Wednesday, April 23, 2008

Encyclopedia Britannica Free for Bloggers

When I was young, I used to read Encyclopedia Britannica. No, not occasionally when I needed to write a book report, but from A to Z. Typically I use wikipedia or citizendium these days, but EB still has a certain nostalgia for me. I was happy to hear about this opportunity for bloggers.

If you’re a Web publisher—a blogger, webmaster, or writer—you can get complimentary access to the complete Encyclop√¶dia Britannica online. It’s a rich trove of reliable and high-quality information that you can use to check quick facts, research topics in depth, or just read to enjoy.

If this promotion succeeds, EB might end up being a major player again.

Herpes Virus as Therapy

Oncolytic viral therapy uses genetically-modified viruses to destroy cancer tumors. A recent blog article describes a novel treatment for human sarcoma tumors that combines "a herpes virus genetically altered to express a drug-enhancing enzyme with a chemotherapy drug." Physician and researcher Timothy P. Cripe of Cincinnati Children’s Hospital Medical Center said “Our study shows the chemotherapy drug cyclophosphamide (CPA) enhances the anti-tumor effectiveness of the oncolytic virus rRp450 in mice carrying aggressive human sarcoma, resulting in significant tumor shrinkage."

As a dsDNA virus closely associated with humans, Herpes is particularly suitable for oncolytic viral therapy. Genetically modified Herpes virus have been rendered non-pathogenic by removing the virulence genes.

The rest of the blog is pretty interesting and I recommend checking it out.

Photo from NCBI.

Tuesday, April 22, 2008

Are Viruses Alive?

I found this interesting web page regarding the biological status of viruses. It's part of a series of pages on Microbial Life - Educational Resources.

I recently claimed that whether viruses were alive or not was largely moot, and that "my belief is that living entities are those that evolve via natural selection, and surely viruses should be included in that category".

Ford Denison countered that, "computer viruses could evolve by natural selection." Are there computer viruses out there evolving by natural selection? That's a scary thought!

Photo: The expansive Sunset Lake of the Black Sand Basin is one of the largest thermal bodies of water in Yellowstone National Park.

Originally uploaded in Microbial Life.

Image 3630 is a 179 by 300 pixel JPEG
Uploaded: Jan27 05

Friday, April 18, 2008

Evolution at Rockefeller

The next few weeks are busy ones for the NYC evilutionary biologist. We have the World Science Festival from May 28-June 1. On May 6 and 8 the New York Botanical Garden is having a symposium on Darwin's Garden. And Rockefeller University is having a Symposium on Evolution May 1-2.

Thursday, April 17, 2008

Six Things Ben Stein Doesn't Want You to Know

Scientific American lists 6 prevarications from Ben Stein's Expelled.

In brief:
1. Stein quotes Darwin selectively to manipulate his message.
2. Ben Stein's speech to a crowded auditorium in the film was a sham.
3. Scientists were interviewed for film under false premises.
4. The "employee" fired from the Smithsonian was never actually employed there.
5. Science doesn't reject creationism because of atheism.
6. Not all evolutionary biologists are atheists as the movie claims.

What's more is that the movie pilfers intellectual property left and right.

See more on how Expelled completely misrepresents the scientific community.

Update: the NY Times calls Expelled "
one of the sleaziest documentaries to arrive in a very long time."

The movie opens tomorrow. I won't be going. If you go, be sure to bring your creationist bingo card. I'll buy lunch for the first person to get five canards in a row. From skeptico.

Darwin's Garden

For those of you in the NYC area or just passing thru, you may want to check out an interesting exhibit coming up at the New York Botanical Garden. It's called Darwin's Garden: An Evolutionary Adventure and is open between Apriil 25th - July 20th 2008.

"The cornerstone of the Garden-wide show is an exhibition of Charles Darwin's original manuscripts, field notebooks, plant collections, and other historical documents chronicling Darwin's progression from a boy with an interest in plants to an evolutionary botanist who revolutionized the world's view of life."

In the Haupt Conservatory, is a display that, "echoes the characteristic architecture of Down House. Just outside the model is a reproduction of the flower garden--bursting with primroses and other seasonal favorites—tended by his wife, Emma. Darwin's greenhouse, its benches lined with carnivorous plants, is nearby, not too far from the kitchen garden where Darwin grew food for his table and flowers for his experiments. Off in the distance is the orchard where Darwin created a “weed garden”--a plot of earth that he cleared and allowed to regenerate on its own so that he could observe natural selection in action."

In addition, a symposium moderated by Edward O. Wilson will be held in early May. The speakers include philosopher Michael Ruse; Rita Colwell, the former director of NSF; Barbara Schaal, vice-president of the National Academy of Sciences; and Ken Miller of Kitzmiller v Dover fame. I'll be attending both sessions if I can get tickets.

Drawing: Darwin's garden at The Mount in 1866.

Wednesday, April 16, 2008

Bacteriophage in the Blogs

It's always nice to read about phages in the news, but I was especially pleased to find a blogger that shares my passion for phages.

I give you Blogging for Bacteriophages.

The latest post covers the difficulties inherent in viral taxonomy. I recently covered this topic in my microbiology course, where I discussed the mosaicism of viral genomes. Another issue raised by the author regards whether viruses are living or non-living. It's a question I am heartily sick of. My belief is that living entities are those that evolve via natural selection, and surely viruses should be included in that category.

Photo from Mimiviridae

Thursday, April 10, 2008

This Week's Citation Classic

This week's citation classic is Haldane J. B. S. 1935. The rate of spontaneous mutation of a human gene. J. Genet. 31, 317–326.

John Burdon Sanderson Haldane was the quintessential eccentric British gentleman, but he made seminal contributions to evolutionary biology as a member, along with E.B. Ford, Sewall Wright and R.A. Fisher, of the Modern Synthesis.

Haldane's interest were broad and wide ranging. In addition to laying the foundations of quantitative evolutionary theory, he was one the first to estimate the mutation rate among humans. Haldane used estimates of the frequency of hemophiliac men in London as a means to quantify the frequency of the x-linked recessive allele responsible for hemophilia.

"If x be the proportion of haemophilic males in the population, and f their effective fertility, that is to say their chance, compared with a normal male, of producing offspring, then in a large population of 2N, (1–f )xN haemophilia genes are effectively wiped out per generation. The same number must be replaced by mutation. But as each of the N females has two X-chromosomes per cell, and each of the N males one, the mean mutation rate per Xchromosome per generation is 1/3(1–f )x, or if f is small, a little less than 1/3(x). Hence we have only to determine the frequency of haemophilia in males to arrive at the approximate mutation rate."

From the available data, Haldane deduced that the mutation rate probably exceeded 10^-5 and suggested between 1 in 100,000 and 1 in 20,000 as a plausible estimate. How close was he? Most estimates of the mutation rate in humans are on the order of 10^-5.

But Haldane wasn't just an armchair scientist.

"One experiment involving elevated levels of oxygen saturation triggered a fit which resulted in him suffering crushed vertebrae. In his decompression chamber experiments, he and his volunteers suffered perforated eardrums, but, as Haldane stated in What is Life, 'the drum generally heals up; and if a hole remains in it, although one is somewhat deaf, one can blow tobacco smoke out of the ear in question, which is a social accomplishment.'" From wikipedia.

In another experiment, he drank hydrochloric acid (HCl) to observe its effects on muscle action.

Haldane's penchant for futuristic ideas and forward thinking rivals Jules Verne. Here are a few ideas that originated from his polymathic brain:

-scientific feasibility of “test-tube babies” brought to life without sexual intercourse (which his friend Aldous Huxley wrote about to great effect in Brave New World.

-the "primordial soup" chemical origin of life in a "hot, dilute soup."

-silicon-based lifeforms

-a hydrogen-based renewable energy economy based on a network of hydrogen-generating windmills.

His famous essay Daedalus contains more of his futuristic thinking.

On Being the Right Size is one of my favorite short essays.

Why I am a Materialist was tremendously influential.

In addition to being an amazing scientist, Haldane was a tremendous wit. His sayings include:

-I have no doubt that in reality the future will be vastly more surprising than anything I can imagine. Now my own suspicion is that the Universe is not only queerer than we suppose, but queerer than we can suppose.

-My practice as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel, or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world.

-An inordinate fondness for beetles. Reply to theologians who inquired if there was anything that could be concluded about the Creator from the study of creation.

-Four stages of acceptance:
(i) this is worthless nonsense;
(ii) this is an interesting, but perverse, point of view;
(iii) this is true, but quite unimportant;
(iv) I always said so.

-No, but I would to save two brothers or eight cousins. Reply when asked if he would give his life to save a drowning brother.

-I will give up my belief in evolution if someone finds a fossil rabbit in the Precambrian.

From Wikiquote.

Monday, April 7, 2008

World Science Festival 2008

If any of you are in the NYC area, you may want to check out the World Science Festival. Many of the events are taking place at the CUNY Graduate Center and NYU.

Here is a list of participants