Personal Genome Scans

Don't count me as one of the people who'll opt for this type of service, though $1,000 isn't all that much to have it done.

Navigenics, 23andMe and deCODE specify that customers own their personal data. But executives keep the door open to use their growing databases for research with commercial or nonprofit partners. Such studies should take place under research protocols, not as an outgrowth of consumer marketing, the CDC’s Khoury argues. For now, he says, the best tool available to personalize medicine is low tech and low cost: family health history.

So we'll move from companies selling your personal information like addresses, phone numbers and the like to selling your genotype. Not for me.

I'm happy ... or am I?

Liberals Miserable, Conservatives Overjoyed.

Honestly, I just think Conservatives are happy right now because they're watching the Liberals rip themselves apart in the Democratic Party Primaries right now. Get that damn thing over and done with!

My question is, where do the moderates fit into this?

Q: Is your glass half empty or half full?
A: It's 50% water, 50% air.

I can relate ...

Compliments of PhDComics.

Isolation Is Fun!

I'm not talking about sitting in a locked room for days upon days, I'm talking about isolating bacteria! Bacteria are everywhere, and depending on where you're considering, they're different from each other. On your skin alone, there are a multitude of different types of bacteria. These bacteria also differ from the bacteria in your mouth, which differ from the ones which are in your gut. Depending on the type of bacteria you're trying to study, you'll need to use different media (either liquid or solid) that you'll use to grow your organism on/in, grow it in the presence of oxygen (aerobic) or not (anaerobic), and supply it with different carbon and nitrogen sources, as well as additional nutrients (Ca, Fe, K, Mg, Mn, etc etc).

Different organisms respond to different culturing methods, and these methods can be exploited by the microbiologist to select for certain types of bacteria. In essence, you're "dissuading" a certain type of bacteria from growing, which allows the others to grow relatively uninhibited. That's what I'm doing today.

I have identified the major players in a bacterial community that we're really interested in, for use in agricultural applications (mainly to remediate animal waste). Now I'm trying to isolate them from each other so we can study them on their own. Now, we might not be able to grow each one of them, but I'd like to isolate at least the ones that are found the most abundantly in the system. Today, I start with a Halomonad. Given the name, these organisms typically like growing in conditions which have higher than normal salt conditions (halophilic - which means "salt loving" as opposed to halophobic which means "salt fearing"). Not all organisms can tolerate such conditions, so we'll use that to our advantage. So what we'll do is make up media containing a range of salt (NaCl) concentrations and plate out some of our bacterial containing solution. If all goes well, only the identified Halomonas strain will grow.

Afraid Of Heights?

This guy obviously isn't. Best of luck to him. He goes in approximately 18 days.

Le Grand Saut.

Viral Outbreak In China Ahead Of Olympcs

Article here.

Although the outbreak is another headache for China's Communist government as it prepares to host this summer's Olympic Games, WHO's China representative, Hans Troedsson, said the disease was not a threat to the Beijing Olympics because the disease mostly sickens young children.

It mostly sickens children, so the Olympians will be safe. Well thank God for that! Sheesh.

NASA in HD

Article here.

More than 100 hours of classic footage from NASA's Mercury, Gemini and Apollo space missions have been restored for high-definition television — and will be made available to the world through the space agency's archives.

Can't wait to see them.

It rained today ...

... so no biking into work. That was a good thing because I had to lug two textbooks, the 1293 page Manual of Environmental Microbiology and the 1069 page Methods for General and Molecular Microbiology from home. I don't think I would have made it if I had to bike to work. BTW, the Manual of Env Micro is an excellent resource.

Primum non nocere - Part I

Translated: First, do no harm.

For those involved in the many scientific disciplines, this is a phrase which should be considered throughout the facets of their professional (and personal) lives. Earlier I mentioned that scientists need to behave responsibly when communicating with the layman because, like it or not, they represent science and scientists in toto. Act irresponsibly, and you tarnish the rest of us. Now, I'm sure that some people will take the Charles Barkley line of defense (i.e., "I'm no role model") and claim that each individual (and their message) should be judged on their own merits ... but we all know that doesn't happen. Never mind that some of the very people taking up this defense probably tend to lump groups of people into convenient, broad brush categories themselves.

Doing harm can come in many forms, but they all have the same outcome - that being, they serve to turn off the individual who is confused, disparaged, insulted or otherwise offended. How does it happen? It happens by talking over the audience, refusing to acknowledge non-scientist inquiries, open mocking of certain groups, and through insults and harassment of opinions and people holding them. I doubt this list is comprehensive, but I think my point is clear. Some people grasp these facts, others do not.

Case in point: Science Blogs. (Well, there goes my invite). I've taken to reading as many of the 71 blogs there as time permits, I stop to leave comments where appropriate, and I truly enjoy a number of them. I think denialism is a great read, and I also enjoy Not Exactly Rocket Science, particularly because Ed Yong spends a lot of time using Research Blogging. As scientists, I believe we need to be cognizant of the fact that our duties don't stop at the edge of the lab bench. That data needs to be interpreted and made known to society. And the thing is, 99.9999999% (a rough estimate) of the population are non-experts in the field we're reporting on. So, part of our role is making sure that we can distill down the important points and give it in digestible chunks for the layman. A lot of blogs do that, and to that end, I think they do the scientific disciplines a great service. The more people are informed the better their ability to grasp the importance of the work, and thusly, the more likely they are to support those efforts (in terms of policy and public funding).

But then, there is the opposite side of the spectrum. These blogs are, IMO, more noise than actual content. They're more screed than treatise. It's almost ironic that one of the entries of the linked blog (on May 4, 2008) was this one, lamenting that television programming devotes so little time to factually representing science. In the meantime, this same individual is taking pot shots at religion, here, and here, and here, and ... well, you get my point. And when he is talking about science, which he admittedly does well, he can't avoid putting in that last jab. And while I don't have the exact site statistics, judging by the numbers of comments left behind in his posts, I'd surmise his blog is one of the (if not the) most visited blogs on the site. So one must ask, what good results from this sort of screed? Other than the fact that he manages to insult a large portion of the members of American society ... the very people who pay the taxes which contribute to his research funding (if he has public sources of funding that is) ... I can't see what good can come of him professing that this is a scientific blog. It is this very type of screed which no doubt led to his being manipulated by Ben Stein. He got suckered because he has a big mouth, and can't keep it shut ... and because of that, the rest of us have to mop up his verbal diarrhea.

In my time doing research, I have found that people, regardless of political or religious affiliation, are more than willing to help you do your research and therefore develop applications which can benefit everyone. I try very hard to put a face to a name, for both their benefit and mine. When you establish that rapport (which for me isn't the most comfortable thing I have to do, being an introvert), you open a number of doors for the betterment of your own scientific program. I don't bite the hand that feeds me, I don't insult someone just because I have a platform to do so, and dozens of people will laud me for it. What exactly would it achieve?

As a microbiologist who currently studies microbial population structures in agriculture, I study microbial relationships which have obviously developed over long periods of time. I am constantly constructing phylogenetic trees ... plotting the evolutionary history of the organisms I am using to develop applications for advanced agriculture. My customers, none of whom are geneticists or microbiologists and who'd I guess are mostly evangelical Christians given my location (and probably have a dim view of evolution, and a probably even lesser understanding of it), see this and don't raise a fuss. They know I'm here to see to their problems and recommend solutions to it. I don't go around insulting their religious beliefs because I know that to do so would only make my life harder. If you don't want to get jabbed by the horns, don't poke the bull with a stick! It's as simple as that. And in the end, when they need to understand evolution, my hope is that they'll remember their discussions with me and they'll come to me for a way to understand it. This way, everyone wins.

Unfortunately, most people remember the bad. Probably because the bad is sexy ... everyone loves looking at the train wreck. Bad news and drama sell. Unfortunately, drama is the last thing scientists should be feeding into. Alas, not everyone feels this way and as a consequence they wind up harming us all.

Flu Epidemic? Stay at home ...

... but not for the reasons you might be thinking about.

To prepare, hospitals should designate a triage team with the Godlike task of deciding who will and who won't get lifesaving care, the task force wrote. Those out of luck are the people at high risk of death and a slim chance of long-term survival. But the recommendations get much more specific, and include:

* People older than 85
* Those with severe trauma, which could include critical injuries from car crashes and shootings.
* Severely burned patients older than 60.
* Those with severe mental impairment, which could include advanced Alzheimer's disease.
* Those with a severe chronic disease, such as advanced heart failure, lung disease or poorly controlled diabetes.

You wouldn't want to get into a car accident and get triaged if you get the flu.

The little ones ...

Recently I was extended an offer to give a science talk to a few classes of elementary school children, an offer which I accepted. A couple of weeks ago, I gave that talk and I must admit that it gave me hope for the future. The kids were well behaved, they were interested, they were intelligent. I spoke about energy and how it affects our lives, and what science is doing to help address the problems these kids hear their parents complaining about at the dinner table at night. The talk wasn't very complex, I didn't get into intricate microbial pathways. Rather, I laid out the basic premises and goals of not only my own research, but the goals and visions of my organization as well. I went in with a "Here is the problem, and here is how my research is going to help all of us."

Unfortunately, I think that message is lost on a lot of scientists. I read blog after angry blog, of scientists railing about stupid laypeople. They mock, they taunt, they openly insult. All of which results in deafening the general public to the good work that scientists do, day after day. However, this is a topic for another day. I'm going to do at least one entry on scientists and their responsibility to inform the public.

So back to the discussion at hand. I was pleased to see that the children ate up my presentation. We had a lengthy Q&A afterwards as well, where I got on the teachers good side by pointing out how a well-rounded education would help them achieve their eventual career goals as well. What floored me the most though was one question asked by one of the students when he asked: Dr. TomJoe, what's the difference in factors between the energy crisis of the Carter administration and the current energy crisis? This kid wasn't any older than 13 years of age, and he asked a question you'd expect from someone much older than him. Heck, you won't find this question being asked by many adults ... yet there he was. If this child can be that inquisitive, and that adept at asking a very important question ... I hope that he will be typical of the future generations. It is our obligation as teachers (for science doesn't stop at the bench) to foster these traits.

The Nitrogen Cycle

This is my first attempt at using Research Blogging, hope I don't mess this up.

At any rate I've been reading a number of articles, for a paper I'm putting together, and I came across this review which I think is pretty good. It goes over the nitrogen cycle, of which I'm primarily concerned with nitrification and denitrification. Nitrification is the biological degradation of ammonia to nitrite and nitrates. Denitification takes nitrite and nitrate and reduces it to (hopefully) dinitrogen gas. I've illustrated (and simplified) the process in the following diagram. I'll also explain the "hopefully" comment towards the end of this entry.



Nitrification, since it is an oxidation reaction, requires oxygen (as one would surmise). Denitrification typically occurs under anaerobic conditions. As a result, the major players for both reactions are typically different, though there is some overlap. There are other processes involved in the nitrogen cycle, such as ANAMMOX (Anaerobic Ammonium Oxidation), Nitrifier Denitrification, and Aerobic Bacterial Denitrification, which have all gained increasing examination amongst scientists but have a long way to go before being as well understood as the classical systems mentioned above.

The field has also revealed that these processes are no longer the domain of bacteria, as once thought, but that the fungi and archaea also play a role in these processes. In fact, fungi in denitrification, and archeae in nitrification and denitrification, may be major players if not THE major players in particular environs.

What has genomics told us? Genome sequencing has definitely sped up the process of understanding, and more importantly, identifying the organisms responsible for these processes. These studies have also shed light on the evolutionary paths these organisms have undergone as well. One such example is that of Nitrosomonas europaea (Ne). This intricate organism lacks all but one single, rudimentary synthesis pathway for siderophore production (citrate). Siderophores bind to iron, which are then picked back up by the organism via a receptor. With few exceptions, iron is a nutrient essential for life, which is why at first glance it makes little sense for Ne to not produce siderophores. However, Ne does encode receptors for many different siderophore types. What does this mean? It means it scavenges off of the siderophores of other organisms. This allows Ne to devote most of its energy into other pathways without having to worry about synthesizing means to acquire iron.

So back to the "hopefully" comment I made earlier. Why are nitrification and denitrification so important? Well, there are several reasons, one of the major ones being that nitrous oxide is a major green house gas (GHG). Nitrous oxide actually has 296 times more of an impact on global warming than carbon dioxide, which sort of makes it a "Big Deal". Nitrous oxide is produced when denitification occurs "incompletely". This incomplete denitrification occurs naturally in the environment. Some organisms don't have the genes which encode for the final step of denitrification, the conversion of nitrous oxide to dinitrogen gas. Sometimes the reason is regulatory, in that the environment is such that nitrous oxide is the final end product. Understanding how and why this occurs is the focus of current research by many individuals.

Hope this sheds some light on these two steps of the nitrogen cycle. I hope to post more on the matter in the future.

References

Hayatsu, M., Tago, K., Saito, M. (2008). Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Science and Plant Nutrition, 54, 33-45. Article here.

Chain, P. (2003). Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology, 185(9), 2759-2773. DOI: 10.1128/JB.185.9.2759-2773.2003

Resources to Learn More About Nitrogen Cycle
Online University Rankings
University of Missouri

I don't mean shoe size

Reducing your Carbon Footprint.

At this website you can calculate the total carbon dioxide emissions you'll incur as a result of a trip, and then offset them. Worth taking a look at if you ask me.

Yer Not The Ocean

I was serious when I said ...

... I was going to do it.

Went out and bought a Slime kit (complete with Slime and air compressor) and repaired both tires on my bike. Washed the bike down and gave it a good rubdown with a microfiber cloth and checked my brakes and gears. Everything looks to be in working order, even though I did notice a couple of broken teeth on the outer chainring (which I'll eventually need to have replaced). So, come Monday, if the weather permits (and part of me is hoping it won't), I'm going to cut down on my carbon footprint a bit!

Clemens is so fuc... screwed

So who hasn't Clemens slept with? I hate the man. The fact that he's a Texass Shorthorn alum (Boomer Sooner!) alone makes him worthy of extreme hatred. Add to this that he pitched for the Evil Empire, the dreaded Yankers, is just the icing on the cake. I can't feel sorry for this bastard one bit. He thought he was untouchable, obviously he was wrong. Should Congress be spending our tax dollars more wisely, rather than wasting it investigating a waste product like Roger? Probably, but you know what ... he's got it coming to him. Say goodbye to the Hall of Fame Roger. Toodles!

Kudos to Obama

For telling it like it is.

Obama has said the tax holiday would save a typical American motorist no more than $28, and likely less according to economists because cheaper gas would increase demand and push up the price, putting more profit into the coffers of the oil companies.

"What working families need right now (is) not more of the same Washington gimmicks that are out of touch with the struggles of working Americans, but real change that will make a real difference in their lives," Obama said.

This is the change I spoke about earlier in my blog. Change that hangs around for awhile, change that is probably going to be uncomfortable for awhile, but pays off in the long run.

"But what we're talking about now is a Washington con game, and I think the American people are smarter than Washington and will see right through it."

Yeah, color me skeptical. I think if history shows us anything at all it is that American people can play the role of sheeple too damn well.

More about that link ...

... between food and fuel.

This article cites Lester Brown, who wrote Plan B 2.0. It's a very informative book, and an excellent read. He's also come out with Plan B 3.0, but I have not had a chance to read it yet.

Anyways, back to the article. There are many issues with using corn grain as a fuel. One of the main reasons is easily seen in your supermarket. Corn diverted to fuel affects more than just the price of corn for consumption. Corn is used as feed for cattle, poultry, and swine. The article relates the following ...

Now, however, the legislation is being criticized for making food more expensive while gasoline prices continue to climb. Rick Perry, a Republican who succeeded Bush as Texas governor, has asked the Environmental Protection Agency to waive half of the "misguided" ethanol requirements because of rising food costs; every penny increase in per-bushel corn prices costs his state's livestock industry $6 million a year, he said.

That increase in cost is eventually transferred to the consumer. I don't know about you, but I'm tired of looking at $7.99/lb for a London Broil and $4.99/lb for chicken breast meat. Matter of fact, I got so tired of it that my wife and I have gone to a mostly vegetarian diet. Fortunately for both of us, there is a farmer's market not too far from my place of employment, and we don't mind eating a lot of vegetables. The loss of corn from the food market also has the effect of placing greater strain on the other food grains. While I'm no economist, I imagine that's at least part of the reason we're seeing an increase in the price of wheat (flour), and rice. As we consume more of these staples, as replacements for corn, our demand for them increases their prices as well. It's a vicious cycle.

Then there is the little nagging fact that corn ethanol might not really be the silver bullet when it comes to saving us from high fuel prices. Why? There just isn't enough of it. Look at the following figure, provided by the University of Tennessee Agricultural Economics Department report 25 x 25 (25% Renewable Energy for the United States by 2025).

That yellow section at the bottom is corn grain (when looking at the report, this figure is found on page 33, it's Figure 11). Through 2025, you can notice that there really isn't an appreciable increase in the amount of corn grain over the next 15 years. Instead, we really need to be looking at the dedicated energy crops (the green section on the chart). Unfortunately, they're not really expected to come online for another 5 years or so. This is, in part, due to the need for increased efficiency for cellulosic ethanol production. One question that can be asked however is, is that even necessary? Thermochemical processes can be brought to bear today, and those crops, which are already being (or are) planted could be used in gasification. Production of methane from that process could be scrubbed clean, essentially becoming "natural gas". Compressed (CNG) and Liquid (LNG) Natural Gas are already used in vehicles across the country. T. Boone Pickens, an oil magnate in Oklahoma has suggested that NG be used on his own website.

While chairman of the National Natural Gas Vehicle Coalition for almost three years, Pickens traveled the country advocating the merits of natural gas. When he left Mesa Petroleum and its management wanted to divest of the natural gas fueling concerns, he purchased them and in 1997 formed Pickens Fuel Corp. He touted natural gas as the best alternative vehicular fuel because it’s a domestic resource that reduces our foreign oil consumption, and enhances America’s energy security; clean (NGV vehicles emit up to 95 percent less pollution than gasoline or diesel vehicles); less expensive than petroleum and hydrogen; and safe (lighter-than-air compressed natural gas is nontoxic and disperses quickly, and has a higher ignition temperature than gasoline and diesel fuel, which reduces the chances of accidental ignition).

Obviously, we're going to experience some growing pains, as we change our infrastructure to adapt. The question is, are we as scrappy and as resourceful as previous generations seem to have been? Honestly, I think it'd be easy for the government to help out as well, when you consider where all our tax dollars are currently being spent. You know this "economic stimulus package"? Why not save that and give it as a tax credit for people who would convert their existing gasoline car into a LNG car instead? I believe the conversion kit costs between $1.5K and $2K. Don't you think that would boost the economy a bit as well? I think there is hope for our country, but this isn't going to be an easy fix. I think the younger generations are ready to make this change, the question is ... are the Baby Boomers? They're the largest voting bloc this election year.

I'm a baseball fan ...

... but Todd Jones is a nincompoop. This is what sticks in my craw.

You’ve stuck around long enough to figure out that your career is not about you; it’s about your teammates and how you leave the game. If somehow you made it better for somebody, you’ve done your job.

I guess when one makes $7,000,000 for playing a game, one can afford to say that. Then again, maybe that "somebody" he's talking about is himself.

For only $10,000 ...

... you too can make ethanol for $1 a gallon with the E-Fuel Microfueler.

As mentioned in the article, there are some problems with this approach:

1. 100% EtOH is illegal as fuel in the United States.
2. Where are you going to buy all this sugar? South of the border*?
   
3. $1/gallon, until you remember you paid 10K for the device!
4. How does this really differ from other stills which are really cheap to make? Is squeezing out that last 5% of water actually that much of a problem for the folks who make grain alcohol?
   

*Inside joke for anyone who travels I-95. South of the Border is a [tourist attraction/eyesore/pimple on the ass of South Carolina/however you view it] that sits about a mile south of the North Carolina border. You can't miss it. You definitely can't miss it because Pedro starts advertising for his place about 90 miles out. Jimminy Christmas, it's annoying. They also claim to sell just about everything and anything.