One of the most readable overviews of the state of science can be found in the article "So Much More to Know" published a few weeks ago in a special edition of Science. For this article, scientists were surveyed on what they saw as the most important unanswered questions in science which could conceivably be solved on the 5-20 year time scale. You may read it here: http://www.sciencemag.org/cgi/content/full/309/5731/78b. Maybe I better rephrase that. You should read it here: http://www.sciencemag.org/cgi/content/full/309/5731/78b. Or better yet, run, do not walk to your nearest internet enabled computer and READ IT!
Why the fuss? If you read this blog occasionally you will realize that one of its purposes, in addition to whatever happens to strike me as interesting, is to educate and provide perspective on science. This article gives a picture of the scientific enterprise in it rawest and most exciting form. It tells us about the unknown in a clear and accessible way. This is the true realm of science, not the ghost of science past you find in a science textbook. These questions will be the stuff of future Nobel prizes and scientific greatness.
I read the article with some relish. It is a wonderful article because it gives a sense of where scientists perceive excitement will be found. For graduate students, hold that thought and try to figure this out for yourself whenever you attend a scientific meeting. You should "sniff the wind" in an abstract sense and see if you can get a feel for the emergence of new paradigms. I will give you two examples from my own experience. In the mid-80s I went to some meetings related to oceanography. At one of those meetings I sat down with a more advanced colleague (he was a Ph. D. student at the time, I was a research assistant) at lunch and we got to asking ourselves what was "new" in the talks at the meeting. This particular meeting was held at a time when the concept of the "biosphere" regulating global climate was "getting traction" as an idea and moving mainstream. For me it was completely and wonderfully new. This notion is still emerging and in some places there remains stubborn resistance (notably the Bush white house).
A second example was two visits I made to PITTCON in the 90s. PITTCON is the premier meeting concerned with analytical chemistry and chemical instrumentation. In 1995, PITTCON was still entrenched in the classical view of analytical chemistry. It was full of atomic spectroscopy, GC, etc. I am not saying there wasn't anything else, but the bulk of what you would have seen there is what you can find in a standard text on analytical chemistry. When I went back a few years later, there had been a sea of change in 4 years. Bioanalysis, DNA sequencing, and other "bio" applications had taken over center stage. This is likely to be the paradigm for many years to come. In other words, people realized that the great unsolved problems in what might be better called "analytical sciences" lie in the direction of biology. Unfortunately, the classic textbooks from which we teach analytical chemistry have not caught up.
The second point I found interesting is a continuation of the status quo in physics. Reading it, you will find the traditional Physics/Philosophy questions about the nature of the universe and dimensions. The "philosophical" position that physics has played in science and life since at least the beginning of the last century (at perhaps going back to Galileo, Descartes, and Newton - Ok, Ok maybe I should say Aristotle and Ptolemy) remains. There are no real surprises there. It is interesting to see this as essentially an old paradigm representing the status quo. What it is missing is the fact that many "traditional" physicists and physics departments have retooled themselves in biophysics while many others struggle to find direction.
A third point of interest is plain as day. Those of you who have not realized that biology is the center of attention, inspiration, and creativity in science need to take a good hard look at this list. Not only are the great problems in biology attracting attention but clearly many people with creativity and imagination have found a home in biological sciences. This bodes well for the strength of the discipline for many years to come. Need I say more? Physics leads the list, but the paradigm this represents is old news while the new focus of imagination is clearly in the biosciences.
The final point was a sense of disappointment and being let down. It is as if they didn't bother to survey chemists. Sure there are one or two (ok maybe three or four) questions that focus on chemistry, but there is a certain spark lacking. Maybe they did talk to a few chemists and they just couldn't give a good account for themselves. What found itself into the list is a set of questions that make you go "huh?" If the best we can come up with to provide 5-20 years worth of excitement for chemists is "the structure of water" and a few other lame notions there is something deeply wrong in the field. It is no wonder that we have trouble attracting students and chemistry departments in places like the UK are being shut down. Let me put it this way. I think of myself as a chemist. I like chemistry. I have worked as a researcher in chemically related fields for roughly 20 years. Even with that background, if someone wrote the definitive paper on the structure of water, I would not give it more than passing interest. I might not even notice. I wouldn't write home. I doubt it would change my outlook on chemistry is any substantive way and I can't imagine making it a centerpiece in my teaching. The question is where are the new paradigms in that question? Even as a chemist I can barely stifle a yawn, call me a Philistine but that's facts. Oh my goodness, let's go out to a secondary or high school to get students excited about the science of chemistry and tell them that we still don't know how many hydrogen bonds between water molecules there are. They are all going to go into medicine. Ok that isn't quite fair since most of our best students want to go into medicine anyway. But, you get my point. As my Ph. D. advisor taught me (he had a unique way of doing this - more on that another day), you gotta ask yourself "Who the hell cares?"
Having come to that conclusion, I decided to spend some time coming up with some questions of my own (not all of them are chemistry oriented). Let me know what you think.
1) Can a chemical sensing system be built that beats a dog? The nose of a dog is a pretty amazing thing. Even in the USA, the center of insane technological approaches to sniffing and screening, when you go through an airport you may find yourself being approached by well mannered dog. There is a reason for that. It means that analytical chemistry can't beat the dog yet for sensitivity, diversity, and cost-effectiveness. Hmm... we have a problem here. I am trying to come up with a question for chemists and here I am taking inspiration from biology. Perhaps I should close up the lab and raise dogs. All kidding aside, what are the unique characteristics of a dog's nose which allow it to beat the best technology the world has to offer. A bloodhound can track a person's scent hours after the fact based on a sniff of clothing. That is simply amazing. I am not aware of a "sniffing" technology that can even recognize the scent of a person, much less track him or her across a field.
2) Is it possible to create a secure operating system for an internet connected computer? Having received a bunch of viruses via e-mail and having noted a spike in the attempts to access my currently "clean" computer I have come to wonder. The triumvirate of virus production, spam, and money seems to be winning the war at present. While there are incremental approaches to new threats that protect for a time, I have not seen any fundamental thoughts on whether it would be possible to create a secure operating system. I suspect this one requires an interdisciplinary answer. My sense is that it will be no more possible to wipe out computer viruses (and related) that it has been to wipe out bacterial disease. I am not convinced that the latter is impossible, but, under the current policies of anti-biotic use, it is unlikely to be anytime soon. I think an analagous situation applies to computers as well.
3) This one is a pretty abstract question, but bear with me. What is the future of dissipative systems in chemistry? What is this guy talking about? A scientist contemplating the characteristics of chemical clocks and related reactions (look up the Beluzov-Zhabotinsky reaction) in the 1960s came up with the concept of dissipative systems. These are structures that form spontaneously in systems far from equilibrium. Perhaps the most approachable dissipative system is the whirlpool that forms in the sink when you pull out the plug. Some argue that the formation of dissipative structures is a characteristic of systems which are far from equilibrium. In undergraduate chemistry, we primarily teach about the thermodynamics of systems close to equilibrium. Systems far from equilibrium appear to have fundamentally different behavior and there seems to be a self organizing principle in at least some of them. This is really a pretty exciting concept and it is to our discredit that we do not try harder to teach these fascinating concepts. As a result, I am convinced there is much gold to be mined if someone were able to harness the self organizing principles in new ways.
So, those are some of the questions that come to mind. Perhaps you have your own questions.
Thursday, July 21, 2005
Friday, July 01, 2005
Computers 3: Computers Save Time (really they do?)
I have been thinking again about computers, again. I started thinking about them because I am finally really convinced that computer use has increased my level of productivity (despite the nearly constant distraction of web surfing). I was always a bit dubious and remember the Mantra “Computers save time” which one was supposed to repeat over and over until it was believed. For years I found the comment a friend inGermany said once (“Computers allow you to do quickly things you otherwise would not have done at all.”) rather funny (because it was true). In otherwords, I really have not been convinced of them as a productivity tool. Instead I thought of them as a distraction except when writing computer programs (I have written in PASCAL, BASIC, and C/C++).
But today I was sifting through my e-mail program trying to sort it out because I get rather a lot of e-mail. I have neglected my in and out box housecleaning for a while since I had a very busy semester. After boredom set in (I get a lot of e-mail remember), I pressed the statistics button on my e-mail program and it told me the following. I have received 21,531 emails. I answer approximately half of these giving a nice round figure of 9135 e-mails sent. This covers a period that begins February 10, 1998 and ends today. This only includes the e-mails I saved, I have thrown out a lot of junk over the years. This is an average of 3,000 e-mails received per year and about 1300 sent. This doesn't give the real picture because the volume of mail (in both directions) has increased enormously in the last few years. For example, I have already sent 1616 e-mails and received 2486 in the first 6 months of 2005.
This is quite astonishing. I had no idea. This amounts to 13 received per day and about 9 sent every single day of 2005. What is remarkable, particularly the outgoing part, is that this is real correspondence. Back before the internet was so popular, I used to write letters. I never averaged 9 a day. Maybe one or two a week to a girlfriend.
I suspect that I am not alone in being quietly turbo-charged toward a huge increase in productive work. I am sure other people, if they took the time, would find something similar. If you put that in perspective, at a rate of $1/letter (probably not far off the mark when you think of postage, paper, pens, envelopes, and remember that much of this is overseas correspondence), the 1616 e-mails I have sent this year will buy a decent computer wich will last for 3-4 years (my last one was 3 and a half when it gave up – the first that I actually wore out before it became obsolete).
Let us put this is pespective. My university really likes memos and things on paper. The fundamentals of the university have not adapted to the electronic age and a lot of paper is pushed around. I am convinced the e-era will be over before we get there. However, since I do all of this composition electronically I still have them all. In the paper correspondence, I have only produced some 234 memos and reqeusts for orders etc. While it is not bad productivity (1-2 memos a week), it is clear that the activation barrier (yes, I am a chemist) to productive work is greater when printing and paper pushing are required than it is for e-correspondence.
What is more, I am not convinced anybody has read all of this correspondence, some vanished into a black hole of sorts. If they wanted to prove to me that they did read it, or look back over any of it now, I doubt they could find it, collate it, and read it. But that is not the case from my end. With a few exceptions, I have every peice of correspondence, every assignment any student has ever sent me, every paper and price quote, all the lab manuals, the marks, as well as a lot of the comments I have made on student work.
Again, this is quite remarkable. The filing cabinet in my office is in hopeless chaos. I try (well sometimes I do) and sometimes can find items in my file drawer, but it might take me an hour or in a bad case an afternoon. If I don't find something, I am never really convinced it isn't in there somewhere. But, I can find nearly anything in my e-correspondence in seconds. I can sift through the 800 MB of e-mail and attachments in seconds. In a worst case, I can search my entire hard drive in a few minutes. Again, this is truly remarkable.
Perhaps you do not believe that this is really productive work and think it is really a distraction. What is the productive work that is covered in this huge volume of correspondence? Ok, let's see how this strikes you. My current out box begins in April of 2005 and continues through to today. It has 325 items in it. 72 of those were sent to addresses with edu or ac (academic) in them. This is mostly e-mail to collegues here and abroad about a variety of academic topics. Some students with campus pipeline accounts are included in this group. 140 went to either hotmail or yahoo addresses of which I estimate 95% is correspondence with students. 29 were to addresses with a .de ending (germany), all but 5 of these were correspondence related to the completion of two papers that were submitted for publication recently. The remaining 50 or so are a mix of correspondence with suppliers (books, chemicals, equipment), colleagues (private e-mail for university staff members), scientific friends (a variety of industry locations), and occaisional notes to family and friends. Looking at this “snapshot” of my correspndence,” I think the big winners are students who recceive 50-60% of the mail in this period. During semesters I have regular correspondence with students. I also on occaision write to former students about a variety of topics (recommendations, jobs, graduate program suggestions, etc.). I should note that the proportion of student correspondence is probably underestimated here because I have already done some housekeeping of my outbox.
So to summerize, I have finally become a believer in computers as productivity tools. I was never so convinced that a computer was anything more than a glorified combination of typewriter and calculator. Now I think it really can boost productivity (it has mine), despite the distractions of surfing (yes, I find it a distraction too).
But today I was sifting through my e-mail program trying to sort it out because I get rather a lot of e-mail. I have neglected my in and out box housecleaning for a while since I had a very busy semester. After boredom set in (I get a lot of e-mail remember), I pressed the statistics button on my e-mail program and it told me the following. I have received 21,531 emails. I answer approximately half of these giving a nice round figure of 9135 e-mails sent. This covers a period that begins February 10, 1998 and ends today. This only includes the e-mails I saved, I have thrown out a lot of junk over the years. This is an average of 3,000 e-mails received per year and about 1300 sent. This doesn't give the real picture because the volume of mail (in both directions) has increased enormously in the last few years. For example, I have already sent 1616 e-mails and received 2486 in the first 6 months of 2005.
This is quite astonishing. I had no idea. This amounts to 13 received per day and about 9 sent every single day of 2005. What is remarkable, particularly the outgoing part, is that this is real correspondence. Back before the internet was so popular, I used to write letters. I never averaged 9 a day. Maybe one or two a week to a girlfriend.
I suspect that I am not alone in being quietly turbo-charged toward a huge increase in productive work. I am sure other people, if they took the time, would find something similar. If you put that in perspective, at a rate of $1/letter (probably not far off the mark when you think of postage, paper, pens, envelopes, and remember that much of this is overseas correspondence), the 1616 e-mails I have sent this year will buy a decent computer wich will last for 3-4 years (my last one was 3 and a half when it gave up – the first that I actually wore out before it became obsolete).
Let us put this is pespective. My university really likes memos and things on paper. The fundamentals of the university have not adapted to the electronic age and a lot of paper is pushed around. I am convinced the e-era will be over before we get there. However, since I do all of this composition electronically I still have them all. In the paper correspondence, I have only produced some 234 memos and reqeusts for orders etc. While it is not bad productivity (1-2 memos a week), it is clear that the activation barrier (yes, I am a chemist) to productive work is greater when printing and paper pushing are required than it is for e-correspondence.
What is more, I am not convinced anybody has read all of this correspondence, some vanished into a black hole of sorts. If they wanted to prove to me that they did read it, or look back over any of it now, I doubt they could find it, collate it, and read it. But that is not the case from my end. With a few exceptions, I have every peice of correspondence, every assignment any student has ever sent me, every paper and price quote, all the lab manuals, the marks, as well as a lot of the comments I have made on student work.
Again, this is quite remarkable. The filing cabinet in my office is in hopeless chaos. I try (well sometimes I do) and sometimes can find items in my file drawer, but it might take me an hour or in a bad case an afternoon. If I don't find something, I am never really convinced it isn't in there somewhere. But, I can find nearly anything in my e-correspondence in seconds. I can sift through the 800 MB of e-mail and attachments in seconds. In a worst case, I can search my entire hard drive in a few minutes. Again, this is truly remarkable.
Perhaps you do not believe that this is really productive work and think it is really a distraction. What is the productive work that is covered in this huge volume of correspondence? Ok, let's see how this strikes you. My current out box begins in April of 2005 and continues through to today. It has 325 items in it. 72 of those were sent to addresses with edu or ac (academic) in them. This is mostly e-mail to collegues here and abroad about a variety of academic topics. Some students with campus pipeline accounts are included in this group. 140 went to either hotmail or yahoo addresses of which I estimate 95% is correspondence with students. 29 were to addresses with a .de ending (germany), all but 5 of these were correspondence related to the completion of two papers that were submitted for publication recently. The remaining 50 or so are a mix of correspondence with suppliers (books, chemicals, equipment), colleagues (private e-mail for university staff members), scientific friends (a variety of industry locations), and occaisional notes to family and friends. Looking at this “snapshot” of my correspndence,” I think the big winners are students who recceive 50-60% of the mail in this period. During semesters I have regular correspondence with students. I also on occaision write to former students about a variety of topics (recommendations, jobs, graduate program suggestions, etc.). I should note that the proportion of student correspondence is probably underestimated here because I have already done some housekeeping of my outbox.
So to summerize, I have finally become a believer in computers as productivity tools. I was never so convinced that a computer was anything more than a glorified combination of typewriter and calculator. Now I think it really can boost productivity (it has mine), despite the distractions of surfing (yes, I find it a distraction too).
Thursday, June 16, 2005
Researchers and Programs in Analytical Sciences
This is a listing of Researchers and Programs in analytical sciences that students thinking of graduate school should know about. I would consider it an honor if one of the students in my courses found there way into one of these labs or programs. When reading this list of people and programs remember they reflect my background and interests.
The point here is that everyone thinks of the big name schools (Harvard, Cambridge, California Insititute of Technology,..) when thinking about great programs for graduate studies. These universities and institutes have excellent reputations and there is a reason for that. However, graduate level research, particularly at the Ph. D. Level is not so simple and there are pockets of excellence in places you might not expect it. For example, in the area of fluorescence spectroscopy (which is dear to my heart) none of these great institutions come to mind. Instead I think of places like: The University of Illinois Urbana Champagne, The University of Maryland Baltimore. The former is a very strong university across the sciences (particularly chemistry) and if you haven't thought about it in the same league as Harvard, maybe you should.
As another example, if you are thinking about optical sciences the University of Rochester and the University of Arizona have been very strong for some time, but within the specialty of microscopy (also dear to my heart) the US as a whole is not very strong and you should look elsewhere (Germany, England, and Australia) because that is where the best are located.
I will try to update this listing as I have time and people and programs come to mind. Please do not get offended if you are not on the list. It is probably a matter of time more than anything else. If you would like to jog my memory please provide a comment or send an e-mail.
Biological sciences:
European Nuerobiology Institute: I visited the European Nuerobiology Institute in Göttingen last summer and ever since I have been trying to get student to think about the International Graduate program offered jointly by the University of Göttingen, The Max Planck Institute for Biophysical Chemistry, The Max Planck Institute for Experimental Medicine and the European Neurobiology Institute. The details may be found here: http://www.gpneuro.uni-goettingen.de/The University of Göttingen has been a very strong University for a very long time (44 Nobel prize winners have studied or worked there). But more important than the reputation of these places for you as a student, I do not know of anywhere in the world where such a combination of resources is being brought to bear on such an important scientific problem. There are Nobel prizes waiting for those who figure out how the brain works. Trust me, I'm a Doctor (well in the Ph. D. sense at least).
Analytical Sciences:
M. Bonner Denton (University of Arizona, US) http://www.chem.arizona.edu/faculty/profile/profile.php?fid_call=dent
Paul Geladi (university of Umea, Sweden)
.http://www.chem.umu.se/dep/ok/staff/people/pg/index.html (Has been very influential in the field of multi-variate image analysis and chemometrics). A bit of a weak web site though.
Jonathon Sweedler (UIUC – Note this University has a very strong analytical chemistry program) http://mrel.beckman.uiuc.edu/sweedler/
Richard Zare (Stanford University) http://www.stanford.edu/group/Zarelab/
Fluorescence and/or Biophysics:
Bob Clegg (UIUC, US) http://www.physics.uiuc.edu/People/Faculty/profiles/Clegg/
Eliot Elson (Washington University of St. Louis). http://www.biochem.wustl.edu/~elelab/ele.htm.
Enrico Gratton (UIUC, US) http://www.physics.uiuc.edu/People/Faculty/profiles/Gratton/
Thomas Jovin (MPI Germany) http://www.mpibpc.gwdg.de/abteilungen/060/
Joseph Lakowicz (UM Baltimore, US) http://www.umbi.umd.edu/~mbc/pages/lakowicz.htm
Doug Magde (UCSD, US) http://www-chem.ucsd.edu/Faculty/bios/magde.html
Nancy Thompson: (UNC Chapel Hill. Note this University has a very strong analytical chemistry program) http://www.chem.unc.edu/people/faculty/thompsonnl/nltindex.html.
Microscopy:
Min Gu (Swinburne University, Australia) http://www.swin.edu.au/bioscieleceng/soll/cmp/profiles/Mingu.html.
Stephan Hell (MPI for Biophysical Chemistry, Germany) http://www.mpibpc.gwdg.de/groups/hell/
Thomas Jovin (MPI for Biophysical Chemistry, Germany) http://www.mpibpc.gwdg.de/abteilungen/060/
Colin Shepperd (National University of Singapore) (Formerly of Oxford University, and University of Sydney). http://www.bioeng.nus.edu.sg/people/colin/index.htm
Enrst Steltzer (EMBL, Heidelberg Germany). http://www-db.embl.de/jss/EmblGroupsOrg/per_546.html
Tony Wilson (Oxford University, UK) http://acara.eng.ox.ac.uk/som/People.html
The point here is that everyone thinks of the big name schools (Harvard, Cambridge, California Insititute of Technology,..) when thinking about great programs for graduate studies. These universities and institutes have excellent reputations and there is a reason for that. However, graduate level research, particularly at the Ph. D. Level is not so simple and there are pockets of excellence in places you might not expect it. For example, in the area of fluorescence spectroscopy (which is dear to my heart) none of these great institutions come to mind. Instead I think of places like: The University of Illinois Urbana Champagne, The University of Maryland Baltimore. The former is a very strong university across the sciences (particularly chemistry) and if you haven't thought about it in the same league as Harvard, maybe you should.
As another example, if you are thinking about optical sciences the University of Rochester and the University of Arizona have been very strong for some time, but within the specialty of microscopy (also dear to my heart) the US as a whole is not very strong and you should look elsewhere (Germany, England, and Australia) because that is where the best are located.
I will try to update this listing as I have time and people and programs come to mind. Please do not get offended if you are not on the list. It is probably a matter of time more than anything else. If you would like to jog my memory please provide a comment or send an e-mail.
Biological sciences:
European Nuerobiology Institute: I visited the European Nuerobiology Institute in Göttingen last summer and ever since I have been trying to get student to think about the International Graduate program offered jointly by the University of Göttingen, The Max Planck Institute for Biophysical Chemistry, The Max Planck Institute for Experimental Medicine and the European Neurobiology Institute. The details may be found here: http://www.gpneuro.uni-goettingen.de/The University of Göttingen has been a very strong University for a very long time (44 Nobel prize winners have studied or worked there). But more important than the reputation of these places for you as a student, I do not know of anywhere in the world where such a combination of resources is being brought to bear on such an important scientific problem. There are Nobel prizes waiting for those who figure out how the brain works. Trust me, I'm a Doctor (well in the Ph. D. sense at least).
Analytical Sciences:
M. Bonner Denton (University of Arizona, US) http://www.chem.arizona.edu/faculty/profile/profile.php?fid_call=dent
Paul Geladi (university of Umea, Sweden)
.http://www.chem.umu.se/dep/ok/staff/people/pg/index.html (Has been very influential in the field of multi-variate image analysis and chemometrics). A bit of a weak web site though.
Jonathon Sweedler (UIUC – Note this University has a very strong analytical chemistry program) http://mrel.beckman.uiuc.edu/sweedler/
Richard Zare (Stanford University) http://www.stanford.edu/group/Zarelab/
Fluorescence and/or Biophysics:
Bob Clegg (UIUC, US) http://www.physics.uiuc.edu/People/Faculty/profiles/Clegg/
Eliot Elson (Washington University of St. Louis). http://www.biochem.wustl.edu/~elelab/ele.htm.
Enrico Gratton (UIUC, US) http://www.physics.uiuc.edu/People/Faculty/profiles/Gratton/
Thomas Jovin (MPI Germany) http://www.mpibpc.gwdg.de/abteilungen/060/
Joseph Lakowicz (UM Baltimore, US) http://www.umbi.umd.edu/~mbc/pages/lakowicz.htm
Doug Magde (UCSD, US) http://www-chem.ucsd.edu/Faculty/bios/magde.html
Nancy Thompson: (UNC Chapel Hill. Note this University has a very strong analytical chemistry program) http://www.chem.unc.edu/people/faculty/thompsonnl/nltindex.html.
Microscopy:
Min Gu (Swinburne University, Australia) http://www.swin.edu.au/bioscieleceng/soll/cmp/profiles/Mingu.html.
Stephan Hell (MPI for Biophysical Chemistry, Germany) http://www.mpibpc.gwdg.de/groups/hell/
Thomas Jovin (MPI for Biophysical Chemistry, Germany) http://www.mpibpc.gwdg.de/abteilungen/060/
Colin Shepperd (National University of Singapore) (Formerly of Oxford University, and University of Sydney). http://www.bioeng.nus.edu.sg/people/colin/index.htm
Enrst Steltzer (EMBL, Heidelberg Germany). http://www-db.embl.de/jss/EmblGroupsOrg/per_546.html
Tony Wilson (Oxford University, UK) http://acara.eng.ox.ac.uk/som/People.html
Wednesday, June 15, 2005
Hurricane and Storm Resources 1: Where to go for the images and advice
Last September I gained new respect for weather systems when hurricane Ivan passed by. While our island was lucky that time, others were not. It is simply a question of time until every island in the Caribbean is hit. What was helpful in the time before Ivan passed was having a fair amount of advanced warning. Ivan was a well established storm by the time it reached 45 degrees W. The papers were a little slow to warn on this one and the University was open the morning before it passed. While it is not necessary to panic every time a storm shows up on the Atlantic, it won't hurt to stock up on noodles, cans, plastic bags, and lay in a store of water when a hurricane forms at 45 degrees west. There are several places to go for information.
These are a series of sites I found useful and I consult some of them daily during the hurricane season.
1) For a quick summary of storms and weather outlook visit:http://hurricane.terrapin.com/. For storms of tropical depression strength or above you will find links to track plots and predicted tracks. Note that storm track prediction is an inexact science. Ivan was predicted to hit us last year but swerved south at the last minute.
2)There are several worthwhile links at the site indicated above to images: http://hurricane.terrapin.com/imagesandmaps.html.en and weather discussion before and after storms: http://www.stormcarib.com/.
3) Unisys provides historical data and current images: http://weather.unisys.com/hurricane/index.html. When you visit this site, you will probably want to scroll down to the middle of the page where you will find current tropical weather satellite images and aviation model forcasts. One link that I like is the sea level pressure maps.
4) The US National Hurricane Center is quite helpful and may be found here: http://www.nhc.noaa.gov/index.shtml.
5)In the links on the US National Hurricane Center site, there is a good set of frequently asked questions: http://www.aoml.noaa.gov/hrd/tcfaq/tcfaqHED.html. My favorite is the question about taping windows. Having dutifully taped my windows for Ivan, I was surprised to learn this was a waste of time and tape.
6) Having learned that tape was not much help, my wife and I constructed a set of plywood shutters based on information and designs found here: http://www.aoml.noaa.gov/hrd/weather_sub/shutters.html. This is something you will want to do in advance. It took us number of weekends to complete these.
7) The European Union operates a satellite (METEOSAT) that covers the whole of africa and the atlantic ocean up to the caribbean. This is an nice view of what is coming for people living in the windward Islands. It can be animated if desired and includes visible, IR, and water vapor imagery. You can acces the site here: http://oiswww.eumetsat.org/IDDS-cgi/listImages?a=0,m=7,f=1,c=2,o=1,s=0,n=6,d=1,v=400,p=0.
8) Here is a good place to go for information about how to deal with potentially contaminated water. http://www.bt.cdc.gov/disasters/hurricanes/recovery.asp#water.
9) Further health related information in English, Spanish, French, and Creole may be found here:http://www.bt.cdc.gov/disasters/hurricanes/recovery.asp.
10) Finally, be very careful about any wounds that come in contact with flood waters. This is a potential route for leptospirosis infection.
Take some time to check your supplies.
These are a series of sites I found useful and I consult some of them daily during the hurricane season.
1) For a quick summary of storms and weather outlook visit:http://hurricane.terrapin.com/. For storms of tropical depression strength or above you will find links to track plots and predicted tracks. Note that storm track prediction is an inexact science. Ivan was predicted to hit us last year but swerved south at the last minute.
2)There are several worthwhile links at the site indicated above to images: http://hurricane.terrapin.com/imagesandmaps.html.en and weather discussion before and after storms: http://www.stormcarib.com/.
3) Unisys provides historical data and current images: http://weather.unisys.com/hurricane/index.html. When you visit this site, you will probably want to scroll down to the middle of the page where you will find current tropical weather satellite images and aviation model forcasts. One link that I like is the sea level pressure maps.
4) The US National Hurricane Center is quite helpful and may be found here: http://www.nhc.noaa.gov/index.shtml.
5)In the links on the US National Hurricane Center site, there is a good set of frequently asked questions: http://www.aoml.noaa.gov/hrd/tcfaq/tcfaqHED.html. My favorite is the question about taping windows. Having dutifully taped my windows for Ivan, I was surprised to learn this was a waste of time and tape.
6) Having learned that tape was not much help, my wife and I constructed a set of plywood shutters based on information and designs found here: http://www.aoml.noaa.gov/hrd/weather_sub/shutters.html. This is something you will want to do in advance. It took us number of weekends to complete these.
7) The European Union operates a satellite (METEOSAT) that covers the whole of africa and the atlantic ocean up to the caribbean. This is an nice view of what is coming for people living in the windward Islands. It can be animated if desired and includes visible, IR, and water vapor imagery. You can acces the site here: http://oiswww.eumetsat.org/IDDS-cgi/listImages?a=0,m=7,f=1,c=2,o=1,s=0,n=6,d=1,v=400,p=0.
8) Here is a good place to go for information about how to deal with potentially contaminated water. http://www.bt.cdc.gov/disasters/hurricanes/recovery.asp#water.
9) Further health related information in English, Spanish, French, and Creole may be found here:http://www.bt.cdc.gov/disasters/hurricanes/recovery.asp.
10) Finally, be very careful about any wounds that come in contact with flood waters. This is a potential route for leptospirosis infection.
Take some time to check your supplies.
Wednesday, May 11, 2005
Educational Philosophy 1: Responsibility is Power.
Most students have heard the adage that “Knowledge is Power.” There is much truth to this, but there is another aspect of power that is equally or more important than knowledge: Responsibility. Many of you may be thinking about giving up reading the rest of this because you have heard it all before about how lecturers and professors think students are irresponsible children and everything was better when they were students and there has been nothing but decline ever since. However, this is not my point at all.
Consider the following. There is no shortage of ignorant people who have been given (or have taken) responsibility. These people can have great power. There is also no shortage of highly intelligent and knowledgeable people who have no power. So, while there is no question that knowledge can be empowering, this is not the whole picture.
What is the point? You can be empowered by people giving you the opportunity to be responsible. You are disempowered when you are not given responsibility. The latter can be a confusing point. You may be given a position that appears to be responsible but unless you are also given the opportunity to carry out those responsibilities it is only form, not substance.
Where is the educational philosophy in all of this? Part of creating responsible adults is giving them responsibility. I tend to give students a lot of project work. There are many reasons for this but among them is giving the students the responsibility to decide what to do the project on, how to do the project, and carry out the work. There is “oversight” of projects which limits the amount of responsibility the students have, but certainly there is more responsibility assigned to the student than in typical lab exercises.
These specifics are not the main point I want to make. Relative to the opportunities I had to carry responsibility as an undergraduate, the students here are severely disempowered. Since, I went through a very different educational system I can not say that there has been an enormous decline since I was in school, only that where I was educated the philosophy of giving students responsibility was very different. For example, as a graduate student I was given a stockroom key. This is something that as an academic staff member I do not have. But that is minor compared to a more dramatic example.
As an undergraduate, I had the benefit of a unique opportunity. As I go through life the uniqueness of that opportunity grows and this note is really a tribute to an educational genius named Dr. Arthur Scott. I never met him. In fact he died while I was an undergraduate, having retired some years earlier. What did Dr. Scott do? He convinced his administration AND government regulatory bodies that undergraduates could operate and run a research nuclear reactor. I am sure he did other things, but the legacy of this person has had a longstanding impact on my life. If you ever read my resume you will see that I was a reactor operator, senior reactor operator, and eventually reactor supervisor. This was all while I was an undergraduate. When I graduated with my degree, I left the region and my license lapsed. I still have a certificate, which I am proud of, and it hangs on my wall.
When I was younger, I used to think of it as a great personal achievement. It certainly is something that not everyone has done, but is it greatness? Not really. The greatness was in Dr. Scott being able to conceive of undergraduate students as capable of such things. In retrospect, certainly when compared to crystallography it wasn’t the most difficult thing I ever did. The physics we were taught was relatively straightforward (I have forgotten most of it – but nothing a reasonably intelligent undergraduate can’t learn). In fact, the TRIGA reactors were engineered – according to rumor – with high school students in mind and I have no doubts that high school students could run a TRIGA if given the responsibility. Most of the operation of the reactor was about following procedures, filling in logs, and sitting around watching meters and chart recorders. Routine operation requires less skill than driving a car.
What was unique was the philosophy of giving young people responsibility. The rest was something most of my students would be capable of doing. It required a bit of effort, but then how many people wouldn’t spend an evening a week for an opportunity to learn how nuclear reactors work and do neutron activation analysis. The course ran for an academic year, for no academic credit. At the end of the year, examiners came from the Nuclear Regulatory Commission and there was a written and practical exam.
The course was open to everyone. Science students are what I am sure you are thinking about, but it wasn’t just for them. Students of humanities also took part and were successfully licensed. Very unique.
Looking at my students from this perspective, I think as an institution we are deficient. While a reactor is a bit of hardware not everyone has, there are other ways we can strive to give students more responsibility. We are not doing enough for them.
Consider the following. There is no shortage of ignorant people who have been given (or have taken) responsibility. These people can have great power. There is also no shortage of highly intelligent and knowledgeable people who have no power. So, while there is no question that knowledge can be empowering, this is not the whole picture.
What is the point? You can be empowered by people giving you the opportunity to be responsible. You are disempowered when you are not given responsibility. The latter can be a confusing point. You may be given a position that appears to be responsible but unless you are also given the opportunity to carry out those responsibilities it is only form, not substance.
Where is the educational philosophy in all of this? Part of creating responsible adults is giving them responsibility. I tend to give students a lot of project work. There are many reasons for this but among them is giving the students the responsibility to decide what to do the project on, how to do the project, and carry out the work. There is “oversight” of projects which limits the amount of responsibility the students have, but certainly there is more responsibility assigned to the student than in typical lab exercises.
These specifics are not the main point I want to make. Relative to the opportunities I had to carry responsibility as an undergraduate, the students here are severely disempowered. Since, I went through a very different educational system I can not say that there has been an enormous decline since I was in school, only that where I was educated the philosophy of giving students responsibility was very different. For example, as a graduate student I was given a stockroom key. This is something that as an academic staff member I do not have. But that is minor compared to a more dramatic example.
As an undergraduate, I had the benefit of a unique opportunity. As I go through life the uniqueness of that opportunity grows and this note is really a tribute to an educational genius named Dr. Arthur Scott. I never met him. In fact he died while I was an undergraduate, having retired some years earlier. What did Dr. Scott do? He convinced his administration AND government regulatory bodies that undergraduates could operate and run a research nuclear reactor. I am sure he did other things, but the legacy of this person has had a longstanding impact on my life. If you ever read my resume you will see that I was a reactor operator, senior reactor operator, and eventually reactor supervisor. This was all while I was an undergraduate. When I graduated with my degree, I left the region and my license lapsed. I still have a certificate, which I am proud of, and it hangs on my wall.
When I was younger, I used to think of it as a great personal achievement. It certainly is something that not everyone has done, but is it greatness? Not really. The greatness was in Dr. Scott being able to conceive of undergraduate students as capable of such things. In retrospect, certainly when compared to crystallography it wasn’t the most difficult thing I ever did. The physics we were taught was relatively straightforward (I have forgotten most of it – but nothing a reasonably intelligent undergraduate can’t learn). In fact, the TRIGA reactors were engineered – according to rumor – with high school students in mind and I have no doubts that high school students could run a TRIGA if given the responsibility. Most of the operation of the reactor was about following procedures, filling in logs, and sitting around watching meters and chart recorders. Routine operation requires less skill than driving a car.
What was unique was the philosophy of giving young people responsibility. The rest was something most of my students would be capable of doing. It required a bit of effort, but then how many people wouldn’t spend an evening a week for an opportunity to learn how nuclear reactors work and do neutron activation analysis. The course ran for an academic year, for no academic credit. At the end of the year, examiners came from the Nuclear Regulatory Commission and there was a written and practical exam.
The course was open to everyone. Science students are what I am sure you are thinking about, but it wasn’t just for them. Students of humanities also took part and were successfully licensed. Very unique.
Looking at my students from this perspective, I think as an institution we are deficient. While a reactor is a bit of hardware not everyone has, there are other ways we can strive to give students more responsibility. We are not doing enough for them.
Friday, April 29, 2005
Essential Skills for Scientists 1:Writing Abstracts
Being able to write, maybe not well but at least well enough, is a very important skill for a scientist. My experience is that it is not enough to only know science while neglecting writing and reading skills. More to the point, the scientists that I know who have gone the furthest are people who are able to communicate well. It is really that simple. If you cannot communicate your findings clearly, you will have difficulty getting people to take you seriously. This somewhat preachy introduction brings me to the topic of the day, the importance of writing good abstracts.
What is an abstract? An abstract is a short 1-2 paragraph text section appearing at the beginning of a paper right below the title and authors' names. It should concisely communicate the essential parts of a study. In science writing it needs to concisely answer the following questions: 1) What was done? 2) How it was done? and 3) What was the result?
This all sounds very easy, but many students have difficulty getting the balance between the different parts right. Here are a few tips to help you write a better abstract:
1) As a quantitative scientist, I like to see clear quantitative statements. For example, suppose you are measuring the amount of fat in milk products. By the time a reader finishes the abstract, they should know how much fat is in the milk products. Consider the following: "Twelve samples of quadruple cream from the South Park dairy were found to contain 75.0±0.3 % fat (w/v)." This speaks to me. Were this your statement, I would say "I like that you told me how much was there and that you gave an estimated uncertainty."
2) How should you answer the question about how you did your work? This is troublesome because some students make the mistake of turning their abstract into a second methods section. The idea is to give the reader a general view of the methods you used. Some people may, for example, be interested in measuring Cd using inductively coupled plasma (ICP) because that is all they have in their lab. These people will appreciate it if you explain that you are measuring Cd by anodic stripping voltammetry (ASV). That way they don't need to read your paper. Alternately, someone else may take a special interest in your work because you are using ASV.
3) As you enter the university level, you should stop including things like "In this practical..." and "The purpose of this series of labs was to introduce us to..." Instead, you should try to integrate the material into a whole that stands on its own. Formal write ups are part of the assignment and are assigned to teach you how to write like a scientist. Insisting on putting sentences where you second guess the reason we assigned a particular lab exercise makes you sound like a secondary or high school student. I don't think that is what you want.
For students who have an interest, I made an aggregate document of all the abstracts received from a group of 56 students for one formal lab write up. You may find it here:http://drhanleydocs.blogspot.com/. This should give you a good idea what a range of abstracts look like. Some have very high information content. I have indicated the one I thought was best. See if you agree.
What is an abstract? An abstract is a short 1-2 paragraph text section appearing at the beginning of a paper right below the title and authors' names. It should concisely communicate the essential parts of a study. In science writing it needs to concisely answer the following questions: 1) What was done? 2) How it was done? and 3) What was the result?
This all sounds very easy, but many students have difficulty getting the balance between the different parts right. Here are a few tips to help you write a better abstract:
1) As a quantitative scientist, I like to see clear quantitative statements. For example, suppose you are measuring the amount of fat in milk products. By the time a reader finishes the abstract, they should know how much fat is in the milk products. Consider the following: "Twelve samples of quadruple cream from the South Park dairy were found to contain 75.0±0.3 % fat (w/v)." This speaks to me. Were this your statement, I would say "I like that you told me how much was there and that you gave an estimated uncertainty."
2) How should you answer the question about how you did your work? This is troublesome because some students make the mistake of turning their abstract into a second methods section. The idea is to give the reader a general view of the methods you used. Some people may, for example, be interested in measuring Cd using inductively coupled plasma (ICP) because that is all they have in their lab. These people will appreciate it if you explain that you are measuring Cd by anodic stripping voltammetry (ASV). That way they don't need to read your paper. Alternately, someone else may take a special interest in your work because you are using ASV.
3) As you enter the university level, you should stop including things like "In this practical..." and "The purpose of this series of labs was to introduce us to..." Instead, you should try to integrate the material into a whole that stands on its own. Formal write ups are part of the assignment and are assigned to teach you how to write like a scientist. Insisting on putting sentences where you second guess the reason we assigned a particular lab exercise makes you sound like a secondary or high school student. I don't think that is what you want.
For students who have an interest, I made an aggregate document of all the abstracts received from a group of 56 students for one formal lab write up. You may find it here:http://drhanleydocs.blogspot.com/. This should give you a good idea what a range of abstracts look like. Some have very high information content. I have indicated the one I thought was best. See if you agree.
Thursday, March 31, 2005
Quiz your analytical knowledge: Projects 1415
I really like this time of year. Why is that? I like this time of year because the students are doing their projects. On the one hand, it is all a bit crazy. CHEM1415, the introductory analytical chemistry course, has nearly 70 students and all of them (except those exempt from labs) do a short project. Each project is meant to be unique and they are allowed to titrate, weigh, and do spectrophotometry (includes atomic methods). It is amazing what you can do with these “simple” starting points. Here is your chance to test your knowledge. Trust me, these projects test mine and every time I run the course I learn something.
So here it goes, how would you do the following analyses?
Acidity and alkalinity of water.
Water Hardness.
Dissolution kinetics of spherical objects.
Carbonate in Detergent.
Calcium in antacids.
Vitamin B12 in supplements.
Acidity of vinegar.
Fluoride in toothpaste (not using an electrode!)
Zinc in supplements.
Antacid strength.
Phosphate in water.
Iron in Spinach.
Biological oxygen demand.
Test of a water purification system to remove calcium.
Free and bound potassium in soil.
Citric acid content in citrus juice.
Acidity of soft drinks.
Lead in plants and soil.
Fatty acid in soap.
Base content of cleanser.
Caffeine in tea.
Ca in milk (2 ways).
Solubility of Calcium Hydroxide.
Free alkali in soap.
Iron content of tap water.
Dissolved Oxygen in Seawater.
Phosphoric acids content of Coca-Cola.
Na (well Cl) content in potato chips.
Volatile acids in wine.
Characterization of the Cabbage juice indicator (pKas).
Caffeine content of sodas.
Aluminum content of deodorant.
Glucose in Urine.
Lead in paint.
Fat content of milk.
Aspirin content of a tablet.
Copper in pennies (two methods).
Pb in seawater.
Hydroquinone in skin lightener.
Fe in supplements. (two different methods)
Caffeine in Chocolate.
Ethanol in drinks (no chromatography!).
Mg and hydroxide content of milk of magnesia.
This is only the first 40 students or so. It is amazing what students can teach you.
I want to thank the technical staff for putting up with the difficulty of running this part of the course.
So here it goes, how would you do the following analyses?
Acidity and alkalinity of water.
Water Hardness.
Dissolution kinetics of spherical objects.
Carbonate in Detergent.
Calcium in antacids.
Vitamin B12 in supplements.
Acidity of vinegar.
Fluoride in toothpaste (not using an electrode!)
Zinc in supplements.
Antacid strength.
Phosphate in water.
Iron in Spinach.
Biological oxygen demand.
Test of a water purification system to remove calcium.
Free and bound potassium in soil.
Citric acid content in citrus juice.
Acidity of soft drinks.
Lead in plants and soil.
Fatty acid in soap.
Base content of cleanser.
Caffeine in tea.
Ca in milk (2 ways).
Solubility of Calcium Hydroxide.
Free alkali in soap.
Iron content of tap water.
Dissolved Oxygen in Seawater.
Phosphoric acids content of Coca-Cola.
Na (well Cl) content in potato chips.
Volatile acids in wine.
Characterization of the Cabbage juice indicator (pKas).
Caffeine content of sodas.
Aluminum content of deodorant.
Glucose in Urine.
Lead in paint.
Fat content of milk.
Aspirin content of a tablet.
Copper in pennies (two methods).
Pb in seawater.
Hydroquinone in skin lightener.
Fe in supplements. (two different methods)
Caffeine in Chocolate.
Ethanol in drinks (no chromatography!).
Mg and hydroxide content of milk of magnesia.
This is only the first 40 students or so. It is amazing what students can teach you.
I want to thank the technical staff for putting up with the difficulty of running this part of the course.
Tuesday, March 29, 2005
My problem with the Q-test (Long)
The Q-test is a simply calculated test statistic that is presented in many textbooks on analytical chemistry as a sufficient criteria for throwing out “outliers” in data sets. Nearly every modern analytical chemistry textbook has a section on this test and it is presented early and often in the University level curriculum. I think it is presented for several reasons. First, it is an easy statistic to compute. There is very little work involved and (I think) textbook writers hope students will spend time pondering the statistics with all the extra time students have after completing the computation. Second, it is a relatively satisfying test because it allows people to eliminate unsatisfactory data. Even I have to confess there is something satisfying about getting rid of a data point that just seemed out of place. Third, it seems to grip the imagination of students in ways that t-tests and F-tests do not. Perhaps, they see it as useful somehow and, therefore, relevant.
Even I can concede all these points. Who can argue against an easy statistical test that catches the imagination of students and leaves a satisfying feeling on successful execution?
Well… me.
What is my problem with the Q-test? Well everything I just said and some. First, philosophically, I am deeply suspicious of people throwing away data. You may argue that the Q-test justifies the exclusion of data, so I am talking rubbish. I will get to this in a moment, but for now just take it as a philosophical disagreement. Second, the Q-test has an underlying assumption of normality. Third, there is a somewhat better test of outliers called Grubb’s test which is recommended in preference to the Q-test by ISO (International Standards Organization). Finally, in my experience as a practicing scientist I have seen far too much removal of inconvenient data. Much was completely unjustified (in particular a certain oil company where I worked which shall remain nameless).
Philosophical objection
Let me begin with an anecdote.
Once upon a time I was headed north along the freeway between the Boston and Manchester, New Hampshire. It was winter and really quite cold. I had a nice energy efficient diesel VW rabbit (Golf for you Europeans). Did I tell you it was cold? I think I did, it was damn cold. I was driving along minding my business and the car started slowing down for no good reason. It went slower and slower and rolled to a stop on the edge of the freeway. I got out and poked around under the hood. Did I tell you it was cold? Just in case you missed it, IT WAS COLD. I didn’t see anything wrong under the hood – didn’t really expect much. I contemplated getting out and walking, but it was too COLD. I got back in the car, turned it with the starter for a while and… it started. I managed to limp to a service station.
You are all wondering, “why is this person telling me this?” The real important question is why did my car stall and me nearly freeze to death? Too much water in my fuel is the answer. Working in an oil refinery a few years later I became suspicious that the real reason was that water is cheaper than diesel fuel and summer and fall diesel fuels can contain more water than winter diesel fuel. In cold weather, the water separates from the fuel, turns to ice, and plugs up the fuel filter. During the warmer months cutting the water content specification “close” or just ignoring the test because it takes too long makes the company money. So, if you throw out or “mend” the numbers (they called it “pencilling” at the oil refinery) you make everyone happy. The guys in the plant are happy because it is less work for them, management is happy because they make more money selling maximum water and every little bit counts… So the pressure is on. Throw out the offending number and ship the product.
Which brings us to the point of the anecdote, if you measure something every day for a month (say water content) and get a particular value then you get a high out-of-specification value, what do you do? Well… Do you apply the Q-test, reject the number, and not tell anyone? Hmm… I didn’t think so. A single value is sufficient to tell if your process is out of control. You do NOT throw that out. Why not? Not only is it bad practice, but you might cause someone lose their toes to frostbite.
Ok. I think I have convinced you not to use the Q-test indiscriminately. Clearly, there are situations where you don’t want to throw out “abnormal” data. What is murky is when it is appropriate to use. I can give you a guideline: Be sure you know what you are doing and why you are doing it, before throwing away ANY data. My philosophical position is throwing away data, “massaging” data, pencilling data, and all related activities can be extremely dangerous to your science. Think of children playing with dynamite. Be sure the little guys know what they are doing, hmm.
Statistical worries.
The problem of removing outliers in its most general sense is the idea that the outlier does not belong to the same distribution as the rest of the data. Sort of a dogs and cats kind of idea. Suppose you did an experiment weighing neighborhood animals. Further suppose that most of the animals in that neighborhood were dogs and relatively big dogs. If you were only looking at the mass you would probably notice a cat. It would appear as an outlier. The cat would weigh much less and when you saw that mass you might try to test whether it fit with the rest of the distribution. This is the concept.
Seems pretty clear, what is the problem? Well in reality there is seldom an a priori reason to remove a value. If we have prior knowledge that a cat has gotten into the dogpile, we would keep the categories separate and there is no need for statistical help. The Q-test is used in cases when there is no a priori reason to tell you that one of your points is a cat rather than a dog. Therein lies the issue. The Q-test tells you the probability that a particular data point is not part of the same distribution and the probability that you are making a wrong decision. The danger lies in the following two issues: bias in application of the Q-test and the rest of the “outlier’s” distribution.
Both of these are rather insidious. Bias is the most obvious. I have yet to see a student (or anyone else) systematically test every single data set for outliers. Rather, the Q-test is usually applied only when someone thinks the outcome of the test might make a difference to their conclusions. If you are doing the latter you are really up to no good. Not at all. Almost assuredly you are trying to establish tenuous conclusions on marginal data. If a single point makes that much difference, maybe you should think about your experimental design a little more carefully or run a few more experiments. Otherwise, you are probably just biasing the conclusions of a marginal experiment in the direction you would like it to go.
The more subtle problem with the Q-test is that that outlier may belong to another distribution. All distributions have “tails.” One may wonder where the rest of the outlier’s distribution is. Yes indeed. If you throw out the one outlier because it belongs to another distribution then philosophically you should remove all the data that belong to that distribution. You may wonder how to do this. I wonder about this too. No one has ever told me. I suspect it is not easy.
For interested students, this isakin to the concept of a and b errors.
What is reality?
This is a big question. As an experimentalist, I see reality as data. To my eyes there is no bad data, only incompletely understood data. Data may reflect artefacts, poor experimental design, or what have you, but… it is always correct. The interpretation may easily be flawed, but the data is always correct. Remember this.
The Q-test assumes that the data are normally distributed. The normal distribution is a theoretical notion (a very useful one, don’t get me wrong), not reality. I do not recall any of the large data sets that I have worked with really conforming to a normal distribution. They all tend to have broader “tails” than “expected.” I am convinced there is something to this, but don’t have the theoretical background to do much about it. I have heard that the Mathematician Mandelbrot (of fractal and Mandelbrot set fame) has been looking at aspects of this problem.
So why am I saying this? Just that data fitting a Normal distribution is less common than you might think. When you throw out data, what you may be doing is “forcing” your data to match a theory which is not applicable. This may be a case of bending reality (data) to fit a preconceived notion. Be careful.
What do you mean?
This is the most important point. What do you mean when you throw out data? Consider the weighing of pennies. You weigh a thousand of them and then throw out a subset. Does this mean these were not pennies? No, it just means they are different pennies. What about the person getting a 100 percent on an exam where the rest of the class was clustered tightly around a mean of 40? Is this person not a student? There is something different about the person, but what do you intend to do once you have made this distinction?
Which brings me to my final point? Throwing out a point should never be done. What you are doing is separating data based on whether it belongs in a single distribution. The process should not stop there. If it is not the same, what does this mean. Can you learn something from this?
Hopefully I have made my point. I am suspicious of the Q-test. It is too easy, it grips the imagination, and is a bit too satisfying for my taste. Use it cautiously if at all. Remember, these tests are not for “throwing away” data. They are for establishing the likelihood that it belongs to another distribution – not for establishing that the data is “bad.”
Even I can concede all these points. Who can argue against an easy statistical test that catches the imagination of students and leaves a satisfying feeling on successful execution?
Well… me.
What is my problem with the Q-test? Well everything I just said and some. First, philosophically, I am deeply suspicious of people throwing away data. You may argue that the Q-test justifies the exclusion of data, so I am talking rubbish. I will get to this in a moment, but for now just take it as a philosophical disagreement. Second, the Q-test has an underlying assumption of normality. Third, there is a somewhat better test of outliers called Grubb’s test which is recommended in preference to the Q-test by ISO (International Standards Organization). Finally, in my experience as a practicing scientist I have seen far too much removal of inconvenient data. Much was completely unjustified (in particular a certain oil company where I worked which shall remain nameless).
Philosophical objection
Let me begin with an anecdote.
Once upon a time I was headed north along the freeway between the Boston and Manchester, New Hampshire. It was winter and really quite cold. I had a nice energy efficient diesel VW rabbit (Golf for you Europeans). Did I tell you it was cold? I think I did, it was damn cold. I was driving along minding my business and the car started slowing down for no good reason. It went slower and slower and rolled to a stop on the edge of the freeway. I got out and poked around under the hood. Did I tell you it was cold? Just in case you missed it, IT WAS COLD. I didn’t see anything wrong under the hood – didn’t really expect much. I contemplated getting out and walking, but it was too COLD. I got back in the car, turned it with the starter for a while and… it started. I managed to limp to a service station.
You are all wondering, “why is this person telling me this?” The real important question is why did my car stall and me nearly freeze to death? Too much water in my fuel is the answer. Working in an oil refinery a few years later I became suspicious that the real reason was that water is cheaper than diesel fuel and summer and fall diesel fuels can contain more water than winter diesel fuel. In cold weather, the water separates from the fuel, turns to ice, and plugs up the fuel filter. During the warmer months cutting the water content specification “close” or just ignoring the test because it takes too long makes the company money. So, if you throw out or “mend” the numbers (they called it “pencilling” at the oil refinery) you make everyone happy. The guys in the plant are happy because it is less work for them, management is happy because they make more money selling maximum water and every little bit counts… So the pressure is on. Throw out the offending number and ship the product.
Which brings us to the point of the anecdote, if you measure something every day for a month (say water content) and get a particular value then you get a high out-of-specification value, what do you do? Well… Do you apply the Q-test, reject the number, and not tell anyone? Hmm… I didn’t think so. A single value is sufficient to tell if your process is out of control. You do NOT throw that out. Why not? Not only is it bad practice, but you might cause someone lose their toes to frostbite.
Ok. I think I have convinced you not to use the Q-test indiscriminately. Clearly, there are situations where you don’t want to throw out “abnormal” data. What is murky is when it is appropriate to use. I can give you a guideline: Be sure you know what you are doing and why you are doing it, before throwing away ANY data. My philosophical position is throwing away data, “massaging” data, pencilling data, and all related activities can be extremely dangerous to your science. Think of children playing with dynamite. Be sure the little guys know what they are doing, hmm.
Statistical worries.
The problem of removing outliers in its most general sense is the idea that the outlier does not belong to the same distribution as the rest of the data. Sort of a dogs and cats kind of idea. Suppose you did an experiment weighing neighborhood animals. Further suppose that most of the animals in that neighborhood were dogs and relatively big dogs. If you were only looking at the mass you would probably notice a cat. It would appear as an outlier. The cat would weigh much less and when you saw that mass you might try to test whether it fit with the rest of the distribution. This is the concept.
Seems pretty clear, what is the problem? Well in reality there is seldom an a priori reason to remove a value. If we have prior knowledge that a cat has gotten into the dogpile, we would keep the categories separate and there is no need for statistical help. The Q-test is used in cases when there is no a priori reason to tell you that one of your points is a cat rather than a dog. Therein lies the issue. The Q-test tells you the probability that a particular data point is not part of the same distribution and the probability that you are making a wrong decision. The danger lies in the following two issues: bias in application of the Q-test and the rest of the “outlier’s” distribution.
Both of these are rather insidious. Bias is the most obvious. I have yet to see a student (or anyone else) systematically test every single data set for outliers. Rather, the Q-test is usually applied only when someone thinks the outcome of the test might make a difference to their conclusions. If you are doing the latter you are really up to no good. Not at all. Almost assuredly you are trying to establish tenuous conclusions on marginal data. If a single point makes that much difference, maybe you should think about your experimental design a little more carefully or run a few more experiments. Otherwise, you are probably just biasing the conclusions of a marginal experiment in the direction you would like it to go.
The more subtle problem with the Q-test is that that outlier may belong to another distribution. All distributions have “tails.” One may wonder where the rest of the outlier’s distribution is. Yes indeed. If you throw out the one outlier because it belongs to another distribution then philosophically you should remove all the data that belong to that distribution. You may wonder how to do this. I wonder about this too. No one has ever told me. I suspect it is not easy.
For interested students, this isakin to the concept of a and b errors.
What is reality?
This is a big question. As an experimentalist, I see reality as data. To my eyes there is no bad data, only incompletely understood data. Data may reflect artefacts, poor experimental design, or what have you, but… it is always correct. The interpretation may easily be flawed, but the data is always correct. Remember this.
The Q-test assumes that the data are normally distributed. The normal distribution is a theoretical notion (a very useful one, don’t get me wrong), not reality. I do not recall any of the large data sets that I have worked with really conforming to a normal distribution. They all tend to have broader “tails” than “expected.” I am convinced there is something to this, but don’t have the theoretical background to do much about it. I have heard that the Mathematician Mandelbrot (of fractal and Mandelbrot set fame) has been looking at aspects of this problem.
So why am I saying this? Just that data fitting a Normal distribution is less common than you might think. When you throw out data, what you may be doing is “forcing” your data to match a theory which is not applicable. This may be a case of bending reality (data) to fit a preconceived notion. Be careful.
What do you mean?
This is the most important point. What do you mean when you throw out data? Consider the weighing of pennies. You weigh a thousand of them and then throw out a subset. Does this mean these were not pennies? No, it just means they are different pennies. What about the person getting a 100 percent on an exam where the rest of the class was clustered tightly around a mean of 40? Is this person not a student? There is something different about the person, but what do you intend to do once you have made this distinction?
Which brings me to my final point? Throwing out a point should never be done. What you are doing is separating data based on whether it belongs in a single distribution. The process should not stop there. If it is not the same, what does this mean. Can you learn something from this?
Hopefully I have made my point. I am suspicious of the Q-test. It is too easy, it grips the imagination, and is a bit too satisfying for my taste. Use it cautiously if at all. Remember, these tests are not for “throwing away” data. They are for establishing the likelihood that it belongs to another distribution – not for establishing that the data is “bad.”
Thursday, February 24, 2005
BIOC2325 1: Importing pictures into ImageJ
ImageJ is a very useful and free program which has been made available by NIH. It also includes many useful plug-ins including gel documentation libraries, 2D FFT filtering, and much more.
If you are interested in a copy, visit: http://rsb.info.nih.gov/ij/. The program itself is a Java update to an earlier program called NIHImage. The author W. Rasband deserves considerable thanks for his assistance bringing quantitative image analysis to biologists – and to us.
The gel documentation system we used to take pictures in lab are in a non-standard image format. By this I mean it is not in one of the commonly recognized image formats like tif, jpg, gif, fits, etc. This means that you will have to load the file using ImageJ’s import features. To do this follow these steps:
1) In imageJ use the file menu and select import->raw
2) This brings up a dialog box for you to select your file. Choose the one you want.
3) When you open the file, a dialog box asking for image type, width, height, offset, etc. will appear. Select the following:type = 8 bit.width 974,height = 1280offset = 300number of images = 1.gap between image = 0.
The three check boxes (“white is zero”, “Little-Endian Byte Order”, and “Open All Files in Folder”) at the bottom should NOT be checked.
If you then say Ok your file should load correctly.
If you have old gel pictures from other classes, you may want to play around with the “Gels” functions. You will find this (at least in the version I am currently using) at the bottom of the “Analyze” menu option.
If you are interested in a copy, visit: http://rsb.info.nih.gov/ij/. The program itself is a Java update to an earlier program called NIHImage. The author W. Rasband deserves considerable thanks for his assistance bringing quantitative image analysis to biologists – and to us.
The gel documentation system we used to take pictures in lab are in a non-standard image format. By this I mean it is not in one of the commonly recognized image formats like tif, jpg, gif, fits, etc. This means that you will have to load the file using ImageJ’s import features. To do this follow these steps:
1) In imageJ use the file menu and select import->raw
2) This brings up a dialog box for you to select your file. Choose the one you want.
3) When you open the file, a dialog box asking for image type, width, height, offset, etc. will appear. Select the following:type = 8 bit.width 974,height = 1280offset = 300number of images = 1.gap between image = 0.
The three check boxes (“white is zero”, “Little-Endian Byte Order”, and “Open All Files in Folder”) at the bottom should NOT be checked.
If you then say Ok your file should load correctly.
If you have old gel pictures from other classes, you may want to play around with the “Gels” functions. You will find this (at least in the version I am currently using) at the bottom of the “Analyze” menu option.
Wednesday, February 16, 2005
The students are on strike
The students are on strike today in protest of a new $700 fee that is (was) to be implemented in the coming year. I don’t think it would be appropriate to comment on the specific issues, either for or against. I do, however, have some strong opinions both on student action in general and state supported education in particular.
First things first, a positive point in all this. I am delighted that students are taking a serious look at something related to their education. If it takes the imposition of a new and unpopular change to get them focused on just what it is we do here in a University, I am all for it. In fact, I think Admin should make a point of irritating them early and often every single year until the end of time. I’d do it myself.
I say that somewhat tongue-in-cheek but, there is a serious undercurrent to my comment which brings me to the second topic. I believe very strongly in state supported education. Education should not just be the playground of the rich and well connected. It should be for all. Everyone should have the opportunity to be educated up to the level of their ability in a way that is not restricted by the wealth of parents. I owe it to my father, who grew up very poor and was perhaps the first university educated man in his family, to speak in support of my beliefs. He never would have been a project leader on the guidance systems for the Apollo rockets that took human beings to the moon and back without the state assistance he was given as a World War II veteran. I owe it to my smart, but not necessarily rich, students as well.
But state support of education is a complex thing. This country is a member of a very special and in my view elite class of nations which provides free public education to those capable of making use of it. This should be a cause for justifiable pride and may also be an underlying factor in its prosperity. A well educated people is the bedrock on which a nation can stand. A well educated electorate informs the public discourse and directs the activities of government. A highly skilled and educated work force can provide the fuel for efficient and prosperous industries.
But state support of free education is a complex thing. This country is in dwindling company with its unqualified support of education. It is in good company, but this countries peers are becoming scarce. I do not know why that is. Worldwide, countries are, one after another, throwing in the towel and imposing greater and greater fees. Free university public education is being pushed to extinction. Again, I do not know why. My wife’s home country recently introduced fees which would have kept her from studying had they existed at the time she was in school. Like my father’s family, my wife’s family was not rich. She worked part-time jobs to support her education. In my home country, University education costs have out paced inflation for some time and in my lifetime it was never free at the undergraduate level. Exceptional students often win scholarships, but the true bedrock of a nation is its middle class, not its elites.
That said, no cost sometimes invites complacency. A sufficient number of students begin to feel entitled, not only to the opportunity to get an education, but to the trappings of education: degrees, certificates, etc. I would say that the vast majority of my students have no idea the gift they are being given. At their age I had no idea either. It was only a few years after I received my undergraduate degree that I began to understand. I was staring out the window one day and counting my blessings. After life itself came the gift of reading and the education that followed. I still remember the two Catholic sisters (Sister Cynthia and Sister Veronica) who taught me to read. I met my wife and most of my closest friends in school. The education I received opened up a world I would otherwise never have dreamed of. It pains me sometimes to see how some (not all) students really do not take the tremendous gift being given to them by their government seriously.
Although I feel strongly that governments should support education, there is nothing that says they have to be equally supportive of everything. At the institution where I did my Ph.D., the greatest number of students were majoring in Communications. Just what we need, more Americans communicating. In Germany, the favoured discipline among students was Geography. All areas of inquiry, do not need to be supported equally. Nations have needs. Some have critical needs. They should feel good about shaping the direction of the students and universities they support.
Equally, some areas of scholarship are bound to be controversial. Sometimes a scholar has to speak the truth to power. As such, a University needs to keep its independence, sometimes stubbornly to allow new and controversial areas to be examined. It is a University after all. Sometimes, new areas of thought need to be explored which initially are perceived as “not useful.” Such topics rightfully belong in a University. A University should take pride in its scholars and its independence.
And therein lies the rub. Free access side by side with responsibility. Governmental management and academic independence. Student desire for degrees and a nation that wants high standards. A “relevant” focus on regional needs and independent thought. Sometimes all these things do not sit well together and there are no easy solutions.
If anything, I hope the students protesting will begin a more expansive examination of their education. It is at the core of both their future and this nation’s future. Higher education is a complex thing.
First things first, a positive point in all this. I am delighted that students are taking a serious look at something related to their education. If it takes the imposition of a new and unpopular change to get them focused on just what it is we do here in a University, I am all for it. In fact, I think Admin should make a point of irritating them early and often every single year until the end of time. I’d do it myself.
I say that somewhat tongue-in-cheek but, there is a serious undercurrent to my comment which brings me to the second topic. I believe very strongly in state supported education. Education should not just be the playground of the rich and well connected. It should be for all. Everyone should have the opportunity to be educated up to the level of their ability in a way that is not restricted by the wealth of parents. I owe it to my father, who grew up very poor and was perhaps the first university educated man in his family, to speak in support of my beliefs. He never would have been a project leader on the guidance systems for the Apollo rockets that took human beings to the moon and back without the state assistance he was given as a World War II veteran. I owe it to my smart, but not necessarily rich, students as well.
But state support of education is a complex thing. This country is a member of a very special and in my view elite class of nations which provides free public education to those capable of making use of it. This should be a cause for justifiable pride and may also be an underlying factor in its prosperity. A well educated people is the bedrock on which a nation can stand. A well educated electorate informs the public discourse and directs the activities of government. A highly skilled and educated work force can provide the fuel for efficient and prosperous industries.
But state support of free education is a complex thing. This country is in dwindling company with its unqualified support of education. It is in good company, but this countries peers are becoming scarce. I do not know why that is. Worldwide, countries are, one after another, throwing in the towel and imposing greater and greater fees. Free university public education is being pushed to extinction. Again, I do not know why. My wife’s home country recently introduced fees which would have kept her from studying had they existed at the time she was in school. Like my father’s family, my wife’s family was not rich. She worked part-time jobs to support her education. In my home country, University education costs have out paced inflation for some time and in my lifetime it was never free at the undergraduate level. Exceptional students often win scholarships, but the true bedrock of a nation is its middle class, not its elites.
That said, no cost sometimes invites complacency. A sufficient number of students begin to feel entitled, not only to the opportunity to get an education, but to the trappings of education: degrees, certificates, etc. I would say that the vast majority of my students have no idea the gift they are being given. At their age I had no idea either. It was only a few years after I received my undergraduate degree that I began to understand. I was staring out the window one day and counting my blessings. After life itself came the gift of reading and the education that followed. I still remember the two Catholic sisters (Sister Cynthia and Sister Veronica) who taught me to read. I met my wife and most of my closest friends in school. The education I received opened up a world I would otherwise never have dreamed of. It pains me sometimes to see how some (not all) students really do not take the tremendous gift being given to them by their government seriously.
Although I feel strongly that governments should support education, there is nothing that says they have to be equally supportive of everything. At the institution where I did my Ph.D., the greatest number of students were majoring in Communications. Just what we need, more Americans communicating. In Germany, the favoured discipline among students was Geography. All areas of inquiry, do not need to be supported equally. Nations have needs. Some have critical needs. They should feel good about shaping the direction of the students and universities they support.
Equally, some areas of scholarship are bound to be controversial. Sometimes a scholar has to speak the truth to power. As such, a University needs to keep its independence, sometimes stubbornly to allow new and controversial areas to be examined. It is a University after all. Sometimes, new areas of thought need to be explored which initially are perceived as “not useful.” Such topics rightfully belong in a University. A University should take pride in its scholars and its independence.
And therein lies the rub. Free access side by side with responsibility. Governmental management and academic independence. Student desire for degrees and a nation that wants high standards. A “relevant” focus on regional needs and independent thought. Sometimes all these things do not sit well together and there are no easy solutions.
If anything, I hope the students protesting will begin a more expansive examination of their education. It is at the core of both their future and this nation’s future. Higher education is a complex thing.
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