Optomechanics Are Rad - Part II

In my last installment, I described the construction of a dip-coating apparatus for applying thin films onto the tips of optical fibers.  With that out of the way, the next step involved the construction of an optics system for measuring the fluorescence produced by a thin film on the tip of an optical fiber.  And so that's what I set about doing today.  Similarly to the dip-coater, I started with a clean breadboard.  Because I am measuring fluorescence with this system, I wanted to minimize any stray light, so I enclosed the breadboard within a black box.  The box is hinged in such a way that the top and front can be opened.

Inside the box, I put my detector - a handheld spectrometer (left) - and my light source - a blue laser (right).  Not shown is the laser's power supply.  This unit is somewhat bulky and, since it doesn't necessarily need to be inside the box, I left it out.  By the way, I apologize for the blurriness of these images; this is the product of a mediocre phone camera combined with shaky hands brought on by a bit too much morning coffee.

I decided that I would take all of my measurements by submerging the fiber tip into a fluid sample, into which I could then inject the analyte that I'm trying to detect and thus monitor any change in the fluorescence output in real time.  I also wanted to illuminate the fiber tip with the laser transversely - or perpendicular to the direction of the fiber - by slicing the laser's coherent beam directly across the tip of the fiber to maximize my excitation intensity.  In order for all this to work correctly, I decided to use a cuvette to hold the sample, therefore minimizing scattering as the beam enters the liquid sample.  So I put a cuvette holder into the box and secured it in place using a few breadboard mounts.  Then I aligned the laser so that the beam was directed through the center of the cuvette holder and bolted it into place.

With the cuvette holder and laser aligned and anchored onto the breadboard, I then needed some way of holding the fiber in place.  In order to make sure that each fiber could be accurately positioned into the path of the laser, I bolted two micro-manipulators onto the breadboard to act as the base of the fiber holder while also allowing me to adjust the X and Y position of the fiber.

Onto the micro-manipulators I then added a fiber holder.  The fiber holder seen in this image came more-or-less preassembled.  The lower section has a turnscrew that clamps the fiber in place and I added the tube seen in the upper section to help keep the fiber straight as it enters the cuvette.  Astute observers might notice that the fiber holder I've used is manufactured by Newport, whereas pretty much every other optomechanic component I've used is manufactured by ThorLabs.  What can I say?  The Newport fiber holder was all I had on hand.  It was a bit of a pain in the ass getting it secured to the ThorLabs components because the dimensions and threading are different between the two manufacturers, but I got things worked out nonetheless.  And once the fiber holder was in place, the whole thing was finished.

To test the system out, I popped an empty cuvette into the cuvette holder and threaded a fiber through the fiber holder and down into the cuvette.  I attached the other fiber terminus - the one with the SMA connector - to the spectrometer and turned on the laser.  Then I used the micromanipulators to position the fiber tip directly into the beam of the laser.  You can see in the picture below that once the laser was incident onto the fiber, the blue laser light was scattered everywhere and fiber tip seemed to glow bright blue.

If there were a thin layer of my novel fluorescence sensor material on the tip of the optical fiber, which there is not because this was just a spare fiber that I found lying around, it would emit a bright green fluorescence when excited by the laser.  The fluorescence emission would be guided through the fiber and into the spectrometer.  The spectrometer is connected via USB to a laptop computer equipped with software that shows the real-time fluorescence spectrum being sent through the fiber.  And there you have it.  Pretty easy to set up and use.  By using a coherent light source along with a fluorescent sensor material coated directly onto an optical fiber, I've negated the need for lenses or other optics.  Once you start adding lenses, alignment becomes a major issue, and the components have to be aligned and adjusted precisely.  On the other hand, this system required only minimal alignment and went from a clean breadboard to a fully functional optical measurement system with about 2 hours of build time.

Now you can hopefully see why these optomechanics systems are so fun.  Once I finished building, part of me wanted to break the whole thing down and start over.  Just like I did with my LEGOs when I was a kid.

Optomechanics Are Rad - Part I

There are a lot of fun things about my job.  And I'd like to devote a couple of posts to one of my favorite aspects of developing optical sensors.  One challenge that arises occasionally is when the optical or fluorescent analysis instruments that we have on hand in the lab are not sufficient for analysis of the optical sensor platforms that I've developed.  This is often the case when dealing with flat, planar substrates onto which a sensor architecture or layer has been applied or when we apply a sensing mechanism onto the tip of an optical fiber.  When this happens, I have to build a bench-top optics system using our inventory of detectors (PMTs and hand-held spectrometers), light sources (LEDs and lasers), and optomechanics components that we keep in the lab just for this type of situation.  And let me just say this:  building a bench-top optics platform is outrageously fun.  It's like playing with LEGOs.  But these LEGOs are bigger, studier, and able to achieve precise alignments.  They also cost thousands of dollars.

My research project is nearing a point at which we will begin applying our fluorescent sensing material onto optical fibers (I'll discuss the application of a sensing mechanism onto optical fibers another time).  This has left me with a couple of specific needs that must be addressed before the project can move forward:  1) the sensor material must be dip-coated onto the optical fiber tip and to do this, the rate of withdrawal of the fiber tip from the precursor solution must be kept constant at a particular rate, and 2) I have to have some way of accurately measuring the fluorescence emission from the layer coated onto the fiber tip.  In this post, I'm going to focus on the dip coating apparatus.  As it turns out, the optomechanics components that are used to build bench-top optics systems are also quite useful for constructing a home-built dip-coater.  Here's how I did it:

First, I started with a plain breadboard.

Next, I bolted one large post into the center of the breadboard.  The large post allowed me to align the entire system vertically.

Onto the post, I clamped a small system of rails.  The top and bottom of the rails are secured using filter/lens holders.  I used these because they have large holes cut out of their centers.  In between the two filter/lens holders is a modified filter/lens holder that has a small metal cylinder attached with epoxy.  The cylinder is just the right size to a hold a 4 ml vial - and this will hold the precursor fluid that is to be dip-coated onto the optical fibers.  While the top and bottom holders are clamped tightly to the rails, the vial holder in the center was left loose, allowing it to slide up and down the rails freely.

Above the rail system I added a small v-clamp.  The clamp will hold the optical fiber in place during the dip-coating process.

Last, I added a small actuator and the accompanying controller.  The actuator moves the vial holder up and down, like an elevator.

When I clamp an optical fiber into place, you can hopefully see how this apparatus works.  The fiber is submerged into the fluid to be dip-coated onto the exposed tip.  Then I just flip a switch on the actuator and the vial holder slowly descends, withdrawing the fiber tip from the liquid.  When the fiber tip has been completely removed from the fluid, it can be removed from the apparatus and the thin layer that has been deposited on the tip is allowed to crosslink and/or cure into a solid film.

Now this setup was pretty simple.  And because no light sources or detectors were involved, alignment of the entire apparatus was not a big deal.  I just needed the little elevator to withdraw the fiber from the fluid at a constant rate.  My next project - which I'll be working on over the next couple of days - will be to build a system for measuring the fluorescence of the thin film dip-coated onto the fiber tip.  This will be slightly more difficult, though using the fiber itself to gather the fluorescence emission does make things much easier.  But more on that to come.

Should I Stay or Should I Go? - Update Style

In regard to the question of whether to start a new blog, thereby leaving this one to a die a quick death, my abnormally beautiful and supremely intelligent wife offered to co-author a blog related to bicycles with me.  Having a co-author would allow me to worry less about posting regularly on the new blog.  This means that I might indeed have enough time to continue updating this blog, while also occasionally posting on another.  So as for now, I am going to keep this blog alive with semi-regular updates.  If it begins to look like I can't keep up with both blogs, I'll make an executive decision at that time.

So it looks like I'll be starting a new blog with my wife.  My wife will author posts focused on cycling fashion - particularly with respect to office-appropriate clothing that is feasible for a bicycling commute.  This is more or less the content of her current blog, which is very good.  She'll also include tidbits about her daily commute.  This is also a feature of her current blog, and most of the notable moments during her commute consist of encounters with asshole motorists.  My posts will likely also include information about my daily commute - dipshit motorists and all - but I plan to focus more on bicycle repair and restoration.

With the holidays imminent, I'm not sure when we'll get the new blog up and running, but I'll post a link to it here when the time comes.  In the meantime, I'll try to keep the science-related updates coming as best I can.

Should I Stay or Should I Go?

I've become a regular reader of a motorcycle blog called Chin on the Tank.  Although the theme is cafe racers and similarly-styled vintage motorcycles, the content varies quite a lot.  The author has a workshop and is a skilled photographer, so he takes a lot of pictures of his shop and the bike projects that he works on.  He also includes information on the local cafe racer scene, promotes motorcycle events, and documents group rides.  It's a fun blog and it's made me yearn for a vintage motorcycle.

Why am I bringing this up, you ask?  Well, as I've mentioned before, I am a bicycle enthusiast of sorts.  In particular, I enjoy restoring older bikes and putting them back on the road.  In my garage I essentially have a fully functioning bicycle workshop and I spend a fair amount of time working on my personal restorations, as well as a pretty steady stream of projects for my friends.  And so I'm considering starting a bicycle blog.  On this blog I would document and detail the projects that I work on.  Posts would include a lot of photographs - particularly before-and-after images of full-on rebuilds.  And I would try to include a lot of information on the restoration process, costs involved, problems and challenges that I came across, etc.  I would probably also talk about group rides that I participate in, and discuss any notable events from my daily bicycle commute.

The reason I'm mentioning this here is because if I start a new blog, it is unlikely that I would be able to continue updating this one.  There are only so many hours in the day, and I'm unable to spend much of them writing blog entries.  I should note that there are a number of other good science blogs out there, whereas I have been unable to find a good bicycle restoration blog.  On the other hand, I sometimes go fairly long periods without having any bike-related projects, and the cold Missouri winter can really cripple my motivation to work out in the garage.  So updates might sometimes be sparse (though it's not like I'm doing a great job of updating this one consistently).  A few things I should note about this:  1) it's likely that a bicycle blog will motivate me to spend more time tinkering in the shop, 2) I can always ditch the new blog and pick this one back up if things aren't working out the way I had envisioned, and 3) I have a fairly substantial back-log of projects, so I could fill the gaps in current projects with old projects that I've worked on in the past.

Thoughts on which direction I should go?  Let me know...stay the course or try something new?

That. Was. Unexpected.

An article at ScienceInsider is reporting that the new spending bill proposed by the House of Representatives is a little more science-friendly than one would have expected.  Not only are the National Institutes of Health and the Department of Energy slated to receive modest budget increases in this bill, but Rick Shindell of SBIR Insider is also reporting that SBIR/STTR program funding has been reauthorized for another 6 years as part of the National Defense Authorization Act.

This is definitely a glimmer of light in what has been an otherwise dim season for scientific research and education funding - see here and here - but I'll definitely take the good news wherever I can find it.

The End of Movember - Update Style

As I mentioned in my previous post, I did indeed shave my moustache on December 1, signifying the end of Movember.  Now that the moustache is gone, I'll be working on my winter beard.  Here is a picture of me without the moustache - not totally clean-shaven, as I was sporting four days worth of growth when this picture was taken; but not looking particularly bearded, either.

I should note that this picture, along with the last one I posted in which I am sporting the moustache, were taken by my lovely wife and featured on her blog, CoMo Cycle Chic.  I should also note that her blog is a lot better than mine.

Anyways, subsequent to last week's post, I received a comment regarding an additional issue concerning beard wearers:  hygiene.  But not just any normal old pirate-on-the-hair-ship hygiene.  The journal article that was brought to my attention by my colleague and good friend KP is titled, 'Microbiological Laboratory Hazard of Bearded Men.'  This study examined the risk that a beard poses to exposing the wearers' friends and family to potentially dangerous microorganisms.  Of course, this only applies to microbiologists or other laboratory workers who often come into contact with such dangerous organisms.  I don't commonly deal with harmful species of bacteria, so this isn't much of a concern for me personally.  But for all of you bearded microbiologists out there:  beware!  You may be exposing your loved ones to more than just unfettered manliness!

The End of Movember

It's now the final day of November and, as I'm sure my wife will be happy about, that means Movember is coming to an end.  I did a half-assed job of participating in Movember.  You see, as November approached, I knew that the month was dedicated to the growing and grooming of a moustache to raise awareness for mens' health issues - particularly prostate cancer.  At that time, I had a well-trimmed full beard.  I had some important business meetings on November 3rd, and I cut my beard short so as to look somewhat professional on that day.  Then on the morning of November 4th, I groomed my facial hair into a tight moustache with the accompanying jazz spot (known more commonly as the soul patch):

Unbeknownst to me at the time, the rules of Movember state that participants must begin the month with a clean-shaven face and subsequently grow and groom the moustache throughout November.  When I learned of this rule - by which time it was nearly a week into November - it seemed futile to start anew.  So I just went with it, meaning that I broke the Movember rules and basically cheated.

Now that Movember is coming to an end, I guess the next step is to shave the 'stache and start growing the traditional winter beard.  And on that note, I thought I'd share some interesting things that I've come across recently regarding beard-growth, bearded men, and beards in general.  First off:  the beard-second.  I first discovered this extraordinary unit of length at The Evolving Scientist.  Wikipedia defines the beard-second thusly, "the beard-second is a unit of length inspired by the light-year, but used for extremely short distances such as those in nuclear physics."  It appears as though the most widely accepted conversion to SI units is 1 beard-second is equal to 5 nanometers.  I deal with lengths at this scale quite often in my work and I'm looking forward to sneaking in a 'beard-second' reference in a future conference presentation.

Less fun is a study described in the journal Heart, Lung and Circulation in 2008.  The article is titled 'Sternotomy and the Beard,' and it describes the difficulties associated with performing a sternotomy on patients with beards.  As it turns out, beards can cause issues with mask ventilation, sterility, and effective skin preparation.  The authors recommend folding the beard over the jaw, toward the patients' face, then securing it in that position using a surgical mask.  This sounds pretty reasonable considering the alternative is to shave the beard off.  I'd hate to wake up from surgery to find my beard gone.  Then again, I don't allow my beard to grow so long that it would interfere with chest surgery.  Yet.

And finally, a research group in Wisconsin examined the effect of beards on high altitude oxygen processing.  The results showed that at a height of 7.5 km, bearded mountain climbers had a 7.3% increase in oxygen respiratory index (ORI).  At 8.0 km, the increase in ORI grew to 10.7%.  And at the summit - approximately 8.8 km - the gap widened to nearly 15%.  That's a pretty significant difference, and good news for mountaineers who are unopposed to beard growth.  Personally, I'll plan on using this little bit of information as further justification for my winter facial growth, even though I don't do much mountain climbing.  Not that I really need any further justification.  Keeping my face warm in the cold Missouri winter is reason enough.

I Promise I'll Do Better

Lately I've been keeping an eye on the stats for this blog.  I noticed that my readership has increased notably over the last couple of months and I'm starting to get some steady traffic.  Of course it stands to reason that this would be happening when I'm extraordinarily bogged down with proposal writing, heavy amounts of lab time, and on top of it all, holiday season.

So to all of you - yes, all three of you - who have been checking in regularly, I apologize for neglecting to update recently.

How about a little update on what I've been so busy with?  Well, the main reason I've been mind-fryingly busy is that I'm working on getting an SBIR proposal submitted while simultaneously getting another one started.  These proposals are company-related and we're trying to get some funding to pursue proof-of-concept studies for one of Emergent Sensor Technologies' core projects.  My colleagues and I are beginning to realize that it may be foolish to depend on SBIR support to initially fund the company, so I'm also working on two proposals for contract-based research for large companies.  In other proposal-writing news, I've been working on getting two proposals that were not funded revised and resubmitted.  These proposals are university-related and are for projects that we are starting at Lincoln University.

Along with cranking out endless grant proposals, I've also been busy in the lab at Mizzou.  Things have started progressing quickly with the MU research team and I'm in the midst of gathering data at a semi-furious pace.  Toss the rapidly approaching holiday season into the mix, and you can get a good idea of why this blog has taken a backseat to my other responsibilities.

Having said all that, I feel a bit despondent about my obvious delinquency.  I'll try to have another update (one with actual science-ish content) by the end of the week.  In the meantime, have a drink to celebrate the successful launch of Curiosity.  It's got a long journey ahead of it and I'm hoping for its safe arrival on the Red Planet.

No Sugar for This Bad Medicine

This sucks.  Wired Science is reporting that cuts to NASA's budget are leaving the agency's planetary science program in a state of limbo.  Questions are being raised about a number of slated missions and NASA's ability to carry out these missions without substantial help from the European Space Agency.  These questions are the result of a drop in NASA's budget of nearly 5% from last year.  And all of this comes on the heels of NASA scrapping their shuttle program, leaving our astronauts to rely on the Russian space program to travel to and from the International Space Station.  It's worth noting that this is a program that has recently seen some notable setbacks, with a Soyuz rocket - the same rocket that launches manned missions into low-earth orbit - crashing shortly after launch in August and the failed launch of a Mars moon probe earlier this month.

I guess this doesn't come as much of a surprise, since I've already discussed the cuts that were anticipated for the budgets of NASA and the NSF.  It's still disappointing, though.  NASA provides us with a wealth of information and new technologies.  They have been analyzing climate change for a number of years, tracking hurricanes, and leading the way in discovering alternative sources of energy.  And now it seems as though our lawmakers are methodically and quietly strangling the agency until there's nothing of substance left.  It's sad to imagine living in a country that has the means but lacks the will to explore the universe, visit other worlds, and discover the wonders that exist right here on our quaint little planet.

A Little More On Energy

I've been hard at work bashing the fossil fuels industry lately.  See previous posts here and here.  I'm beginning to wonder why I didn't get my degree in a field related to energy production.  But I know why; it's because I really enjoy my work in chemical and biological sensor development.  And being an advocate for alternative energy while working in the energy sector has got to be one of the most frustrating situations ever.  Besides, I can always apply my current expertise to the energy production industry to try to help aid the development of alternative energy sources in a more indirect way.

Since I've been on a tear about fossil fuels, I thought I'd better share Paul Krugman's latest column, which is also devoted to the energy production industry.  It's a great glimpse into the present and future state of solar energy from the viewpoint of a Nobel prize-winning economist, whose opinion I deeply respect.  He also addresses some of the major issues with fossil fuel extraction, with a particular emphasis on the burgeoning and highly destructive fracking technique.  I should note that he also has a brief follow-up blog post in which he clarifies a couple of ideas that he didn't have space to address effectively.

I also thought I'd share a few thoughts while I'm on this subject.  First of all, I would like to reiterate that I am not an expert in the field of energy production.  I don't do a very good job of keeping up with the latest research or technology in this area, mainly because I have no vested interest in it beyond wanting mankind to be more responsible citizens of our planet.  On the other hand, I'm a relatively intelligent person.  I'm also pretty good at reading data.  So what I've done in previous posts - such as this one and this one - is look at the actual data in the references that the authors cite and make sure that the studies were sound and that the data matches the authors' claims.  After all, I don't have to be an expert to spot bullshit.

As of right now, I'm not sure if I'll continue to take the hatchet to the ACCCE's ridiculously idiotic website or not.  But either way, there will definitely be more on these issues to come.

Keep That Middle Finger in the Air

I happened to catch one of the clean coal television commercials that I mentioned in a previous post.  The advertisement - I wasn't able to find it on YouTube, otherwise there would be a link here - along with the corresponding website, are hosted by the American Coalition for Clean Coal Electricity (ACCCE).  One quick thought before I briefly discuss what I found on their website:  I think an advocacy group that tries to help make coal-based energy cleaner is a good thing.  Coal-fired power isn't going anywhere for a while, and if we can make it less destructive in the meantime by utilizing technology that decreases harmful emissions from power plants, I'm all for it.  But that's not what the ACCCE is.

The ACCCE website claims that "the environmental performance of coal-based generation for traditional emissions such as SO2, NOx and particulate matter has been significantly improved."  On the original page, this sentence is a link, presumably to a cited reference for this claim.  When you click on this link, however, it takes you to another page on the americaspower.org site.  So now at this new page, I have to click on yet another link to see the reference that they've cited.  This next link takes me to an EPA air pollution trends database.  From here, in order to see the data that the ACCCE cited, I have to open an Excel file that contains the data.

So that's what I did.  And I learned a few things.

The ACCCE's claim that SO2 and NOx emission have been reduced is true.  In fact, these reductions have been fairly dramatic.  Although I would hasten to add that these reductions are probably largely due to the EPA regulations that the ACCCE is so vehemently against.  This is an odd stance:  touting results as your own victory when you are opposed to the causes behind those results.  And what about the claim that particulate matter emissions have been significantly improved?  Not so much.  Since 1970, the amount of particulate matter with a diameter of 2.5-10 microns produced from electrical utilities has been reduced; that much is true.  But particular matter with a diameter of 2.5 or smaller has increased, and done so by nearly four-fold.  Other emissions that have seen increases over the years include carbon monoxide and volatile organics.  And ammonia emissions, which were non-existent in the power production industry through 1995, have increased steadily, reaching 37,000 tons in 2011.

So exactly how clean is coal?  Not really all that clean.

Is Illegal Kidney Trafficking Just the Beginning?

I first heard about the story of the man in New York who was brokering black market kidney transplants yesterday on NPR news.  Then I ran across it again this morning on Wired Science.  The guy got busted by the FBI trying to arrange an illegal kidney transplant.  After the sting, he told investigators that he had brokered several other such deals.  He claims that the transplant procedures took place in U.S. hospitals by experienced surgeons and that the Isreali donors were well compensated.  And that's all good; it would be some pretty frightening shit if the procedures were being done in a roadside motel or an old meat locker or something similarly disturbing.

It's important to note, though, that a kidney transplant is not as easy as changing the fuel filter on an old Chevy pickup.  In particular, immunological markers have to be matched effectively to reduce the risk of the patient having a major foreign body response to the organ.  And even then, the chances of complications after the procedure are not trivial.

But I can't help thinking that this case could be a sort of omen; how runaway medical care costs and high rates of uninsured Americans could be fostering a culture of illegal, black market medical practices.  Not only do people die while on a waiting list for donor organs, but they also die because they can't afford the transplants.  The man who was arrested in New Jersey for trafficking kidneys was charging $160,000.  Seems fairly steep, but would it have cost any less if the patient had gone through official channels to get the kidney?  And how long would they have had to wait on a list before receiving the needed organ?  According to one website, the average waiting time for a kidney is 3 to 5 years.  That's a long time to wait if you are dying a slow, painful death.  And the average transplant cost, according to one study, is just shy of $90,000.  Add to that the $135,000 that it will cost to be on kidney dialysis for the 3 years that you're waiting for a suitable donor organ and suddenly $160,000 for an illegal kidney starts to look like a pretty attractive option.

My guess is that there will be more cases like this in the future, especially if the new Affordable Care Act is repealed.  And you want to know what we can do to make sure that these types of instances don't become commonplace?  Support universal health care.

Giving 'Em The Good 'Ol One-Finger Salute

I've been seeing a few television advertisements, such as those from some sort of Clean Coal organization and Conoco-Phillips, making some odd claims lately.  The Conoco-Phillips commercials show actors posing as young, supposedly intelligent college students discussing how natural gas is "cleaner."  Uh...cleaner than what, exactly?  Cleaner than most other fossil fuel industries like coal and petroleum?  Alright, I can go along with that.  But the big push right now is in the renewable energy sector; solar, wind, and to a lesser degree, biofuels.  If these ass-clowns are trying to tell me that natural gas is "cleaner" than solar energy, they need to go take a walk.

But the Clean Coal commercials are what really raise my ire.  These advertisements make dire predictions about EPA regulations killing jobs and destroying our economy.  I've lately found myself raising my middle finger to salute these advertisements when they appear.  To say the least, I find them unfathomably disgusting.  Paul Krugman has a delightful summation of a study that looks at the quantitative economic impacts of pollution, with regard to health and productivity effects, for various industries.  The researchers then compared these values to the economic value that the industry contributes.  The study indicates that there are some industries that actually have an overall negative impact on the economy.  To take a quote from the abstract:

Solid waste combustion, sewage treatment, stone quarrying, marinas, and oil and coal-fired power plants have air pollution damages larger than their value added. The largest industrial contributor to external costs is coal-fired electric generation, whose damages range from 0.8 to 5.6 times value added.

So there you go.  Want to stop killing jobs and boost the economy?  Regulate the shit out of the coal industry.

By the way, this issue really sticks in my craw, so expect more on this in the coming days and weeks.

Drill, Baby, Drill!

But not for oil.  For life.

I just think this is too cool:  a group of geologists from the British Antarctic Survey are planning to drill down through 3,000 meters of Antarctic ice to reach a sub-glacial lake, called Lake Ellsworth, that remains unfrozen due to geothermal heating.  The researchers will be looking for signs of life in the waters deep below the surface, as well as taking other measurements to learn more about this strange place.

Thinking about it makes me shake my head in disbelief.  Sub-glacial lakes that could potentially harbor life?  This planet is so freakin' awesome!

Hello From My Comfy Pink Chair

Holy cow.  It's been a hectic couple of weeks.  I officially started working at Mizzou late last week.  I am now a staff researcher for the International Center for Nano/Micro Systems and Nanotechnology in the Department of Electrical and Computer Engineering.  My official title is Research Scientist.  Over the last week I've been getting somewhat conflicting descriptions of my responsibilities, but I'm relying on my PI and my own ideas of how the project should proceed to hammer out a research plan.  Sticking to that plan will be another story.  But I suppose that's the nature of research.

In the meantime, I'm still working part-time at Lincoln University.  In fact, my start date at Mizzou pulled me away from setting up our new Raman spectroscopy system in our lab at LU.  I'm looking forward to getting back down there tomorrow and getting that instrument running.  We're still waiting to get a new refrigerator and some optomechanics supplies, and also have a big floor centrifuge moved downstairs.  But the lab is really coming together.  It's kind of a shame that, with my colleague and I dropping to part-time, the shiny new lab will be pretty badly underutilized.  Hopefully having the new lab running smoothly will help kick-start the sensors research program at LU and my supervisor can bring in some new lab rats to use the lab at something more closely resembling full capacity.  It's not as easy as it sounds, though, as the LU Department of Life and Physical Sciences does not have a graduate program, so he's unable to bring in graduate student researchers.  He mostly depends on post-docs like myself and undergrads to staff the lab.

One last thing:  I'm squatting in a nice roomy corner office for right now while the MU Bioengineering Department does some rearranging.  However, there is a possibility that I will be staying in this office permanently.  The office has a 3-sided desk and a receptionist counter, both of which are pink.  I also have a matching pink chair.  It is truly awesome and I really do hope that I get to stay in this office:

I mean, seriously, how can you not dig that color scheme?

Faster Than the Speed of Light is Pretty Fast - Relatively Speaking

As you've probably heard by now (or not, depending on whether you are a flaming nerd or not), a research group based primarily at CERN claims to have sent a neutrino, an elementary subatomic particle, zipping across Europe faster than the speed of light.  According to early reports, the neutrino reached its destination -  after traversing a 732 km distance - 60 nanoseconds faster than it should have had it been traveling its expected speed, which is a tiny fraction under the speed of light.  This is a big deal because according to Einstein's theory of special relativity, the speed of light is the ultimate speed limit for all physical matter.

But is it really THAT big a deal?  I say no, not particularly.

If you'd like to know why it's not really as tremendous a breakthrough as some would have you think, check out posts at Wired Science and The Evolving Scientist.  Here are a few quick thoughts about this study, as illustrated by posing questions to myself:

Does this disprove Einstein's theory of special relativity?  Of course not.  This is one small, albeit significant aspect, of this particular theory.  I should also point out that this is only one of Einstein's many contributions to our understanding of physics.

Are these results conclusive?  Not necessarily.  Other groups, such as the U.S.-based FermiLab, are already working on repeating the study to see if they can get the same results.  Additionally, the European group claims to have taken important sources of error into account when analyzing their data.  But that doesn't mean that they were able to consider every source of error, and so other physicists were immediately pointing out potential sources of error with this study.

If these results turn out to be conclusive, how important are they?  They're pretty important, but no more so than any other notable scientific discovery.  That's kind of the point.  Science is not static.  It moves forward.  Our knowledge is advanced with each new discovery, and new discoveries are happening every single day.  And that's why science is so cool.

Imprinted Polymers AND Carbon Nanotubes? Is That Even Allowed?

I ran across a paper a few days ago that caught my eye for two reasons.  The first reason is that the paper deals with applications of molecularly imprinted polymers, and applies molecular imprinting to a sensing scheme that I hadn't previously considered.  The second reason for my keen interest in this paper is that the analyte that the authors are trying to detect with their sensor is a cardiac protein called Troponin T (TnT), which is what much of my Masters research focused on - developing a fluorescence-based immunosensor for TnT.  The paper, titled Artificial antibodies for troponin T by its imprinting on the surface of multiwalled carbon nanotubes: Its use as sensory surfaces (subscription is likely required) is published in the October 2011 edition of Biosensors and Bioelectronics, which is one of my favorite journals.

I should probably briefly explain why TnT is important.  Cardiac TnT is part of a greater, multi-protein Troponin complex, and is found exclusively in cardiac muscle tissue.  When necrosis of cardiac tissue occurs, a hallmark of heart attack, the Troponin complex fragments into its three individual subunits (TnI, TnC, and TnT).  These subunits then become bloodborne and can be detected in the blood using standard laboratory testing.  Under normal, healthy conditions, the subunits are absent from the blood.  The current laboratory testing techniques for detection of TnT to diagnose heart attack are unfortunately somewhat lengthy, and there is a great deal of interest in developing a much more rapid diagnostic test that is both accurate and sensitive.  This was the goal of a large part of my Masters research.  And obviously, this is the goal of the authors of the paper described herein.

I'm not going to go into depth on the technical details of the sensing system that the authors developed, but it's important to have a general understanding of how the thing works.  The researchers started with multi-wall carbon nanotubes (MWCNTs) and chemically modified them, allowing them to bind covalently to TnT when it was introduced.  The MWCNTs with bound TnT were then coated in a functional polymer capable of forming a number of weak noncovalent bonds with the TnT.  Then, when the TnT was removed using a chemical extraction procedure, a molecularly imprinted binding site for TnT was left behind.  I've described this process previously, and it is diagrammed in the figure below, which is from the paper.

The MWCNTs coated in molecularly imprinted polymer were then suspended in PVC and coated onto a wire electrode.  The electrode was then exposed to a solution of TnT and voltage measurements were used to determine TnT binding.

Although I found this paper quite fascinating and an interesting use of molecularly imprinted materials, I have to say that the methods the authors used are somewhat flawed.  The most glaring problem that I noticed was the extraction procedure to remove the TnT template.  The authors claim that the TnT was removed by introducing the MWCNTs with the imprinted polymer to a solution of oxalic acid.  Now, I'm not all that familiar with oxalic acid, but I'm not entirely sure that this extraction procedure is robust enough to disrupt the covalent amide bond that was used to link the TnT to the surface of the MWCNT.  This would explain why the authors observed large peaks that are normally associated with proteins when x-ray spectroscopy measurements were taken.  Another fairly major problem is that the modified MWCNTs were embedded in PVC for the potential measurements.  Although TnT is not an abnormally large protein, it is a protein nonetheless, and is therefore a substantially sized molecule in the grand scheme of things.  Due to its size, it is unlikely that TnT would be able to infiltrate the PVC matrix.  That would mean only those MWCNTs that are exposed at the surface of the PVC layer would be able to effectively bind to TnT, rendering the rest of the MWCNTs - probably a majority of them - inaccessible to the analyte.


All in all, the idea behind this project is pretty cool.  It was poorly executed, though, and I have difficulty believing that they actually got the results that they claim to have gotten.  I can think of a number of ways to go about developing a carbon nanotube-based electrochemical sensor that uses molecular imprinting to impart selectivity, and I can honestly say that I wouldn't have decided on the method described here.

A Few Notes on Antibodies: Part 2

Now that I've covered the basic function of antibodies and how they're made, I think I'll turn my attention to immobilization techniques.  There are a number of different ways to stick antibodies onto a solid surface, and the strategy that is used is mostly dependent on the type of surface you're working with.  Gold, for example, is pretty easy.  This is because the cystein residues that are present all over the antibody structure will bind - albeit fairly weakly - to gold.  There is a natural attraction between the thiol group of the cystein residue and the gold.  So when you expose IgG antibodies to gold at a nice comfortable pH of 7.5-8.5, the antibodies will adsorb onto the gold surface.  Although this method is easy and relatively effective, it does not create a very stable bond.

To immobilize antibodies with a stronger binding scheme, the protein must be covalently attached to the surface.  This type of covalent linkage between a surface and a protein is often used when the surface is glass.  Glass is a material whose surface is surprisingly easy to modify using a class of compounds called silanes.  Silane molecules are most often based around a single silicon atom.  The silicon atom has three ethoxy or methoxy groups.  These groups will covalently bind to glass, creating extremely stable bonds that are also able to crosslink with other nearby silanes to further stabilize the silane layer.  The fourth valence electron is bound to an organic species - usually a functional group connected to the silicon via a short hydrocarbon linker.  One of the more common silanes used in immobilization techniques is mercaptopropyl(triethoxysilane), and its structure looks like this:

By looking at the structure, you can clearly see the three ethoxy groups (O-CH3) bound directly to the Si atom, and the one mercapto group (SH) connected to the Si atom by a three-carbons (propyl) bridge.

So once the surface of the glass is functionalized with a silane layer, it is much more reactive than the fairly inert native glass surface.  The next step would then be to connect the functional layer of the modified glass surface to one of the amino acids of the IgG antibody.  This is accomplished through the use of a crosslinker.  To give give an example, the crosslinker that I have the most experience with is GMBS (long chemical IUPAC name:  4-Maleimidobutyric acid N-hydroxysuccinimide ester).  And this is what it looks like:

GMBS is known as a heterobifunctional crosslinker because the two ends of the molecule are different and are reactive towards different type of functional groups.  In this case, the maleimide group on the left binds covalently to the mercapto group of the functionalized glass.  The succinimidyl ester on the right then binds to amine groups found on the peptide chains that make up the antibody protein.  Once this reaction successfully completes - which happens fairly quickly - you end up with a glass surface that is coated in IgG antibodies.  And therefore, the surface is now capable of selectively binding the antigen of interest.

One last note about antibody immobilization: the the steric position of the antibodies on the glass is important.  By simply crosslinking the protein directly to the glass surface, you have no way of controlling the position of the antibody.  For instance, the crosslinkage could occur at or near the antigen binding site of antibody.  This would mean that this particular antibody would end up immobilized 'upside down,' with the antigen binding sites so close to the glass surface that the antigen would be unable to bind.  To remediate this problem, you can first crosslink special proteins, such as Protein A or Protein G, to the surface.  Protein A and Protein G have a binding site that is specific to a highly conserved region near the 'bottom' of the antibody, on the opposite side of the IgG from the antigen binding sites.  After immobilization of Protein A or G, you can introduce the antibody, it will bind to the Protein A or G, and you end up with a surface in which all of the antibodies are pointed 'up' with the antigen binding sites exposed and available.

A Few Notes on Antibodies: Part 1

During my doctorate research, I shifted my research focus from more traditional biosensor technologies, such as immunosensors, to sensing applications of molecularly imprinted polymers.  However, I still dabble in immunosensors fairly often, and my expertise and previous experience in antibody-based sensors comes in handy, particularly for other researchers who come to me with questions and guidance in this field.  Here at LU, my research group is currently waiting to receive a fluorescent microscope that we recently ordered.  When the new scope arrives, I will be using it to conduct a study examining targeted antibody immobilization onto gold electrodes.  The plan is to block specific areas of our sensor substrate so that antibodies will only be able to bind to certain regions.  When fluorescent bacteria are introduced, they'll bind specifically to the antibodies, and this phenomenon should be clearly visible under the fluorescent microscope.  So in the spirit of beginning this work, I thought I'd discuss some of the basics of antibodies and antibody immobilization.  I'm going to be brief, so I may have to turn this into a series of posts.

First off, I need to clarify one thing:  when I say antibody, I am referring solely to immunoglobulin G (IgG) antibodies.  Next, I guess I should describe what antibodies are and what they do.  The IgG antibody is a relatively high molecular weight protein.  It's produced by our immune cells (B cells) in response to infection.  When the antibodies are produced during infection, they bind to the bacterium or virus or whatever, coating its surface and acting as a sort of signaling beacon.  Other immune cells are able to detect this beacon and attack and destroy the infection.  So in a very general sense, that's the natural function of antibodies.

This natural function of the IgG antibody is made possible by one of its most important properties; selectivity.  The IgG antibody is a large Y-shaped protein that looks something like this:

At the top ends of the two 'arms' of the antibody are binding sites that are capable of binding to one single antigen, which is the target bacteria or virus or whatever, and only that one antigen.  This is what is referred to as selectivity.

Researchers like me who are interested in using the properties of antibodies for biosensors and other applications must be able to readily produce or purchase these antibodies.  As it turns out, there is a fairly effective way of harvesting the antibodies that are selective for a particular antigen of interest.  Let's say, for instance, that you want an antibody that is selective for the flu virus.  To produce these antibodies, you would take a syringe that contained the flu virus and inject it into the lumen of the gut - or some other space where the antigen would not leak out into the bloodstream - of a mammal.  The mammal used is commonly a mouse, rabbit, or goat.  The B cells infiltrate the gut lumen of the animal and begin churning out antibodies that are selective for the flu virus.  Then you would go back and draw out the fluid from the lumen of the gut and purify the antibodies that were produced.  And there you have it - anti-influenza antibodies.

Having only touched the surface of this topic, there will definitely be more to come.

Learning Curve

Whoa...Blogger has made some changes to their interface, so hopefully my confusion won't result in any illegible posts.  I must say, though, that they've simplified things nicely.  Perhaps too simple, as it's been difficult for me to figure out how to do tasks that used to be almost second nature. 

For example, the old interface had a navigation bar at the top of the page, with one of the nav buttons displaying the word 'STATS.'  When clicked, you were taken to a page in which you could view various statistics and information on your readership (number of blog and individual post views, redirect URLs, etc.).  To get to that same stats page with the new interface is a little less intuitive.  There is a button near the top of the page with an icon that resembles a piece of paper with text on it.  Next to that is an upside down triangle.  When you click on the upside down triangle, a drop-down box opens that contains a list of link options.  One of the options is 'Stats,' and when you click on it, you are directed to the statistics page that I described previously.

Don't get me wrong, the interface is very sleek and I think I'll come to prefer it to the old one.  It's just going to take some getting used to.  I hope.

For Your Viewing Pleasure

As I've said before, and will probably say again, I've always been fascinated by the workings of our universe and the magnificence of space. I try to make it over to NASA's website to check out their Image of the Day Gallery once in a while, and I'm always amazed at how awesome the featured pictures are.

Today, I ran across this article at Wired Science. A Rice University researcher took 14 years of images of high-energy jets released from forming stars from the Hubble Space Telescope and pieced them together into a series of seamless animations. The result? I would call it staggering, eerie, beautiful. But you're welcome to come up with your own adjectives.

The video below includes a small selection of the animations. The rest can be found here.

Seeing Red, In More Ways Than One

As the co-owner of a small high-tech business, Emergent Sensor Technologies (EST), I have a vested interest in the federal Small Business Innovation Research (SBIR) program, and to a lesser degree, the Small Business Technology Transfer Research (STTR) program. These programs were originally designed to give small businesses kick-start funding to pursue highly advanced and innovative research projects that might be too risky to undertake otherwise. The end goal of the program? To create jobs. And this makes a lot of sense considering national job growth is fueled almost solely by small businesses. In fact, when EST is awarded its first SBIR, we plan to hire new employees nearly immediately, with additional employees to be added within 1.5-2 years after the date of the award.

Unfortunately, the SBIR program, like many other federal science-related programs, is on the chopping block. According to Rick Shindell of SBIR Insider,

The news on SBIR reauthorization is not good. In fact, at this time, the odds for obtaining reauthorization by the September 30, 2011 deadline is grim, and congress seems to have no taste for what would be the 13th continuing resolution (CR or extender) of the program. In short, the SBIR/STTR programs are likely to lapse, at least for a time, but perhaps permanently.

I don't think I should have to state explicitly that this is an utter travesty, but I'm going to anyways: This is an utter travesty.

It's become clear that in Washington, D.C., job growth and economic development has taken a back seat to deficit reduction. This, despite high unemployment and a depressed economy for the foreseeable future. It's a shame that balancing our federal budget, a matter which has very little effect on the majority of Americans, is being touted as some sort of pressing problem, all at the expense of our country's future. It shows a real lack of foresight and vision. And it's paving the way for us to be overcome as the world's most powerful nation, leaving us whimpering and grabbing at China's coattails.

You Say Scientific Reference, I Say Reprobate

As an avid bicyclist, bicycle aficionado, and all-around bike-lover, I have a great respect for the bicycle helmet. Beyond general self-awareness and following the rules of the road, the bicycle helmet is one of the few ways a cyclist can help ensure his or her own safety. That's why I was taken aback when I came across a supposed bicycle advocacy website that purposefully denounced the use of helmets, citing their "scientific reference on helmets." Their reference is for the so-called 'Bicycle Helmet Research Foundation.' I should warn you that, should you decide to visit this reference website, your head might explode due to the sheer volume of stupid that will be racing over the internet directly into your brain.

Here's what the 'research institute' is all about. They've compiled a bunch of research studies that show that bicycle helmets make cyclists safer. They take these studies and tear them apart, looking for any gaps or holes that can be used to decry the findings and conclusions of the study. Then they look at a bunch research studies that show that helmet-wearing cyclists are not statistically significantly safer than non-helmeted cyclists, which they take as gospel. This is, of course, because these studies back the conclusion that they had obviously settled upon beforehand: helmets may or may not make bicyclists safer, so no one should use them.

Basically the authors have decided that they don't like helmets, so they dig up a bunch of literature to justify themselves, often failing to understand or purposefully misconstruing the conclusions of the papers that they've cited. I should probably be a little more fair and honest about this; the authors are actually against mandatory bicycle helmet legislation. No matter their underlying goals, though, it really is quite despicable.

How about this instead: Helmet use has been estimated to reduce head injury risk by 85 percent, according to the Insurance Institute for Highway Safety (IIHS). Oh and by the way, I'd say the biggest difference between the IIHS and these turds who run the anti-helmet website is that the IIHS isn't made up of a bunch of quacks trying to come to a preconceived conclusion.

Overall, the website reminded me a lot of the websites of climate change skeptics. Obviously subjective and including only the evidence required to illuminate their own narrow viewpoint. And I think it's rather pathetic that this is what these people have devoted their time to. Not wearing bicycle helmets seems to have caused them to take a few too many blows to the head, if you know what I mean. But I guess we're all entitled to our point of view, no matter how idiotic it may be.

Toot My Horn

My most recent manuscript submission has been published online. As I promised in a previous post to link to the paper on my blog, you can find the article here (probably requires a subscription). This paper doesn't include any mind-blowing discoveries, so I'm not going to spend a whole lot of time hashing out all the details of the study. But here's a brief picture of what was done...

The paper is titled, "Comparison of molecular imprinted particles prepared using precipitation polymerization in water and chloroform for fluorescent detection of nitroaromatics." First off, I've described the process of molecular imprinting and how the molecular imprinted polymers work; you can find this information here if you'd like to know more. In essence, a molecularly imprinted polymer is a plastic material that starts as a liquid-phase precursor solution containing the template molecule that you want to imprint. When the material polymerizes, creating a rigid solid, the template is physically and chemically bound within the material. A chemical extraction process is then used to remove the template molecules within the material. This leaves behind binding sites in the polymer that, when re-exposed to the template, are able to specifically rebind the molecule. In this case, I used two different template molecules, TNT (the explosive) and its little brother DNT. Both of these compounds are nitroaromatics and are important in the detection of bombs, IEDs, landmines, etc.

For this study, I prepared the imprinted polymer particles using precipitation polymerization. In precipitation polymerization, the liquid precursor of the imprinted polymer contains an excess of solvent. When there is enough solvent, one section of forming polymer in the solution is unable to link up to another forming section of polymer in the solution because of all the solvent that is between them. Because of this, discrete particles of imprinted polymer are formed within the solution.

The selection of what type of solvent to use for this process is very important, as it determines how effectively the imprinted polymer binding sites will bind to the template molecule. In previous work, I experimentally determined that chloroform was the best solvent for imprinting nitroaromatic molecules. But here's the catch: molecularly imprinted polymers bind the template molecule best when they are exposed to the molecule in the same solvent that was used to form the imprinted polymer, and I wanted to expose the imprinted polymer to the template molecule in a water environment. So there's a trade-off going on. On the one hand, I already knew that chloroform was the most effective solvent for imprinting. But on the other hand, water would be the ideal solvent if I planned to expose the imprinted polymer to the template in water.

So I set out to compare the two solvents, chloroform and water, but a funny thing happened along the way. I used scanning electron microscopy (SEM) images to look at the polymer particles and found that they were nothing alike. In the image below, (a) is the SEM of the particles produced in chloroform and (b) is of the particles produced in water. The images showed us that not only was the chemistry of the two polymers different because of the solvents, but the entire morphology was different as well.

To test which polymer would bind the TNT and DNT templates best, I doped the imprinted polymer particles with a fluorescent dye. When the template bound to the binding sites of the imprinted polymer, it would then quench the fluorescence of nearby dye molecules, which could be detected using a spectrometer. By carefully analyzing the data from these studies, I found that chloroform was the most effective solvent. This meant that the increased imprinting efficiency of the chloroform-based polymer was more important than using the same solvent for polymerization and rebinding. These results weren't much of a surprise, but they could be very beneficial for other researchers working in this field, as they can now refer to my paper rather than conducting this fairly time-consuming study on their own.

Not Exactly Robot Overlords, But Still...

Some of you may have already come across this, because it's making big news. But researchers at Argonne National Laboratory have developed what they are calling 'self-assembled colloidal asters.' You can check out the abstract here, but the full article is available by subscription only. These colloidal asters are essentially little micro-robots. They are manipulated with a magnetic field and can perform simple tasks as a cohesive group of colloid particles. If you're interested, I recommend reading Wired Science's article on this, which also includes some pretty cool videos of the little dudes in action.

Today's Vocabulary Word: Theory

I'm going to go ahead and essentially plagiarize an entire post from one of my new favorite blogs, The Evolving Scientist. I even stole one of the images from their post! Last month, they addressed an issue that has been close to my heart since I was a fledgeling scientist, beating my head against the wall trying to explain evolution by natural selection to the church kids on the school bus. And that issue is the definition of a scientific theory.

I'm not going to rehash their entire post, because they've done an outstanding job of explaining what a theory is and how it is different from a law, as well as how a theory is different from the layman's common definition. But the difference between scientific theory and law is summed up nicely by the image above. A theory is not an educated guess, as many believe (that would be a hypothesis). Instead, a theory is defined (by the Oxford English Dictionary) as 'a scheme or system of ideas or statements held as an explanation or account of a group of facts or phenomena.' In simple terms, a theory is used to explain a set of often complex observations. A law, on the other hand, is a description of an observation, and is often used as a predictive measure when certain conditions exist.


These ideas are, more or less, part of the scientific method, in which observations are used to verify hypotheses and generate scientific theories, thus increasing our understanding of the world around us. This process was spelled out by Francis Bacon in 1620, in one of the greatest works ever written, Novum Organum Scientarium. PZ Myers has a phenomenal post on his blog, Pharyngula, that discusses Novum Organum and its place as a marvelous triumph in human history. If you feel like being inspired by science and our quest for knowledge, it's required reading.

Piece By Tiny Little Piece

A quick update before heading off to a meeting: the old lab refrigerator - the one with the Natural Light in it - has been hauled out of the lab by the LU Facilities guys. That freed up a lot of space in the laboratory and got rid of a pretty wretched eyesore. Unfortunately, the old calorimeter is still there. They weren't able to take it along with the fridge because it is still connected to the water supply. This means we'll have to wait for the plumber to come disconnect the instrument, then we'll have to wait for the Facilities guys to come back to pick it up. So it may be there for a while longer.

We're also waiting to have an old non-functional floor centrifuge picked up. The centrifuge is in a lab in the basement. Once they've hauled it away, we're going to move the functional centrifuge that's currently in our lab down to take the old one's place. Then we'll be putting the new refrigerator in the space left by the centrifuge.

After all this is done, it's going to look pretty awesome in the new lab. Everything will be arranged very efficiently and we'll have lots of extra space on the bench top for all of the equipment that has been ordered or will be ordered in the near future.

Speaking of equipment, I also moved our spectrofluorometer up into the lab from downstairs. This is a pretty big deal since it's the instrument that we use most often for fluorescence measurements. It wasn't easy, since the fluorometer is a pretty big unit - taking up most of the bench that it now sits on. I had to break the instrument itself in half and carry it up into the lab on a cart. Then I had to bring up all of the drivers and amplifiers and other peripheral equipment that runs the machine. It's a fairly delicate and complicated instrument, so it took me some time to get it put back together and hooked up properly, but it's going to be nice to have it in our lab where it will be easily accessible. It was starting to become a real pain in the ass to prepare the samples in the new lab, then carry them downstairs to the old lab to take the measurements.

Putting on the Blinders

Back in the early days of this blog, I made mention of the James Webb Space Telescope (JWST). The JWST is set to take the place of the Hubble, now that the Hubble is in semi-retirement. Then, as now, I'm really excited about the JWST. One of its primary missions will be to peer back to the beginnings of the Universe; back to the time when light first came into existence.

That is seriously awesome. It's like time travel, but not.

And now, on top of everything else falling apart around us, it looks like congress may use the federal budget deficit as an excuse to cut the program. A program, by the way, this is nearly complete. As I learned via Pharyngula today, cancellation of the JWST project is eminent. I recommend following that last link and reading the column by Lawrence Krauss. It is powerful, concise, and says more about this potential tragedy than I ever could.

Getting Into It

I've been trying to broaden by horizons a little bit by expanding the number and scope of other blogs that I read each morning. A while back I posted a list of the blogs that I've been reading as I sit down with a cup of coffee to check my email and take care of other morning duties. I guess it's now time to add another recommendation to the list. I've been getting into a blog called The Evolving Scientist. The blog is authored by a group of five graduate students at the University of Kentucky, which I have a bit of fondness for as I spent some time on the UK campus when my then-girlfriend, now-wife was working at the Frankfort State-Journal.

The authors of The Evolving Scientist do some fun things with their blog. The tag line changes almost daily but retains a theme of 'five guys with a love of science.' I should note here that they've added another author to the list within the last few days, and this addition has made their tag line a little misleading. Not only is the group now composed of six authors, but the newest author is female. So I guess it's more like 'five guys and one chick with a love of science.'

Anyways, the blog is lighthearted and enjoyable to read. The authors are all biologists, though, so I only have a passing interest in their more technical entries. They also feature a podcast, which I must admit, I have not listened to. It seems as though this is the centerpiece of the blog, and I may be totally missing out on something. But I prefer to spend my mornings reading rather than plugging earbuds into my head and zoning out. And you can forget about listening and reading simultaneously. I wouldn't retain information from either source. It would be as if I hadn't read the blog or heard the podcast. My brain would just sort of shut down. It does that more often than I'd like to admit.

You Call That a Review? Part II

Just quick follow-up note to my post titled 'You Call That a Review?' The post described the lame reviewer comments that I received for a manuscript that I recently submitted to an academic journal. I mentioned near the beginning of that post that I believed my paper would inevitably be published. Sure enough, I received word over the weekend that my paper has been accepted for publication. No idea yet when this will happen, but when the electronic version goes up , I'll link to it here on this blog. I'll also try to provide a few notes as well - in less technical terms than the paper itself.

Do You Want The Bad News or The Bad News First?

First, I'm going to start with what is probably the least significant bad news in the grand scheme of things. I arrived onto campus this morning to find that my building does not have air conditioning. As I write this, it is not quite 9:00 am, and the thermostat in my office just hit 80 degrees and is rising fast. I mean, seriously, it's like the hottest week in human history and the air conditioning decides to peter out now? Let me tell you, if it wasn't 9 am, I'd be packing up my computer and heading to the pub to do my proposal writing with a cold refreshing craft beer. Not that I have anything against enjoying an adult beverage in the morning. The pub just isn't open yet.

Now for the other bad news, which is somewhat more important than my mild discomfort. While reading through one of my new favorite blogs, The Evolving Scientist, I ran across this post. It looks like NASA and the NSF are going to see significant cuts in their budgets. And that means less money being sent down the pipe to researchers like me in the form of research grants. Even more troubling is that this will also mean less money being spent on science education, which is one of NSF's primary directives. I suppose this was inevitable, as we are currently creeping through what is being called the Lesser Depression - the result of the 2008-2009 economic recession and the subsequent and continuing lack of action by the federal government. It still really sucks, though.

You Call That a Review?

I received reviewer comments back from a journal to which I submitted a manuscript last month. Overall, I'm fairly pleased because I think my paper is going to be inevitably selected for publication. I read over the reviewer comments and addressed the reviewers' concerns as I revised the manuscript. And that's when I noticed some striking differences between the comments of the two reviewers.

The first reviewer's comments went something like this: "The manuscript was well-written and study design is sound. Along with a few minor grammatical errors, I have several recommendations..." The reviewer then went on to point out that graphs could be redesigned to be more readable, and that some of the data could be modeled differently so as to be more clear and produce stronger conclusions.

The second reviewer, by contrast, barely pointed any of the paper's assets, deciding instead to use the brief comments section to criticize the manuscript. Normally, I don't mind critical reviews. In fact, I prefer them to overly doting comments, as it's difficult to better my writing without a strong critique. But in this case, 4 of the 5 reviewer comments were along the lines of "the authors should have performed a study that examined..." And then the reviewer proceeded to describe some specific experiment or study that was not at all within the scope of the manuscript. In fact, when I wrote my response to the reviewer comments, I had to point out three times that the studies described by the reviewer were beyond the scope of the current paper, but that they could possibly be the focus of future studies.

I've come across reviewer comments like these before. It sometimes seems as though a reviewer is simply trying to flaunt their intelligence, rather than actually supplying the author with any useful information. It's frustrating and it doesn't help make the manuscript better. So I may just be venting, but I'd also give this recommendation to any future journal reviewer: think about the scope of the manuscript and what information the authors are trying to convey with the results during the review process. Just because you think you're smarter than the authors doesn't mean you really are.

I Think I Need My Own Personal Intern

Holy cow. I knew that the end of the summer was going to be busy, what with a number of SBIR solicitations being released all at around the same time. But now I'm also having to focus on an academic research proposal, revising a manuscript that was just accepted-pending-revisions, and helping to draft a proposal for a Homeland Security funding opportunity.

I've put doing any actual research in the lab on hold for right now. This makes things a little less overwhelming, since I'm able to spend my days in the office cranking out pages. It feels a lot better when I'm able to easily see how productive I've been when I finally close my computer's lid, shut off the lights, and head home for the day.

But all-in-all things are still pretty crazy. Maybe that's why I found this so soothing when I ran across it this morning (the link will only be available until Aug 7). All the slow, fluid motion. All the rhythmic circling. All the...blue. When the video loaded on my screen, all I could do was settle back in my chair, sip my coffee, and daydream that I was actually there in the exhibit with all the beautiful and wondrous creatures.

And now back to the real world. I'm going to try to keep updates coming in the same, semi-erratic pace that I've been keeping lately. We'll see how that goes. When taking a break from staring at a screen and typing on the keyboard, one of the last things I want to do with that time is to stare at that same screen, typing on that same keyboard. Just don't hate me if posting is even more erratic than usual.

Last Bits of the Lab Overhaul

Our new lab space at Lincoln University's Foster Hall is coming along splendidly. Nearly all of the old equipment has been cleared. Supplies that will not be used have either been pilfered by other researchers or hauled downstairs to be stored. And best of all, we have begun regularly using the lab space for sample preparation and other research activities. We are still waiting on a number of instruments and equipment to arrive, but orders - especially of large items - take forever to go through the bureaucratic mess that is LU's purchasing department. But in the meantime, we've cleared a lot of lab bench space for the new equipment to take up residence. Some of the more crucial items that we're waiting on include a refrigerator and an optics table. Once we have the optics table set up, we'll be all set to move the spectrofluorometer and a new microscope into the lab.

Unfortunately, there are two pieces of equipment that are taking up valuable real estate in the lab that we're having trouble getting rid of. The first is an ancient calorimeter, which is integrated into the benchtop and is connected to a dedicated water line. We've had to request that LU facilities and maintenance come to disconnect it and break it down so that it can be hauled down to surplus.


The other item of interest is this old refrigerator. It is packed with biological samples, and of course I was the one who discovered that it had stopped working. I opened the door of the unit to discover a most putrid odor - and a tepid can of Natural Light in the butter dish. We're waiting on the owner of the samples in the fridge to receive a new refrigerator so that he can remove the contents and we can have the old non-functional machine hauled away.


All in all, it's coming together. At least the lab is now useable, which is more than I could have said a month ago. When the last of the old equipment is gone, I'll post some pictures of the lab. Hopefully we'll have some of our fancy new instruments installed by then. I'm wishing now that I would have taken some pictures before we started cleaning so that I could do a before-and-after comparison. But alas, you'll just have to take my word for it that the lab was in a very sorry state of affairs before we moved in.

Things Are Not What They Appear

So I finally received my Arsenic in the mail the other day. Actually, it's not Arsenic, per se, but a salt compound called sodium arsenate. When the salt is dissolved in water, you then have a mixture containing sodium ions and arsenate ions. Arsenate, commonly referred to as As[V] due to its pentavalent electron structure, is often encountered in nature. And detection and monitoring of arsenate is a research effort of notable interest due to its high toxicity - it is Arsenic after all.

We've set about developing a detection method for arsenate, which is based on one overarching principle of the substance: As[V] quenches fluorescence. This is theoretically true, as the arsenate ion should act as a potent electron acceptor. There are several research groups using fluorescent silole compounds to detect the presence of As[V] via electron quenching in such a manner. See here (subscription required) and here.

But there's a problem with all this. I tried to replicate Stern-Volmer quenching plots for As[V] last week and...well...let's just say I didn't get the same results. My results were not necessarily bad; just unexpected. I'm sure that the data will end up in a manuscript shortly. And once the paper is published - which will be in, like, two years - I'll post a link to it on this blog. Until then, you'll just have to imagine what the data looked like...