The Aggie Transcript is is a forum for undergraduate UC Davis students to share news, original writing, and art related to the life sciences.Here are some recent posts:
Thank you for being a CAMERA user during its operation as a resource for
environmental genomics. During the past few years, CAMERA has been able to
offer a number of important community resources, including an exceptionally
well curated environmental genomic database, the ability for researchers to
deposit molecular sequence datasets with associated environmental
parameters (metadata), open access to computational resources to enable
metagenomic comparisons, educational resources, and helpdesk services.
These efforts have been funded through the Gordon and Betty Moore
Foundation (GBMF) Marine Microbiology Initiative and the National Science
Foundation to serve the needs of the marine microbiology community and
other users.
In particular, the CAMERA compute resources, which include large-scale
BLAST capabilities and other workflow-enabled analysis capabilities
(RAMMCAP), were generously supported by the GBMF, the San Diego
Supercomputer Center, the NSF XSEDE program, and commercial Cloud computing
resource providers (CODONiS).
Due to the termination of GBMF support, CAMERA can no longer accommodate
the computational needs of the community. Therefore, starting July 1, 2014,
CAMERA will begin to shut down the CAMERA portal and will no longer accept
any new workflow submissions. The results of workflows submitted by July 1,
2014 will be available to users through July 15th. Urgent requests for the
temporary use of CAMERA workflow resources beyond July 1, 2014 will be
considered on a case-by-case basis.
If you are a current or prior CAMERA user and would like to retrieve
personal data from the system, we strongly encourage you to do so now.
As announced earlier this year, CAMERA will continue to maintain free and
open access to its rich collection of curated data and metadata via the
CAMERA Data Distribution Center (DDC), which includes links to the Marine
Microbial Eukaryote Transcriptome Sequencing Project. In conjunction with
the portal shutdown, CAMERA will also no longer accept user data
submissions past July 1st (but data submissions currently in progress will
be completed and made available via the DDC).
Please contact us at camera-info@calit2.net regarding matters pertaining to
the use of CAMERA.
Thank you so much for your support and participation!
I have decided today is "Support a Science Writer" day - just bought "Gulp" by @mary_roach pic.twitter.com/A82dAfwZ88
— Jonathan Eisen (@phylogenomics) May 24, 2014
Loving Gulp by @mary_roach - something to laugh at & learn about on every page (best parts to me are the footnotes) pic.twitter.com/Ye6KxDVZNF
— Jonathan Eisen (@phylogenomics) May 25, 2014
@phylogenomics @missmolamola Hear podcast w/ M. Roach on Gulp, Stiff, Packing for Mars and more http://t.co/xiyh1vZqTz
— Charles Margulis (@kvetchingguru) May 25, 2014
There's bacteria in the placenta, similar to those in mouth. But the oral hygiene msg seems hugely premature to me. http://t.co/WfVWfMpCT4
— Ed Yong (@edyong209) May 21, 2014
well @edyong209 that is not the only issue w/ that article
— Jonathan Eisen (@phylogenomics) May 21, 2014
And then a mini conversation happened
@phylogenomics Tell me more.
— Ed Yong (@edyong209) May 21, 2014
I think @edyong209 @phylogenomics are right, and besides lots of more testable good reasons to brush your teeth before bed.
— Nick Loman (@pathogenomenick) May 21, 2014
@phylogenomics Is it the implicit assumption that the presence of bacteria in the placenta is a bad thing? Cos that annoyed me too
— Ed Yong (@edyong209) May 21, 2014
well @edyong209 1) is this a living microbiome or just DNA? 2) adaptationism in giving "purpose" 3) no mention of prior work
— Jonathan Eisen (@phylogenomics) May 21, 2014
@phylogenomics @edyong209 Re point 3, from 9 months ago-- http://t.co/o79GA2QbUC
— carlzimmer (@carlzimmer) May 21, 2014
.@phylogenomics @edyong209 given human history and oral health, if impacts pregnancy so much, how are any humans still alive and reproducing
— Dr. SPONCH (@SponchPhD) May 21, 2014
@edyong209 @phylogenomics bacteria are bad everywhere right?
— Vincent J. Lynch (@VinJLynch) May 21, 2014
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| Coyote hunting rodents off in the distance |
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| Ring necked pheasant |
@phylogenomics Information can't be removed if it's in the public interest. See: http://t.co/FcOKDttRn1
— Debbie Kennett (@DebbieKennett) May 15, 2014
Your home's odor may be making you sick; microbial volatile organic compounds http://t.co/8M7U84L5Oi via @USATODAY
— Airmid Healthgroup (@AirmidHealth) May 13, 2014
Bad days evaporate into nothingness with a warm cat pic.twitter.com/x5U8v9Z2Wj
— Jonathan Eisen (@phylogenomics) February 27, 2014
The investigators found no significant differences in the primary outcome or any of the secondary outcomes, which included the Inflammatory Bowel Disease Questionnaire and the EQ5D health status assessmentThe researcher seems enthusiastic about FMT still but certainly this means that FMT for IBD is not going to be like FMT for CDiff (just wanted to make sure I got in a lot of abbreviations there). I am sure there will be much more to come on FMT and it would be good to see more detail on what was presented at the meeting (a paper, or poster, or such). But for now, this hopefully will temper some of the overselling of FMT that is going around (e.g., Overselling the microbiome award: Mercola/Perlmutter on fecal transplants for severe neurological dysfunction).
According to James Kaufman, a research manager at the Almaden Research Center, the move to study metagenomics -- the study of systems of micro-organisms -- came from what he called a tipping point in big data. As more and more government-funded institutions study organisms and bacteria, they've collected more information about them, and submitted much of their work to centralized databases. "So there's a growing library of genomes across the field of life," Kaufman said. "That made possible metagenomics."What? Metagenomics has been around for a long time. Sure, many people in the field are taking advantage of so called big data, but there was no "tipping point" needed to launch the field. This is just completely misguided.
The result: We can now look at and understand whole ecosystems at the bacterial level. One example of how that manifests is what IBM refers to as the Human Microbiome Project. According to an IBM document, that's about characterizing "microbial communities found at multiple human body sites to discover correlations between changes in the microbiome with changes in human health."So - there have been dozens of high profile papers from the Human Microbiome Project. There are hundreds of web pages with information about the project. It was started years and years ago. And the reporter quotes an "IBM document" to tell us what the Human Microbiome Project is? And even worse the reporter says "what IBM refers to as the Human Microbiome Project" like they ran it / designed it. Good that they refer to it as the Human Microbiome Project. You know why? Because that is what it is known as to all the other $(&@)(* people in the whole (%&# world.
This kind of work is not entirely new, but the scientists who will be gathering at IBM Research this week are grappling with one conundrum: they don't know what they don't know. So a big topic of conversation, and a big part of what IBM would like to see advanced, is "the ability to do metagenomics on the scale of a city or the world....That will depend on software services available in the cloud," Kaufman said. "It has to be cheap, easy, and accessible from anywhere. That's what we're really good at."Once again making it seem like IBM is somehow leading this field. Not to pick on IBM here. I am glad they organized the meeting. But either the reporter just got handed a press release from IBM and wrote it up, or did not do any type of background research, or both. Sure IBM would like to see this. But so would lots of other people. Why make this all about IBM? There are so many people who have done interesting work in the area of "microbiology of the built environment" - why are none of them even discussed? What exactly is the point of this article if not to simply be a PR piece for IBM? Aaaaaarg.
I truly love the work Bil Gates and the Gates Foundation have been doing over the last years. Absolutely wonderful stuff. But I have a bone (or perhaps a proboscis) to pick with this latest effort: The Deadliest Animal in the World | Bill Gates. The article discusses some "facts" about how many people different animals kill. And it uses this to argue for the need for more attention to be placed on mosquitoes. I agree with the conclusion. Mosquitoes are a big deal and need much much much more work and attention. But the data is just, well, not sound. Here is the problem I have
"But even more concerning, say experts like Dr. Martin Blaser, director of the human microbiome program at the New York University Langone Medical Center and author of Missing Microbes, is how these antibiotics are affecting the makeup of both good and bad bacteria that live within us – our microbiome. The first big cost of antibiotics is resistance,” he says. “But the other side of the coin is [the fact that] antibiotics are extinguishing our microbiome and changing human development.”Extinguishing our microbiome? Really? The evidence simply does not support such a claim. I personally think antibiotics may be contributing to messing up the microbiome in many people and that this in turn might be contributing to the increase in a variety of human ailments (e.g., I mentioned this issue in my TED talk and many many times here and elsewhere). But "extinguishing"? Not even close. In fact, many of the published sutdies done so far suggest that the human microbiome is pretty resilient in response to antibiotics. Really serious overselling of the impact of antiobitcs by Blaser.
If I prescribe a heart medicine for a patient, that heart medicine is going to affect that patient,” says Blaser. “But if I prescribe an antibiotic, that antibiotic will affect the entire community to some degree. And the effect is cumulative.Yes antibiotics can affect more than one person because microbes (and resistance) can spread. But "the effect is cumulative"? I do not think that has been shown.
That may also help to protect our microbiomes, which in turn could slow the appearance of chronic diseases such as obesity, cancer and allergies.What? Now antibiotics cause obesity? And allergies? And cancer? Sure - there is good reason to think that antibiotic usage plays a role in obesity and allergies. The evidence is not yet completely overwhelming but it is certainly a reasonable notion. But how did cancer get thrown in here?
Outstanding group of individuals, and the organizational and management structure appears sound with clear roles and responsibilities of theme faculty. There is a large focus on developing this for microbiome research, but Eisen seems to be the only team member with this expertise, and may not have the bandwidth to coordinate this on such a large project alone, especially given his high time commitment to his blog.I started drafting a letter to the reviewer - partly about how great I think I am and partly to vent some anger ... here is the beginning:
Dear Reviewer
But then I realized this was a bit too much. I should not let this comment lead me to get defensive about my career, my blog, etc. Plus, I was spending too much time on this. (The above took 2 minutes and 12 seconds to write and then another 1 minute and 11 seconds to highlight and link up and ponder). So I decided to be more concise
- Fuck you.
- Apparently getting elected to the American Academy of Microbiology this year was due to my blogging.
- I have 31907 citations in Google Scholar. What the fuck do you have?
- My blog is in fact about EXACTLY what we were talking about in the proposal, you fucking piece of fucking shit.
- Fuck you.
- You are right in a way - I have little time to spare. Did I somehow not do something you wanted me to do? Fine. Say that. But focusing on my blog just shows you are a ...
Dear Reviewer
Fuck you.
Love,But then I realized, cursing was not the solution. Maybe love would be better?
Jonathan Eisen
Dear Reviewer
Thank you for your insight. I will do my best to spend less time blogging in the future.
Love,But this still did not seem right. So I decided that the best option was to do nothing. So that is what I am doing. Nothing. No response. No blog post. Nothing. There. I feel better already.
Jonathan Eisen
BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes. The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO's future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up. Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding. Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.
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Fecal transplantation, in cases of severe neurological dysfunction where poor gut flora appears to be a contributing factor. Your microbiome is critical for multiple reasons, including regulating the set point of inflammation, producing neurotransmitters like serotonin, and modulating systems associated with brain function and brain health. This form of therapy is now the standard of care for life-threatening C. difficile infections.Yup. He is recommending fecla transplants to treat severe neurological dysfunction. Not the first person to suggest a connection between microbes and neurology. Not the first person to say that maybe trying to change the microbiome might be an interesting thing to test as a treatment for some issues. But with no caveats here they just jump right in to using this to treat neurological dysfunction. This is just grossly over the top and will likely mislead many many people with neurological dysfunctions into thinking fecal transplants are a known effective treatment. I wonder if Dr. Perlmutter will start offerring home fecal transplant kits for sale on his web site (which I will not link to here).
@phylogenomics I've read your blogs about lack of diversity on conference panels, thoughts on UC drought summit's? https://t.co/PsH1dOikc9
— Elizabeth Case (@elizabeth_case) April 25, 2014
Renée Schroeder
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http://dx.doi.org/10.4161/rna.28566 Robin R Gutell Pages 170 - 171 http://dx.doi.org/10.4161/rna.28393 Peter B Moore Pages 172 - 174 http://dx.doi.org/10.4161/rna.27428 Ralph Wolfe Page 175 http://dx.doi.org/10.4161/rna.27429 Mark A Ragan, Guillaume Bernard and Cheong Xin Chan Pages 176 - 185 http://dx.doi.org/10.4161/rna.27505 James A Shapiro Pages 186 - 196 http://dx.doi.org/10.4161/rna.27506 Eugene V Koonin Pages 197 - 204 http://dx.doi.org/10.4161/rna.27673 Ann Reid Pages 205 - 206 http://dx.doi.org/10.4161/rna.27701 John D Rummel Pages 207 - 209 http://dx.doi.org/10.4161/rna.27702 Bojan Zagrovic Pages 210 - 212 http://dx.doi.org/10.4161/rna.27718 Michael W Gray Pages 213 - 216 http://dx.doi.org/10.4161/rna.27799 Kenneth R Luehrsen Pages 217 - 219 http://dx.doi.org/10.4161/rna.27800 Sahotra Sarkar Pages 220 - 224 http://dx.doi.org/10.4161/rna.27883 Harry F Noller Pages 225 - 231 http://dx.doi.org/10.4161/rna.27970 Roger A Garrett Pages 232 - 235 http://dx.doi.org/10.4161/rna.28228 Larry Gold Pages 236 - 238 http://dx.doi.org/10.4161/rna.28305 James R Cole and James M Tiedje Pages 239 - 243 http://dx.doi.org/10.4161/rna.28306 Mark Martin Pages 244 - 247 http://dx.doi.org/10.4161/rna.28002 Nigel Goldenfeld Pages 248 - 253 http://dx.doi.org/10.4161/rna.28640 Robin R Gutell Pages 254 - 272 http://dx.doi.org/10.4161/rna.28718 Harris A Lewin Pages 273 - 278 http://dx.doi.org/10.4161/rna.28866So - it is another Thanksgiving Day and in addition to thinking about family, and football, and Alice's Restaurant, I also think a lot a...
