the microbes closer to us – those that live in and on us (the human microbiome) – those that live in and on plants and animals and other organisms we care about – and those that live in the places where we spend much of our time (the microbes of the built environment). I mean – come on – everyone is talking about fecal transplants now in public – in cover stories of the NY Times Magazine and in Ted talks.

  • Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too. 
  • The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology. 
  • Citizen Science is growing by leaps and bounds in other areas (e.g., check out http://www.scistarter.com). 
  • Crowdsourcing (not the same thing as Citizen Science – more on this another time perhaps) is also growing in leaps and bounds. 
  • Crowdfunding is providing new ways to fund scientific activities. 
  • Sensors of all kinds are getting cheaper and easier to use and are being deployed widely. 
  • Many people are becoming more and more interesting in recording information about themselves and sharing it with others. 
  • The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research. 
  • Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used. 

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include 

  • Germophobia is rampant and fueled by media hype and marketing forces. 
  • We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on 
  • Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know – claiming that probiotics will cure all ailments for example. 
  • Some information about microbes that is out there on the web is, well, less that ideal 
  • The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most. 

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

  • Ethics 
  • Funding 
  • Openness and sharing 
  • Visualization 
  • Analysis tools 
  • Communication 
  • Outreach 

And of course – the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project – well – why not? Get your act together.

Anyway – got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

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Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.

UPDATE: Notes from the Session Added 5/23

Here are some notes from the meeting:
Meeting Report: ASM 2013 in Denver, Day 1
ASM 2013, Day 1: From Oceans to Guts
Citizens doing Science, or Science on Citizens? (ASM 2013: Post 1)
Symbionticism: ASM 2013 LINKS
Storify by SPONCH

My storify embedded below

//storify.com/phylogenomics/asm2013-citizen-microbiology/embed//storify.com/phylogenomics/asm2013-citizen-microbiology.js[View the story “#ASM2013 Citizen Microbiology” on Storify]

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Thanks to Software Carpentry (@swcarpentry) for coming to #UCDavis

Quick post here.  Jenna Lang in my lab has a post at microBEnet about the recent workshop that the Software Carpentry folks ran at UC Davis: Software Carpentry comes to UC Davis! | microBEnet: The microbiology of the Built Environment network.  It was a major success.  For those who don’t know Software Carpentry’s mission is is to build basic computing skills among researchers.  From their web site:

Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn’t rare.

A great idea and done really well.  Others out there should consider hosting or attending one of their Boot Camps and checking out their materials on their web site.  See for example their videos and their reading list and their lessons.  They really do great things …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

ICG Europe starts w/ "Omics & the future of man" & sticks to men the rest of the time

Fun.  Another day.  Another YAMMGM (yet another mostly male genomics meeting).  This one is the International Conference on Genomics Europe 2013.  I have copied the program as it is now here and then highlighted the men and women as far as I can tell.  And, well, it is not very balanced.  It starts off, ironically, with “Omics and the future of man” and then stays on both omics and alas, men, for most of the meeting.  The first woman does not talk until 5 pm on the first day.  Nothing against BGI per se.  But they seem to be repeat offenders in having meetings with mostly male speakers.  A difference between countries?  Perhaps.  But unfortunate and unpleasant nevertheless.

Sessions with speakers:

Plenary Session 1: Omics and the future of man

  • 09:00-09:10: Opening ICG-Europe 2013 & Welcome: Hans Galjaard, Chairman of the Department of Clinical Genetics at Erasmus University
  • 09:10-09:55: Talk 1: Huanming Yang, BGI, China
  • 9:55-10:25: Talk 2: Jeremy Nicholsen, Head of the Department of Surgery and Cancer, Imperial College London, UK
  • Topic: Molecular Phenotyping and Systems Medicine Approaches in Personalised and Public Healthcare

Chairman: Prof.Huanming Yang, BGI, China

Plenary Session 2 :

  • 11:00-11:30: Talk 1 (30 min): Jun Wang, CEO, BGI, China
  • 11:30-12:00: Talk 2 (30 min): Karsten Kristiansen, Head of the Department of Biology, University of Copenhagen, Denmark
  • 12:00-12:30: Talk 3 (30 min): Nils Brunner, Director of the Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Denmark
  • Topic: Docetaxel resistance in vitro: Known mechanisms and novel pathways in breast cancer
  • Chairman: Prof. Jun Wang, BGI, China

Plenary Session 3: Plant and Animal Genomics

  • 13:30-13.55: Talk 1: Rajeev K. Varshney, Director-Centre of Excellence in Genomics, ICRISA, Hyderabad, India
  • Topic: “Little” is “more” for chickpea and pigeonpea
  • 13.55-14.20: Talk 2: Michael Bevan, Genomics and Functional Genomics of Bread Wheat for Crop Improvement, John Innes Centre, Norwich, UK
  • Topic: Genomics and Functional Genomics of Bread Wheat for Crop Improvement
  • 14.20-14.45: Talk 3: Michel Georges, Unit of Animal Genomics, University of Liège, Belgium
  • 14.45-15.15: Talk 4: Tomas Marques, ICREA Research Professor, Universitat Pompeu Fabra, Spain
  • Topic: Great Ape genetic diversity
  • 15.15-15.35: Talk 5: TBC
  • Chairman: Prof. Marc Van Montagu , VIB, Belgium

Session 4: Cancer genomics and Transcriptional Regulation

  • 16:00-16:20: Talk 1(20 min): Stein Aerts, Heading the Laboratory of Computational Biology, K.U.Leuven, Belgium
  • Topic: Probing into the genome, transcriptome, and regulatory network of T-cell acute lymphoblastic leukemia
  • 16:20-16:40: Talk 2(20 min): Lars Bullinger, Assistant Professor, University of Ulm, Germany
  • Topic: Genomics in acute myeloid leukemia (AML) – clinical translation of findings
  • 16:40-17:00: Talk 3(20 min): Diether Lambrechts, Assistant Professor, K.U.Leuven & VIB, Belgium
  • Topic: Mutation signatures of mismatch repair deficiency in cancer genomes
  • 17:00-17:20: Talk 4(20 min): Lynnette Fernandez-Cuesta, University of Cologne, Germany
  • Topic: Characterization of lung neuroendocrine tumors
  • 17:20-17:40: Talk 5(20 min): Henrik Ditzel, University of Southern Denmark, Denmark
  • Chairman: Dr. Jan Cools (K.U.Leuven, VIB)

Workshop：Innovation-Entrepreneurship and Venture creation-1

  • 14:30-14:50: Talk 1 (20 min): Boo Edgar, Program Director, Innovation and entrepreneurship; The Sahlgrenska Academy, University of Gothenburg
  • 14:50-15:10: Talk 2 (20 min): Martin Bonde, Chairman of Danish Biotech association
  • 15:10-15:30: Talk 3 (20 min): Søren Møller, Managing Investment Director, Novo Seeds
  • Chairman: Johan Cardoen
  • 16:00-16:20: Talk 1(20 min): Johan Cardoen, Managing Director VIB
  • 16:20-16:40: Talk 2(20 min): Patrick Van Beneden, GIMV
  • 16:40-17:00: Talk 3(20 min): Ann De Beuckelaer, Flanders Bio

Session 5: Human Disease- Structural Genomic Variation and Function

  • 09:00-09:30: Talk 1 (30 min): Wigard Kloosterman, UMC Utrecht, The Netherlands
  • Topic: Cause and Consequence of Complex Genomic Rearrangements
  • 09:30-10:00: Talk 2 (30 min): Michael Talkowski, Instructor, MGH, Harvard University, USA
  • Topic: Sequencing unique human genomes reveals novel loci in autism and predictive phenotypes in prenatal diagnostics
  • 10:00-10:30: Talk 3 (30 min): Thierry Voet, K.U.Leuven
  • Chairman: Prof. Edwin Cuppen , Hubrecht Institute

Session 6: Metagenomics

  • 09:00-09:30: Talk 1 (30 min): Hui Wang, The Centre for Ecology & Hydrology, UK
  • Topic: Virus discovery by using deep sequencing data
  • 09.30-10:00: Talk 2 (30 min): TBC
  • 10:00-10:30: Talk 3 (30 min): Bjoern Textor, New England Biolabs GmbH
  • Topic: Direct Selection of Microbiome DNA from Host DNA
  • 11:00-11:30: Talk 1 (30 min): Jeroen Raes, Scientific Collaborator, VUB&VIB
  • 11:30-12:00: Talk 2 (30 min): Rob Knight, Associate Professor, Colorado University
  • Topic: Characterizing microbial effects of family structure, including our furry family members?
  • 12:00-12:30: Talk 3 (30 min): Ruth Ley, Cornell University
  • Topic: Host control of the microbiome
  • Chairman: Dr. Jeroen Raes (VUB, VIB)

Session 7(3 talks: include Q&A 5 mins): Human Disease – Clinical Genetics

  • 11:00-11:35: Talk 1(35 min): Han Brunner, Department of Human Genetics, Radboud University Nijmegen Medical Centre, The Netherlands
  • Topic: Clinical Genetic Diagnostics by Genome Sequencing.
  • 11:35-12:05: Talk 2(30 min): Wang Wei, BGI Health, Shenzhen, China
  • Topic: Non-invasive prenatal testing (NIPT): Current clinical application and future outlook
  • 12:05-12:45: Talk 3(30 min): Gabor Vajta, BGI Europe, Copenhagen, Denmark and Central Queensland University, Rockhampton, Australia in concert with Du Yutao, BGI Health, Shenzhen, China
  • Topic: Pre-implantation Diagnostics by Blastocyst Biopsy, Vitrification and Genome Sequencing
  • Chairman: Prof. Lars Bolund, Aarhus University

Session 8: Health and Translational Medicine-1

  • 13:30-13:55: Talk 1(25 min): Vince Gao, BGI
  • Topic: Development of Clinical Service at BGI Health
  • 13.55-14:20: Talk 2(25 min): Attila Lorincz, UK
  • Topic: Clinical Validation of Genomic and Epigenomic Biomarker Panels
  • 14:20-14:45: Talk 3(25 min): Maurizio Ferrari, Director of Clinical Molecular Biology and Cytogenetics Laboratory, and Head of Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele, Milan, Italian
  • Topic: From bench to bedside: new advanced molecular techniques for genetic diagnosis
  • 14:45-15:10: Talk 4(25 min): Carlos Simón Vallés, Board Certified and Full Professor of Obstetrics and Gynecology at the University of Valencia,Spain
  • Topic: Clinical Application of the endometrial receptivity array
  • 15:10-15:35: Talk 5(20 min): To be selected from submitted abstracts
  • Chairman: Dr. Vince Gao , BGI

Session 9: Human disease

  • 13:30-13:55: Talk 1(25 min): Lars Bolund, Professor of Clinical Genetics at Aarhus University, Denmark, and Adjunct Professor of Human Genetics at Copenhagen University, Denmark
  • Topic: Chronic Disorders, Rare Genetic Variants and Pig Models of Degenerative Disease Processes
  • 13:55-14:20: Talk 2(25 min): Tao Dong, Head of anti-viral T cell immunology group, MRC Human Immunology Unit, Oxford University, UK
  • 14:20-14:45: Talk 3(25 min): Hartmut Wekerle, Honorary Professor, Max Planck Institute of Neurobiology, Martinsried, Germany
  • 14:45-15:10: Talk 4(20 min): Ramneek Gupta, The Technical University of Denmark, Danmark
  • 15:10-15:30: Talk 5(20 min): Anders Børglum, Professor, Aarhus University, Denmark
  • Chairman: TBC

Session 10: Health and Translational Medicine-2

  • 16:00-16:20: Talk 1(20 min): Diana M Eccles, Academic Vice President of the Clinical Genetics Society, Southampton General Hospital, UK
  • 16:20-16:40: Talk 2(20 min): E. Gomez Garcia, Maastricht University, the Netherlands
  • 16:40-17:00: Talk 3(20 min): Pascal Pujol , Chu Montpellier, France
  • 17:00-17:20: Talk 4(20 min): Atocha Romero, Hospital Clinico San Carlos, Spain
  • 17:20-17:40: Talk 5(20 min): Ian Campbell, Peter MacCallum Cancer Centre, Australia
  • Topic: Identification and validation of familial cancer susceptibility genes using massively parallel sequencing
  • Chairman: Prof. Yves-Jean Bignon, Centre Jean Perrin

Workshop: Ethical, Legal and Social Implications (ELSI)

  • 16:00-16:20: Talk 1(20 min): Lone Frank, Denmark
  • 16:20-16:40: Talk 2(20 min): Pascal Borry, K.U.Leuven, Belgium
  • 16:40-17:00: Talk 3(20 min): TBC
  • Chairman: Prof. Huanming Yang, BGI

Session 11: Biobanks

  • 08:00-08:30: Talk 1 (30 min): Zhang Yong, BGI, China
  • 08:30-09:00: Talk 2 (30 min): Kristian Hveem, Chief Scientific Officer, Nord-Trondelag County, Norway
  • 09:00-09:30: Talk 3 (30 min): Shaoliang Peng, National University of Defense Technology, China
  • Topic: Bioinformatics and Computational Biology on TianHe Supercomputer
  • Chairman: Dr. Zhang Yong, BGI

Workshop: Use of Omics Technology for Personalized Medicine

  • 08:00-08:30: Talk 1 (30 min): Jenny Wei, R&D Information China, AstraZeneca global R&D
  • Topic: Genomics for Personalized Medicine: From Discovery to Clinic
  • 08:30-09:00:Talk 2 (30 min):André Rosenthal, CEO, Signature Diagnostics AG
  • Topic: Next-Gen Sequencing Tests for Prognosis and Prediction of Response to Therapy of Patients with Colorectal Cancer Using Somatic Mutation Signatures
  • 09:00-09:30: Talk 3 (30 min):Radoje Drmanac, Complete Genomics, Inc. Mountain View, California, U.S.A.
  • Topic: Accurate whole genome sequencing as the ultimate genetic test enabling personalized disease prevention and treatment
  • Chairman: TBC

Session 12: Bioinformatics

  • 10:00-10:30: Talk 1 (30 min): Nathaniel Street, Assistant professor, Umea University
  • Topic: Sequencing the Norway spruce genome reveals a unique history of repeat expansion
  • 10:30-11:00: Talk 2 (30 min): Sofie Van Landeghem, Ghent University, VIB, Belgium
  • Topic: Mining the literature to enhance integrative network biology
  • 11:00-11:30: Talk 3 (30 min): Mario Caccamo, Acting Director at The Genome Analysis Centre, Norwich, UK
  • Topic: Next Generation Genomics for Complex Crops
  • Chairman: Prof. Yves Van De Peer (U.Ghent, VIB)
For related posts see
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Aquarium 16S library submitted today

Seven months after starting the sample collections we finally submitted our pooled 16S library today for sequencing.  We have somewhere around 90 samples from a few different types of aquariums and our community succession experiment.  Now time for everyone to learn QIIME!

 

Twisted tree of life award #15: NBC News on "Junk DNA mystery"

Oh for fu$*# sake.  Really MSNBC?  I mean, I know perhaps I should not expect much from some in the press but this is just awful: ‘Junk’ DNA mystery solved: It’s not needed.

Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage).  This article has some complete and utter crap:

Some parts that I have issues with:

  • The headline: “‘Junk’ DNA mystery solved: It’s not needed.”  The headline is silly but alas it is consistent with what is in the article.
  • “So-called junk DNA, the vast majority of the genome that doesn’t code for proteins“.  So – they have redefined junk DNA as all non coding DNA?
  • “For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn’t seem to contain genes or turn genes on or off.”  Apparently there is an entity out there known as “The Genome”.  
And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.
  • “At least for a plant, junk DNA really is just junk — it’s not required.”  Except that they did not show this – they just showed that one plant can have a small genome and not have a lot of “junk” as they call it, which of course does not really say anything about what “junk” does or does not do in other organisms.
  • “Nobody’s really known what junk DNA does or doesn’t do” apparently calling into question the some 10,000 plus papers on the topic.

Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes.  Oh and the organism is complex.  Therefore, apparently, it follows that

“The findings suggest junk DNA really isn’t needed for healthy plants — and that may also hold for other organisms, such as humans.”

And this leads us to ‘Junk’ DNA mystery solved: It’s not needed.

So – basically – if ONE FUCKING ORGANISM DELETES SOME OF IT’S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

Aaaaaaaaaaaaaaaaaaargh.

And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.

Past winners:
UPDATE 5/17/13
Some other discussions of this paper and related to my critique (though not always agreeing with me)
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Sitting in the lab

I’m sitting here in the lab looking at our google doc and it’s looking pretty good! We only have a few final dilutions to do and we’ll be on our way to sequencing! I’m waiting for David to come back from lunch so he can update me on the next steps.

 

I’m excited for what’s to come!