Soil May Be More Complex Than We Ever Thought

I am really excited about this press release (courtesy Science Daily), detailing how researchers at Cornell University used X ray spectroscopy to examine soil organic matter at the nano-scale. For reference, our sense of scale is generally in the meter to centimeter (0.01 m) range. Then there are millimeters (0.001 m), micrometers (0.000001 m; a typical bacterium is 1 to 2 micrometers), and then nanometers (0.000000001 m; a typical virus is about 50 to 100 nanometers in diameter). So, we are talking extremely fine scale: in fact, these are the highest resolution images produced of soil to date.

What the research team found was that while soil organic matter might look and behave as a fairly homogenous substance at typical human scales, even from soil to soil, organic matter takes on entirely different properties at the nano-scale.

"There is this incredible nanoscale heterogeneity of organic matter in terms of soil," said Johannes Lehmann, a Cornell associate professor of crop and soil sciences and lead author of the study. "None of these compounds that you can see on a nanoscale level looks anything close to the sum of the entire organic matter."

For me, these observations have implications for microbial ecology. The materials observed by the science team serve as food and energy sources, as well as physical substrates for attachment for a variety of bacteria. So if the distribution of food and niche space is this diverse at the nano-scale, imagine the incredible diversity of life forms and their bizarre survival strategies to be found in a single gram of soil! There can be completely different processes taking place, mediated by completely different species of organisms across distance scales smaller than the breadth of a baby’s hair. Before you get too excited, let me emphasize that such ideas about soil have been around for some time - they are not original by me, nor new. But, even if they seem to be completely rational and logical in the absence of such hard evidence, such fine scale observations provide critical support for these ideas. All of these things working together, the living and non-living components functioning in rich combinations at extremely small scales, give us soil. And soil, in turn, has given us food, building substrates, polymers, antibiotics, and more. Truly, the whole is greater than the sum of its parts.

Laser Elevator

I have one of those friends who is constantly sending me links: photos, videos, articles, you name it. Most of the time it just gets deleted - I mean, who has time to look at 20-30 links a day, every day, on top of the Internet time wasting they already had planned? But I digress.

One of the recent links was a web-comic from the site xkcd. The comic was OK, but what I found even more interesting - well, WAY more interesting - was this treatise on solar sails and laser elevators. I love the diagrams (definitely my style of explaining scientific concepts) and the way the whole thing is explained. I hope you enjoy it, too.

How the Bacteriophage got its Tail...?

Disclaimer: All images in this post are from the ICTV picture gallery and copyrighted by their respective owners. This website is not for profit. Please don't sue me.

Bacteriophages, or simply “phages,” are viruses that infect prokaryotes – bacteria and archaea. Phages come in many shapes and sizes, including filamentous Inoviridae such as phage fd pictured below

and icosahedral Microviridae such as phi-X 174 shown here:

Phages that infect hyperthermophiles seem to be even more bizarre, including bottle- and lemon-shaped particles. But your garden-variety bacteriophages also include the only classes of virus particles known to have “tails.” The tails are tube-like structures protruding from one of the capsid vertices, often with additional architecture like base plates, spikes, or thin fibers located at the tips. Phages with tails can be classified into three categories:

Podoviridae – short, non-contractile tails (above);

Myoviridae – sheathed, contractile tails(above);

or Siphoviridae – long, flexible, non-contractile tails (above).

These tails are non-motile, so they don’t function as a means of locomotion. The tail tips (and the more elaborate architecture found there) mediate the infection process upon contact with the appropriate surface receptor on the host cell, sort of like a key in a lock. For example, phage lambda, a Siphoviridae, uses the maltose receptor on E. coli as its gateway. Normally, E. coli uses the receptor to gather the sugar maltose from its suroundings, but lambda has co-opted this natural feature of its host cell surface biochemistry to its own purposes.

My question is this: why so many different kinds of tails? And why have a tail at all? The only phages for which tails seem necessary are the Myoviridae. Due to their contractile nature, the tail apparatus is essential in penetrating the cell membrane and in passing the viral nucleic acid into the host cell. But what about these other, non-contractile tail types? Rather than at the end of a tail, why not simply place the receptor recognition complex on one of the vertices – problem solved. Some of the Siphoviridae tails can be over 200 nm long. This seems like a liability, especially considering that if a phage particle loses its tail, it is rendered “dead” or inactivated. So, beyond the Myoviridae, what is the evolutionary advantage to a phage tail, and what is the advantage of the different types? There has to be one, or the tails wouldn't still be around. Are they essential in packaging the viral DNA? In chaperoning viral DNA into the host cell during infection? Are they useful in extending the “reach” of a given phage particle? I am still looking for reasonable answers. If you have any information on the subject, feel free to chime in!

David Baltimore across the Internet

David Baltimore is quite an accomplished scientist: 1975 Nobel laureate in physiology or medicine (but which one, dammit!), basically for the discovery of the reverse transcriptase enzyme; president of the American Association for the Advancement of Science; president of CalTech in Pasadena; and the list of honors goes on. Well, you have the Internet right there if you want to find out; I'm not going to catalog all his field day awards here. Anyway, being the virus scholar that I am, I was familiar with Baltimore's Nobel research, and his classification scheme for viruses based on their relationship to mRNA. More recently, I knew he was seriously involved in research to develop an HIV vaccine. This PBS Frontline interview dating from May 30, 2006 provides some excellent background, both on the man and the mission.

Lately, there has been a small explosion of Internet activity surrounding David Baltimore. First up, this piece from the Feb. 18th NY Times. During a special session at the AAAS annual meeting, Baltimore openly criticized the Bush administration's repressive tactics and exploitation of science to support its own policies.

"It's no accident that we are seeing such an extensive suppression of scientific freedom," he said. "It's part of the theory of government now, and it's a theory we need to vociferously oppose." Far from twisting science to suit its own goals, he said, the government should be "the guardian of intellectual freedom."

Huzzah! Now, if we could only have embraced that zeitgeist from the beginning of these eight years of hell. But I digress. On the Feb. 1 installment of NPR's Talk of the Nation, Baltimore was the guest, and weighed in with similar sentiments: restoring respect to scientists and restoring funding to important scientific endeavors. We really have fallen from grace, particularly if one were to compare the stature of today's scientists with those of the likes of Max Delbruck, John von Neumann, or Francis Crick. Of particular interest to me were the rarely heard (anymore) topics of space exploration and population control. Asimov would have been pleased that these were brought up - though severely disappointed at how little we've done in either sphere at this point. The program can be heard here and is about 25 minutes in duration.

Finally, Good news, everyone! Baltimore was also quoted as more-or-less acknowledging defeat in the quest for an HIV vaccine.

Prof Baltimore added: "Against that background, the vaccine community has tried its best. It initially made an attempt to control the virus through antibodies, but found that the virus was quite solidly protected against that mode of attack. It then switched to trying the other arm of immune protection, the cellular immune system. That has never been mobilised to protect against a virus because it was not through to be powerful enough. Sure enough, in full-scale clinical trial the first such candidate vaccine gave no protection.''

He said the scientific community was still doggedly trying for a cellular vaccine breakthrough, as well as persevering with antibodies. "But the community is depressed because we see no hopeful route to success,'' said Prof Baltimore. He added: "Some years ago I came to the conclusion that our community had to seriously undertake new approaches or we might find ourselves with a world-wide epidemic and no effective response. That is just where we are today.''

But not to worry: blast away that dejection with this spirited response from another science blogger I have only recently discovered - and someone who is likewise interested in viruses! So while this may be the end of the road for the particular approach headed up by Baltimore and colleagues, clearly we have yet to exhaust all our options. That, and the determined attitude of scientists like ERV, is truly good news.

A man, a plan, a canal

My plan here is to discuss science related material: everything from recent publications and media hype to my biased observations on the processes of research, publication, and science education. As a goal, I'd like to update the site two or three times a week, but even that may be pie in the sky. We'll find out soon enough, like all good organic chemistry students, that the experimental yield is usually miserably lower than the theoretical yield.

Up and Running

I've been meaning to start up a science blog for some time now. I used to co-write at another site which is now defunct. Things got too busy I guess... but the absence of an outlet through which I could share my thoughts, even if only to the five friends who actually read my material, has weighed on me more than I thought possible. So, it is with great pleasure that I sit down at the keyboard once again to air my opinions and place my ignorance on display.

In this pilot episode of Good News, let's talk about space travel, why not? Actually, I'm going to let George Dyson do the talking courtesy of TED. The TED website (which stands for Technology, Entertainment, Design) is really something else... like YouTube, only smarter. Props to Greg Laden for digging up the link in the first place.