>> carole: i am here to introduce matthew todd,who's here at the university of sydney to talk about crowdsourcing chemistry and thetropical disease initiative. so please welcome, matthew todd.>> todd: okay. so, first, i should say... >> carole: you don't need to use this one.>> todd: oh, is it one of these two? okay, i can stand here on this one, all right. so,first, i should say, thanks, carole, for introducing me and hosting the visit. thanks also to,christy burner, who also ultimately set up the visit. and, yeah, i'm an organic chemist.so hopefully i'm going to do a bit of chem 101 to make everyone familiar with what i'mtalking about. but also, i'm going to be talking
a little bit about open science. and the purposeof my visit today really is to preach that we need tools and applications. so, one ofthe reasons coming to google is that your apps are very intuitive and so on, and weneed things for conducting science in the open which we currently don't have, and oneof the reasons we don't have them is because people haven't designed very intuitive userinterfaces for things to be used by scientists to record their work in the lab. the otherreal reason for coming to google today is because i recently bought a nexus one phone,and i lost the little black sleeve that comes with it and i'm hoping to get a new one, so,if you have one. okay. so, there's going to be a little bit of chemistry and a littlebit of stuff about science and how we do it
and maybe how we should we do it. so it'squite a wide range of things and obviously, if you have any questions, please just stickout your hand and we'll go. okay, so a little bit of--i think i still got animation in here,a little of bit of chemistry at the start. okay. so i'm an organic chemist. i teach inresearch organic chemistry in the university of sydney in australia. and what does thatmean? well, we make molecules. i have graduate students and post-docs and undergraduate whomake molecules. so we put atoms together in specific ways. and one of the interestingthings about this is that as you do chemistry for a long time and you learn a lot aboutorganic chemistry, you learn about how to do this and you become proficient at doingthis both in your mind and also with your
hands. so you become good at putting thingstogether, bringing atoms together in specific ways to make complicated molecules and thiscan be done in several different ways. what we do is we buy things from commercial cataloguesand then we use chemistry in a rational way to put things together. and we make importantmolecules that may be are useful for pharmaceuticals or agrichemicals or fragrances and so on.and to do that, sometimes you want to make a really complex molecule which has certainproperties, and you have to know how to do that, how to put an atom here, an atom therein specific ways. and it can be quite complicated. in some ways as it's shown on the top here,the molecule might be going from the top-left might be obviously related to the thing thatyou can buy. so on the right-hand side there,
you got things in the box, which you can easilybuy and put these things together in a kind of like a lego manner and build up a complexmolecule, which maybe has some nice property. in other ways, there maybe something availablefrom nature, like the molecule in the middle on the right, which you can easily transforminto something that you might want. so you can buy that in large quantities from somenatural source and you can convert it into something that you might want to use. so theseare kind of ways of using nature initially to make things which are kind of complicated.but in many cases, the molecule that you might want, for example, that thing on the bottom-righthere is very--it's structurally unrelated to anything that you can buy or find. andin order to make that you might have to think
in a very lateral way about how you can buythings and combine those things to make a complicated molecule. and frequently, we findthis, some molecule that we--that have some potent biological property, is not simplymade by a logical combination of starting materials. and this is the right creativeprocess, so a lot of people say that there's a lot of art in organic synthesis. to makea complex molecule, you have to have a deep appreciation for the subject and think aboutit a lot and perceive hidden patterns. now, the reason why this is interesting for mewas because this struck a cord as the parallels between this and a chess game have made before.a chess game also has certain rules that you follow. and in order to get to some finalpoint, some complicated position or some winning
position, you have to follow a certain paths,and the number of paths diverge from the starting point combinatorially. so the number of possiblegames of chess, obviously, is a huge number. the number of different ways of combiningsmall molecules to get larger molecules is also colossal. so the question that came tome was, well, "can we analyze how to make a big molecule with a computer?" and, well,the answer is obviously yes, but no one's done it. well, people have tried, but theprogress is quite slow. the contrast that struck me is that deep blue, obviously a computerprogram, deep gary kasparov of chess, this is the defining moment for a.i., i guess,for computer power and also software development. something as complicated as chess could bemastered by a computer and beat the current
reigning world champion; well, this hasn'thappened in organic chemistry so far. for some reason, people have not designed softwareyet, he would have made inroads, certainly, but haven't design software yet that can reallytake on the masters, the big professors at various universities around the world, haveput molecules together. so this--i wrote this article about this, appealing for maybe someprogress and the application of modern computational techniques to making organic molecules. andso far this hasn't happened. now the thing i'm talking about today is related to this,why haven't we--why haven't people developed tools that help scientists to do science onlineand in the open? that is the--that is i guess the message, why can't we do that yet? okay,so away from chemistry for a second, i sub-reported
it to my lab and one of them is working inan area of neglected tropical diseases. and now, there are various diseases in the world;cancer, aids, big diseases; and malaria, too. there are some which are neglected, whichmeans purely that the amount of money being spent on them and the amount of time beingspent on them is relatively small compared to their impact socially. and there are severalexamples, here's a graph from a website that lists several that usually have rather complicatednames to say, but the one that i'm interested in is this thing called schistosomiasis, whichis used to be called bilharzia. it's a parasitic disease carried primarily in the regions shownon this map. so it's mainly a sub-saharan problem. and it's a particularly nasty disease,it's a parasitic disease and a parasite infects
you and lays eggs in you and these are excretedinto fresh water and then this can be taken up--the parasite matures and is taken up bya snail in fresh water and then the snail--the parasite matures again in the snail and thatexcretes it into freshwater and then you pick it up again. there's a cycle rather like malariawith a mosquito as the intermediate host, but instead, now, you have a snail and freshwater.and it's unpleasant for several reasons, one is that the egg burden in you and your majorinternal organs can become very bad and you begin to get very sick. you don't necessarilydie from this disease but it affects you by morbidity, so it makes you very sick, andit means that children for example who get the disease are not--can't develop properly.they tend to have stunted growth and they're
very tired, they're not going to go to schooland this kind of things. so neglected tropical diseases like these often measured by somethingcalled a daly, a disability-adjusted life year, which doesn't take into account thenumber of people who die, but it tries to quantify the impact of a disease on a society.and by that measure, schistosomiasis is actually a big problem. it affects more than 200 millionpeople have the disease and another 200 million people are at risk, pretty colossal numbersactually. now this is unpleasant but thankfully there is a good drug for it. as with manytropical diseases, actually, there are drugs available to treat these things. they're nottremendously good drugs necessarily but they're inexpensive, small, easy to make, and a fewpeople around the world have been suggesting
that we really need to focus on this, thatmaybe the drugs aren't fantastic but at least they're there and we can use them and thatwe can distribute them for a low price. so for example in schistosomiasis, the gatesfoundation way back 2002, i think, but maybe i'm going to be corrected on that, fundedsomething called the schistosomiasis control initiative which operates out of imperialcollege in london. the guy who heads it up is professor alan fenwick. now, his idea wasthat we have one drug available to treat schistosomiasis, and i'll come to that in a minute. and whatwe really need to do is distribute this drug enormously widely to reduce the morbidityof the infected populations. so we take the drug and we just distribute it to whole populationsof countries, and this is not happening in
select countries in africa and other countriesin africa have also begun their own national control program. so there's an article herein public library of sciences, neglected diseases, the whole journal devoted to neglected diseases--africa's32 cents solutions for hiv/aids. it turns out also that this drug used for schistosomiasiscan also be used to try and slow the transmission of hiv/aids in africa so there's renewed interestin the drug also from the position of hiv. so in general, the idea is that we try anduse things that we already have. so here is the drug that's used for schistosomiasis.now, this is a very small molecule. these--for those of you who dropped out of chemistry,organic chemistry--the lines are bonds, right? so when a line changes directions, it's acarbon atom. and where there seem to be double
lines, that means there's two bonds betweenthe couple of the carbons, the oxygen's obviously the o, and the nitrogen is n. they have doubleand single bonds, there are rings there, but this is a small molecule, this is a very smallmolecule. and this drug was found through a screen. it's not a naturally occurring compound.it was found through a screen of similar compounds. initially, actually, for a similar diseasein cattle, and i don't know the story of how it was worked out but it helps people andi don't necessarily want to know that story, but it was found out and the drug was developed.now, this is a very molecule and can be made cheaply. so this drug through market forceactually, is now made by chemical in shin poong out of south korea who supply the schistosomiasiscontrol initiative with the supply of praziquantel
to this drug. and it's quite striking thatthis drug is now available for around 12 or 11 euro cents per gram, which is absolutelyremarkable. if you look up most study materials, you might want to buy to try and make thismolecule, they will be available from all the net. so really, it has been optimizedand optimate, it's of patent, obviously. the drug has been optimized and optimized andis now available for a very low price. so this is great news. sadly, the news may beis actually too good. when a drug is this cheap and is being distributed to this manypeople and killing this many parasites, you have a problem. if you--evolution tells usthat if you try and kill something, it's going to do something to try and stop being killed,right? so the parasite presumably is going
to become resistant to this or develop tolerance.and this is a big issue for schistosomiasis because there are no other drugs availableto treat this disease. so we're in a very dangerous situation, we're using a drug totreat literally millions of people. sometimes whole countries and villages and cities arebeing treated with this drug and there are no backups for when this drug fails. now,there are obviously some people who will say that resistance will not appear and otherswho say it will appear, and there's this debate going on. my take it on this is better tobe safe than sorry so a lot of the research that we're doing in my lab to do with schistosomiasisis to, for example, develop new analogs of this drug before they need it. so drugs witha slight modification. it turns out in medicinal
chemistry if you have a drug like this andsuddenly it becomes ineffective through the development of resistance, you can changea little bit of it. you can introduce a little group on the left, a little group on the rightand you might be able to regain potency. so we were trying to look at--thinking aboutsimple modifications to the structure which is, i guess, that's what we do, we make molecules.another thing we might want to do is try to find how the drug works. and still after morethan 30 years of use, the mechanism of action of this compound isn't known, which is quiteextraordinary; apparently, quite a common situation in that in parasite medicine. however,there's one thing that we can do right now. and we were in touch the world health organizationto try and discuss how we can keep this drug
good for as long as possible. and the worldhealth organization's perspective is that we need to try and use this drug maximal whileit's still good. and there's a simple thing we can do to try and postpone the developmentof resistance. and what you do is you increase the dose of the drug, right? so you give moreof the drug to try and kill off partially resistant parasites. one of my students wasgiving a talk about this and accidentally, he said that what you should do is give moreof the drug to kill off the partially resistant people. you really get the wrong message.the point is the parasites become resistant, and you don't want that to happen, so youwant--if there are some parasites which are partially resistant, you want to try and killingthose off by increasing the dose, 15-20%.
unfortunately, the amount of drug you haveto take is large. this is a 600 milligram pill. and the field workers who've come toconferences which i've been, tell me the compliances is a real issue. if you're trying to giveliterally tens of millions of people a drug, sometimes in very remote areas, if the drugis too big or tastes bad, it won't be taken. people maybe naturally suspiciously of artificialcompounds, right? we call it pills. it also turns out the praziquantel tastes terrible.so there's another compliance issue. so if you can't necessarily make the pill biggerbut you want to increase the dose, so how do you do that? well, we as chemists, we seea way of doing this. okay. this--just a little bit more chem 101 something--this is an issuein organic chemistry. let's take a few minutes
out. this is an issue of organic chemistrythat i wish the public understood. it's one of the most profound and beautiful aspectsof the universe. and this is not known generally by the public, a fundamental feature of organicmolecules. okay, so organic molecules are--they're three-dimensional, unlike some of the drawingswhich i put up of two-dimensional things, they're three-dimensional things, they'rereal things with depth structure. and the larger the molecule is like proteins and dna,this structure becomes very large, they're three-dimensional objects. it turns out thatthree-dimensional objects can have this property called chirality. and this is all about amirror image. so if you mention some object, let's take a symmetrical object like ball.and if you take a mirror image of that object
that the ball you generate in the mirror looksjust like the first thing you start it with. so the two mirror images are superpimposable,they're the same thing basically. other objects--familiar objects don't have this property. the mirrorimage is not superpimposable back on itself. actually, the majority of things you see innature are asymmetric like this. your hands are a good example. your hands extensivelylooks the same but if you'll try and put and back on each other, you can't they're notsuperimposable, which is why your right hand doesn't fit in your left hand quite frankly.this is very important in nature because it turns out the molecules in nature, almostall molecules in nature above from water and ions and things have this property, that theyhave a certain three-dimensional orientation
in space. and almost all the molecules innature have one orientation, not the other one. so if you imagine just for a second thatyou're walking along that street and you meet someone you know, and you want to shake theirhand. that works one way around, so if i get my right hand to someone and they use theirright hand, we have a good handshake, right? if one is using their left hand then handshake'sall wrong. and this is an important thing. when two molecules like these meet, you canhave different kinds of interactions. and it's very important if we get it right, soall of these drugs that we now take which are now approved by the fda, you have to defineexactly the three-dimensional arrangement of atoms in space and it can't be a mixtureof the two. this was made tragically obvious
by the narration of the solidimide story.solidimide is showing those two structures on the right of the screen. and the differenceonly really is in the structure is that in one case, see what a nitrogen is, you kindof have a hash line, that implies that, that atom is behind the rest of molecule. and onthe right hand molecule, the nitrogen has a kind of thick wedge going to it, that impliesto half the molecule is in front of the rest of the molecule. these two things are mirrorimages, they're not superimposable. and if you take one, it has a very different effectfrom the other. so it turns out that one acts as a sedative they're saying for morning sickness,i think, but the--one of these other molecule inhibits the formation of limbs on fetuses.and so this was tragically realized when these
babies were born deformed through this drug.and since then, it's been definitely required that we have to specify exactly what we givepeople when they take drugs. it turns out actually this molecule inter-converts thetwo when it's in the body so it's not that easy. but the principle remains the same,that one of them is very bad for you and one of them isn't. this has rather nicer implicationsin the case of the molecules on the bottom-left here, this is limonene. and the reason i'vegot this picture of my wife up there holding lemons and oranges is, one is a picture ofher and one's a mirror image and there's lemons and oranges in both hands. one of these moleculesis responsible for the smell of lemons and one is responsible for oranges, so they'retwo mirror image molecules. if you smell one,
you get lemons, if you smell a mirror imagemolecule, you get lemons. so it's very important that we have molecules that specify exactlythe three-dimensional arrangement in space. now, why am i'm telling you this? well, probablybecause i think it's the most beautiful thing, one of the most beautiful things i've everseen. that it is a very profound thing about the way the world is. and i'd love to explainthis more widely but of course i'm in a job. however, this is relevant to praziquantel,the drug that i'm talking about. so the structure i gave you before didn't have that littlewiggly h on the top. now that little--that carbon in the middle there, where the h isattached, is very special. it's got four different things attached to it. and that means thatmakes a small molecule chiral. it means that
in one case if you imagine the hydrogen that'son the left there, it would kind of wedge in and it's coming towards you. and then onthe right side, you've got the hydrogen going away from you; these two molecules are mirrorimages. you don't really see that because i've turned it around but they're mirror images.the one on the left is the drug that works. and the one on the right, doesn't do anything.in fact, it has mild side effects. and in fact, the one on the right that doesn't doanything is the one that tastes bad. so we just want the one on the left, that's it.how easy is that to do? why don't we just--instead of making both and giving both to people,so it tastes bad and there's too much drug, why don't we just give the one on the leftwhich has the right orientation? well, that's
actually quite difficult. so, these moleculesare difficult to make when you have to specify exactly the orientation in three-dimensionsof where all the atoms are. and to give you a sense of that, i guess if you think aboutthe ball here on the bottom-left, it's a symmetrical structure. it's very easy to make somethinglike this because you kind of like have a spinning wheel and it's simple to make somethingthat's symmetrical and round, right? in the middle plugging plus one, i wanted--on theboard a plus one, disclaimer, this is a more difficult thing to make. this is--it's not--sorry,it's still symmetric but it's less symmetric than the ball. suddenly you've got to makethe round part, which is quite easy, but putting the handle you going to have to do that byhand. this is a more complicated structure.
when you get to asymmetric structures likethis rodan sculpture, that's actually very difficult to make, right? because you've gotto, with your hands, put things in various different places. so the less symmetric somethingis the more difficult it is to make, i guess. and a lot of molecules in nature are extremelyun-asymmetric. they have little bit here and there that you have to install by not, well,kind of by hand, except because the molecules are very small, so how we do this? well, ofcourse, we have to design other molecules that act as our hands and install things incertain places. it's very demanding. it's an area called asymmetric synthesis in organicchemistry and hope that people throughout their whole careers like me too to this area.how do we make molecules in three-dimension?
so it's very demanding. and so, unfortunately,praziquantel has this feature. and if you want to make one rather than the other, it'sdifficult. making both at the same time, it's very straightforward, easy. but making onerather the other is difficult. so this is where we were a few years ago, we thought,well, the world health organization wants just the one active form of the drug, it'scalled an antimo, the active, in-antimo of the drug, they don't want an inactive one.they want that because then they can reduce the pill size by half. and the pill doesn'ttaste bad. it's smaller and you can increase the dose even a little bit. so it's a muchmore effective pill. the problem is that as soon as you're trying to make one an antimorather than the other, it becomes an expensive
thing. people like me have to get involvedand i have to think about ways of doing that. how do you install that hydrogen on one faceof the molecule rather the other when a molecule is so small you can't put it there with yourhands? so we were thinking about this, and unfortunately, drug is already very cheap,so how can i justify assigning academic resources to reducing the price of something? i wouldbe fired if i do that, right? that's not academic work to try and try grossly reduce the priceof something, interest will be out in several years. this is not a problem that is solvableby the academia by any means. we would--we, obviously, in the business we're trying toget out high impact research in new frontiers. we're not in the business of reducing thecost of anything. on the other hand, if we
turn to industry, they would not be interestedat all in this problem because there's not money to be made in tropical diseases. there'sno money to be made in taking an already cheap drug and try to modify it little bit. so,there's no real market value for that. this is already a very, very cheap process to make,the combination of the two in-antimos. so, we were left with this problem a few yearsago. i was thinking well, this is an important public health problem that the world healthorganization would like to solve. we can't sell it with academia and we can't sell itwith industry. and this seems like an en passe, right? what do we do? if i try to--this graphis meant to indicate that if i try to assign people to increase the ee, this will be anenantiomeric excess, which is a measure of
how much of one of those molecules they haverather than the other. and you try and increase by piling dollars in the programs, it doesn'treally--you get to this point where you can't anymore assign anymore resources to this problem.you got to reach a breaking point we say, i simply can't justify this anymore. and simply,as you assign more people to this problem, you think, "well, is this really worth ourwhile? how we do this in traditional models, we can't do that." so in the case of this--wefelt, well, i was actually in my honeymoon at the time and i was thinking, "how do wesolve this problem?" what i need to do is try and collaborate with as many people asi can. so this is new to me a few years ago. and it turns out that of course, well youguys know a little about this. you guys know
all about open source things. the idea ofopen source is being somehow illustrated by this comparison between a cathedral and abazaar. so in academic research in chemistry, by and large we operate on the cathedral model.i'm the professor in charge of students and i have my resources and my grants. and wework usually pretty much on isolation using the supposed intelligence of me and my studentsto try and solve problems. we're this autonomous unit. we do collaborate occasionally, we selectpeople, but we are a closed unit. and we were thinking about how to try to solve this problemand we couldn't. the contrast between a cathedral is the bazaar, where anyone can contributeand everyone's opinion is valid and you listen to many people as possible to try to solvethis problem. now, you guys will know more
a lot than i do. so this is new to me andi haven't read the requisite literature about this but this was the essential contrast thatwe were seeing then. basically, we don't operate in science on the bazaar model, we use thecathedral. so we don't tend to discuss problems openly with strangers and a large number ofpeople we don't know and try and get a solution through the community, this doesn't reallyhappen. you tend to publish papers in academic journals and people might respond to that.but it's a slow process, there's not direct discussion between people unless you activelycollaborate. these are very different models. and as i understand it things have gone verywell for the bazaar model and open source. so, from my naã¯ve non-computer science perspective,it seems as if projects like firefox, chrome,
wikipedia, these things have gone extremelywell, extremely powerful programs, they develop really quality products. i think a lot ofpeople tend to associate, outside the movement; people tend to associate open source withendeavors which are purely done by volunteers and which are not funded. and of course thisis wrong. from what i hear, a lot of projects that are open source have involved a fundedkernel of activity to which people then respond and help out. the example that maybe that'srelevant here is as i understand it, the chrome browser was developed by guys here. but it'sopen source that people beyond these walls can help change, modify and update it. that'smy understanding and i hope to be proved right on that. and so, schematically, i put thesetogether. this is two--again rather naã¯ve
ideas by how you do things in two differentways. i shouldn't have pointed that out. i should have put some women rather than menicons, sorry, i just, i was in a bit of a rush. so in the left here, you have the traditionalway of doing science which involves people working in labs, submitting articles to peer-reviewedjournals, waiting a few months. and then the reviewers of that article, who are anonymoususually, maybe one or two people say, "yes" or "no." the article gets published and thenpeople read that in a literature and then people design their own response to it, dotheir own research. publish an article again. the times scale is quite lengthy here, itinvolves months of waiting around while the review process happens. and in some cases,peer review is of course flawed, i don't want
to get in that discussion right now but peerreview is an excellent system but it does have these big flaws that sometimes you canget referees who are maybe not impartial, maybe they have vested interest, maybe sometimesthere's only like one referee on an article and then that appears in print in it's thensaying sanction as being valid. typically, articles published in academic lecture don'thave feedback on them. if you want to criticize an article you have to publish a substantialpaper that refers back to the original. it's not a very interactive process. it's alsofairly slow, so the calendar icons indicates that it's a slow process and costs a lot ofmoney. we apply for a lot of money to do this. and in some cases, we're competing with peoplewho are doing similar research to us. so in
many cases, we may be duplicating effort.on the right, the idea here is that instead of doing that, why don't we post the problemto the community, have as many people as we can reach helping us out with the scientificproblem and publish our results in real-time which are then in peer-reviewed after theyappear, so after publication. this is not a model that operates in science at the moment.this is not how we do things at all. science operates pretty much on the basis of peer-review,before publication not after publication. so wikipedia is an aftermath to a lot of scientistsbecause corrections happen after something is made public. notice that--since open scienceis doing on the right there that data would then be published in real-time as it's acquiredand people would be able to respond as they
see fit and collaborate with you in real-time,even though you may not know who these people are. this is very important qualification,is this not the same thing as an open access in journals. open access is where of courseyou can read things for free, but the research may have been done in a very traditional way.open access is a very worthwhile pursuit. journals--it's very important that journalsare open access but it's not the same thing as an open source or open science, where communityparticipants can actually have an input into the project itself. so if, for example, idesign an organic synthesis of the molecule, anyone, and i posted that as an open scienceproject, anybody in the world could then come along and say, "no, i don't need you to dothat. you should try this and in fact, i'm
going to try it on my lab and i'll get backto you with what's going to--with the results of that synthesis." so anyone can change theproject and repost it for further community input. that's a very different way of doingthings. okay. so i should mention that a lot of people are doing this already. some people,they know who they are. up in the top-left there, for example, is jean-claude bradley,who's at drexel university in this country who has enabled usefulchem project, the usefulchemproject, which is--its aim is to do open science where he's trying to make molecules that willeventually be used to treat malaria. jean-claude actually practices something as a proponentof something called open notebook science. the extreme form i guess of open science whereyou're lab work is on the web completely for
every--everybody to see. so every single datumis published on the web. there's a picture of steve cook who has a biophysics lab inthe university of arizona, who also has--everything he's doing is on the web, and a bunch of otherpeople. even billy clark, cameron neylon and daniel mitchell who are among several zealotsof the open science movement and they're very frequent commentators on how we should dothis. so there's a very passionate community, lots of people i haven't mentioned, passionatecommunity about this. but it's still incredibly small and we tend to have meetings where weall get together and talk about this thing. and the outside world, the larger scientificarea doesn't tend to pick up on what we're doing, unfortunately. however, there are exampleson the web of lots of projects which we've
used open methods. this is a small guide boardof all of these things and they vary a lot. so, for example, on the top-right, the genbankinitiative; that's not really open science, it's a depository of information where peoplecan deposit genetic information that can be retrieved free. this isn't really open sciencebecause you're not really changing things and collaborating on the site. but it's opendata, a very important massive open data resource. the fold it program is an interesting one.if you haven't seen it, it's a game which the public can play to try and help peopleto work at how proteins fold. so in a very ingenious bit of software development, somebodymade a computer program to allow the public to get involved with them. it turns out thepublic are very intuitive about this and have
really good ideas about how protein shouldfold amazingly. the open dinosaur project is something where the public are being involvedin measuring bones of dinosaurs from the literature and collecting data. galaxy zoo is somethingsimilar in astrophysics where people are classifying galaxies. these are what--these are projectswhere public input is required and need to use effectively. on the other hand, there'ssomething called the tropical disease initiative which was started by several people includinga guy who gave a talk here called marc marti-renom, which is a sister site to the site that i'minvolved with. there's also a big movement for trying to find drugs, for example, fortb called the open source drug discovery project which is an indian project, which was startedfairly recently. and then on the bottom-left
here it has something called chemspider whichis a community center resource for chemistry, very unusual. chemistry has an unusual history.we have a lot of very powerful, very wealthy organizations who've become involved in collectingand curating chemical data. and these things are usually--these applications are usuallyquite expensive and universities tend to buy subscriptions to these things to gain accessto information. if you know any university which has that kind of resource--that hasthese resources, then it can be quite difficult to get your hands on that kind of information.the chemspider is something which is on the web and anyone can upload chemical data tochemspider. so it became a community centered resource and with recent approaches by theroyal society of chemistry, who is keen to
promote this. so this is a selection of differentthings where open projects are involved or open data are involved. and some of them likethe galaxy zoo and open dinosaur project are actually where this community input, so publicinput to the project. open wetware, the last thing i want to mention, is a site where anyonecan have a lab book online, free and post data of any kind that they wish. it's a veryimpressive initiative, operates on the basis of the wiki. so in order to have a page onthis, you do have to be a little bit savvy with how to write wiki pages. but it is completelyfree and open and anyone can have a lab and a lab book on the site. so it's very impressive.we sorted out, a few years ago, with this website called the synaptic leap. so if youwould like to see more about it, please just
google us and have a look at it. the ideahere is it's a basic--a blog functionality. and we posted our problems with schistosomiasison this website. the intention of the site is actually to be an open science site foranyone to conduct any projects they want in anything to do with biomedical research. westarted with the schistosomiasis project because there's a philanthropic angle, i guess. theidea of spending some of your spare time helping us out when this project is to do with a neglectedtropical disease, gives participants, you know, good karma, right? so people feel goodabout contributing to this. but really, it's--the aim of it is to have something which is wider,so you can do any kind of collaborative biomedical research on the site. so up on the top there,there's the schisto research community and
on the bottom there's an example of somethingthat my post i recently did, which is a chemical reaction which we did in the lab. and beneaththat diagram is all the data about how that worked and what happened, including the rawspectral data of what we did. now i just want to mention something about this. this is alimited functionality. it still operates as a blog. it's built on drupal. and i don'tknow about you, but whenever i see a blog post which is interesting and for which thereare several comments, maybe 10 or so comments, by the time the comments get to about 10 orso, i chill down, like a comic book and i'm reading them. a blog functionality is reallyquite limiting. it's--you can't do a huge amount with this. and in terms of communityinput, it's actually quite limited in what
people can do. what we really want is to havethis, but much more intuitive and functional. at the moment, it's very linear and very flat.we're doing our best with this, but i think we need something that's much more intuitive.and that's really what i'm trying to get at here. just before i get on to the nitty-grittyof that, just a couple of other advantages of open science; more generally, the ideaof doing this on the web. so the project we're posting here, of course, is asking the communityto help us device a synthesis for this molecule for a very, very low price. the other advantagesof doing science like this, on the left, is transparency. you might have heard about thecontroversy surrounding the climate change emails in the u.k., the university anglia.this idea that the public thought of that
was science that was being hidden from publicview, where perhaps some research allegedly was being suppressed because it didn't agreewith the idea of climate change. this doesn't do science any good to have this kind of publicperception of what we're doing. and it--there's a real advantage in doing open science isthat everything is transparent and you can see what's going on and nothing is hidden.and i think in terms of public engagement with science that's going to be very important.in the middle of this picture is a starfish, again, this is a probably an it analogy, thestarfish and the spider. open projects don't have leaders. i mean, i am the leader of theproject that we're doing at the moment, but i don't have to be. the project is the importantthing and if i decide to do something else
or if i called to write to do something else,then somebody else will take over. it's a leaderless organization, which is a big advantagefor open projects. somebody can take over; anybody can take over and anyone can takeon site projects and lead things. the third picture is meant to imply speed. to me, oneof the big advantages of open science is speed of progress. i – my theory is the one thingthat we're trying to test out in the next few years is an open science project whereanybody can contribute and experts identify themselves, we'll operate faster than a closelab project. that's the hypothesis. and we are hoping to try and test that in the nearfuture. but we're starting with our synaptic leap project for this drug. the picture ofthe plankton here is meant to remind me that
the one important lesson we've learned withopen science over the brief period that we've been doing it is something which, i think,is very well known to you, it professionals, who have been working in open source, whichis that it's not enough to post a problem and have the community input. you have topost data first; you have to post results, a kernel of activity to which people respond.and this was very clear to us with the synaptic leap which, for the first couple of yearsof its existence, was very quiet because we had no funds in our resources to put peopleon the project. we then went the long route and asked the australian government for fundingfor this project with the world health organization as our sponsoring partner. and we secureda grant for this project in may 2008, which
took a while to get signed off, but is nowactive. now, we have somebody working on the lab who's posting real research data as it'sgoing on. and that means the people have a lot more to get their teeth stuck into. we'vejust started, but it means the people can now respond to us. it's crucial i think inany open science endeavor, any open source endeavor to have sometimes a funded kernelof activity which people can respond to. that's our important lesson. okay, so i want to saysomething about experimental science and then i want to do my appeal for applications. sothis is the real nitty-gritty. being an experimental chemist, being an organic chemist is verylike being a chef. you have things, your resources, you buy things in, you combine them with variousapparatus, which you have in the lab. a lot
of the things in the chemistry lab have acollaborate that's in the kitchen, it's amazing. you have, you know, a gas flame in the kitchen,we have bunsen burner. you tend to boil things off, maybe you want to reduce something andtake water off something; we have something with that in the lab. lots of things thatwe use in the lab are very similar to the kitchen--kitchen kind of chemistry. there'sa picture on my students. (inaudible) who--his bench is right to the left there, and he hasall the stuff laid there and his team covered which is the thing he uses for toxic stuffis behind him. a bench chemist will come in early in the morning, 8 o'clock in the morning,to think about what they're going to do. they'll design an experiment, they'll get their chemicalstogether and use glass and glassware and metal
things and a bunch of different things todo their chemistry. they'll run a reaction. they'll effectively taste it, as you do whenyou're a chef by sticking a spoon in and then licking it. in the chemistry lab, you neverdo that. but you--there are ways of testing what's happening in your reaction. and thenyou isolate the thing you've tried to make. you analyze it with some instruments and thenyou write up what you've done. this is what a chemist does in our life. the analysis iskind of complicated. as a chef, you taste things because your tongue is a very sophisticatedthing. in the lab, you have to take the molecule that you think you've made and put it intosome very large expensive instrument, which then analyzes if that's the right thing. there'sa lot of data here. for example, the instrument
we use the most, we take all molecules andwe put it into this large super conducting magnet. and we spin this molecule very quicklyand we blast it with electromagnetic radiation. and rather like when you hit a bell, you listento what comes off the molecule after you've done that. so, when you strike a bell you'regoing to listen to the tone. and, of course, what you get off the bell is always a sortof vibrational data which is very complicated, and your ear transforms that into one note.similarly, with something called animospecstropy in the lab, we take molecules and we blastit with this radiation; we get this very complicated signature that comes off. we use to make allthe (inaudible) transform and get these lines on a piece of paper. and the signature onthose lines and how they appear allows me
to say "yes, that's the molecule we thoughtit was" or "no, it isn't." lots of big instruments' generating lots of data. but in a typicalday, a student will use all these different things. if that student is meant to tell anotherstudent how they did something, how did they do that? well, they can write up somethingin the traditional paper. that often hides little things that you might have done whichare special, in a same way that a recipe book--often recipes don't work, you don't quite followthe instructions right or something was just missed out or the decimal point wrong somewhere.if you want to capture the research process, you need ways of doing that that are reallyquite data-rich. so you want to be able to capture things with audio and video. you'dlike to be able to post raw data to a website
rather than the interpreted lines that wetend to get, so maximizing amount of data that you publish. and really, you want somethingwhich is quite intuitive and rich because you want somebody to follow what you've done.for example, also in the lab, that's me talking to one of my students, althea. we have thesefumes covered with kind of prospects covers and often you write on it, you write on whiteboardat the back here. if you're going to collaborate with someone, you want to be able to easilycollaborate with them as if you were sitting next to them with a coffee, talking aboutscience. and really, at the moment, we can't do that outside my lab. we can't collaboratewith people who are outside and sitting outside my lab. if we've got a problem, we go downthe corridor and talk to a colleague. but
if we want to throw this project open to theworld, we need a really intuitive way of collaborating as we would in a normal lab. how do we dothat? and how do we maximize the input that people are going to give us? well, somethingwhich, i think maybe some of you will know as it professionals, is something called "stackoverflow," maybe some of you have heard about, which is a site where you can post code andask people to help you out solving certain problems. with code, that works really wellbecause you can cut and paste code and stick it on a webpage and people can rapidly respond.it's also a very nice idea because you can have medals awarded to you for valor of service,right, and your reputation increases. so it's a good way of trying to develop a reputationfor yourself as someone who help people solve
a problem. of course that's good for text,but for experimental science, this just doesn't really exist. something has been started,chempedia lab by a guy in san diego, richard paloka, who has taken the basic functionalityand tried to use it for chemistry. at the moment, it's quite text-heavy, but it's avery good idea to try and use the same idea in experimental science because what we needis something again that's still very much more intuitive and allows data-rich thingsto be posted, allows links to online pages where all your data are posted, allows linksto online lab books for science. so basically, the structure we need is something which isan intuitive lab book online, where all of the data are linked with your experiment andwhich can easily be analyzed by somebody else
as part of a collaboration and collaborateis composed to your webpage. >> [indistinct]>>todd: ...type text and that's fine. and then you can post something like that, butthere is no chemical content in this that works and they're not understood by a machineto be referring to molecules or chemicals. so the text is quite dead and if anythingwas going to search this, you wouldn't really have a lot of input from the computer aboutwhat is chemical information, what isn't. to be able to take text and convert that tosomething which is chemically rich, so where wood is associated with a molecule and canbe searched and analyzed and indexed would be tremendous for html xml. and a guy called[indistinct] wrote the language called cml
which is chemically rich mark-up languageand has worked with microsoft and it has a reword here. where did microsoft to developa chem. word add-in, where a word document can be searched by a machine and the chemicalinformation can be annotated and extracted automatically. so when you hover over a word,you get a structure and you can change the structure and that changes the word. so ina phd thesis, for example, this become a very rich document where all the chemicals arepart of the actual fabric of the text and are not simply words. now an example that'sjust recently brought to my attention with something called chemicalized dot org, thistakes any given webpage and extracts chemical information. and you can see, what's happenedhere is that in the usual latin text you got
on pages, it spotted beta carotene, whichis a molecule and if you hover your mouse over that, you get the structure of the molecule.if you click on that, you get taken to a page where there's a bunch of chemical informationabout the molecule. this is very useful and it makes, for example, html pages are richfor chemists; that means it can be searched very effectively. we could do with somethinglike this actually for drupal, so given that drupal is open source. what we really needis an extra button on this menu up here which says, "okay, take the text that i've justentered here, scan it for chemical information and please annotate these individual wordsso the page, when it's published, it's clear that these molecules are in there." so ifi write the word "benzinc" and i click this
little button, it's [indistinct] moleculeand then on the html pages published, that becomes an active word that commend the searcheffectively and can be annotated in this way. that will be a very nice project that we coulddo which would enhance drupal a great deal for chemists and make the resulting web pagesthat we make much more functional. okay, so the last--just, just summary--the summaryof where we are--this is my son, harvey; he's playing with his first molecule, which isgreat; start him early you know? but this is--this is how i feel with this, with openscience. i have absolutely no idea where we are going to be definitely going and how weare going to get there, but it feels right. it feels--so, science that is trying to openwhere anybody can help us out and nothing
is kept secret is the real spirit of science.it's fast and it's transparent and it's generous of spirit. this project that we're doing wherewe are trying to get the price down of this drug with the world health organization, we'vegot another two and three quarter of years to solve that problem. it needs to work; wehave to be able to show that by massively distributing a collaboration like this, whereeverything is in the open. we need to show that we can do that and we need input fromchemists all around the world, particularly process chemists who work in industry, tohelp us with this problem. the price constraint is extremely severe and it's a real challengefor organic chemistry. of course, what we would like to do eventually with open scienceis to move beyond philanthropy. we are doing
a project which is organic chemistry but wesaw--it's, it's hard for physical science, but it does have philanthropic element wherepeople might contribute because they feel good. what would be nice is try and move intoan area which is academically hard where there's a lot of activity at the moment and peopleare competing with each other to show that an open science project could actually generatepapers and results faster than traditional close collaborations. that would be quiteexciting, but it's not something that we're doing right now. generally, the dollar signthere indicates that countries weren't maybe thought by many people about open source.open science also may well need funded kernels of activity where projects are--small projectsare funded and lots of the scientific community
can respond to us. now that to me, would beextremely attractive if i was a funding agency who want to de-fund scientific projects--ifi was a government agency, i want to de-fund scientific projects. what i would do is tryingto fund a kernel of activity and then have, have a wider group of people help me out,so we leverage more activity for my funding dollars. there is an advantage there, of course,that i've covered before is that once the funding runs out, the project doesn't haveto stop; it's this leaderless organization, the project can continue. and i guess thelast thing is a more general point that open data are very important. the idea that openscience of course share data with many people as possible; and this is always going to bea good thing; that if we have data in labs
which the public have funded through taxes,those data should be available for any body to see. and open science obviously necessitatesopen data as part of its reason for being. and so, my main appeal, of course, though,so is--just to close--is that at the moment, we do not have really good intuitive toolsfor scientists to collaborate over large distances effectively. we have tools that are--thatrequire tutorials to use. my students are very busy; they're very busy making moleculesin the lab. and they--i know what's going to happen if i ask them to try and learn howto write a wiki page or sit through a tutorial about how to use something. they are goingto say they're just too busy. those are my students; and some of them are most receptiveto this that i know of. trying to ask an experimental
science student to learn something beforethey can post their data online, to me, is like asking, "gordon ramsey to learn arabic"right, this is silly. he wants to do his cooking and generate a product. he doesn't have tolearn a language to be able to do that. and with chemists and experimental science students,we need applications--applications which do not have tutorials on them so that scientistscan rapidly gain and comment on each other's work and share data effectively. so, giventhat i've never needed to look at tutorial for google app; i can't hear, right. so, iuse gmail and google docs and picasso without reading anything. i just started using itbecause it was intuitive. if we could develop that for a lab book, for an open shared electroniclab book, that would be fantastic. we--my
lab is collaborating with a guy called jeremyfrey of the university of south hampton to try and link online electronic lab books tomachines in a chemistry school. so, data are meshed with an experimental technique. ifwe could expand this to have a front-end that was incredibly intuitive to use, i think we'dgo places. and i think a lot of scientists would love to do--to share what they are doingif they had an effective intuitive tool to do that. and that's really my appeal, is forsomething about to happen. a dialogue between it guys and experimental guys, phd studentin the lab and know what they need to try and develop a real killer app for an onlineshared electronic notebook. okay, so with that, i won't take anymore of your time. ijust want to thank carol again, and chris,
and thank you, guys for coming along and listeningto this idea. thanks. >> [indistinct]>> science is still going to get tenure and paying in all kind of stuff and how does thatwork with conventions or spread outs or [indistinct]. >> todd: yeah. okay, so the idea that if youopen everything up to the world, you're going to commit professional suicide, yes. i mean,i--that's--at the moment, i think that that's certainly the perception. there are some bravesouls who are doing it anyway, a couple of people i just mentioned. it's interesting.the--there is this sense, there is this--i'm sorry, there's this prejudice that if youpublish data online, you can't then put it into an academic journal. and actually, forsome of the high impact chemistry journals,
that's true. so i can't publish in certainbig journals if i've already released data. in many cases, that is not true. so i--ifi have published everything on the web and i've decided to summarize it on a paper andthen submit to nature, they'll take that paper. so there are also journalists which are happyto do that, but this is a test case. how many journals will take those kinds of papers andhow effective are they? i think that if you can do that, if you can still publish yourwork in journals, which are traditional journals, then i think you'll be okay. the questionabout whether you'll get scooped is another thing. so if you have a great idea and youthen put it on the web, what are you going to do? of course, if something is commerciallysensitive and you want to patent it, then
of course you can't do that; that's off limits.that's something is not--and it's something which you don't foresee to have commercialinterests. my theory is that by opening it up and by recruiting more collaborators, yourscience will actually go faster; that's my theory. but i--no one has done that yet; idon't' know if it's going to work. there was a nice example last year, i think, a guy calledshean cuttler who is a biologist; he's with riverside, i think, who had a nice resultthat he found. he's a pump biologist--had a nice result that he found and rather thanpublishing his nice result, he went to actively recruit his competitors. and then together,they published a much larger piece of work in the journal science, which is an incrediblyhigh impact paper and amazing and well-sited.
the idea is that you can go and actively getpeople to help you out. it's an anthem with a lot of scientists who may be don't usuallywant to trust their competitors with what they've done. but i think this is--this isthe next exciting frontier to me is whether it accelerates your science. if it does, theni think [indistinct] committees would be rather excited about it. all right, thanks--thanksguys.
If you want to know about herbal product visit IBHIndo Herbal Indonesia. Also best herbal product for diabetes visit Obat Diabetes Alami - Obat Herbal Diabetes Paling Ampuh. Visit Jual Obat for online shoping herbal medicine.