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).

For my first talk at a scientific meeting I discussed using RecA as a marker for phylogenetic studies (and had a slide where I had text saying RecA was cool).  Over the years I have continued to try and study RecA or at least use it for studying microbial diversity in some way.  See for example

Anyway – in this context I was excited to see a new paper on RecA-structure-function-evolution studies: PLoS Genetics: Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites from Olivier Lichtarge and others.  In the paper they use Lichtarge’s Evolutionary Trace method to study RecA.

The paper is worth a look and if you are interested in structure-function-evolution types of studies and need a good protein to work on, I would suggest you look at RecA and its relatives … They are Cool.

Oh and for the fun of it — I have found some of my slides from that talk in 1995.  Here they are

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.

Among the key links & tools discussed:

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

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.

So – what was wrong?  Well, I was starting to get more and more jaded with bad press releases about science papers.  And I felt ours had at least one really lame part – my quote

So if you’re interested in making clean fuels, this microbe makes an excellent starting point.

Well, WTF?  I have never done anything with biofuels and I really knew nothing about them then.  That quote should never have been in the press release and I am not sure I even said it.

Other parts of the PR are OK I think but I wish that quote had never been in there.  I note – I do like the end though

What we want to have is a field guide for these microbes, like those available for birds and mammals,” Eisen says. “Right now, we can’t even answer simple questions. Do similar hot springs , a world apart, share similar microbes? How do microbes move between hot springs? Our new work will help us find out.

I agree with that.   I have indeed been obsessed with a Field Guide to the Microbes for a long time …

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:


Gut microbes are essential components of the human organism—helping us metabolize food into energy, produce micronutrients, and shape our immune systems. Having a particular pattern of gut microbes is also increasingly being linked to medical conditions including obesity, inflammatory bowel disease, and diabetes. Recent studies now indicate that our resident intestinal bacteria may also play a critical role in determining one’s risk of developing cancer, ranging from protection against cancer to promoting its initiation and progression. Gut bacteria are greatly influenced by diet and in this review we explore evidence that they may be the missing piece that explains how dietary intake influences cancer risk, and discuss possible prevention and treatment strategies.

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

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 …