Jonathan Eisen's Lab

Draft post cleanup #15: Now this is how to write a scientific paper

Yet another post in my “draft blog post cleanup” series. Here is #15, from May 2010.

I had written:

Just found an old fax I received from my brother of a paper published in 1974 in Scientia Sinica. “Studies of the insulin crystal structure: the molecule at 1.8Å resolution.” Sounds pretty straightforward right? But then you read the paper: Here is the abstract (could not find a PDF so scanned in the fax I got).

I note, I stopped here because I could not figure out how to upload a PDF here. But I did figure out how to upload it to FriendFeed. But I think in the end it would be good to have a version of this post on my blog. So, well, here it is. And now I have included scans of the fax:

Request for input – are there any rules regarding posting text of one’s own NSF (or other) grant proposals?

In response to a series of posts from Karen James (who is a biologist now in Maine and is director of the HMS Beagle Project) on Twitter, I am posting here to ask for input from the crowd. On Twitter, Karen has been discussing her putting together an NSF proposal and was then celebrating a few days ago when it was done.

I have posted some of the twitter conversation below. But to get directly to the point the question I have for everyone here is – are there any rules at the National Science Foundation that would prevent one from sharing with others a grant proposal that one has submitted? Are there any rules against this at any agency? I think there are none but apparently some are telling Karen otherwise.

Any information on this would be useful. Some of the twitter conversation is below:

kejames
So, @phylogenomics and others, with whom is it appropriate to share a submitted NSF proposal? Anyone? No one? Something in between?
1/12/12 6:15 PM

phylogenomics
@kejames what do you mean by “appropriate”
1/12/12 6:15 PM

johnhawks
@kejames If I were you, I’d share the whole thing in public and make the reviews public as well. But I’m a minority view.
1/12/12 6:16 PM

kejames
@johnhawks Thanks, I’ve thought of that, actually. It is a federal agency after all. I’d need to redact confidential budget info, though.
1/12/12 6:18 PM

johnhawks
@kejames Yes, and possibly key personnel. My attitude is the success rate is so low, it can’t hurt and might draw visibility pre-review.
1/12/12 6:19 PM

kejames
@phylogenomics Best practice. My instinct is to share it with colleagues, collaborators and associates I think might be interested in it.
1/12/12 6:16 PM

phylogenomics
@kejames what is the potential reason to not share?
1/12/12 6:17 PM

kejames
@phylogenomics That’s what I’m asking. Is there any rule or custom that prohibits sharing it far and wide?
1/12/12 6:19 PM

phylogenomics
@kejames none that I know of – only reason not to is if you are worried about people “stealing” your ideas
1/12/12 6:19 PM

kejames
@phylogenomics Not worried about that in the slightest. If anything sharing it widely establishes it as “my” idea. Thanks.
1/12/12 6:20 PM

kejames
@johnhawks Or I could ask the key personnel if they’re okay w/ it. I think it would be nice to include them if they want to be included.
1/12/12 6:21 PM

phylogenomics
@kejames I think Rosie Redfield posts hers on her blog http://t.co/g73Xb2Yz
1/12/12 6:25 PM

kejames
@phylogenomics Thanks for that. I notice she just posts the project description itself, none of the other “stuff”and doesn’t list names.
1/12/12 6:28 PM

DoctorZen
@kejames NSF proposals are your choice who to share with. Probably not best to post publicly, though.
1/12/12 6:25 PM

kejames
@DoctorZen Why not? As @phylogenomics notes, @RosieRedfield posts her grant proposals on her lab’s website: http://t.co/peWEmnvs
1/12/12 6:29 PM

kejames
Anyone else besides @phylogenomics @doctorzen @johnhawks want to weigh in on how broadly I should share my just-submitted NSF proposal? 1/2
1/12/12 6:31 PM

kejames
@rdmpage @RosieRedfield @DoctorZen @johnhawks @phylogenomics @kzelnio So I asked the collaborators on the proposal. One replied… 1/2
1/13/12 4:50 AM

kejames
@rdmpage @RosieRedfield @DoctorZen @johnhawks @phylogenomics @kzelnio 2/2…”Sharing not wise! Could disqualify proposal.”
1/13/12 4:51 AM

rdmpage
.@kejames @rosieredfield @doctorzen @johnhawks @phylogenomics @kzelnio In other words fear of what grant agency will do trumps being open 😦
1/13/12 5:10 AM

DoctorZen
@rdmpage I support being open; not sure every step always needs to be public. @kejames @rosieredfield @johnhawks @phylogenomics @kzelnio
1/13/12 5:18 AM

rdmpage
.@DoctorZen @kejames @rosieredfield @johnhawks @phylogenomics @kzelnio I agree, it’s not that it HAS to open, but that it COULD be
1/13/12 5:27 AM

phylogenomics
@kejames @rdmpage @RosieRedfield @DoctorZen @johnhawks @kzelnio WTF? As far as I know there are NO NSF issues w/ sharing a proposal
1/13/12 7:00 AM

phylogenomics
@kejames @rdmpage @RosieRedfield @DoctorZen @johnhawks @kzelnio Yes, need to discuss w/ collabs & get permission but not angst any rules
1/13/12 7:02 AM

phylogenomics
@rdmpage @DoctorZen @kejames @rosieredfield @johnhawks @kzelnio agree w/ Rod – issue was whether it could be posted, not if it had to be
1/13/12 7:04 AM

kejames
@phylogenomics I’m following up w/ him to find out what he meant He’s a seasoned NSF grantee and reviewer. Have also contacted NSF directly.
1/13/12 7:08 AM

Storification of Tweets from talk by Jane Lubchenco at #UCDavis

Jane Lubchenco, head of NOAA, gave a talk at UC Dav is yesterday and I made a “Storify” version of some tweets from it. I am putting it below the “fold” here since it takes up a lot of space and I cannot figure out how to put the “click here for more” feature in the middle of a storify embed.
http://storify.com/phylogenomics/jane-lubchenco-head-of-noaa-talk-at-ucdavis.js[&amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/jane-lubchenco-head-of-noaa-talk-at-ucdavis” target=”_blank”&amp;amp;amp;amp;gt;View the story “Jane Lubchenco, head of NOAA, talk at #UCDavis” on Storify&amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;gt;]

Letter from Chancellor Katehi to #UCDavis Community

Posting this email I received for those interested. Not sure what will happen this quarter in terms of Occupy UC Davis actions and related issues … but will post as things develop.

Dear UC Davis Community,

Happy New Year! I am writing to welcome everyone back to campus and to share my thoughts about the coming year at UC Davis.

The many conversations we’ve had about the events of last November affirm that our pursuit of academic excellence can succeed only if our campus remains a safe and welcoming place for all voices and forms of expression.

As we work to ensure this, we must not forget the understandable frustration that has fueled protests. After repeated cuts in state support for California’s public universities and a near doubling of tuition the past four years, many of our students and their families have reached a breaking point. Rising student debt and a still-struggling economy have only made things worse. Students have every right to expect that we will stand with them in fighting to reverse these very troubling trends.

In the coming year, I will personally and persistently advocate for additional state and federal investment in our university to help ease this financial burden and make UC Davis more available and accessible to deserving students. We also will steward our resources wisely, seek to protect academic programs to the extent possible, and do everything possible to fund more student scholarships and fellowships.

Ours is a preeminent public university. As we all strive to enhance its many qualities and distinctions, let us be proud of what is taking place every day in our classrooms, laboratories, health centers and other centers of excellence. All of you, in some way, are benefiting our region, state, nation and world. All great universities place students at the center of their work. We cannot and will not rest until we provide our students the best learning environment and services possible.

I also am committed to focusing on the positive role of UC Davis in economic development and its positive impacts on communities, our state and beyond. A stronger regional, state and global economy will provide our graduates with the career and service opportunities they deserve.

In support of this goal, I have initiated an extensive effort involving faculty, students and staff to assess and evaluate our 2020 Initiative. Central to that task is our ability to convert this concept into a plan that is implementable, aligns well with and supports our values and principles as a land-grant university.

The 2020 Initiative can be a bold blueprint for UC Davis to meet its financial challenges while broadening access to California students and allowing our university to become an even more vital engine of economic development.

Much work lies ahead. We expect to receive in coming weeks the results of various inquiries regarding the events of last November. We will receive critical reports regarding the future of UC Davis athletics. And we will hear the concerns and ideas generated by the fifty faculty, staff and students helping to study and shape the proposed 2020 Initiative.

I look forward to sharing and discussing these important subjects with you.

Sincerely,

Linda P.B. Katehi

Draft post cleanup #14: Video of Talk of mine from 2005

Yet another post in my “draft blog post cleanup” series. Here is #14 from July 2010.

Embedded here is a video of a talk I gave in 2005 at the NIH entitled “More Questions Than Answers Insights into DNA Repair Processes from Genome Sequencing Projects”

http://videocast.nih.gov/embed.asp?file=12774

Google scholar missing paper issue clarified, though not corrected, but glad Google responded

Below is a thread relating to a reference missing from Google Scholar

From: jonathan.eisen@gmail.com

Subject: Missing reference in Google Scholar

Date: Sat, 24 Dec 2011 15:12:07 +0000

The following important and highly cited reference is somehow missing from Google Scholar although it was there a few months ago – it would be useful to have it back:

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC.

Nature. 1999 Dec 16;402(6763):761-8.

PMID: 10617197 [PubMed – indexed for MEDLINE]

Thanks for your recent email to Google Scholar. We’ve included answers to a number of frequently asked questions in our response below. If you have a question or concern that is not addressed by these answers, please reply to this email for further assistance.

Adding content to Google Scholar:
Please contact your publisher or the institutional repository for your
university to add your papers to Google Scholar.
Detailed guidelines for publishers and other websites can be found below.
http://scholar.google.com/intl/en/scholar/publishers.html
http://scholar.google.com/intl/en/scholar/inclusion.html

Incorrect bibliographic information in Google Scholar results:
Please click on the erroneous result and contact the owner of the website where we found it. Please ask them to follow the technical guidelines below to help fix the indexing of their articles.
http://scholar.google.com/intl/en/scholar/inclusion.html

I can’t find my paper anymore! My citation count has gone down!
That can happen because we index scholarly articles available to us on the Web, and the Web changes. Chances are that some website that used to host your paper or papers that cite it no longer do so. Please contact your publisher about adding your papers or correcting their bibliographic data. Unfortunately, we’re unable to include papers that are no longer available on the Web.

Two of my papers are listed as one… Some citations aren’t counted…
Please reply to this message with detailed examples of the problem. Please include the queries you used as well as the specific articles in question. Google Scholar is based on automated indexing algorithms. We’re unable to make individual changes, but specific examples will help improve the automated techniques and will result in improved results for all users.

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Please contact the vendor of your link resolver (e.g., SFX) to make any changes regarding library links. If you are moving to a different link resolver, please contact both the previous vendor and the new vendor. Detailed information is available on our help page for libraries at http://scholar.google.com/intl/en/scholar/libraries.html

Feature requests and suggestions:
We are actively developing new features for Google Scholar. We take note of all feedback that we receive and add some of the ideas to our growing list of feature requests. Although we are unable to respond to every suggestion, we will be sure to email you if we have follow-up questions.

We’re working hard to provide easy access to scholarly literature, and your feedback will assist us in improving this program.

If you continue to have questions or concerns about Google Scholar, please reply to this email and one of our specialists will assist you.

My concern is not addressed by these answers. My concern is that I am an author on a paper that is listed in Pubmed and used to be listed on Google Scholar but it has disappeared for some reason. The citation is below. It is a reasonably important biology paper and thus it would be good in general (and good for me) if it could be “rescued” and show up in Google Scholar again. Thanks

Jonathan Eisen

Hello Jonathan,

In this case the clustering algorithm mis-detected two articles with
similar metadata as being the same article, which you can see at:
http://scholar.google.com/scholar?cluster=8097588176412115112&hl=en&as_sdt=0,5

We’re not currently able to perform manual correction on individual
entries in our database since the indexing is done automatically by
robots, but we use examples like this one as we continue to improve the clustering algorithm. Thanks for letting us know about the issue.

Sincerely,

The Google Scholar Team

OK – testing "threaded commenting" on my blog

Just saw this post from Blogger and am testing it here – seems like it could be a better commenting system — Engage with your readers through threaded commenting | Blogger Buzz

Let me know if there are any opinions on the matter …

Diplomacy fails? Military options off the table? Let’s assassinate the scientists

While I for one do not want Iran to have nuclear weapons I think this is disturbing: Iranian nuclear scientist killed in Tehran explosion – latimes.com

So – basically – the decision by some agency or agencies (US, Israeli, others) seems to be – let’s go after the scientists. Why do they do this? Well, because nobody seems to have the skills or desire to develop an international consensus or diplomacy for an alternative response. Not that dealing with Iran would be easy. And not that military options would be good. But sad in many ways that the option of choice is to kill the scientists behind the work. If all other options had been tried – this might be reasonable – but it does not seem to me that all other options have been tried yet …

Wrap up of tweets from Joe Derisi talk

Just a quick post here – for those not following on Twitter – Joe Derisi gave a talk at UC Davis 1/9 and I posted some tweets about it. Here they are:

phylogenomics
Joe DeRisi getting ready for his talk at the #ucdavis Genome Center this am http://t.co/OwZbM2nn
1/9/12 9:57 AM

phylogenomics
Joe Derisi’s first slide : “Bees, viruses, and plastids: a seminar in two parts” – I think he needs to work on his math http://t.co/0nPjChlc
1/9/12 10:05 AM

phylogenomics
DeRisi works with mobile honeybee colony trucks that travel around the country to service pollination needs
1/9/12 10:09 AM

phylogenomics
DeRisi – one of the problems with figuring out what is causing CCD is we do not know much about “normal” healthy colonies
1/9/12 10:09 AM

phylogenomics
Bee trucks start in Mississippi in winter, spring in Dakotas, then To california for almonds
1/9/12 10:10 AM

phylogenomics
DeRisi got into bee studies because of colony collapse disorder CCD
1/9/12 10:13 AM

phylogenomics
DeRisi – grinds up bees and then assays them with “bee pathogen chip” and sequencing
1/9/12 10:13 AM

phylogenomics
Derisi discussing his new Plos one w/ SFSU paper showing phorid flies associated with bees
1/9/12 10:16 AM

phylogenomics
Derisi says if you want your paper to get 1000s of hits you should mention Zombies somewhere as they did w/ “Zombie bees”
1/9/12 10:18 AM

phylogenomics
Derisi: zombie bees are cool but the phorids are probably not associated with CCD
1/9/12 10:19 AM

phylogenomics
DeRisi found six major pathogens associated w/ bees: Nosema, phorids, spiroplasma, notovirus, and others
1/9/12 10:22 AM

phylogenomics
DeRisi – sequencing ground up bees – most reads are host or pathogens they know about – says key to characterizing new viruses is assembly
1/9/12 10:23 AM

phylogenomics
DeRisi mentioning their PRICE assembler – an inductive assembly method
1/9/12 10:25 AM

notSoJunkDNA
URL for PRICE is http://t.co/bRGiY7Rz
1/9/12 10:30 AM

phylogenomics
Why I love Joe Derisi “there will be a manuscript on the assembler someday… But the software is available for free now”
1/9/12 10:27 AM

phylogenomics
DeRisi pooled together Bee samples prepped with various methods so that he could get diverse viruses covered
1/9/12 10:29 AM

phylogenomics
DeRisi – lake sinai virus 2 is present in up to 10^11 copies per bee
1/9/12 10:35 AM

phylogenomics
DeRisi – also present in bees – Crithidia – a trypanosome – related to known pathogens of other insects
1/9/12 10:36 AM

phylogenomics
DeRisi – Crithidia also increases in abundance in winter
1/9/12 10:36 AM

phylogenomics
DeRisi – sequenced and assembled genome of Crithidia – genome is interesting
1/9/12 10:37 AM

phylogenomics
DeRisi – part two – the essential function of the Plasmodium apicoplast
1/9/12 10:38 AM

phylogenomics
DeRisi – history of Studies of plasmodium apicoplast – organelle bound by four membranes – likely b/c result of secondary symbiosis
1/9/12 10:39 AM

phylogenomics
Derisi discussing sequencing of apicoplast genome in 1990s by Gardner, McFadden, etc
1/9/12 10:40 AM

phylogenomics
DeRisi – experiments suggest IPP is the sole essential product of apicoplast biology
1/9/12 10:47 AM

Another seminar at #UCDavis 1/11 – Evan Eichler – #TooManyChoices

Well, this is going to be awkward. I really really want to hear this upcoming talk by Evan Eichler. But alas, Jane Lubchenco – head of NOAA – is talking at the same time. And sorry Evan, but Jane wins – this time (never heard her speak before).

UC Davis M.I.N.D. Institute’s 2011-2012 Distinguished Lecturer Series

SPEAKER: Evan E. Eichler, Ph.D.
TOPIC: Copy Number Variation, Exome Sequencing and Autism
DATE: Wednesday, January 11, 2012
TIME: 4:30 pm – 6:00 pm
LOCATION: M.I.N.D. Institute Auditorium (2825 50th Street, Sacramento)

Biographical / Presentation Information (attached and pasted below):

Evan E. Eichler, Ph.D., is a Professor and Howard Hughes Medical Institute Investigator in the Department of Genome Sciences, University of Washington School of Medicine. Dr. Eichler is a leader in an effort to identify and sequence normal and disease-causing structural variation in the human genome. His research group provided the first genome-wide view of segmental duplications within human and other primate genomes. The long-term goal of his research is to understand the evolution and mechanisms of recent gene duplication and its relationship to copy number variation and human disease. A graduate in biology of the University of Saskatchewan, Canada, he received his Ph.D. in 1995 from the Department of Molecular and Human Genetics at Baylor College of Medicine, Houston. After a Hollaender post-doctoral fellowship at Lawrence Livermore National Laboratory, he joined the faculty of Case Western Reserve University in 1997 and later the Department of Genome Sciences at the University of Washington in 2004. He was a March of Dimes Basil O’Connor Scholar (1998-2001), appointed as an HHMI Investigator (2005), and awarded an AAAS Fellowship (2006) and the American Society of Human Genetics Curt Stern Award (2008). He is an editor of Genome Research and has served on various scientific advisory boards for both NIH and NSF.

Copy Number Variation, Exome Sequencing and Autism.
It has become apparent that genetic structural variation contributes significantly to both neurocognitive and neuropsychiatric disease. I will present a detailed study of the genomes of children with developmental delay compared to adult controls and show that as much as 14% of pediatric disease, including autism, epilepsy and intellectual disability, is caused by deletions and duplications of large segments of the genome involving multiple genes. These mutations can be either inherited or found in the parents of children depending on the size of the event. I will present evidence from exome sequencing of over 200 parent-child trios with sporadic autism and show how these data may be used to pinpoint novel genes underlying CNV (copy number variation) burden, as well as provide insight into new pathways. We find that some of the same disease-causing mutations can manifest very differently and in particular be more severe if they occur on a background of other compounding mutations. We predict that the overall burden of rare and private severe mutations will correlate with different outcomes ranging from autism, intellectual disability and epilepsy. We propose that the early development of the brain is particularly sensitive to the timing and expression of many different genes and that multiple genetic perturbations within specific pathways can lead to disease with varying severity.

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