For $&%# sake, Bentham Open Journals, leave me alone

For crying out loud, I am still getting crappy spammy mail from various "Bentham Open" journals. The most annoying part to me of Bentham Open is that they try to make it seem that anything published in an Open Access journal is better than anything published in a non Open Access journal. While I personally believe publishing in an OA manner is great, lying about the benefits of OA is not a good thing.

For example they ask and answer the following question "WHY PUBLISH IN OPEN ACCESS JOURNALS? " Their answers include:

• Your article will obtain more citations.
• Your article will be peer-reviewed and published very fast.
• Your article can be read by potentially millions of readers, which is incomparable to publishing in a traditional subscription journal.
• All published open access articles will receive massive international exposure and as is usually the case for open access publications, articles will also receive high citations.

Yes, that is right, the crappiest, most boring, most idiotic article in an OA journal will receive "massive international exposure" and "high citations."

I know, criticism of Bentham Open may seem biased coming from me, a PLoS insider. So, just in case you were not aware that just about everyone else out there cannot stand them, here are some reading assignments:

• A short post about Bentham Open
• Editor will quit over hoax paper : Nature News
• Spam journals or open journals?
• Re: Bentham Science Publishers
• Gunther Eysenbach's random research rants: Black sheep among Open
• Some background on Bentham Open, but just some - Peter Suber, Open ...
• Open and Shut?: The Open Access Interviews: Matthew Honan
• Jeffrey Beall, summed up by Peter Suber.

And so on.

Open Evolution: Kudos to SMBE for creating a new Open Access publication - Genome Biology and Evolution

Another sign that Open Access is spreading.  SMBE, which publishes the journal MBE (Molecular Biology and Evolution) is announcing the creation of a new journal - Genome Biology and Evolution (GBE).  And happily it will be an Open Access journal being published by Oxford under the Oxford Open system (not quite a full creative commons license like PLoS journals, but pretty good).  I am VERY pleased to see this, especially since I quit the Editorial Board at MBE mostly because they were not moving fast enough to Open Access for me.  Kudos to SMBE, Bill Martin (the new Editor in Chief of GBE) and all the folks at Oxford for doing a good thing.

Freeing My Father's Scientific Publications Update

Well, I have made some progress already in my quest I began on Father's Day to free up the scientific publications of my father (see The Tree of Life: Freeing My Father's Scientific Publications).

I wrote to the powers that be at the journal "Endocrinology" asking about when back issues might be made available. And I got a VERY quick reply from someone from Highwire Press which is the place that puts out Endocrinology on the web

Dear Jonathan Eisen,

The Endocrine Society is currently in the process of loading back issues for all of their journals. It will most likely be six months before back content is online.

The person who wrote back was almost apologetic about how long this might take but I am personally very pleased. Given that Endocrinology says the make all articles more than a year old available for free, this likely means that my father's three papers in Endocrinology will soon be available for free online. This then changes my tally to:

Pubmed Central: 3
Free access: 17
Fee access: 11
Unavailable: 4

Getting better. Of course, I want them all to be as widely available as possible so I am still going to work to move everything up the list towards Pubmed Central. Also, my brother suggests (in the comments to my previous post) that since my father was a government employee we should be able to just post his papers online. I think this is a good option but I still will be working on the "official" channels to see what happens.

Since I made the original posting there have been some useful comments about what I might do on some other sites. See for example, this FriendFeed discussion (I have just discovered FriendFeed and it seems quite cool but I am not sure if everyone can see this discussion or not so please let me know if this link does not work).

I will keep posting on my progress as well as what I learn about Copyright, Free Access, etc.

Freeing My Father's Scientific Publications

Today is Father's Day. It was a great day for me, hanging out with my kids and wife and doing things around town here in Davis (we kind of made it Father's Weekend and did some activities on Saturday too). Despite the wonderful weekend, this day is also filled with melancholy for me when I think about my father, Howard Eisen, who died when I was a freshman in college. I miss him greatly. But whenever I think about him I think about how he almost certainly would be really proud that his two sons (me and my brother Michael at Berkeley) are now scientists.

You see, my father was a scientist too --- an MD who did research at the NIH, focusing mostly on hormone receptors. Given my propensities for putting things on the web and trying to disseminate scientific information, I cam up with a plan last night to create some sort of web page in his honor with some information about his work and his life.

The thing is, I actually know little about his work, because while I was growing up, my parents never really talked about the details of their work (my mom is a scientist too). Sure, we went to the NIH occasionally and most of my parents friends were scientists. And they talked sciency talk. But they did not really discuss details of their work. I think in the end, this is partly why my brother and I did not shun the family business and went into science.

So, of course, being the obsessed Open Access advocate, the first thing I decided to look at was what publications of my fathers I could get my hands on. This was both to read them and to make them available on this tribute page.

So - my first step in this journey was to search Pubmed for Eisen HJ. And then I had to remove the publications by another Eisen HJ. And so I was left with 35 publications in PubMed (I know he had some other articles as well as chapters in books and such but this is a good start). So then I asked - which of these were available online in one way or another. According to Pubmed 24/35 were available online. Of those available online:

• Pubmed Central: 3
  
• Free access: 13
  
• Fee access: 8
  
• Unavailable: 11.

This made me both happy and sad. I was glad to see some of his publications in Pubmed Central (thanks to PNAS and the Biochemistry Journal for putting them there). It was also good to see many available for free, even if this was only at some journals site. So - thanks to journals like J. Biol. Chem. for making the material available online for free. But I was a bit saddened to see how many of his papers, which are now all over 20 years old, being available only for a fee. And I was also a bit saddened to see how many had not yet made it into the digital world.

So - what to do next? Well, my goal is to get access to all his papers and then to free them up to the world. So my first step was to see if any of the ones that Pubmed did not have links for might be available online anyway. And indeed a few were. For example, Pediatric Research back issues are available online. And these are free. In addition, his papers in Biochemistry, J. Steroid Biochemistry and Advances in Genetics is available for a fee but it is not linked from Pubmed. So with this information the new tally was

• Pubmed Central: 3
  
• Free access: 14
  
• Fee access: 11
  
• Unavailable: 7

Getting digitized.
So for those 7 that are currently unavailable (at least anywhere I could find) digitally, my next step is to try and lobby the journals to make them available. For some journals, this has some hope (well, not per se my lobbying, but they may make them available). For example, Endocrinology has some back issues available but just not all the way back to some of my father's publications in that journal. So, I wrote to the journal Endocrinology using the link from the journal site and asked what their plans were for older issues. And I will post here if I get a response. (( UPDATE - THESE ARE TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.)) I am doing the same for all the other unavailable publications, although some of the journals seem to not exist anymore.

Convincing "free" access journals to deposit old papers in PMC.
My next goal is to see if the "free" access journals have any plans to submit stuff to Pubmed Central. Yes, I know PMC is not perfect, but I believe it is better to have things in PMC than just on a journals website. So I am writing to all these journals to find out if they have any plans to deposit this material.

Freeing up the "fee for access" papers.
My final initial goal, and probably the most challenging, is to figure out ways to make the papers that are current "fee for access" available for free. If these were my papers, I suppose I could put many of the PDFs on my own web site. Perhaps I can do this for my father's publications (does the right to do this get passed down?). Of course, first I have to get the PDFs and it just seems weird to me to have to pay to get access to papers my father wrote. Another possibility is that the journals would let me pay an OA fee to free up these old papers. I am going to look into that although I cannot really afford it. A final possibility would be to get the papers into PMC without the journals explicit agreement. Perhaps because my father was a government employee, the copyright would allow depositing in PMC? I do not know.

So right now, the process is incomplete. I am actually learning a good deal about OA from looking into older papers rather than just all the new papers I tend to focus on. And hopefully in the process I can free up all of my father's papers so that his scientific legacy does not fade away as rapidly due to lack of access. And then next maybe I can focus on my grandfather's publications.

Anyway -- here is a list of my father's publications with links and/or comments on their availability.

1. Simons SS Jr, Pumphrey JG, Rudikoff S, Eisen HJ. Identification of cysteine 656 as the amino acid of hepatoma tissue culture cell glucocorticoid receptors that is covalently labeled by dexamethasone 21-mesylate. J Biol Chem. 1987 Jul 15;262(20):9676-80. PMID: 3597435.


2. Cresteil T, Jaiswal AK, Eisen HJ. Transcriptional control of human cytochrome P1-450 gene expression by 2,3,7,8-tetrachlorodibenzo-p-dioxin in human tissue culture cell lines. Arch Biochem Biophys. 1987 Feb 15;253(1):233-40. PMID: 3813564.


3. Eisen LP, Reichman ME, Thompson EB, Gametchu B, Harrison RW, Eisen HJ. Monoclonal antibody to the rat glucocorticoid receptor. Relationship between the immunoreactive and DNA-binding domain. J Biol Chem. 1985 Sep 25;260(21):11805-10. PMID: 3840164


4. Antakly T, Eisen HJ. Immunocytochemical localization of glucocorticoid receptor in target cells. Endocrinology. 1984 Nov;115(5):1984-9. PMID: 6208016. UPDATE - TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.


5. Harmon JM, Eisen HJ, Brower ST, Simons SS Jr, Langley CL, Thompson EB. Identification of human leukemic glucocorticoid receptors using affinity labeling and anti-human glucocorticoid receptor antibodies. Cancer Res. 1984 Oct;44(10):4540-7. PMID: 6331880


6. Reichman ME, Foster CM, Eisen LP, Eisen HJ, Torain BF, Simons SS Jr. Limited proteolysis of covalently labeled glucocorticoid receptors as a probe of receptor structure. Biochemistry. 1984 Oct 23;23(22):5376-84. PMID: 6391542


7. Nebert DW, Eisen HJ, Hankinson O. The Ah receptor: binding specificity only for foreign chemicals? Biochem Pharmacol. 1984 Mar 15;33(6):917-24. Review. PMID: 6324804


8. Nebert DW, Brown DD, Towne DW, Eisen HJ. Association of fertility, fitness and longevity with the murine Ah locus among (C57BL/6N) (C3H/HeN) recombinant inbred lines. Biol Reprod. 1984 Mar;30(2):363-73. PMID: 6704471


9. Foster CM, Eisen HJ, Bloomfield CD. Covalent labeling of rat thymocyte and human lymphoid glucocorticoid receptor. Cancer Res. 1983 Nov;43(11):5273-7. PMID: 6577947


10. Karenlampi SO, Eisen HJ, Hankinson O, Nebert DW. Effects of cytochrome P1-450 inducers on the cell-surface receptors for epidermal growth factor, phorbol 12,13-dibutyrate, or insulin of cultured mouse hepatoma cells. J Biol Chem. 1983 Sep 10;258(17):10378-83. PMID: 6309801


11. Mariani G, Kortright KH, Eisen HJ, Adamson RH, Waldmann TA. A methodological approach for the study of protein synthesis by cell cultures in vitro. J Nucl Med Allied Sci. 1983 Jul-Sep;27(3):237-47. PMID: 6198498


12. Simons SS Jr, Schleenbaker RE, Eisen HJ. Activation of covalent affinity labeled glucocorticoid receptor-steroid complexes. J Biol Chem. 1983 Feb 25;258(4):2229-38. PMID: 6687388.


13. Tukey RH, Hannah RR, Negishi M, Nebert DW, Eisen HJ. The Ah locus: correlation of intranuclear appearance of inducer-receptor complex with induction of cytochrome P1-450 mRNA. Cell. 1982 Nov;31(1):275-84. PMID: 6186383


14. Legraverend C, Hannah RR, Eisen HJ, Owens IS, Nebert DW, Hankinson O. Regulatory gene product of the Ah locus. Characterization of receptor mutants among mouse hepatoma clones. J Biol Chem. 1982 Jun 10;257(11):6402-7. PMID: 6896205


15. Nebert DW, Negishi M, Lang MA, Hjelmeland LM, Eisen HJ. The Ah locus, a multigene family necessary for survival in a chemically adverse environment: comparison with the immune system. Adv Genet. 1982;21:1-52. Review. PMID: 7036691. Available online for fee but not linked from Pubmed.
    


16. Eisen HJ, Schleenbaker RE, Simons SS Jr. Affinity labeling of the rat liver glucocorticoid receptor with dexamethasone 21-mesylate. Identification of covalently labeled receptor by immunochemical methods. J Biol Chem. 1981 Dec 25;256(24):12920-5. PMID: 6895516


17. Hannah RR, Nebert DW, Eisen HJ. Regulatory gene product of the Ah complex. Comparison of 2,3,7,8-tetrachlorodibenzo-p-dioxin and 3-methylcholanthrene binding to several moieties in mouse liver cytosol. J Biol Chem. 1981 May 10;256(9):4584-90. PMID: 7217100


18. Stevens J, Eisen HJ, Stevens YW, Haubenstock H, Rosenthal RL, Artishevsky A. Immunochemical differences between glucocorticoid receptors from corticoid-sensitive and -resistant malignant lymphocytes. Cancer Res. 1981 Jan;41(1):134-7. PMID: 7448753


19. Nebert DW, Eisen HJ, Negishi M, Lang MA, Hjelmeland LM, Okey AB. Genetic mechanisms controlling the induction of polysubstrate monooxygenase (P-450) activities. Annu Rev Pharmacol Toxicol. 1981;21:431-62. Review. PMID: 7016012


20. Marković RD, Eisen HJ, Parchman LG, Barnett CA, Litwack G. Evidence for a physiological role of corticosteroid binder IB. Biochemistry. 1980 Sep 30;19(20):4556-64. PMID: 7426614. Available online to purchase though no listed in Pubmed.
    


21. Eisen HJ. An antiserum to the rat liver glucocorticoid receptor. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3893-7. PMID: 7001446


22. Hannah R, Simkins R, Eisen HJ. Synthesis of alpha-fetoprotein and albumin by fetal mouse liver cultured in chemically defined medium. Dev Biol. 1980 Jun 15;77(2):244-52. PMID: 6156873


23. Okey AB, Bondy GP, Mason ME, Kahl GF, Eisen HJ, Guenthner TM, Nebert DW. Regulatory gene product of the Ah locus. Characterization of the cytosolic inducer-receptor complex and evidence for its nuclear translocation. J Biol Chem. 1979 Nov 25;254(22):11636-48. PMID: 500663


24. Rechler MM, Eisen HJ, Higa OZ, Nissley P, Moses AC, Schilling EE, Fennoy I, Bruni CB, Phillips LS, Baird KL. Characterization of a somatomedin (insulin-like growth factor) synthesized by fetal rat liver organ cultures. J Biol Chem. 1979 Aug 25;254(16):7942-50. PMID: 468799


25. Simkins RA, Eisen HJ, Sparks JW, Glinsmann WH. Development of glucogenesis from galactose by fetal rat liver explants in organ culture. Dev Biol. 1978 Oct;66(2):353-60. PMID: 700252


26. Simkins RA, Eisen HJ, Glinsmann WH. Functional integrity of fetal rat liver explants cultured in a chemically defined medium. Dev Biol. 1978 Oct;66(2):344-52. PMID: 81156


27. Eisen HJ, Glinsmann WH. Maximizing the purification of the activated glucocorticoid receptor by DNA-cellulose chromatography. Biochem J. 1978 Apr 1;171(1):177-83. PMID: 646815


28. Eisen HJ, Glinsmann W. Partial purification of the glucocorticoid receptor from rat liver: a rapid, two-step procedure using DNA-cellulose. Biochem Biophys Res Commun. 1976 May 17;70(2):367-72. PMID: 180989


29. Eisen HJ, Ginsberg AL. Letter: Disulfiram hepatotoxicity. Ann Intern Med. 1975 Nov;83(5):673-5. PMID: 1200504. Back issues not currently available.
    


30. Eisen HJ, Glinsmann W. Partial purification of glucocorticoid receptor from rat liver using DNA-cellulose. J Steroid Biochem. 1975 Jul;6(7):1171-3. PMID: 170470. AVAILABLE FOR FEE BUT NOT LINKED FROM PUBMED.
    


31. Glinsmann WH, Eisen HJ, Lynch A, Chez RA. Glucose regulation by isolated near term fetal monkey liver. Pediatr Res. 1975 Jul;9(7):600-4. PMID: 125868. AVAILABLE FREE EVEN THOUGH MEDLINE DOES NOT HAVE LINK.
    


32. Eisen HJ, Goldfine ID, Glinsmann WH. Regulation of hepatic glycogen synthesis during fetal development: roles of hydrocortisone, insulin, and insulin receptors. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3454-7. PMID: 4357871


33. Eisen HJ, Glinsmann WH, Sherline P. Effect of insulin on glycogen synthesis in fetal rat liver in organ culture. Endocrinology. 1973 Feb;92(2):584-8. PMID: 4682869. Wrote to ask if they will become available.  UPDATE - TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.
    


34. Hellman DE, Eisen HJ, Goodman HM. The effects of hypophysectomy on phosphorylase activity in adipose tissue and muscle. Horm Metab Res. 1971 Sep;3(5):331-5. PMID: 4332655


35. Eisen HJ, Goodman HM. Growth hormone and phosphorylase activity in adipose tissue. Endocrinology. 1969 Feb;84(2):414-6. PMID: 4303531. Wrote to ask if they will become available. UPDATE - TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.