January 30, 2012
Category: Knoxville '82: Where Miscellany Thrive
A news story in ScienceNOW this week describes how City University of New York is planning to rearrange its "General Education" requirements so that non-majors who take science don't have to take lab courses anymore. Scientists at CUNY are, predictably, annoyed and upset. Even non-majors should get to muck around in lab with their own hands a bit before going off to whatever other majors and interests they have.
Here at LSU we've been discussing almost the Exact Same Issue in the Honors College for the past few weeks and coming to the Exact Opposite Conclusion to CUNY. We are re-designing an Honors version of Introductory Biology for Non-majors - and everyone is on board with the need for an associated laboratory in the course - even though (get this): the lab is not even a General Education requirement at LSU. Doing some science experiments with your own hands completely changes your perspective on it -- every scientist knows that -- we don't design expensive, staff-intensive, time draining, space-hogging teaching labs just for the fun of it - we design them because without them, you're only getting part of the picture.
So, for commitment to educating our future non-scientist leaders in the basics of science, the score this week is: LSU: 1 and CUNY: 0. (of course in the competition for good nearby pizza, the score is the opposite, thus creating a stalemate at present). Sadly, however, outside of the Honors College, as noted above, LSU's non science majors face some of the same incompleteness of their general science education, since labs are not part of the General Education requirements.
Not having some decent science literacy is a bit crippling for anyone who wants to be a future societal leader in any field. In the same way that not having some familiarity with foreign languages or art likewise makes for poorer scientists. And both situations make for poorer citizens.
Posted by Vince LiCata at 10:28 PM • 1 Comments • 0 TrackBacks
September 23, 2011
Category: Knoxville '82: Where Miscellany Thrive
Yanling Yang, who just graduated with a Ph.D. from my lab, has a paper in the just published November issue of Biophysical Chemistry. The entire issue of the journal celebrates the 25th Anniversary of a conference called "The Gibbs Conference on Biothermodynamics", and each of the papers is from the laboratory of one of the organizers of one of the previous 25 annual meetings (I co-organized #24). Despite the restricted invitation list, however, all the papers were peer reviewed (some quite viciously according to reports) and some required several months of revisions to qualify for the issue.
Our lab's contribution focuses on how the thermodynamics of binding of DNA polymerases different DNA structures might influence the balance between replication and repair in the cell. Yanling examined DNA molecules with normal replication start sites, along with DNA molecules with nicks and gaps between bases, and DNA molecules with mismatches near the polymerase binding site. One of the major questions was: do the "same" enzymes from two different organisms (in this case the Pol I DNA polymerases from E. coli and Thermus aquaticus) actually perform the "same" functions in the two different organisms? The thermodynamic results of this paper suggest that there are some serious differences between these two "homologous" enzymes, such that the E. coli enzyme is more advanced in being able to recognize different DNA structures.
The schematic below illustrates this in cartoon fashion by illustrating how Klentaq (from Thermus aquaticus) sees a primer-template (i.e. a "normal" replication start site) as being equal to a DNA with a gap in it. In contrast, Klenow (from E. coli) binds the primer-template DNA with much higher affinity than it binds the gapped DNA.
The paper compares the binding preferences among a large number of different DNA structures, and consistently finds that the E. coli enzyme is capable of distinguishing among all these DNAs (and binding to them with differing affinities), while the T. aquaticus enzyme sees and binds to almost every DNA exactly equivalently. We spend some time discussing how this might shift the balance between repair and replication in the two different organisms, and discussing how evolutionary time has made this enzyme more subtle and sophisticated in its DNA substrate choices.
As always, if your institution does not have access to the paper and you would like a copy, I will be happy to send you one.
Posted by Vince LiCata at 5:59 PM • 1 Comments • 0 TrackBacks
September 13, 2011
Category: Advisory Board Room
...but actually somewhere else...
So what's going on? The short version is that this is a goodbye post. The long version goes a little like this:
1. For a while now, I've been using twitter, primarily as a place to highlight interesting things. It has more or less replaced my blogging output. These tweets are often science-y, visual in nature, and with (of course) the occasional dose of Chewbacca. However, it soon became obvious to me that I should start blogging again so that such things could be compiled: more so because I'm a big fan of using these odd snippets to segue into scientific discussions in class. With twitter (as lovely as it is), it was just too easy to lose these interesting links. With blogging, I figured there would be more features to archive things more effectively. Plus, this was an easy way to make sure there was a consistent stream of content (kind of like using twitter to blog).
2. I really wanted to start writing again. What I mean here, is that I'm quite out of practice. You consistently hear from other folks that writing is a little like a muscle. It needs more than the occasional flex, but rather a full-on regime of exercise. Things at work have been busy (aren't they always?), but writing is definitely something that I've missed doing, and something that I feel I need to practice all over again. I can also add that the last post I did for boingboing.net was a major proverbial kick in my ass. Clearly my editorial spider sense is off, and so (as they say) practice, practice, practice...
3. Here is the heart of the matter. My really wanting to do something, and actually doing it are two very different things. Indeed this whole desire to start writing again was initiated by an act of irony. That is, I've just sent in a friendly "thanks for the memories" email to Scienceblogs, who were asking to renew contracts etc. Here, I declined because I really wasn't doing much at the World's Fair (again with the busy excuse). For whatever reason, I wasn't necessarily inspired by having an outlet at Scienceblogs. Because of this, it was only fair to ask to be taken off Scienceblogs - hence the reason why you are reading this goodbye post.
Ironically, this course of action is what is getting me to blog again. By ending things here, it feels like an opportunity to start fresh: and fresh starts can be incredibly exciting and invigorating. In many ways, the idea of having a new online home is making me want to write more - does that make sense? Plus, this is also a chance to have full aesthetic control over how a blog might look, which is something I've always kind of wished I could do. I've never been a fan of websites that were overly busy looking, so getting to do my minimalist thing was definitively an advantage.
In any event, this is to say that overall, Scienceblogs was a great experience, and was a wonderful way to connect with similar folks around the globe. Sharing this platform with Ben and Vince (and indeed the rest of the community, bloggers and managers alike) over the years has been an absolute privilege. For that I am grateful, but now it is time to move on.
4. And where will I move on to? As mentioned above, I'm keen to try this independently for while. I've been collecting my tweets for the last few weeks at Popperfont, so that seems as good a place as any to "have a go."
And what will I blog about? Mostly, the content that my twitter account points to, but hopefully there will be some meaty stuff here and there as well.
Specifically, I'm keen to produce a weekly (this might be optimistic but I will do my best) series, which I'm going to call "sciencegeek fundamentals." In essence, the aim of these pieces is to discuss and go over some key scientific concepts, but in a manner that is hopefully engaging to readers and possibly unconventional. We'll start next week, but to give you a sense of the sort of writing I gravitate to, you can take a gander at some of my clips, as well as consider the working title of my first "sciencegeek fundamentals" piece (The scientific method by way of Chewbacca).
As well, I'm already working on a book for children where the scientific method is central to the plot (It's called Lizzie Popperfont and the Collider Whale Tale). No expectations here... just enjoying myself as I put ideas down and work out the narrative. Who knows - maybe one of these days, we'll try to find an agent and and publisher for this endeavor.
5. Finally... what's with the name "Popperfont?" Nothing too deep... just kind of rolls nicely on the tongue, and with my inherent interest in creative arts and science, I thought the mix of Karl Popper and Typology sort of works.
cheers
dave
@dnghub
popperfont.wordpress.com
Posted by David Ng at 1:25 PM • 2 Comments • 0 TrackBacks
September 4, 2011
Category: Knoxville '82: Where Miscellany Thrive
The "Dance Your Ph.D." contest is on again for 2011. This unusual and highly interesting experiment in science outreach continues to be shepherded by John Bohannon, and continues to attract new sponsors -- this years sponsor is TEDx Brussels.
So what is this? Basically: you create an interpretive dance that "explains" your Ph.D. research and videotape it. Sounds easy, eh? No words, no powerpoint, just dancing. And you want the audience to walk away with a reasonable understanding of what you did or are currently doing your Ph.D. on. Send in a video and John will collect them all on his website (which is also linked from the Science website, since he is a contributing writer at Science). Then, on October 10th (yes, SOON!), me and about 8 other judges will pick some winners: with prizes ranging from $500 to a trip to Brussels. But one of the most rewarding "prizes" is the making of the video itself.
So check it out and start planning your dance video:
http://gonzolabs.org/dance/
the site tells you how to apply and has links to all previous entries.
(A previous WorldsFair post about the 2010 "Dance your Ph.D.", which also includes some videos, is here.)
Posted by Vince LiCata at 12:36 PM • 1 Comments • 0 TrackBacks
August 14, 2011
Category: Movie discussion • The Film Building
Even in the small theater where I saw Rise of the Planet of the Apes, it was clear that this is, to some degree, a father and son movie - there were several father and son pairs in the audience - more than I've seen in any other movie. "Yes, son, now you will see why our planet eventually will be taken over by apes." "Yes, dad, now you will see how CGI replaces this Roddy McDowell person you keep talking about."
Caution: spoilers.
Andy Serkis's Caesar and the rest of the ape-men were wonderful, as was slow build of the story. I also loved that the apes' goal was not world domination but to spend some time in the Muir Woods (although apparently this changes later in the series). The filmmakers clearly spent a lot of time getting the apes and orangutans and chimpanzees "right". I was a bit hesitant about seeing it at first since I don't like James Franco's so called "acting" (really mostly a lot of frowning) - but the ape-actors and the rest of the ensemble so overshadowed him that I barely retched at all. It was also nice that the writers and the filmmakers concentrated all of their inaccuracies into his character - somehow it seemed easier to take a bad actor playing a badly written character (and compared to Caesar, Franco's character, and the portrayal of science in the movie, seemed to have been written by a monkey).
Read on »
Posted by Vince LiCata at 12:47 PM • 1 Comments • 0 TrackBacks
June 23, 2011
Category: Knoxville '82: Where Miscellany Thrive
Reblogitation (pronounced with a "j" sound for the "g", of course): the blogospheric phenomenon of reposting, and re-reposting, and re-re-reposting the information from the "apparent first" or "most snarky" report (or blog post) about a news item.
Mother-post: the "apparent first" or "most snarky" report of an item, that then provides "the facts" for most of the other stories about that item online (even those that don't reference or link to the mother-post).
The flurry of recent news about the question "Should evolution be taught in public schools?" that was asked of the recent crop of MIss USA contestants is fascinating for a number of different reasons. It is a wonderful attention getter for the contest, taking away the usual annual spotlight on the structural misogyny and objectification of the contest. (She says "misogyny", he says "philogyny"...let's call the whole thing off). And it is double-bonus fantastic that the winner is a self-proclaimed "huge science geek" -- hooray for Miss USA!
Interestingly, the reported number of contestants who believe evolution should be taught in schools has been bizarrely scattershot. The numbers are all over the place, even though everyone seems to be looking at the same video -- but one set of numbers seems to "dominate the web".
Read on »
Posted by Vince LiCata at 2:18 PM • 4 Comments • 0 TrackBacks
June 8, 2011
Category: Ethics Palace: Where ethical questions go to live or die
(You can follow Dave on twitter @dnghub)
30 MINUTES, 70 FATES.
You don't know it, but as I write this piece, there is some serious procrastination going on. My attention span is weak and sidetracked constantly by a variety of diversions, and if you must know, it's taken me close to half an hour to write these first two sentences. Still, one could argue that none of us are strangers to procrastination, and 30 minutes is relatively short - only a minor instance of time in the grand scheme of things.
But a lot can happen in thirty minutes. Earlier, I had been looking over some 2009 UNAIDS statistics, and noting the numbers issued in the report. They are all very big, big enough certainly to require the pressing of buttons on calculators. More to the point, I learn that during my thirty minutes, approximately 70 people died from HIV/AIDS in Sub-Sahara Africa. That's 1.3 million victims each year - in Sub-Sahara Africa alone. Many of these were parents leaving orphans, and many were young children just leaving. Most troubling, however, is the fact that all of them suffered their fate with a loss of dignity.
Why do I say this? I say this because people shouldn't have to die from HIV/AIDS. There are good medicines out there, and they can control the disease. In fact, for those in the developed world, HIV/AIDS is now considered a chronic disorder, not a death sentence. If you are diagnosed, you are no longer forced to take a shortcut to demise. You can still have a long life, you can still be productive, and you can still live with dignity.
Unfortunately, this wasn't an option for those who passed away. For them, the medicines were out of reach. They were simply too expensive. And from this, you come to realize a cold hard fact in this narrative: that the fate of a person living or dying from HIV/AIDS is determined by their income. This statement is fairly straightforward, with no mincing of words, or confused rhetoric. But for most, it feels fundamentally wrong, and yet, it is a simple reality of how the world works today. Why it works in this way, however, is complicated.
Read on »
Posted by David Ng at 5:13 PM • 6 Comments • 0 TrackBacks
May 2, 2011
Category: Ethics Palace: Where ethical questions go to live or die
It's election time again and, as is the norm, we see teachers using the opportunity to talk to their students about things such as Prime Ministers, parliaments, senates, and, well, basically - how this thing we call the "Canadian Government" is meant to work. My own daughter who is in Grade 4 is in such a class, and has been asking me all sorts of questions: the most prevalent of which is "Who is Alice Wong?" Not a surprising question, since her face is fairly ubiquitous in Richmond, BC where I live, being set against the many blue Conservative signs and placards (she is our incumbent MP).
Because we've had a few elections of late, I have a habit of how I deal with such questions from my kids - these opportunities to talk politics. So far, being an educator and scientist myself, my training forces me to be objective, focusing primarily on the different philosophies that each of our political parties represent, including the general pros and cons of each. I tell my children that who you choose is a personal decision driven by what you think is important. Above all, voting is a privilege, as is the act of receiving a vote if you are campaigning. I think it best to not indoctrinate your kids with your own views, but rather to succinctly tell them that voting is something special, and deserves some effort to be informed on the issues. If you take that view, the rest will happen naturally.
Unfortunately, this time around, and to my surprise, I found myself facing my daughter and uttering the following: "I'm not really a big fan of Alice Wong." This was quite a shift of attitude, and here is why: I have no issue with Conservative ideas and values (I actually agree with some of them), but I am tremendously concerned with the actions of the current Canadian Government.
How I came to this conclusion is due to many issues, but the one that has lit the proverbial "fire in my belly," is a law that would fix policy to allow life saving drugs to be made at lower cost. There's merit in this because it permits individuals, desperate in places like Africa, to be able to afford them. HIV/AIDS has the most disconcerting narrative: if you are diagnosed with HIV, now considered a chronic disease with very effective medicines, the choice between living and dying is based on your income. It's that cold.
This law was called Bill C-393. And it was a good one. It was aimed to be innovative and to fix the previous law, which wasn't working at all. It took care to protect Canadian pharmaceutical companies so that such generic drugs could only be sold to markets that weren't in the industry's bottom line. It had a built in "let's monitor" clause. It was backed up by robust expert peer review, involving economists, policy analysts, health experts. Cost to taxpayers: zero. Because of all of these facts, it was passed by the Parliament in March - even many Conservatives broke rank and voted for it.
However, in a truly frustrating string of events, it was left to die in Senate, when Tory Senators (a large portion of which were appointed by Harper) continually delayed voting on it, until it was killed by default with the call of the election. A mini screenplay to describe this would consist of four acts, each one with the same dialogue: "We'd like to adjourn because such and such would like to speak, but oh, he's left for the day, can we do this tomorrow?"
Why were there these four days of delay? Apparently, it's because the pharmaceutical industry would rather keep things as is, even going so far as to distribute misleading counter arguments, all of which have been firmly discredited by the aforementioned expert peer review process. All of which were delivered top down to the mailboxes of Conservative Senators, and the rest, as they say, is history.
I know that critiquing Miss Wong in front of my daughter is somewhat unfair (despite being one of the few who voted against Bill C-393 in parliament), but she is representative of the bigger problem. She is a small cog in a remarkably unsettling machine. I know the value of strong leadership, but this should not trump ethical leadership. Can you imagine my daughter at school, learning not about how the "Canadian Government" works, but instead, the "Harper Government?"
Posted by David Ng at 11:48 AM • 9 Comments • 0 TrackBacks
April 12, 2011
Category: Ethics Palace: Where ethical questions go to live or die • Gift Shop & Haberdashery • Nature, as in parts, bits, molecular and stuff
I just noticed that there's a workshop being offered from June 13th to June 18th, 2011, in Vancouver, Canada, that provides technical and hands-on training for "scientists and non-scientists interested in human cloning." This course has a price tag of $1400 (does not include transportation, room and board) and apparently provides the following:
"This professional course (which can accept only 12 clients) will guide participants through the various methodologies involved in the production of a human clone. This includes extensive lectures on the various techniques as well as a significant portion of the course being hands-on sessions where clients will become adept at blastocyst tissue culture maintenance. Note that this course also includes a full day devoted to practicing on equipment that allows robotic micro-injection of nucleic material into host cell nuclei, and that the workshop includes 8 hours of equipment access time, after the workshop is finished."
Unreal right? Well, o.k. - it is actually unreal. I'm only kidding here, if only to let you know that I will be offering a professional workshop (same dates, same pricetag, and same locale) where molecular cloning is actually covered, although this is more in the vein of general molecular biology techniques used in biomedical research, or molecular characterization of any life science related endeavour.
Additional details on the course can be seen at the above link, or below the fold.
Read on »
Posted by David Ng at 12:53 PM • 0 Comments • 0 TrackBacks
