[3dem] RE: 3dem Digest, Vol 74, Issue 3

Fri Oct 11 09:00:00 PDT 2013

Apologies, my previous message was sent by mistake.
Alessandro

Alessandro Costa, PhD
London Research Institute
Clare Hall Laboratories
Cancer Research UK
South Mimms
Herts EN6 3LD, UK

Tel (within UK): 01707 625740
Tel (international): +44 1707 625740

E-mail: alessandro.costa at cancer.org.uk
http://www.london-research-institute.org.uk/research/alessandro-costa
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Sent: Friday, October 11, 2013 4:48 PM
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Subject: 3dem Digest, Vol 74, Issue 3

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Today's Topics:

   1. Re: Don't blame your thermometer... (the story continues)
      (Marin van Heel)
   2. EM position open at Duke University (RJ Perz-Edwards, Ph.D.)

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Message: 1
Date: Fri, 11 Oct 2013 11:53:42 +0100
From: Marin van Heel <marin.vanheel at googlemail.com>
Subject: Re: [3dem] Don't blame your thermometer... (the story
        continues)
To: "Penczek, Pawel A" <Pawel.A.Penczek at uth.tmc.edu>,
        "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Message-ID: <5257D8B6.7050303 at googlemail.com>
Content-Type: text/plain; charset="windows-1252"

The saga continues...

Marin

          Protein Data Bank in Europe (PDBe)
          <https://www.facebook.com/proteindatabank?ref=stream&hc_location=stream>

          Controversy continues over the validity of the cryo-electron
          microscopy structures of the HIV-1 envelope glycoprotein
          complex http://dx.doi.org/doi:10.1073/pnas.1307382110
          <http://dx.doi.org/doi:10.1073/pnas.1307382110>
          http://pdbe.org/emd-5447.

          Richard Henderson's article in PNAS (http://bit.ly/17pHW2q) is
          accompanied by letters from Subramaniam
          (http://bit.ly/1c2Qfq4), van Heel (http://bit.ly/1ac3xNA) and
          a response from Mao (http://bit.ly/1hE0p0Z
          <http://www.facebook.com/l.php?u=http%3A%2F%2Fbit.ly%2F1hE0p0Z&h=CAQGdA-hTAQG0DkJHPvtisdEmgsMpEGB4gajAcMuymMGi5A&s=1>).

(Yes Pawel, you read me right, that is what was behind my original
posting...)

======================================================

On 28-Aug-13 3:29 PM, Penczek, Pawel A wrote:
> Hi,
>
> "cheating" is a strong a loaded term.  Most mistakes are made by overzealous and sometimes not fully knowledgeable users.
> Given a tool that is not entirely correctly advertised as a panacea against mistake the dangers paradoxically increase.
>
> I am not aware of any statements that would specify what resolution a reference should be in "golden standard" procedure.
>
> Regards,
> Pawel.
>
>
> On Aug 28, 2013, at 9:20 AM, Steven Ludtke <sludtke at bcm.edu> wrote:
>
>> Ouch, now I can see a real 'discussion' arising.
>>
>> One minor correction to your statement. They did, indeed, claim to do a 'gold standard' refinement in that paper, however, they used the same (high resolution) reference for both of the 'independent' refinements. They claimed a final resolution of ~6 ? which is higher than the '11 ? reference'. Then again, I suspect that the '11 ? resolution' reference was not rigorously filtered to 11 ?. So, they used the word 'gold standard' without following the procedure it is supposed to embody.
>>
>> You are correct, of course, even so that there are many many ways to 'cheat' any standard. Nonetheless, it isn't a bad idea to develop standards which at least make it more difficult to do so, and also dramatically reduce the possibility of _unintentional_ cheating. There is very little anyone can do about someone who's determined to cheat. (That isn't intended as a comment about the PNAS manuscript, which I suspect could only be resolved at this point if they decided to make their raw data publicly available).
>>
>> On Aug 28, 2013, at 8:56 AM, "Penczek, Pawel A" <Pawel.A.Penczek at uth.tmc.edu> wrote:
>>
>>> My reading of Marin's parabole is that he is trying to clarify issues surrounding some of the exaggerated claims that surfaced
>>> in few recent years and espoused in the papers listed by Steve.
>>>
>>> While by themselves they are innocuous the danger is that for some they can provide a false sense of self-confidence: I used
>>> the well-documented "prevention" method therefore my structure is beyond doubt and reproach.
>>>
>>> Regrettably, it is not quite so and while additional validation never does any harm by itself it is not sufficient to prove the
>>> results are correct.  A determined person can alway squeeze out helices and phosphate bonds from the data.
>>>
>>> A very good illustration of perils associated with the uncritical use of "golden standard" is provided by Richard Henderson interviewed in Science:
>>>         Is High-Tech View of HIV Too Good to Be True?
>>>
>>> *   Jon Cohen
>>>
>>> *   Science 2 August 2013: 443-444.
>>>
>>> Regards,
>>> Pawel A. Penczek, Ph.D.
>>>
>>> ====================================================
>>>
>>> On Aug 28, 2013, at 6:27 AM, Marin van Heel <marin.vanheel at googlemail.com<mailto:marin.vanheel at googlemail.com>> wrote:
>>>
>>>
>>> Thought of the day:
>>>
>>> If you overheat your house, do you blame your thermometer?
>>> It is rather your own responsibly to change your thermostat settings!
>>> If you over-fit your 3D reconstruction, do you blame the FSC resolution measure?
>>> It is rather your own responsibility to avoid overfitting by reference bias.
>>> There is no such thing as a biased FSC (Fourier Shell Correlation). Neither is there a ?gold standard? FSC!
>>> Yes, you CAN do deviously biased data processing to try to prove you are better than everybody else.
>>> But what ever you do, please don?t blame your thermometer.
>>>
>>> Cheers,
>>> Marin
>>>
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Message: 2
Date: Fri, 11 Oct 2013 15:34:04 +0000
From: "RJ Perz-Edwards, Ph.D." <rj.perz-edwards at duke.edu>
Subject: [3dem] EM position open at Duke University
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Message-ID: <987F9D1C-4B09-4642-B6CF-7CA685374697 at cellbio.duke.edu>
Content-Type: text/plain; charset="utf-8"

Are you looking for a job in EM, but also interested in learning more? We???re hoping you???ll join our team in the lab of Dr. Michael Reedy, at Duke University, in Durham NC.  We study the in situ mechanism of force generation by myosin motors and the regulation of myosin by tropomyosin-troponin, using the exquisitely well-ordered flight muscles of the giant waterbug, Lethocerus.  We???re striving for a 1-ms, 1-nm resolution ???movie??? of how muscle works by integrating time-resolved cryo-EM with real-time muscle physiology monitored by live action X-ray diffraction movies.
Job opening is flexible and we will consider any level candidate from bachelor's degree and up, including post-docs or research scientists.  Exact job title and pay level will depend on your experience.  Current funding is guaranteed until 2017-2018.
Ideally, you are well versed in routine biological TEM, including fixation, embedding, thin sectioning, and negative stain.  You should also have experience in, or willingness and ability to learn, 3D cryo-EM and electron tomography, including single particle methods, iterative helical real-space reconstructions and sub-volume averaging.  EM will be most (~75%) of your duties, but you will also assist with muscle physiology and X-ray diffraction experiments as needed.
Please contact Robert Perz-Edwards (hiring manager), and send me your CV, including contract information for 2-3 references.
Robert J Perz-Edwards, PhD
Assistant Research Professor, Reedy Lab
Cell Biology, Duke University
Box 3011 (US Mail)
303 Research Drive, Sands Bldg, Rm 457
Durham, NC 27710
919-684-5674
rjpe at cellbio.duke.edu<mailto:rjpe at cellbio.duke.edu>

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