Draft post cleanup #22: Fun emails for another Jonathan Eisen

Yet another post in my "draft blog post cleanup" series.  Here is #22.  Written 5-5-2007 ...
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I have decided to start posting some of the more fun real emails I have gotten relating to some of my scientific work or supposedly related to it.

The best I get are usually not related to my work but instead are related to another Jonathan Eisen out there. There is this other person with my name who has written some off-kilter books about conspiracy theories. And every once in a while I get an email means for him. For example, here is one (with some personal information about the sender removed)

Draft post cleanup #21: Tracking progress on the vertebrate tree of life

Yet another post in my "draft blog post cleanup" series. Here is #21; from March 2010:

A very interesting paper came out recently from colleagues of mine at UC Davis:  Rapid progress on the vertebrate tree of life.  I did not know they were working on this but perhaps should have.  It has some fun/interesting analysis of the accumulation of phylogenetic knowledge over time.  For example see Figure 1

Cumulative phylogenetic information amassed for the last 16 years. The accumulation of sequences for vertebrates in GenBank (a), papers using the term 'phylogeny' or 'phylogenetics' in the Web of Science database (b) and phylogenetic resolution (measured as the proportion of nodes with at least 50% bootstrap support) in the vertebrate tree of life resulting from these research efforts (c). In all cases, the data are cumulative from the start of each analysis. Phylogenetic resolution is calculated as in Table 1. Trend lines are exponential in (a), and second order polynomial in (b) and (c).

Draft post cleanup #20: Retaking the biology GRE

Yet another post in my "draft blog post cleanup" series.  Here is #20:

In 2008, I had this idea that it would be interesting for biology faculty to retake the Biology GRE and see how they do.  I never got around to trying to register to take it and thus never wrote about it ...  Any Profs. out there who have gone back and taking the GREs?

Draft post cleanup #19: Spam and biased spam at that

Yet another post in my "draft blog post cleanup" series.  Here is #19 from September 2011:

I am sure many others out there who blog have gotten this kind of message:

We at Onlinephdprograms.com recently came across your blog and were excited to share with you an article “15 Fictional Professors We Wish Were Real” was recently published on our blog and we hoped that you would be interested in featuring or mentioning it in one of your posts.

(http://www.onlinephdprograms.com/15-fictional-professors-we-wish-were-real/)

Either way, I hope you continue putting out great content through your blog. It has been a sincere pleasure to read.

Thanks for your time,
Liz Nutt

I assume that these posts that are written for this, and various other sites, are all about driving up Google Search ranking somehow.  So I normally avoid writing about them.  But I thought I would in this case because, well, their post annoyed me because of the 15 functional professors they wrote about, only one is female.  Really, that is the best they could do?  In three minutes of web surfing (e.g., browsing this site and this one) I have come up with a list of fictional female professors who certainly could have been included in their list.  And many are much more interesting than some they wrote about.  Here are some examples:

• Eleanor Arroway - Jodie Foster's character in Contact
• Susan Calvin - character in Isaac Asimov's I Robot series

....

But then I stopped because I was disappointed I could not find more functional female professors to add to my list.  I do think the list posted by the OnlinePhD site could certainly have had more women on it ... but I never posted the post because I had a hard time coming up with a lot of examples ... but now that I am trying to revive draft posts ... well ... I will put this out there even if it is an incomplete thought

Draft post cleanup #18: Epernicus

Yet another post in my "draft blog post cleanup" series.  Here is #18, from July 2008.

Well, was going to write about Epernicus in 2008 as an interesting tool for networking scientists.  I still have an account there which I just updated a bit.  But I am not sure if Epernicus is being used much anymore.  I have focused a lot on a similar system: Mendeley though they have differences.

Draft post cleanup #17: Obama overqualified for application to be president

Yet another post in my "draft blog post cleanup" series.  Here is #17 from October 30, 2008.  I note - I never posted it because I tend to avoid politics here on the blog --- but three+ years later I think it is OK ...

Dear Mr. Obama

Thank you for your application for the position of 

President of the United States

Unfortunately we are unable to consider you for this position because you have been deemed overqualified.  

Draft post cleanup #16: Science and Title IX

Yet another post in my "draft blog post cleanup" series.  Here is #16 from July 2008.

I had seen an article that surprised me: Findings - John Tierney - Science Has Become the New Frontier for Title Nine - NYTimes.com

In the article Tierney discussed how the Title IX statute which forbids discrimination based on gender in education and has been applied extensively to athletic endeavors was beginning to be applied to science.  Not sure what has become of this over the last 3+ years --- if anyone knows more please post ...

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).

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"

Draft post cleanup #13: Twisted tree of life award: MSNBC, Aliens and Photosynthesis

Yet another post in my "draft blog post cleanup" series.  Here is #13 from July 2010.

I wanted to give this article a "Twisted Tree of Life Award":

How to find aliens: Follow the photosynthesis - Technology & science - Space - Space.com - msnbc.com

It is pretty painful to me.  Basically the people they are quoting argue that since "complex" life on Earth requires oxygen and since oxygen only comes from photosynthesis, therefore we should look for planets where photosynthesis is possible as the place where life is most likely to be interesting.  Uggh.  So many things in the article I did not like ... but just not enough time I guess to bitch about it then.  I will leave it to readers to decide for themselves I guess ...

Draft post cleanup #12: RecA is cool (and interesting)

Yet another post in my "draft blog post cleanup" series.  Here is #12:

I have been interested in RecA and related proteins for many many years.  In particular I have been interested in structural and functional evolution of RecA and its relatives.  This all started when for my second scientific paper I helped a post doc in the lab where I was doing my PhD do some structure-function-evolution studies (with a little help from Chris Lee, then in Mike Levitt's lab, and my brother, then in Don Wiley's lab).

Draft post cleanup #11: Tree Hugging

Yet another post in my "draft blog post cleanup" series.  Here is #11 from September.

Just a quick one.  In August a nice review paper came out on phylogenetic analysis software: Learning to Become a Tree Hugger | The Scientist.  By Amy Maxmen it is a "A guide to free software for constructing and assessing species relationships".  Definitely worth checking out.

Draft post cleanup #10: trip to LA artificially sweetened by Carolyn de la Peña

Yet another post in my "draft blog post cleanup" series.  Here is #10:

Went on a mini trip to UCLA for a mini meeting in November. It seemed appropriate that I brought with me to Los Angeles, land of empty pleasures - the new book from UC Davis Professor Carolyn de la Peña - "Empty Pleasures" on the history of artificial sweeteners. So I took a picture of the book overlooking part of LA from my hotel room:

The book is great read by the way ...

Draft post cleanup #8: Don't let a hospital kill you - CNN.com

Yet another post in my "draft blog post cleanup" series.  Here is #8 from 5-1-2008
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Saw an interesting article today on CNN.Com: Don't let a hospital kill you - CNN.com.  It has some useful suggestions for how to protect yourself from infection in a hospital.  In many cases we have an excessive fear of germs which can be a bad thing.  But in hospitals, staying clean is almost certainly a good idea ...

Draft post cleanup #7: Scamming Pubmed Central Deposition Rules

Yet another post in my "draft blog post cleanup" series.  Here is #7, from February this year.

I continue to be a bit annoyed by the Pubmed Central system for depositing your own papers there.  Well, actually, not annoyed with the existence of the system.  But am annoyed that you can only do it if you have an NIH grant ID associated with the paper you are depositing.  I am tempted to set up a system for sharing NIH grant IDs that would allow non NIH funded researchers to scam the system and to get their papers into Pubmed Central.  Almost certainly, people at NIH would not like this, but not sure whether this would be considered "illegal" or just "annoying".

And I am still unclear as to why Pubmed does this.  Genbank is NIH funded but will take sequences from any researcher no matter the source of funding for the work.  Anyway - I have not set up a NIH grant ID sharing system but if you want to submit an article to Pubmed Central and do not have an NIH grant ID, you might want to just ask someone who has one for a grant covering a similar topic at a similar time period.  I do not think NIH would figure out that the grant did not actually fund your work.  And you could even use the NIH grant search engine that pops up when you use the manuscript submission system or search Pubmed directly.  Not that I would recommend anyone break their rules or anything like that.

Draft post cleanup #6 from 2005: Hydrogen producing microbe mea culpa

Yet another post in my "draft blog post cleanup" series.  Here is #6. From 2005. (Yes, the bottom of my draft list).  In fact, this would have been my second blog post if I had posted it ...

I had written

OK, so a few months ago we published a paper on a hydrogen producing microbe and issued a press release. I think the paper we published was pretty cool - lots of interesting science.

Then we (me and our public affairs person) wrote a press release about the project. We were fortunate enough to have the press release picked up by all sorts of bloggers and web commentary groups. Examples include Softpedia (article here) and probably most importantly Slashdot.

Draft post cleanup #5: Best Science Paper Endings Award: Linking the Kama Sutra & Amoebas

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #5:

I was reading an article on MSNBC: Amoebas: Sexier than anyone knew - Technology & science - Science - LiveScience - msnbc.com

The article discusses a paper: "The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms" from the Proceedings of the Royal Society B.  The paper is freely available and it is definitely scientifically interesting.  But the last sentence is phenomenal and deserves some sort of prize

"When discussing the sex of amoeboid protists, the existing evidence does not evoke chastity but rather Kama Sutra"

So I am starting a new award here - the "Best Science Paper Endings Award"

Draft post cleanup #4: Gut microbes and cancer

Yet another post in my "draft blog post cleanup" series.  Here is #4:

Interesting article in the Scientist August 1, 2011:
Sharing the Bounty | The Scientist by Michelle Rooks and Wendy Garrett.

It is based on an article from the journal F1000 reports by the same authors.

The article in essence reviews other studies that suggest a possible link between microbes in one's gut and the risk of development of certain cancers.  It is worth a look.

See abstract below:

Draft post cleanup #3: The Open Knowledge Foundation

Yet another post in my "draft blog post cleanup" series.  Here is #3 from just a few weeks ago:

Interesting article in PLoS Biology:  PLoS Biology: The Open Knowledge Foundation: Open Data Means Better Science.  It discusses many issues in open science especially as they relate to open data.

Some links from this paper are worth checking out

• http://www.opendefinition.org/okd/
• http://science.okfn.org/About/
• http://www.earlham.edu/~peters/fos/bethe​sda.htm
• http://sciencecommons.org/projects/publi​shing/open-access-data-protocol/
• http://www.pantonprinciples.org/
• http://www.isitopendata.org/

This article reminds me that I keep meaning to push for the development of a "Datawatch" system much like the "RetractionWatch" systems of Ivan Oransky. I have discussed this with Ivan but we have not yet gotten around to doing it ... 

Draft blog post cleanup #2: Metagenomics meets animals

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #2:

Saw an interesting story on Genome Web: 'Denizens' of the Deep | The Daily Scan | GenomeWeb.  I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals.  They collected sloughed off cells and other material from a lake and surveyed it for animal DNA.  This seems like a very cool derivative of metagenomic approaches and has enormous potential.  But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post.  Damn non open access journals ...