Heading down the homestretch ...

... my tenure packet is due to reviewers on the 7th. That means that, since the 7th is a holiday, I really need to get it turned in by the 4th. That is the same day I have an invited presentation to a state agency. So, I'm going to be super busy again. I'll probably resume full-fledged blogging next week.

The only thing I have left to say is: Boomer Sooner!

I fully expect a total thrashing of BYU at the hands of Oklahoma this weekend.

Latest addition to the lab ...

... to be viewed while singing Stevie Wonder's Isn't She Lovely.

Isn't she lovely.
Isn't she wonderful.
Isn't she precious.

The newest addition to the lab*. A Roche LightCycler 480 Real Time PCR system (PDF, 6 pages). We're currently waiting for the electricians to install a new line (and IT to get her computer connected to our intranet) so we can fire this beauty up, but once we do ... bye bye BioRad iCycler iQ RT-PCR system. Ok, we're not getting rid of it, but we are going to use it much less frequently.

Eventually, my hope is to get a robotic liquid-handling system to do DNA preps and setup RT-PCR reactions to feed the 480. When I get those items procured, then I can buy the 384 well plate heat block** and upgrade the 480 to quadruple our output for a single run.


*The picture isn't of our machine. I lifted this picture off the web. But we do have one which looks just like it, and it's beautiful.

**The 96 and 384 well blocks are interchangeable.

Soon, you can call me ...

... Uncle Tommy. My sister is dilated one centimeter and the kidlet is pointed downwards. I'm in the pool for the 22nd of September, but she may not go that long. In the meantime, a couple of days ago, this arrived:It's as soft as can be, super plush, and the lady at the swanky toy shop I got it from said all her customers love them. It's from BestEver. Exciting times!

PS: The kidlet is going to be spoiled rotten, and Uncle Tommy will surely be to blame (at least mostly).

You've got to give it to FOXNews ...

... at least they can come up with some good puns.

Title of Story: New Park Offers X-Rated Views of NYC Hotel Guests

Closing Line of Article: The hotel won an award from the Municipal Arts Society of New York for best new building erected last year.

*rimshot*

Any health care reform ...

... should answer this question.

Isn't it a shame that after all this time and with skills honed by decades of experience, many of us can no longer afford to work as a physician?

... and address this issue ...

Good luck recruiting primary care specialists when we are projected to be short 39,000 by 2020, according to the American Academy of Family Physicians. And nearly half of all doctors surveyed by the Physicians' Foundation have said that over the next three years they plan to reduce the number of patients they see or stop practicing entirely.

What do the Dems have planned to address this?

Manuscript Update

I really should be working on my tenure case right now, but ... it's numbed my mind past the point of functioning at this point. So, since I said I would, here is my manuscript update and some thoughts on the process. So, I'm batting .500 (1 for 2) in my current spate of first author manuscript submissions.

1. Manuscript One: Sent it off to Applied and Environmental Microbiology only to get reviews telling me it was "too applied". Was told that it "... read like an engineer wrote it". Too applied? Written like an engineer? WTF? Well listen folks, when I write about an applied microbiological process, what do you expect? The system is actually used in an engineered management setting. It was a novel/interesting study because under similar situations experienced by other systems under these conditions (and we checked several), ours performed between 200% and 800% more efficiently. There was not a single previously published study which outperformed our system. That didn't seem to make much of a difference. Oh well. But, hey ... aside from a 100+ day wait through the peer process when we directed it towards another journal it wound up being accepted by said journal which has a higher impact factor than AEM. Win for me.

Take home message: Just because a particular set of reviewers doesn't like your paper doesn't mean your paper isn't worthy of publication. When you get back a review, sit down, check over those reviews and if they're a load of bullturd, make the revisions you do need, reformat it, and send it back out. Try to get that process done within a couple of weeks. There is no use, if you do not plan on making major revisions, to let it sit on your desk for much longer. All it will do is delay the time it takes to get it accepted elsewhere. If you get a similar review the next time, then you should reconsider your science, but if your science is sound, don't give up on the paper.

2. Manuscript Two: Sent it to my new favorite journal (Soil Science Society of America Journal). It received a quick turn-around, and I was able to watch the entire process online. Not only that, but the journal strives to make the peer review process double-blind. Within reason, all identifying information is stripped from the manuscript. Obviously, if you cite yourself a lot, figuring out who sent in the manuscript is not a problem, but overt naming of the manuscript submitter is taken out of the paper. I like this style of review. Unfortunately, the paper was not accepted (was told when I resubmit, I should submit it as a new manuscript since it would really amount to a new work). However, the three reviewers sent back to me the most detailed and helpful review I've ever received. In total, they spent about eight pages combined detailing my experimental methods and the interpretations of my data and told me what they agreed with, and what they disagreed with. When they disagreed, they spent considerable time telling me why. In essence, they left me with a blueprint of what they would accept for publication. The things they disagreed with really didn't come as too much of a surprise for me, and the bonus is that the things they did suggest, we've already done (and figured we'd use in another publication). So, now all I need to do is switch around the data in the two manuscripts and send it back off.

I'm not sure if they figured I was new to this field and wanted to walk me through their world, or if this is standard for the journal. I figure I'll find that out with my next submission. However I was stunned by the level of detail put into a review for what amounted to a rejected manuscript.

Take home message: Appreciate criticisms of your manuscript. While this may seem to contradict the first take home message, I think we can all tell the difference between a simply negative review and valid criticism. If the reviewer spends no time detailing why they disagree with your premise, but simply tells you to take it elsewhere, the peer review system has failed. That's not a review. It's passing the buck. So when you do get thorough reviews, appreciate them, take them to heart, let them allow you to grow as a scientific investigator.

Before these two manuscripts, I had never had a manuscript rejected before. Perhaps I was just lucky, but it was bound to happen eventually. Fortunately I learned valuable lessons with these two manuscripts. I do not delude myself into thinking that my pooh doesn't stink. In case #2 I definitely can see the areas where I stretched, and the reviewers didn't buy it. They figured the data I was presenting would be good for different analyses, just not the one I was trying to answer with that particular manuscript. I can buy that, and I'll do (have done) the work and get them back out as quickly as I can. The point for me is that I use this as a moment of growth. I could have gotten pissy and sent out #2 to a lower-tier journal and probably have gotten it in, but I saw this situation as different than situation #1. It also reinforces that I need to be thorough, helpful, and honest when doing my own peer-reviews. That is how the system succeeds and works as intended.

Biggest Wii-related Time Sinks

Listed in order (greatest to least*)

1. LEGO Batman (Wii)
2. LEGO Star Wars (Wii)
3. Monster Lab (Wii)
4. My Aquarium (WiiWare)
5. Link's Crossbow Training (Wii)

*Least is a relative term. It's still a time sink, and is still keeping me away from the things I should be doing. Though I did manage to pull myself away this weekend and spend forever mowing my lawn with my newly purchased reel mower.

Job Announcement

Received this from the people who develop Greengenes. If you're just beginning a career in bioinformatics, this sounds like a good place to start.

Hello Greengenes pro!

I'm including you in this job announcement since you have used multiple tools on the Greengenes 16S rRNA analysis web site. I'm guessing you are likely aware that Greengenes is both a DNA database and a web service and we've been funded to grow in both areas. If you know a recent Bachelors-level graduate with solid programming skills whose looking for an entry level full-time position, please forward them this link to the job description:

http://jobs.lbl.gov/LBNLCareers/details.asp?jid=23315&p=1sid=2027

Thanks for considering this opportunity and for all your helpful suggestions over the years.

Please note, this is listed as a "term" position. According to the position description, you'll be hired for one year. Your term position may be extended after that or converted into a career position depending on your performance and future funding.

Guess who?

We need a new government for a new century, humble enough not to try to solve all our problems for us, but strong enough to give us the tools to solve our problems for ourselves.

I'm telling you right now ...

... if there is a work stoppage in the NFL in 2011, I'll permanently take my interest/support/fandom/money elsewhere. My team (the Jets) are not good enough for me to even feign interest after they tell me to go kiss my rear end because they're going to hold out for more money. Most of them already make more money in one year than I make in an entire lifetime. I'm supposed to support them for their greedy grab to make more?

Once again I ask ...

... is the major problem people have with the health care reform the "government option"? If so, can't the people writing the bill just say "To hell with it, we'll yank that part of the bill"? Is it so integral to the reform that the reform is worthless without it?

If this is the extent of the problem, then it seems to me rather easy to fix it. Part of me thinks that if this was the only major issue, it would have been fixed already, but then I remember who works in Washington DC on these issues and I begin to think that maybe it is that simple after all.

Addendum: Recently I blogged about the state of Massachusetts and their "universal health care". It seems that not everyone is pleased with that system either. The author of the OP-ED thinks we should head in the opposite direction of what I suggested and expand Medicare to cover all US citizens. Of course, if I read it correctly, the author implies that this would be the end of insurance companies:

A modest, progressive tax would replace what people currently pay out of pocket. This program would pay for itself by eliminating the wasteful administrative costs and profits of private insurance companies, and save $8 billion to $10 billion in Massachusetts alone.

Without profits, these companies cease to exist. How many times has the United States of America intentionally undercut a business (seemingly contra-capitalism) to install such massive programs? I can imagine it having happened before, but I can't think of any offhand ... at least at the magnitude we're now potentially talking.

Menaquinone 6 (MK-6)

Anyone know where to buy this damn thing? I can't believe that I cannot find a single chemical and/or pharmaceutical company that produces this quinone for sale for research purposes. Sigma sells MK-4 (it's Vitamin K2), but what about MK-6? Nada. Grrrr!

Boobies!

Came across this article in the New Scientist. It's a lovely piece of modern day molecular biology doing some forensic work to rediscover a species that was thought to have died out a couple of hundred years ago. The bird in question is the Tasman Booby (Sula tasmani).

It has been speculated that this bird has been extinct since around 1790, though evidence has suggested that these birds might still be around. From my reading of the papers, it appears that the call for extinction of the Tasman Booby was based on the examination of fossil material. However the authors believe that the previous study was instead looking at fossil remains of S. dactylatra, the Masked Booby, that were in the upper size range of that species.

The authors first performed morphometric data. Their results were presented as follows:

Contrary to van Tets et al. (1988), our comparison of new skeletal material revealed a size overlap between modern and fossil specimens for all standard humerus measurements.

Such an overlap was not seen by van Tets et al. (see Table 1 reproduced below).So how does that happen? The authors of this manuscript state that van Tets et al. in their studies made a bit of a faux pas. Seems that they "failed to acknowledge" the fact that all the fossil specimens in their study were female, and the modern specimens in their study were male. Like a number of birds, the Booby presents with what is known as reversed sexual size dimorphism. In other words, the females are larger than the males. Whoops.

Anywhoo ... Steeves et al. complement the morphometric data with genetic data by performing mitochondrial DNA sequencing. Phylogenetic analysis of these sequences revealed that mitochondrial DNA extracted from three of the six fossil specimens (nothing was recoved from the remaining fossils) were identical to an existing species of Booby, Sula dactylatra fullagari. Based on this, they proposed that all North Tasman Sea boobies should be known as Sula dactylatra tasmani. With this Steeves et al. have extracted the Tasman Booby from the Book of the Dead!

Reference
Steeves, T., Holdaway, R., Hale, M., McLay, E., McAllan, I., Christian, M., Hauber, M., & Bunce, M. (2009). Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea Biology Letters DOI: 10.1098/rsbl.2009.0478

A very reasonable argument ...

... made by Rob Knop (blogger at Galactic Interactions) to creationist Christians. Here is the most important point, if you ask me, as to why creationists should not feel threatened about these arguments: Jesus himself taught in parables. IOW, if Jesus himself didn't teach using a strictly literal style, why would he (as God the Father) give us a series of books (Scripture) limited in such a strictly literal fashion?

I told Rob I'd give him some link-love, and we're definitely both on the same side of this issue, so here it is. He has several good posts, IMNSHO, on the subject. They're worth a read.

Northeastern USA Ecosystems Under Attack

By the White-Nose Fungus. It is decimating bat populations in the Northeastern United States.

First observed in Howe Caverns near Albany, N.Y., in early 2006, white nose syndrome has spread north to New Hampshire and Vermont and south to Virginia. At least a million bats in six species have already perished, and death rates at infected hibernacula range between 90 and 100 percent.

Ninety to one hundred percent.

However, it's not just the bats which suffer, the rest of the ecosystem suffers as well:

... because bats are essential to the control of nocturnal flying insects, the outbreak could upset local ecologies, weaken the health of forests and even affect crop yields.

So how much money have we set aside to combat this fungus and syndrome? A total of 1.1 million dollars. A paltry sum of money to fight something of this magnitude.

This past May, 25 U.S. Senators and Representatives signed a letter to Interior Secretary Ken Salazar urging emergency funding for agencies with the expertise to “determine a cause and develop solutions to this crisis.”

It's been requested that at least $17 million be set aside for immediate research efforts. Write your congressional representatives and ask them to support research to combat this disease.

You know that antibacterial soap you use?

It's winding up in the environment.

Triclosan, an antibacterial chemical found in everyday bathroom and kitchen products, is accumulating in dolphins at concentrations known to disrupt the growth and development of other animals.

Whatever happened to good, old fashioned soap? Ivory Soap folks. Ivory Soap.

So how does it work (in disrupting development)?

Triclosan is strikingly similar to thyroid hormone, so it might bind to hormone receptors, said Helbing, author of the frog study. Because frog and mammal endocrine systems are similar, triclosan can potentially “affect how hormones work in ways that aren’t intended” in dolphins, and maybe even humans, she said. Altering thyroid function in humans and animals might cause abnormal brain development and other developmental defects.

LEGO Update

So I'm over 80% of the way finished with LEGO Star Wars. It's taken me over 50 hours, and now that I've gotten all the low hanging fruit, I'm stuck trying to finish up all the timed challenges and getting those last little minikit bits in all the hard to reach places.

Which is probably why my attention has shifted more towards my latest Wii game ... LEGO Batman! It too is a cool game. Not as in-depth at the Star Wars game is, but the overall game play remains the same, making it a fun game, especially if you enjoyed Star Wars. When I played my PS2 regularly, I loved the RPG style games, though the really good ones, like the Baldur's Gate (I and II) and the Champions of Norath, were hard to come by. So when you chanced upon them, you played them all. The LEGO games are sort of like that.

Enaging in risky behavior ...

... and by that I mean eating unsafe foods. Here are some excerpts:

Should I drink milk after its use-by date? What about eggs?

Drinking milk a day or two after its use-by date shouldn't be an issue. But if you notice changes in flavor, consistency, smell -- don't take any chances, Nelken said.

For eggs, the USDA recommends using within three to five weeks of the date of purchase. The "sell-by" date will usually expire by then, but the eggs are safe to use.

Eggs and milk should be stored in the coldest areas of the refrigerator, not on the door, since it's four to five degrees warmer there.

That's good to know. Have you looked at the price of eggs lately?

Should I drink the water after the expiration date has passed on the bottle?

"What happens with water is absolutely nothing," Beattie said. Water is safe to drink even past its expiration date (as long as there's no leakage in the bottle), but the water may taste different.

According to the Food and Drug Administration, bottled water is considered to have an indefinite safety shelf life if it is produced and stored properly. While the federal agency does not require an expiration date for bottled water, many manufacturers elect to put expiration dates.

"What happens is that people feel more comfortable with bottled water with a code date," Beattie said. "There is no safety factor beyond that. Manufacturers feel that quality of water may deteriorate or become more neutral."

People actually buy water still? Haven't people learned that when they are buying bottled water, they're probably buying someone else's tap water?

Get a water filter unit for your faucet and a nice BPA-free water bottle.

If you have a couple of hours to spare tonight ...

... you might want to take in the Perseid Meteor Shower.

The Moon is least troublesome during the early evening hours of August 11th. Around 9 to 11 p.m. local time (your local time), both Perseus and the Moon will be hanging low in the north. This low profile reduces lunar glare while positioning the shower's radiant for a nice display of Earthgrazers.

It's one of the best times of the year to view meteor showers.

A good read ...

... on agriculture and what most of us take for granted, can be found here.

Farming has always been messy and painful, and bloody and dirty. It still is. This is something the critics of industrial farming never seem to understand.

h/t Mike at the Big Stick.