Informed Voters

Results of a Pew Poll: Only 26% of Americans know that it takes 60 votes to break a fillibuster.

Only 32% of Americans know that the Senate version of the health care bill was passed without a single Republican vote.

Speaking of Republican votes. Today, every Republican senator voted against re-establishing pay-as-go. These are the guys that are so concerned about deficit spending.

UPDATE: Concerning restablishing pay-go Steve Benen says: "Republican obstructionism has reached the level at which they oppose ideas they support."

Ode to My Path Students

Our lives are filled with joys and strife,
And what is death but part of life?
Will come the day that we must die,
And leave behind those learning why.

Education is hanging around until you've caught on.

-- Robert Frost

70% of Polled Share Pres. Obama's Priorities

An "instant poll" conducted right after President Obama's speech last night indicated that 70% said President Obama "shares their priorities for the country". This was "up from 57 percent before the speech."

This is good. Doesn't this mean that President Obama should have no problem moving forward on his priorities since 70% of the country supports him? I bet not. Having a majority of the votes in the U.S. Senate these days no longer guarantees passage of legislation. You need 60 votes to pass legislation now.

Colorful Dinos

This changes everything. All future movies that show dinosaurs will have to do away with grey-colored, lizard-skin look. Oh yeah, and we've got to add feather too. This should be great news to all you chicken-lovers. You are now the proud owners of the decendents of dinosaurs.

How do you determine the color of a dinosaur from fossil imprints? Well, it has do be done indirectly. Paleontologists have discovered fossils of feathered dinosaurs. When these feathers were examined microscopically, dark rod-shaped structures were seen that at first were thought to be bacteria. Turns out they are melanosomes, structures that contain the pigment melinin. The melanosomes are not only present in feathers but also in the skin. You can read more about this discovery here.

MA New Senator - Full Frontal Nudity?

Ok, you can debate the recent MA election for the US senate all day. But let's say the Democrats had a really powerful, electable female candidate (not Coakley in other words). Would this women still be electable if she had posed completely nude for a magazine? I don't think so. So now the "moral" conservatives have a senator that has a full frontal nudity centerfold available for viewing by those nice conservative moral women (and more likely the conservative men).

Having Your Pig & Eating It Too

Petri pork is almost here. Grow pork in a dish using pig stem cells. Cool!

Don't Forget the Bush II Federal Debt

With the constant chatter of how President Obama and the Democratic Congress is spending the US to death, it's good to be reminded every now from whence that debt came. Here's David Axelrod in today's Washington Post:

The day the Bush administration took over from President Bill Clinton in 2001, America enjoyed a $236 billion budget surplus -- with a projected 10-year surplus of $5.6 trillion. When the Bush administration left office, it handed President Obama a $1.3 trillion deficit -- and projected shortfalls of $8 trillion for the next decade. During eight years in office, the Bush administration passed two major tax cuts skewed to the wealthiest Americans, enacted a costly Medicare prescription-drug benefit and waged two wars, without paying for any of it.

Axlerod also reminds us that Obama is proposing far more cuts in government than are the Republicans. Don't believe him? Then maybe an article in the conservative Washington Times might convince you. Unfortunately, many of President Obama's proposed cuts do not make it through Congress. Why? Well I suspect it's because constituents of congressional reps do not actually want government cuts as much as they proclaim they do.

Just ask conservative Doug Hoffman what government cuts he would make if elected to Congress. We want cuts that affect the other guy, not us.

Short History of DNA

 

The Census - What is it good for?

Yeah OK, the census asks some pretty personal questions. But what do they do with all that information? Robert J. Samuelson gives us an example in his Washington Post column today.

You may think that the last place to find a portrait of a nation is a book full of numbers. But turn to Page 673 of the Statistical Abstract of the United States, and you find these intriguing figures. About three-quarters of Americans (76.1 percent in 2007, to be exact) get to work by driving alone. Only 10.4 percent carpool, while 4.9 percent use public transportation and 2.8 percent walk. On average, Americans spend 25.3 minutes commuting each way. The state with the longest commuting time is New York, at 31.5 minutes; the states with the shortest are North and South Dakota, at about 16 minutes, followed closely by Montana and Nebraska, at 17.6.

In addition to the Libary of Congress, the U.S. Census Bureau provides a wealth of information. The 2010 Statistical Abstract can be found here.

I'm Back, but I Never Really Left

My winter sabatical is nearly over as I return to my office to order lab supplies, fill out workload and office hours schedules, prepare course syllabi, write new and rewrite old lectures etc. My first real big job is to work on a couple of presentations concerning fluid and electrolyte balance - a very complicated topic.

My annual New Year's trip to Washington, DC was another success. After living in the DC area for many years, there are still many places I've never visited or visited in a serious way. The Library of Congress is one of those places.

The LOC building itself is pretty spectacular and is located next to the Supreme Court on Capital Hill.

But it's what's inside that is really spectacular. It's probably one of the most beautiful buildings on the "Mall" and you really need a guided tour to appreciate the building's history. It's the largest library on Earth with 142 million items located on over 650 miles of shelves.

Above is a picture of the great hall (main entrance) taken from Wikipedia. The silver colored material around the ceiling is actually made of aluminum, a very difficult, expensive material to come by in those days. I have my own pictures but I haven't downloaded them off the camera yet.

The Library was destroyed by the British in 1814 but most of it's then 3000 books were replaced with over 6,000 books purchased from Thomas Jefferson. Unfortunately, another fire in 1851 destroyed about two-thirds of those books. One of the current exhibits at the LOC is the library of Thomas Jefferson which is being reconstituted either with the original books or replacement copies of the books. Some of the books will never be replaced because they are unavailable.

The reading room and the dome above it abound with architectural history.

Yes, you can actually use the library as a research library, but you must first become a registered reader. This is like applying for a library card that is good for two years.

But the primary reason I wanted to explore the LOC was to visit the exhibit on "Exploring the Early Americas". I wanted to see the first map ever drawn to use the word "America". This is the Martin Waldseemüller map of the world drawn in 1507 and given to the library by Germany.

The word "America" is printed on the continent of South America.

The LOC is a library but it is also a museum with changing exhibits. You really need to visit the library to appreciate the building and the exhibits. However, the LOC website is probably one of the most extensive and information filled sites ever published. And, don't forget...this is the Library of Congress, so you can find out what specifically is going on in Congress on a day-to-day basis using the "Thomas" portion of the website.

Run, Don't Walk to See Avatar in 3-D

Run, don't walk, to your nearest 3-D capable movie theater to see Avatar. Don't waste your money on the 2-D version. We went to the Cumberland 12 theaters in Plattsburgh to see Avatar in 3-D. Movies will never be the same. The best I can describe the experience is that it is like looking out a window at something happening, not looking at a screen. The "alien" planet is absolutely beautiful. The movies isn't full of 3-D "gimmicks", like things flying out at you (although sometimes....). There are instances where you want to reach out and touch cool little floating or flying alien animals. The movie has many messages that apply to the political situation today. The main message I took away from the movie is that it is much easier to reign destruction on a people if you can somehow convince yourself to hate them.....to make them seem less than yourself or just different. This movie is going to win awards if only for the new technology used in making an unforgetable experience. One technical question however. Many of the alien animals are hexapods rather than tetrapods, but the alien "humans" are tetrapods like us. I believe even the alien "monkeys" were heptapods. How did the alien "humans" end up evolved into tetrapods?

Science is Beautiful

Here is a good reason to visit Rochester, NY. An almost exact replica of a 1976 late Baroque pipe organ has been reconstructed in Christ Church Episcopal. It's a copy of a pipe organ built by Adam Gottlob Casparini of East Prussia and cost $3 million. There is nothing modern about this organ. It needs to be pumped by a human and has over 2200 pipes. It is handmade and even the cabinetry is made from 19th century wood. It is the nearest we have to being able to hear Bach's music as he himself heard it.

You can read more about the pipe organ here and even listen to it being played.

Happy Saturnalia

Hallelujah! - CALM

One of the most important pieces of legislation ever has been voted on by the House of Representatives. The "Commercial Advertisement Loudness Mitigation Act" or CALM has passed the House on a voice vote. This act requires that TV advertisements be no louder than the programs during which they appear.

Climate Change Emails

Those hacked climate emails prove global warming is hoax, right?

Bacteriophage Therapy History (Part 3)

Use of phage therapy in the USA declined drastically with the advent of antibiotic therapy. But this was not the case in Eastern Europe. The Eliava Institute, founded in 1923 in Tbilisi, Georgia, by Giorgi Eliava, continues to this day to research phage therapy. In fact, there is a Phage Therapy Center to this day in the Republic of Georgia that takes patients for phage therapy treatment.

There are hundreds of published research reports on phage therapy. A large number of these are to be found in non-English journals published in the former Soviet Union and Poland. Stefan Slopek, of the Laboratory of Bacteriophages, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, published a series of papers in the 1980's, on the effectiveness of phage therapy against infection with several different bacterial pathogens including multi-drug resistant bacteria. A review of the work was published by Slopek in 1987. Slopek reported that of 550 patients treated with phage therapy, "positive results were found in 508 cases (92.4%)". Most of these cases were infections with drug resistant bacteria.

More recently, at the same Institute in Poland, Gorski reported that "1307 patients with suppurative bacterial infections caused by multidrug-resistant bacteria of different species were treated with specific bacteriophages (BP)". And that, "BP therapy was highly effective; full recovery was noted in 1123 cases (85.9%)".

Reports concerning phage therapy of staphylococcal infections of the lung, sepsis in newborns, urinary tract infections, infections of surgical wounds, and eye infections have been published. Unfortunately, in many cases the trials were not completed in a manner to allow rigorous evaluation of the results.

Research on phage therapy does continue in the USA. In fact, rather than using the whole phage virus which can be attacked by the human immune system and in some cases by the bacteria themselves, a phage lysin can be used to attack the bacterial cell wall.

More information about phage therapy can be found at this Evergreen International Phage Biology Meeting website. An extensive list of the phage therapy literature can be found here.

Bacteriophage - Therapy History (Part 2)

Bacteriophages are viruses that can infect and destroy bacteria. This fact was actually used, prior to the discovery and widespread use of antibiotics, to treat certain infections.

Who discovered bacteriophages is the subject of debate. Most credit Frederick Twort (1915), an English bacteriologist, and Felix d'Herelle (1917), a French-Canadian microbiologist with the independent discovery of bacteriophages.

Frederick Twort
Felix D'Herelle

But in 1896 another British bacteriologist, Ernest Hankin, observed that water from the Ganges river in India had a marked inhibitory effect against Vibrio cholerae. Furthermore, he observed that the substance was susceptible to heat and could pass through a fine porcelain filter. The first phage was not visualized until 1939 by Helmut Ruska using an electron microscope.

D'Herelle used phages to treat dysentary and was probably the first to use phages therapeutically. In one experiment, he purified a phage preparation and ingested it himself to insure its safety. The next day he gave the preparation to a 12 year old boy suffering from severe dysentary. The boy's symptoms ceased after a single dose of the phage and he fully recovered from the dysentary.

The first published report of using phage as a therapeutic treatment was in 1921 by Bruynoghe and Maisin who used phage therapy to treat staphylococcal skin disease. Felix D'Herelle eventually started a commercial laboratory in Paris to produce phage preparation marketed to treat 5 different bacterial infections. The company later became L'Oreal.

In the USA in the 1940's the Eli Lilly Company manufactured phage preparations for human use. These preparations were specific for staphylococci, streptococci, E. coli and several other bacteria. It was a subject of debate of how effective these phage preparations were in treating infections.

Unfortunately (and fortunately) the large scale production of penicillin also occurred in the 1940's and commercial production of phages ceased in most of the world.

Bacteriophage (Part 1)

What are bacteriophage? Bacteriophages (or phages) are viruses that infect bacteria rather than eukaryotic cells. The word bacteriophage comes from "bacteria" and "to eat" because many phages literally destroy the bacteria they infect.

Bacteriophage T4 is a classic example of phage virus. It infects the E. coli bacterium. Below is a diagram of a T4 phage and an actual electron micrograph of the phage.
The T4 phage looks alot like the lunar lander doesn't it? The "legs" of the T4 phage allow for attachment to the E. coli host bacterium and the phage "tail" is hollow to allow for the injection of the phage DNA into the bacterium. You can see an animation of the T4 phage infecting a bacterium here.

Viruses have two different types of life cycles called lytic and lysogenic. The lytic life cycle is the more common type of life cycle used by viruses and it results in the destruction of the bacterium or cell. The below excellent diagram, from the U. of Delaware, shows the lytic life cycle of a T4 phage.
Basically, the bacterium is infected, the phage takes over the metabolic machinery of the bacterium, reproduces itself and destroys the bacterial host cell thus releasing more virus available to infect new host cells.

The lysogenic cycle is different and is pictured below.
In this phage "life style", the phage DNA is actually incorporated into the bacterial genome. This newly integrated phage DNA is referred to as a prophage. The advantage of this life cycle is that every time the bacterium divides, the DNA of the prophage is replicated along with the bacterial genome. At some time in the future, the prophage can be induced to enter the lytic phase where new phages are reproduced and the bacterial cell is destroyed, releasing the phage virions.

So phages are good because they infect and destroy bacteria. Well not so fast. Phages are also known to increase the disease-causing capability (virulence) of some bacteria. For instance, the toxin produce by Vibrio cholerae bacterium diarrhea and rapid dehydration of the infected person, is due to infection of the bacterium with CTX phage. The toxin which causes cholera is actually encoded by the phage genome and not the bacterial genome. It is possible that phage infection of bacteria could be responsible for the evolution of more virulent bacteria. Other toxins reported to be encoded by phages include shigalike toxin in some pathogenic E. coli strains, botulinum toxin, diptheria toxin and erythrogenic toxin. This is serious business because it may be possible for phage to transfer virulence genes from disease-causing bacteria to unrelated bacteria which normally do not cause disease. You can read more about this phenomenon here.

On Homosexuality, Civil Rights and Christian Judgement

It all started a few weeks ago with a letter to the editor of the Adirondack Daily Enterprise written by a very brave soul. The letter concerned gay marriage as a civil right. The letter generated 85 comments on the ADK website. What is surprising to me is the number of comments supporting the letter writer. I was not so surprised by the comments made by local homophobes.

A few days ago another letter to the editor was published in the ADK. This letter was written by a local bible-thumper and stated that homosexuals are sinners. As you might imagine (or maybe not) the letter has so far generated over 140 comments. The discussion rapidly devolved into whether what the bible says is worth the paper it is printed on. Interesting reading.

Many Cancer Treatments Not Cost Effective

There is an article in today's Washington Post with some information that I expect many people do not want to hear. The bottom line is that treatment for most cancers is ineffective and very expensive.

At the moment, there is a giant disconnect between patients, the cost of care and the clinical benefit of the treatment -- a disconnect that has caused us to lose perspective. When it comes to cancer care, we're not getting what we pay for.

But we are talking about someone's life! Yeah, well maybe spending thousands of dollars a month on ineffective cancer treatments might make you feel like you are doing something rather than nothing, but all that is really happening is....well, nothing.

How did we get to where we are in cancer treatment? In spite of the billions of dollars spent on the "war on cancer" we actually have no "evidence-based medicine" on which treatments are effective. Accepting this situation means, I guess, that maybe we will have "rationing" and "death panels" in some areas of medicine where treatments are just not effective. Maybe more time and money need to be put into counseling patients about their untreatable conditions rather than tens of thousands of dollars on the hope of a miracle cure.

Speaking of "death panels" read this. There is sometimes a limit on what an emergency room can do for you.