Friday, October 01, 2010

Thursday, September 30, 2010

Plagiarism rampant in Chinese science journals

There have been several discussions on plagiarism lately on the intertubez (note to self: compile list), so when the following article was sent to my email this afternoon (via Biotechniques) I took note.
Over 31% of submissions to the National Natural Science Foundation of China English-language publications show signs of copying, self-plagiarism, or copyright infringement, according to Helen Zhang, journal director at the Zhejiang University Press in China.
Almost a third?!?
In an article published earlier this year in Learned Publishing, Zhang and her colleagues analyzed manuscripts submitted to the three journals between October 2008 and May 2009. They discovered evidence of plagiarism in 151 out of 622 papers, or about 22.8% of submissions during that seven-month period. In a recent opinion piece published in Nature, Zhang reports that continued data collection analysis shows that the problem is only escalating as the percentage of plagiarized submissions has increased to 31%.
So why all of this plagiarism? The authors of the study claim that it "is a result of the academic world’s emphasis on publishing quantity over quality". I've frequently referred to it as the LPU (least publishable unit) but it seems that some researchers are taking it even further than that.

QR Codes

I've been enamored with the idea of QR codes lately. Over at LabSpaces, I mentioned that I'd like to include them on my next round of business cards.

I've found two applications which have proven useful in my quest to QR code things.

The first is a web app by Kaywa. If you give them a URL, they will generate a QR code image for you which you can then download and do anything you want with.

The second is ScanLife, which produces an app that I have for the BlackBerry. It takes some getting used to, but if you hold your camera back far enough (I'd say at least 6 to 10 inches) it'll actually work fairly well. There are also applications for the desktop where you use a webcam as a barcode reader.

Tomorrow is going to be a big day ...

... I can feel it already.

Wednesday, September 29, 2010

Latest Manuscript

Went into manuscript tracker for the latest first author manuscript I put together. It's the one on the topic that I find totally uninteresting but which yielded some interesting results. Other than a delay getting it into the hands of the associate editor, things have been going smoothly. Maybe too smoothly. One of the reviewers took a total of five days to get their review back. Usually these things sit for a couple of weeks before the reviewer hands them in, and I'm wondering if this is a case of the jury not taking much time to deliberate.

I've got two likely scenarios running through my mind*:
1. Reviewer is someone I don't know, but didn't like the work and tubed it.
2. Reviewer is someone I do know and they gave me a favorable review.

I hope it's #2. What do you think?

*The ones I consider to be the most likely.

Remainder of the day

I'll be AFB (away from blogger) until I finish the revisions for one of the latest manuscripts my collaborators and I submitted. We've gotten one of the two accepted, and we hope to get this one accepted ASAP.

ETA: Only took a couple of hours, not as bad as I thought it would be.

Wednesday Micro Hits

So the hump day has begun. As such, it's time for my second weekly rollout of my Wednesday Micro Hits. Here is where, instead of rattling off small blog entries of mundane thoughts, I coalesce them into one. Ergo, I only waste a fraction of your time!

1. Debating a AAAS membership. I don't really need a subscription (hard-copy or online) of Science, but their new t-shirt (Ways to Demonstrate Science) is really cool. Can't find a picture of it online yet, but if I do soon, I'll link to it here.

2. According to Google Analytics, I've had 14,434 (~40/day) pageviews in the past year. As a standalone amateur blogger, I'll take that as some good numbers.

3. My tri-society has informed me that I have been a member for five years. I guess if I sit down and do the math I have been in the field for roughly that period of time now. I didn't think it had been that long. I guess time flies when you're having fun?

4. If you think agriculture is contributing to global warming, think again.
The study included carbon dioxide and other gases such as methane emitted by rice paddies. It found that, overall, the intensification of farming helped keep the equivalent of 600 billion tonnes of CO2 out of the atmosphere – roughly a third of all human greenhouse-gas emissions between 1850 and 2005.

5. I think I'd like one of these for Christmas. However I don't live in a drought-ridden area. At least not most years.
The Waterboxx, invented by Pieter Hoff, is a low cost device that can help plants to survive in drought-ridden areas.

6. To everything there is a season. At least that is what the verse in Ecclesiastes (3:1) says. Then why do we and our medical community spend so much money delaying the inevitable?
Americans increasingly are treated to death, spending more time in hospitals in their final days, trying last-ditch treatments that often buy only weeks of time, and racking up bills that have made medical care a leading cause of bankruptcies.

Tuesday, September 28, 2010

Watch this space ...

... I have some news I'll reveal in the upcoming days.

Monday, September 27, 2010

Writing Reviews

A couple of weeks back an interesting discussion was had (well, it appears to be over) at DrugMonkey's Scientopia page, on the issue of citation practices. I chimed in with my own practice ... I don't give a rats patooie what journal the manuscript is in, as long as it was good science. And that would have been it, had not someone uttered something I found completely unfathomable.
I do not have adequate time to do all of the fact-checking myself for every reference in my 200-reference review article.
Excuse me? I responded here ...
Say what? You include references into an article without fact-checking them yourself? I can understand going through the abstract, skimming the R&D, and reading the conclusions … but if you can’t be bothered to read the damn article, why are you citing it?!
... and here ...
Yah … I’m following up my own reply. If by fact-checking you mean subsequent articles which support and/or refute said article … IMNSHO, if it’s important enough to cite, then it’s important enough to know the history behind the article and how it was received IN THE FIELD YOU’RE WRITING A REVIEW ARTICLE IN. If you don’t know the history behind the literature in said field, let someone else write the review article.
I also said ...
What I said is that if you’re in a field you should at least know the relevant literature, especially if you’re writing a review on said literature. Cold-citing an article? Piss poor.
I continue to stand by those comments. Why would anyone cite an article without taking a look at and understanding said article? How would you even know where to begin, to properly cite the article, when you have no idea what was contained within the manuscript and/or how it was perceived post-publication? Taking someone else's word for it? Sure, but how do you know they got it right?

I was damn sure then, and I remain damn sure now, that if you can't bother to pick up the manuscript yourself, read at the very least the Abstract, Results & Discussion, and Conclusions (if your journal has them) yourself ... skim them at the very least ... you have no business reporting on that article in your own article/review. I don't care if you have one week to write the article, or one year. You should have at least a passing familiarity with the work in order to cite it.

But hey, I was just being argumentative, right?

But wait, it gets better. I then find a blog entry on the discussion. Stumbled across it really. It does its very best to completely misconstrue the entire point of my comments over at DM's blog ...
There have been implications on the interwebz that I totally cannot do a good job of this if I am a non-expert and if I do not spend infinity bajillion hours researching Mango Skin Allergies. That I will do the world of science a serious injustice if I do not provide the very best reference for every point in my article. That it takes a real expert to know the field, the history of the field, to put all of the confusing shit in the context of the field, appreciate the field, take the field out for some lobster, and try to put the moves on the field after dinner.

Bulls**t indeed Candid Enginner. Bulls**t that for someone with a graduate degree your reading comprehension is abysmal. No one, not me, nor anyone else at DM's blog stated that you must spend countless hours on the review (though a week really is crap IMNSHO) or that you must provide the very best reference, or that you must be a real expert to know the field, or know every minute detail of the history of field. I did say that ... you should understand the damn papers you are going to cite! And yes, you should also know how those papers relate to the field. Now, since she didn't clarify what she meant by "fact check" I suppose we can't truly understand what she was trying to say, but honestly I think a fairly reasonable conclusion is that "fact checking" meant (at least in part) how the manuscript fits in the "big picture" of the entire field.

To which I say ... if you personally don't know how the manuscript truly fits into the big picture of the field (because you didn't check for yourself, because you're busy writing super-important-review) ... how the heck are you writing a review on it?


Now, I'm willing to be educated on this issue. It's possible that I may have overlooked an argument which really makes sense on this issue, but so far I haven't. Not really.

Oh, and by the way ... when writing a review, it helps to keep the people who are going to take credit/blame on said review in the loop. Otherwise you wind up wasting tons of time. Telling a field they don't know how to do their work in the field is going to make so many enemies for your PostDoc adviser that it's irresponsible to even consider writing such a treatise. It's one thing to play fast and loose with your own career. It should be a crime to play fast and loose with someone elses.

Wednesday, September 22, 2010

Scientific Misconduct

The Genomic Repairman has a blog entry up asking about scientific misconduct. He found an instance of two journal articles from the same group that used an identical figure in a set of 2008 and 2010 reports. Is this scientific misconduct? If they didn't cite it, you betcha ... and even if they did cite it, they could be butting their heads up against copyright issues with the 2008 journal. Any way you cut it, if you can't be bothered to change things up, like oh I dunno redoing the experiment to generate a new figure, you deserve to be hoisted up by your own petard.

I have a similar tale as a graduate student, but this one didn't involve me stumbling across two publications of a science enemy. Instead, I came across the scientific misconduct of one of my departments professors.

I came across this misconduct early on in my journey as a graduate student. It was before my second year was completed and a friend and I were studying for our general exam. We would alternate between the building he worked in, the building I worked in, and the campus library. This day we were in his building and we had taken a break. I was in the hall looking at the lab posters and came across the work of Professor M. Professor M had several of their papers tacked to the board as well and I was leafing through them.

Something caught my eye.

I noticed that in two papers on the same subject, published back-to-back (but in different journals), looked awfully similar. In Manuscript A, there were several tables. In Manuscript B, there were several figures. I took note of it and went back to studying. Later that evening I went to the library and printed out the two manuscripts ... and began lining up the tables and figures.

They matched.

Whiskey. Tango. Foxtrot. I slept on it and then brought the evidence to my adviser the next morning. He was not pleased, but there was no denying it. This was a clear cut case of double publishing. My adviser said he'd take care of it, and took the evidence I collected. That was the last I heard of it. Now, there were several other instances of moral turpitude concerning Professor M, the combination of which forced him out of our department and university altogether. I'm not sure what role his double publishing played, and to be honest I have never looked for a retraction of either paper. I suppose I could go and check now (check back for an ETA). I don't know if Professor M rues the time spent at our university, but I do know what the immediate consequences of Professor M's actions were ...

Department Chair at a different university.

ETA: Both publications still exist in the literature, with neither ever being retracted.

Wednesday Micro Hits

One. It's definitely misconduct.

Two. I feel naked when I don't wear an undershirt underneath my polo.

Three. Let the poor guy die in peace. Quit asking him if he's going to convert on his deathbed. Honestly, he's already on his deathbed so asking him is silly.

Four. The Archaea are the next great frontier in microbiology. If anyone wants to carve out their niche in microbiology, seriously consider this line of research. There is so much about the Archaea that we don't know, but we do know that they contribute A LOT to environmental processes.

Five. This twitter thing is pretty interesting. Don't know if I'll stick with it, but so far it's been fun and a bit of a time hog.

Six. I love my new Streetcars shoes. Got the Carerra's (#5703) and they're as comfortable as my Ecco's.

Tuesday, September 21, 2010

Joyful Video Tuesday ...

... because the alternative sucks.

Caught in the crossfire

Humans suffer collateral damage as microbes battle it out. Guess we've become the microbe's turf eh?
When S. pneumoniae is forced to share space with Haemophilus influenzae, another common and ordinarily asymptomatic bacterium, the two begin a tussle for space. But H. influenzae has an extra trick up its sleeve, calling on our immune system to help get rid of its competitor by recruiting white blood cells called neutrophils, which surround and attack the S. pneumoniae bacteria.
This of course forces S. pneumoniae to respond ...
Many strains of S. pneumoniae exist, each coated with a thick sugar capsule. In some strains, the capsule is particularly protective, and appears to act as armour against the host's immune response. This allows the bacterium to enter the blood stream where it can go on to replicate and cause serious diseases such as pneumonia, bacteraemia (blood infection), septicaemia and meningitis.

Monday, September 20, 2010

Tuesday, September 14, 2010

retraction: *smile*

And this story does not make me happy to be a Jets fan today. First caught wind of this last night during the game, and read more about it today. Rex Ryan needs to get a better grip on his club.

Tuesday's Three Things

1. I'm hopeful for Percy Harvin. Hopefully sleep apnea was the cause behind his migraines and that his treatments will prevent him from getting any others. I wonder how many other people who suffer from migraines also have sleep apnea?

2. Will the Jets win a game this season? They played like total crap last night. I hope Cromartie isn't a Jet by next weeks game, and Dustin Keller needs to figure out what side of the first down marker is the right side to go out of bounds on. Pathetic.

3. Losing your wallet stinks.

Monday, September 13, 2010

It's pretty obvious ...

David Procopio, a spokesman for the state police, which is probing Staupe’s death, said it’s unclear how Staupe got the cyanide to Milford.
... how the lab tech got the cyanide -- which she used to off herself -- all the way to her house in Milford. She put it in a bag, put it in her pocket and walked home. Chemical inventory, in my experience, is one of the most overlooked things in a lab. I mean, come on folks ... how many times have you grabbed a bottle of Chemical A, B or C ... only to find it empty? It happens all the time. Hence, if it happens all the time ... people can walk off with things more often than we'd like to admit. Of course, situations like this will only result in more work for labs, to document chemicals and their continued status ... so thanks for that Emily. Then again, perhaps it's not such a bad thing.

Next question: Is the PI of the lab in which Emily worked, responsible in some way, shape, or form?

ETA: This article states that she was laid off, but still had keys to laboratories. Was she given some additional time to work in the labs, making her key-ownage valid, or does the university have a really poor policy to repo'ing keys of individuals they've just canned?

An Open Letter to both PC-ORD and Microsoft

Dear PC-ORD and Microsoft,

I wish you both could get your crap together. Could you at least talk to one another, civilly, for just a bit?

PC-ORD, why do you insist on only analyzing files saved in Lotus Workbook format? Who the hell uses the .wk1 extension anymore? Does Lotus even continue to exist? And Windows ... why did you make it such that Windows Excel 2007 won't save in .wk1 format, and that Excel 2003 only does so after you have to go in and edit the registry? Talk about freaking impossible! My institution wants me to let go of 2003, and I refuse to do so. I really have no choice in the matter! Not until one of you gets your act together and decides to play nicely with the other!

In the meantime, I shall hate you both.

Thomas Joseph

Boomer Sooner!

University of Oklahoma 47
Free Shoes University 17

What a glorious day to be a Sooner fan! I will admit, I was very nervous about this game, but we put on a show and won convincingly. Next year, Tallahassee!

Friday, September 10, 2010

Looking for a career in science?

Received the following in an email today:
When you're looking to move up the career ladder, look to ASCP's Online Career Center. It's the place where you'll find hundreds of jobs with top employers in your field.

Recruiters from top laboratories and hospitals like ARUP, Abbott, Roche, The Johns Hopkins, Beckman Coulter, Spectrum Labs, Cleveland Clinic, and many local facilities are there looking for you.

Start your search for the best job today at:


It might suck to be a Mets fan, but stories like this make me glad I'm a Jets fan too.


Sad but true.

I'd say today is a sad day to be a Met's fan, but what does that really mean anymore? It's always a sad day to be a Met's fan.

Thursday, September 09, 2010

Wednesday, September 08, 2010

I've seen it all ...

... got a review back a day or two ago on a manuscript from a journal we were submitting to. I won't mention the name of the journal, other than the initials were Plant and Soil, and the reviews were horrible. Reviewer 2 was a particularly pleasant person who left us the following gem of a comment: "No!!!"


Oh, and buttmonkey, the reason we didn't use effluent was because when you use effluent you add a multitude of confounding factors. We were looking at the effect of a single variable, that element being the whole impetus of the study. Idiot.


If this program crashes one more time, I'm going to have a fit*!

*Another one at any rate.

PS: Figured out that starting by deleting peaks from the end does not cause the program to crash. It only crashes if you start by deleting peaks from the front. It also only crashes when you load up a second signal after processing the first. Go figure.

Busy ...

... data crunching. Be back later.

Tuesday, September 07, 2010

Tuesday Video

Feels like a Monday.

Face my destroyer.
I was ambushed by a lie.
And you judged me once for falling.
This wounded heart will rise.

And burn my shadow away.

Thursday, September 02, 2010

Where is my silver lining!

I really think someone stole it. I should have stayed in bed today, honestly.

1. Trying to work with ChemSoft, only to be continually frustrated. When I choose the option "Print > To File" and click "Print" nothing happens. The dialog box closes and that's that. After killing a couple of trees testing other options, I finally find a folder that has about a bazillion Excel files now. Fun stuff. Next time Agilent ... at least tell us where the damn file is being saved!

2. Found an article today while perusing F1000 that is directly related to my own work. Said article comes to a similar conclusion on a particular genes abundance that I made, which means we're not the first ... but it's from a heavy hitter so it's a nice bit of confirmation. Problem? Yah, because it was packaged to be submitted today. Now I need to dust it off, make the edits and then glance over it again to ensure I didn't goof anything up.

3. Bought a new bed, which was sorely* needed. When are they dropping it off? They gave me like a five hour window ... which means I need to head home soon and wait for them. I know with the way today is going that they'll show up an hour after the five hour window is over.

4. ChemSoft crashed, and now I can't get it to work again, which means I'll need to uninstall and then reinstall. I HATE, with a white hot fire that burns my brain, this program!

*Ha ha ha, I made a pun.

Woo hoo!

I've been invited to guest speak at a Conference ... in China!

BIT’s 1st Annual World Congress of Marine Biotechnology (WCMB-2011)
Time: April 25-29, 2011
Place: Dalian, China

Dear [redacted],
We would like to extend our invitation to you to be a speaker at our upcoming event: BIT’s 1st Annual World Congress of Marine Biotechnology (WCMB-2011) which will help to bring together scientists, managers, faculties, decision makers among all organizations engaged in marine biotechnology and encourage the development of commercialization of marine biotechnology. As we know your work in this field is a clear example of the leadership, so we would like to highlight your effort at our conference which will take place during April 25-29, 2011 in Dalian, China, with the theme of “Ocean, Life and Sustainability”. We express our sincere wish for your participation in this conference and make an oral presentation at one session of Track 5: Marine Bioenergy and Engineering, The details of the sessions are:

Track 5-1: Algae and Seaweed Biomass
Track 5-2: Marine Bioethanol
Track 5-3: Marine Biodiesel
Track 5-4: Marine Biogases
Track 5-5: Algal Biofuels Commercialization

WCMB-2011 will take the form of plenary lectures, oral presentations, posters, exhibitions and project matchmaking; it covers topics from breakthroughs in Marine Biotechnology R & D, Algal Biotechnology, Marine Natural Products and Valuable Materials, Marine Bioenergy and Engineering, Marine Resources and Environment Bioremediation to applications of Marine biotechnology. WCMB-2011 will provide an ideal platform for marine biotechnologist to debate and deliberate on issues that are critical for the progress of this emerging area and identify the challenges and opportunities for the development of Marine Biotechnology.

Your participation as a speaker at this year’s world congress would add great value for your organization and our attendees. Please contact Ms. Doris Han at if you are able to participate. Thank you for your timely consideration of this invitation, and we look forward to hearing from you soon.

In addition, this major international event will be held in Dalian, one of the most beautiful coastal cities. After the conference, you are welcomed to join the Tech tour to experience the traditional Chinese culture and enjoy the delicious food in China.

The details of the conference, please visit:

Best Regards,

Ms. Doris Han
Organizing Committee of WCMB-2011
26 Gaoneng St., F4
Dalian Hightech Zone
Dalian, LN 116025, China
Tel: 0086-411-84799609 ext 813
Fax: 0086-411-84799629

PS: We expect your precious comments or suggestions on the structure of our program, also your reference to other speakers will be highly appreciated. We look forward to receiving your replies on the following questions.

1. Are you interested in delivering a speech in one of these sessions? Which session?

2. What is the title of your speech?

3. Do you want to co-organize one of the sessions or have any suggestions about our scientific program?

Full Program

Track 1: Breaking R & D in Marine Biotechnology

Track 1-1: Marine Molecular/Cell Biology and Physiology
Track 1-2: Marine Ecology and Microbiology
Track 1-3: Marine Organismal Molecular Biology & Biotechnology
Track 1-4: Genomics, Proteomics & Metabolomics in Marine Biotechnology
Track 1-5: Marine Metagenomics and Bioinformatics
Track 1-6: The Marine Biotechnology Research Toolkit
Track 1-7: Marine Extremophiles
Track 1-8: Marine Nanobiotechnology and Biomaterials
Track 1-9: Sustainable Aquaculture and Fishery
Track 1-10: Conservation, Bioinvasion and Climate Change

Track 2: Algal Biotechnology and Phycology

Track 2-1: Algae Ecology, Cell Biology, Biochemistry, and Systematics?
Track 2-2: Algae and Cyanobacteria in Extreme Environments
Track 2-3: Micro-algal Biotechnology
Track 2-4: Algal Cultivation Techniques toward Seaweed Farming and Aquaculture
Track 2-5: Biotechnology Improving Algal Production & Productivity
Track 2-6: Algae Photobioteactors
Track 2-7: Robust Algal Processing & Downstream Production
Track 2-8: Algae in Health, Nutrition, Cosmetic and Feed Industries
Track 2-9: Harmful Algae Blooms and Green Tide
Track 2-10: Applications of Algae in Wastewater Treatment, Carbon Capture & Recycle

Track 3: Marine Natural Products and Valuable Materials

Track 3-1: Resources, Isolation and Identification of Bioactive Marine Natural Products
Track 3-2: Marine Chemistry of Natural Products
Track 3-3: Eicosanoids from Algae
Track 3-4: Marine Peptide and Protein and its Functions
Track 3-5: Marine Microalgae Polysaccharides
Track 3-6: Marine Enzymes with Unique Functions
Track 3-7: Natural Products and Materials from Sponges
Track 3-8: Marine Biopolymers and Applications
Track 3-9: Materials in Preventing Marine Corrosion
Track 3-10: Novel Composite Materials for Marine Applications

Track 4: Biomedical Applications of Marine Biotechnology

Track 4-1: New Drug Screening from Marine Microorganism Metabolites
Track 4-2: Discovery of Marine Biomarker, and Biological Active Compounds
Track 4-3: Marine Products for Biomedical Assay
Track 4-4: Anticoagulant and Anti-thrombic Marine Products
Track 4-5: Antiviral and Antibacterial Marine Natural Products
Track 4-6: Anti-Tumor, Anti-metastatic Marine Natural Products
Track 4-7: Other Biomedical Applications of Marine Biotechnology

Track 5: Marine Bioenergy and Engineering

Track 5-1: Algae and Seaweed Biomass
Track 5-2: Marine Bioethanol
Track 5-3: Marine Biodiesel
Track 5-4: Marine Biogases
Track 5-5: Algal Biofuels Commercialization

Track 6: Marine Resources and Environment Bioremediation

Track 6-1: Metagenomics and Synthetic Genomics for New Marine Resources
Track 6-2: Marine Industry Processes and Products
Track 6-3: Bioremediation for Bacterial Biofilms and Biofouling
Track 6-4: Bioremediation for Spilled Oils on the Sea
Track 6-5: Novel Marine Biotechnology for Conservations and Environment Protections

Track 7: Business Forum on Marine Biotechnology

-5 Open Sessions for Free Organizations by both Tech and Product Suppliers and Investors
-Open Space for Interactive Forum (please propose)
Problem is ... I don't do any marine microbiology. So, is this an elaborate case of spam? Is it a scam? I hesitate to click on the link (heck, I probably should not have even provided it).

One of those days ...

Wednesday, September 01, 2010

Blast from the Past

If you don't know the proper conditions with which to precipitate DNA using EtOH, here is an article that will show you how it's done ... old school style* (PDF, 2 pages).

Moral of the story: Spin your DNA down for 30 minutes.

*Old school in this case being 1985.

It's Always Something ...

Currently playing on iTunes: Hells Bells by AC/DC.

So just got back a review on a manuscript I'm a 2nd author on. It's a collaboration I struck up with the help of a senior researcher at the institution I work at. He was friends with a couple of guys, and they needed some microbial work done. Since I'm the lone microbiologist here, the match was made fairly easily. Bonus, they've become good drinking buddies (and at this point owe me lots and lots of free beer).

At any rate, we put together a manuscript on a problem that my collaborators face in their neck of the woods. It involves agent X, used to deal with issue A. When exhausted, it is disposed of in manner NG (which stands for "not good"), which creates issue B, and effects crop 1 and 2. Got all that?

It's some fairly straightforward work, and I was asked to look at the impacts on microbial diversity. They shipped me samples, I did my work, I wrote it up and sent it off to them. They worked it into the overall manuscript, we beat and banged on it a bit and then sent it off. Well we got the reviews back last week.

Reviewer 1: Loved it. Had nothing but praise for it. Comments were all of a paragraph in length. Either they did a last minute review and couldn't be bothered with it or not, I have no idea. I love Reviewer 1 regardless.

Reviewer 2: Someone pee'd in their Wheaties before they did this review. They picked every nit that could be picked. Heck, they even took issue with my use of the word "microbial". I mean really, dude? All told, their review was three single space pages long. We've all decided that we don't like Reviewer 2, but would love to take Reviewer 1 out for a beer.

So now ... off to address the comments of Reviewer 2. Hopefully we address them to the satisfaction of the Associate Editor so this puppy doesn't have to go out for a re-review.

Tuesday, August 31, 2010

Odd packing?!?!

Taping a cellphone to a Pepto-Bismol bottle and stuffing it in your suitcase is NOT an example of odd packing. I still don't know why, if you had them flagged before they left the US, you let them get to Amsterdam. Whiskey Tango Foxtrot TSA!

Monday, August 30, 2010

No hablo Español.

But I'm trying to rectify that. Just installed Rosetta Stone's Latin American Spanish, Level 1 onto my work laptop. Now I just need to find time to wear the dorky headset and I should be able to curse in a foreign language in no time!

Anyone ever use Rosetta Stone, and what did you think of it?

Woo hoo!

A plethora of PLFA data arrived on Friday, which means for most of today I'll be analyzing the data and prepping it for my next collaborative manuscript. Probably not much blogging today unless the data analysis breezes by.

Friday, August 27, 2010

Tuesday, August 24, 2010

Urine Luck

Using urine to power daily life.
Botte's brainwave was to use urine instead of water. By weight, urine contains roughly 2 per cent urea, and each urea molecule contains four hydrogen atoms, which, crucially, are less tightly bound to the molecule than the hydrogen in water. Splitting these bonds would require less energy, making hydrogen production more efficient.

Last year, Botte's team reported that they had been able to generate hydrogen from urine using an electrolytic cell with cheap nickel-based electrodes running at only 0.37 volts- much less than the 1.23 volts it takes to split water (Chemical Communications, 2009, p 4859). Pure hydrogen bubbled off at the cathode, while nitrogen and carbon dioxide formed at the anode.
Doing this would have two advantages. First, you can generate electricity. Second, it removes the urea from the environment. Urea is broken down to ammonia (NH3) which can cause environmental problems such as ecosystem acidification and eutrophication.

Food Recall

Listeria monocytogenes contamination of lunch meat.
The products subject to recall include:

* 25.5-pound cases of "Marketside Grab and Go Sandwiches BLACK FOREST HAM With Natural Juices Coated with Caramel Color" with the number 17800 1300.
* 28.49-pound cases of "Marketside Grab and Go Sandwiches HOT HAM, HARD SALAMI, PEPPERONI, SANDWICH PEPPERS" with the number 17803 1300.
* 32.67-pound cases of "Marketside Grab and Go Sandwiches VIRGINIA BRAND HAM With Natural Juices, MADE IN NEW YORK, FULLY COOKED BACON, SANDWICH PICKLES, SANDWICH PEPPERS" with the number 17804 1300.
* 25.5-pound cases of "Marketside Grab and Go Sandwiches ANGUS ROAST BEEF Coated with Caramel Color" with the number 17805 1300.
* The packages also bear vendor number "398412808" and the USDA mark of inspection.
All the above were sold at Wal-Mart.

The US has a "zero tolerance" policy with L. monocytogenes. That means that when inspecting food, even if one colony of Lm shows up, the food needs to be removed from the market. It's not a bug that plays well with people, especially pregnant women.

Monday, August 23, 2010

I hate cats ...

... to the people in my neighborhood who let their cats roam freely ... if you'd like to come pick up the trash in front of my house that your cats ripped open and dragged over my front lawn between 6AM and 8AM, I won't stop you.

This really doesn't come as a surprise ...

... if you're on Facebook, you cannot block the founder Mark Zuckerberg. Though I doubt he'll spend all his free time looking at my page, it is something people should consider carefully. While it doesn't appear to be the case that anyone else is blockable yet, the time may come when someone figures out how to do it and pilfers people's private information.

Probably not hugely newsworthy, but yet another reminder to keep the information on Facebook to a minimum.

Thursday, August 19, 2010

Too much literature?

Either I read too much literature, or I am citation happy. This latest manuscript is pushing 100+ citations. The journal I am sending this article too doesn't have a reference limit, but it's still an awful lot of the literature I'm going back to. Oddly enough, I've had to make links back to articles from the 1970's because from that time, to the time we did this study ... no one reported on these linkages from a molecular biology standpoint, at least in this particular ecosystem.


Seems that the Genomic Repairman is having a music crisis. Here, I have over 120 GB of music, with very little I wish to listen to. However, I do have a few bands that I have on my iPod which I've turned to.

1. Them Crooked Vultures - A sweet mix of Queens of the Stone Age (Josh Homme), Nirvana/Foo Fighters (Dave Grohl), and Led Zeppelin (John Paul Jones). What isn't to like about this super band?

2. Queens of the Stone Age - Awesome beats, kick-butt lyrics.

3. Shinedown - Sound of Madness, awesome song.

4. Brand New - Daisy and The Devil and God Are Raging Inside Me are two of the best albums of the first decade of the new millenium.

5. Beastie Boys - And if you don't like it, then hey **** you!

6. Here Come the Mummies - Most people will not have heard of this band, but if you love funk ... you'll love these guys. And they'll love you right back!

Link Love

I'm starting to update my blog links because a few people can't sit still long enough to keep my links relevant. At any rate, if anyone would like to do a little quid pro quo, drop me a link to your blog, put my blog up as a link on yours, and I'll include yours here.

Bed Bugs

Saw a report on the Today Show (video) this morning about bed bugs in NYC movie theaters. Seriously, whiskey tango foxtrot. Problem is, bed bugs are not all that easy to treat, and you can pick them up almost anywhere (especially if you stay at a hotel that is infested). Perhaps it's time to bring back DDT?

Then again, this blog entry in 2009 states that bed bugs are not as susceptible to DDT as we might think.

Wednesday, August 18, 2010

When men drink ...

... saw this "science-related" article on MSNBC. It supposedly is on the "beer goggle effect".
To make matters even worse, another study shows liquor makes guys more likely to misinterpret a friendly female glance as a bold come-on.
So they spend some time discussing what this all means, and then come up with a "solution".
What to do? Women who want to just have a good time -- and not go home with a guy -- would be smart to dress conservatively, says University of Texas psychology professor Kim Fromme. "That's the more obvious cue."
That's right ladies. When men drink, you need to dress more conservatively. Got to love how the burden shifts from the individuals actually undertaking a behavior and the individuals who are more than likely minding their own damn business.

Tuesday, August 17, 2010


Correlations of my latest gene abundance data set and environmental variables. The sheet is roughly 30 inches by 25 inches. Think this would make a good supplementary data set? ;)

Thursday, August 12, 2010

One two many cooks ...

... so I've begun writing a new manuscript. We have a number of additional collaborators that we generally would not have, so I decided to, before I started my outline of the manuscript, email everyone and ask how they envisioned this manuscript taking shape. I detailed where I was thinking I'd take the manuscript (in philosophical terms ... not vacation destinations). I went so far as to let them know of the journal it was going to, and that I had already talked to the editor-in-chief of the journal about this manuscript (which is somewhat off the beaten path of what they routinely deal with) and that he was extremely receptive to this article.

I figured this was a nice courtesy email, and didn't expect much fallout from it. Yah, I was stupid. Turns out that everyone else has their own idea on the path this manuscript should take, and while some parallel my own ideas, the heaviest hitter on this manuscript (other than the one who is writing it, moi) is the most esteemed member of the group. So ... what to do? I can certainly see their point of view, but the approach they want me to take (and which other people have fallen in line with now), while it is the safe approach, does not bring the problems I wish to address front and center. It's not that I'm intending on making a huge splash with this paper, though if it happens to partly revolutionize the field I'll gladly take as much credit as people are willing to give me, but I really hate beating around the bush. My collaborators are much more conservative, thinking that you don't upset the status quo, you go for the sure bet, you play it safe, you don't fight the reviewers, you get results, and you accept it and be happy about it. With most publications, I'm happy to take that course of action. I did not want to take that action with this manuscript. Bollocks.

Where I disagree with Drugmonkey ...

... and I'm sure he's devastated. However, he's just plain wrong in celebrating the demise of Supplementary Material from the Journal of Neuroscience. I say as much in his comments section, but I'm going to start a discussion (for the two or three people who read this blog) here anyways. It's my perogative!

At any rate, Bobby Brown aside, here is what I had to say to his celebrating.
I seriously hope that not all journals go this route, and I’ll tell you why . As part of my postdoc, we did an MLST project on a common pathogen in the food industry. We managed to get strains from all over the world, from state and federal agencies, and from international organizations. In the end, the project had several hundred isolates. Where were we supposed to list them and all the supporting data (date collected, place collected, food it was isolated from, serotype, etc etc)? In the article itself? It would have taken a dozen or so pages just for that one table! And that’s not including the several phylogenetic trees we generated all of which took up an entire page. It would have been half the issue if we had incorporated it all into the text. It seemed that that was a PERFECT use of the supplementary material section. Instead of the editors taking proper control of their reviewers and authors, they’ve banished the practice altogether … bye bye baby, but at least we don’t have to worry about that bathwater any longer.
I'm not the only one who thought that there were good uses for Supplementary Material, and I do think that my anecdote is one good example of why Supplementary Material needs to remain as an option. In an age where we can generate millions of base pairs of data sequence in a few short hours, but where journal issues are not increasing accordingly in size, something has to give. I know there are repositories for most data of this sort (such as GenBank for sequence and GEO for microarray data), but I think we still need the Supplemental Material option for certain descriptive elements of a manuscript.

I agree with J. Neurosci when they said that additional experiments added as Supplemental Material were allowing things to get out of hand, but as I said in my comment ... instead of cracking down on such practices, they just threw the baby out with the bathwater. If all journals take this route, things are going to get a bit hairy. I know a couple of my manuscripts, where I provide background information that would dominate a manuscript's page total if I could not include it as Supplemental Material, is descriptive in nature, and is provided as a courtesy to the reader* would have a hard time finding a place to published. So, why is it too much to ask that journals, and their editors, spend a bit more time sorting the issue out, rather than torpedoing it wholesale? I bet part of the issue is money ... it's probably no small fee to host that data in perpetuity.

*It also saves me countless emails being asked for that last bit of information which some people might hope to glean some ideas from for their own data sets, but which for me didn't factor at all in my own study.

Invasion of my aural space

Aural Space - Aural space is a term used to describe moments when listeners are hearing a lack of noticeable sound.

Sometimes when I am at work and at home, I prefer to have that "background noise" going on. I make no attempts to drown it out by having a television on, or a radio, or my computer playing tunes. I figure that if I'm in my office, or my home ... I should be able to choose which noises I want going on within my immediate space. Sometimes at home my dogs disagree, and they'll bark til the cows come home, but I can live with that ... for the most part.

What I cannot live with, is websites which have now taken to playing video automatically. ESPN dot com is notorious for this, and it drives me freaking batty. I go to ESPN dot com to read the news, not hear it. If I wanted to hear it, I'd go to my television and turn on ESPN the channel. It's a downright pain in the rear, and a total invasion of my aural space.

I remember way back when, when Al Gore had just invented the internets, that putting MIDI music files on ones website was cool ... the tin-sounding music really added pizazz to any website that featured it. Ok, not really ... it was cool for all of a couple minutes but really started sucking as soon as the file looped back and played the same crappy music all over again. But it seemed like most people figured it out pretty quickly (except for anyone who has a Geocities or Homestead account) and discontinued their use.

There are a few other websites, most of which evade my memory right now, which I've caught doing this as well ... but ESPN dot com is, by far, the worst offender in my book.

Anyone else have any other websites which have taken up this annoying habit?

Wednesday, August 11, 2010

What am I reading today?

An article from 1972. Characterization of the Oxidized and Reduced Zones in Flooded Soil. I can't believe you still need a subscription to view this article. How long do copyright protections exist for articles published prior to 1978?
The oxidized and reduced layers in flooded soil were characterized by vertical distribution of the oxidation-reduction (redox) potential and concentrations of manganous manganese, ferrous iron, sulfide, nitrate, and ammonium. Redox potential was measured with a special motor-driven assembly which advanced a platinum electrode at a rate of 2 mm/hour through the flooded soil profile. Vertical distribution of reduced forms of manganese, iron, and sulfur and of nitrate and ammonium was determined by freezing and slicing the flooded soil into segments 1 or 2 mm thick. The apparent thickness of the oxidized layer was different when evaluated by the distribution of the various components in the profile, with the sulfide profile indicating the thickest oxidized zone, the manganese profile indicating the thinnest oxidized zone, and the iron profile showing an intermediate thickness. The thickness of the oxidized layer increased with duration of flooding.

Another issue with GenBank

So received an email today from GenBank that started with the following:
Complete feature annotation has not been included for some or all of the sequence(s) you have submitted. We prefer to accept sequences that have been annotated by the submitting authors.
Of course they prefer to accept sequences that have been annotated by the submitting authors. It's one less thing they need to do, and I completely get that ... no problem with that from me.

So what annotation was missing? Protein translations for the sequences from my phylogenetic study of environmental samples. It's not a very large sample set (more than fifty, under a hundred) but it was (I believe) enough to get the job done for what we were looking at. We looked at a real time PCR amplification product, which was slightly on the long side (a tad over 400 base pairs) as far as qRTPCR goes. It's a partial sequence of the gene we are looking at, so I have no idea how things look 5' or 3' of the gene in question. As a matter of fact, the gene has about a 1000 base pairs of sequence upstream of the site we are looking at, and extends about an additional 250 to 300 base pairs downstream of our site as well. It's a fairly big gene which encodes a pretty large protein product.

So GenBank wants to know the protein translation of these clones from this environmental study. Me? I think it's a waste of time. Since they're partial sequences, we have no way of knowing if this sequence is even going to be used to make a protein. Since there is over 1,000 bp of sequence upstream, with any number of potential stop codons or frameshift's before we even get to the sequence in question ... it seems like a fruitless exercise. Do we really need these environmental sequencing projects, similar to mine and many many others, cluttering up BLAST reports? GenBank calls them "conceptual translations" and they DO show up in blastp reports. Since there are so many of them, they oftentimes dominate those reports. Now, I know GenBank has a "exclude uncultured/environmental sample sequences" as an option (which can be found under "Exclude" oddly enough) but it seems silly IMNSHO to automatically incorporate the thousands of these sequences in these reports. I suppose there are pro's and con's to each approach, and I know some people prefer to use protein sequences; though I've always read we want to find possible silent substitutions so you can't go wrong in choosing/preferring to use DNA sequences.

I don't know. Maybe my inner-curmudgeon is getting the better of me today. It just seems that, especially when it pertains to environmental samples, there can be something as "too much information" especially when that information is based on conceptual models. Do I think that these sequences are wrong simply because they're rooted in bioinformatics? No, I do not. I just don't see the utility in providing them in each and every case. Especially since it'd be simple enough to work them up when you download the DNA sequences. Of course, one would argue that it's simple enough to just submit them.

Educate me folks.

Food for thought ...

... very interesting article on staying connected. Could I do without a cell phone? Probably.


Iceberg four times the size of Manhattan works its way into the Arctic Ocean shipping lane. So who cares? Well, just about every oil rig in the Arctic Ocean.
Large enough to threaten Canada's offshore platforms in the Grand Banks off Newfoundland. Wohlleben said iceberg control companies can redirect smaller icebergs, by towing them or spraying them with water cannons.

"I don't think they could do with an iceberg that large," she said. "They would have to physically move the rig."
Fun stuff, huh?

Tuesday, August 10, 2010

BankIt - I hate you GenBank

Why I can't set my "Clone ID" to use the "Sequence ID" is beyond me. Why does it have to be "You use the same property for every item, or construct some stupid tab-delimited table to upload"? Why not have a damn button which says "You want to use the Sequence ID for the Clone ID"? How hard is that? Does no one ever do that?


Manuscript out the door. Now onto the next one. Fun fun!

In the meantime, I'm jamming to the following iTunes mix ...

Don't Talk to Strangers - Dio
Mexico - Incubus
Dream Brother - Jeff Buckley
Life in Technicolor - Coldplay
Dyers Eve - Metallica
Dam That River - Alice in Chains
Next To You - The Police
We Build Then We Break - The Fray
Get Off My Cloud - The Rolling Stones
Been Around the World - Cracker

Maybe I won't get a smartphone ...

... after I read this article.
Many people are banking on their iPhones, for example. Watch out. Citigroup recently revealed that its mobile-banking application for the iPhone was secretly storing personal information, possibly including account numbers, access codes, and balance information.
So nice.

Friday, August 06, 2010

Tuesday, August 03, 2010

Friday, July 30, 2010

Mix Tapes ...

... are cool. Though technically, they're more like Mix CD's now, eh?

1. I'm a Believer - The Monkees
2. Bus Stop - The Hollies
3. God Only Knows - The Beach Boys
4. Just You 'N Me - Chicago
5. Never My Love - The Association

Thursday, July 29, 2010

Thor ...

... looks like it's going to be pretty darn awesome.

China - Food for Thought

Read this commentary over at Reuters and it raises some interesting points, but the most interesting point IMNSHO was raised by a commenter who said:
Population control takes many forms, does it not? Every government is guilty and bloody handed. Do they care? Unlikely.
As I was reading that commentary, that very thought was going through my head. I simply do not think that China cares about its population*, and if a number of them die so that China can progress economically, then they died for a good cause. It's a horribly shortsighted position to take, considering the long term effects that pollution will have, but at least to me it appears a route that China is willing to take. I don't think anything will happen in the near future unless the people demand it, and that can't happen or won't be allowed to happen.

*We already know China has stringent population control measures in place, so we know they consider themselves overpopulated to begin with.

Friday, July 23, 2010

Weekend Reading

Effects of Medium Composition on the Growth of Chlorella vulgaris During Photobioreactor Batch Cultivations
A promising alternative to petroleum-derived fuels lies in microalgae-produced biodiesel. Compared to major terrestrial crops, microalgae have higher rates of oil and biomass production and appear to be the only source of renewable biodiesel that can meet global demand for transport fuels. Chlorella vulgaris may be suitable for biodiesel production due to its faster growth and easier cultivation compared to other strains. Lipid production is achieved in two steps: a biomass production phase, and a lipid production phase, in which the lipid content of algal cells is increased by submitting them to environmental stress such as nitrogen starvation. As a preliminary step towards the optimization of the biomass production step, the effect of different nutrient concentrations in TAP medium on the photobioreactor cultivation of C. vulgaris was studied. The results showed good growth of Chlorella vulgaris in 2X TAP, reaching a biomass concentration of 6.0 g/liter. Growth inhibition was observed at concentrations of the nitrogen source, NH4Cl, between 500 and 1000 mg/liter in the medium. Varying the concentration of the phosphorus source, K2HPO4 in the medium had no effect on cell growth within the range studied, provided phosphorus sufficiency is ensured. Other medium components are non-limiting at the levels studied.

... and ...

Semi-continuous Cultivation of Chlorella vulgaris for Treating Undigested and Digested Dairy Manures
The present study, based on a previous batch-wise experiment, investigated a lab-scale semi-continuous cultivation of green microalgae Chlorella vulgaris (UTEX 2714), as a useful means for nutrient reduction as well as production of algal biomass which can be used as potential feedstock for the production of biofuel and other commodities, on 20x diluted dairy manures. Both undigested and digested samples were applied in parallel experiments for comparison regarding the requirements of hydraulic retention times (HRTs), removal efficiencies of nitrogen, phosphorus, and chemical oxygen demand (COD), biomass productivities, and CO(2) sequestration abilities. It was demonstrated that algae grown in undigested dairy manure achieved removal rates of 99.7%, 89.5%, 92.0%, and 75.5% for NH (4) (+) -N, TN, TP, and COD, respectively, under a 5-day HRT, while the HRT had to extend to 20 days in order to achieve 100.0% removal of NH (4) (+) -N in digested one with simultaneous removals of 93.6% of TN, 89.2% of TP, and 55.4% of COD. The higher organic carbon contained in undigested dairy manure helped boost the growth of mixotrophic Chlorella, thus resulting in a much shorter HRT needed for complete removal of NH (4) (+) -N. Moreover, algae grown in digested dairy manure provided more penitential than those grown in undigested one in CO(2) sequestration per milligram of harvested dried biomass (1.68 mg CO(2)/mg dry weight (DW) vs 0.99 mg CO(2)/mg DW), but did not surpass in total the amount of CO(2) sequestered on a 15-day period basis because of the better productivity gained in undigested dairy manure.

Guess I'm going to be interested in algae this weekend. What about everyone else?

Tuesday, July 20, 2010

The hotties of science

Over the past few days there has been a bit of discussion about the place of women in science. Part of it revolves around this ill-advised post which clearly objectifies women. Creepily, in my not so humble opinion. Sheril Kirshenbaum of the Intersection responded in a very calm and rational manner, and some other bloggers have weighed in as well. I found the discussion particularly interesting given the fact that Newsweek just had an article discussing the "Beauty Advantage" and how looks do matter, more than we'd like to admit actually, and that women do have it worse. So it goes without saying, but needs to be said despite some people's objections, that everyone really should use a more critical eye towards their own verbal regurgitation's ... before they spew them into the workplace, cyberspace, the street, or wherever they happen to be at the time.

Remember, it's better to keep your mouth closed and be thought a fool than to open it and remove all doubt.

With that said, one thing that was unfortunately lost in the entire discussion is that we can talk about the hotties of science without objectifying anyone. Yes, there are many good looking men and women in science -- myself included -- but it still overlooks another important facet ... the science itself.

So with that, I would now like to present the true hotties of science, or at least the ones I can pull from the top of my head.

1. Pyrolysis. Pyrolysis is a process by which organic material is exposed to extremely high temperatures and often pressure, in the absence of oxygen. This material is broken down into several components for the generation of energy. It is a player in the emerging biofuel discussion and has the benefit of being able to use multiple feedstocks. A common utilizable energy product from pyrolysis is methane which can then be used for natural gas in homes, vehicles, workplaces, you name it. It can also be used to generate bio-oils (PDF, 42 pages) for liquid fuels. As mentioned, people have looked at a number of feedstocks including cellulose and other plant materials, such as rice husks and even coconut shells. Oh, and people have looked at cooking swine manure as well (PDF, 8 pages) with excellent results.

2. Gasification. Gasification is the dizygotic twin sister of pyrolysis. Like pyrolysis, gasification is playing a visible role in the bioenergy discussion. Pretty much anything that contains carbon can be gasified, and fossil fuels such as coal are often gasified to produce electricity. Since the process typically occurs at over 700 degrees Celsius, this is a very hot science topic indeed. There are several approaches to gasification, as well as feedstocks. Gasification of biomass (PDF, 23 pages) has been studied to a great degree (PDF, 64 pages).

3. Thermo-tolerant bacteria. Now we get into my own wheelhouse! The blood always gets pumping when talk turns to the extremophiles, groups of organisms which live in the most inhospitable of environments. From the extremes in pH and temperature, to salinity and arid environments ... places we would never expect life on earth, seemingly harbors entire communities. These organisms have been used as models for exobiology, and been used in applied science the world over. Heck, one can easily argue that if it were not for the thermophile Thermus aquaticus (from which we got Taq polymerase), we would never have experienced the genomic revolution.

4. Lasers. I blurbed about this already today, but man weaponized lasers are pretty cool/hot/awesome/no longer the stuff of science fiction alone. Maybe the end-product isn't science itself, but to get it to that point some serious applied science needed to be performed, and these systems are the end result. These directed-energy weapons (DEWs) literally evaporate their targets. That's some serious heat!

5. The Hubble Telescope and Astronomy. Ok, so the telescope itself isn't hot per se, but what it typically views generates some pretty serious heat. The core of our own star, Sol, tips the thermometer at a mere 15,000,000°C, which by all estimates is pretty hot. Launched in 1990, the Hubble Telescope continues to produce amazing pictures of our universe today. Recently, astronomers detected a "monster star" which outweighs our own sun by ~300 fold.

6. Climate Change. So, is the world really getting warmer? It's a debate that has certainly generated a lot of heat, which in and of itself warrants it's placement on this list. I wish I could say that there are things that both sides could agree on, but I'm not so sure that there are. There is plenty of research being conducted on greenhouse gases, such as nitrous oxide, methane, and carbon dioxide. Scientists continue to look into how these gases are generated, how to reduce/sequester them, and the impacts they play on the environment. From my own vantage point, these gases are all part of two important nutrient cycles, nitrogen and carbon (PDF, 33 pages). Life goes on, and one thing is for sure ... marmots are getting bigger.

7. Heat shock proteins. There is a reason life can tolerate extremes in temperatures. Some cannot handle the extremes as well as others, but we all have a way of dealing with increases and decreases. The heat shock proteins regulate the responses of cells when exposed to elevated temperatures. There are a variety of proteins which handle this chore, and they are found in a range of organisms as well, from bacteria, to insects, to mammals. In addition, some of these proteins have been manipulated to serve a biotech purpose. You have to love applied science sometimes.

So, that's but a small primer on the hotties of science. As I think of some more, I'll definitely add them to the list. If commenters wish to add to the list, provide them in the comments or send me a link to your own posts. Perhaps the most important imparted lesson from this entire mess is that if we can find it in ourselves to look beyond things such as the gender of coworkers, collaborators and peers, and instead focus on the areas of science which really matter ... we'll wind up opening doors to bigger and better things. One can always hope.

ETA: Updated on 07/22/2010 to expand the list.

Nightmare cruise

Thousands of spiders found on ship from South Korea. It was a cargo ship, rather than a cruise ship, but still. Gah!
The Guam Department of Agriculture says hundreds of large spiders and thousands of smaller ones were seen when stevedores began offloading insulation and beams for housing units from the ship, the M.V. Altavia.
They blocked the offloading of materials for fear that the influx of spiders would damage the local ecosystem. I don't blame them.


Killer lasers.

Tuesday, July 13, 2010

Goodbye George ...

... Steinbrenner dead.

I never liked the Yankees. Heck, I hate the Wankees. But you have to give it to George Steinbrenner ... he wanted to win. I would like that in the owner of my favorite team. You hear that Wilpon?

Friday, July 09, 2010

One Funny, One Serious ...

... note.

Based on this article.The funny is the picture of a bunch of mice, on the right hand side. The caption: These mice have preferences. Seriously? That's your caption? Duh.

Now, for the serious stuff.
A GENE has been discovered that appears to dictate the sexual preferences of female mice. Delete the gene and the modified mice reject the advances of the males and attempt to mate with other females instead.
Which gene, and how?
The gene the team deleted is for an enzyme called fucose mutarotase, which adds the sugar fucose to proteins. Park believes that disabling the gene exposes parts of the developing mouse brain linked with sexual preference in adult life to extra oestrogen. The hormone masculinises the brain in mice - though not in people.

In a normal female mouse fetus, this extra oestrogen would be "filtered out" by a substance called alpha-fetoprotein. But AFP only functions properly when adorned with fucose. So without the gene that makes the enzyme, AFP cannot keep the flood of oestrogen at bay.

As a result, the female mouse brain develops as if it were a male. "The mutant female mouse underwent a slightly altered developmental program in the brain to resemble the male brain in terms of sexual preference," says Park.
I don't really intend to get into the whole nature/nurture debate on homosexuality. To me, I honestly don't care if it is a personal decision, or has some sort of genetic basis, or is a mixture of both, or varies dependent upon the person.

What I do care about is the road that such studies could go down. So what if scientists could establish a link between a single gene and lesbianism? Seems like it'd be to screen for. That is where my concerns arise. And they are not concerns I hold alone. The US Council of Catholic Bishops have a page discussing the moral implications of prenatal testing. Here is the "money quote" from that page, and they cite Pope John Paul II in his encyclical Evangelium Vitae (The Gospel of Life).
But since the possibilities of prenatal therapy are today still limited, it not infrequently happens that these techniques are used with a eugenic intention which accepts selective abortion in order to prevent the birth of children affected by various types of anomalies. Such an attitude is shameful and utterly reprehensible, since it presumes to measure the value of a human life only within the parameters of “normality” and physical well-being, thus opening the way to legitimizing infanticide and euthanasia. (no. 63)
Bold emphasis is mine. I do not think it is such a large leap to think that some people would consider homosexuality to be considered an "anomaly" just like one might view a child with Down's Syndrome to be considered an "anomaly". I think we need to be very careful when we head down these roads. It is one thing to wish to understand the things we experience in this world. I think it is another thing entirely to create tests to screen for them afterward. I don't think any small amount of irony should be lost on the fact that the Catholic Church -- an institution that many (not all, but many) of the more liberal-minded people in this country despise -- would be the first to step up in the defense of all people who could be construed as an "anomaly".

Further reading: Evangelium Vitae

I don't do chain emails ...

... but the information in this one was pretty sound (in my estimate) so I'm posting it here. So here is some advice, for those that want it and/or need it.

1. Give people more than they expect and do it cheerfully.

2. Marry a man/woman you love to talk to. As you get older, their conversational skills will be as important as any other.

3. Don't believe all you hear, spend all you have, or sleep all you want.

4. When you say, 'I love you,' mean it.

5. When you say, 'I'm sorry,' look the person in the eye.

6. Be engaged at least six months before you get married.

7. Believe in love at first sight.

8. Never laugh at anyone's dreams. People who don't have dreams don't have much.

9. Love deeply and passionately. You might get hurt but it's the only way to live life completely.

10. In disagreements, fight fairly. No name calling.

11. Don't judge people by their relatives.

12. Talk slowly but think quickly.

13. When someone asks you a question you don't want to answer, smile and ask, 'Why do you want to know?'

14. Remember that great love and great achievements involve great risk.

15. Say 'bless you' when you hear someone sneeze.

16. When you lose, don't lose the lesson.

17. Remember the three R's: Respect for self; Respect for others; and Responsibility for all your actions.

18. Don't let a little dispute injure a great friendship.

19. When you realize you've made a mistake, take immediate steps to correct it.

20. Smile when picking up the phone. The caller will hear it in your voice.

21. Spend some time alone.

Thursday, July 08, 2010

If I were to assemble ...

... a soccer *ahem* football team, I would insist on the following:

1. The uniforms would be red.
The psychologists found that when the competitors appeared to be wearing red, they were awarded an average of 13% more points than the blue competitors, even though every athlete was presented in both colors at some point. What’s more, points awarded seemed to increase after the blue athlete was digitally transformed into a red athlete and decrease when the red competitor changed to blue.
2. I would field my team with short players.
Based on evolutionary and linguistic research which has revealed that people associate the size of others with concepts such as aggression and dominance, Van Quaquebeke and Giessner speculated that ambiguous fouls are more likely to be attributed to the taller of two involved players.
3. I'd insist on playing all my games at home.
Analysing over 2,500 English Premiership matches, researchers discovered that referees were statistically more likely to award yellow and red cards against the away team – even when home advantage, game importance and crowd size were taken into account.
4. I'd ensure that my team always played left to right (leftward).
It's been documented that individuals who read languages which flow left-to-right are more likely to have a negative bias for events moving in the opposite direction, from right-to-left. In the Penn study of twelve members of the University of Pennsylvania's varsity soccer teams (all native English speaking), researchers found that participants viewing the soccer plays were more likely to call a foul when seeing a right-to-left attack.
Doing all of this, my team would be unbeatable!

Wednesday, July 07, 2010

World Cup 2010

La Furia Rojas!


ETA2: And I win the pool!

Tuesday, July 06, 2010

I love Maglites ...

... and after this article, I love them even more.
Maglica is obsessed with upgrading automation and fine tuning work flow in the plant to wring out speed and efficiency — the only way, he says, that he can compete with imports from China where labor is so much cheaper. The company has invested tens of millions in automation against pressures to go overseas — a strategy that has worked remarkably well, according to distributor Rich.

“The amazing thing with Maglite is we have sold their product for at least 10 years and they have never had a price increase,” he says. “I’ve never seen anybody not have a price increase every year. Not any other product line we’ve ever sold … and the quality has remained.”
If you need a flashlight, spend the couple extra dollars it'll cost you to buy a Maglite. I have a couple which I've had for over a decade a piece. The only thing that has worn down on them is the batteries.

Friday, July 02, 2010

River in the Road

by: Queens of the Stone Age

Fast approaching monsters,
Marching in a row,
Grab what slips your mind,
And what your memory won't hold.
Run, darling run.
I'll stall them if I can,
You'll escape and I'll be left rotting on the vine.

Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.
Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.

Run, darling run.
I'll stall them if I can,
You'll escape and I'll be left rotting on the vine.

Avert the children's eyes,
Forget left untold,
Don't look back to see,
The blood,
River in the road.

Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.
Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.

Get sweet revenge with my blood,
River in the road .

Tuesday, June 29, 2010

Video Tuesday

What happens when coal is gone?

But a combination of sources, perhaps including saltwater-grown plants, could get us there in the relatively near term. “Oil will disappear and there’ll be no change at the gas pump because there’ll already be technologies in place,” predicts Laughlin. “The good news is once you build these [Fischer-Tropsch] plants, you can use anything, including garbage, for the biofuel conversion. The big problem is the initial capital cost.” We can adapt the facilities over time.

Thursday, June 24, 2010

Who wants to live forever?


I've got to admit, the thought is somewhat intriguing. And just think ... all this awesome scientific knowledge I possess, what a shame to let it all go to waste!

iTunes - Next Ten

1. Welcome to the Working Week - Elvis Costello
2. (Don't Fear) The Reaper - Blue Oyster Cult
3. Mr. Brightside - The Killers
4. Albert Goes West - Nick Cave and the Bad Seeds
5. Champion Sound - Fatboy Slim
6. Nice to Know You - Incubus
7. Fight With Tools - Flobots
8. Highway 61 Revisited - Bob Dylan
9. The Needle and the Damage Done - Neil Young
10. Walking On the Moon - The Police

Video Thursday

Going through my iTunes, I came across this gem from a bit back. My goodness, what was I thinking? Catchy beat, those crazy Europeans.

Biofuel Roadmap

Document issued by USDA. From an article at Biofuels Digest:
The USDA projected in its report that the US, in order to meet its 2022 RFS target of 36 billion gallons of renewable fuel, would produce 13.4 billion gallons formed educated energy crops, including perennial grasses, energy cane, and biomass sorghum; 500 million gallons from oilseed crops, 4.3 billion gallons from crop residues (corn stover, straw), 2.8 billion gallons from woody biomass (logging residues only) and 15 billion gallons from corn starch ethanol.
The report, entitled "A USDA Regional Roadmap to Meeting the Biofuels Goals of the Renewable Fuels Standard by 2022" can be found here (PDF, 21 pages).

Asian Carp in the Great Lakes? I have a solution ...

... just let BP into Lake Michigan. That'll kill off the carp!

Asian carp found less than six miles from Lake Michigan.
CHICAGO – An Asian carp was found for the first time beyond electric barriers meant to keep the voracious invasive species out of the Great Lakes, state and federal officials said Wednesday, prompting renewed calls for swift action to block their advance.

Commercial fishermen landed the 3-foot-long, 20-pound bighead carp in Lake Calumet on Chicago's South Side, about six miles from Lake Michigan, according to the Asian Carp Regional Coordinating Committee.
What a mess we've made of our world. I always say that life doesn't come with a "reset" button, but in this case I really wish we had one.

Wednesday, June 23, 2010

My hatred of BP ...

... grows by the minute.

BP "oil containment practices" threatening extremely endangered wildlife populations.
"They drag a boom between two shrimp boats, and whatever gets caught between the two boats, they circle it up and catch it on fire. Once the turtles are in there, they can’t get out," Ellis said.

Ellis said he had to cut short his three-week trip rescuing the turtles because BP quit allowing him access to rescue turtles before the burns.
... and ...
Ellis said most of the turtles he saw were Kemps Ridley turtles, a critically endangered species. Harming or killing one would bring stiff civil and criminal penalties and fines of up to $50,000 against BP.
$50,000? Chump change for BP at this point.

I will NEVER buy gas from a BP station ever again. EVER.

Tuesday, June 22, 2010

To the Algerian witchdoctor ...

... that gave his favorite team a tie in the World Cup against England. Can you leave the pigeon home for the game against the United States? Thanks.

Tuesday, June 15, 2010

Science as fad ...

One of the most impressive, and revolutionizing, advancments in science (IMNSHO) was the ability to sequence DNA. And not just sequence DNA, but sequence billions upon billions of base pairs in minimal time.

The problem now is ... it's gone mainstream.
The first full genome was sequenced in 2003 after 13 years of work. Today, analyzing a genome takes three months and costs about $40,000.
You know it's gone mainstream when people are chatting up sequencing Ozzy Osbourne's genome. Oh of course, it's all for the "betterment of man" because some of us may go on a decades long bender and will need to know if our genes can handle it ... right?

Monday, June 14, 2010

Smile at someone today ...

... you never know what effect it may have on them.
A smile cannot, of course, save everyone; the motivations behind suicide are too varied. But simple kindness can be surprisingly effective. Mental health professionals tell the story of a note left behind by a man who jumped off San Francisco's Golden Gate Bridge. If one person smiles at me on the way to the bridge, the man wrote, I will not jump.

Thursday, June 10, 2010

In the last stages ...

... of pushing out a manuscript for review. I'm feverishly trying to get this darn thing presentable, and since it's on a project I hate, it's not going well. But I'm motivated now so I'm spending much energy on it. Trying to juggle personal life as well, which is also cutting down on my time. In the meantime, enjoy some QotSA.

Thursday, June 03, 2010


Sack-tapping, a new form of bullying. My goodness gracious. What is wrong with people?!?!

Wednesday, June 02, 2010

I like Mark Shea ...

... article on Copernicus.