The Giant's Shoulders X

The latest edition of The Giant's Shoulders is up at Stochastic Scribbles. I particularly like the Open Helix's pick. It's an article on computational sequence analysis ... from 1962!

Belated Birthdays

The Evilutionary Biologist is now 5 days into its second year of existence.

I was late last year too.

If I ever get a cake, I'd like one like the one Arthur Kornberg got. It has some Rube Goldberg action going on there. Check out the hi res version.

Irony

New Scientist published an editorial by Simon Baron-Cohen on media distortion of Science.

Is this... uhh... the same New Scientist that claimed Darwin Was Wrong on the cover?

Larry Moran, Jerry Coyne and PZ Myers among others called them out on this.

Fight Infection with Infection

There was a recent article in Popular Science magazine on bacteriophage therapy. Scientists, including d'Herelle the discoverer of phages, have long recognized the value of phage therapy. In fact, the protagonist of Sinclair Lewis's novel Arrowsmith (publ. in 1925) cured the residents of a fictitious Caribbean island of plague using phage.

Despite its early popularity, phage therapy never quite caught on in the West. Most speculate that the arrival of antibiotics precluded their widespread acceptance, except in the former Soviet Union (e.g. Georgia).

The article discusses some of the advantages of phage therapy.

They prey only on bacteria, never human cells, they rarely spread from person to person, and, perhaps most important, bacteria have trouble becoming immune to them. As living organisms, phages are constantly changing and adapting in tandem with their host bacteria to kill them more effectively. Phage therapy could therefore eliminate the vicious cycle in which bacteria evolve resistance to antibiotics, necessitating the development of new, even more powerful drugs, at which point the process begins all over again.

I'm skeptical that phages rarely spread from person to person (but the research on this is minimal if not nonexistent), and bacteria DO become immune. In fact, bacteria frequently win arms races with phage in coevolution experiments.( A good example is the trap cells I used in my virus trap experiments. Several attempts to generate phage able to infect these trap cells have failed). Nonetheless, the article is correct in that, unlike antibiotics, phage evolve. This is a powerful tool to generate new phage variants.

Unfortunately, as the article points out, this precise point makes it difficult for phage treatments to past muster at the FDA.

Although there have been no reports of adverse effects resulting from mutations, phages that don't normally nest inside the human body could potentially swap genes with other phages that do and produce foreign proteins that trigger an immune reaction. And it's impossible to say exactly how a virus might mutate when exposed to different bacteria, says Paul Sullam, a microbiologist at the University of California at San Francisco.

FDA regulation, which some would say is excessive, has slowed phage therapy research in the US.

"People in this country have a right to be incensed that we have a very different situation here than in Europe with regards to phage," says Betty Kutter, a phage researcher at Evergreen State College. "Our whole regulatory environment has been one major thing that has slowed people down."

So where does one go when they have an uncurable infection? The Eliava Institute of of Bacteriophage, Microbiology and Virology.

Randy Wolcott calls Eliava the "mother ship of phage research," a worldwide Mecca for people suffering from antibiotic-resistant infections. Only it doesn't look like the sort of place you'd want to go with a health problem. When Wolcott visited to hunt down alternatives for his patients, the four-story facility bore a closer resemblance to a neglected sanatorium. The walls were unpainted, the rooms were dark, and the equipment looked like museum pieces. "The conditions were abysmal," he says. "Yet the science is amazing."

Perhaps, as Rockefeller's Vincent Fishetti says , the way to go is phage-based therapy.

This distinction might seem arcane to nonbiologists, but in Fischetti's mind, it's a crucial one. While Wolcott sees phages as a major therapeutic coup, Fischetti sees them as merely an intermediate step toward a new generation of even better bacteria-fighters. He contends that the uphill regulatory battle phages face, as well as the risk of mutations, make them too big a gamble for American drug companies. "Phages are going to be a boutique treatment, nothing more," he says. So he is taking an alternative approach, purifying the phage to extract the lysin, the enzyme it uses to dissolve the bacterial cell wall and kill the bacterium. Having observed that lysins were the phages' "active ingredients," Fischetti aims to harvest the lysins from them and turn them into stable antibacterial drugs. If successful, he could accomplish a double feat previously thought impossible: getting the bacteria-fighting benefits of phages to patients, while doing an end run around the regulatory Rube Goldberg machine that researchers like Wolcott face.

Incidentally, I am currently hosting a doctoral student from the Eliava Institute, Sophie Rigvava, who is characterizing the phages of Enterococcus faecalis in my laboratory.

I've posted a few times on phage therapy here, here, here and here.

Photo: Phages [in orange] prey on a lone bacterium, using prong-like proteins to anchor themselves to the cell before they inject their genes into it Lee D. Simon/Photo Researchers

Darwin Rocks

A small team of evolutionary ecologists from Tuebingen, Germany, just finished a rock music clip about evolution which is called "Struggle for love", together with a computer program that allows the user to "select and evolve" music tunes following biological principles. This program was also used to generate the underlying tunes for the song.

All this is the result of a one-year project that was generously supported by the VolkswagenFoundation (www.volkswagenstiftung.de) following a creativity contest called "Evolution Today". We cooperated with composers, musicians, film-makers, informaticians and a whole series of creative students, about one hundred in total!

Both the clip and the program are meant to attract the attention from non-biologists and make them think and talk about evolution. Hence, if you like it, please feel free to share it with your friends, relatives and students.

The Darwin Rocks! Team:
Johannes Faber
Suska Sahm
Gregor Schulte
Nico Michiels

Science journalism: Supplanting the old media?

This week's issue of Nature has an interesting article on scientific blogging. Geoff Brumfiel asks whether science blogging will replace a declining scientific journalism.

In part because of a generalized downturn, especially in newspaper revenues, the traditional media are shedding full-time science journalists along with various other specialist and indeed generalist reporters. A Nature survey of 493 science journalists shows that jobs are being lost and the workloads of those who remain are on the rise (for full results see http://tinyurl.com/c38kp6). At the same time, researcher-run blogs and websites are growing apace in both number and readership. Some are labours of love; others are subsidized philanthropically, or trying to run as businesses.

I think diversity in media is a great thing. Throughout the 80s and 90s, it was apparent that the media was coming under the control of a few large corporations e.g. the News Corp, Time Warner etc. Controlling the media means controlling the message. The rise of the internet makes monopolizing the means of communication more difficult.

However, the article cites the example of Robert Lee Hotz, a science journalist for The Wall Street Journal, who doubts that blogs can fulfill the additional roles of watchdog and critic that the traditional media at their best aim to fulfill.

I seriously doubt this. In my opinion, investigative journalism is best a bottom-up enterprise. With the advent of venues such as wikileaks and reddit, anyone can be an investigative journalist.

Others say that science reporting will fail to reach a broad audience.

Press releases and blogs will not find the same broad audience once served by the mass media, says Peter Dykstra, who was executive producer of CNN's science, technology, environment and weather unit until it was closed down last year. Now at the Woodrow Wilson International Center for Scholars, an independent think tank in Washington DC, he says that science and environment news will be "ghettoized and available only to those who choose to seek it out".

So citizens will have to be active consumers of media rather than spoon fed "the news" during a 6:30 PM nightly broadcast? Oh catastrophe!

The idea that science journalism will suffer because major newspapers and tv stations are dropping coverage is ridiculous. What was that coverage anyway?

"You get a press release that is slightly rehashed by somebody in the newsroom and it goes in the paper! It's wrong, its sensationalist, it erodes the public trust in scientific endeavour," says Bora Zivkovic, author of A Blog Around the Clock on ScienceBlogs and an online community manager for the Public Library of Science journals. Myers takes a similar view. "Newspapers realize that they can get their audience by peddling crap instead of real science," he says. Not surprisingly, those who came to blogging from journalism — such as Carl Zimmer, who writes for a range of publications, including The New York Times, and blogs at Discover — tend to disagree. But Larry Moran, a biochemistry professor at the University of Toronto, Ontario, who blogs at Sandwalk, seemed to speak for many bloggers when he recently wrote "Most of what passes for science journalism is so bad we will be better of [sic] without it".

If anything blogging has enhanced scientific coverage. PZ Meyer's Pharyngula is getting 500k hits per week. The best thing is that scientists are generating news, reporting it, commenting on it and interacting with the general public in a manner that was impossible pre-web. Talk about tearing down the Ivory Tower! Readers can ask questions of actual scientists in the comment box, receive expert answers and opinions, and the end result will likely be a more science literate, engaged society.

The Giant's Shoulders #9

"The Giants' Shoulders" is a monthly science blogging event, in which authors are invited to submit posts on "classic" scientific papers. Information about the carnival can be found here. The last Giants' was hosted at Greg Laden's Blog. The next issue will be hosted at Stochastic Scribbles.

The name "The Giants' Shoulders" refers to a passage in a letter from Issac Newton to his rival Robert Hooke dated February 5, 1676: "What Descartes did was a good step. You have added much several ways, and especially in taking the colours of thin plates into philosophical consideration. If I have seen a little further it is by standing on the shoulders of Giants." It's a bit of a taunt, really. Oh if I seem smarter than you, it's because I understand the work of our forebears much better than you. Newton and Hooke were famously at odds.

The phrase is believed to significantly predate Newton. Wikipedia attributes it to Bernard of Chartres based on a passage in 1159 in John of Salisbury's Metalogicon.

"Bernard of Chartres used to say that we are like dwarfs on the shoulders of giants, so that we can see more than they, and things at a greater distance, not by virtue of any sharpness of sight on our part, or any physical distinction, but because we are carried high and raised up by their giant size."

This month we celebrate the following works of genius. I've posted them in the order in which they were received.

1. "The irreducibility of the space of curves of given genus" by Pierre Deligne and David Mumford in 1969 was submitted by Charles Siegel of Rigorous Trivialities. The significance of the paper is, as Siegel writes, "Aside from the great achievement of solving this long standing open problem, the real value here is that Deligne and Mumford made algebraic geometers start taking the notion of stacks seriously, because they could be used to solve actual mathematical problems. Nowadays, stacks are essential to large branches of mathematics research."

2. Quantum Science Philippines submits Einstein's 1905 article on E = hf or The Equation That Changed The World. Here Einstein claimed that light was not only emitted in integral units or bundles of energy but it was also absorbed in such bundles - bundles that came to be known as photons.

3. GG of Skull in the Stars serves up this goodie on the unification of light and magnetism: “Experimental Researches in Electricity,” published in the Philosophical Transactions (vol 136, pp. 1-20) in 1846. GG writes, "The more I read of Michael Faraday’s work, the more I am in awe of the scientist’s insights and abilities." We all should be.

4. My own contribution to this list is comes from the Venerable George Williams who, in the words of no less a luminary than Stephen Pinker, "was instrumental in making natural selection an intellectually rigorous theory". In 1959 Williams published, "Pleiotropy, natural selection, and the evolution of senescence. Evolution, 11: 398-411" thus providing one of the first intellectually rigorous hypotheses for the question of "Why Do We Get Old and Die?" Click here to find out Why!

5. Kylie Sturgess of PodBlack Cat cites Expert Performance. Its Structure and Acquisition by K. Anders Ericsson and Neil Chamess (1994) and writes about talent versus training debate. Are poets born that way or do they become poets after years of hard work? She concludes, "I think research demonstrates how some Expert Performances were indeed gained from Structure and Acquisition. And I didn’t even have to go much further than the Romantic era poetry." Read more here.

6. A fascinating article was submitted by Scicurious of Neurotopia, Philip, APW. "On the nature of death" Philosophical Transactions of the Royal Society of London, 1834. As Scicurious writes, "Dr. Philip undertook in this publication to explain the nature of death. Not what happens after death. He was very specific that he would not cover anything "metaphysical". His concern was, well, with HOW people die."Phillip realized that breathing was critical to staying alive, thus was the first to attempt "artificial resuscitation".

7. Materialia Indica's Guru serves up this classic in materials science: L. Vegard. 1921. Die Konstitution der Mischkristalle und die Raumfüllung der Atome. Zeitschrift für Physik. The popularity of the law [stems from] the fact that the lattice parameter change with concentration is one of the important pieces (and, as Denton and Ashcroft note in their paper, rather fundamental piece) of information in understanding many interesting properties of alloys — for example, the wiki entry on the law mentions the determination of semiconductor band gap energies — and, a linear relationship is the minimum that one needs to assume.

8. Greg Laden, biological anthropologist extraordinaire and author of Greg Laden's Blog, thinks we all should read Mark Pagel (2009). Natural selection 150 years on Nature, 457 (7231), 808-811 DOI: 10.1038/nature07889. Pagel addresses the question: How has Darwin's theory of Natural Selection fared over the last 150 years, and what needs to be done to bring this theoretical approach to bear as we increasingly examine complex systems, including human society?

9. Underemployed, grumpy, aging liberal John J. McKay of Archy has been busy lately and submitted four posts about mammoths: Fragments of my research - VII, Fragments of my research - VIII, Mastodon nightmares and A mammoth literary mystery. There's a wonderful melange of Eurasian history, skullduggery and entertainment; very much worth a read.

10. The eternal student John Wilkins of Evolving Thoughts writes about Polly Winsor's article in Taxon. Winsor thinks taxonomy was critical for Darwin's Big Idea; "she holds that what set up Darwin's problems was the hierarchical arrangement of organisms in the Linnean system that had effectively swept all before it in the early 19th century." Fascinating article.

11. Grad student Jeremy Yoder of Denim and Tweed cites Verne Grant's 1949 discovery of cleverly indirect evidence that pollinator isolation shapes the evolution of flowers. More than fifty years after Grant's study, pollinator isolation is a well-established mechanism for speciation. And the principle that Grant proposed, that increased divergence in floral traits is a sign of pollinator isolation, is still very useful.

12. And our last post is from Providentia who writes about psychologically profiling Hitler. The work was done by the Office of Strategic Services (the predecessor of the CIA) and was published here. (It's no longer top secret).

That's it for this month's edition of The Giant's Shoulders. Tune in next month at Stochastic Scribbles.