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	<title>InkSpot. Science. On Demand</title>
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	<link>http://www.inkspotscience.com/blog</link>
	<description>Collaboration between scientists, in any field, anywhere.</description>
	<pubDate>Wed, 10 Feb 2010 07:54:49 +0000</pubDate>
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	<language>en</language>
			<item>
		<title>Selling Coals to Newcastle</title>
		<link>http://www.inkspotscience.com/blog/index.php/2010/02/10/selling-coals-to-newcastle/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2010/02/10/selling-coals-to-newcastle/#comments</comments>
		<pubDate>Wed, 10 Feb 2010 07:38:54 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[business]]></category>

		<category><![CDATA[drug discovery]]></category>

		<category><![CDATA[outsourcing]]></category>

		<category><![CDATA[peakdale]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=32</guid>
		<description><![CDATA[Bigup to Peakdale Molecular for their recently announced deal with Pfizer to supply 50 chemists, working in Pfizer labs, in Kent.  Well they&#8217;re not selling coal, and Sandwich is about as far from Newcastle as you can get and still be in England, but you know what I mean.
So what does this mean for [...]]]></description>
			<content:encoded><![CDATA[<p>Bigup to <a href="http://www.peakdale.co.uk/">Peakdale Molecular</a> for their recently announced <a href="http://www.earthtimes.org/articles/show/peakdale-molecular-limited-announces-innovative,1143958.shtml">deal with Pfizer</a> to supply 50 chemists, working in Pfizer labs, in Kent.  Well they&#8217;re not selling coal, and Sandwich is about as far from Newcastle as you can get and still be in England, but you know what I mean.</p>
<p>So what does this mean for the industry in the UK, if anything. Well firstly it means no let up in the trend by big Pharma to back out of doing their own research. In fact this is one of three pieces of news that seem to mark an acceleration of what started a number of years ago. The others being AstraZeneca <a href="http://www.astrazeneca.com/_mshost3690701/content/resources/media/investors/AZN-Q4-2008/q4-results-2008-narrative.pdf">announcing</a> that they are going to lay off 1 in 9 staff. At the same time they have frozen the pensions, which is a sign that they are not going to want to cushion the redundancies any more. In the cuts last year, the pay-offs were so generous, when asked for volunteers, one third of Cancer Research put up their hands to go. <a href="http://industry.bnet.com/pharma/1000360/glaxosmithkline-employees-fume-over-latest-round-of-layoffs/">GSK also</a> are in the same mood for layoffs causing consternation and bemusement for <a href="http://pipeline.corante.com/archives/2010/02/04/gsk_day.php">many employees</a>.</p>
<p>It seems that they are all are heading for the outsourcing door, located in China and India where chemistry is cheap. So what is Pfizer doing with Peakdale? And how come Peakdale still survive as a specialist small molecule organic chemistry company based in the UK? There is one answer: expertise and trust. No there are two answers: expertise, trust and &#8230;<br />
<span id="more-32"></span></p>
<p>Maybe Tony Brown will tell us why? I can only guess that it is that Pfizer want to get the costs off their books, but are nervous about reducing their research to the point where they are totally reliable on producers overseas, especially when there remain major concerns about quality and IP protection. How many of the 50 staff then are Pfizer chemists that will be laid off and re-hired by Peakdale, cushioned by a golden bridge to profitability for several years? Whatever the reasons, it is better news from Pfizer than from AZ and GSK (but they were always the clever ones) and suggests that at least one company has management prepared to think beyond &#8220;cheaper is better&#8221;. It is only better if you are hiring people that really understand what they are doing and who you can trust to deliver. Good luck to both Peakdale in their new partnership. It shows that there is at least one alternative to &#8220;slash and burn&#8221; in restructuring the industry.</p>
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		<title>Open QSAR</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/11/09/open-qsar/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/11/09/open-qsar/#comments</comments>
		<pubDate>Mon, 09 Nov 2009 19:42:18 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<category><![CDATA[biologics]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=29</guid>
		<description><![CDATA[Open QSAR is a new site for the development and assessment of comparative QSAR modelling methodology (meta QSAR) as well being available for QSAR model building and multi-property prediction. The site uses an automated QSAR building and prediction software system that has been developed over the last few years and which is known as the [...]]]></description>
			<content:encoded><![CDATA[<p><a href="http://www.openqsar.com">Open QSAR</a> is a new site for the development and assessment of comparative <a href="http://en.wikipedia.org/wiki/Quantitative_structure-activity_relationship">QSAR</a> modelling methodology (<a href="http://www.slideshare.net/DavidLeahy/meta-qsar">meta QSAR</a>) as well being available for QSAR model building and multi-property prediction. The site uses an automated QSAR building and prediction software system that has been developed over the last few years and which is known as the <a href="http://www.discoverybus.com">Discovery Bus</a>.</p>
<p>At this stage the site displays 15,000 QSAR models as well as validation data for around 100 properties extracted from the WOMBAT database of Prof. Tudor Oprea of the University of New Mexico. We evaluate the models against criteria outlined by Tropsha et al in their paper &#8220;The Importance of Being Earnest&#8221;,   QSAR Comb. Sci. 22 (2003), 69.<br />
We will shortly be extending this to include the remainder of the WOMBAT database as well as the recently released <a href="http://www.ebi.ac.uk/chembldb/">ChEMBL</a> database comprising 2 million data points for over 5,000 targets. This study, which we are calling the &#8220;Mother of All QSAR&#8217;s&#8221; is supported by Microsoft Research who are providing the Azure cloud computing nodes that we need to reduce the time required from several years to a few weeks. We expect this study to create a comprehensive QSAR model library that can be used for multi-property predictions in drug discovery. We are now testing its use for predictions and will make that available for use shortly. It is also our intention to offer the site for training models.</p>
<p>This is the first of a series of posts on the technical capabilities of this new resource and announcements as it develops. We would be grateful for feedback and questions.</p>
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		<title>The Micro Pharma</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/11/09/the-micro-pharma/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/11/09/the-micro-pharma/#comments</comments>
		<pubDate>Mon, 09 Nov 2009 18:02:13 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[drug discovery]]></category>

		<category><![CDATA[micropharma]]></category>

		<category><![CDATA[open science]]></category>

		<category><![CDATA[open source drug discovery]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=27</guid>
		<description><![CDATA[Pre-clinical drug discovery has traditionally been the preserve of large fully integrated pharmaceutical companies (FIPCO’s) in established geographical centres in the UK, US and Europe. It relied on tight integration of laboratory facilities and drug design expertise within monolithic mega-research facilities. As laboratory science has become more industrialised and experimental data resources become more widely [...]]]></description>
			<content:encoded><![CDATA[<p>Pre-clinical drug discovery has traditionally been the preserve of large fully integrated pharmaceutical companies (FIPCO’s) in established geographical centres in the UK, US and Europe. It relied on tight integration of laboratory facilities and drug design expertise within monolithic mega-research facilities. As laboratory science has become more industrialised and experimental data resources become more widely available through the internet, drug discovery is moving out from the mega-Pharma into thousands of small mid-size Biotech or Pharma research businesses. These new “mini-Pharma” entrants usually focus on developing some biological insight emerging from academic research into potential drug development candidates and then license those to the mega-Pharmas that have the financial muscle to carry the costs of clinical development.</p>
<p>Although the mini-Pharma companies are smaller and operate more cost-effectively, they often operate as smaller versions of their larger role models. Their productivity may sometimes be higher, but they are not radically different. They remain expensive to set up, fixed costs are high and the majority fail commercially. Nevertheless, driven by unmet medical needs, growing populations and increasing wealth, there is a very large market for new clinical development candidates to fill the empty pipelines of the large FIPCO’s.</p>
<p>The revolution in information technology and emerging developments such as the semantic web, cloud computing as well as community data and software resources is now creating the right circumstances for a second wave of change. This change will be driven by solutions for managing information, extracting knowledge and making decisions in virtual organisations which will create opportunities for new entrants to this very valuable market, especially those with strong IT expertise. The new entrants will be “micro-Pharmas” that minimise fixed costs through accessing on demand, pay-as-you-go laboratory and computing services and exploit Web 2.0 technologies to access globally available services and expertise “on demand”. Driven by their expertise in Information systems, they will deliver new medicines at low unit cost and lower risk. These new micro-drug discovery companies will stimulate local markets for services and grow expertise core in biotechnology activities that create wealth for their investors and communities.</p>
<p>In this emerging landscape for Pharmaceutical research, the mega-Pharmas will increasingly focus on clinical development and commercialisation, in-licensing their products from high productivity mini- and micro-Pharmas. Services will be acquired from the best providers that operate globally and offer services on demand.</p>
<p>This emerging landscape creates new businesses opportunities in the provision of on demand services and in the formation of micro-Pharmas which may operate as businesses, charitable foundations or potentially as participants in open source drug discovery.</p>
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		<item>
		<title>Independent Science</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/10/27/independent-science/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/10/27/independent-science/#comments</comments>
		<pubDate>Tue, 27 Oct 2009 11:35:32 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[business]]></category>

		<category><![CDATA[open innovation]]></category>

		<category><![CDATA[science shared]]></category>

		<category><![CDATA[consultancy]]></category>

		<category><![CDATA[EU Grant]]></category>

		<category><![CDATA[grants]]></category>

		<category><![CDATA[independent science]]></category>

		<category><![CDATA[independent scientist]]></category>

		<category><![CDATA[product]]></category>

		<category><![CDATA[science 2.0]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=26</guid>
		<description><![CDATA[In a post earlier in the year I talked about the independent scientist and how very experienced people were stepping out of their careers with sufficient income to engage in science as independents, assuming that they could find ways to reproduce the networks and tools that they needed. In a somewhat plaintive cry from a [...]]]></description>
			<content:encoded><![CDATA[<p>In a post earlier in the year I talked about the independent scientist and how very experienced people were stepping out of their careers with sufficient income to engage in science as independents, assuming that they could find ways to reproduce the networks and tools that they needed. In a somewhat plaintive cry from a commenter, I was asked how that might  work if you didn&#8217;t have a made-up pension or other income following a well paid career but wanted to continue working in research. Roughly translated, I think that means &#8220;this may work for you old gits, but what about us that still have our hair and eyesight&#8221;. Having confidently said I would reply soon, it has taken me 5 months to think of an answer. Hubris. </p>
<p>Because I am not sure you can. At least, I can see ways to make an independent living as a young scientist, but it may not be end up being research and it may mean that you do a  lot of things that you don&#8217;t want to do. It depends a lot on what your research  area is, what motivates you and how committed you are. So how could you do this?<br />
<span id="more-26"></span><br />
First of all, independence and the ability to decide what you do and how you do it is a very desirable thing, but it doesn&#8217;t come easy. The nearest you got to independence in research used to be an academic environment in the days when there wasn&#8217;t so much time pressure on academics to both teach and bring in money from grants and consultancy work. By independence, I think we are probably talking about self-employment, bringing in your own funding and managing your own costs. The downside of this life is that you have to be constantly alert to where your income is coming from. It means you need to be always thinking about 3 things. The first is visibility. This means how much time have you got (before the money runs out). It is derived from the most conservative estimate you can make of projected income minus your running costs. If your visibility is less than a year there should be an amber light flashing. Anything less than 6 months and it&#8217;s a red. Anything less than 3 months and its time to ring up the folks and see if your old bedroom is still available. All the time you will need to be working on reducing your costs and working very hard on the second thing you need to be constantly thinking about, which is what options do I have? You need options. Most opportunities (i.e. things that generate income) that you will work on won&#8217;t come off, so you have to work on lots of options. All the time. particularly when you relax and think that you have got a deal or a grant. They often fall through at the last minute. The third thing is validation. What is it you are doing and how much evidence do you have that it will work? Or is useful? Everything you do as an independent, i.e. without a permanent job, has to be about maximising these three things. Visibility, Options and Validation.</p>
<p>None of this is of much use though until you have sat down and thought really hard about your research and what you want to do, from two perspectives, the benefits of the research, and the costs of doing it. Working out the benefits of your research is surprisingly difficult. The internal benefits, that is benefits to you personally are easy and they centre around the science and technology that interests you. The hardest thing in all of this is visualising and expressing the external benefits, i.e. benefits to the &#8220;customer&#8221; or the organisation that may be prepared to pay you an income. I still find this the hardest bit. Fundamentally, like most scientists, I get excited by new ideas, new technologies and &#8220;how thing&#8217;s might be&#8221;. Backing off from all that enthusiasm and reframing things in terms of benefits to others is actually very tough. What you are doing in thinking through benefits is to work out who you potential customers are. As an aside, if you don&#8217;t like the idea of &#8220;customers&#8221; or the word, you might want to take a step back from this  whole thing. If you don&#8217;t have your own income, you need to find other people who will provide it. Customers don&#8217;t buy technology or science, they buy solutions to their problems. So you need to think carefully about the benefits of your research to a potential customer, and frame your funding proposals in terms of what they think their problems are, not what you think they should be. </p>
<p>As an example of this let me take a trivial example. let&#8217;s suppose you&#8217;ve come up with some algorithm that solves the NP-complete problem. First of all, congratulations. You get the &Uuml;ber-Propeller Head Prize of the decade. Now its understandable why you&#8217;d want to market yourself as the person who solved the NP-complete problem, because its one in the eye for all your fellow Propeller Heads. However, don&#8217;t do  this. Firstly there are very few people who understand what you are talking about (your market is small) and they don&#8217;t sign cheques (your market is very small). You will get a lot of interest, open doors and give lots of presentations, but the people listening so carefully aren&#8217;t really going to pay for anything. They are trying to do two things. Firstly they want to prove you wrong. Second, they want to find out how you did it so they can do it themselves. What you really need to do is go to the Avon Ladies and explain that you will reduce their costs of sales by 20% and that will increase their profitability by £x/year. See how hard that is? If I&#8217;d solved the NP-complete problem I&#8217;d want to shout about it too, not reduce my triumph to such a trivial level. You may not like this but remember the Golden Rule</p>
<blockquote><p>The Golden Rule. Them what&#8217;s got the gold, makes the rules</p></blockquote>
<p>&#8230;, and if you want to get paid you will need to follow the customer&#8217;s rules. Alongside thinking about the benefits of what you do, who might value that, and who are your customers might be, you need to think about your costs. If its a lab based activity, then you have kit, space and consumables to deal with. You can do it. I know a chemistry company that started with the founder assembling chemicals for sale in his garage. Is there someone who will loan you space and access to kit in  return for something you can offer them? Maybe you can do a deal to work part time for them helping them solve their problems while having a some time left to do your own thing. Maybe you can come to an agreement to use their facilities for some future return on investment. Maybe you can get some kit from a fire sale and start off in your garage? Have you thought of moving to a country where the cost of living is lower and the authorities might be interested in getting in people with your skills? Maybe they would give you some kind of incentive? There may be grants that can help. Obviously this depends very much on where you wish to be based, but in the UK, the Government Grants for Research and Development (micro, research and development levels) are an option. One possibility is via the EU Framework grants which unlike the EPSRC and BBSRC, are not exclusive to academic institutes. You can bid for them as Joe Bloggs Ltd. If you put a consortium grant proposal together with yourself as project leader you can put all your personal costs against the grant. Like all grants you will be subject to the vagaries of the assessment and competence of the referees, but as I said you will need to run multiple options. By the way, these grant giving bodies are still customers. You still have to think carefully about what benefits they are looking for and why what  you are offering will deliver those benefits. Who else would benefit from your research? Any local businesses? People you could do a  little bit of work for to get some money coming in?<br />
How will you deliver the benefits, as a product or as a service? A service such as providing consultancy is a treadmill. Every time you win a contract of some kind you turn right round and go to to win the next one. However, you can get started quickly, the lead in time is to getting the contract. If it is a product, you need development time, maybe a year or more to develop whatever it is to being commercially viable. You need support while you do this of some kind, which means investment. That might be your savings, combined with a working (and very understanding) spouse. Maybe its an investor. Even when you have built the product you still need to market and sell it. That is usually harder to do than invent the product in the first place. So this is what I mean by saying I am not sure that a someone without a basic income can do research without it becoming something that isn&#8217;t really research or not what you want to do. By looking hard at funding realities we inevitably come to thinking of how you operate as a business. Maybe a small consultancy business perhaps, but a business no less. Your service comes from your research expertise, any product needs to come from your imagination. I believe in  business and science-based business in particular. I would encourage any young scientist to consider taking their skills and ideas directly to the market. It is how you can win independence. It takes courage and hard work, but it&#8217;s worth it. However, what matters is what you want to do with your life. Self-employment will give you a kind of independence, but it you have to think carefully about what is right for you.</p>
<p>If your research is software or data analysis based, then your costs are about as low as they could be, especially with pay-as-you-go computiing from Amazon, Microsoft and others coming along and the availability of open source scientific software  and collaboration tools. Also the web gives multiple low cost routes to global markets which is starting to create a different set of possibilities for research scientists attaining their independence. Many of these are things we are working on offering through Inskpot, but its probably better to address those through the Inkspot site directly.</p>
<p>I would encourage any scientist, young or not so, to look into options for attaining their research independence. There are ways that it could be done outside of the conventional career structure, but it does require a very significant shift in thinking and it may change what you have to do by so much that it isn&#8217;t research any more. Good  luck to you.</p>
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		<title>Nutters on the Bus</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/10/26/nutters-on-the-bus/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/10/26/nutters-on-the-bus/#comments</comments>
		<pubDate>Mon, 26 Oct 2009 10:52:36 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<category><![CDATA[science shared]]></category>

		<category><![CDATA[regulatory affairs]]></category>

		<category><![CDATA[toxicology]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=25</guid>
		<description><![CDATA[Having argued in the previous post that open science lets the general public engage in science and that this is a Good Thing, I&#8217;d like to backtrack slightly and qualify my remarks. I think open science will be a bit like public transport. For some things it can get you places quicker and it has [...]]]></description>
			<content:encoded><![CDATA[<p>Having argued in the previous post that open science lets the general public engage in science and that this is a Good Thing, I&#8217;d like to backtrack slightly and qualify my remarks. I think open science will be a bit like public transport. For some things it can get you places quicker and it has a community value, but is not for everyone or for all journeys. It means that you have to mix with the public, and you can meet some interesting people that way, but you do have to be a little circumspect. Most importantly, you don&#8217;t want to sit near the Nutter on the Bus and if you do, whatever else happens, don&#8217;t make eye contact.<br />
<span id="more-25"></span><br />
They can be hard to spot at first, the nutters, perhaps not until the bus gets underway and you realise you&#8217;re stuck with them, and you know that they know that you&#8217;re stuck with them. You can recognise the nutter by a sort of starey-eyed intensity which expresses an absolute conviction that they, and they alone, have the Knowledge-that-Will-Save-the-World. In their eyes, you have come within range and now you must listen. They have always talked aloud to themselves, and now they blog. <a href="http://www.guardian.co.uk/environment/georgemonbiot">Some</a> even make a living out of it. Selling their outrage to create traffic for their clients. Their convictions are dogmatic, religious and they are fundamentally anti-science, reason and evidence. Indeed, in previous ages, they would have been the witch-finders, the hell-fire priests, the druids. They think they are engaging in scientific discussion, but it is a bastardised sort of science with smearing the unbelievers at its core. So as an example, anyone who works in the private sector, has ever worked in the private sector, or has ever collaborated with anyone in the private sector or spoken at a conference that was, even in part funded by the private sector  is fundamentally corrupt and <a href="http://www.guardian.co.uk/environment/blog/2009/oct/14/bees-scientific-research">their ideas, work and opinions are therefore discredited and can be ignored</a>. Any other counter-arguments are dismissed by a vague waiving in the direction of partially relevant facts and frequent use of the term &#8220;debunked&#8221;. As in &#8220;the work of <em>insert name of eminent scientist here</em> has been debunked by <em>insert reference to Wikipedia pages controlled by your fellow starey-eyed ones here</em>&#8220;. There is a kind of suppressed outrage in much of what they say which prevents them from listening and hearing any part of the answers given to their questions they pose. They don&#8217;t listen, because they don&#8217;t have to. They already know The Truth.</p>
<p>I came across one such group a few months ago while walking past the shiny new Oxford Chemistry building on my way to a workshop. They were a large group of animal rights protestors with banners calling scientists murderers. They have been there for a few years now attacking the University and its scientists for the new primate centre being constructed along the same road. Thankfully, the authorities finally got round to stopping their all day chanting and verbal abuse of the scientists working in the buildings nearby, so they were quiet and on the surface, harmless. I crossed the road anyway. You don&#8217;t want to make eye contact with a nutter. </p>
<p>I am personally very interested in animal reduction in science, and mainly work in areas (in vitro testing, PBPK simulation and QSAR modelling) that are important tools in drug and pesticide research, and also have great potential for reducing the use of animals.  I served on expert committees of<a href="http://ecvam.jrc.it/"> ECVAM</a>, the EU funded centre for developing alternatives to animal testing, particularly as a result of the EU regulations to control the use of chemicals, REACH (what the EU gives &#8230;). Those of us that attended the expert review groups were pretty much of the same view that a combination of in vitro testing in human tissues combined with computational methods were actually more predictive of human and environmental exposure and risk than some of the very crude animal tests in use. However, I became pessimistic when I realised that the issue didn&#8217;t have much to do with the best scientific methods, and that the regulators and therefore industry just wouldn&#8217;t expose themselves to criticism and potential product withdrawal. The new animal testing required by REACH may be expensive and time consuming, but it is not as expensive as withdrawing a product. It wasn&#8217;t that the alternatives weren&#8217;t good enough, it was that they will never be good enough to satisfy the demands of the new commandment,  &#8220;the precautionary principle&#8221;. So they won&#8217;t take the best scientific position, they will do what they have to, to avoid making eye contact with the nutters on the Green bus. In fact, now that REACH defines the requirements, it may significantly increase testing, regardless of its scientific value, simply because companies will see that, as expensive as the testing is, and however destructive or scientifically pointless, it will put them and their products in a solid defensive position against any possible criticism or new findings. Because they know as do we when we stop to think about it, that it doesn&#8217;t matter what tests are done, to the starey-eyed ones, all chemicals are toxic, by definition. QED, the debate is over. The only defence is to say &#8212; &#8220;we did exactly the testing that we were told to do. We obeyed every rule you threw at us&#8221;. The scientific basis for those tests is irrelevant.</p>
<p>Thomas Hartung was Director of ECVAM when I served on those advisory committees. He is an experienced academic toxicologist who supports the REACH legislation but was active in the EU to try and ensure that science and evidence would be at the heart of the new testing regime and the impact (and REACH has a staggeringly large impact on animal use) should be  minimised. From the sound of a <a href="http://network.nature.com/groups/naturenewsandopinion/forum/topics/5338">recent letter</a> to Nature, he and others are growing increasingly concerned that all that work is coming to nothing. Thus, yet again, the &#8220;Law of Unintended Consequences&#8221; trumps the &#8220;Precautionary Principle&#8221;.</p>
<blockquote><p>&#8220;Our results suggest that generating data to comply with REACH will require 54 million vertebrate animals and cost 9.5 billion Euros over the next 10 years. This is 20 times more animals and 6 times the costs of the official estimates.</p></blockquote>
<p>However, Thomas&#8217; well reasoned arguments mean very little to the green <a href="http://blogs.edf.org/nanotechnology/2009/08/26/talk-about-over-reaching-anti-reach-screed-gets-nearly-everything-wrong/">Nutter on the Bus</a> who deploys the usual smear and innuendo, loosely referenced arguments and outrage against him and his co-author. Scientists can&#8217;t win here. They are caught between two groups of the starey-eyed competing for their own peculiarly narrow view of the world. We now have two nutters on the same bus. Maybe we could slide off at the next stop and let them have a go at each other? </p>
<p>So a polite request to the Oxford animal rights people. Please move your campaign of intimidation to outside the office of the <a href="http://www.greenparty.org.uk/news/1605">Green Party</a>. Carry on your dialogue of the deaf with each other. Neither of you have any interest in science or scientists. Leave us out of it.</p>
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		<title>Beyond the Pale</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/10/23/beyond-the-pale/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/10/23/beyond-the-pale/#comments</comments>
		<pubDate>Fri, 23 Oct 2009 20:01:16 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[open innovation]]></category>

		<category><![CDATA[science shared]]></category>

		<category><![CDATA[democratic science]]></category>

		<category><![CDATA[open science]]></category>

		<category><![CDATA[open source]]></category>

		<category><![CDATA[open source drug discovery]]></category>

		<category><![CDATA[public]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=24</guid>
		<description><![CDATA[Enthusiasts for open science come from many backgrounds and see different advantages. For me, open science is what science is supposed to be. Open publishing of results and data in such a way that the &#8220;educated layman&#8221; can repeat the work, check its validity and potentially come to alternative conclusions. After all science is the [...]]]></description>
			<content:encoded><![CDATA[<p>Enthusiasts for open science come from many backgrounds and see different advantages. For me, open science is what science is supposed to be. Open publishing of results and data in such a way that the &#8220;educated layman&#8221; can repeat the work, check its validity and potentially come to alternative conclusions. After all science is the process, the debate, not the corpus.  The corpus changes with new data, new interpretations and new theories, it&#8217;s the continuity of debate which is constant. Not all scientific research should be open. It requires confidentiality to take research through to a commercial product, but if there is an expectation of gaining credit from the work, then it should be.  The other argument is that open data and open publishing create radically new opportunities for mining information and realising the potential of the semantic web in building new kinds of scientific understanding.</p>
<p>All of these are noble goals and scientists that go open, publish their data, software methods and conclusions, especially if they do it &#8220;live&#8221; as in Open Notebook Science are pioneers in an exciting new world of collaborative, transparent scientific discovery. One such pioneer is Steve McIntyre, whose blog I link to here, who operates fully &#8220;live&#8221; in the open publishing and archiving of data, his software and interpretations as he does the work and leaving himself open to continuous peer review by all comers at his blog as well as elsewhere, If he makes a mistake (which is unusual) it is quickly challenged. There are many good examples of his work to see on his blog and a recent <a href="http://www.climateaudit.org/?p=7374">analysis</a> of his is representative. As an experiment in the sociology of open science and a window into what open science might look like, I find it fascinating to observe.</p>
<p>However, despite his site winning the Science blog of the year in 2008, his pioneering of open notebook science and his blog&#8217;s  very high traffic, I don&#8217;t see any recognition of what he does in open science <a href="http://www.openscience.org/blog/">&#8220;circles&#8221;</a>or in the mainstream scientific debate about open publishing. I don&#8217;t know why that is, because I see the same comments on his site about the importance of open data, transparency and rigorous analysis as elsewhere. What&#8217;s more he doesn&#8217;t just talk about it, he does it for real and does it well. I can&#8217;t help wondering whether this is  because he is a <em>climate change denier</em>, someone whose scientific analysis undermines the basis of claims for man-made global warming. As such it is possible he is largely ignored because he is seen as &#8220;Beyond the Pale&#8221; and excluded from the respect I think he (and others) are due for their courage in working openly and publishing live.<br />
I agree he is &#8220;Beyond the Pale&#8221;, but not in the modern sense of being outside what should be regarded as acceptable to polite society. Rather, I think he is Beyond the Pale as in its original meaning and if interpreted in that way, what he does, how he works and the reaction he gets has very important lessons for any scientist, whether working in the open or not.<span id="more-24"></span><br />
The term originally came from that period in Anglo-Irish history when the Irish tribal leaders briefly stopped fighting each other and combined to drive the Anglo-Norman knights back into a small area in Dublin, where they surrounded themselves with a wooden fence or &#8220;Pale&#8221;. Beyond the Pale were the barbarians (or rightful inhabitants depending on your take) and Beyond the Pale was a dangerous place to venture. For traditional scientists working in official positions in universities, government institutes, business etc, Beyond the Pale lies the general public, the great unwashed. It used to be that they could be safely ignored. Debate was to be held within the confines of the &#8220;Peer Reviewed Literature&#8221;, specialist conferences and tea rooms of the place of work. Open Science or not this is no longer the case. The internet opens data and scientific debate to the public, and they want to get in. It doesn&#8217;t matter whether you the scientist wants this, or whether you plan to participate in this open science thing. The new world will be one of open analysis and open debate, whether you like it or not. It will happen more quickly if your research has significantly policy implications or is politically sensitive. The man made global warming hypothesis is clearly one of those topics, but so is new drug research, especially anything related to drug safety and animal use. Open Source Drug Discovery would attract huge public attention. Then there is the wide swathe of environmental research, GM crops or population genetics related to the historical movement of peoples.  It is going to be like permanent review. No more sighs of relief that you&#8217;ve seen off the referees, when the editor accepts your latest seminal contribution. The barbarians are out there waiting their turn to have a go at your work and you&#8217;d better get used to it. So what should we do, huddle behind the fence and sling the occasional arrow to keep them at bay? I think not.</p>
<p>The best way to prepare yourself of course is to do good science and be your own sternest critic. However for all other advice, I would have a good look at how the official <a href="http://realclimate.org">Climate Scientists</a> have dealt with Steve McIntyre over the last 10 years, and then do the opposite. So amongst many other errors of judgement I would suggest that you don&#8217;t refuse to release your data &#8220;because you only want to find something wrong with it&#8221;. Don&#8217;t refuse to release your data for 10 years until forced to do so by a journal. If you&#8217;ve lost your raw data and don&#8217;t remember how you analysed it then don&#8217;t lie, you will get found out eventually. Don&#8217;t accuse your critics of corruption, stupidity or venality. Remember what the lawyers say. &#8220;When my case is strong I bang on the facts, when it&#8217;s weak I bang on the table&#8221;. Don&#8217;t ignore, sneer, patronise, insult or otherwise get distracted from the facts. To the neutral observer, this makes you look weak and unprofessional. Most importantly of all, don&#8217;t bring politics into it, at least not if you want to be respected for your scientific objectivity.</p>
<p>Stay calm, accept what criticism is justified, challenge the rest with facts and rational argument. Talk to the barbarians, don&#8217;t throw stuff at them.  That way, if your interpretations are right you will win, and if you really are wrong, &#8230; we all win.</p>
<p>Open Science is what it says on the tin, open. The Web is pulling the fence down, and anyone can join in.</p>
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		<title>Bacon and Eggs</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/05/31/bacon-and-eggs/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/05/31/bacon-and-eggs/#comments</comments>
		<pubDate>Sun, 31 May 2009 21:02:43 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[Regeneration]]></category>

		<category><![CDATA[Uncategorized]]></category>

		<category><![CDATA[business]]></category>

		<category><![CDATA[science shared]]></category>

		<category><![CDATA[cities]]></category>

		<category><![CDATA[Civic University]]></category>

		<category><![CDATA[commitment]]></category>

		<category><![CDATA[industrial revolution]]></category>

		<category><![CDATA[involvement]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=22</guid>
		<description><![CDATA[The great Northern cities of England grew out of the world&#8217;s first industrial revolution and its specialisations for Cotton (Manchester), Wool (Bradford), Ships (Newcastle) and other products. The Universities, often started and funded by successful Victorian entrepreneurs to do research to devise newer products, also contributed to better educational opportunities for many and the growth [...]]]></description>
			<content:encoded><![CDATA[<p>The great Northern cities of England grew out of the world&#8217;s first industrial revolution and its specialisations for Cotton (Manchester), Wool (Bradford), Ships (Newcastle) and other products. The Universities, often started and funded by successful Victorian entrepreneurs to do research to devise newer products, also contributed to better educational opportunities for many and the growth of new knowledge that improved health care, nutrition and the environment.  They and their founders saw themselves as Civic Universities, adding to the culture of the city as well as its wealth. They committed their time, energy, knowledge and innovation to their local citizens, and they did it because that is what they were for.</p>
<p>Today&#8217;s Universities operate as businesses, selling their time, energy, knowledge and innovation to their fellow citizens for as much as they can get. They compete with real businesses. They may say that they are Civic Universities, and they may appear to be involved in the life of their city, but they don&#8217;t show the commitment of their predecessors. They may be involved, but they are not committed.</p>
<p>An investor of mine once explained the difference between involvement and commitment when I had said something about &#8220;being involved&#8221; in the new business we were launching. &#8220;Involvement&#8217;s no good to me&#8221;, he said, &#8220;I need commitment. Just like with Bacon and Eggs, the Hen may be involved, but the Pig is committed&#8221;.<br />
<span id="more-22"></span></p>
<p>Universities play an essential role in the growth and regeneration of a city and region. Regions that can establish a high performance <a href="http://www.triple-helix-7.org/theme-paper.htm">Triple Helix</a> alongside Government and business have been shown to benefit from faster growth. However, the Universities can&#8217;t be just involved in this, they need to be committed, like the Pig.</p>
<p>Since Universities lose money from their &#8220;control the IP and sell it&#8221; strategy they could easily demonstrate their commitment by abandoning the (fairly recent) attempt to control all the activities of the academics. This is not &#8220;unbusiness-like&#8221; since real businesses are ruthless about cutting unprofitable services and the Universities make their money from Teaching not Tech Transfer.</p>
<p>Let the academics own all their own work, ideas, know-how and &#8220;IP&#8221;. Close down the Tech Transfer offices, tear up pointless contracts, NDA&#8217;s and elaborate schemes for sharing future revenues that never exist. Get out of the way of collaboration between the academics and business. Let scientists in Universities talk to and work with scientists in industry as they wish, when they wish. Rescue them from the endless project delays while contracts are developed and signed. Help them to bootstrap their start-ups by allowing them to spend 20% of their time on developing the idea. Stop bullying them with &#8220;conflict of interest&#8221;. Stay out of commercialisation and let them work with government agencies, investors and angels that can help. Let them give of their ideas freely to business or get paid for their advice if the company wishes to do that.</p>
<p>A Civic University commits to the city it lives in and takes its reward from its prosperity. By releasing the energy of its people from the shackles of the obsession with selling IP, it can attract more investment, more students and more research collaborations while at the same time demonstrating its commitment to its fellow citizens.  </p>
<p>Open Innovation. Courtesy of the Pig.</p>
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		<title>Walled Gardens</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/04/02/walled-gardens/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/04/02/walled-gardens/#comments</comments>
		<pubDate>Thu, 02 Apr 2009 17:05:00 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[business]]></category>

		<category><![CDATA[science shared]]></category>

		<category><![CDATA[Economic Development]]></category>

		<category><![CDATA[Tech Transfer]]></category>

		<category><![CDATA[Triple Helix]]></category>

		<category><![CDATA[walled gardens]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=21</guid>
		<description><![CDATA[There is a nice quote in Wikinomics which I like,  particularly the bit about walled gardens

“What was different? The losers launched web sites, the winners launched vibrant communities. The losers built walled gardens. The winners build public squares. The losers innovated internally. The winners innovated with their users. The losers jealously guarded their data and [...]]]></description>
			<content:encoded><![CDATA[<p><span>There is a nice quote in Wikinomics which I like,  particularly the bit about walled gardens<br />
</span></p>
<p><e><span style="font-size: 8.5pt; font-family: 'Verdana','sans-serif'; color: #444444;">“What was different?<span> </span>The losers launched web sites, the winners launched vibrant communities.<span> </span>The losers built walled gardens.<span> </span>The winners build public squares.<span> </span>The losers innovated internally.<span> </span>The winners innovated with their users.<span> </span>The losers jealously guarded their data and software interfaces.<span> </span>The winners shared them with everyone.”</span></e></p>
<p>The quote is largely referring to new-style on-line business and the importance of engaging users and helping them to establish communities, but it seems to me that this is also very relevant advice for the modern University. Universities make money from Teaching, Research and Technology Transfer. They are usually good at teaching and can turn a profit, because they generally know what they are doing. Research Contracts bring in cash, although less than they might if they got their overheads down.  However, most Universities lose money from spin-out and licensing, and this is bad for them, bad for the academics and most importantly, it is very bad for the community in which they live. </p>
<p>Why is this?  They build Walled Gardens.<br />
<span id="more-21"></span><br />
 In a recent report by Hefce (Higher Education Funding Council for England) which summarises the financial performance of English Universities, showed that a 22% increase in funding in IP protection (to over £20M) had led to a 1% increase in income. Note &#8212; income, not profit. Most Universities run their IP protection activities at a loss, and I bet that very few University managers assume that this situation is likely to change when they are putting together their spending plans. Amongst the asinine comments that I pulled out of the article were &#8230;</p>
<p><em><span style="font-size: 8.5pt; font-family: 'Verdana','sans-serif'; color: #444444;"> &#8230; most IP is junk, &#8230; in order to get the full benefit of the important stuff a lot of investment has to be made &#8230; </span></em><br />
Anyone want to buy more lottery tickets?</p>
<p><em><span style="font-size: 8.5pt; font-family: 'Verdana','sans-serif'; color: #444444;"> &#8230; the fall in income &#8230; was not yet a concern because it could be 25 years for the investment to pay off &#8230;<span></em><br />
25 years?? Could pay off? </p>
<p>The strategy of &#8220;investing&#8221; in IP protection that can be sold to make money for the University is deeply flawed. It fails in its primary objective of making money and stifles innovation. A recent opinion piece by <a href="www.aimresearch.org/about-aim/directors/andy-neely">Andy Neely</a> of the Advanced Institute of Management said that more than half of business people surveyed blamed University policy including issues of confidentiality, ownership of intellectual property as well as commercially unrealistic expectations for creating a barrier to fruitful cooperation with business. The &#8220;<a href="http://www.ncl.ac.uk/nubs/staff/research/triplehelix.htm">Triple Helix</a>&#8221; model for regional development argues that it is the combination of three partners, Universities, Government and Business that is the engine for economic growth. The Walled Garden strategy of the Universities means that the supply of ideas for innovation-based growth is limited to what the University gatekeepers sitting in Tech Transfer offices will let out.</p>
<p>It seems to me that the public Universities are funded by the taxpayer and their public duty is to deliver what the community wants most, growth and jobs. The walled garden strategy does not deliver this and the Universities fail in their public duty to support their communities.</p>
<p>A great Civic University should be a public square, not a walled garden.</p>
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		<title>Heroes and Villains</title>
		<link>http://www.inkspotscience.com/blog/index.php/2009/01/08/heroes-and-villains/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2009/01/08/heroes-and-villains/#comments</comments>
		<pubDate>Thu, 08 Jan 2009 22:27:46 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<category><![CDATA[business]]></category>

		<category><![CDATA[drug discovery]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/?p=19</guid>
		<description><![CDATA[I am part way through watching Series 3 of &#8220;Heroes&#8221;, and enjoying the interesting twists of character and plot. For those that don&#8217;t know it, the basic premise is that an unusual set of genetic mutations have produced new kinds of individuals that are able to suspend the laws of physics and fly, move in [...]]]></description>
			<content:encoded><![CDATA[<p>I am part way through watching Series 3 of &#8220;Heroes&#8221;, and enjoying the interesting twists of character and plot. For those that don&#8217;t know it, the basic premise is that an unusual set of genetic mutations have produced new kinds of individuals that are able to suspend the laws of physics and fly, move in time, read minds, or whatever else the scriptwriters can come up with in time for the next episode. Very enjoyable stuff, even if (or because of) the science being so &#8220;creative&#8221;. Still, where would popular culture be without warp drive and inertial dampeners? The latest series has an interesting twist in that some of the Heroes of the first and second series are now turning into Villains and some of the Villains are becoming Heroes. Even so, I still don&#8217;t buy the argument that Syler should be let off his conduct (i.e. slicing off the skulls of his victims in order to suck out the brains) in the earlier series, just because he has an eating disorder and his mother had him adopted.  So it is getting confusing and unsettling, but very watchable.</p>
<p>When it comes to the Pharmaceutical industry and health care, popular culture has no such uncertainty about who is the hero and who is the villain. The litany of complaint is well known. Drug companies extort obscene profits from the sick, corrupt honest scientists and doctors through bribes, abuse the poor of the third world as human guinea pigs, and force dangerous, untested new drugs on us. We know that because we read it in the news and watch films like &#8220;the Fugitive&#8221; and &#8220;the Compleat Gardener&#8221;.</p>
<p>Still, it&#8217;s only entertainment, no harm done, and anyway, everyone knows who is the villain  &#8230;<br />
<span id="more-19"></span><br />
So, imagine the case where there is a new drug for pain relief free from the damaging side effects of the older treatments it replaces. Some issue is raised in the scientific literature about possible increased incidence of heart problems (from 0.25% to 0.5%) in the elderly and a journalist short of copy spins these findings into a health scare story (&#8221;Drug Causes Heart Attacks&#8221;). The editor scents something that they can run with to fill the paper in a slow news week, but wants to move the story to the front pages. With more effort the paper digs out a report of some earlier animal studies which, with hindsight and knowledge that wasn&#8217;t available to the scientists of the drug company 5-10 years earlier, might, just might, have suggested the heart problems could have been predicted. The story now changes from the complexity of the real scientific issues (which none of the journalists understand and readers find boring), to the perfidy of the drug company who &#8220;covered up&#8221; the results deliberately. A Texas lawyer advertises for people to come forward to participate in a class action suit and a test case of 75 year old (with a history of arthritis and heart disease) who died of a heart attack while also taking the drug results in an award of $250 million against the drug company. Inspired by this, a novel is written by a famous thriller writer about a drug company using murder and bribery to cover up drug testing deaths in Africa and becomes an international best seller. A blockbuster film is made with an A list cast, one of whom wins an Oscar. At the podium she says modestly, with a single tear arranged for the close up, that she is proud to tell the story of &#8220;all those that have suffered&#8221;. Politicians see the film and hammer the FDA for their inadequacy and cosying up to the drugs industry and the FDA cranks up the barriers to new drug approval one more notch. The drug company withdraws the drug and its $1 billion a year revenues and, followed by all the other drug companies, puts in place new and more costly testing to make sure they can defend themselves from a similar situation in the future.</p>
<p>Serves them right you say. The Villains got caught trying to make money unethically and were punished for it. The Heroes, the journalists, the newspaper owners, the famous author, lawyers, the studio and the actors were only interested in the public good and poor, helpless (and highly photogenic) Africans. No doubt the actors give their $10M fees to people working in tropical diseases and the lawyers forgo their 30% cut of the damages to pay for AIDS medicines in the third world.</p>
<p>I have been in the industry for 25 years, 15 of which were in a large Pharma. There are things I think they don&#8217;t do well, but there are far more they do right. We live much longer than our parents did. We have cured or ameliorated major diseases and continue make big improvements in the treatment of killer diseases such as cancer. These improvements come from the hard work and expertise of hundreds of thousands of decent, highly ethical scientists and engineers working in the industry, across the globe.  They have delivered enormous benefit to society over the last 100 years.</p>
<p>However, the industry is now <a href="http://business.timesonline.co.uk/tol/business/industry_sectors/health/article5438553.ece">in serious trouble</a> and so are we. As regulations get tighter, fewer new medicines are approved and each one is more expensive. Financial performance has dropped and investors are turning away. This is not new, and the large Pharma&#8217;s have survived because the Venture-funded Biotechs have been making up the shortfall in new medicines. However, the flow of new venture-backed drug discovery has dried up and few new ideas get funded. You might want to start imagining the consequences of no new medicines.</p>
<p>Heroes, Villains, your call.</p>
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		<title>Inkspot Steps Up</title>
		<link>http://www.inkspotscience.com/blog/index.php/2008/12/20/inkspot-steps-up/</link>
		<comments>http://www.inkspotscience.com/blog/index.php/2008/12/20/inkspot-steps-up/#comments</comments>
		<pubDate>Sat, 20 Dec 2008 21:52:55 +0000</pubDate>
		<dc:creator>David Leahy</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://www.inkspotscience.com/blog/index.php/2008/12/20/inkspot-steps-up/</guid>
		<description><![CDATA[We are now working with the first closed Beta version of the Inkspot Science on demand site as well as the workflow design desktop client that currently acts as an IDE for adding services, managing data and sharing both.&#160; The Inkspot desktop client is a very nice implementation of a workflow design tool that makes [...]]]></description>
			<content:encoded><![CDATA[<p>We are now working with the first closed Beta version of the Inkspot Science on demand site as well as the workflow design desktop client that currently acts as an IDE for adding services, managing data and sharing both.&#160; The Inkspot desktop client is a very nice implementation of a workflow design tool that makes it easy to build workflows from standard blocks and manage these on the Inkspot server. We have been adding specialist blocks for data mining and cheminformatics and plan to extend these depending on what the beta test users need. I particularly like the scripting block which lets me write simple R scripts which are implemented using an Rserve server on the Inkspot site. The (currently) small number of blocks for cheminformatics were added using a few bits of the <a target="_blank" href="http://apps.sourceforge.net/mediawiki/cdk/index.php?title=JChemPaint">CDK toolkit</a> along with some charting, modelling and data manipulation tools.&#160; We are expecting to be adding a great deal more in the near future connected with research projects that we are keen to support and would be happy to work with collaborator groups to tailor the content, particularly if those groups would be willing to help us improve the site and help us direct its development. </p>
<p>The server site has a simplified version of the workflow editor as well as a “lab notebook” blogging mechanism that makes it easy to add scientific content such as data, workflows, references and so on. This is an early focus of what we are doing to simplify the process of data analysis and communication. Of course the site allows the user to form groups and share objects, although the default is private.&#160; We have two major research collaborations already underway and I hope to be able to say more about both soon. Although it is early days for us, we the site is making excellent progress and we are excited about the prospects in the coming year.&#160; </p>
<p>If you have a research project that could benefit from using Inkspot as a hosting and collaboration mechanism, or if you’d like to use the site in your business get in touch and we will arrange a web demo and conversation. </p>
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