Live: “Better, Stronger, Faster” – A World Science Festival Event

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Better, Stronger, Faster: The Future Of The Bionic Body

Date: Saturday May 31, 2014
Time: 02:00 PM-03:30 PM
Venue: Kaye Playhouse at Hunter College
Moderator: Bill Blakemore
Participants: John DonoghueJennifer FrenchJoseph J. FinsP. Hunter Peckham

The deaf begin to hear. The blind begin to see. Once damaged hearts begin to pump blood. Forget “wearable tech”—we’ve entered a zone where deploying engineering and circuitry inside the human body can help erase disabilities and, more controversially, enhance human capacities beyond their evolutionary limits. Peek into a future where technology will have the capacity to make us stronger, faster and by some measures, better.

Catch the livestream coverage of this event here and follow my liveblogging coverage here.

Live: “Ripples from the Big Bang” – A World Science Festival Event

big bang

Image Credit: RedOrbit

Ripples From The Big Bang: Listening To The Beginning Of Time

In March, a major breakthrough in understanding the origin of universe took the scientific community–and the general public–by storm. A team lead by astronomer John Kovac, using a powerful telescope at the South Pole, reported evidence of ripples in the fabric of space time produced by the big bang, a long-sought prediction of our most refined approach to cosmology, the inflationary theory. Amidst the worldwide celebration, though, some have been quietly suggesting that the champagne has been uncorked prematurely. Join a singular conversation, among the world’s most respected pioneers in cosmological theory and observation, that will explore the state of the art in the ongoing quest to understand the beginning of the universe.

Date: Friday May 30, 2014
Time: 08:00 PM-09:30 PM
Venue: NYU Skirball Center for the Performing Arts
Moderator: Brian Greene
Participants: Andrei LindeAlan GuthAmber MillerJohn KovacPaul Steinhardt

Follow my liveblogging coverage here.

Great video that clearly explains how gravitational waves were discovered and their significance to our understanding of the universe – See more at: http://astrobob.areavoices.com/2014/03/18/gravity-waves-confirm-universe-ballooned-after-big-bang/#sthash.oUM4zPHO.dpuf

inflationary theory

By LARRY BUCHANAN and JONATHAN CORUM of The New York Times

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Of course, no discussion involving Andrei Linde is complete without the heartwarming moment when Linde first received the wonderful news of the amazing discovery:

Update: The World Science Festival tweeted some of my posts!

Update on Camelopardalids

The May Camelopardalids’ peak did not reach the predicted rate of 200 meteors per hour but instead averaged around 5 to 6 meteors per hour last night. Here is what some of the various astronomy Web sites are saying about the shower, in hindsight…

SpaceWeather.com:

Although this [the 5 to 10 meteors per hour] is a far cry from predictions, it is hardly a surprise. The parent comet, 209P/LINEAR, is faint and currently produces only a small amount of dust. Most forecasters acknowledged that there might be less dust in Earth’s path than the models suggested.

Another possibility is that the shower is not a dud, just delayed. If models mis-located the debris zone, an outburst could still occur later on May 24th.

Universe Today:

Based on a few reports via e-mail and my own vigil of two and a half hours centered on the predicted maximum of 2 a.m. CDT (7 UT) Saturday morning the Camelopardalid meteor shower did not bring down the house. BUT it did produce some unusually slow meteors and (from my site) one exception fireball with a train that lasted more than 20 minutes.

Nevertheless, several observers shared their meteor shower photos:

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Cat Connor caught some meteors Friday night – the night of the Camelopardalid shower – over Mono Lake in California. The double streak on the left in this shot might be the upper stage of Japan’s Daichi-2 booster venting fuel. Read more at Phil Plait’s Bad Astronomer blog.

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Steve Lacy caught this beautiful fireball the night of the Camelopardalid meteor shower.

Many people saw fireballs, or very bright meteors, on the night of the Camelopardalid meteor shower. This one is from Kevin Palmer, who was observing from Green River State Wildlife Area in Illinois.

Many people saw fireballs, or very bright meteors, on the night of the Camelopardalid meteor shower. This one is from Kevin Palmer, who was observing from Green River State Wildlife Area in Illinois.

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The Inaugural Comet LINEAR Meteor Shower Tonight!

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A meteor streaks across the sky against a field of stars during a meteorite shower early August 13, 2010 near Grazalema, southern Spain. (Photo credit: Jorge Guerrero/AFP/Getty Images)

Tonight, the earth will pass through a cloud of debris from Comet 209P/LINEAR, discovered in 2004. The resulting new meteor shower, the Camelopardalids, is expected to peak Friday night into Saturday morning. Mid-latitudes in North America are predicted to have the best views. Models suggest that the best viewing hours are from 2 a.m. to 4 a.m. EDT on May 24. Initial predictions placed the zenithal hourly rate at 1,000 per hour, which would’ve pushed the meteor shower into the storm category. Realistically, we will probably see about 200 to 400 meteors at the shower’s peak, or 5 meteors/minute! The Camelopardalids have the potential to beat out the Perseids for the title of best celestial spectacle of the year, according to a report on RedOrbit.com. Since this meteor shower may become an annual event, people are already calling it the May Camelopardalids.

According to earthsky.org, the meteors will radiate from the constellation Camelopardalis (camelopard), an obscure northern constellation. Its name is derived from early Rome, where it was thought of as a composite creature, having characteristics of both a camel and a leopard. This constellation is in the northern sky, close to the north celestial pole, making this meteor shower better for the Northern Hemisphere than the Southern Hemisphere. If you are unable to see the meteor showers outside, the Slooh space camera has got you covered with a live broadcast. Watch the celestial show, starting tonight at 11 p.m. EDT.

meteor shower, Camelopardalids

The radiant point of the Camelopardalid meteor shower is in the far-northern sky, not far from Polaris the North Star. For this reason, this shower is better for the Northern Hemisphere. Chart via skyandtelescope.com

The Twice-Forbidden Fruit: A Quest to Create a Living Tree of Knowledge

apple tree, NPR

Image Credit: Catalin Petolea/iStockphoto.com

Last semester in my biology lab class, my peers and I read some research on DNA sequencing as a form of information storage, including a paper from the lab of George Church. We compiled information from several sources into a research paper, and I have shared mine below:


DNA’s Potential for Digital Information Storage Solutions

The onset of the Information Age has given rise to a need for more efficient methods for data storage and retrieval, as archiving data has become an increasingly complex task. In light of this problem, solutions such as cloud computing have been proposed as the savior of storage and now constitute a burgeoning market. However, to quote Einstein, “We can’t solve problems by using the same kind of thinking we used when we created them.” The key to our data storage problems may not lie in thinking bigger but in thinking smaller. DNA offers the possibility for storage of large amounts of data in a small amount of space. Additionally, data storage in the form of DNA can withstand the test of time, unlike many currently used data storage methodologies. DNA-based storage has potential as a practical, cost-effective solution to the digital archiving problem.

Although successful on a small scale, a significant limitation to the large-scale practical application of DNA-based information storage lies in the difficulty of synthesizing long strands of DNA de novo. George M. Church and his colleagues at Harvard Medical School were the first to attempt to tackle this problem using next-generation DNA synthesis and sequencing technologies. Rather than work with a single long stretch of DNA, the team opted to use shorter, overlapping fragments which together contain all the necessary information, yet individually are easier to manipulate. To move beyond the limited encoding of uppercase text which served as the basis of previous approaches, the team chose to encode an entire book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, which included 53, 426 words, 11 JPEG images, and one JavaScript program. The text was converted into a 5.27-megabit stream, and the resulting bit sequence was converted to DNA code using a 1-bit per base encoding. Following PCR to amplify the library, the sequence was read using an Illumina HiSeq next generation sequencer. All data blocks were recovered with a total of 10 bit errors out of 5.27 million, most of the errors being located within homopolymer runs (Church et al., 2012).

Researchers at the European Bioinformatics Institute used a similar strategy to create a way to store data in the form of DNA. In their study, Nick Goldman and his colleagues managed to create a code that is resistant to error and can last for at least 10,000 years (Goldman, et al., 2013). As was the case in the Harvard study, this code was created using short strings of DNA, which were broken up into overlapping fragments that ran in both directions (Church et al., 2012; Goldman, et al., 2013). In an effort to improve upon Church’s work, Goldman’s coding scheme did not allow for repeats in order to reduce error in DNA reading and writing. Goldman’s method ensures that no homopolymers are generated, significantly reducing high throughput sequencing errors. Given that a majority of errors associated with the Church method can be ascribed to homopolymers, the Goldman strategy is much less error prone than its predecessor (Church et al., 2012; Goldman, et al., 2013).

To test the efficacy of Goldman’s method, five files were encoded: all 154 of Shakespeare’s sonnets (ASCII), Watson and Crick’s seminal paper, “Molecular Structure of Nucleic Acids” (PDF), a medium resolution color photo (JPEG), an excerpt from Martin Luther King’s 1963 “I Have a Dream” Speech (MP3), and the Huffman code used to convert bytes to base-3 digits (ASCII). From these files, corresponding pieces of DNA were synthesized into base pair sequences. Four out of the five resulting DNA sequences were fully decoded without intervention. The fifth file contained 2 gaps, 25 bases each, but inspection of neighboring regions allowed researchers to hypothesize the missing fragments and manually insert the 50 missing bases, resulting in original files that had been reconstructed with 100% accuracy (Goldman, et al., 2013).

Church and Goldman were not the first to hypothesize about DNA’s powerful potential for information storage. Researchers at the University of Phoenix conducted a study comparing and contrasting the structure and function of computer hard drives and DNA. The study proposed that the same properties necessary for information processing in the hard drives of digital computers also reside in the DNA of eukaryotic cells. David D’Onofrio and Gary An identified four essential properties of information in a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting, and (4) translation from stored to usable form. D’Onofrio and An asserted that both the DNA complex and the computer hard drives contain these components characteristic of centralized information storage and processing systems. While computer hard drives and the DNA of living organisms seem to exhibit functional equivalence, D’Onofrio and An acknowledged that there are places where the analogy breaks down. For example, biological systems do not have an external source for a map of their stored information or for a set of instructions; instead, they must possess an organizational template within their intermolecular structure. For this reason and several others, the authors of this study are weary to think of hard drives and DNA interchangeably. The implication is that attempts to disrupt DNA sequences by manipulating its components will invariably lead to unintended consequences, suggesting that the use of DNA for storage solutions is ill advised (D’Onofrio and An, 2010). While some, such as D’Onofrio and An, may approach the idea of DNA storage solutions with hesitancy, others, like Church and Goldman, champion DNA storage solutions as the beginning of a new digital frontier.

References:

Church, G.M., Gao, Y., Kosuri, S. 2012. Next-Generation Digital Information Storage in DNA. Science. 337(6102): 1628.

D’Onofrio, D.J. and An, Gary. 2010. A Comparative Approach for the Investigation of Biological Information Processing: An Examination of the Structure and Function of Computer Hard Drives and DNA. Theor Biol Med Model. 7(3).

Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E.M., Sipos, B., Birney, E. 2013. Toward Practical High-Capacity Low-Maintenance Storage of Digital Information in Synthesized DNA. Nature. 494 (7435): 77-80.


Now, an artist from George Church’s lab, Joe Davis, plans to use synthetic biology to insert a DNA-encoded version of Wikipedia into a 4,000-year-old strain of apple to create a a living, literal tree of knowledge. He calls his endeavor Project “Malus ecclesia.” (Malus, the genus name for all apples, means both “evil” and “apple tree” in Latin. Ecclesia translates to “church,” an homage to George Church.) The process of inserting this extra information into an apple’s genome is akin to writing in the margins of a book; he will not alter any of the apple’s existing genome–responsible for the apple’s appearance, texture, and taste–but add to it. Furthermore, since the English version of Wikipedia contains two and a half billion words and the space in the bacterial genome is limited to a few thousand words, Davis plans to spread Wikipedia’s information out across many apples and many trees, which will likely compose a large grove. Because the Animal and Plant Health Inspection Service of the U.S. Department of Agriculture has strict regulations concerning the consumption of genetically altered plants, the engineered apple, when complete, will be twice forbidden.

What do you think of this project to create a living tree of knowledge? Are there potential advantages to storing information in this manner as opposed to using a digital platform? [Added December 20, 2014: Perhaps the only pertinent question left is, “Are you, are you coming to the tree?”] Leave your thoughts in the comments section below!

An American Pekin Duck in Memorial Park

Memorial Park IMG_3433 duck IMG_3438IMG_3434 IMG_3440

Happy 104th Birthday, Dorothy Hodgkin!

Dorothy Hodgkins Google Doodle

Google Doodle displaying the structure of a penicillin molecule, which Dorothy Hodgkin discovered using X-ray crystallography

Today, Google celebrates the legacy of British chemist Dorothy Hodgkin with a doodle on its homepage. Dorothy Crowfoot Hodgkin, born May 12, 1910 in Egypt but raised in England, was fascinated by crystals from a young age and received a book authored by Nobel Prize-winning physicist William Henry Bragg on her 16th birthday, sparking her interest in X-ray crystallography. Hodgkin studied physics and chemistry as an undergraduate at Somerville College at the University of Oxford and received her doctorate in chemistry from Cambridge University. Despite being diagnosed at only 24 with rheumatoid arthritis, which eventually crippled her hands and feet, Hodgkin never ceased in her pursuit of scientific truth.

She was awarded the Nobel Prize in Chemistry in 1964–making her the third woman to win the award after Marie Curie and Irene Joliot-Curie–for elucidating the structures of Vitamin B12 and penicillin using X-ray crystallography, the same technique that Rosalind Franklin employed to illuminate the double helical structure of DNA. X-ray crystallography allows a researcher to discern a molecule’s three-dimensional arrangement of atoms by shooting X-rays at a crystallized sample of the substance of interest and then observing the pattern of diffracted X-rays as they bounce off the electrons of the atoms in the crystal. The structure of penicillin, which Hodgkin discovered while working alongside colleague Ernst Chain in 1946, is shown in the Google doodle; Hodgkin’s model is on display at the Science Museum in London. In announcing her prize, the Swedish Academy of Science praised Hodgkin’s “exceptional skill, in which chemical knowledge, intuition, imagination, and perseverance have been conspicuous.” In 1969, after 35 years of work, Hodgkin was also able to decipher the structure of insulin.

Aside from her scientific endeavors, Hodgkin was also an active humanitarian. From 1976 to 1988, she served as chair of the Pugwash Conferences on Science and World Affairs, an international organization of scholars and public figures inspired by a manifesto written by Albert Einstein and Bertrand Russell and aimed at reducing and eliminating the threat posed to humanity by nuclear weapons and war.

Hodgkin won the Lenin Peace Prize and earned the Order of Merit, Britain’s most respected royal order, making her the second woman to have done so after Florence Nightingale, who was also born this day in 1820. The Order of Merit is limited at any time to 24 members who have excelled in science, art, letters, or the armed services. Hodgkin was the first woman to win the Copley Medal and remains the only British woman to have ever received a Nobel Prize in the sciences. She died in July 1994, at age 84, after suffering a stroke. Upon her death, The Times of London observed, “She will always be remembered for her discovery of the structure of penicillin, of the antipernicious anemia factor vitamin B12 and of the diabetic hormone, insulin.” An obituary beautifully described her in this way:

“She pursued her crystallographic studies, not for the sake of honours, but because this was what she liked to do. There was magic about her person. She had no enemies, not even among those whose scientific theories she demolished or whose political views she opposed. Just as her X-ray cameras bared the intrinsic beauty beneath the rough surface of things, so the warmth and gentleness of her approach to people uncovered in everyone, even the most hardened scientific crook, some hidden kernel of goodness.”