Please see below an ad for a postdoctoral position at the NIH in
Bethesda.
NIH funded Postdoctoral Fellowship, structural biology
Cell Biology and Biophysics Unit, National Institute of Neurological
Disorders and Stroke (NINDS)
Location: NIH Main Campus, Bethesda, Maryland
Start Date: flexible
Description: Postdoctoral positions are available in the Cell Biology
and Biophysics Unit headed by Dr. Antonina Roll-Mecak at the National
Institute of Neurological Disorders and Stroke. The Roll-Mecak lab
combines biophysical and cell biological approaches to understand the
mechanism underlying intracellular organization and movement, with a
focus on the microtubule cytoskeleton. Our lab is located in the
Porter Center for Neuroscience on the NIH main campus in Bethesda. The
NIH has a long tradition of research excellence in cytoskeletal
biology and offers a stimulating environment for postdoctoral fellows
interested in interdisciplinary training in cell biology and
biophysics. The research facilities at NIH are outstanding and the lab
has access to state-of-the-art equipment such as crystallization
robots, liquid handling systems, TIRF and confocal microscopes. For
more information, please visit: http://intra.ninds.nih.gov/rm_lab/
The position will be fully funded by the NIH. We are looking for
candidates who wish to work on challenging structural biology problems
related to the microtubule cytoskeleton and have a strong background
in X-ray crystallography, protein overexpression and purification. The
lab offers excellent training opportunities in motor biophysics and
imaging.
Other details: Candidates should have less than 2 years of
postdoctoral experience and a strong publication record. Please send
a CV, a one-page research experience summary, a summary to research
interests and contact information of three references to [log in to unmask]
Please write “Postdoctoral application” in the subject header.
----- Original Message -----
From: CCP4BB automatic digest system <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, 10 Dec 2009 19:00:01 -0500 (EST)
Subject: CCP4BB Digest - 9 Dec 2009 to 10 Dec 2009 (#2009-338)
There are 32 messages totalling 3040 lines in this issue.
Topics of the day:
1. Solvent content of crystals vs. resolution? (7)
2. molprobity and coot, dots do not update
3. Crystallography position at CSIRO, Melbourne
4. Coot 0.6 Released (3)
5. Practical workshop on the use of longer wavelength in Structural Biology -
ESRF 18-19 February 2010
6. FW: pdb-l: Retraction of 12 Structures (9)
7. Postdoctoral positions
8. Difficult MR structures (3)
9. LG announces 3D display
10. Retraction of 12 Structures (3)
11. pdb-l: Retraction of 12 Structures (2)
----------------------------------------------------------------------
Date: Wed, 9 Dec 2009 19:10:27 -0500
From: Christian Biertuempfel <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
Hi Jeremiah,
It is interesting that I have just told a student about this feature
today. You can pull up the information from the pdb directly (advanced
search) or have a look into the following article:
Kantardjieff, K. A. & Rupp, B. Matthews coefficient probabilities:
Improved estimates for unit cell contents of proteins, DNA, and
protein-nucleic acid complex crystals. Protein Sci, 2003, 12, 1865-71
Cheers,
christian
Jeremiah Farelli wrote:
> Hello all,=20
>=20
> Does anyone know of some relevant literature (or a general idea really)=
that
> discusses protein crystal solvent content vs. average resolution? I am
> under the impression that the higher the solvent content, the lower the
> average resolution....but I'd like to see some sort of data to back thi=
s up.
>=20
> Thanks!
>=20
_______________________________________________________________________
Dr. Christian Biert=FCmpfel
Laboratory of Molecular Biology
NIDDK/National Institutes of Health phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________
------------------------------
Date: Wed, 9 Dec 2009 20:11:30 -0500
From: Alexandra Deaconescu <[log in to unmask]>
Subject: molprobity and coot, dots do not update
Hi everyone:
I am trying to reduce my clashscore in Coot using Molprobity. I can get the dots to display alright, but they do not update when I change the rotamer/angles. Here's my .coot
(define *probe-command* "/gdata1/deacona/molprobity/molprobity3/bin/linux/probe")
(define *reduce-command* "/gdata1/deacona/molprobity/molprobity3/bin/linux/reduce")
(set-find-hydrogen-torsion 1)
(set-do-probe-dots-on-rotamers-and-chis 1)
(set-do-probe-dots-post-refine 1)
(set-rotamer-lowest-probability 0.5)
Anything I need to add to the file?
Thanks a lot,
Alex
--
Alexandra M. Deaconescu, Ph.D.
Damon Runyon Cancer Research Foundation Postdoctoral Fellow
Grigorieff Laboratory
Brandeis University
Rosenstiel Center
415 South St. MS-029
Waltham, MA 02454
For deliveries:
c/o Grigorieff Laboratory
Brandeis University
415 South St.
Kalman Receiving Dock
Waltham, MA 02454
------------------------------
Date: Thu, 10 Dec 2009 03:06:57 +0000
From: Tom Peat <[log in to unmask]>
Subject: Crystallography position at CSIRO, Melbourne
Hello All,
An opportunity is available immediately for a Research Scientist in x-ray=
crystallography at the CSIRO Molecular and Health Technologies division.=20=
Applications are accepted through the CSIRO employment website:
https://recruitment.csiro.au/asp/job_details.asp?RefNo=3D2009%2F966=20
(the job reference number is 2009/966)
International applicants are welcome and encouraged.
Part of the advertisement and a blurb on CSIRO is copied below, but more
information on CSIRO can be obtained on the following web site:=20
http://www.csiro.au/=20
And more specifically the CMHT division:
http://www.csiro.au/org/CMHT.html=20
Questions can be directed to me (Tom Peat) at the following email address=
:
[log in to unmask]
We seek an enthusiastic and highly motivated protein crystallographer to
join the Structural Biology research group in Parkville. You will be
responsible for protein structure determination and structure-function
studies. You will work in a team and will liaise with other CSIRO divisio=
ns
and external collaborators to carry out their structural biology
requirements. You must have an interest in automation and high throughput=
methodology. You will have a PhD or equivalent qualification with
postdoctoral research experience in protein crystallography.
You will be able to operate independently, but will enjoy working in a te=
am
environment. You will develop your own research projects as well as liais=
ing
with collaborators both within and outside CSIRO. Your interests are
predominately protein structure-function studies, including structure-bas=
ed
drug design. You will have a strong commitment to safe laboratory practic=
e
and abide by OHS&E regulations.
The Commonwealth Scientific and Industrial Research Organisation is
Australia's national science agency and one of the largest and most diver=
se
research agencies in the world. At CSIRO Molecular and Health Technologi=
es
our scientists work in partnership to address key challenges in health an=
d
in a range of industries requiring smart materials. Talented scientists a=
re
undertaking biotechnology and advanced materials research drawing on a lo=
ng
history of chemistry and molecular, cellular and structural biology to
develop and grow their capabilities. We form strong collaborative
relationships with industry, universities, Cooperative Research Centres
(CRCs) and research institutions to deliver leading edge research. Our
vision is to transform industries and improve health and wellbeing by
delivering creative molecular technologies.
------------------------------
Date: Wed, 9 Dec 2009 22:36:33 -0500
From: lei feng <[log in to unmask]>
Subject: Re: Coot 0.6 Released
--_8cfd6a45-c171-4437-9674-2edc1d649a21_
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Hello Paul
I am wondering =2C do we need uninstall the previous version of coot to ins=
tall this?=20
thanks
=20
_________________________________________________________________
Windows Live Hotmail is faster and more secure than ever.
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cid=3DPID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_1:092009=
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<body class=3D'hmmessage'>
Hello Paul<BR><BR><BR>I am wondering =2C do we need uninstall the previous =
version of coot to install this?=A0<BR><BR><BR>thanks<BR><BR><BR><BR><BR> =
<br /><hr />Windows LiveT Hotmail is faster and more secure tha=
n ever. <a href=3D'http://www.microsoft.com/windows/windowslive/hotmail_bl1=
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target=3D'_new'>Learn more.</a></body>
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--_8cfd6a45-c171-4437-9674-2edc1d649a21_--
------------------------------
Date: Thu, 10 Dec 2009 00:55:22 -0500
From: Roger Rowlett <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
I think that higher solvent content crystals are more likely to have
higher resolution, but I can't remember the reference. I'm sure one of
the CCP4bbers knows.
Cheers,
Roger Rowlett
On 12/9/09, Jeremiah Farelli <[log in to unmask]> wrote:
> Hello all,
>
> Does anyone know of some relevant literature (or a general idea really) that
> discusses protein crystal solvent content vs. average resolution? I am
> under the impression that the higher the solvent content, the lower the
> average resolution....but I'd like to see some sort of data to back this up.
>
> Thanks!
>
--
Sent from my mobile device
------------------------------
Date: Thu, 10 Dec 2009 08:36:54 +0000
From: Paul Emsley <[log in to unmask]>
Subject: Re: Coot 0.6 Released
lei feng wrote:
>
> I am wondering , do we need uninstall the previous version of coot to
> install this?
>
No. Many group use more than one version of Coot.
Ah, but perhaps you mean WinCoot? My (limited) experience is that you
can install right over the top of the old one.
Paul.
------------------------------
Date: Thu, 10 Dec 2009 09:56:47 +0100
From: "Bernhard C. Lohkamp" <[log in to unmask]>
Subject: Re: Coot 0.6 Released
>>
>> I am wondering , do we need uninstall the previous version of coot to
>> install this?
>
> No. Many group use more than one version of Coot.
>
> Ah, but perhaps you mean WinCoot? My (limited) experience is that you
> can install right over the top of the old one.
WinCoot can be installed on top of each other. And of course there is a
0.6 version available as well. From Paul's page or here:
http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-download.html
B
------------------------------
Date: Thu, 10 Dec 2009 10:01:13 +0100
From: Anastassis Perrakis <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
The other way round.
High solvent==low resolution
Low solvent==high resolution
Since the resolution limit depends on subjective criteria (source,
dose, I/sigI limit) in our test we always had a better correlation
between Wilson B (rather than resolution) and solvent content.
A.
Sent from my iPhone
On 10 Dec 2009, at 06:55, Roger Rowlett <[log in to unmask]> wrote:
> I think that higher solvent content crystals are more likely to have
> higher resolution, but I can't remember the reference. I'm sure one of
> the CCP4bbers knows.
>
> Cheers,
>
> Roger Rowlett
>
>
> On 12/9/09, Jeremiah Farelli <[log in to unmask]> wrote:
>> Hello all,
>>
>> Does anyone know of some relevant literature (or a general idea
>> really) that
>> discusses protein crystal solvent content vs. average resolution?
>> I am
>> under the impression that the higher the solvent content, the lower
>> the
>> average resolution....but I'd like to see some sort of data to back
>> this up.
>>
>> Thanks!
>>
>
> --
> Sent from my mobile device
------------------------------
Date: Thu, 10 Dec 2009 10:47:23 +0100
From: mjvanraaij <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
how about this for a general idea:
resolution is related to order in the crystals, more order =3D =20
diffraction to higher resolution
the order is determined by crystal contacts, stronger crystal contacts =20=
=3D more order
more solvent means, on average, less close packing and less crystal =20
contacts
(of course, there are cases where only a few strong crystal contacts =20
make for a very highly ordered crystal diffracting to high resolution, =20=
so there are quite a few exceptions of high solvent content being =20
compatible with high resolution diffraction)
or is this too simplistic?
(and widely known?)
Mark J. van Raaij
Dpto de Bioqu=EDmica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
researcherID: B-3678-2009
On 10 Dec 2009, at 00:56, Jeremiah Farelli wrote:
> Hello all,
>
> Does anyone know of some relevant literature (or a general idea =20
> really) that
> discusses protein crystal solvent content vs. average resolution? I =20=
> am
> under the impression that the higher the solvent content, the lower =20=
> the
> average resolution....but I'd like to see some sort of data to back =20=
> this up.
>
> Thanks!
------------------------------
Date: Thu, 10 Dec 2009 11:46:57 +0100
From: Daniele de Sanctis <[log in to unmask]>
Subject: Practical workshop on the use of longer wavelength in Structural Biology - ESRF 18-19 February 2010
--00235400ec76b7715a047a5d86cd
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Dear all,
We are pleased to announce the
*
*
*Practical workshop on the use of longer wavelengths in Structural Biology
*The routine accessibility, on some macromolecular crystallography (MX)
beamlines at SR sources, of photons in the energy range 8 =96 6 keV has lea=
d
to an increase in the exploitation, for structure solution in MX, of the
small anomalous signals from sulphur and phosphorous available at such
energies. However, due to experimental difficulties, this approach to
structure solution has not yet reached its full potential.
A Practical Workshop on the use of longer wavelengths in Structural Biology=
*
*will be organised at the ESRF, Grenoble on the 18th-19th of February 2009.
Long wavelength data will be collected on the ID29 MAD Beamline which is
equipped to provide state-of-the-art facilities for long wavelength data
collection (i.e. third harmonic rejection mirror, use of minikappa device t=
o
reorient the crystals for more accurate Friedel pairs measurement and use o=
f
He-filled cone to minimise air scattering and absorption).
The number of participants is limited to six. Students will be tutored
directly on the beam line where data processing and on-line attempts at
structure solution will also take place. Participants are encouraged and
should be prepared to bring crystals of their own 'real' cases where phasin=
g
using longer wavelengths (particularly S-SAD or P-SAD) might prove
tractable.
Travel and subsistence costs will be covered by the ESRF. Applications
comprising a full CV, a letter of motivation, a supporting letter from the
supervisor and a detailed characterisation of the sample (cell parameters,
number of anomalous scatterers, resolution limit, space group, DF/F etc)
should be sent electronically to [log in to unmask] before the *24th o=
f
January 2010*.
On behalf of the organisers
Claudine Brun, Daniele de Sanctis, Gordon Leonard, Christoph
Mueller-Dieckmann
--=20
Daniele de Sanctis, PhD
Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869
--00235400ec76b7715a047a5d86cd
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<p class=3D"MsoNormal">Dear all,<br><br>We are pleased to announce the<br><=
/p><p class=3D"MsoNormal"><b><span lang=3D"EN-GB"><br></span></b></p><p cla=
ss=3D"MsoNormal"><b><span lang=3D"EN-GB">Practical workshop on the use of l=
onger
wavelengths in Structural Biology<br>
<br>
</span></b><span lang=3D"EN-GB">The routine accessibility, on some macromol=
ecular
crystallography (MX) beamlines at SR sources, of photons in the energy rang=
e 8
=96 6 keV has lead to an increase in the exploitation, for structure soluti=
on in
MX, of the small anomalous signals from sulphur and phosphorous available a=
t
such energies.=A0 However, due to experimental difficulties, this approach
to structure solution has not yet reached its full potential. <br>
<br>
A Practical Workshop on the use of longer wavelengths in Structural Biology=
<b> </b>will
be organised at the ESRF, Grenoble
on the 18th-19th of February 2009.=A0 Long wavelength data will be collecte=
d
on the ID29 MAD Beamline which is equipped to provide state-of-the-art
facilities for long wavelength data collection (i.e. third harmonic rejecti=
on
mirror, use of minikappa device to reorient the crystals for more accurate
Friedel pairs measurement and use of He-filled cone to minimise air scatter=
ing
and absorption).<br>
<br>
The number of participants is limited to six. Students will be tutored dire=
ctly
on the beam line where data processing and on-line attempts at structure
solution will also take place. Participants are encouraged and should be
prepared to bring crystals of their own 'real' cases where phasing =
using longer
wavelengths (particularly S-SAD or P-SAD) might prove tractable. <br>
<br>
Travel and subsistence costs will be covered by the ESRF. Applications
comprising a full CV, a letter of motivation, a supporting letter from the
supervisor and a detailed characterisation of the sample (cell parameters,
number of anomalous scatterers, resolution limit, space group, </span><span=
style=3D"font-family: Symbol;" lang=3D"EN-GB">D</span><span lang=3D"EN-GB"=
>F/F etc) should
be sent electronically to <a href=3D"mailto:[log in to unmask]" target=
=3D"_blank">[log in to unmask]</a> before the <b>24th of January 2010<=
/b>.<br>
<br>
On behalf of the organisers<br>
<br>
Claudine Brun, Daniele de Sanctis, Gordon Leonard, Christoph Mueller-Dieckm=
ann</span></p>
<br clear=3D"all"><br>-- <br>Daniele de Sanctis, PhD<br><br>Structural Biol=
ogy Group<br>ESRF, Grenoble, France<br>Tel 33 (0)4 76 88 2869<br>
--00235400ec76b7715a047a5d86cd--
------------------------------
Date: Thu, 10 Dec 2009 09:16:17 -0500
From: Ibrahim Moustafa <[log in to unmask]>
Subject: FW: pdb-l: Retraction of 12 Structures
Hi all,
I want to share the following e-mail received from pdb-l.
It is sad to see something like that!
regards,
Ibrahim
------ Forwarded Message
From: Michael Sadowski <[log in to unmask]>
Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST)
To: <[log in to unmask]>
Subject: pdb-l: Retraction of 12 Structures
Dear All,
Better check your data!
Apologies to those who have seen this.
S.
-----
"The University of Alabama at Birmingham has issued a statement indicating
that a former UAB researcher may have fabricated or falsified data about
protein structures that are contained in the Protein Data Bank.
The university did not include a name of the researcher, but the Birmingham
News this week reported that the scientist is H.M. Krishna Murthy and an
independent review by BioInform of the PDB shows that Murthy is associated
with all of the proteins that UAB said were falsified.
The newspaper said that a probe of Murthy's research has been underway since
2007.
"After a thorough examination of the available data, which included a
re-analysis of each structure alleged to have been fabricated, the committee
found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID,
1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than not
falsified and/or fabricated and recommended that they be removed from the
public record," the university said in its statement this week."
-----
http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr
icated-protein-structures-now-protein-dat?utm_source=feedburner&utm_medium=f
eed&utm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29
http://main.uab.edu/Sites/reporter/articles/71570/
http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m
ay_be.html
TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .
------ End of Forwarded Message
------------------------------
Date: Thu, 10 Dec 2009 09:29:32 -0500
From: "Edward A. Berry" <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
mjvanraaij wrote:
> how about this for a general idea:
>
> resolution is related to order in the crystals, more order = diffraction
> to higher resolution
> the order is determined by crystal contacts, stronger crystal contacts =
> more order
> more solvent means, on average, less close packing and less crystal
> contacts
> (of course, there are cases where only a few strong crystal contacts
> make for a very highly ordered crystal diffracting to high resolution,
> so there are quite a few exceptions of high solvent content being
> compatible with high resolution diffraction)
>
> or is this too simplistic?
> (and widely known?)
Sounds very reasonable to me. One the positive side (and this may be what
Roger was thinking of), for a given amount of protein in the asymmetric unit,
increased solvent content means a larger unit cell and finer sampling of the
molecular transform, -> more reflections and thus a greater data/param ratio
at a given resolution. Also solvent flattening becomes more powerful.
Ed
------------------------------
Date: Thu, 10 Dec 2009 09:42:14 -0500
From: Roger Rowlett <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
Ah. Found the paper: Kantardjieff & Rupp (2003) Prot. Sci. 12, 1865.
"Matthews coefficient probabilities: Improved estimates for unit cell
contents of proteins, DNA, and protein-nucleic acid complex crystals."
There is a nice figure showing that data from the PDB shows a clear
correlation between lower solvent content and increasing resolution.
This is what one would expect on physical principles, but I can't find
the paper I read that suggested that in practice the reverse correlation
can be true. I'm probably remembering incorrectly what Ed is referring to.
Cheers,
Roger Rowlett
Edward A. Berry wrote:
> mjvanraaij wrote:
>> how about this for a general idea:
>>
>> resolution is related to order in the crystals, more order = diffraction
>> to higher resolution
>> the order is determined by crystal contacts, stronger crystal contacts =
>> more order
>> more solvent means, on average, less close packing and less crystal
>> contacts
>> (of course, there are cases where only a few strong crystal contacts
>> make for a very highly ordered crystal diffracting to high resolution,
>> so there are quite a few exceptions of high solvent content being
>> compatible with high resolution diffraction)
>>
>> or is this too simplistic?
>> (and widely known?)
>
> Sounds very reasonable to me. One the positive side (and this may be what
> Roger was thinking of), for a given amount of protein in the
> asymmetric unit,
> increased solvent content means a larger unit cell and finer sampling
> of the
> molecular transform, -> more reflections and thus a greater data/param
> ratio
> at a given resolution. Also solvent flattening becomes more powerful.
> Ed
------------------------------
Date: Thu, 10 Dec 2009 10:06:55 -0500
From: "Bailey, Douglas (NIH/NCI) [E]" <[log in to unmask]>
Subject: Postdoctoral positions
--_000_3359F4D2714C8148A596B5BAAFE51C8BBDF7FBFCNIHMLBX11nihgov_
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Postdoctoral positions available in the Protein Expression and X-ray Crysta=
llography of National Cancer Institute
The Macromolecular Crystallography Laboratory (MCL), Center for Cancer Rese=
arch (CCR), National Cancer Institute (NCI), National Institutes of Health =
(NIH) is seeking applications for postdoctoral fellowships from exceptional=
candidates for 2 of their Sections of the MCL. Dr. Jacek Lubkowski is seek=
ing a candidate with a recent Ph.D. degree and a strong publication record =
in the areas of gene cloning, protein expression in eukaryotic systems, and=
protein purification. Dr. Lubkowski's research focuses on the structural p=
roperties of Janus kinases, members of the TREM family of receptors, and de=
fensins; and correlating these properties with biological functions. Dr. Da=
vid S. Waugh is seeking either a candidate with similar qualifications who =
is interested in leading an effort to develop novel technology for the prod=
uction of recombinant proteins in eukaryotic organisms or a candidate who i=
s already an accomplished protein crystallographer and who wishes to contin=
ue working in this field while also learning cutting-edge techniques for th=
e production of recombinant proteins and protein engineering. Dr. Waugh's r=
esearch interests revolve around methods development for the production of =
recombinant proteins, X-ray crystallographic studies of virulence factors f=
rom potential agents of bioterrorism, and structure-assisted development of=
therapeutic agents for the treatment of cancer. MCL is equipped with state=
-of-the-art X-ray equipment and complete infrastructure for the preparation=
and characterization of functional recombinant proteins. Additional suppor=
t is available from a broad range of core services. US citizenship is not r=
equired but proficiency in English is essential. Please submit curriculum v=
itae including contact information for three references via e-mail to Dr. L=
ubkowski ([log in to unmask]<mailto:[log in to unmask]>) or Dr. Waugh=
([log in to unmask]<mailto:[log in to unmask]>).
Salary is commensurate with research experience and accomplishments. With n=
ationwide responsibility for improving the health and well being of all Ame=
ricans, the Department of Health and Human Services oversees the biomedical=
research programs of the National Institutes of Health.
--_000_3359F4D2714C8148A596B5BAAFE51C8BBDF7FBFCNIHMLBX11nihgov_
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<p style=3D'text-align:justify'><b><font size=3D3 face=3D"Times New Roman">=
<span
lang=3DEN style=3D'font-size:12.0pt;font-weight:bold'>Postdoctoral position=
s
available in the Protein Expression and X-ray Crystallography of National
Cancer Institute</span></font></b><span lang=3DEN><o:p></o:p></span></p>
<p style=3D'text-align:justify'><font size=3D3 face=3D"Times New Roman"><sp=
an
lang=3DEN style=3D'font-size:12.0pt'>The Macromolecular Crystallography Lab=
oratory (MCL),
Center for Cancer Research (CCR), National Cancer Institute (NCI), National
Institutes of Health (NIH) is seeking applications for postdoctoral fellows=
hips
from exceptional candidates for 2 of their Sections of the MCL. Dr. Jacek
Lubkowski is seeking a candidate with a recent Ph.D. degree and a strong
publication record in the areas of gene cloning, protein expression in
eukaryotic systems, and protein purification. Dr. Lubkowski's research focu=
ses
on the structural properties of Janus kinases, members of the TREM family o=
f
receptors, and defensins; and correlating these properties with biological
functions. Dr. David S. Waugh is seeking either a candidate with similar
qualifications who is interested in leading an effort to develop novel
technology for the production of recombinant proteins in eukaryotic organis=
ms
or a candidate who is already an accomplished protein crystallographer and =
who
wishes to continue working in this field while also learning cutting-edge
techniques for the production of recombinant proteins and protein engineeri=
ng.
Dr. Waugh's research interests revolve around methods development for the
production of recombinant proteins, X-ray crystallographic studies of virul=
ence
factors from potential agents of bioterrorism, and structure-assisted
development of therapeutic agents for the treatment of cancer. MCL is equip=
ped
with state-of-the-art X-ray equipment and complete infrastructure for the
preparation and characterization of functional recombinant proteins. Additi=
onal
support is available from a broad range of core services. <st1:place w:st=
=3D"on"><st1:country-region
w:st=3D"on">US</st1:country-region></st1:place> citizenship is not require=
d but
proficiency in English is essential. Please submit curriculum vitae includi=
ng
contact information for three references via e-mail to Dr. Lubkowski (<a
href=3D"mailto:[log in to unmask]"
title=3D"blocked::mailto:[log in to unmask]">[log in to unmask]</a>) =
or Dr.
Waugh (<a href=3D"mailto:[log in to unmask]"
title=3D"blocked::mailto:[log in to unmask]">[log in to unmask]</a>).<o:p=
></o:p></span></font></p>
<p><font size=3D3 face=3D"Times New Roman"><span lang=3DEN style=3D'font-si=
ze:12.0pt'>Salary
is commensurate with research experience and accomplishments. With nationwi=
de
responsibility for improving the health and well being of all Americans, th=
e
Department of Health and Human Services oversees the biomedical research
programs of the National Institutes of Health.<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN style=3D'f=
ont-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN style=3D'f=
ont-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:1=
0.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span style=3D=
'font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</body>
</html>
--_000_3359F4D2714C8148A596B5BAAFE51C8BBDF7FBFCNIHMLBX11nihgov_--
------------------------------
Date: Thu, 10 Dec 2009 10:40:08 -0500
From: Narayanan Ramasubbu <[log in to unmask]>
Subject: Difficult MR structures
Deal All:
I have a 2.0 A data for a SeMet protein (native crystal not available
yet!) that has 6 Se sites.
The cell comes out to be 65 67 101 and the angles are all very close to
90. The data set was collected in house with Cu 1.5418 A
We integrated and scale in orthorhombic and the statistics are reasonable.
There are 4 homologous structures and all of them have a sequence
identity of 15-16 %.
I have tried Phaser, AMoRe, EPMR with varying templates
with polyala, polyser and varying the resolutions.
I have also done a modeller and found best match with one of the four
structures. I have used this derived model as well for input.
I would like to know whether there other options (I am working on
getting a good synchrotron data set at the peak wavelength for Se).
Thanks
Subbu
PS: I am also trying P1 just in case.
------------------------------
Date: Thu, 10 Dec 2009 16:25:14 +0100
From: Vellieux Frederic <[log in to unmask]>
Subject: Re: Difficult MR structures
Dear Subbu,
One more thing you can do is to search with an ensemble of structures (4
in your case) for molecular replacement.
Fred.
Narayanan Ramasubbu wrote:
> Deal All:
> I have a 2.0 A data for a SeMet protein (native crystal not available
> yet!) that has 6 Se sites.
> The cell comes out to be 65 67 101 and the angles are all very close
> to 90. The data set was collected in house with Cu 1.5418 A
>
> We integrated and scale in orthorhombic and the statistics are
> reasonable.
>
> There are 4 homologous structures and all of them have a sequence
> identity of 15-16 %.
>
> I have tried Phaser, AMoRe, EPMR with varying templates
> with polyala, polyser and varying the resolutions.
>
> I have also done a modeller and found best match with one of the four
> structures. I have used this derived model as well for input.
>
> I would like to know whether there other options (I am working on
> getting a good synchrotron data set at the peak wavelength for Se).
>
> Thanks
> Subbu
> PS: I am also trying P1 just in case.
>
>
------------------------------
Date: Thu, 10 Dec 2009 17:38:06 +0100
From: Anastassis Perrakis <[log in to unmask]>
Subject: Re: Difficult MR structures
In my experience, even when rather magically Phaser works with 20-25% ident=
ity, with 2.0 data you cannot always proceed to change and refine your stru=
cture.
I would focus on the Se synchrtron data, or collect a very redundant set at=
the home source, which should allow you to find the Se and do some good ph=
asing.
Tassos
________________________________________
From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Narayanan Ra=
masubbu [[log in to unmask]]
Sent: Thursday, December 10, 2009 4:40 PM
To: [log in to unmask]
Subject: [ccp4bb] Difficult MR structures
Deal All:
I have a 2.0 A data for a SeMet protein (native crystal not available
yet!) that has 6 Se sites.
The cell comes out to be 65 67 101 and the angles are all very close to
90. The data set was collected in house with Cu 1.5418 A
We integrated and scale in orthorhombic and the statistics are reasonable.
There are 4 homologous structures and all of them have a sequence
identity of 15-16 %.
I have tried Phaser, AMoRe, EPMR with varying templates
with polyala, polyser and varying the resolutions.
I have also done a modeller and found best match with one of the four
structures. I have used this derived model as well for input.
I would like to know whether there other options (I am working on
getting a good synchrotron data set at the peak wavelength for Se).
Thanks
Subbu
PS: I am also trying P1 just in case.
------------------------------
Date: Thu, 10 Dec 2009 12:11:03 -0500
From: Bard Joel <[log in to unmask]>
Subject: Re: LG announces 3D display
Perhaps more tantalizing:
http://www.engadget.com/2009/10/22/sonys-360-degree-3d-prototype-displays-b=
lown-minds-video/
There's a YouTube of it too:
http://www.youtube.com/watch?v=3DlAS55_RngoQ
If a higher resolution version could be made it might be of interest to =
our community. It sounds like Sony doesn't have current commercialization =
plans so we might want to lobby them.
I've also seen claims that Sony will come out larger with 3D TVs using =
active stereo in 2010.
Joel
=20
>>> "David J. Schuller" <[log in to unmask]> 12/04/09 7:21 PM >>>=20
http://www.pcworld.com/article/183644/lg_announces_3d_high_definition_lcd_d=
isplays.html
"LG Announces 3D High Definition LCD Displays"
23", "full HD" (which I think means 1920 x 1080)
No mention of connectors or ports,
No mention of compatibility with existing products (e.g. nVidia 3D
Vision)
"No target release date was announced," and no price mentioned.
In short, a rather useless article. But tantalizing.
--=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
You can't possibly be a scientist if you mind people
thinking that you're a fool. - Wonko the Sane
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[log in to unmask]
------------------------------
Date: Thu, 10 Dec 2009 11:59:49 -0600
From: Jacob Keller <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise,
how would one author alone perpetrate this kind of thing? He pretends to go
to the synchrotron, comes back with the hkl file, and goes from there? What
about the crystals? Grows some lysozyme crystals, labels as protein x,
proceeds to go "to the synchrotron" and then...? This whole thing is really
hard to imagine--is there an "initiation" procedure in that lab, when the
"noble lie" is revealed to all would-be authors?
Jacob Keller
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [log in to unmask]
*******************************************
----- Original Message -----
From: "Ibrahim Moustafa" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Thursday, December 10, 2009 8:16 AM
Subject: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
> Hi all,
>
> I want to share the following e-mail received from pdb-l.
>
> It is sad to see something like that!
>
> regards,
> Ibrahim
>
>
> ------ Forwarded Message
> From: Michael Sadowski <[log in to unmask]>
> Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST)
> To: <[log in to unmask]>
> Subject: pdb-l: Retraction of 12 Structures
>
> Dear All,
>
> Better check your data!
>
> Apologies to those who have seen this.
>
> S.
>
> -----
>
> "The University of Alabama at Birmingham has issued a statement indicating
> that a former UAB researcher may have fabricated or falsified data about
> protein structures that are contained in the Protein Data Bank.
>
> The university did not include a name of the researcher, but the
> Birmingham
> News this week reported that the scientist is H.M. Krishna Murthy and an
> independent review by BioInform of the PDB shows that Murthy is associated
> with all of the proteins that UAB said were falsified.
>
> The newspaper said that a probe of Murthy's research has been underway
> since
> 2007.
>
> "After a thorough examination of the available data, which included a
> re-analysis of each structure alleged to have been fabricated, the
> committee
> found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID,
> 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than
> not
> falsified and/or fabricated and recommended that they be removed from the
> public record," the university said in its statement this week."
>
> -----
> http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr
> icated-protein-structures-now-protein-dat?utm_source=feedburner&utm_medium=f
> eed&utm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29
>
>
> http://main.uab.edu/Sites/reporter/articles/71570/
>
> http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m
> ay_be.html
>
>
>
>
> TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
> https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .
>
>
> ------ End of Forwarded Message
>
------------------------------
Date: Thu, 10 Dec 2009 10:04:08 -0800
From: Peter Zwart <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
> He pretends to go to the synchrotron, comes back
Thats what I do all the time. Instead, I go to lane splitters /
jupiter for pizza and beer.
P
------------------------------
Date: Thu, 10 Dec 2009 18:46:17 +0000
From: Nathaniel Echols <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
--000e0cd1a3f0f5dd41047a643835
Content-Type: text/plain; charset=ISO-8859-1
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller <[log in to unmask]
> wrote:
> I assume this is the denouement of the Ajees et al debacle a while back?
> Does this mean all authors on all of those papers were complicit? Otherwise,
> how would one author alone perpetrate this kind of thing? He pretends to go
> to the synchrotron, comes back with the hkl file, and goes from there? What
> about the crystals? Grows some lysozyme crystals, labels as protein x,
> proceeds to go "to the synchrotron" and then...? This whole thing is really
> hard to imagine--is there an "initiation" procedure in that lab, when the
> "noble lie" is revealed to all would-be authors?
>
I'm curious about this too, but it is actually very likely that some
(perhaps the majority) of the co-authors were unaware of the fraud,
especially those whose name is only present on a single paper. I didn't
look closely, but I recognized one name of someone who certainly doesn't
need to fake anything at this point in his career; I would be shocked if he
had any clue what was going on. Likewise, if there were co-authors from
entirely different fields, I'm sure they wouldn't know what a Wilson plot is
supposed to look like. Many excellent scientists have been burned like this
before; wouldn't you assume that your collaborators are acting in good
faith?
There are two other things to keep in mind:
1. The standard for co-authorship is often very low. This is a problem by
itself, and it's one reason why Nature (and a few others) now list author
contributions by name.
2. Rumor has it that in some labs, the PI may take the data and solve the
structure personally, cutting out the postdoc or grad student who did most
of the benchwork. (I've seen one or two author contribution sections that
indicated this had occurred.) After all, spinning dials and looking at
electron density is the "fun" part of crystallography. Who is going to
second-guess the professor when a recommendation letter (and future career)
is at stake?
-Nat
--000e0cd1a3f0f5dd41047a643835
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller <span dir=3D"ltr"><<a href=
=3D"mailto:[log in to unmask]" target=3D"_blank">[log in to unmask]
rthwestern.edu</a>></span> wrote:<br><div class=3D"gmail_quote"><blockqu=
ote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, 204, 204=
); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I assume this is the denouement of the Ajees et al debacle a while back? Do=
es this mean all authors on all of those papers were complicit? Otherwise, =
how would one author alone perpetrate this kind of thing? He pretends to go=
to the synchrotron, comes back with the hkl file, and goes from there? Wha=
t about the crystals? Grows some lysozyme crystals, labels as protein x, pr=
oceeds to go "to the synchrotron" and then...? This whole thing i=
s really hard to imagine--is there an "initiation" procedure in t=
hat lab, when the "noble lie" is revealed to all would-be authors=
?<br>
</blockquote><div><br>I'm curious about this too, but it is actually ve=
ry likely that some (perhaps the majority) of the co-authors were unaware o=
f the fraud, especially those whose name is only present on a single paper.=
=A0 I didn't look closely, but I recognized one name of someone who cer=
tainly doesn't need to fake anything at this point in his career; I wou=
ld be shocked if he had any clue what was going on.=A0 Likewise, if there w=
ere co-authors from entirely different fields, I'm sure they wouldn'=
;t know what a Wilson plot is supposed to look like.=A0 Many excellent scie=
ntists have been burned like this before; wouldn't you assume that your=
collaborators are acting in good faith?<br>
<br>There are two other things to keep in mind:<br><br>1. The standard for =
co-authorship is often very low.=A0 This is a problem by itself, and it'=
;s one reason why Nature (and a few others) now list author contributions b=
y name.<br>
<br>2.=A0 Rumor has it that in some labs, the PI may take the data and solv=
e the structure personally, cutting out the postdoc or grad student who did=
most of the benchwork.=A0 (I've seen one or two author contribution se=
ctions that indicated this had occurred.)=A0 After all, spinning dials and =
looking at electron density is the "fun" part of crystallography.=
=A0 Who is going to second-guess the professor when a recommendation letter=
(and future career) is at stake?<br>
<br>-Nat<br></div></div>
--000e0cd1a3f0f5dd41047a643835--
------------------------------
Date: Thu, 10 Dec 2009 14:07:20 -0500
From: Roger Rowlett <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<font face="Verdana">This kind of unfortunate situation only reinforces
the notion that there must be some sort of laboratory
oversight/communication/mentoring/documentation procedures in place. In
my research lab (populated by a postdoc and a bunch of undergraduates)
raw images and data processing log files are visible to everyone on the
central XRD server, there is a lot of intra-laboratory communication
about every structure that is processed, and lots of required
documentation that must go onto our electronic laboratory
notebook/wiki. While a determined individual could still find a way to
perpetrate fraud, it is a lot more difficult when there are a lot of
eyes looking at every structure, and raw data and documentation is
widely visible within the lab. This is not a bad thing for
co-authorship purposes, also.<br>
</font><br>
Nathaniel Echols wrote:
<blockquote
cite="mid:[log in to unmask]"
type="cite">On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:[log in to unmask]" target="_blank">[log in to unmask]</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I
assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit?
Otherwise, how would one author alone perpetrate this kind of thing? He
pretends to go to the synchrotron, comes back with the hkl file, and
goes from there? What about the crystals? Grows some lysozyme crystals,
labels as protein x, proceeds to go "to the synchrotron" and then...?
This whole thing is really hard to imagine--is there an "initiation"
procedure in that lab, when the "noble lie" is revealed to all would-be
authors?<br>
</blockquote>
<div><br>
I'm curious about this too, but it is actually very likely that some
(perhaps the majority) of the co-authors were unaware of the fraud,
especially those whose name is only present on a single paper. I
didn't look closely, but I recognized one name of someone who certainly
doesn't need to fake anything at this point in his career; I would be
shocked if he had any clue what was going on. Likewise, if there were
co-authors from entirely different fields, I'm sure they wouldn't know
what a Wilson plot is supposed to look like. Many excellent scientists
have been burned like this before; wouldn't you assume that your
collaborators are acting in good faith?<br>
<br>
There are two other things to keep in mind:<br>
<br>
1. The standard for co-authorship is often very low. This is a problem
by itself, and it's one reason why Nature (and a few others) now list
author contributions by name.<br>
<br>
2. Rumor has it that in some labs, the PI may take the data and solve
the structure personally, cutting out the postdoc or grad student who
did most of the benchwork. (I've seen one or two author contribution
sections that indicated this had occurred.) After all, spinning dials
and looking at electron density is the "fun" part of crystallography.
Who is going to second-guess the professor when a recommendation letter
(and future career) is at stake?<br>
<br>
-Nat<br>
</div>
</div>
</blockquote>
<div class="moz-signature">-- <br>
<font face="Verdana">
<hr>Roger S. Rowlett<br>
Professor<br>
Department of Chemistry<br>
Colgate University<br>
13 Oak Drive<br>
Hamilton, NY 13346<br>
<br>
tel: (315)-228-7245<br>
ofc: (315)-228-7395<br>
fax: (315)-228-7935<br>
email: <a class="moz-txt-link-abbreviated" href="mailto:[log in to unmask]">[log in to unmask]</a><br>
</font>
</div>
</body>
</html>
------------------------------
Date: Thu, 10 Dec 2009 11:11:31 -0800
From: Bernhard Rupp <[log in to unmask]>
Subject: Re: Solvent content of crystals vs. resolution?
> I can't find the paper I read that suggested that in practice the
> reverse correlation can be true.
Of course it can. Those are conditional probability distributions
that tell you what is most likely the case. The distributions
tell you just how possible that is with its corresponding probability.
No contradiction here at all. One interesting case Dale Tronrud
reported to me where he got a zero probability was in a previous
edition of the calculator where I rounded the printout too
aggressively. Then it turned out to be just as expected :-)
On top of it, there goes nothing into the distribution that would
allow you to realize if cooling procedures or whatever played
a determining role in an *individual* case.
Best, BR
Cheers,
Roger Rowlett
Edward A. Berry wrote:
> mjvanraaij wrote:
>> how about this for a general idea:
>>
>> resolution is related to order in the crystals, more order = diffraction
>> to higher resolution
>> the order is determined by crystal contacts, stronger crystal contacts =
>> more order
>> more solvent means, on average, less close packing and less crystal
>> contacts
>> (of course, there are cases where only a few strong crystal contacts
>> make for a very highly ordered crystal diffracting to high resolution,
>> so there are quite a few exceptions of high solvent content being
>> compatible with high resolution diffraction)
>>
>> or is this too simplistic?
>> (and widely known?)
>
> Sounds very reasonable to me. One the positive side (and this may be what
> Roger was thinking of), for a given amount of protein in the
> asymmetric unit,
> increased solvent content means a larger unit cell and finer sampling
> of the
> molecular transform, -> more reflections and thus a greater data/param
> ratio
> at a given resolution. Also solvent flattening becomes more powerful.
> Ed
------------------------------
Date: Thu, 10 Dec 2009 13:06:36 -0600
From: "Tanner, John J." <[log in to unmask]>
Subject: Retraction of 12 Structures
Some of you might be curious about the "Ajees et al debacle" that Jacob mentioned in his message. Here are two links:
Nature Brief Communication that questioned the validity of one of Murthy's structures:
http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html
Murthy's rebuttal:
http://www.nature.com/nature/journal/v448/n7154/full/nature06103.html
Jack
--
John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: [log in to unmask]
http://www.chem.missouri.edu/TannerGroup/tanner.html
________________________________
From: Jacob Keller <[log in to unmask]>
Reply-To: Jacob Keller <[log in to unmask]>
Date: Thu, 10 Dec 2009 11:59:49 -0600
To: <[log in to unmask]>
Conversation: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise,
how would one author alone perpetrate this kind of thing? He pretends to go
to the synchrotron, comes back with the hkl file, and goes from there? What
about the crystals? Grows some lysozyme crystals, labels as protein x,
proceeds to go "to the synchrotron" and then...? This whole thing is really
hard to imagine--is there an "initiation" procedure in that lab, when the
"noble lie" is revealed to all would-be authors?
Jacob Keller
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [log in to unmask]
*******************************************
----- Original Message -----
From: "Ibrahim Moustafa" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Thursday, December 10, 2009 8:16 AM
Subject: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
> Hi all,
>
> I want to share the following e-mail received from pdb-l.
>
> It is sad to see something like that!
>
> regards,
> Ibrahim
>
>
> ------ Forwarded Message
> From: Michael Sadowski <[log in to unmask]>
> Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST)
> To: <[log in to unmask]>
> Subject: pdb-l: Retraction of 12 Structures
>
> Dear All,
>
> Better check your data!
>
> Apologies to those who have seen this.
>
> S.
>
> -----
>
> "The University of Alabama at Birmingham has issued a statement indicating
> that a former UAB researcher may have fabricated or falsified data about
> protein structures that are contained in the Protein Data Bank.
>
> The university did not include a name of the researcher, but the
> Birmingham
> News this week reported that the scientist is H.M. Krishna Murthy and an
> independent review by BioInform of the PDB shows that Murthy is associated
> with all of the proteins that UAB said were falsified.
>
> The newspaper said that a probe of Murthy's research has been underway
> since
> 2007.
>
> "After a thorough examination of the available data, which included a
> re-analysis of each structure alleged to have been fabricated, the
> committee
> found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID,
> 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than
> not
> falsified and/or fabricated and recommended that they be removed from the
> public record," the university said in its statement this week."
>
> -----
> http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr
> icated-protein-structures-now-protein-dat?utm_source=feedburner&utm_medium=f
> eed&utm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29
>
>
> http://main.uab.edu/Sites/reporter/articles/71570/
>
> http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m
> ay_be.html
>
>
>
>
> TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
> https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .
>
>
> ------ End of Forwarded Message
>
------------------------------
Date: Thu, 10 Dec 2009 19:30:23 +0000
From: Paul Emsley <[log in to unmask]>
Subject: Re: Retraction of 12 Structures
Tanner, John J. wrote:
> Some of you might be curious about the "Ajees et al debacle" that Jacob mentioned in his message. Here are two links:
>
> Nature Brief Communication that questioned the validity of one of Murthy's structures:
>
> http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html
>
> Murthy's rebuttal:
>
> http://www.nature.com/nature/journal/v448/n7154/full/nature06103.html
>
> Jack
>
Notice that John E. Volanakis (not at the Center for Biophysical
Sciences and Engineering, Alabama) and Girish J. Kotwal (also not at the
Center for Biophysical Sciences and Engineering, Alabama) were not
authors of the rebuttal to Janssen et al.. They seem to have shown some
backbone (or were sufficiently detached for independent thinking).
Paul.
------------------------------
Date: Thu, 10 Dec 2009 16:34:54 -0500
From: Matthew Franklin <[log in to unmask]>
Subject: Re: pdb-l: Retraction of 12 Structures
> "After a thorough examination of the available data, which included a
> re-analysis of each structure alleged to have been fabricated, the
> committee
> found a preponderance of evidence that structures 1BEF, 1CMW,
> 1DF9/2QID,
> 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely
> than not
> falsified and/or fabricated and recommended that they be removed from
> the
> public record," the university said in its statement this week."
I think it's worth pointing out, as I did when this came up last time, that=
one needs to read this list of PDB codes very carefully, and in a font tha=
t distinguishes 0 from O, and 1 from I. It would be very unfortunate, for =
example, if an innocent bacterial enzyme structure (2HRO) was called into q=
uestion in some people's minds because of the apparent fabrication of the s=
tructure 2HR0.
Once again, I'd like to get the community's thoughts: should we ask the PDB=
to stop using 0 and 1 in its IDs?
I'll get off the soapbox now.
- Matt (who has nothing to do with any of these structures...)
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
Confidentiality Note:
This e-mail, and any attachment to it, contains privileged and confidential=
information intended only for the use of the individual(s) or entity named=
on the e-mail. If the reader of this e-mail is not the intended recipient,=
or the employee or agent responsible for delivering it to the intended rec=
ipient, you are hereby notified that reading it is strictly prohibited. If =
you have received this e-mail in error, please immediately return it to the=
sender and delete it from your system.
Thank you.
------------------------------
Date: Thu, 10 Dec 2009 21:41:21 GMT
From: Boaz Shaanan <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
This is a multi-part message in MIME format.
----598d688321bc4d514933
Content-Type: text/plain; charset=utf-8
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
If that=27s of any consolation for us crystallographers=2C this =22situa=
tions=22 arise in other fields too=2E Here is another example=2E See thi=
s link=3A
http=3A//www=2Ebiotechniques=2Ecom/news/Glycosylation-methods-paper-retr=
acted/biotechniques-182060=2Ehtml
=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Boaz
----- Original Message -----
From=3A Roger Rowlett =3Crrowlett=40COLGATE=2EEDU=3E
Date=3A Thursday=2C December 10=2C 2009 21=3A07
Subject=3A Re=3A =5Bccp4bb=5D FW=3A pdb-l=3A Retraction of 12 Structures=
To=3A CCP4BB=40JISCMAIL=2EAC=2EUK
This kind of unfortunate situation only reinforces the notion that there=
must be some sort of laboratory oversight/communication/mentoring/docum=
entation procedures in place=2E In my research lab (populated by a postd=
oc and a bunch of undergraduates) raw images and data processing log fil=
es are visible to everyone on the central XRD server=2C there is a lot o=
f intra-laboratory communication about every structure that is processed=
=2C and lots of required documentation that must go onto our electronic =
laboratory notebook/wiki=2E While a determined individual could still fi=
nd a way to perpetrate fraud=2C it is a lot more difficult when there ar=
e a lot of eyes looking at every structure=2C and raw data and documenta=
tion is widely visible within the lab=2E This is not a bad thing for co-=
authorship purposes=2C also=2E
Nathaniel Echols wrote=3A
On Thu=2C Dec 10=2C 2009 at 5=3A59 PM=2C Jacob Keller =3Cj-keller2=40md=2E=
northwestern=2Eedu=3E wrote=3A
I assume this is the denouement of the Ajees et al debacle a while back=3F=
Does this mean all authors on all of those papers were complicit=3F Oth=
erwise=2C how would one author alone perpetrate this kind of thing=3F He=
pretends to go to the synchrotron=2C comes back with the hkl file=2C an=
d goes from there=3F What about the crystals=3F Grows some lysozyme crys=
tals=2C labels as protein x=2C proceeds to go =22to the synchrotron=22 a=
nd then=2E=2E=2E=3F This whole thing is really hard to imagine--is there=
an =22initiation=22 procedure in that lab=2C when the =22noble lie=22 i=
s revealed to all would-be authors=3F
I=27m curious about this too=2C but it is actually very likely that some=
(perhaps the majority) of the co-authors were unaware of the fraud=2C e=
specially those whose name is only present on a single paper=2E=C2=A0 I =
didn=27t look closely=2C but I recognized one name of someone who certai=
nly doesn=27t need to fake anything at this point in his career=3B I wou=
ld be shocked if he had any clue what was going on=2E=C2=A0 Likewise=2C =
if there were co-authors from entirely different fields=2C I=27m sure th=
ey wouldn=27t know what a Wilson plot is supposed to look like=2E=C2=A0 =
Many excellent scientists have been burned like this before=3B wouldn=27=
t you assume that your collaborators are acting in good faith=3F
There are two other things to keep in mind=3A
1=2E The standard for co-authorship is often very low=2E=C2=A0 This is a=
problem by itself=2C and it=27s one reason why Nature (and a few others=
) now list author contributions by name=2E
2=2E=C2=A0 Rumor has it that in some labs=2C the PI may take the data an=
d solve the structure personally=2C cutting out the postdoc or grad stud=
ent who did most of the benchwork=2E=C2=A0 (I=27ve seen one or two autho=
r contribution sections that indicated this had occurred=2E)=C2=A0 After=
all=2C spinning dials and looking at electron density is the =22fun=22 =
part of crystallography=2E=C2=A0 Who is going to second-guess the profes=
sor when a recommendation letter (and future career) is at stake=3F
-Nat
-- =
Roger S=2E Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton=2C NY 13346
tel=3A (315)-228-7245
ofc=3A (315)-228-7395
fax=3A (315)-228-7935
email=3A rrowlett=40colgate=2Eedu
Boaz Shaanan=2C Ph=2ED=2E
Dept=2E of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone=3A 972-8-647-2220 =3B Fax=3A 646-1710
Skype=3A boaz=2Eshaanan=E2=80=8E
----598d688321bc4d514933
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Content-Transfer-Encoding: quoted-printable
If that=27s of any consolation for us crystallographers=2C this =22situa=
tions=22 arise in other fields too=2E Here is another example=2E See thi=
s link=3A=3Cdiv=3E=3Cbr=3E=3C/div=3E=3Cdiv=3E=3Ca href=3D=22http=3A//www=
=2Ebiotechniques=2Ecom/news/Glycosylation-methods-paper-retracted/biotec=
hniques-182060=2Ehtml=22=3Ehttp=3A//www=2Ebiotechniques=2Ecom/news/Glyco=
sylation-methods-paper-retracted/biotechniques-182060=2Ehtml=3C/a=3E=3Cb=
r=3E=3Cbr=3E=3C/div=3E=3Cdiv=3E=3Cbr=3E=3C/div=3E=3Cdiv=3E=26nbsp=3B=26n=
bsp=3B =26nbsp=3B =26nbsp=3B =26nbsp=3B =26nbsp=3BBoaz=3C/div=3E=3Cdiv=3E=
=3Cbr=3E----- Original Message -----=3Cbr=3EFrom=3A Roger Rowlett =26lt=3B=
rrowlett=40COLGATE=2EEDU=26gt=3B=3Cbr=3EDate=3A Thursday=2C December 10=2C=
2009 21=3A07=3Cbr=3ESubject=3A Re=3A =5Bccp4bb=5D FW=3A pdb-l=3A Retrac=
tion of 12 Structures=3Cbr=3ETo=3A CCP4BB=40JISCMAIL=2EAC=2EUK=3Cbr=3E=3C=
br=3E
=3Cspan=3E=3Cp=3E
=
=3Cspan bgcolor=3D=22=23ffffff=22 text=3D=22=23000000=22=3E=3C/span=3E=3C=
/p=3E=3Cp=3E
=3Cfont face=3D=22Verdana=22=3EThis kind of unfortunate situation only r=
einforces
the notion that there must be some sort of laboratory
oversight/communication/mentoring/documentation procedures in place=2E I=
n
my research lab (populated by a postdoc and a bunch of undergraduates)
raw images and data processing log files are visible to everyone on the
central XRD server=2C there is a lot of intra-laboratory communication
about every structure that is processed=2C and lots of required
documentation that must go onto our electronic laboratory
notebook/wiki=2E While a determined individual could still find a way to=
perpetrate fraud=2C it is a lot more difficult when there are a lot of
eyes looking at every structure=2C and raw data and documentation is
widely visible within the lab=2E This is not a bad thing for
co-authorship purposes=2C also=2E=3Cbr=3E
=3C/font=3E=3Cbr=3E
Nathaniel Echols wrote=3A
=3C/p=3E=3Cblockquote cite=3D=22mid=3Af0cef88f0912101046k4089e7fan67a85b=
e1aafed433=40mail=2Egmail=2Ecom=22 type=3D=22cite=22=3EOn Thu=2C Dec 10=2C=
2009 at 5=3A59 PM=2C Jacob Keller =3Cspan dir=3D=22ltr=22=3E=26lt=3B=3C=
a href=3D=22javascript=3Amain=2Ecompose(=27new=27=2C=27t=3Dj-keller2=40m=
d=2Enorthwestern=2Eedu=27)=22 target=3D=221=22=3Ej-keller2=40md=2Enorthw=
estern=2Eedu=3C/a=3E=26gt=3B=3C/span=3E
wrote=3A=3Cbr=3E
=3Cdiv class=3D=22gmail=5Fquote=22=3E
=3Cblockquote class=3D=22gmail=5Fquote=22 style=3D=22border-left=3A 1p=
x solid rgb(204=2C 204=2C 204)=3B margin=3A 0pt 0pt 0pt 0=2E8ex=3B paddi=
ng-left=3A 1ex=3B=22=3EI
assume this is the denouement of the Ajees et al debacle a while back=3F=
Does this mean all authors on all of those papers were complicit=3F
Otherwise=2C how would one author alone perpetrate this kind of thing=3F=
He
pretends to go to the synchrotron=2C comes back with the hkl file=2C and=
goes from there=3F What about the crystals=3F Grows some lysozyme crysta=
ls=2C
labels as protein x=2C proceeds to go =22to the synchrotron=22 and then=2E=
=2E=2E=3F
This whole thing is really hard to imagine--is there an =22initiation=22=
procedure in that lab=2C when the =22noble lie=22 is revealed to all wou=
ld-be
authors=3F=3Cbr=3E
=3C/blockquote=3E
=3Cdiv=3E=3Cbr=3E
I=27m curious about this too=2C but it is actually very likely that some=
(perhaps the majority) of the co-authors were unaware of the fraud=2C
especially those whose name is only present on a single paper=2E=26nbsp=3B=
I
didn=27t look closely=2C but I recognized one name of someone who certai=
nly
doesn=27t need to fake anything at this point in his career=3B I would b=
e
shocked if he had any clue what was going on=2E=26nbsp=3B Likewise=2C if=
there were
co-authors from entirely different fields=2C I=27m sure they wouldn=27t =
know
what a Wilson plot is supposed to look like=2E=26nbsp=3B Many excellent =
scientists
have been burned like this before=3B wouldn=27t you assume that your
collaborators are acting in good faith=3F=3Cbr=3E
=3Cbr=3E
There are two other things to keep in mind=3A=3Cbr=3E
=3Cbr=3E
1=2E The standard for co-authorship is often very low=2E=26nbsp=3B This =
is a problem
by itself=2C and it=27s one reason why Nature (and a few others) now lis=
t
author contributions by name=2E=3Cbr=3E
=3Cbr=3E
2=2E=26nbsp=3B Rumor has it that in some labs=2C the PI may take the dat=
a and solve
the structure personally=2C cutting out the postdoc or grad student who
did most of the benchwork=2E=26nbsp=3B (I=27ve seen one or two author co=
ntribution
sections that indicated this had occurred=2E)=26nbsp=3B After all=2C spi=
nning dials
and looking at electron density is the =22fun=22 part of crystallography=
=2E=26nbsp=3B
Who is going to second-guess the professor when a recommendation letter
(and future career) is at stake=3F=3Cbr=3E
=3Cbr=3E
-Nat=3Cbr=3E
=3C/div=3E
=3C/div=3E
=3C/blockquote=3E
=3Cdiv class=3D=22moz-signature=22=3E-- =3Cbr=3E
=3Cfont face=3D=22Verdana=22=3E
=3Chr=3ERoger S=2E Rowlett=3Cbr=3E
Professor=3Cbr=3E
Department of Chemistry=3Cbr=3E
Colgate University=3Cbr=3E
13 Oak Drive=3Cbr=3E
Hamilton=2C NY 13346=3Cbr=3E
=3Cbr=3E
tel=3A (315)-228-7245=3Cbr=3E
ofc=3A (315)-228-7395=3Cbr=3E
fax=3A (315)-228-7935=3Cbr=3E
email=3A =3Ca href=3D=22javascript=3Amain=2Ecompose(=27new=27=2C=27t=3Dr=
rowlett=40colgate=2Eedu=27)=22=3Errowlett=40colgate=2Eedu=3C/a=3E=3Cbr=3E=
=3C/font=3E
=3C/div=3E
=3C/span=3E
=3C/div=3E=3CBR=3E=3CBR=3EBoaz Shaanan=2C Ph=2ED=2E=3Cbr=3EDept=2E of Li=
fe Sciences=3Cbr=3EBen-Gurion University of the Negev=3Cbr=3EBeer-Sheva =
84105=3Cbr=3EIsrael=3Cbr=3EPhone=3A 972-8-647-2220 =3B Fax=3A 646-1710=3C=
br=3ESkype=3A boaz=2Eshaanan=3C/BR=3E=3C/BR=3E=E2=80=8E
----598d688321bc4d514933--
------------------------------
Date: Thu, 10 Dec 2009 22:39:07 +0100
From: Anastassis Perrakis <[log in to unmask]>
Subject: Re: Retraction of 12 Structures
It seems that at least some of the primary authors, were starting PhD stude=
nts.
For Ajees, as far as i know, he was given the mtz as soon as he joined the =
lab, told that they have this data for a while, and asked to see
if the new software would do it. Not difficult to imagine.
A.
=3D=3D
I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise=
,
how would one author alone perpetrate this kind of thing? He pretends to go
to the synchrotron, comes back with the hkl file, and goes from there? What
about the crystals? Grows some lysozyme crystals, labels as protein x,
proceeds to go "to the synchrotron" and then...? This whole thing is really
hard to imagine--is there an "initiation" procedure in that lab, when the
"noble lie" is revealed to all would-be authors?
Jacob Keller
------------------------------
Date: Thu, 10 Dec 2009 16:43:08 -0500
From: Ezra Peisach <[log in to unmask]>
Subject: Re: pdb-l: Retraction of 12 Structures
Matthew Franklin wrote:
>
>
> Once again, I'd like to get the community's thoughts: should we ask the PDB to stop using 0 and 1 in its IDs?
>
> I'll get off the soapbox now.
>
>
I would be all for it... Having tried to downloade 1o08 and gotten it
screwed up.... Especially when journals use a sans-serif font - things
get interesting....
Ezra
------------------------------
Date: Thu, 10 Dec 2009 21:59:59 +0000
From: Sean Seaver <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
Thanks for bringing this article to our attention. I went ahead and crea=
ted
a table of the PDBs in question including links to the structures, journa=
ls
and citations. My hope is that it will save others time trying to track
down this information.
http://bit.ly/5KqaRF
Hope it helps.
Sean
------------------------------
Date: Thu, 10 Dec 2009 22:06:07 +0000
From: Paula Salgado <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
--00032555f9caa0d627047a67035b
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
Actually, I don't think that should be any consolation at all... As
scientists, from whatever field, we should be appalled by this kind of
mischief from anyone that calls themselves scientists. Not only it has
effects on further research, delaying science sometimes by years, but it
just gives an appalling image of science and scientists. And of course, is
unethical and wrong...
Today is a sad moment for crystallography and science.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
Dr Paula Salgado
Division of Molecular Biosciences
Department of Life Sciences
Faculty of Natural Sciences
Biochemistry Building, 5th Floor
Imperial College London
South Kensington Campus
SW7 2AZ
London
Tel: 02075945464
2009/12/10 Boaz Shaanan <[log in to unmask]>
> If that's of any consolation for us crystallographers, this "situations"
> arise in other fields too. Here is another example. See this link:
>
>
> http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/b=
iotechniques-182060.html
>
>
> Boaz
>
> ----- Original Message -----
> From: Roger Rowlett <[log in to unmask]>
> Date: Thursday, December 10, 2009 21:07
> Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
> To: [log in to unmask]
>
> This kind of unfortunate situation only reinforces the notion that there
> must be some sort of laboratory
> oversight/communication/mentoring/documentation procedures in place. In m=
y
> research lab (populated by a postdoc and a bunch of undergraduates) raw
> images and data processing log files are visible to everyone on the centr=
al
> XRD server, there is a lot of intra-laboratory communication about every
> structure that is processed, and lots of required documentation that must=
go
> onto our electronic laboratory notebook/wiki. While a determined individu=
al
> could still find a way to perpetrate fraud, it is a lot more difficult wh=
en
> there are a lot of eyes looking at every structure, and raw data and
> documentation is widely visible within the lab. This is not a bad thing f=
or
> co-authorship purposes, also.
>
> Nathaniel Echols wrote:
>
> On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller <
> [log in to unmask]> wrote:
>
>> I assume this is the denouement of the Ajees et al debacle a while back?
>> Does this mean all authors on all of those papers were complicit? Otherw=
ise,
>> how would one author alone perpetrate this kind of thing? He pretends to=
go
>> to the synchrotron, comes back with the hkl file, and goes from there? W=
hat
>> about the crystals? Grows some lysozyme crystals, labels as protein x,
>> proceeds to go "to the synchrotron" and then...? This whole thing is rea=
lly
>> hard to imagine--is there an "initiation" procedure in that lab, when th=
e
>> "noble lie" is revealed to all would-be authors?
>>
>
> I'm curious about this too, but it is actually very likely that some
> (perhaps the majority) of the co-authors were unaware of the fraud,
> especially those whose name is only present on a single paper. I didn't
> look closely, but I recognized one name of someone who certainly doesn't
> need to fake anything at this point in his career; I would be shocked if =
he
> had any clue what was going on. Likewise, if there were co-authors from
> entirely different fields, I'm sure they wouldn't know what a Wilson plot=
is
> supposed to look like. Many excellent scientists have been burned like t=
his
> before; wouldn't you assume that your collaborators are acting in good
> faith?
>
> There are two other things to keep in mind:
>
> 1. The standard for co-authorship is often very low. This is a problem b=
y
> itself, and it's one reason why Nature (and a few others) now list author
> contributions by name.
>
> 2. Rumor has it that in some labs, the PI may take the data and solve th=
e
> structure personally, cutting out the postdoc or grad student who did mos=
t
> of the benchwork. (I've seen one or two author contribution sections tha=
t
> indicated this had occurred.) After all, spinning dials and looking at
> electron density is the "fun" part of crystallography. Who is going to
> second-guess the professor when a recommendation letter (and future caree=
r)
> is at stake?
>
> -Nat
>
> --
> ------------------------------
> Roger S. Rowlett
> Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: [log in to unmask]
>
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan=E2=80=8E
--00032555f9caa0d627047a67035b
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
<div><br></div>Actually, I don't think that should be any consolation a=
t all... As scientists, from whatever field, we should be appalled by this =
kind of mischief from anyone that calls themselves scientists. Not only it =
has effects on further research, delaying science sometimes by years, but i=
t just =C2=A0gives an appalling image of science and scientists. And of cou=
rse, is unethical and wrong...<div>
<br></div><div>Today is a sad moment for crystallography and science.=C2=A0=
</div><div><br></div><div><div><br></div><div>=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</div>=
<div><br></div><div>=C2=A0Dr Paula Salgado</div>
<div><br></div><div>=C2=A0Division of Molecular Biosciences</div><div>=C2=
=A0Department of Life Sciences</div><div>=C2=A0Faculty of Natural Sciences<=
/div><div>=C2=A0Biochemistry Building, 5th Floor</div><div>=C2=A0Imperial C=
ollege London</div><div>
=C2=A0South Kensington Campus</div><div>=C2=A0SW7 2AZ</div><div>=C2=A0Londo=
n</div><div><br></div><div>Tel: 02075945464</div><br><div class=3D"gmail_qu=
ote">2009/12/10 Boaz Shaanan <span dir=3D"ltr"><<a href=3D"mailto:bshaan=
[log in to unmask]">[log in to unmask]</a>></span><br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">If that's of any consolation for us cry=
stallographers, this "situations" arise in other fields too. Here=
is another example. See this link:<div>
<br></div><div><a href=3D"http://www.biotechniques.com/news/Glycosylation-m=
ethods-paper-retracted/biotechniques-182060.html" target=3D"_blank">http://=
www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniq=
ues-182060.html</a><br>
<br></div><div><br></div><div>=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Boaz<=
/div><div><div class=3D"im"><br>----- Original Message -----<br>From: Roger=
Rowlett <<a href=3D"mailto:[log in to unmask]" target=3D"_blank">rrow=
[log in to unmask]</a>><br>Date: Thursday, December 10, 2009 21:07<br>
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures<br>To: <a href=
=3D"mailto:[log in to unmask]" target=3D"_blank">[log in to unmask]</=
a><br><br>
</div><div><div></div><div class=3D"h5"><span><p>
=20
<span bgcolor=3D"#ffffff" text=3D"#000000"></span></p><p>
<font face=3D"Verdana">This kind of unfortunate situation only reinforces
the notion that there must be some sort of laboratory
oversight/communication/mentoring/documentation procedures in place. In
my research lab (populated by a postdoc and a bunch of undergraduates)
raw images and data processing log files are visible to everyone on the
central XRD server, there is a lot of intra-laboratory communication
about every structure that is processed, and lots of required
documentation that must go onto our electronic laboratory
notebook/wiki. While a determined individual could still find a way to
perpetrate fraud, it is a lot more difficult when there are a lot of
eyes looking at every structure, and raw data and documentation is
widely visible within the lab. This is not a bad thing for
co-authorship purposes, also.<br>
</font><br>
Nathaniel Echols wrote:
</p><blockquote type=3D"cite">On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller=
<span dir=3D"ltr"><<a>[log in to unmask]</a>></span>
wrote:<br>
<div class=3D"gmail_quote">
<blockquote class=3D"gmail_quote" style=3D"border-left:1px solid rgb(204,=
204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">I
assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit?
Otherwise, how would one author alone perpetrate this kind of thing? He
pretends to go to the synchrotron, comes back with the hkl file, and
goes from there? What about the crystals? Grows some lysozyme crystals,
labels as protein x, proceeds to go "to the synchrotron" and then=
...?
This whole thing is really hard to imagine--is there an "initiation&qu=
ot;
procedure in that lab, when the "noble lie" is revealed to all wo=
uld-be
authors?<br>
</blockquote>
<div><br>
I'm curious about this too, but it is actually very likely that some
(perhaps the majority) of the co-authors were unaware of the fraud,
especially those whose name is only present on a single paper.=C2=A0 I
didn't look closely, but I recognized one name of someone who certainly
doesn't need to fake anything at this point in his career; I would be
shocked if he had any clue what was going on.=C2=A0 Likewise, if there were
co-authors from entirely different fields, I'm sure they wouldn't k=
now
what a Wilson plot is supposed to look like.=C2=A0 Many excellent scientist=
s
have been burned like this before; wouldn't you assume that your
collaborators are acting in good faith?<br>
<br>
There are two other things to keep in mind:<br>
<br>
1. The standard for co-authorship is often very low.=C2=A0 This is a proble=
m
by itself, and it's one reason why Nature (and a few others) now list
author contributions by name.<br>
<br>
2.=C2=A0 Rumor has it that in some labs, the PI may take the data and solve
the structure personally, cutting out the postdoc or grad student who
did most of the benchwork.=C2=A0 (I've seen one or two author contribut=
ion
sections that indicated this had occurred.)=C2=A0 After all, spinning dials
and looking at electron density is the "fun" part of crystallogra=
phy.=C2=A0
Who is going to second-guess the professor when a recommendation letter
(and future career) is at stake?<br>
<br>
-Nat<br>
</div>
</div>
</blockquote>
<div>-- <br>
<font face=3D"Verdana">
<hr>Roger S. Rowlett<br>
Professor<br>
Department of Chemistry<br>
Colgate University<br>
13 Oak Drive<br>
Hamilton, NY 13346<br>
<br>
tel: (315)-228-7245<br>
ofc: (315)-228-7395<br>
fax: (315)-228-7935<br>
email: <a>[log in to unmask]</a><br>
</font>
</div>
</span>
</div></div></div><font color=3D"#888888"><br><br>Boaz Shaanan, Ph.D.<br>De=
pt. of Life Sciences<br>Ben-Gurion University of the Negev<br>Beer-Sheva 84=
105<br>Israel<br>Phone: 972-8-647-2220 ; Fax: 646-1710<br>Skype: boaz.shaan=
an=E2=80=8E
</font></blockquote></div><br></div>
--00032555f9caa0d627047a67035b--
------------------------------
Date: Thu, 10 Dec 2009 15:19:51 -0800
From: Bernhard Rupp <[log in to unmask]>
Subject: Re: FW: pdb-l: Retraction of 12 Structures
This is a multi-part message in MIME format.
------=_NextPart_000_0685_01CA79AC.389CB3D0
Content-Type: text/plain;
charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
I wish to point out (as I unsuccessfully did to Nature) that
by just READING the infamous Table 1 (data collection and refinement =
stats,
hidden in the supplemental material) any review worth its name should=20
immediately have raised multiple red flags. Check for yourself.
Also the B-factor distribution is worth a look (Fig 13-20 in my paper =
weight).
=20
Also, the report by Zbysek Otwinowsky is most gripping forensic yarn.
=20
http://bones.swmed.edu/people.html
=20
BR
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of =
Paula Salgado
Sent: Thursday, December 10, 2009 2:06 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
=20
=20
Actually, I don't think that should be any consolation at all... As =
scientists, from whatever field, we should be appalled by this kind of =
mischief from anyone that calls themselves scientists. Not only it has =
effects on further research, delaying science sometimes by years, but it =
just gives an appalling image of science and scientists. And of course, =
is unethical and wrong...
=20
Today is a sad moment for crystallography and science.=20
=20
=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
=20
Dr Paula Salgado
=20
Division of Molecular Biosciences
Department of Life Sciences
Faculty of Natural Sciences
Biochemistry Building, 5th Floor
Imperial College London
South Kensington Campus
SW7 2AZ
London
=20
Tel: 02075945464
=20
2009/12/10 Boaz Shaanan <[log in to unmask]>
If that's of any consolation for us crystallographers, this "situations" =
arise in other fields too. Here is another example. See this link:
=20
http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/b=
iotechniques-182060.html
=20
Boaz
----- Original Message -----
From: Roger Rowlett <[log in to unmask]>
Date: Thursday, December 10, 2009 21:07
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
To: [log in to unmask]
This kind of unfortunate situation only reinforces the notion that there =
must be some sort of laboratory =
oversight/communication/mentoring/documentation procedures in place. In =
my research lab (populated by a postdoc and a bunch of undergraduates) =
raw images and data processing log files are visible to everyone on the =
central XRD server, there is a lot of intra-laboratory communication =
about every structure that is processed, and lots of required =
documentation that must go onto our electronic laboratory notebook/wiki. =
While a determined individual could still find a way to perpetrate =
fraud, it is a lot more difficult when there are a lot of eyes looking =
at every structure, and raw data and documentation is widely visible =
within the lab. This is not a bad thing for co-authorship purposes, =
also.
Nathaniel Echols wrote:=20
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller =
<[log in to unmask]> wrote:
I assume this is the denouement of the Ajees et al debacle a while back? =
Does this mean all authors on all of those papers were complicit? =
Otherwise, how would one author alone perpetrate this kind of thing? He =
pretends to go to the synchrotron, comes back with the hkl file, and =
goes from there? What about the crystals? Grows some lysozyme crystals, =
labels as protein x, proceeds to go "to the synchrotron" and then...? =
This whole thing is really hard to imagine--is there an "initiation" =
procedure in that lab, when the "noble lie" is revealed to all would-be =
authors?
I'm curious about this too, but it is actually very likely that some =
(perhaps the majority) of the co-authors were unaware of the fraud, =
especially those whose name is only present on a single paper. I didn't =
look closely, but I recognized one name of someone who certainly doesn't =
need to fake anything at this point in his career; I would be shocked if =
he had any clue what was going on. Likewise, if there were co-authors =
from entirely different fields, I'm sure they wouldn't know what a =
Wilson plot is supposed to look like. Many excellent scientists have =
been burned like this before; wouldn't you assume that your =
collaborators are acting in good faith?
There are two other things to keep in mind:
1. The standard for co-authorship is often very low. This is a problem =
by itself, and it's one reason why Nature (and a few others) now list =
author contributions by name.
2. Rumor has it that in some labs, the PI may take the data and solve =
the structure personally, cutting out the postdoc or grad student who =
did most of the benchwork. (I've seen one or two author contribution =
sections that indicated this had occurred.) After all, spinning dials =
and looking at electron density is the "fun" part of crystallography. =
Who is going to second-guess the professor when a recommendation letter =
(and future career) is at stake?
-Nat
--=20
_____ =20
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [log in to unmask]
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan=E2=80=8E=20
=20
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<div class=3DSection1>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>I
wish to point out (as I unsuccessfully did to Nature) =
that<o:p></o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>by
just READING the infamous Table 1 (data collection and refinement =
stats,<o:p></o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>hidden
in the supplemental material) any review worth its name should =
<o:p></o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>immediately
have raised multiple red flags. Check for =
yourself.<o:p></o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>Also
the B-factor distribution is worth a look (Fig 13-20 in my paper =
weight).<o:p></o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'><o:p> </o:p>=
</span></p>
<p class=3DMsoPlainText><span =
style=3D'font-family:"Verdana","sans-serif";
color:blue'>Also, the report by Zbysek Otwinowsky is most gripping =
forensic yarn.</span><o:p></o:p></p>
<p class=3DMsoPlainText><o:p> </o:p></p>
<p class=3DMsoPlainText><a =
href=3D"http://bones.swmed.edu/people.html">http://bones.swmed.edu/people=
.html</a><o:p></o:p></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>=C2=A0=C2=A0<o:p>=
</o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif";color:blue'>BR<o:p></o:p></sp=
an></p>
<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>
<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'> CCP4 =
bulletin board
[mailto:[log in to unmask]] <b>On Behalf Of </b>Paula Salgado<br>
<b>Sent:</b> Thursday, December 10, 2009 2:06 PM<br>
<b>To:</b> [log in to unmask]<br>
<b>Subject:</b> Re: [ccp4bb] FW: pdb-l: Retraction of 12 =
Structures<o:p></o:p></span></p>
</div>
<p class=3DMsoNormal><o:p> </o:p></p>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<p class=3DMsoNormal>Actually, I don't think that should be any =
consolation at
all... As scientists, from whatever field, we should be appalled by this =
kind
of mischief from anyone that calls themselves scientists. Not only it =
has
effects on further research, delaying science sometimes by years, but it =
just
gives an appalling image of science and scientists. And of course, =
is
unethical and wrong...<o:p></o:p></p>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=3DMsoNormal>Today is a sad moment for crystallography and =
science. <o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p =
class=3DMsoNormal>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=3DMsoNormal> Dr Paula Salgado<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=3DMsoNormal> Division of Molecular =
Biosciences<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> Department of Life Sciences<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> Faculty of Natural Sciences<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> Biochemistry Building, 5th =
Floor<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> Imperial College London<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> South Kensington Campus<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> SW7 2AZ<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> London<o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=3DMsoNormal>Tel: 02075945464<o:p></o:p></p>
</div>
<p class=3DMsoNormal><o:p> </o:p></p>
<div>
<p class=3DMsoNormal>2009/12/10 Boaz Shaanan <<a
href=3D"mailto:[log in to unmask]">[log in to unmask]</a>><o:p></o:p><=
/p>
<p class=3DMsoNormal>If that's of any consolation for us =
crystallographers, this
"situations" arise in other fields too. Here is another =
example. See
this link:<o:p></o:p></p>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><a
href=3D"http://www.biotechniques.com/news/Glycosylation-methods-paper-ret=
racted/biotechniques-182060.html"
target=3D"_blank">http://www.biotechniques.com/news/Glycosylation-methods=
-paper-retracted/biotechniques-182060.html</a><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=3DMsoNormal> =
Boaz<o:p></o:p></p>
</div>
<div>
<div>
<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><br>
----- Original Message -----<br>
From: Roger Rowlett <<a href=3D"mailto:[log in to unmask]" =
target=3D"_blank">[log in to unmask]</a>><br>
Date: Thursday, December 10, 2009 21:07<br>
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures<br>
To: <a href=3D"mailto:[log in to unmask]" =
target=3D"_blank">[log in to unmask]</a><o:p></o:p></p>
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<p><span style=3D'font-family:"Verdana","sans-serif"'>This kind of =
unfortunate situation
only reinforces the notion that there must be some sort of laboratory
oversight/communication/mentoring/documentation procedures in place. In =
my
research lab (populated by a postdoc and a bunch of undergraduates) raw =
images
and data processing log files are visible to everyone on the central XRD
server, there is a lot of intra-laboratory communication about every =
structure
that is processed, and lots of required documentation that must go onto =
our
electronic laboratory notebook/wiki. While a determined individual could =
still
find a way to perpetrate fraud, it is a lot more difficult when there =
are a lot
of eyes looking at every structure, and raw data and documentation is =
widely
visible within the lab. This is not a bad thing for co-authorship =
purposes,
also.<br>
</span><br>
Nathaniel Echols wrote: <o:p></o:p></p>
<blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'>
<p class=3DMsoNormal>On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller
<[log in to unmask]> wrote:<o:p></o:p></p>
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<p class=3DMsoNormal>I assume this is the denouement of the Ajees et al =
debacle a
while back? Does this mean all authors on all of those papers were =
complicit?
Otherwise, how would one author alone perpetrate this kind of thing? He
pretends to go to the synchrotron, comes back with the hkl file, and =
goes from
there? What about the crystals? Grows some lysozyme crystals, labels as =
protein
x, proceeds to go "to the synchrotron" and then...? This whole =
thing
is really hard to imagine--is there an "initiation" procedure =
in that
lab, when the "noble lie" is revealed to all would-be =
authors?<o:p></o:p></p>
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<p class=3DMsoNormal><br>
I'm curious about this too, but it is actually very likely that some =
(perhaps
the majority) of the co-authors were unaware of the fraud, especially =
those
whose name is only present on a single paper. I didn't look =
closely, but
I recognized one name of someone who certainly doesn't need to fake =
anything at
this point in his career; I would be shocked if he had any clue what was =
going
on. Likewise, if there were co-authors from entirely different =
fields,
I'm sure they wouldn't know what a Wilson plot is supposed to look =
like.
Many excellent scientists have been burned like this before; wouldn't =
you
assume that your collaborators are acting in good faith?<br>
<br>
There are two other things to keep in mind:<br>
<br>
1. The standard for co-authorship is often very low. This is a =
problem by
itself, and it's one reason why Nature (and a few others) now list =
author
contributions by name.<br>
<br>
2. Rumor has it that in some labs, the PI may take the data and =
solve the
structure personally, cutting out the postdoc or grad student who did =
most of
the benchwork. (I've seen one or two author contribution sections =
that
indicated this had occurred.) After all, spinning dials and =
looking at
electron density is the "fun" part of crystallography. =
Who is
going to second-guess the professor when a recommendation letter (and =
future
career) is at stake?<br>
<br>
-Nat<o:p></o:p></p>
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<p class=3DMsoNormal>-- <span =
style=3D'font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><span
style=3D'font-family:"Verdana","sans-serif"'>
<hr size=3D2 width=3D"100%" align=3Dcenter>
</span></div>
<p class=3DMsoNormal><span =
style=3D'font-family:"Verdana","sans-serif"'>Roger S.
Rowlett<br>
Professor<br>
Department of Chemistry<br>
Colgate University<br>
13 Oak Drive<br>
Hamilton, NY 13346<br>
<br>
tel: (315)-228-7245<br>
ofc: (315)-228-7395<br>
fax: (315)-228-7935<br>
email: [log in to unmask]</span><o:p></o:p></p>
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<p class=3DMsoNormal><span style=3D'color:#888888'><br>
<br>
Boaz Shaanan, Ph.D.<br>
Dept. of Life Sciences<br>
Ben-Gurion University of the Negev<br>
Beer-Sheva 84105<br>
Israel<br>
Phone: 972-8-647-2220 ; Fax: 646-1710<br>
Skype: boaz.shaanan=E2=80=8E </span><o:p></o:p></p>
</div>
<p class=3DMsoNormal><o:p> </o:p></p>
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End of CCP4BB Digest - 9 Dec 2009 to 10 Dec 2009 (#2009-338)
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Alexandra M. Deaconescu, Ph.D.
Damon Runyon Cancer Research Foundation Postdoctoral Fellow
Grigorieff Laboratory
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Rosenstiel Center
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