Showing posts with label Cambridge. Show all posts
Showing posts with label Cambridge. Show all posts

June 05, 2008

Progress in Abiogenesis: Protocells Capable of Replicating DNA Without Enzymes

This story goes in the bin marked "Woa!"

A Harvard research team led by Jack Szostack has created protocells in the laboratory made from non-living components. These very primitive, cell-like structures have an outer membrane composed of nothing more than fatty acids. The membrane can allow nucleotides to enter the cell from outside where they can be assembled into DNA without the need for the cell to synthesize any enzymes at all. It's a chemical process that probably mimics an early step in the rise of life on earth.

While we don't know for sure if this is how it all began, this discovery is at the very least a good possibility of how the first living organisms came into being based on relatively simple physical laws.

A New Way to Think About Earth's First Cells

A model protocell containing DNA; click the image for more informationA team of researchers at Harvard University have modeled in the laboratory a primitive cell, or protocell, that is capable of building, copying and containing DNA...

The protocell's fatty acid membrane allows chemical compounds, including the building blocks of DNA, to enter into the cell without the assistance of the protein channels and pumps required by today's highly developed cell membranes. Also unlike modern cells, the protocell does not use enzymes for copying its DNA.

Supported with funding from the National Science Foundation and led by Jack W. Szostak of the Harvard Medical School, the research team published its findings in the June 4, 2008, edition of the journal Nature's advance online publication...

When fatty acids are in an aqueous environment, they spontaneously arrange so that their hydrophilic, or water-loving, "heads" interact with the surrounding water molecules and their hydrophobic, or water-fearing, "tails" are shielded from the water, resulting in the formation of tiny spheres of fatty acids called micelles.

Depending upon chemical concentrations and the pH of their environment, micelles can convert into layered membrane sheets or enclosed vesicles...

When the team started its work, the researchers were not sure that the building blocks required for copying the protocell's genetic material would be able to enter the cell.

"By showing that this can happen, and indeed happen quite efficiently, we have come a little closer to our goal of making a functional protocell that, in the right environment, is able to grow and divide on its own," said Szostak...
The image below links to an animation that demonstrates how micelles (the fatty acid membranes mentioned above) are formed and change at different pHs:
Amazingly cool stuff, this. The mystery of how life began becomes less and less a mystery as time and science progress. Given a few fatty acids and some chemicals, including liquid water, it seems more likely than not that life or something very much like it is almost bound to spring up. Once there are micelles, given enough time things come into being that look a lot like your cells!

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May 12, 2008

Irreligious Things to Do in Massachusetts: Humanists and Skeptics

Tomorrow at 7:00 PM, the Greater Worcester Humanists will be meeting at the Unitarian Universalist Church at 90 Holden Street to discuss Religion and Politics in an Election Year. There will be a panel discussion and QA session. Panelists for the meeting are:

  • Rev. Richard Simpson, Rector of St. Francis Episcopal Church in Holden
  • Fr. Frank Scollen, Priest at St. Peters Catholic Church in Worcester
  • Rev. Aaron Payson, Minister of the UU Church in Worcester
  • Mr. Tahir Ali, Public Affairs Rep. of the Worcester Islamic Mosque
  • Mr. David Niose, President of the Greater Worcester Humanists.
  • Moderator: Rev. David Miller, Minister Emeritus of the UUC
GWH has also made available video from the last meeting on April 8. The speaker, zoologist Abigail Hafer of Curry College, gave a talk entitled "Unintelligent Design." The video is in three parts:

On Monday, May 26, it's time for another meeting of Boston Skeptics in the Pub. The meeting this time will be at Tommy Doyle's in Harvard Square, which is at 96 Winthrop Street, Cambridge. The speaker will be Patty Pieniadz former director of Narconon Connecticut, who left the Cult of Scientology after 27 years of membership.

Both of these events are free of charge, so if you're within range of Worcester and Cambridge, c'mon out and get rational and/or skeptical and/or drunk (at least at the Boston Skeptics meeting; leave the brewskis at home for GWH).

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May 09, 2008

Yesterday's Festivities: Phylogeny Symposium and Such

Yesterday was consumed, happily enough, by attending the Plant Biology Initiative symposium at Harvard. As it was entitled Phylogeny Informs Biology, it probably comes as no surprise that the theme of the day was the many ways in which phylogenetic techniques are being applied to modern biology and the findings that are being produced because of this.

Traffic was awful and caused us to arrive a bit late which made us miss the opening remarks and the very beginning of Debashish Bhattacharya's seminar on endosymbiosis and the origins of plastids in eukaryotic cells. Nonetheless, I found it the most interesting session of the day (not to take anything away from the other presentations, I just find the topic particularly interesting). Erika Edwards presented her research on the application of phylogenetic techniques in sorting out the question of the importance of C3 vs. C4 photosynthesis schemes in grasses are involved in atmospheric carbon cycling through the investigation of biases in stable isotope utilization. After the first break, Lee Taylor presented on orchids of genus Corallorhiza, a devious bunch of plants that have gone from being a mutualist with mycorrhizal fungi to being a predator. In this genus, the plants have given up producing leaves and roots and the like and instead have taken to eating the hyphae that provide mineral nutrients in exchange for photosynthate in other orchids-fungus relationships. They're nasty things if you're a hapless fungal symbiont! In this instance, the driving evolutionary force is a jump between Thelephoraceae and Russulaceae, one which forms very neat clades under phylogenetic analysis. Again, Taylor's talk was particularly interesting to me because Thelephoraceae is a sister group to the polypores. Next up, David Hibbett spoke about automated taxonomy and particularly a program called MOR, which is currently under development.

The Harvard folks were very generous with lunch. Yes, they gave us sandwiches, but these were some particularly good sandwiches. My lab and members of the Pringle lab split off for a mycological luncheon in the herbarium. I learned that one of the graduate students in that lab is also doing work involving polypores, though she's looking at community structure. We'll probably be collaborating on some things, swapping specimens and collecting and the like. Funny how our paths keep crossing; I first met her in Oakland in 2000 or 2001, and now here we are on the other side of the country overlapping our work on clades that not many others are engaged with lately. Near the herbarium I noted the first mushroom fruiting bodies of the season, a number of very robust Pholiota, and now am particularly inspired to go collecting this weekend. It's a sign, I tell you!

After lunch, Susanne Renner spoke on the application of phylogeny to the question of the biogeographical diversification of plants, a session which ended with her declaration of the death of vicariance hypotheses in favor of tremendous pools of seeds limited not by dispersal but establishment. Then it was back to the grasses with Caroline Stromberg who spoke on her work using phytoliths to date the origin and diversification of grasses; it looks like they were already around by the end of the Cretaceous, pushing back their age by several million years beyond current estimates. Finally, the day's presentations ended with Michael Donoghue's talk on the application of phylogenetic analysis in resolving the evolutionary history of angiosperms, particularly Dipsacales. He also gave the concluding remarks before the symposium ended and the reception began. Donoghue is a very engaging and entertaining speaker and certainly was a good remedy to the sleepiness induced by the sporadic air conditioning in the room in which the symposium took place.

When all is said and done, it's interesting to see how large a role the reconstruction of evolutionary history plays in diverse aspects of biology and how it unites mycology, plant biology, paleontology and other such disciplines. As John Timmerman pointed out based on his attendance at an entirely different symposium, there really are controversies in evolutionary biology, but they're about the specifics, not about evolutionary theory itself. The theory, in fact, is what allows us to discover the evidence that resolves the controversies in evolutionary history, the specifics of what happens. The controversies we heard about yesterday — from whether or not the biogeographical history of grasses was driven by the rise of ungulates to whether the Cucurbitae originated in Africa or Asia — are questions for which evidence can be discovered, and not just when someone happens to find a fossil. Evolutionary biology in general is the basis upon which these histories can be reconstructed and resolved using molecular characters and biogeographical evidence. What's happening in phylogeny these days is really pretty amazing stuff for those who can make some attempt to keep up with it.

In fact, all anyone can do is make an attempt. There's so much new discovery and so much happening in general that it's probably not possible for anyone to stay on top of all of it. Still, one must make some attempt. Even a small fraction is a lot of knowledge. Anyone who says that there's "no evidence" for evolution can be accurately assessed as someone who refuses to look for any by even doing so much as reading a paper every so often.

In his concluding remarks yesterday, Michael Donoghue said that these were exciting times. He's right, but maybe a bit conservative in his verbiage. I'd call them frenetically hyperactive times, exciting in proportion to their subject matter to the same extent that jumping out of an airplane is proportionate to pedaling a tricycle.

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May 03, 2008

Evolution in Cambridge: Free and Open Symposium at Harvard

Need something to do this Thursday? Going to be close to Cambridge, MA and itching to catch up on the latest research in plant evolution, plant-fungus interactions and global biome change? Of course you are!

The Fourth Annual Plant Biology Symposium will be held on Thursday, May 8 at Harvard. It's free and open to the public. From the website:

A wealth of new information, from whole genome sequences to inventories of the earth's biota, is rapidly transforming biology. Simultaneously, ongoing progress in resolving phylogenetic relationships among the more than 1.7 billion species in the tree of life provides the framework in which these data can be used to address long standing questions in plant biology. The 4th Annual Plant Biology Symposium at Harvard is aimed at highlighting the exciting ways in which phylogenies are being used in a wide range of studies, from global biome change to endosymbiosis.
Click the graphic below for more info:

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April 17, 2008

Edward Lorenz Passes: Butterflies Observe Moment of Not Flapping

Edward LorenzEdward Lorenz, the father of Chaos Theory whose ideas revolutionized thinking about dynamic systems across every discipline one can name, passed away yesterday at age 90. His ideas marked a revolution in the sciences on par with Einstein and Newton. Suffice to say that mankind's collective intelligence declined just a few points at the moment of his death — strongly supporting his theories, ironically enough.

Edward N. Lorenz, a Meteorologist and a Father of Chaos Theory, Dies at 90

Edward N. Lorenz, a meteorologist who tried to predict the weather with computers but instead gave rise to the modern field of chaos theory, died Wednesday at his home in Cambridge, Mass. He was 90...

In discovering "deterministic chaos," Dr. Lorenz established a principle that "profoundly influenced a wide range of basic sciences and brought about one of the most dramatic changes in mankind's view of nature since Sir Isaac Newton," said a committee that awarded him the 1991 Kyoto Prize for basic sciences.

Dr. Lorenz is best known for the notion of the "butterfly effect," the idea that a small disturbance like the flapping of a butterfly's wings can induce enormous consequences.

As recounted in the book "Chaos" by James Gleick, Dr. Lorenz's accidental discovery of chaos came in the winter of 1961. Dr. Lorenz was running simulations of weather using a simple computer model. One day, he wanted to repeat one of the simulations for a longer time, but instead of repeating the whole simulation, he started the second run in the middle, typing in numbers from the first run for the initial conditions.

The computer program was the same, so the weather patterns of the second run should have exactly followed those of the first. Instead, the two weather trajectories quickly diverged on completely separate paths.

At first, he thought the computer was malfunctioning. Then he realized that he had not entered the initial conditions exactly. The computer stored numbers to an accuracy of six decimal places, like 0.506127, while, to save space, the printout of results shortened the numbers to three decimal places, 0.506. When typing in the new conditions, Dr. Lorenz had entered the rounded-off numbers, and even this small discrepancy, of less than 0.1 percent, completely changed the end result...

Dr. Lorenz published his findings in 1963. "The paper he wrote in 1963 is a masterpiece of clarity of exposition about why weather is unpredictable," said J. Doyne Farmer, a professor at the Santa Fe Institute in New Mexico.

The following year, Dr. Lorenz published another paper that described how a small twiddling of parameters in a model could produce vastly different behavior, transforming regular, periodic events into a seemingly random chaotic pattern.

At a meeting of the American Association for the Advancement of Science in 1972, he gave a talk with a title that captured the essence of his ideas: "Predictability: Does the Flap of a Butterfly's Wings in Brazil Set Off a Tornado in Texas?"...
Lorenz was one in 1,000,000.0000000001. Butterflies the world over are today observing a moment of not flapping to mark the passing of one of the most distinguished scientists of our time.

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April 09, 2008

Barker v. D'Souza at Harvard

On April 22, the Humanist Chaplaincy at Harvard will be hosting a debate between Neocon Reconstructionist Dinesh D'Souza, author of What's So Great About Christianity and the Freedom from Religion Foundation's Dan Barker, author of Losing Faith in Faith. The student-moderated debate has been entitled "Christianity vs. Atheism?"

The debate is scheduled to begin at 8:00 PM at Memorial Church and is free to the public with no reservations necessary.

Which brings up a question: what is it about Humanists and Tuesday nights, anyhow? Perhaps I should write What's So Great About Tuesdays? It's not a great night for me. I have to give my students their lab practical (which amounts to their final exam) for Intro Bio that day, then hop a train and haul my sorry mycological butt to Cambridge. I do believe I'll have to squeeze in a visit to Dunkin' Donuts along the way. Since returning to the Northeast, I have rekindled my love affair with their coffee. It reanimates me regularly after 5:00 PM.

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