tag:blogger.com,1999:blog-107215532024-03-07T05:34:12.389+00:00martyn amosMartyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.comBlogger239125tag:blogger.com,1999:blog-10721553.post-48817583463862058622012-10-30T11:20:00.001+00:002012-10-30T15:05:31.356+00:00Publishing spamThis week, my colleague Susan Stepney posted an <a href="http://susan-stepney.blogspot.co.uk/2012/10/it-truly-is-excellent-paper.html">interesting blog article</a> on the emerging phenomenon of "publishing spam" - unsolicited emails sent to academics in an attempt to flatter them into submitting a paper for publication. Unfortunately, such publications generally come with significant page charges attached. While the notion of page charges is not, in itself, inherently bad (most open access publishing <a href="http://www.rin.ac.uk/our-work/research-funding-policy-and-guidance/paying-open-access-publication-charges">relies on it</a>), problems arise when they are levied by so-called "predatory publishers" - operations set up <i>specifically </i>to harvest fees from sometimes gullible academics (who may be desperate to add papers to their CVs in an attempt to gain tenure, or even gain a first position). The number of such outfits is growing rapidly, and they are <a href="http://www.nature.com/news/predatory-publishers-are-corrupting-open-access-1.11385">discussed in detail here</a>.<br />
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Susan was discreet enough to redact the name of the publisher in her case; I, however, have been contacted <i>several </i>times by the same operation, despite several requests for my address to be removed from their mailing list. I therefore have no qualms about reproducing here the email I've just sent to them. MASAUM appear on the most popular <a href="http://scholarlyoa.com/publishers/">list of predatory publishers</a>, and so I can only conclude that their primary aim is to make money, rather than disseminate good scholarship.<br />
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<b>To whom it may concern:</b></div>
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Despite several requests to you to remove my email address from your contact list, you still persist in sending me your academic spam. I am therefore copying this message to members of your "editorial board", in the hope that they will come to realise the precise nature of your operation.</div>
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Your messages are unsolicited and unwelcome. No credible organization would garner publications by sending out boiler-plate invitations in the way that you do. It is clear that the only objective of your operation is to gather publication fees from desperate and/or gullible academics. The role of academic editors is to use their contacts in order to solicit submissions. The people you list in your email should be made aware of the fact that associating themselves with MASAUM will do their careers a lot more harm than good; seeing such an editorship on a CV would immediately cause me to call into question a colleague's judgement, since they have clearly not done their homework on the precise nature of your business model. I would encourage them to resign immediately.You are listed in a directory of predatory publishers</div>
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http://scholarlyoa.com/publishers/</div>
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and it is clear that such a listing is well-deserved.</div>
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Please do not contact me again. </div>
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<b><br /></b>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com6tag:blogger.com,1999:blog-10721553.post-2634459282459936202012-04-02T16:48:00.002+00:002012-04-02T16:50:24.293+00:00ImagesAfter removing some Blogger folders from my new Android phone, I quickly realised that they were actually <i>synced</i> with my blog (as opposed to just being copied). As a result, I've lost any images posted to my blog. I've tried to restore the most recent ones, but the rest are gone. Ho hum.Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com2tag:blogger.com,1999:blog-10721553.post-65955552040343372312012-03-14T10:58:00.002+00:002012-04-05T22:49:11.794+00:00Come and work with us - Ph.D. in Digital Design<span style="font-weight:bold;">MIRIAD/DRI Studentship in Digital Design</span><br /><br /><span style="font-style:italic;">Ref: JA2012/3</span><br /><br />The Manchester Institute for Research and Innovation in Art and Design (MIRIAD) and the Dalton Research Institute (DRI) at Manchester Metropolitan University (MMU) seek qualified candidates for a fully-funded, three-year full-time Ph.D. studentship in the area of digital design.<br /><br />The use of computers and associated technologies has a long history in art, design, architecture and other affiliated disciplines. Research at the intersection of informatics and art/design is developing quickly, due to the increasing availability of high-performance computers, and the accessibility of various software packages and programming tools and techniques. Recently, though, a new wave of digital creativity has emerged that seeks to go beyond the simple application of software to problems in art and design. Practitioners in this area are using novel computing techniques, in a ‘bottom up" fashion, to generate entirely new representations, structures and designs. Examples of this (from ongoing work at MMU) include the design of 3D structures using methods inspired by embryonic development, and the evolution of rules for pattern formation.<br /><br />The successful candidate will be jointly-supervised by leading academics in both MIRIAD (Art & Design) and the DRI (Science and Engineering), and will belong to both Research Institutes. MIRIAD and the DRI are embarking on an ambitious programme of formal collaboration, and the student will be expected to contribute fully to this. Trained in art/design/architecture or a related discipline, you will have substantial computational skills, at least to the level of having a good working knowledge of scripting and/or programming languages. You should be prepared to cross disciplines during the course of your research, and be willing to play a role in bridging the gaps between disparate research fields.<br /><br />More details at <br /><br /><a href="http://www.mmu.ac.uk/research/studentships/arthum.php#art">http://www.mmu.ac.uk/research/studentships/arthum.php#art</a><br /><br />The deadline for all applications is <span style="font-weight:bold;">10th April 2012 (new deadline!)</span>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-68739105264433027592012-03-08T21:45:00.012+00:002012-04-02T17:01:26.125+00:00On public engagement (Part I)Last week I was privileged to be invited to speak to participants in the University of Sheffield's <a href="http://www.sheffield.ac.uk/faculty/science/training-and-development/sheffield-crucible">Crucible</a> programme. The idea is to create "outward facing researchers", who are capable of thinking and working in an inter-disciplinary fashion, exchanging knowledge and reaching out to wider society. I was asked to talk to them about public engagement, so here's a summary of my presentation (split into a number of parts).<br /><br />The notion of "the good, the bad and the ugly" is <a href="http://www.ippr.org/publications/55/1829/the-good-the-bad-and-the-ugly-housing-demand-2025">often used</a> as a device with which to <a href="http://www.flyte.biz/resources/newsletters/06/09-paypal-good-bad-ugly.php">frame</a> a discussion. I thought I'd use it, but with a minor modification, as I couldn't really think of any truly <i>ugly</i> experiences of public engagement. <br /><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/goodbad.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 222px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/goodbad.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5717647753680227586" /></a><br /><br />We first need to define what we <i>mean</i> by "public engagement". I was quite happy to go with the National Co-ordinating Cente for Public Engagement <a href="http://www.publicengagement.ac.uk/what">definition</a>:<br /><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/nccpe.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 111px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/nccpe.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5717649739169205458" /></a><br /><br />The phrases to emphasise here are "connect and share their work", "mutual benefit", "sharing knowledge, expertise and skills", "trust, understanding and collaboration", and the inevitable "impact".<br /><br />In my view, what public engagement is emphatically <i>not</i> about is "selling" an institution or a particular piece of work.<br />People taking a more positive view of an institution should be a beneficial <i>side-effect</i> of effective public engagement, rather than an end in itself. In my experience, people know when they are being sold to, and it can often be counter-productive. Good, honest attempts to truly <i>engage</i> will always leave people with a favourable impression, whereas sales tactics generally give off a whiff of desperation and tackiness.<br /><br />I then invoked my utterly unscientific idea of the "axes of involvement" to categorise different types of public engagement (with which I've been personally involved. On the x-axis we have the level of "audience" participation (running from "passive" to "actively involved in delivering the product", and on the y-axis we have audience numbers (on a log scale, running from single individuals to thousands of people).<br /><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/axes.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 241px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/axes.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5717652039417356994" /></a><br /><br />On the left-hand side we have activities such as my book <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/gm.html"><i>Genesis Machines</i></a>, which was read by thousands of people (honest!), but involved a very low level of "participation" (a few people emailed me after reading the book, but there was no real interaction involved). On this side we also have our <a href="http://martynamos.blogspot.com/2011/03/weeknote-35-we-20311.html">exhibit</a> in the Museum of Science and Industry; again, seen by potentially thousands of visitors, but which involves them passively watching a video interview.<br /><br />To the right we have more participative activities, such as <a href="http://diybio.madlab.org.uk">DIYbio Manchester</a>, or Manchester Methods (see the video below):<br /><br /><center><br /><iframe width="280" height="200" src="http://www.youtube.com/embed/zh1NIEW79IA" frameborder="0" allowfullscreen></iframe> <br /></center><br /><br />Both of these activities, by their very nature, might involve handfuls of individuals (up to maybe 50 or 60), but they're a lot more <i>hands on</i> in terms of their participation. <br /><br />I therefore decided to call projects to the left "broadcasting" activities (lots of communication, not much feedback, large numbers), and those to the right "collaboration" activities (lots of participation, lots of feedback, smaller numbers). I also identified four different activity <i>types</i>: Writing, Presenting, Teaching and Working.<br /><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/axes2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 245px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/axes2.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5717654710057482802" /></a><br /><br /><b>Writing</b> is often the most obvious route into public engagement. It was certainly mine; my first popular science book was published in 2006, as a direct result of my entering the Wellcome Trust Book Prize in 1999. I didn't win, but I <i>was</i> shortlisted (and was delighted to learn that the panel that year included Douglas Adams), and the winner was the acclaimed <a href="http://www.wellcome.ac.uk/News/Media-office/Press-releases/2002/WTD002882.htm"><i>Right Hand, Left Hand</i></a>, by Chris McManus. Afterwards, Toby Mundy, who was publishing the winner, contacted me to discuss the possibility of my working up my synopsis into a full book, which would appear some years later. This led, in turn, to appearances at the <a href="http://martynamos.blogspot.com/2006/08/genesis-machines-publication-event.html">ICA</a>, turns at both Edinburgh Science and <a href="http://www.genomicsnetwork.ac.uk/esrcgenomicsnetwork/events/pastevents/edinburghinternationalbookfestival/title,1080,en.html">Book</a> Festivals, <a href="http://www.thesundaytimes.co.uk/sto/ingear/tech_and_net/article169032.ece">newspaper</a> features, appearances on <a href="http://www.bbc.co.uk/radio4/science/thematerialworld_20061116.shtml">Radio 4</a>, and so on (I was greatly helped in all of this by having an <i>excellent</i> publicist in <a href="http://www.guardian.co.uk/uk/2000/mar/25/3">Annabel Huxley</a>). <br /><br /><b>Message 1</b> is therefore <b>Write, Write, Write!</b>. <i>Accessible</i> articles can really open up your field to outsiders; you can either post them on your blog (where they form a useful ready-made archive of soundbites for interested journalists), or enter them into competitions. Leading writer Ed Yong has <a href="http://www.guardian.co.uk/science/2011/may/13/wellcome-trust-science-writing-prize">described</a> how winning the Wellcome Trust Science Writing Prize kick-started his own career, and the Guardian has a <a href="http://www.guardian.co.uk/science/series/secrets-science-writing">large list</a> of tips for successful writing.<br /><br /><b>Next time</b>: Presenting.Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-90159665300113944912012-02-19T19:43:00.008+00:002012-11-13T12:59:26.934+00:00Warning: (Center for) Advanced Modeling and Optimization, and a plagiarism case.<span style="font-size: 100%;">Since I described the </span><a href="http://martynamos.blogspot.com/2012/02/my-worst-plagiarism-case-yet.html" style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">plagiarism of one of our papers</a><span style="font-size: 100%;">, one of the authors has been in touch to (a) apologize, and (b) confirm his agreement to retract the paper. He's been perfectly helpful, which is more than can be said for the editor of the journal in which the paper appears.</span><br />
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Both the author and myself have contacted him several times, without reply, so I'm now taking the opportunity to name both him and his journal. I do this in the hope that it will discourage potential authors from submitting papers to an operation that publishes plagiarised work and then refuses to even <i>acknowledge</i> the fact, let alone investigate it.</div>
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<a href="http://camo.ici.ro/journal/jamo.htm"><i>Advanced Modeling and Optimization</i></a> is an "electronic international journal" edited by <a href="http://camo.ici.ro/neculai/nandrei.htm">Neculai Andrei</a> of the "<a href="http://camo.ici.ro/">Center for Advanced Modeling and Optimization</a>" in Romania. It's rather obscure, but the fact that its content is freely-available means that papers it "publishes" will often be used in preference to others if authors have no access to better sources (one of the few down-sides of open access publishing).</div>
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As a result, <a href="http://camo.ici.ro/journal/vol6/v6b4.pdf">the paper in question</a>, containing swathes of <i>our work</i>, has attracted a fairly respectable 19 citations, including mentions in papers published in <i>decent</i> journals. </div>
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I would therefore ask you to consider this case before citing the following paper:</div>
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<span style="font-size: 100%;">DNA Simulation of Nand Boolean Circuits. </span><span style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">H. Ahrabian and </span>A. Nowzari-Dalini.</div>
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<i>Advanced Modeling and Optimization</i> <b>6</b>:2, 2004.</div>
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If you're thinking about submitting a paper to <i>Advanced Modeling and Optimization</i> (or even citing a paper in which it appears) I'd also ask you to consider the scientific credibility of the journal, given its lax reviewing and non-existent quality assurance processes.</div>
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<b>EDIT 13/11/12:</b> The paper has (finally) been withdrawn.</div>
Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-5132840702126300532012-02-07T17:16:00.011+00:002012-04-02T17:05:30.902+00:00Big in Iran(With apologies to <a href="http://www.youtube.com/watch?v=c98qdFQF7sw">Alphaville</a>).<div><br /></div><div>After yesterday's post on plagiarism, I didn't think it could get any worse. I was wrong.</div><div><br /></div><div>Another search turned up a<i> second</i> Iranian remix of our (clearly legendary) 1997 paper on DNA-based Boolean circuits. Again, ours is on the left:</div><div><br /></div><div><br /></div><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/plag3.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 187px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/plag3.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5706444480906230402" /></a><br />This version is due to Mahnaz Kadkhoda and Ali A. Poyan, of the University of Birjand and Sharood University of Technology respectively, and it <a href="http://dl.acm.org/citation.cfm?id=1343593.1343711&coll=GUIDE&dl=">appeared</a> in the proceedings of the <i>Second International Conference on Quantum, Nano and Micro Technologies</i> (2008). Notice, once again, the direct copying of sections of text.<div><br /></div><div>I've made the full versions of <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/Docs/CTAG-97009.pdf">our paper</a> and <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/Docs/04455931.pdf">their paper</a> available here, as they serve to illustrate the point made yesterday about a culture of "remixing" existing work, adding a little spin and then releasing it as one's own. Although there are differences between the two papers, they aren't technically significant. In this case, they've simply inverted our scheme, and thus claimed a new method which is "much faster and easier" (it isn't, as it still requires a fairly brutal gel extraction step).</div><div><br /></div><div><b>But there's more.</b></div><div><br /></div><div>By Googling a selected phrase from the original paper, we also find our text embedded in <a href="http://wenku.baidu.com/view/def5783610661ed9ad51f3d9.html">this paper</a>, due to Zoraida, Arock, Ronald and Ponalagusamy, from the National Institute of Technology in India.</div><div><br /></div><div>At this point, I've decided to give up chasing the matter, if only for the sake of my sanity. There are only so many rabbit-holes one can jump down in fruitless pursuit of plagiarists.</div><div><br /></div><div><br /></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-81140757436292252232012-02-06T22:52:00.016+00:002012-04-02T17:05:08.245+00:00My worst plagiarism case yet<div style="text-align: justify;"><span style="text-align: left; ">I've </span><a href="http://martynamos.blogspot.com/2010/11/blatant-plagiarism.html" style="text-align: left; ">written before</a><span style="text-align: left; "> about having our stuff plagiarized. In the past, the cases I've found have </span><span style="text-align: left; ">been generally low-impact, in that the places in which the ripped-off material appeared have been low-</span><span style="text-align: left; ">key (eg. news articles, course materials). When contacted, the miscreants have either ignored me, or apologised. In </span><i style="text-align: left; ">this</i><span style="text-align: left; "> particular case, things got a lot more weird.</span></div><div><br /><div><div>Full (and ironic) disclosure: the sections of the paper that were ripped off were actually written by my co-author, <a href="http://www.csc.liv.ac.uk/~ped/">Paul Dunne</a>.</div><div style="text-align: center;"><br /></div><div>A few years ago (in 2007), while searching for a reference to back up an assertion I'd made about NAND gates, I came across a paper on simulating Boolean circuits using DNA. "Looks familiar", I thought, and a side-by-side comparison shows just <i>how</i> similar it was to a 1997 <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/Docs/CTAG-97009.pdf">paper</a> I wrote with Paul (our paper is on the left):</div></div><div style="text-align: left;"><br /></div><div style="text-align: left;"><br /></div><div><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/plag1.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 192px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/plag1.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5706171132134500930" /></a><br /><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/plag2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 140px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/plag2.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5706171310152920306" /></a><br /><br /></div><div>At the time, I contacted the senior author, who I'll call Dr A, for reasons which will become clear shortly.</div><div><br /></div><div>I received a response from Dr A, saying that there had been a "misinterpretation", and decided not to pursue it any further. However, I recently found myself coming across the paper again after following a different trail of references. According to Google Scholar, it's been cited 18 times in the past four or so years, which is a decent number. That's 18 citations to a paper that borrows large conceptual chunks from our original idea, as well as taking whole sections verbatim. </div><div><br /></div><div>Happily for us, <i>our </i>original paper has been cited many more times than the plagiarized version, but I was rather annoyed to see this bastardised "ghost" version mopping up after it. So, I sent another email to Dr A; this time they sent me a fairly detailed response (on January 31 2012, the date is important), arguing how their method is subtly different to ours. I wasn't entirely happy with this, so I sent them the side-by-side comparison (above). Here's the response I got:</div><div> <p class="p1"><span><b>In the first slide, exactly above the highlighted text, I cited you paper. In second slide, I used some text from your paper in problem definition. The definition of Boolean network was very good in your paper and I used it. I thought, this kind of use is fair, and show the value of the paper (you paper).</b></span></p></div><div>It's true that our paper was cited, but the text was lifted without any form of quotation. Most telling is the explanation along the lines of "I liked it, so I took it."</div><div><br /></div><div>I wasn't particularly happy with this, so I responded</div><div><br /></div><div><b>I am pleased that you recognize that this is a case of plagiarism; I do not accept the "imitation is the sincerest form of flattery" argument.</b></div><div><span><br /></span></div><div>The response I got was quite shocking:</div><div><br /></div><div><span><b>...unfortunately I have cancer and I'm dying and I do not live more than one month.</b></span></div><div><span><b><br /></b></span></div><div>Huh. I responded to say "I'm sorry to hear that", and then left it, but Googled Dr A on a hunch.</div><div><br /></div><div>It turned out that Dr A <i>actually</i> died in November of last year. I'm not naming her here directly, because I have no desire for her to show up in connection to a post about plagiarism when she is in no position to defend herself. Nonetheless, it seemed as if <i>someone</i> was posing as her, and responding to her emails through her official University account.</div><div><br /></div><div>I responded:</div><div> <p class="p1"><b>I don't mean to be disrespectful, but I am sure that you are not Dr A. The reason I say this is that I believe she died at the end of last year. So, please explain who you are, and why you are continuing to use her email address. This is not about plagiarism now, it's more about establishing who I am actually speaking to.</b></p> </div><div>The person then responded, explaining that they were an ex-student of Dr A (let's call him Mr M), and she had given them her email password prior to her death. Whether or not she had given them permission to <i>pose</i> as her is another question entirely.</div><div><br /></div><div>I then pointed out to Mr M that he seemed to know a lot about the paper's contents, given that he was not listed as a co-author. His response:</div><div> <p class="p1"><b>I am a computer programmer. I wrote the programs of Dr. A's papers. For this paper, I wrote the simulation program for testing the algorithm.</b></p></div><div>So, this guy wrote some simulation code (the results of which are described in the paper), but <i>wasn't listed as a co-author</i> (or even acknowledged). He <i>was</i> paid for his services, I established later.</div><div><br /></div><div>This all seemed pretty grubby to me at that stage, so I contacted the <i>other</i> author to explain what had happened. On the surface he was very angry, and told me that he had had Mr M's access to Dr A's email revoked. However, when I suggested to him that the paper should be retracted (as <a href="http://publicationethics.org/files/COPE_plagiarism_discussion_%20doc_26%20Apr%2011.pdf">suggested</a> for non-trivial cases of plagiarism), he fell strangely quiet. </div><div><br /></div><div><b>Edit 9/2/12:</b> He's agreed to retract the paper.</div><div><br /></div><div>The reason that I'm highlighting this right now is that this week I received a paper to review, which came from Dr A's country (Iran). Without giving anything away, the paper contained several plagiarised figures from various sources, and drew <i>far</i> too heavily on a Ph.D. thesis with which I am familiar. I initially tried to dismiss it as coincidence, but then some cursory research into Iran's research culture led me <a href="http://www.timeshighereducation.co.uk/story.asp?storyCode=412811&sectioncode=26">here</a> and <a href="http://www.nature.com/nature/journal/v462/n7275/full/462847a.html">here</a>.</div><div><br /></div><div>I was particularly struck by the observation in the Times Higher article that "People who are under pressure to get publications out sometimes look to research done in another language, add their twist to it and publish it..", which certainly seems to be the case here.</div><div><br /></div><div>I don't feel qualified to comment on the complex political, cultural and social reasons for endemic plagiarism, but I very much doubt that tackling plagiarism is high on the Iranian government's agenda right now.</div><div><br /></div><div><br /></div><div><br /></div><div><br /></div><div><br /></div></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com3tag:blogger.com,1999:blog-10721553.post-70123117085577875332012-01-17T22:38:00.015+00:002012-04-02T13:56:50.127+00:00More press coverage for Pete<a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/pete.jpg"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 245px; height: 320px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/pete.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5698735123495743890" /></a><br />After last week's appearance in the <i>Times Higher</i>, I'm glad to see that Pete's <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028747">research</a> has been picked up by the local press. There's a pretty impressive shot of him in today's <i>Manchester Evening News</i>, accompanied by an article that does a decent enough job of presenting our work. Yakub Qureshi seems to give the impression that we've creating some big new piece of modelling software, when what Pete <i>actually</i> did was to analyse existing evacuation simulations using a novel technique based on information theory. This "mutual information" measure appears to have become conflated with the notion of "<a href="http://pre.aps.org/abstract/PRE/v51/i5/p4282_1">social forces</a>", but I'm glad that the quote in the final paragraph was kept, as it accurately sums up what we did. I gather Pete is greatly enjoying his new status as an official "disaster expert".<br /><br />Unfortunately, though, I appear to have forgotten the cardinal rule: when talking to a journalist, <b>there is no such thing as an "off the cuff" remark</b>. I remember vaguely mentioning the computer game The Sims, as a way of trying to get across the notion of <a href="http://en.wikipedia.org/wiki/Agent-based_model">agent-based modelling</a>. Yakub has enthusiastically run with this idea, and, sure enough, there's a picture of The Sims 2. Why, I'm not sure. I don't <i>think</i> the next version will include smoke modelling or exit awareness profiling, but this has only served to remind me that tiny, inconsequential remarks will suddenly become the <b>entire focus of the article</b>, unless you're very, very careful.<br /><br /><a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/uma.jpeg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 169px; height: 320px;" src="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/images/uma.jpeg" border="0" alt="" id="BLOGGER_PHOTO_ID_5698737859270474690" /></a>Take this example, from the Liverpool <i>Daily Post</i>, April 22, 1998. I'd not long been awarded my Ph.D., which happened to be the first in the field of DNA computing. I was talking to a local reporter, and, while explaining the labelling of the bases making up DNA strands (A, G, C, T), pointed out, in passing, that the name of the film <i><a href="http://www.imdb.com/title/tt0119177/">Gattaca</a></i> (starring Uma Thurman) is a string over this alphabet (and, indeed, will be <a href="http://www.straightdope.com/columns/read/1830/does-the-title-of-the-movie-em-gattaca-em-refer-to-a-dna-sequence">commonly found in the average human genome</a>). When the final piece appeared, describing this complex scientific research, <i>sure enough</i>, there's a picture of... Uma Thurman.Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-70797603261609442722012-01-14T00:18:00.007+00:002012-01-25T16:09:39.014+00:00Weeknote #46<a href="http://2.bp.blogspot.com/-kG4_ZcrD85s/TxDKUjahl7I/AAAAAAAAAYo/GJnrQ9HmvRQ/s1600/crush.jpeg"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 274px; height: 320px;" src="http://2.bp.blogspot.com/-kG4_ZcrD85s/TxDKUjahl7I/AAAAAAAAAYo/GJnrQ9HmvRQ/s320/crush.jpeg" border="0" alt="" id="BLOGGER_PHOTO_ID_5697275983076366258" /></a><br />There's been a bit of a gap since the last weeknote, mainly due to Christmas, followed by the start of term and the usual last-minute rush before a big European Commission funding deadline...<br /><br />The <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028747">crush paper</a> I recently published with Pete and Steve has attracted a certain amount of media attention; the story (see the scan to the right) was used as the centrepiece in the campus roundup section of yesterday's <i>Times Higher Education</i>, and we're expecting local newspaper coverage next week. Apart from the obvious high quality of the science and the significant potential impact of the work ;-) I'm convinced that one of the reasons that the story has been given such prominence is that we published the paper in an <a href="http://en.wikipedia.org/wiki/Open_access">open-access</a> journal. If the paper had been buried away behind a journal paywall, I'm not sure people would have been so keen to cover it, and <i>anyone</i> who sees the story and searches for the work will be able to read it, whether they're affiliated to a University or not (and not be asked for $30 for the privilege, or whatever the going rate is...) Of course, we had to pay $1,350 to have the paper published (<i>not</i> considered for publication...), but we could have applied for a fee waiver had we been unable to find the money (and reviewers/editors don't know the payment status when they consider papers).<br /><br />The proof is in the <a href="http://www.plosone.org/article/metrics/info%3Adoi%2F10.1371%2Fjournal.pone.0028747#usage">access statistics</a>; the paper was published just over three weeks ago, and it's been viewed over 800 times already. It's been <a href="http://www.johndcook.com/blog/2010/06/23/write-only-articles/">argued</a> that the average number of readers for an academic article is about <b>5</b>, so this is clearly an improvement!Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-19429597129365923182011-11-19T16:46:00.003+00:002011-11-19T16:57:06.853+00:00Weeknote #45Quite an eventful week; I was over in Brussels on Tuesday, as one of the two external reviewers of the <a href="http://www.sapere-project.eu/">SAPERE</a> project. Quite apart from hearing about their results, it was quite interesting to see how another project operates in terms of management and so on. While I was away I received the formal notification that our paper on mutual information for crush detection (written with Pete Harding and Steve Gwynne) had been accepted by <i><a href="http://www.plosone.org">PLoS ONE</a></i>.<br /><br />The acceptance couldn't have come at a better time, as Pete had his Ph.D. viva on Wednesday. I'm delighted to report that he passed with minor corrections, so congratulations, Dr Harding!Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-14657118768937911902011-10-25T16:12:00.004+00:002011-11-08T12:22:33.257+00:00Talking TuringI did a few radio interviews last Thursday, ahead of the Turing/Morphogenesis event. Here's a recording of one of them, done with Heather Stott for BBC Radio Manchester. It's worth a listen, if only for the brief, stunned silence when I blurt out "He grew breasts!"<br /> <p><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" width="275" height="55" id="divplaylist"><param name="movie" value="http://www.divshare.com/flash/playlist?myId=16034134-25a" /><embed src="http://www.divshare.com/flash/playlist?myId=16034134-25a" width="275" height="75" name="divplaylist" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer"></embed></object>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com1tag:blogger.com,1999:blog-10721553.post-76302121192042403682011-10-24T08:35:00.009+00:002011-10-24T10:02:24.513+00:00Turing and MorphogenesisYesterday I was privileged to take part in an <a href="http://www.manchesterliteraturefestival.co.uk/events/23rd-october/alan-turing-morphogenesis-jane-rogers">event </a>held as part of the <a href="http://www.manchesterliteraturefestival.co.uk/">Manchester Literature Festival</a>. Many months ago I was invited by Ra Page of <a href="http://www.commapress.co.uk/">Comma Press</a> to suggest "Eureka" moments in science, one of which might act as inspiration for a short story to be written by an established author. One of my suggestions was Alan Turing's theory of <a href="http://en.wikipedia.org/wiki/Morphogenesis">morphogenesis</a>; while this idea has proved to be a "slow burn" rather than a phase transition in science, it marked the beginning of a new mathematical and <i>computational</i> era in biology. I was delighted that <a href="http://www.janerogers.org/">Jane Rogers</a> picked up the idea, and she produced a marvellous story for the <i><a href="http://www.commapress.co.uk/?section=books&page=Litmus">Litmus</a></i> collection (<a href="http://www.independent.co.uk/arts-entertainment/books/reviews/free-radicals-the-secret-anarchy-of-science-by-michael-brooksbrlitmus-short-stories-from-modern-science-edited-by-ra-page-2331766.html"><i>Independent</i> review</a>). I supplied a short afterword to the story as part of the collection, which formed the basis for my notes for yesterday's event.<div><br /></div><div>It was an absolute pleasure to work with Jane; we met only once before the story was written, but she produced a wonderfully humane depiction of Turing, as well as an accurate rendition of the science. It was great to meet up with her again yesterday; I'm sure the past few months were a bit of a blur for Jane after she was long-listed for this year's <a href="http://www.themanbookerprize.com/perspective/articles/1516">Man Booker Prize</a>.</div><div><br /></div><div>The event was held at the <a href="http://www.madlab.org.uk/">MadLab,</a> which I know well from our partnership on the <a href="http://diybio.madlab.org.uk/">Manchester DIYbio</a> project. Although there were only 40 or 50 seats available, we sold out, which made for a nice atmosphere. Craig Pay took some photos, which are <a href="http://www.facebook.com/media/set/?set=a.293443774016365.86006.100000522333039&type=1&l=c2c4bfddc2">available here</a>.</div><div><br /></div><div>Jane read an edited (for length) version of her story, and then I offered a brief commentary, before Ra asked some questions and then opened up the discussion to the floor. Ra was kind enough to pre-warn us of the questions, so I made some notes (below) ahead of time (of course, I ended up <i>ad-lib</i>bing quite a lot, but I wanted to ensure that I didn't miss out any important details).</div><div> <p class="p1"><span class="s1"><b>Martyn: Do you think the myth&mystery that surrounds Turing's life (and death) has helped or hindered his legacy as a scientist?</b></span></p><p class="p1">I think Turing’s legacy is clear and unambiguous from a scientific perspective; he’s rightfully acknowledged as one of the fathers of computer science. Every time we use anything with a processor chip in it we owe a debt of gratitude to Turing for his foundational work. Leads onto the more general issue of what we, as a society, owe him, and I think he’s been incredibly badly-served in terms of his general legacy. I think this is partly to do with institutional/societal squeamishness about his sexuality and the way in which he was treated as a result of it, although Gordon Brown did <a href="http://news.bbc.co.uk/1/hi/8249792.stm">make some steps</a> a few years ago to begin to address this. Hopefully the <a href="http://www.mathcomp.leeds.ac.uk/turing2012/">2012 Centenary</a> celebrations will help to address this. I also believe that Leonardo di Caprio is <a href="http://www.guardian.co.uk/film/2011/oct/12/leonardo-dicaprio-codebreaker-alan-turing">rumoured</a> to play Turing in a forthcoming biopic, so we'll wait and see what effect that might have...</p> <p class="p2"><b>Martyn: When you say the morphogenesis theory has only recently been corroborated, could you explain how it has exactly, and why has it taken so long? </b><span class="s1"></span></p><p class="p1">At first, his work was largely ignored by experimentalists, because they thought that it relied on a number of unproven hypotheses. Very soon, though, the existence of “natural Turing patterns” was demonstrated by Belousov and Zhabotinsky (<a href="http://en.wikipedia.org/wiki/Belousov%E2%80%93Zhabotinsky_reaction">B-Z reaction</a>), who showed that one could obtain a number of patterns (spots, spirals, rings, etc.) in a dish simply by mixing several chemicals. Again, though, its sceptical response led to Belousov effectively resigning his commission from science. Only recently has work in fish, chicks and mice lent experimental support to Turing’s idea, but the real contribution was to show how order can arise <i>spontaneously</i> from disorder. It gave us a whole new way of looking at natural systems.</p> <p class="p1"><span class="s1"><b>Martyn: Carrying on from this, how typical or atypical is Turing as a figure/personality in the many wider fields he influenced (computer science/AI, chaos theory & synthetic biology)?</b></span></p><p class="p1">I think that we are lucky if we get one Turing in every generation. If there exist common features between some of the leading figures in my field and Turing, it’s the fact that they <i>connect</i>. <a href="http://en.wikipedia.org/wiki/Leonard_Adleman">Len Adleman</a>, who founded my own field of molecular computing, is a leading mathematician (he received a share of the <a href="http://en.wikipedia.org/wiki/ACM_Turing_Award">Turing Award</a> for his co-invention of the <a href="http://en.wikipedia.org/wiki/RSA">RSA</a> encryption scheme) came up with the idea for <a href="http://en.wikipedia.org/wiki/DNA_computing">DNA-based algorithms</a> while reading James Watson's <i>The Molecular Biology of the Gene</i>. Erik Winfree's father was <a href="http://en.wikipedia.org/wiki/Arthur_Winfree">Art Winfree</a>, another pioneer of computational biology. They are the only father and son team to hold<a href="http://en.wikipedia.org/wiki/MacArthur_Fellows_Program"> MacArthur</a> "genius grants", and <a href="http://en.wikipedia.org/wiki/Erik_Winfree">Erik</a> now looks at computational properties of biochemical systems.</p> <p class="p1"><span class="s1"><b>Martyn: Is this a common feature in the biographies of great scientific pioneers - the need for a counter-argument, a listener, a foil, or an adversary - whether real or imaginary?</b></span></p> <p class="p1"><span class="s1">I think what readers of biographies or popular science have in common with those of fiction is the need for a good narrative. Quite often popular science tries to present the work outside of its human context, which I think is a mistake. </span></p> <p class="p2">Other characters or institutions can serve to bring out the human characteristics, frailties, etc. of scientists. <a href="http://en.wikipedia.org/wiki/Richard_Feynman">Richard Feynman</a> is often portrayed as a robust character, but his heartbreaking <a href="http://discardedlies.com/entry/?52984_">letter to his dead wife</a> shows a tenderness that we don’t get from pictures of him <a href="http://server.physics.miami.edu/~curtright/FEYNMAN63.GIF">playing the bongos</a>.<span class="s1"></span></p> <p class="p1"><span class="s1">People also love a <i>race </i>- it gives a story a natural energy and drive. Rivalries or counter-arguments also serve to shed light onto the scientific process itself - not just the investigation, but the <i>politics</i> and <i>history</i> of it (eg. Watson and Crick versus <a href="http://en.wikipedia.org/wiki/Rosalind_Franklin">Rosalind Franklin</a>).</span></p></div><div><br /></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-73240396718213511582011-09-21T19:54:00.002+00:002011-09-21T20:42:43.547+00:00Weeknote #44I can't quite believe that the summer has gone, and that we're about to launch into another term. The first year students are already here, and I spoke to them today about the importance of research, not just to academics, but to the University as a whole (and, of course, to them, as students and members of that community). I talked about some of the work we've been doing on swarm intelligence, and pointed out that much of that stuff has originated in student projects. I cited Matthew, my Ph.D. student, as an excellent representative of the "grow your own" ethos we're trying to develop at MMU; his SimZombie project led to Ph.D. studies, and he's now developing that work in parallel with his "proper" research. If anyone's interested, I've made my slides available <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/OUT/induction.pdf">here</a> (warning: 15Mb PDF).<div><br /></div><div>We had a research away day last week, and I also attended a meeting in London to hear about the panel-specific aspects of the forthcoming <a href="http://www.ref.ac.uk">Research Excellence Framework</a>. An unexpected bonus was the chance to chat to my old mate <a href="http://www.macs.hw.ac.uk/~dwcorne/">Dave Corne</a>, with whom I used to work at Exeter.</div><div><br /></div><div>One of the important points to come out of our internal REF workshop was the need to increase the visibility of our publications, both past and present. With that in mind, I've slightly revamped my own <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/papers.html">publications page</a>. When I was a Ph.D. student, one of the most soul-sapping aspects of writing was the construction of the bibliography, so I've added <a href="http://www.bibtex.org/">BibTeX </a>entries for the majority of my papers and books. I've also managed to dig out PDF versions of several publications I thought I'd lost for ever.</div><div><br /><div><br /></div><div><br /></div></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-37892453303865052042011-09-13T09:46:00.003+00:002011-09-13T10:04:50.639+00:00Weeknote #43Last week Naomi and I travelled down to Bristol for a network meeting of the <a href="http://www.epsrc.ac.uk">EPSRC </a>Bridging the Gaps projects. Our <a href="http://www.nanoinfobio.org">NanoInfoBio</a> project has now technically finished, although we do have £50K of continuation funding to take us into 2012. We were hosted by the <a href="http://www.uwe.ac.uk/research/heat/">University of the West of England BTG project</a>, and the meeting went very well. Several projects offered a single slide on "The Good, the Bad and the Beautiful", and ours were as follows: <div><br /></div><div><b>Good:</b> The use of seed-corn funding (eg. £5K) to nurture ideas from initial "blue sky" sessions, through to prototyping and then subsequent large funding.</div><div><br /></div><div><b>Bad:</b> Nobody came to coffee. We had real trouble getting people to socialise and mix on an informal basis. Several projects reported similar problems with both real and virtual interactions.</div><div><br /></div><div><b>Beautiful:</b> The realisation of one of our stated aims, which was to "grown our own" researchers. We are now seeing MMU undergrads working on NIB-supported Ph.D. projects, and they will hopefully stay on to become valued members of staff, and help to train a next generation of inter-disciplinary researchers.</div><div><br /></div><div>It was an inspiring meeting, and it helped me to realise just how much we've accomplished with the project in two short years. The real challenge now is to embed the lessons we've learned into institutional thinking, and the targeted continuation funding will make a significant impact on research activities ahead of the <a href="http://www.hefce.ac.uk/research/ref/">REF</a> in 2014.</div><div><br /></div><div>On a personal level, it was also a pleasure to catch up with <a href="http://www.dcs.kcl.ac.uk/staff/mml/">Mike Luck</a>, who's now Head of Department at King's College London (a post recently held by my Ph.D. supervisor, Alan Gibbons, until his retirement). I first met Mike as a potential Ph.D. student, when he was showing around applicants at University College London. When I eventually fetched up at the University of Warwick, Mike had, by then, taken an academic post there, and remembered me from the tour. He does great work on multi-agent systems, and I'm pleased to see him doing so well.</div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-35704402802421826032011-09-03T10:53:00.003+00:002011-09-03T11:05:07.284+00:00Speakers for SchoolsI'm pleased to be able to participate in a new initiative to get volunteer speakers into schools, to share their knowledge, experience and advice. <a href="http://www.speakers4schools.org/">Speakers for Schools</a> (which will formally launch next month) was founded by Robert Peston (BBC Business Editor), and enjoys the support of people such as Jon Snow, Jeremy Paxman, Alastair Campbell, Yvette Cooper, Martha Lane Fox, Lauren Laverne and Martin Rees.<div>
<br /></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-15231895032201107952011-09-03T10:43:00.001+00:002011-09-03T10:46:15.860+00:00Call for papers on "Biological and Chemical IT"<div><i><a href="http://www.elsevier.com/wps/find/journaldescription.cws_home/506017/description#description">BioSystems</a></i> invites manuscripts for a special issue dedicated to </div><div>“Biological and Chemical Information Technologies”.</div><div>
<br /></div><div>Following the COBRA <a href="http://www.cobra-project.eu/biochemit2011.html">Workhop on Biological and Chemical </a></div><div><a href="http://www.cobra-project.eu/biochemit2011.html">Information Technologies</a> (BioChemIT), held at the European </div><div>Conference for Artificial Life, Paris, August 8th 2011, the organizers </div><div>invite members of the community to contribute to a collection of </div><div>papers dedicated to this growing area of research.</div><div>
<br /></div><div>Topics include (but are not limited to): </div><div>
<br /></div><div>Biological/chemical information technologies; molecular and </div><div>chemical computing; protocells and synthetic cells; molecular </div><div>robots; integration of information processing with (bio-)chemical </div><div>production; nano-bio-info interface; cellular engineering, artificial </div><div>neurons; programmable information chemistry; unconventional </div><div>computing substrates; synthetic biology; computational and </div><div>mathematical studies.</div><div>
<br /></div><div>For more information, see the full <a href="http://www.cobra-project.eu/public/biosystems_cfp.pdf">call for papers</a>.</div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-45064011555531123842011-08-19T22:06:00.010+00:002011-08-19T23:08:45.885+00:00Weeknote #42Much to report; the <a href="http://www.ecal11.org/">European Conference on Artificial Life</a> was held in Paris at the start of the month. Our <a href="http://www.cobra-project.eu/">COBRA</a> project organized a <a href="http://www.cobra-project.eu/biochemit2011.html">satellite workshop</a> the day before the main conference, which went very well. Our meeting covered the broad area of "biological and chemical IT", and topics included synthetic biology, artificial cells and robotics. A special issue of the journal <i>BioSystems</i> will be edited around the themes of the meeting, with an open call for papers to be issued shortly.<div>
<br /></div><div>We're fortunate enough to have one of the artificial life <a href="http://www.ecal11.org/pioneers/">pioneers</a> (<a href="http://www.santafe.edu/about/people/profile/Steen%20Rasmussen">Steen Rasmussen</a>) as a COBRA collaborator (another pioneer, <a href="http://www.ecltech.org/ecltech_j/index.php/research/people/21-people/23-npackard.html">Norman Packard</a>, is also involved via the <a href="http://www.ecltech.org/ecltech_j/">European Center for Living Technology</a> in Venice) , and their panel discussion was entertaining and thought-provoking. Steen has blogged about this (and the wider conference) <a href="http://steennewmexico.wordpress.com/author/steennewmexico/">here</a>.<div>
<br /></div><div>Our Ph.D. students Matthew Crossley and Henry Dorrian recently attended the <a href="http://www.multidisciplinary.soton.ac.uk/events/2011/08/sccs-11-winchester-student-conference-complexity/">Student Conference on Complexity Sciences</a> in Winchester, which sounds like <i>exactly</i> the sort of thing I wish had been around when I was a student (I did attend the Santa Fe Institute complex systems summer school in 1995, but that was for a whole <i>month</i>). Anyway, Henry presented a poster, and Matthew gave a talk, both of which were very well-received. Indeed, Matthew reported that one of the invited speakers, <a href="http://en.wikipedia.org/wiki/Robert_May,_Baron_May_of_Oxford">Robert May</a> (AKA The Lord May of Oxford, former President of the Royal Society and Chief Scientific Advisor to the government, among his many roles) had quietly taken him to one side to offer particular praise and encouragement for his work on <a href="http://www.springerlink.com/content/8j683687141144l0/">agent-based models of epidemiology</a>, and how they might be used in public engagement/education activities. To say that Matthew was "chuffed" might be a slight under-statement...</div></div><div>
<br /></div><div>We were delighted by a <a href="http://webcache.googleusercontent.com/search?q=cache:3xnb6PSxGmYJ:www.independent.co.uk/arts-entertainment/books/reviews/free-radicals-the-secret-anarchy-of-science-by-michael-brooksbrlitmus-short-stories-from-modern-science-edited-by-ra-page-2331766.html+%22These+days+science+is+either+nothing+or+it's+the+new+religion%22&cd=4&hl=en&ct=clnk&gl=uk&source=www.google.co.uk">recent review of Litmus</a>, which appeared in the <i>Independent </i>a couple of weeks ago. <a href="http://www.pforbes.org/">Peter Forbes</a> (I'm an admirer of his book <i>The Gecko's Foot</i>) describes the collection as "...not a test but an open sesame into some of science's most intriguing passages." I was also pleased to see that the morphogenesis story written by <a href="http://www.janerogers.org/">Jane Rogers</a> (for which I acted as scientific consultant and wrote the afterword) attracted particular attention in the review. Jane's just been long-listed for the <a href="http://www.themanbookerprize.com/perspective/articles/1516">2011 Man Booker Prize</a>, so well done and good luck to her! <i>Litmus</i> is <a href="http://www.commapress.co.uk/?section=books&page=Litmus">available to buy here</a>, and now might also be a good time to plug an event Jane and I are doing in October, jointly with the Manchester Science and Literature Festivals (details to right).</div><div>
<br /></div><div>Finally, as I was typing this note I got an email from Springer to tell me that the journal version of our paper on using genetic algorithms to solve the Zen Puzzle Garden game has now <a href="http://www.springerlink.com/content/v136033315u374w4/">appeared in print</a> in the journal <i>Natural Computing</i>. I'm particularly pleased about this paper, not because it's hugely ground-breaking, but because it originated from an undergraduate student project.</div><div>
<br /></div><div>Although Paris was half-and-half work and pleasure (I was accompanied by my wife, while our daughter stayed with her grand-parents in Northumberland), next week <i>really is</i> a holiday (visiting family in Suffolk). That means IMAP server passwords deleted from my phone, no tweeting, <i>the lot</i>. I'm sure it will do me good.</div><div>
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<br /></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-39538092717358783832011-07-18T10:13:00.006+00:002011-08-25T11:34:26.614+00:00Weeknote #41A couple of meetings to report on this week; last Wednesday the <a href="http://www.nanoinfobio.org/">NanoInfoBio</a> board met to discuss progress. Although the project is due to finish next month, we were recently granted an additional £50K of funding by the <a href="http://www.epsrc.ac.uk/">EPSRC</a>, which will allow us to extend it into 2012.<span class="Apple-style-span"> </span>As I said in an email to the EPSRC this morning, the project really has had a disproportionately positive effect on the Faculty and the University, and the next challenge is to see how we can retain our momentum after the formal funding finishes.<div>
<br /></div><div>The other meeting of interest was held at the <a href="http://www.madlab.org.uk/">MadLab</a> on Thursday, where the <a href="http://diybio.madlab.org.uk/">DIYbio</a> organizing team got together to plan our next set of activities. The "big event" will be a DIYbio summit on October 29-30, to be held as part of the 2011 <a href="http://www.manchestersciencefestival.com/">Manchester Science Festival</a>. More details to follow. </div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-45307244161041621482011-07-12T12:06:00.005+00:002011-07-12T12:27:31.463+00:00Weeknote #40<a href="http://4.bp.blogspot.com/-DBhqGUn3I_4/Thw5ph83HBI/AAAAAAAAAWU/hbPpcGGCXPg/s1600/2011-07-07%2B10.02.59.jpg" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 240px; height: 320px;" src="http://4.bp.blogspot.com/-DBhqGUn3I_4/Thw5ph83HBI/AAAAAAAAAWU/hbPpcGGCXPg/s320/2011-07-07%2B10.02.59.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5628437019957337106" /></a>To Berlin, for the latest general meeting of the <a href="http://www.bactocom.eu/">BACTOCOM</a> project. I'd never actually visited the city before, which came as a bit of a surprise, so I was glad that we had time to take a walking tour on Thursday morning, before the work began. I took some photos, which are available <a href="http://www.facebook.com/media/set/?set=a.10150367984862907.439993.656772906&l=36f386a9af">here</a>. We got lots done (drafting our response to the first year review from the European Commission, and kicking ideas around for a follow-on project), before Nils and Ilka (and their <i>numerous</i> students!) put on a great BBQ. On Friday we put in a few more hours before breaking for lunch, followed by a seminar and then a visit to the adjacent <a href="http://www.naturkundemuseum-berlin.de/en.html">Natural History Museum</a> (the highlights being the <a href="http://www.naturkundemuseum-berlin.de/en/presse/hintergrundinfos/brachiosaurus.html">World's Tallest Dinosaur Skeleton</a> (officially), and the slightly creepy but strangely compelling storage room, with thousands of specimens held in glass jars). Friday was rounded off with dinner in the <a href="http://www.guardian.co.uk/travel/2008/oct/11/berlin-germany">Schlesisches Tor</a> district. I also got to chat (briefly) with <a href="https://twitter.com/#!/li5a">li5a</a> about <a href="http://diybio.madlab.org.uk">DIYbio</a>, so hopefully that will lead to a future link-up. All in all, a great meeting and visit.Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-9560009523472616072011-06-28T21:37:00.008+00:002011-06-28T22:27:35.949+00:00Shady publishingI was recently asked, by an anonymous individual, for my opinion on an unsolicited email that contained an offer to publish their thesis. To a young academic this might sound like an attractive proposition (more so in the arts and humanities than in the sciences, where journal articles still rule) - log a quick publication, get on Amazon and maybe even make some money.<br /><br />However, if we dig a little beneath the surface we quickly uncover some pretty cynical practices. Others have documented in detail the shady nature of these companies (see <a href="http://accrispin.blogspot.com/2009/09/victoria-strauss-vdm-verlag-dr-mueller.html">here</a>, <a href="http://ask.metafilter.com/67149/What-kind-of-unsolicited-publishing-query-is-this">here</a> and <a href="http://www.writingnetwork.edu.au/content/email-lap-offering-publish-my-masters-thesis">here</a>); suffice to say, the overwhelming advice is <b>Don't Do It</b>.<br /><br />I thought I'd do my own research on the specific company that approached my colleague; LAP Publishing. Although several people have already commented at length on the various problems with their approach, and how these should all serve as significant red flags (see the last link above), perhaps the most damning evidence I found came from <b>their own website</b>.<br /><br />I visited their <a href="https://www.lap-publishing.com/">main website</a>, and soon saw a page of <a href="https://www.lap-publishing.com/site/author-comments/38">author comments</a>. I'm absolutely sure that these are all <i>completely genuine</i>, and not at all fabricated; after all, who could <i>make up</i> a book with a title such as "RETURNS TO EDUCATIONAL INVESTMENTS IN A TRANSITIONAL ECONOMY: AN INVESTIGATION OF KAZAKHSTAN’S LABOR MARKET IN 2005"? It's even <a href="http://www.amazon.com/RETURNS-EDUCATIONAL-INVESTMENTS-TRANSITIONAL-ECONOMY/dp/3838300572/ref=sr_1_1?ie=UTF8&qid=1309297705&sr=8-1">available on Amazon</a>, although I'd advise you to turn off 1-Click Ordering before taking a look - you might not be able to stop yourself.<br /><br />The best bit about this page, though, is the testimonials from the <i>authors themselves</i>:<br /><br /><span class="Apple-style-span">"My experience with Lap Lambert Academic Publishing has been an experience I will never forget."</span><br /><br />Well, that one could go one of two ways.<br /><br /><span class="Apple-style-span">"Their superb customer service and support of me was the first point I noticed in my first communication with company."</span><br /><br />Hmm, not sure about the grammar there, but we'll persevere.<br /><br /><span class="Apple-style-span">"Within three short months, with their assistance I have now published six books..."</span><br /><br />A book every <b>two weeks</b>!<br /><br />Ok, so this getting a little suspect. No serious publisher would <i>ever</i> use such mangled English in their testimonials (or, indeed, actually <i>need</i> such things from their authors), or imply that, through them, you can knock out books at a rate that would make even <a href="http://en.wikipedia.org/wiki/Barbara_Cartland">Barbara Cartland</a> question her commitment.<br /><br /><div>This isn't a post to say "let's laugh at the foreigners and their bad use of English". It's simply a comment on an absence of editorial standards that is so complete as to let these unedited "testimonials" go live on the company's own website.</div><div><br /><div>These last two really are the final nails in the coffin:<br /><br /><span class="Apple-style-span">"I must tell you that your contribution of publishing this book is very helpfulness and valuable for globalization of Ergonomics/Human Factors. […] I am appreciated of your contributions and also your kindly support and assist."<br /><br />"This was very convenient process, because personal and printed advise were so excellent!"</span><br /><br />Case closed.</div></div>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-35141001634190080462011-06-27T19:08:00.006+00:002011-06-27T21:42:09.409+00:00Public Service AnnouncementNote to dimwit colleagues: "Reply" != "Reply all", which is especially important when the original email was stupidly sent, <i>individually</i>, to <b>every single member of staff in the University</b>.<br /><br />I just got a message that said, in its entirety, <br /><br />"Ditto.", <br /><br />and which was sent to <b>1,591</b> people. It's like we've travelled back in time to 1995, when people were "still getting the hang of email".<br /><br />Unfortunately, the original error seems to be propagating, as more and more people weigh in (the first message was from University management, warning us of the implications of taking strike action).Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-15568000443318108012011-06-20T21:12:00.003+00:002011-06-20T21:32:11.074+00:00Weeknote #39Two weeks since the last weeknote, not <i>too</i> bad...<br /><br />Angel and I have had the journal version of our population-based oscillator paper accepted by <i>BioSystems</i>; you can find a preprint version <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/Docs/oscill_biosystems.pdf">here</a>.<br /><br />Two new members have joined the Novel Computation Group; Jon Parkinson is an undergraduate who'll be working over the summer on ant colony optimisation, and Paul Robson is an M.Sc. student working on predation/avoidance strategies, using Matthew's SimZombie package.<br /><br />This week we have an open day, followed by a <i>day</i> of Moodle training (...), followed by another day of professional development review training. <br /><br />Naomi, Lindsey and myself popped over to Sheffield Hallam last week to talk at their <a href="http://research.shu.ac.uk/engineering-for-life/events.html">Research Cafe</a>. SHU and MMU were both successful in the same round of <a href="http://www.epsrc.ac.uk/about/progs/cdi/priorityareas/Pages/bridgingthegap.aspx">Bridging the Gaps</a> funding from the EPSRC, and their <a href="http://research.shu.ac.uk/engineering-for-life/index.html">Engineering for Life</a> network shares similar features with our own <a href="http://www.nanoinfobio.org">NanoInfoBio</a> project.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/-b5dMdKgqBRk/Tf-6Q5Rb-gI/AAAAAAAAAVA/Ttm01M5HbVQ/s1600/2011-06-19%2B16.32.20.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 240px; height: 320px;" src="http://4.bp.blogspot.com/-b5dMdKgqBRk/Tf-6Q5Rb-gI/AAAAAAAAAVA/Ttm01M5HbVQ/s320/2011-06-19%2B16.32.20.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5620415659396299266" /></a><br />We managed to get over to Derbyshire at the weekend, for a fourth birthday party (and sneaky fathers' day celebration). Alice had a good go at the dino-pinata.Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-20957990905612178422011-06-06T22:15:00.006+00:002011-06-06T22:40:53.659+00:00Weeknote #38<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/-28oF84UI9yQ/Te1SCFX4evI/AAAAAAAAAU4/E7DkIBCXxyA/s1600/2011-06-03%2B13.07.32.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 240px; height: 320px;" src="http://4.bp.blogspot.com/-28oF84UI9yQ/Te1SCFX4evI/AAAAAAAAAU4/E7DkIBCXxyA/s320/2011-06-03%2B13.07.32.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5615234506156440306" /></a>Saturday saw us fly back from a week in Madrid, where I'd been on <a href="http://www.bactocom.eu">BACTOCOM</a> business. I was there to talk to Alfonso, our computational collaborator, and to give a series of lectures on molecular computing and synthetic biology to the M.Sc. and Ph.D. students. I've made the slides available <a href="http://www2.docm.mmu.ac.uk/STAFF/M.Amos/Docs/UPMslides.zip">here</a> (3.8Mb download).<br /><br />I had a day off on Friday, so we took Alice to the Museo Reina Sofia, which I always try to visit when in Madrid. I discovered the artist <a href="http://www.lygiapape.org.br/">Lygia Pape</a>, and was absolutely transfixed by her <a href="http://premierartscene.com/magazine/biennale-arsenale/">Tteia installation</a> (although I think I might have ruined the moment by making a joke about tripping up and being sliced like a boiled egg...) Her early (1950s) "Draws" geometric work also greatly appealed to me, but I can find little of it online. <br /><br />Last week saw the publication of an interesting paper by Erik Winfree and Lulu Qian, on evaluating Boolean circuits using DNA. I was asked for comment by both <i>Nature</i> and <i>New Scientist</i>, and my post covering this is below (or <a href="http://martynamos.blogspot.com/2011/06/chemical-computation.html">here</a>).<br /><br />We (ie. the <a href="http://www.cobra-project.eu">COBRA</a> project board) managed to submit our paper for the <a href="http://www.fet11.eu">FET11</a> proceedings, <i>just</i> ahead of the deadline (not helped by some last-minute wobbles caused by dodgy version control - mainly my fault).<br /><br />This week is dominated by prelim. exam boards, although we do have a meeting of the <a href="http://diybio.madlab.org.uk">DIYbio</a> team tomorrow, and I'm seeing a new M.Sc. student (agent-based modelling) and summer intern to chat about their projects. Next week I'll be over at Sheffield Hallam to talk to their Bridging the Gaps project, doing my bit as an external examiner, and attending <i>final</i> exam boards.<br /><br /><a href="http://twitter.com/share" class="twitter-share-button" data-text="Weeknote 38" data-count="none" data-via="martynamos">Tweet</a><script type="text/javascript" src="http://platform.twitter.com/widgets.js"></script>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-39949319928243764282011-06-04T23:51:00.010+00:002011-06-06T13:41:53.610+00:00Chemical computationLulu Qian and Erik Winfree's <a href="http://www.sciencemag.org/content/332/6034/1196.abstract">recent paper</a> on simulating Boolean circuits using DNA has attracted quite a lot of <a href="http://www.bbc.co.uk/news/science-environment-13626583">attention</a>. I was asked by both <i>Nature</i> and <i>New Scientist</i> to offer comments on their work, which I happily did (<a href="http://www.nature.com/news/2011/110602/full/news.2011.343.html">here</a> and <a href="http://www.newscientist.com/article/dn20539-seesaw-logic-gates-make-dna-computing-easier.html">here</a>). <br /><br />While the <i>New Scientist</i> quote is clearly taken directly from an early-morning Skype conversation, the <i>Nature</i> story (understandably) used only a small snippet of my "take". In the context of the article, it <i>could</i> appear that I was being overly-negative about what is actually a remarkable piece of work. For the record, here's the entire text that I sent the author of the piece, with the bit that was actually <i>used</i> highlighted in <b>bold</b>:<br /><br />"This is an important development in the search for truly 'hands free' molecular computing. The paper describes a real fusion of computing and the life sciences, which moves us one step closer towards programmable information chemistry. As the authors themselves acknowledge, scaling up their approach might be difficult, but they've described one possible path for its future development, through physical localization of elements. As John Reif points out in the commentary, <b>the biggest challenge will be to get this type of construction to work inside living cells</b>, where it might find a number of applications in sensing and control."<br /><br /><a href="http://twitter.com/share" class="twitter-share-button" data-text="My take on DNA logic gates @ScienceMag" data-count="none" data-via="martynamos">Tweet</a><script type="text/javascript" src="http://platform.twitter.com/widgets.js"></script>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com0tag:blogger.com,1999:blog-10721553.post-86388978481942915052011-05-25T13:38:00.004+00:002011-05-25T18:05:52.237+00:00Who says Universities aren't forward thinking?Our local hospitality operation has recently put in place an automated booking system, which allows grant holders to request and approve catering for meetings, etc. This is great, as it avoids (in principle) orders going missing, and so far it seems to have worked well.<br /><br />Each request is assigned a "ticket number", and I noticed that the system designers appear to have learned the lessons of the <a href="http://en.wikipedia.org/wiki/Year_2000_problem">Millennium Bug</a>, and allowed plenty of room for new requests. The order I approved today, for example, is request number<br /><br /><b>REQ000000000721</b><br /><br />which, assuming there were 720 previous requests since the system began, allows for 1,000,000,000,000 unique requests (that's a <i>trillion</i>).<br /><br />Even if we assume a <i>million</i> requests a day, 365 days a year, we've still got over 2,700 years before the system runs out of space. <br /><br /><small>By which time we might have introduced some variety into the menu.</small>Martyn Amoshttp://www.blogger.com/profile/07492865372027822011noreply@blogger.com1