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Matthew Todd › Comments
'Lifeless' prion proteins are 'capable of evolution' http://news.bbc.co.uk/2...
Not read this yet, but sounds deeply cool.
- Matthew Todd
Beyond Traditional Cross Couplings: The Scope of the Cross Dehydrogenative Coupling Reaction. Caroline J. Scheuermann. 2009; Chemistry - An Asian Journal - Wiley InterScience - http://www3.interscience.wiley...
Althea. Soo. Useful review on CDCs by former Queen Mary student! Althea's paper featured.
- Matthew Todd
from Bookmarklet
One-Pot Organocatalytic Asymmetric Synthesis of 3-Nitro-1,2-dihydroquinolines by a Dual-Activation Protocol. Yi-Feng Wang. 2009; Chemistry - An Asian Journal - Wiley InterScience - http://www3.interscience.wiley...
Not a reaction we're doing, but catalyst holds something that looks very much like a nitronate. Ahamed, Michael, Nilupa
- Matthew Todd
from Bookmarklet
"100 Incredible Lectures from the World’s Top Scientists"
- Matthew Todd
Reductive and Transition-Metal-Free: Oxidation of Secondary Alcohols by Sodium Hydride - Journal of the American Chemical Society (ACS Publications) - http://pubs.acs.org/doi...
Jean-Claude Bradley liked this
"This manuscript has been withdrawn for scientific reasons"
- Matthew Todd
from Bookmarklet
The actual reasons are quite interesting - it would have been good for the authors to add an explanation of what happened with appropriate links to the blogosphere where experiments were repeated. What they reported was important as a caution for anyone using NaH wishing to avoid possible side reactions. All or nothing publishing is not a very efficient way to communicate science in this case.
- Jean-Claude Bradley
Another case where useful information is labelled "unpublishable" and wasted.
- Bill Hooker
My new Nature paper: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea (w/ CC license - yay) - http://www.nature.com/nature...
Ruchira S. Datta, Christopher Fields, rowlikeagirl and 16 other people liked this
Kudos for getting the CC license!
- Bill Hooker
Absolutely =)
- Graham Steel
I note that the data for the project, in addition to being in Genbank and at the JGI IMG sites, is now available in Biotorrents at http://www.biotorrents.net/details...
- Jonathan Eisen
Jonathan - How did you get the CC license?
- Michael Nielsen
I wrote briefly about the CC license thing on my blog a while ago here: http://phylogenomics.blogspot.com/2008... ... I think it is only done for papers reporting new genome sequence data.
- Jonathan Eisen
Ah, very nice. It's useful to know about that policy from Nature. When I publish material related to open science I usually have a chat with my editor about licensing - this is the kind of thing that will be useful to bring up in future discussions.
- Michael Nielsen
Nature announced a Creative Commons license for all genome papers in December 2007: http://dx.doi.org/10...
- Martin Fenner
Worth noting that this was in response to strong community demands coming out of the controversy over the public and private genome projects as I understand it. Other communities take note (looking at you structural biology...)
- Cameron Neylon
Two cancer genomes published in Nature last week also have Creative Commons license: http://dx.doi.org/10... and http://dx.doi.org/10...
- Martin Fenner
Well, for many years (dating way back ...) Nature made genome papers available for free - and amazingly to me they have stuck to this. I do not think this was due to the public vs. private debates per se but I guess we could ask some of the old timers. Chris Gunter, who was an Nature back then and handled many of the genome papers, was involved in some way with this "openness" policy. The move to CC licenses in 2007 was a pleasant surprise too ...
- Jonathan Eisen
Kudos also for getting the Nature paper. Merry Christmas.
- Matthew Todd
I wrote a bit more about the paper and the story behind the story here: http://phylogenomics.blogspot.com/2009...
- Jonathan Eisen
Thanks for the fascinating blog post. As one commenter said, longer than the Nature paper itself. I wish we had more blog posts like this where authors write about their just published papers.
- Martin Fenner
from iPhone
+1 Martin! Even better if authors were allowed to write to write their papers the way they want and wouldn't have to write blog posts - hint: paper: four pages, supplement: 10 pages. Supplements must be among the most absurd outgrowths of our decrepit publishing system...
- Björn Brembs
Well, Bjorn and Martin, I agree and disagree. Certainly, forcing papers to be a certain length, to me, is silly, and is Yet Another Reason I like PLoS, since they have no specific restrictions on page lengths in most cases. And I completely agree that supplemental material is mostly inane. In fact, in my PLoS One, PLoS Bio and other PLoS papers I have tried to put as little as possible...
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- Jonathan Eisen
@Jonathan: I wrote the comment before I read the largely biographical blog post :-) Either way, being forced to be concise is indeed (often? sometimes?) a good thing, but can be done without the insane page limits of some journals. On the other hand, who but the author would have the right to force brevity? Put another way, shouldn't an author be allowed to completely spoil their work...
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- Björn Brembs
Unfortunately there is still a lot of work to be done before we can easily find all blog posts talking about a particular paper. Nature and other journals should follow the lead of PLoS with linking to blog posts directly from the paper webpage. And tools such as Researchblogging.org, Nature.com Blogs or Streamosphere should do a better job of aggregating all blog posts about a particular paper together.
- Martin Fenner
Bjorn: 1) Author should indeed be in charge of length in my opinion as well as form in many other ways 2) Does not hurt to have editors who suggest things that might make a paper better. 3) As for understandability, I think part of the review of a paper, including in journals like PLoS One, should be whether or not what is written correctly explains what was done and correctly explains...
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- Jonathan Eisen
Harsh Reaction to Chemistry Claims Cast Doubt on Reactome Paper : ScienceInsider - http://blogs.sciencemag.org/science...
Jean-Claude Bradley, Steve Koch, Neil Saunders and Cameron Neylon liked this
Issues with peer review here, but it sounds like open data might have helped. "In private chats and online postings, chemists began expressing skepticism about the reactome array as soon as the article describing it was published, noting several significant errors in the initial figure depicting its creation. Some also questioned how a relatively unknown group could have synthesized so many complex compounds. The dismay grew when supplementary online material providing further information on the synthesized compounds wasn’t available as soon as promised. “We failed to put it in on time. The data is quite voluminous,” says co-corresponding author Peter Golyshin of Bangor University in Wales, a microbiologist whose team provided bacterial samples analyzed by Ferrer’s lab."
- Matthew Todd
from Bookmarklet
Maybe we should do a round-up of high profile peer review "failures" from this year? Between this, hydride oxidation and the withdrawn crystal structures its not been a good year really...
- Cameron Neylon
Yes, on that note see http://www.coronene.com/blog...
- Matthew Todd
Official Google Blog: The meaning of open - http://googleblog.blogspot.com/2009...
Cameron Neylon liked this
File under "must read later unless Cameron does first."
- Matthew Todd
from Bookmarklet
I'm reading it - not sure how soon I'll have something useful to add though - brain has gone into terminal end of year decline...
- Cameron Neylon
Ok. Brief response - a lot of it is motherhood and apple pie and it would be nice to see a clearer line drawn between where they take the decision not to open source but if that is really the tenor of inside communications and Googlers take this kind of thing seriously (and the contacts I have had with various people within Google all suggest that this is the case) then it is very...
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- Cameron Neylon
Pd(III) catalysis insight - http://www.rsc.org/chemist...
Missed this earlier this year - Pd(III) implicated in oxidative C-H activation cycles.
- Matthew Todd
from Bookmarklet
Bad snowflakes - http://www.nature.com/nature...
"Parts of the world are once again knee-deep in images of snow crystals for the Christmas and New Year festivities. Unfortunately, the grand diversity of naturally occurring snow crystals is commonly corrupted by incorrect 'designer' versions — as illustrated by the faux octagonal snowflakes depicted in a Nature online subscription advertisement and, ironically, captioned “...for anyone who loves science”."
- Matthew Todd
The Vega Science Trust - Richard Feynman - Science Videos - http://www.vega.org.uk/video...
University of Auckland Feynman Lectures
- Matthew Todd
from Bookmarklet
Computational Organic Chemistry » Enantioselective Michael Addition - http://comporgchem.com/blog...
Bachrach post on the lack of modelling in a recent cinchona-catalysed Michael addition paper.
- Matthew Todd
from Bookmarklet
Twitter, Facebook, and Open Access …. 2009; Angewandte Chemie International Edition - Wiley InterScience - http://www3.interscience.wiley...
Deepak Singh, Bora Zivkovic, Andrew Spong and Noel O'Boyle liked this
"10.1002/anie.200906501" Requires subscription, obviously.
- Matthew Todd
from Bookmarklet
is this going to raise my blood pressure?
- D0r0th34
@D, yes. Now that I have read it http://ff.im/d9OMw, it's barely worth reading. But that's often true (innit) of TA editorials about OA.
- Graham Steel
it certainly is... and it's from Angewandte Chemie to boot, so that's more or less what I expected. will pass on actually reading it.
- D0r0th34
(1) Guilt by association: Links Open Access to Twitter and Facebook as buzzwords. (2) Fallacious argument: Open Access = Publish under pressure (huh?) => Reduction in Quality. (3) Economic argument: This is the only strong argument, but is undermined by silly arguments (1) and (2).
- Noel O'Boyle
sounds about what I'd anticipated
- D0r0th34
As a journal editor there are many valid arguments for or against Open Access, but this editorial by Peter Gölitz includes many misconceptions. Example: "... the earnings of a journal are directly dependent on the number of articles published. Only fools believe that editors wouldn't then tend towards acceptance of a manuscript in the many borderline cases." It is my understanding that...
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- Martin Fenner
Why Don't Chemists Communicate? (Or Do We?). In the Pipeline: - http://pipeline.corante.com/archive...
suelibrarian, Duncan Hull, Matthew Todd and 5 other people liked this
Derek Lowe's thoughts on social networking for chemists.
- Martin Fenner
from Bookmarklet
Iteresting that he kind of skirts the issue "chemists don't do big experiments"...yes that's because we maintain a 19th century way of working in most cases in most academic labs. Very different in industry but there is a still a lot of one person at one bench making one compound - which I can't help but feel would be unthinkable in other disciplines...
- Cameron Neylon
no new ideas, really, it's the same reasons the original author gave - I keep hoping some chemist will prove all of this wrong or come up with some examples of information and communication technologies that are needed and will be used.
- Christina Pikas
I think we should not try calling it 'the scientist', but also accept that there are several personality types. Here my blog comment http://bit.ly/8BQcqd
- joergkurtwegner
Joerg - indeed there are individual differences on top of any regularities or similarities we can detect across groups ( I questioned the utility of talking about whole disciplines). I think we can probably say that collaborating openly online is ingrained and typical in some areas and is extraordinary and atypical in other research areas.
- Christina Pikas
Left my comments on the site. Would be interesting if we could decide that Chemistry is somehow different from other disciplines. FF and other online communities are full of bio/cheminformatics guys, i.e. people with a predisposition to sharing online through bespoke software? What about zoology, or geology, or areas of science less impacted by software?
- Matthew Todd
@Christina - Can you point to more references or information on this topic? Which areas are standing out, and even more interesting why are they outstanding?
- joergkurtwegner
The Fourth Paradigm: Data-Intensive Scientific Discovery - Microsoft Research - http://research.microsoft.com/en-us...
"In The Fourth Paradigm: Data-Intensive Scientific Discovery, the collection of essays expands on the vision of pioneering computer scientist Jim Gray for a new, fourth paradigm of discovery based on data-intensive science and offers insights into how it can be fully realized."
- Matthew Todd
from Bookmarklet
CJO - Abstract - Praziquantel: its use in control of schistosomiasis in sub-Saharan Africa and current research needs - http://journals.cambridge.org/action...
Jean-Claude Bradley liked this
"10.1017/S0031182009000493" New PZQ review
- Matthew Todd
from Bookmarklet
A Dark Tale Behind Two Retractions -- Service 326 (5960): 1610 -- Science - http://www.sciencemag.org/cgi...
Jean-Claude Bradley liked this
"The notices published in Science last month and online in the Journal of the American Chemical Society (JACS) in September were brief: Two papers from a prominent chemistry lab were being retracted because the results couldn't be replicated. Part of the story behind the retractions is anything but straightforward, however. It involves an extortion attempt and a threat of suicide." Needs subscription, sorry.
- Matthew Todd
from Bookmarklet
"Zhang's lab notebooks, describing his experiments in detail, were missing"
- Jean-Claude Bradley
Who can point me to a drug where tautomerism is involved in its mode of action?
Duncan Hull, Matthew Todd and Mike Chelen liked this
I heard of warfarin having functional implications due to tautomerism, did you checked that ?
- Khader Shameer
No, but will do so now... thanx for the pointer! (others: more ṕointer always welcome)
- Egon Willighagen
Enol tautomer as biological switch - http://www.ncbi.nlm.nih.gov/pubmed...
- Neil Saunders
Surprised that "drug tautomer" only throws up 96 PubMed records - many of which are computational studies (docking etc.) Perhaps > 1 tautomer under physiological conditions is rare? Or avoided by design?
- Neil Saunders
Hate to be a pedant, but do you mean that a less thermodynamically favourable tautomer of a drug is the bound/active form?
- Matthew Todd
@Matthew: our group is writing a book on pharmaceutical bioinformatics (cheminformatics, QSAR, proteochemometrics), and we are trying to have all examples pharmaceutically relevant... tautomerism is a source of variance in cheminformatics (as is pKa, resonance structures, conformations, ...), so discussed in the book... any effect of tautomerism on drug activity would be good enough
- Egon Willighagen
@Neil you got a DOI? Your PubMed page does not link anywhere at uu.se and Google Scholar does not give hits on the title other than PubMed...
- Egon Willighagen
PDF would do fine too of course... first.lastname _at_ gmail :)
- Egon Willighagen
@Egon That's odd. No DOI - reference is Adv Exp Med Biol. 2003;527:601-8. Can't get PDF. Best I can do is this Google book link - http://bit.ly/78w6rV.
- Neil Saunders
Ah, sorry... did not realize it was a book :(
- Egon Willighagen
Regiodivergent Ring Opening of Chiral Aziridines -- Wu et al. 326 (5960): 1662 -- Science - http://www.sciencemag.org/cgi...
"10.1126/science.1180739" Two enantiomers, one catalyst, two products
- Matthew Todd
from Bookmarklet
Novel Rearrangement « Naturalproductman’s Blog - http://naturalproductman.wordpress.com/2009...
Heterocyclic rearrangement mechanism problem for future cohorts of Chem3115.
- Matthew Todd
from Bookmarklet
Funding cuts mark 'sad day for British science' |Science | guardian.co.uk - http://www.guardian.co.uk/global...
"Britain's physics community is reeling from a "disastrous" day of funding cuts that will force scientists to withdraw from major resarch facilities and see PhD studentships fall by a quarter."
- Matthew Todd
from Bookmarklet
I'm intrigued that no-one seems to have picked up what I think is the real bomb shell. Diamond phase III operating costs will be funded by scaling back the ESRF subscription...and presumably no support for additional money for new build. No mention of anything similar for ISIS/ILL tensioning but it has to come.
- Cameron Neylon
Neglected Tropical Diseases: Multi-Target-Directed Ligands in the Search for Novel Lead Candidates against Trypanosoma and Leishmania - Journal of Medicinal Chemistry (ACS Publications) - http://pubs.acs.org/doi...
"10.1021/jm9004835" Review
- Matthew Todd
from Bookmarklet
The Nature of the Extraordinary Finish of Stradivari’s Instruments. Jean-Philippe Echard. 2009; Angewandte Chemie International Edition - Wiley InterScience - http://www3.interscience.wiley.com/journal...
Picked up from http://www.chemcafe.net/antonio... No magic ingredients, it seems.
- Matthew Todd
from Bookmarklet
Formats Chem3D exports to
Hi Mat, could you please send me the file as simple JPG or any other ordinary image file? I couldn't find a suitable free exporter or viewer. However I have downloaded a demo version of "Molecular Modeling Pro Plus" which I can use to view the files in 3D ( if they're overly complex for 2D) and then just model in my own app. BTW which method of communication do u prefer- forum or email?
- Bachir Kazzi
Either - email easier for small technical things and nitty-gritty, forum for sharing files?
- Matthew Todd
Hi Mat, well I finally got my animation reel together and thought I'd show you if you were still interested. http://bachanimation.com/images... sorry it took so very long.
Hang on - you did these? Seriously?
- Matthew Todd
Hi Mat. Sorry I want to just be clear on this so as not to be misleading- I did all the character/creature animation- Not the models/character design/rendering (in the first 3/4 of the showreel). In studios they give me a character and props and I animate them. The last inanimate objects in the show-reel I modelled. One of them, the spider (designed by someone else) appears in a Louie...
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- Bachir Kazzi
OK, still very impressive and I suspect what I have in mind would be easy. I need molecules animated in 3D, mainly in black and white (essentially animated versions of structures you see drawn in text books) roughly in the style of this: http://www.youtube.com/watch.... As a starting point can you take a regular line representation of a benzene ring in black and white and have it rotate on its axis?
- Matthew Todd
Yep- that sounds simple enough. Do you have an email i can send it to? it shouldnt take very long to model animate render and compress into a quicktime for you. Have you got skype? maybe it might be easier to make adjustments on the go.
- Bachir Kazzi
it took 5min. But i need an email to post you a link to the uploaded quicktime. (i'm using yousendit)
- Bachir Kazzi
OK, use m.todd@chem.usyd.edu.au for now...
- Matthew Todd
That's absolutely perfect Bachir. OK, fantastic. Can you add in an OH group on the ring somewhere, have it spin twice then have an arrow appear pointing to the OH (which turns red) and the word "acidic" appear in red letters? This may sound odd, but is representative of what I'd like to do, so bear with me.
- Matthew Todd
lol.. I'll take that as a compliment- thanks :) Yeah I did. I worked as a professional animator for 5 years. I still work during the year- thats why i got too busy to put the reel together earlier.
- Bachir Kazzi
from email
OK, that's beyond awesome. Wow. I need to get together a more detailed description of something more complex. Do you have time to put together something that maybe runs for one minute, with more complex structures, provided I guide you as to the exact chemical content? With a prototype animation we can apply for funding to develop this properly - i.e. cost for your time. If I wanted to...
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- Matthew Todd
:). Yeah that should be fine- I'd prefer something a bit shorter though as it can get time consuming say 30 sec? but if it's a minute you need then that's ok too. Could you please send me an example of a simple file output from chem draw... that way I can see if its compatible with my software and if the 3d Mesh is usable- what file formats can it export to? does it do .Obj files or .max or .3ds files?
- Bachir Kazzi
OK, posted formats separately. 30 seconds absolutely fine. Email for sample output file?
- Matthew Todd
Cool 30 seconds it is. I guess an eps, tga and cdx file would be nice- sorry it's just that I'll try and find a way to make it easier and quicker for us if I can experiment with the file formats and some plugins. I was referring to an OBJ file before- it's an industry standard 3d file that is used to cross apps between cad and other 3d packages- that way i'd have saved time modelling...
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- Bachir Kazzi
OK, send me an email so I can send you a sample.
- Matthew Todd
bachir.kazzi@gmail.com
- Bachir Kazzi
Hi Mat, just wondering have you sent something through yet?- no rush, just wondering if you have and it hasn't gone through thats all.
- Bachir Kazzi
Not yet - will soon.
- Matthew Todd
Bachir - separately posted (in my teaching room) the formats Chem3D saves molecules as. Any of these any good - I have a structure I'd like to send you.
- Matthew Todd
Column: Totally Synthetic - http://www.rsc.org/chemist...
Khalid Mirza liked this
Althea - example of the Ono procedure we talked about.
- Matthew Todd
from Bookmarklet
Wondering when/if friendfeed search will be unbroken again.
Chieze Okoye, MVB (Curmudgeon of FF) and Mike Chelen liked this
Still broken? /checks - so it is. It's been weeks now. The kind of issue that makes you wonder about the long-term future.
- Neil Saunders
it is working for me ... very ... slowly ...
- Mike Chelen
Working fine for me - what's up?
- Matthew Todd
Strike that - it's screwed.
- Matthew Todd
For me, "search everybody" works very slowly, "search my friends" gives a service unavailable error.
- Neil Saunders
It was working for me last night but is broken now...damnit, anyone got $10M to build something for us?
- Cameron Neylon
Yes, that research group with the recent grant to build "FB for Science", they have the money and the mandate. Now, how do we get them to build a FriendFeed instead of a Facebook?
- Bill Hooker
In early next year my grant to do something like that should be decided :-)
- Björn Brembs
Preparation of Zwitterionic Hydroquinone-Fused [1,4]Oxazinium Derivatives via a Photoinduced Intramolecular Dehydrogenative-Coupling Reaction - Organic Letters (ACS Publications) - http://pubs.acs.org/doi...
Althea/Soo - interesting "side reaction" of DDQ here. Amines?
- Matthew Todd
from Bookmarklet
BenchFly: How to Calculate an Rf Value - Zusammen - http://zusammen.metamolecular.com/2009...
Funky graphics describing how to measure a TLC Rf. However, quote Rfs to 2 d.p. and every TLC needs at least 3 lanes in reality...
- Matthew Todd
from Bookmarklet
Drug Companies Since 1950. In the Pipeline: - http://pipeline.corante.com/archive...
"Given that many large pharmaceutical companies estimate they need to produce an average of 2–3 NMEs per year to meet their growth objectives, the fact that none of them has ever approached this level of output is concerning"
- Matthew Todd
from Bookmarklet
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