For those who read this blog but don’t follow me on Twitter or elsewhere just thought I would share my new project with you: The Eisenome. Please join in.
Just got this email regarding Nature Precedings.
Dear registrant:
As you are an active user of Nature Precedings, we want to let you know about some upcoming changes to this service. As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Submitted documents will be processed as usual and hosted provided they are uploaded by midnight on April 3rd. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.
Be assured that Nature and the Nature research journals continue to permit the posting of preprints and there is no change to this policy, which is detailed here.
Nature Precedings was launched in 2007 as NPG’s preprint server, primarily for the Life Science community. Since that date, we have learned a great deal from you about what types of content are valued as preprints, and which segments of the research community most embrace this form of publication. While a great experiment, technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived.
Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area. We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.
Interestingly, there is no announcement at the Nature Precedings site itself. I assume the email I received is real (it really looks real) though you never know these days. It’s too bad. I like the concept of a preprint server for biology. Interestingly, one of the alternatives to NP is FigShare (which is pretty cool) which recently became part of the Digital Science group which is a sister group to Nature. Hmm … wonder what the conversations at joint tea parties between Nature and Digital Science group are like. Could be fun.
Seriously? Scientists look to mummies for obesity cure. I mean – yes – I do think it is possible that antibiotic use has screwed up the human microbiome across the planet and that might have led to other problems. But for 3$&#$# sake there are 1,000,000 plus other things that have changed since the time of the mummies from diet, to pollution, to longevity, to urbanization, to sedentariness, to TV, to … well … almost everything. So – sure – the microbiome in “the ancients” might be different (I don’t see a paper here). But the headlong “look for mummies for obesity cure” is pretty darn misleading. And thus I am giving MSN one of my coveted “Overselling the microbiome” awards.
There is an interesting story going around the web. An example of the coverage is here at the Huffington Post: Birth-Control Pill Helped Boost Women’s Wages, New Study Shows. As for all stories I read about new scientific findings, for this one I looked for the research paper or report behind the story. The Huff. Post story seemed a bit strange in this regard reporting “Bailey and her colleagues report in a National Bureau of Economic Research working paper due to be published in July in the American Economic Journal: Applied Economics.” Weird – to be published in July. Why report on it now? So I sniffed around at other news stories about this topic and found one that said the working paper was published online. So a little more sniffing (i.e., Googling) led me to the National Bureau of Economic Research (a private non profit entity). And there, eventually, I found
The Opt-In Revolution? Contraception and the Gender Gap in Wages
Martha J. Bailey, Brad Hershbein, Amalia R. Miller
NBER Working Paper No. 17922
Issued in March 2012
When I tried to get the paper I discovered it was $5. Not so bad. I prefer of course, free and open publication. Especially if the research and salaries of the authors were paid for by Government grants. But I did not have the zeal to dig into the funding behind the work. And 5$ really is not much money. So I decided WTF – let’s buy it. Alas, then I discovered that I could not just buy the paper but that I had to create a user account of some kind, and I stopped at that point. Too complicated for a bit of a whim. So much for buying the paper.
Then I saw further down on the page
Information about Free Papers
You should expect a free download if you are a subscriber, a corporate associate of the NBER, a journalist, an employee of the U.S. federal government with a “.GOV” domain name, or a resident of nearly any developing country or transition economy.
Most of this makes sense to me except the .GOV part. Why exactly do they make articles available for free to those who work for the US Federal Government but not for others, like, say, the taxpayers who pay for the US Federal Government? Again, I get that publishers have to make a living somehow and I was even ready to pay for this article because the fee was low and it seemed interesting. But I am a bit perplexed and annoyed that people that have a .GOV domain address get stuff for free. This smells funny to me. You can’t even give pencils to some people working for the US Federal Government due to gift rules. But apparently you can give away research papers that are not available to others. What is the logic behind this? Aargh. Well. Maybe I will download the paper when I within a .GOV domain. But it will feel icky in some way.
Just a quick post here. There is a nice review by Monya Baker on de novo genome assembly in Nature Methods: De novo genome assembly: what every biologist should know : Nature Methods : Nature Publishing Group. It is currently freely available though not sure if that is permanent or not …
Love the start which quotes my colleague Ian Korf
Asked how mature the field of genome assembly is, Ian Korf at the University of California, Davis, compares it to a teenager with great capabilities. “It’s got bold assertions about what it can do, but at the same time it’s making embarrassing mistakes,” he says
The paper is definitely worth a look …
Sequencing reference genomes for various built environments requires a series of steps. The first part of the procedure is to sample an environment that possibly has interesting microbes. For an example one might sample a toilet, public tables, floors or human associated items. There are 2 ways to sample something, direct plating or indirect plating. Direct plating is done by directly swabbing the area of interest with a sterile swab then directly swabbing onto a plate. Indirect plating is done by swabbing the area then putting the swab directly into media and allowing growth to occur, then plating.
The next step after growing the samples is to dilution streak. Dilution streaking is a method used to isolate a single organism by systematically reducing the amount of bacteria in different parts of the nutrient plate. To dilution streak, first sterilize an inoculation loop and run it through a colony in the sample plate. Take the inoculation loop and create a heavy “pool” of microbes in one corner of the new plate. After doing this, sterilize the inoculation loop again and drag it through the pool creating a zig zag pattern. Repeat this step one more time using the previous pattern as the “pool”. This allows individual colonies to form.
After the individual colonies have grown, it is time to make over night cultures. To do this take 5ml of the appropriate media and with the sterilized inoculation loop, scrap a colony and put it into the liquid. After the overnight culture as grown we can extract genomic DNA by doing genomic preparations. Genomic preparation involves lysing the membrane and nuclei, which allows the DNA to flow into the solution. Cellular proteins and other impurities are then removed using salt-precipitating solution and isopropanol. Lastly, the genomic DNA is suspended in rehydration solution for further analysis. After this, we must confirm there is actually genomic DNA. To do this, we use an agarose gel. A mold of agarose solution is created with wells. The mold is placed in a “gel box” with TAE buffer. The genomic DNA and a UV-fluorescing dye are loaded into the wells and a current of 120 V is run through it for 20 minutes. This separates the DNA fragments. We then analyze the DNA fragments under a UV light. If DNA fragments are present, that means there is genomic DNA.
The next step is to do a 16S PCR. A PCR is involves ribosomal RNA which is highly conserved, and is done to amplify this ribosomal RNA. This procedure involves a master mix made up of Taq Buffer, Q Buffer, dNTP, P1 P2 Primers, Taq polymerase, water and DNA. Then we must confirm the PCR using agarose gel electrophoresis. Always have a positive and negative control and ladders. The gel allows us to see if the PCR was correctly done with a presence of a band at 1300bp and by looking at the size of the bands.
After 16S PCR is confirmed the PCR is cleaned up. This step requires Buffer NT-Bind 16S DNA to membrane, NT3 buffer-wash PCR reagents, dry silica membrane, and Elution- Buffer NE. The cleaned PCR is then TOPO cloned. To TOPO clone, use the Invitrogen protocol and kit. Take a few micro liters of PCR product and mix with TOPO vector, the enzyme ligates the PCR product to the vector. Then the plasmid is transformed into E.Coli by mixing the TOPO reaction with E.Coli and incubating on ice. The cells are then heat shocked to allows plasmids to enter. Then the cells are allowed to repair so ampicillian resistance can be expressed. Spread the transformation onto LB carbenicillian plates and incubate overnight. Plasmid preps are then made by first picking the correct colony and grow in an over night culture. Then the plasmids are isolated from the E.Coli following the Qiagen kit protocol. Various buffers are added to break down cell walls and precipitate protein then transfer into QIAprep spin column to capture plasmid DNA. Add more buffers to isolate plasmid DNA from genomic DNA then elute plasmid DNA into clean microcentrifuge tube by washing out the spin column.
The plasmid is then quantified using plasmid quantification procedures. Use a spectrophotometer to measure how much DNA was isolated during the plasmid prep. This shows us the amount of DNA that is in the sample, this is important because a certain amount of DNA is needed before the sample can be sent to be sequenced. Use the dsDNA function and mix 1 micro liter of sample with 99 micro liters of water. Multiply the reading by 100 to take into account the dilution factor. After getting the readings the plasmids and/or the PCR is diluted to specific concentrations and transferred to the UC Davis DNA sequence center. A few days later the results are sent back to us. Using the Geneious program we edit and analyze the gene sequence. We copy and past the cleaned up sequence onto Blast website to compare the sequence of our 16s to other organism. Lastly we use Genome online database (GOLD) to see genome sequencing projects relating to our organism. We check the complete, incomplete and targeted projects to see what has been done thus far. From here we decide whether or not to go further into research.
Just got an announcement for a meeting from Elsevier that I have absolutely no potential connection too. It is yet another example of Science Conference Spam. Not really shocking to get it from Elsevier to be honest. But one part of the email struck me. This was the end of the message which I post below:
DATA PROTECTION NOTICE
This email has been sent to xxxxxxx from Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, using 22 Times B.V. technology and platform. This is a one-off email sent to you in the belief that it will be of interest. We will not add your name and email address to our database unless you request further information. If you wish to ensure that you will not receive a future marketing message from us about these products or services, please send a reply message to exclusionlist@elsevier.com. We respect your privacy and do not rent or sell your personal information to any non-affiliated third parties without your consent, except as may be stated in our privacy policy at: Elsevier privacy policy.
For the 22 Times privacy policy, please visit: 22 Times B.V. privacy policy.
We obtained your name and email address from ISI Thomson Scientific, 3501 Market street, Philadelphia, PA 19104 USA. If you wish to be removed from the ISI Thomson Scientific mailing lists, please click here ISI Thomson Scientific.
Copyright © 2012 Elsevier B.V. http://www.elsevier.com. registered office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, under number 33156677, VAT number 002967455B65. All rights reserved.
This is a typical SPAMMY system where you get added to a list without requesting it. So – want to know what the “22 Times” privacy policy is? Well if you click the link you get
I can guess what it says but fortunately for those like me that don’t read Dutch, Google offers to translate. So I clicked on that offer just to be sure: “Page not found.” Great policy. Maybe I am supposed to pay to access it? I note – I have not posted the actual original link in the email because it has what appears to be some tracking information embedded in it. This I guess is what one could call an empty promise of privacy?
Anyway, next I clicked on the link for the Elsevier Privacy Policy. This time there is an actual policy there. Not surprisingly it is not very focused on the people at the other end. Here it is below, with some highlighting by me
Elsevier Website Privacy Policy
Elsevier is committed to maintaining your confidence and trust with respect to the privacy of the personally identifiable information we collect from you. This privacy policy sets forth our practices regarding collection, use and disclosure of information collected through or in connection with the Elsevier corporate website and all other Elsevier websites that post a link to this privacy policy (each a “Site”).
Collection and Registration of Personal Information
We may request users of this Site to provide personal information. The information collected directly from a user may include contact information such as the user’s name, e-mail address, and postal address.
In order to access certain content and to make use of the full functionality and advanced personalization features of the Site we ask you to register by completing and submitting a registration form, which may request additional information, such as work setting or principal professional field.
Automatic Collection of Information
This Site automatically collects certain information from your web browser regarding your use of the Site. Examples of information collected automatically from all users include the Internet Protocol (“IP”) address used to connect your computer to the Internet; computer and connection information such as browser type and version, operating system, and platform; and full Uniform Resource Locator (“URL”) click stream data, including date and time, and content you viewed or searched for on the Site.
This Site also collects information through the use of “cookies” or similar technologies. Cookies are anonymous, unique alphanumeric identifiers sent to your browser from a website’s computers and stored on your computer’s hard drive. The type of information collected as a result of a cookie being stored on your computer is specific to your computer. “Session” cookies collect information about your use of the Site (e.g., whether you are logged in) and to give you a more personalized browsing experience and help you navigate the Site more efficiently from page to page. These cookies are temporary and are deleted when you close your browser. “Persistent” cookies gather statistical information about repeat usage from your computer or workstation. In general, cookies do not contain personally identifiable information, but when you furnish your personal information through the Site, this information may be linked to the non-personally identifiable data stored in cookies sent to your browser from the Site.
We and our affiliated group companies and service providers may use cookies, “web beacons” or clear .gifs, or similar technologies to collect and use this information for the purposes of usage analysis (including for the purposes of reporting and paying royalties and license fees to third-party providers, such as authors, societies and other copyright holders and content distributors as well as tracking and analyzing user preferences and trends), delivery and management of our advertising, promotions and surveys, quality control and administering, customizing and improving the Site.
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We use the personal information that you provide for such purposes as:
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Pseudonymous analysis to create a profile used to determine the habits, interests or other characteristics of users for purposes of research, analysis and anonymous reporting; and
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We may on occasion also match or combine the personal information that you provide with information that we obtain from other sources or that is already in our records, whether collected online or offline or by predecessor or affiliated group companies, for such purposes.Disclosure of Personal Information to Third Parties
Access to your personal information is restricted to our employees, agents, representatives, service providers, and entities for which we are acting as an agent, licensee or publisher, such as societies, for the purposes set forth above. Your personal information may be used by all of our trading names and affiliated group companies and transferred to other countries for processing. These countries may not have similar data privacy laws, but if we transfer your information in this way, we will take steps to ensure that your information continues to be protected.
We also may share your personal information with our affiliated group companies worldwide and/or with non-affiliated third parties that wish to send you information about their products and services that may be of interest to you. We will not pass your personal information to such third parties if you indicate that you do not wish us to do so.
If this site offers an online content database or learning service (“Service”) and you access the Service through an institution-sponsored subscription, your personal information and certain usage data gathered through the Service, such as the number of items you downloaded, any non-subscribed items you accessed, and test scores, may be shared with your institution for the purposes of usage analysis, subscription management, course management, and testing and remediation. If your institution is a corporation or other business entity, additional usage data, such as the types of records you viewed and the number of searches you ran, also may be shared for the purposes of cost attribution and departmental budgeting.
We will not otherwise disclose any personal information without your consent except under the following circumstances:
in response to subpoenas, court orders, or legal process, or to establish or exercise our rights to defend against legal claims;
if we believe it is necessary to investigate, prevent, or take action regarding illegal activities, suspected fraud, safety of person or property, violation of our policies, or as otherwise required by law; and
if Elsevier, this Site, or a related asset or line of business is acquired by, transferred to or merged with another company.
Access and Changes to Your Registration Information and PreferencesRegistered users may access their identified contact information and other registration information and correct any discrepancies or update information upon log in at any time. The accuracy of such information is solely the responsibility of the user. No access is given to other data that may have been collected about users.
If you wish to receive alerts, newsletters, special offers or promotions from us, please indicate your preferences when you register or amend your preferences upon log in at any time. If you wish to cease receiving any of this information, amend your preferences either upon log in or by using the “opt-out” or unsubscribe option or other means provided within the communications you receive. We reserve the right to notify you of changes or updates to the Site whenever necessary.
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Our Commitment to Data Security
We endeavor to keep your personal information confidential and protected against unauthorized access, loss, misuse or alteration through the use of appropriate administrative, physical and technical safeguards. The personal and demographic information about each user is stored on systems that are subject to appropriate physical and electronic security measures, and we limit employee access to and use of such information.
About This Privacy Policy
The foregoing is the current privacy policy of the Site. We reserve the right to change this policy at any time without notice. Any changes to this policy will be posted on this web page.
This Site may contain links to other websites that are beyond our control. Other websites to which you link may contain privacy policies that are different from this privacy policy. This privacy policy will not apply to data collected by or provided to other websites.
The websites of certain divisions or business units within the Elsevier group of companies may have privacy policies that are different from this privacy policy. In such cases, the privacy policy of that website will be posted and will supersede the terms of this policy in the event of a conflict.
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If you have any questions or comments regarding this privacy policy, please contact:
Elsevier Data Protection Officer
Elsevier Limited
The Boulevard
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Email: DPO@elsevier.comIf at any time you believe that we have not adhered to this privacy policy or you have a complaint regarding the way your personal information is being handled, please contact the Elsevier Data Protection Officer. Disputes under this privacy policy will be resolved by the Elsevier Data Protection Officer, who will use commercially reasonable efforts to promptly investigate and, if necessary, to correct any problem.
Last revised: 28 May 2010
I don’t know about you but I am not feeling too comforted by this policy. For comparison here are some links to privacy policies of other science publishers:
Well, let’s see if Nature Publishing Group actually does the right thing here. A few days ago I showed that they were charging for access to “genome sequencing” papers that were supposed to be freely available (see Hey Nature Publishing Group – When are you going to live up to your promises about “free” genome papers? #opengate #aaaaaarrgh). And in researching this I then discovered that Nature Publishing Group has been charging for access to corrections of articles (see Nature’s access absurdity: Human Genome Paper free but access to corrections will costs $64 and Corrections Scamming at Nature: Tantalizing clues, to see errors just pay more money #Seriously?).
So – after finding out that “corrections” for freely available papers at Nature cost money to get access to I decided to snoop around at Nature Publishing Group’s archives to see how they have handled corrections.
If you search for “Corrections” in Nature Publishing Group’s journals, you see that many / most are labelled as “free” and in fact, they do seem to be free. That is until about 5 years ago. As far as I can tell, most “Corrections” published prior to September 2007 are not freely available.
For example see this correction where we are told
“In the News & Views article “Chemical biology: Ions illuminated” by Christopher J. Chang (Nature 448, 654–655; 2007) an error crept into part a of the accompanying figure.”
Tantalizing. To find out more you need just pay $18.
Or in this correction:
“In the News & Views article “Organic chemistry:A tuxedo for iodine atoms” by Phil S. Baran and Thomas J.”.
Not so tantalizing. But nevertheless the full correction can be yours for just $18.
Or this one:
The story ”That’s no laser, it’s a particle accelerator” (Nature 443, 256; 2006) incorrectly stated that the device described could accelerate electrons to 0.15% of their initial speed.
This is one of my favorites:
“A misleading statement appeared in the News and Views article “Cardiology: Solace for the broken-hearted?” by Christine L.”
Want to know what was misleading? $18.
How about this one:
In Karim Nader’s News and Views article “Neuroscience: Re-recording human memories” (Nature 425, 571–572; 2003) the citation of reference 6 was unclear. The reference concerned — Siegel, J.
“On page 875 of this Article, there are some typographical errors in the equations used in the computer model. The errors are in the third and fourth full paragraphs on this page.”
Some don’t even have any clues. For example in this one we just know the problem is in an article on Transatlantic robot-assisted telesurgery. Or in this one the issue is with ancient homes for hard-up hermit crabs.
I could go on and on and on.
The corrections one needs to pay to see go back to the 1800s. For example in 1893 J. J. Walker wrote:
“The next two paragraphs will require slight modifications accordingly; and the last will, of course, be unnecessary. I owe this correction to a correspondence with which Prof. W.”. Alas, we can’t know the rest without – wait for it – without paying $32.
I think we should have a context. Find the correction for which the free part is the most absurd or tantalizing. I don’t know if other closed access journals do the same thing but it would be great to know …
UPDATE: Some more fun stuff from Nature. There is a paper from Nature in 2005 “Making sure corrections don’t vanish online“. It is, of course, available for just $18.
Jonathan Eisen's Lab 