The best writing in science papers: Part II

Guest post by Stephen Heard (scientistseessquirrel.wordpress.com)

Over 2 years ago now, Jonathan posted “The best writing in science papers: Part I”.  I stumbled across that post and searched excitedly for Part II – only to discover there wasn’t one.  Well, now there is, as Jonathan has kindly allowed me to guest-post this.

Jonathan’s Part I identified the butterfly-taxonomy papers of Vladimir Nabokov as containing flashes of beautiful writing, and I agree (although my favourite bits differ from his).  But Jonathan wondered if picking Nabokov (an acclaimed novelist) was “a bit unfair” and he later told me he’d never done a Part II because other examples were too hard to find! 

Actually, other examples can be found, and not only in the papers of scientists who are also accomplished novelists.  I collected a few in my recent paper “On whimsy, jokes, and beauty: can scientific writing be enjoyed”.  For example, here is Nathaniel Mermin on a surprising result in quantum mechanics:
      “There are no physical grounds for insisting that [Alice] assign the same value to an observable for each mutually commuting trio it belongs to – a requirement that would indeed trivially make her job impossible. The manner in which the nine-observable BKS theorem brings Alice to grief is more subtle than that. It is buried deep inside the mathematics that underlies the construction that makes it possible, when it is possible, to do the VAA trick.”
Here is Bill Hamilton setting up a simulation model of antipredator defence via herding:
      “Imagine a circular lily pond.  Imagine that the pond shelters a colony of frogs and a water-snake…Shortly before the snake is due to wake up all the frogs climb out onto the rim of the pond… [The snake] rears its head out of the water and surveys the disconsolate line sitting on the rim… and snatches the nearest one.  Now suppose the frogs are given opportunity to move about on the rim before the snake appears, and suppose that initially they are dispersed in some rather random way.  Knowing that the snake is about to appear, will all the frogs be content with their initial positions? No…and one can imagine a confused toing-and-froing in which [desirable positions] are as elusive as the croquet hoops in Alice’s game in Wonderland.”
And here is Harry Kroto describing the structure of C60 buckyballs:
     “An unusually beautiful (and probably unique) choice is the truncated icosohedron...All valences are satisfied with this structure, and the molecule appears to be aromatic.  The structure has the symmetry of the icosahedral group.  The inner and outer surfaces are covered with a sea of πelectrons.”
Finally, read this by Matthew Rockman – too much, too good, to even excerpt here.

So, “regular” scientific writers can achieve beauty, too (and please share your own favourite examples in the comments). But I’d have to agree with Jonathan that we don’t do so very often. Why not? I can think of three possibilities:

It could be that writing beautifully in scientific papers is a bad idea, and we know it. Perhaps readers don’t respect scientists who resist the conventional turgidity of our writing form. I don’t think this is true, although I’m aware of no formal analysis.

Or it could be that beauty is a good idea, but well-meaning reviewers and editors squash it. In my paper I argue that beauty (like humour) can recruit readers to a paper and retain them as they read; but that reviewers and editors tend to resist its use. But again, there’s no formal analysis, so I was forced to make both halves of that argument via anecdote.

Or it could be we just don’t have a culture of appreciating, and working to produce, beauty in our writing. I think this is most of the explanation: it’s not that we are opposed to beauty as much as it doesn’t occur to us that scientific writing could aspire to it.

All of which makes me wonder: if we wanted to make beauty more common in scientific writing, how could we do that?  Well, that could make for a really long post.  I’ll mention a few thoughts, and encourage you to leave more in the comments.  

First, we could write with small touches of beauty in our own papers.  Of course, that’s not as easy as it sounds, because most of aren’t trained or oriented that way.  To oversimplify, it’s a chicken-and-egg problem: most of us come from science backgrounds that lack a culture of beauty in writing.  Perhaps we even came to science as refugees from the arts and humanities where beauty is more valued.  That’s true for me, at least; and I know a fair bit about how to write functionally, but almost nothing about how to write beautifully.  But if there’s a path to writing beauty, it probably starts in reading beauty, wherever it can be found.  Nabokov? Sure... but also science blogs, lay essays and books aboutscience and nature (for a start, sample the science writing of Rachel Carson, Lewis Thomas, Karen Olsson, Barbara Kingsolver, or John McPhee), and really, anything we can get our hands on.  And when we read, we can be alert for language that sparkles, so as to cultivate an ear for beauty and to build a toolbox of techniques we can deploy in our own writing.  (For some other thoughts on this, see Helen Sword’s book “Stylish Academic Writing”).

Second, and much easier, we could encourage beauty in the writing of others.  As reviewers and editors, we could decide that style and beauty are not incompatible with scientific writing.  We could resolve not to question touches of style, or unusual but beautiful ways of writing, in the work we are judging.

Finally, we could publicly recognize beauty when we see it.  We could announce our admiration of beautiful writing to the authors who produce it or to colleagues who might read it.  What Jonathan and I have done with these posts is a small start on this, and I’ve promised myself I’ll praise wonderful writing whenever I can.  Thinking bigger, though, wouldn’t it be great if there was an award for the best scientific writing of the year?  I don’t mean the best science – we have plenty of awards for that – but the best writingto appear in our primary literature.  Such awards exist for lay science writing; if one existed for technical writing I’d be thrilled to make nominations and I’d volunteer to judge. 

As Jonathan and I both found, examples of beautiful scientific writing do seem to be unusual; and those that exist aren’t well known.  I don’t think it has to be this way.  W could choose to change our culture, a little at a time, to deliver (and to value) pleasure along with function in our scientific writing.

-----

By the way: I became interested in beauty in scientific writing while working on a guidebook for scientific writers.  It’s not available yet, but to learn more about it, see my web site.  For more of my (somewhat scattered) thoughts on writing and on doing science, visit my blog.

UPDATE 1/25/15

Now posted on Heard's Blog.


A long (and I think good) listen: Tim Ferriss podcast on "the microbiome"

So - I have been travelling a lot lately.  On one of my trips - to Las Vegas and neighboring areas - I was interviewed by Tim Ferriss for his blog.  Jessica Richman of uBiome was also interviewed - she was in SF, Ferriss was somewhere else, and I was on the phone in Vegas.  As soon as it was over I got caught up in the work I was doing there (field work for a new NSF Funded Project on "microbial dark matter".  Anyway - the interview was entertaining and I think interesting.  And then it came out while I was on the road again for another trip.  So I am just getting around to posting about it now.  Anway - here are some links for the podcast.

Ferriss' blog post about it: Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome…

Direct links
I note - I have never done such a long interview for a show before (it was about two hours) but Ferriss was remarkably adept at making it relaxing and fun (for me at least).  Even the part about Jim Watson ...

UC Davis MARS Symposium Wrap Up #globalfood #UCDavisMARS

Yesterday I went to a symposium at UC Davis that was the launching of a new partnership between UC Davis and the Mars Corporation. I note - I have been collaborating with some people at Mars on multiple microbiome related projects and generally have had great interactions with the people there. I am not directly involved in the planning for this new partnership between UC Davis and Mars and thus I was interested in hearing more about it at the symposium.

The symposium was at the Mondavi Center on UC Davis campus and I zipped in on my bike through the cold (for Davis) air and got there just before they opened the doors to the main theater. I saw a few folks I knew milling around in the lobby and said hello and then went inside with some people from my lab for the "show".

 I will try to write more about this later but just one note - I found some of the big picture discussions about the importance of the nexus between food, agriculture and health to be pretty inspiring. For now - I hope the Storify I made and embedded below will give some idea as to the goings on of the symposium.

Surprise 28th

 photo JenniSurpriseBirthdayParty-0001_zps05dc828c.jpg

I've been meaning to write about my beautiful surprise birthday party for, oh, over a month now... but you know, busy-ness and the holidays and excuses excuses excuses. On this dreary Monday morning, however, I've finally gotten to it, and I'm having such a nice time reliving this oh-so-sweet evening.

On Decemeber 5th, I turned 28, which is weird all unto itself, seeing as how my twenties are creeping to a close and in some ways I still feel so young and others I feel so old. In some ways I feel so accomplished, and others I feel so panicky for not being further along. But that's another post for another day.

Also on December 5th, a few friends threw me a surprise birthday party, which was, indeed, an actual surprise!  In the last year or two, I've grown close to a beauty named Brittany who started her own event rentals company (Birch & Brass Vintage Rentals) here in Austin, of which I've helped to photograph the inventory over the course of many sweaty photo shoots and hundreds of beautiful pieces. Brittany is so, so good at styling perfect tablescapes and vignettes, and I always wished I knew her before our wedding or some other excuse to have her style an event for me.

Well now, thanks to her expertise and kindness, I have this incredibly perfect little party to look back on fondly, much thanks to Shalyn's gorgeous photos of the evening. I was so in shock that night, I barely took in all the details. Another reason that photography is so important: to capture and freeze time so you can go back and enjoy special moments over and over again.

There was fried chicken and other southern-style comfort foods (my absolute favorites), rum punch (another fave), cake and cupcakes and doughnuts (because you KNOW I love my sweets), a ridiculous piñata I had to whack about 47 times before it finally broke, and karaoke and quality time with sweet friends I was so grateful to for taking the time out of their Friday night to attend.

Thank you so much, Brittany, for one of the most thoughtful things anyone has ever done for me, and to Celine & Justin for hosting and for handling all of the mess that comes with that, and to Shay for taking the most beautiful photos and creating the most gorgeous little placecards, and to Kelsey & Jona, John & Kirsten, Kate, Emilie, Federico, and of course Matthew, all for attending.

Here's a few photos from the evening... thanks for stopping by today!

 photo storyboard001_zpscba61278.jpg

 photo storyboard002_zpscba61278.jpg

 photo JenniSurpriseBirthdayParty-0005_zps486a1206.jpg

 photo storyboard003_zpsba242305.jpg

 photo JenniSurpriseBirthdayParty-0024_zpscf352684.jpg

 photo storyboard004_zps2b97dc05.jpg

 photo storyboard005_zpsbc7c4f84.jpg

 photo JenniSurpriseBirthdayParty-0022_zpsa7e1ba3e.jpg

 photo storyboard006_zps3b7e8690.jpg

 photo JenniSurpriseBirthdayParty-0042_zps0c9e7922.jpg

 photo storyboard007_zps4833c1e8.jpg

 photo storyboard010_zpsb4a76f6a.jpg

 photo JenniSurpriseBirthdayParty-0046_zps90837672.jpg

 photo storyboard008_zps9e42402a.jpg

 photo storyboard009_zps781726b5.jpg

 photo storyboard011_zps112b432b.jpg

 photo storyboard012_zpsaef862a4.jpg

 photo JenniSurpriseBirthdayParty-0071_zps787539b2.jpg

 photo JenniSurpriseBirthdayParty-0074_zps815cbaf1.jpg

 photo JenniSurpriseBirthdayParty-0076_zpsa067dfed.jpg

 photo JenniSurpriseBirthdayParty-0080_zpse2ec28b5.jpg

 photo JenniSurpriseBirthdayParty-0083_zpsc866d164.jpg

Postdoc position in Computational Biology / Infectious Disease w/ Ashlee Earl at the Broad

My friend, the brilliant Ashlee Earl is recruiting a post doc ... posting this for her.


POSTDOC – COMPUTATIONAL BIOLOGIST (INFECTIOUS DISEASE)
Requisition Number: 1571 http://www.broadinstitute.org/careers/job-openings/job-openings-0

The goal of the Bacterial Genomics Group at Broad is to develop and implement genomic and metagenomic methods to answer pressing questions related to bacteria and their role in human health. Specifically, we seek to understand the evolution and spread of bacterial pathogens (and antibiotic resistance) including the interactions that these pathogens have with their host and host-associated microbiota. We devise and carry out large-scale studies that employ genomic, metagenomic and transcriptomic data sets to understand human pathologies caused by e.g., Mycobacterium tuberculosis, carbapenem resistant Enterobacteriaceae, enterococci and uropathogenic Escherichia coli. We do this in close collaboration with clinical and academic researchers from across the Broad community and around the globe.

We are seeking a creative and highly motivated postdoctoral researcher in Computational Biology.  The ideal candidate should be broadly conversant with bioinformatics techniques for genomic data analysis including metagenomic analysis. They should also be familiar with microbial ecology principles, statistics and have made significant contributions to their area of study.

Responsibilities include:

  • Developing data analysis strategies, writing algorithms and deploying computational tools for the exploration of large genomic, metagenomic and metatranscriptomic data sets
  • Collaborating closely with experimental and computational researchers to interpret analytical results for publication
  • Communicating scientific findings in writing and orally

A Ph.D. in Computer Science, Bioinformatics, Biostatistics, Physics, Biological Sciences or a related field

  • Must be proficient in working in the Unix environment.  Solid coding proficiency in some combination of Python, Perl, Scala, Java, C/C++ and R. Experience with cluster computing and parallelization preferred.
  • Comfort and experience with programming for biological data analysis
  • Demonstrated ability to analyze and interpret metagenomic data
  • Excellent ability to communicate scientific material
  • Excellent collaborative skills and unrelenting enthusiasm for genomic science


EOE/Minorities/Females/Protected Veterans/Disabilities

Haloferax volcanii, model archaea, and me

When I was a graduate student I was looking around for an extremophile - especially an evolutionarily novel one.  And I settled on this species Haloferax volcanii - a model halophilic archaeon largely because Ford Doolittle and colleagues had started to turn it into a genetic model organism (and because Patrick Keeling, from Ford's lab convinced me it was a good thing to do).  So I started work on this species - doing DNA repair studies in the lab.  See my PhD thesis for some of the work I did which I never published outside of the thesis for multiple reasons.  But I continued to be interested in this species.  And when I was working at TIGR, an NSF Program Officer approached me asking me to help get the genome sequencing done for this species.  So, well, I did: The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.  And I became interested in other haloarchaea and eventually started working with Marc Facciotti, in the lab next to mine, in sequencing from across the diversity of the haloarchaea: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response.

Anyway - enough about me.  The whole point here is to point people to a new paper:  BMC Biology | Abstract | Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery.  Further evidence for the use of Haloferax volcanii as a model species.  Tools continue to become available for genetic and experimental studies in this species.  So - if you are looking for an unusual and interesting organisms to work on - consider working on this species ...

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus

Well, this press release is from October:Study Suggests Altering Gut Bacteria Might Mitigate Lupus But I just discovered it and it definitely deserves an award.  An Overselling the Microbiome Award.  The PR, sadly and amazingly from the American Society for Microbiology which should know better, discusses a paper from the ASM Published journal Applied and Environmental Microbiology.  The PR does an OK job discussing what was in the paper - a study of the microbiome in mice including those that are a model for lupus.  The researchers characterized the microbiome is mice with and without the lupus model disease and also compared over time and between sexes.  And they found some interesting correlates of microbial patterns that are found during flare ups of lupus for example and also in drug induced worsening of symptoms.  But they never showed ANY causal connection between any of the mcirobes and the lupus like disease.  And the never showed ANY benefit of treating the lupus-like symptoms in the mice.  Yet amazingly they go over board in making such claims including
Title: STUDY SUGGESTS ALTERING GUT BACTERIA MIGHT MITIGATE LUPUS.
No - the study did not suggest that at all.  The authors suggested that, yes.  And the study is consistent with that.  But it is also consistent with altering gut bacteria having NO EFFECT on lupus.  So this title is simply deceptive.

In the text other statements are like this:
These results suggest that the gut bacteria may contribute to lupus.
Stunningly, the PR includes some really inappropriate comments including:
Nonetheless, Luo suggests that people with lupus should eat Lactobacillus-containing probiotics, such as live culture yogurts, to reduce lupus flares.
Seriously?  Shame on ASM for allowing this garbage to be in the PR. No evidence at all is presented that this is helpful.

Also in the PR:
More generally, "The use of probiotics, prebiotics, and antibiotics has the potential to alter microbiota dysbiosis, which in turn could improve lupus symptoms," says co-principal investigator Husen Zhang. Ultimately, says Luo, fecal transplant might prove valuable as a treatment for lupus.
Again, shame on ASM.  No evidence is presented for this either.

And then the PR ends with
"We were inspired in part to perform this research by a study on type 1 diabetes, which found that that disease is dependent on gut microbiota," says Zhang. "Like type 1 diabetes, lupus is an autoimmune disease that is even more prevalent [than type 1 diabetes] in women."
What?  I know of no research that shows that type 1 diabetes is dependent on gut microbiota.  I really don't even know what to say here.

This is one of the worst Press Releases I have ever seen in terms of misleading statements about microbiomes.  And ASM should be embarassed about it.  And ASM should retract it.  And ASM should never ever put out something like this again.  And for this, I am awarding a coveted "Overselling the Microbiome Award" to ASM for putting out this inappropriate press release.  If any with lupus goes out and gets even remotely worse from taking such probiotics, prebiotics, or antibiotics, ASM will bear some of the responsibility for their problems.  Shameful.



UPDATE 1: Jan 2, 2015

I did some searching for "probiotics" and "lupus" and found some much more tempered claims from other places. For example in "Lupus Studies Point to Gut Microbes, Epigenetics"
 "The long-standing anecdotal patient reports of certain diets worsening or improving flares might be more real than we thought. They should be studied more systematically, now that we know that almost any dietary component acts on the gut microbiota, [which] in turn has profound effects on the immune system," Dr. Kriegel said. He also warned that patients should not assume that the various "probiotic" products now available to consumers would have a beneficial effect in lupus. "Probiotics could theoretically even worsen a disease state, since it is possible that physiologic immune responses against benign commensals could fuel autoimmune responses via cross-reactivity (as we hypothesize) or other mechanisms," he said.
Dr. Kriegel concluded, "I think the best will be to wait until we have a better understanding of which commensals or commensal-derived products might be driving which autoimmune disease and then target those with a diet that is known to modulate these strains or products. Ideally, the field will also develop eventually novel types of antibiotics or vaccinations against certain commensals. Such approaches would allow us, in the future, to more specifically modulate the gut microbiota in autoimmunity." 
Now that is responsible commenting on lupus and the microbiome.  Too bad ASM allowed complete BS to get into this PR instead of more reasonaed statements.

See also

Total Pageviews

Popular Posts

الجمعة، 16 يناير 2015

The best writing in science papers: Part II

Guest post by Stephen Heard (scientistseessquirrel.wordpress.com)

Over 2 years ago now, Jonathan posted “The best writing in science papers: Part I”.  I stumbled across that post and searched excitedly for Part II – only to discover there wasn’t one.  Well, now there is, as Jonathan has kindly allowed me to guest-post this.

Jonathan’s Part I identified the butterfly-taxonomy papers of Vladimir Nabokov as containing flashes of beautiful writing, and I agree (although my favourite bits differ from his).  But Jonathan wondered if picking Nabokov (an acclaimed novelist) was “a bit unfair” and he later told me he’d never done a Part II because other examples were too hard to find! 

Actually, other examples can be found, and not only in the papers of scientists who are also accomplished novelists.  I collected a few in my recent paper “On whimsy, jokes, and beauty: can scientific writing be enjoyed”.  For example, here is Nathaniel Mermin on a surprising result in quantum mechanics:
      “There are no physical grounds for insisting that [Alice] assign the same value to an observable for each mutually commuting trio it belongs to – a requirement that would indeed trivially make her job impossible. The manner in which the nine-observable BKS theorem brings Alice to grief is more subtle than that. It is buried deep inside the mathematics that underlies the construction that makes it possible, when it is possible, to do the VAA trick.”
Here is Bill Hamilton setting up a simulation model of antipredator defence via herding:
      “Imagine a circular lily pond.  Imagine that the pond shelters a colony of frogs and a water-snake…Shortly before the snake is due to wake up all the frogs climb out onto the rim of the pond… [The snake] rears its head out of the water and surveys the disconsolate line sitting on the rim… and snatches the nearest one.  Now suppose the frogs are given opportunity to move about on the rim before the snake appears, and suppose that initially they are dispersed in some rather random way.  Knowing that the snake is about to appear, will all the frogs be content with their initial positions? No…and one can imagine a confused toing-and-froing in which [desirable positions] are as elusive as the croquet hoops in Alice’s game in Wonderland.”
And here is Harry Kroto describing the structure of C60 buckyballs:
     “An unusually beautiful (and probably unique) choice is the truncated icosohedron...All valences are satisfied with this structure, and the molecule appears to be aromatic.  The structure has the symmetry of the icosahedral group.  The inner and outer surfaces are covered with a sea of πelectrons.”
Finally, read this by Matthew Rockman – too much, too good, to even excerpt here.

So, “regular” scientific writers can achieve beauty, too (and please share your own favourite examples in the comments). But I’d have to agree with Jonathan that we don’t do so very often. Why not? I can think of three possibilities:

It could be that writing beautifully in scientific papers is a bad idea, and we know it. Perhaps readers don’t respect scientists who resist the conventional turgidity of our writing form. I don’t think this is true, although I’m aware of no formal analysis.

Or it could be that beauty is a good idea, but well-meaning reviewers and editors squash it. In my paper I argue that beauty (like humour) can recruit readers to a paper and retain them as they read; but that reviewers and editors tend to resist its use. But again, there’s no formal analysis, so I was forced to make both halves of that argument via anecdote.

Or it could be we just don’t have a culture of appreciating, and working to produce, beauty in our writing. I think this is most of the explanation: it’s not that we are opposed to beauty as much as it doesn’t occur to us that scientific writing could aspire to it.

All of which makes me wonder: if we wanted to make beauty more common in scientific writing, how could we do that?  Well, that could make for a really long post.  I’ll mention a few thoughts, and encourage you to leave more in the comments.  

First, we could write with small touches of beauty in our own papers.  Of course, that’s not as easy as it sounds, because most of aren’t trained or oriented that way.  To oversimplify, it’s a chicken-and-egg problem: most of us come from science backgrounds that lack a culture of beauty in writing.  Perhaps we even came to science as refugees from the arts and humanities where beauty is more valued.  That’s true for me, at least; and I know a fair bit about how to write functionally, but almost nothing about how to write beautifully.  But if there’s a path to writing beauty, it probably starts in reading beauty, wherever it can be found.  Nabokov? Sure... but also science blogs, lay essays and books aboutscience and nature (for a start, sample the science writing of Rachel Carson, Lewis Thomas, Karen Olsson, Barbara Kingsolver, or John McPhee), and really, anything we can get our hands on.  And when we read, we can be alert for language that sparkles, so as to cultivate an ear for beauty and to build a toolbox of techniques we can deploy in our own writing.  (For some other thoughts on this, see Helen Sword’s book “Stylish Academic Writing”).

Second, and much easier, we could encourage beauty in the writing of others.  As reviewers and editors, we could decide that style and beauty are not incompatible with scientific writing.  We could resolve not to question touches of style, or unusual but beautiful ways of writing, in the work we are judging.

Finally, we could publicly recognize beauty when we see it.  We could announce our admiration of beautiful writing to the authors who produce it or to colleagues who might read it.  What Jonathan and I have done with these posts is a small start on this, and I’ve promised myself I’ll praise wonderful writing whenever I can.  Thinking bigger, though, wouldn’t it be great if there was an award for the best scientific writing of the year?  I don’t mean the best science – we have plenty of awards for that – but the best writingto appear in our primary literature.  Such awards exist for lay science writing; if one existed for technical writing I’d be thrilled to make nominations and I’d volunteer to judge. 

As Jonathan and I both found, examples of beautiful scientific writing do seem to be unusual; and those that exist aren’t well known.  I don’t think it has to be this way.  W could choose to change our culture, a little at a time, to deliver (and to value) pleasure along with function in our scientific writing.

-----

By the way: I became interested in beauty in scientific writing while working on a guidebook for scientific writers.  It’s not available yet, but to learn more about it, see my web site.  For more of my (somewhat scattered) thoughts on writing and on doing science, visit my blog.

UPDATE 1/25/15

Now posted on Heard's Blog.


الخميس، 15 يناير 2015

A long (and I think good) listen: Tim Ferriss podcast on "the microbiome"

So - I have been travelling a lot lately.  On one of my trips - to Las Vegas and neighboring areas - I was interviewed by Tim Ferriss for his blog.  Jessica Richman of uBiome was also interviewed - she was in SF, Ferriss was somewhere else, and I was on the phone in Vegas.  As soon as it was over I got caught up in the work I was doing there (field work for a new NSF Funded Project on "microbial dark matter".  Anyway - the interview was entertaining and I think interesting.  And then it came out while I was on the road again for another trip.  So I am just getting around to posting about it now.  Anway - here are some links for the podcast.

Ferriss' blog post about it: Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome…

Direct links
I note - I have never done such a long interview for a show before (it was about two hours) but Ferriss was remarkably adept at making it relaxing and fun (for me at least).  Even the part about Jim Watson ...

UC Davis MARS Symposium Wrap Up #globalfood #UCDavisMARS

Yesterday I went to a symposium at UC Davis that was the launching of a new partnership between UC Davis and the Mars Corporation. I note - I have been collaborating with some people at Mars on multiple microbiome related projects and generally have had great interactions with the people there. I am not directly involved in the planning for this new partnership between UC Davis and Mars and thus I was interested in hearing more about it at the symposium.

The symposium was at the Mondavi Center on UC Davis campus and I zipped in on my bike through the cold (for Davis) air and got there just before they opened the doors to the main theater. I saw a few folks I knew milling around in the lobby and said hello and then went inside with some people from my lab for the "show".

 I will try to write more about this later but just one note - I found some of the big picture discussions about the importance of the nexus between food, agriculture and health to be pretty inspiring. For now - I hope the Storify I made and embedded below will give some idea as to the goings on of the symposium.

الاثنين، 12 يناير 2015

Surprise 28th

 photo JenniSurpriseBirthdayParty-0001_zps05dc828c.jpg

I've been meaning to write about my beautiful surprise birthday party for, oh, over a month now... but you know, busy-ness and the holidays and excuses excuses excuses. On this dreary Monday morning, however, I've finally gotten to it, and I'm having such a nice time reliving this oh-so-sweet evening.

On Decemeber 5th, I turned 28, which is weird all unto itself, seeing as how my twenties are creeping to a close and in some ways I still feel so young and others I feel so old. In some ways I feel so accomplished, and others I feel so panicky for not being further along. But that's another post for another day.

Also on December 5th, a few friends threw me a surprise birthday party, which was, indeed, an actual surprise!  In the last year or two, I've grown close to a beauty named Brittany who started her own event rentals company (Birch & Brass Vintage Rentals) here in Austin, of which I've helped to photograph the inventory over the course of many sweaty photo shoots and hundreds of beautiful pieces. Brittany is so, so good at styling perfect tablescapes and vignettes, and I always wished I knew her before our wedding or some other excuse to have her style an event for me.

Well now, thanks to her expertise and kindness, I have this incredibly perfect little party to look back on fondly, much thanks to Shalyn's gorgeous photos of the evening. I was so in shock that night, I barely took in all the details. Another reason that photography is so important: to capture and freeze time so you can go back and enjoy special moments over and over again.

There was fried chicken and other southern-style comfort foods (my absolute favorites), rum punch (another fave), cake and cupcakes and doughnuts (because you KNOW I love my sweets), a ridiculous piñata I had to whack about 47 times before it finally broke, and karaoke and quality time with sweet friends I was so grateful to for taking the time out of their Friday night to attend.

Thank you so much, Brittany, for one of the most thoughtful things anyone has ever done for me, and to Celine & Justin for hosting and for handling all of the mess that comes with that, and to Shay for taking the most beautiful photos and creating the most gorgeous little placecards, and to Kelsey & Jona, John & Kirsten, Kate, Emilie, Federico, and of course Matthew, all for attending.

Here's a few photos from the evening... thanks for stopping by today!

 photo storyboard001_zpscba61278.jpg

 photo storyboard002_zpscba61278.jpg

 photo JenniSurpriseBirthdayParty-0005_zps486a1206.jpg

 photo storyboard003_zpsba242305.jpg

 photo JenniSurpriseBirthdayParty-0024_zpscf352684.jpg

 photo storyboard004_zps2b97dc05.jpg

 photo storyboard005_zpsbc7c4f84.jpg

 photo JenniSurpriseBirthdayParty-0022_zpsa7e1ba3e.jpg

 photo storyboard006_zps3b7e8690.jpg

 photo JenniSurpriseBirthdayParty-0042_zps0c9e7922.jpg

 photo storyboard007_zps4833c1e8.jpg

 photo storyboard010_zpsb4a76f6a.jpg

 photo JenniSurpriseBirthdayParty-0046_zps90837672.jpg

 photo storyboard008_zps9e42402a.jpg

 photo storyboard009_zps781726b5.jpg

 photo storyboard011_zps112b432b.jpg

 photo storyboard012_zpsaef862a4.jpg

 photo JenniSurpriseBirthdayParty-0071_zps787539b2.jpg

 photo JenniSurpriseBirthdayParty-0074_zps815cbaf1.jpg

 photo JenniSurpriseBirthdayParty-0076_zpsa067dfed.jpg

 photo JenniSurpriseBirthdayParty-0080_zpse2ec28b5.jpg

 photo JenniSurpriseBirthdayParty-0083_zpsc866d164.jpg

الجمعة، 9 يناير 2015

Postdoc position in Computational Biology / Infectious Disease w/ Ashlee Earl at the Broad

My friend, the brilliant Ashlee Earl is recruiting a post doc ... posting this for her.


POSTDOC – COMPUTATIONAL BIOLOGIST (INFECTIOUS DISEASE)
Requisition Number: 1571 http://www.broadinstitute.org/careers/job-openings/job-openings-0

The goal of the Bacterial Genomics Group at Broad is to develop and implement genomic and metagenomic methods to answer pressing questions related to bacteria and their role in human health. Specifically, we seek to understand the evolution and spread of bacterial pathogens (and antibiotic resistance) including the interactions that these pathogens have with their host and host-associated microbiota. We devise and carry out large-scale studies that employ genomic, metagenomic and transcriptomic data sets to understand human pathologies caused by e.g., Mycobacterium tuberculosis, carbapenem resistant Enterobacteriaceae, enterococci and uropathogenic Escherichia coli. We do this in close collaboration with clinical and academic researchers from across the Broad community and around the globe.

We are seeking a creative and highly motivated postdoctoral researcher in Computational Biology.  The ideal candidate should be broadly conversant with bioinformatics techniques for genomic data analysis including metagenomic analysis. They should also be familiar with microbial ecology principles, statistics and have made significant contributions to their area of study.

Responsibilities include:

  • Developing data analysis strategies, writing algorithms and deploying computational tools for the exploration of large genomic, metagenomic and metatranscriptomic data sets
  • Collaborating closely with experimental and computational researchers to interpret analytical results for publication
  • Communicating scientific findings in writing and orally

A Ph.D. in Computer Science, Bioinformatics, Biostatistics, Physics, Biological Sciences or a related field

  • Must be proficient in working in the Unix environment.  Solid coding proficiency in some combination of Python, Perl, Scala, Java, C/C++ and R. Experience with cluster computing and parallelization preferred.
  • Comfort and experience with programming for biological data analysis
  • Demonstrated ability to analyze and interpret metagenomic data
  • Excellent ability to communicate scientific material
  • Excellent collaborative skills and unrelenting enthusiasm for genomic science


EOE/Minorities/Females/Protected Veterans/Disabilities

الجمعة، 2 يناير 2015

Haloferax volcanii, model archaea, and me

When I was a graduate student I was looking around for an extremophile - especially an evolutionarily novel one.  And I settled on this species Haloferax volcanii - a model halophilic archaeon largely because Ford Doolittle and colleagues had started to turn it into a genetic model organism (and because Patrick Keeling, from Ford's lab convinced me it was a good thing to do).  So I started work on this species - doing DNA repair studies in the lab.  See my PhD thesis for some of the work I did which I never published outside of the thesis for multiple reasons.  But I continued to be interested in this species.  And when I was working at TIGR, an NSF Program Officer approached me asking me to help get the genome sequencing done for this species.  So, well, I did: The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.  And I became interested in other haloarchaea and eventually started working with Marc Facciotti, in the lab next to mine, in sequencing from across the diversity of the haloarchaea: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response.

Anyway - enough about me.  The whole point here is to point people to a new paper:  BMC Biology | Abstract | Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery.  Further evidence for the use of Haloferax volcanii as a model species.  Tools continue to become available for genetic and experimental studies in this species.  So - if you are looking for an unusual and interesting organisms to work on - consider working on this species ...

الخميس، 1 يناير 2015

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus

Well, this press release is from October:Study Suggests Altering Gut Bacteria Might Mitigate Lupus But I just discovered it and it definitely deserves an award.  An Overselling the Microbiome Award.  The PR, sadly and amazingly from the American Society for Microbiology which should know better, discusses a paper from the ASM Published journal Applied and Environmental Microbiology.  The PR does an OK job discussing what was in the paper - a study of the microbiome in mice including those that are a model for lupus.  The researchers characterized the microbiome is mice with and without the lupus model disease and also compared over time and between sexes.  And they found some interesting correlates of microbial patterns that are found during flare ups of lupus for example and also in drug induced worsening of symptoms.  But they never showed ANY causal connection between any of the mcirobes and the lupus like disease.  And the never showed ANY benefit of treating the lupus-like symptoms in the mice.  Yet amazingly they go over board in making such claims including
Title: STUDY SUGGESTS ALTERING GUT BACTERIA MIGHT MITIGATE LUPUS.
No - the study did not suggest that at all.  The authors suggested that, yes.  And the study is consistent with that.  But it is also consistent with altering gut bacteria having NO EFFECT on lupus.  So this title is simply deceptive.

In the text other statements are like this:
These results suggest that the gut bacteria may contribute to lupus.
Stunningly, the PR includes some really inappropriate comments including:
Nonetheless, Luo suggests that people with lupus should eat Lactobacillus-containing probiotics, such as live culture yogurts, to reduce lupus flares.
Seriously?  Shame on ASM for allowing this garbage to be in the PR. No evidence at all is presented that this is helpful.

Also in the PR:
More generally, "The use of probiotics, prebiotics, and antibiotics has the potential to alter microbiota dysbiosis, which in turn could improve lupus symptoms," says co-principal investigator Husen Zhang. Ultimately, says Luo, fecal transplant might prove valuable as a treatment for lupus.
Again, shame on ASM.  No evidence is presented for this either.

And then the PR ends with
"We were inspired in part to perform this research by a study on type 1 diabetes, which found that that disease is dependent on gut microbiota," says Zhang. "Like type 1 diabetes, lupus is an autoimmune disease that is even more prevalent [than type 1 diabetes] in women."
What?  I know of no research that shows that type 1 diabetes is dependent on gut microbiota.  I really don't even know what to say here.

This is one of the worst Press Releases I have ever seen in terms of misleading statements about microbiomes.  And ASM should be embarassed about it.  And ASM should retract it.  And ASM should never ever put out something like this again.  And for this, I am awarding a coveted "Overselling the Microbiome Award" to ASM for putting out this inappropriate press release.  If any with lupus goes out and gets even remotely worse from taking such probiotics, prebiotics, or antibiotics, ASM will bear some of the responsibility for their problems.  Shameful.



UPDATE 1: Jan 2, 2015

I did some searching for "probiotics" and "lupus" and found some much more tempered claims from other places. For example in "Lupus Studies Point to Gut Microbes, Epigenetics"
 "The long-standing anecdotal patient reports of certain diets worsening or improving flares might be more real than we thought. They should be studied more systematically, now that we know that almost any dietary component acts on the gut microbiota, [which] in turn has profound effects on the immune system," Dr. Kriegel said. He also warned that patients should not assume that the various "probiotic" products now available to consumers would have a beneficial effect in lupus. "Probiotics could theoretically even worsen a disease state, since it is possible that physiologic immune responses against benign commensals could fuel autoimmune responses via cross-reactivity (as we hypothesize) or other mechanisms," he said.
Dr. Kriegel concluded, "I think the best will be to wait until we have a better understanding of which commensals or commensal-derived products might be driving which autoimmune disease and then target those with a diet that is known to modulate these strains or products. Ideally, the field will also develop eventually novel types of antibiotics or vaccinations against certain commensals. Such approaches would allow us, in the future, to more specifically modulate the gut microbiota in autoimmunity." 
Now that is responsible commenting on lupus and the microbiome.  Too bad ASM allowed complete BS to get into this PR instead of more reasonaed statements.

See also