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...