LIFE

THE CRAWFOORD PRIZE IN BIOSCIENCES 2007

[7.18.07]

The Royal Swedish Academy of Sciences has awarded the annual $500,000 Crafoord Prize in Biosciences for 2007 to Robert L. Trivers, Rutgers University, "for his fundamental analysis of social evolution, conflict and cooperation".

His pioneering ideas on the evolution of the social behaviour of animals form the basis of much of sociobiology and its research on how cooperation and conflict arise in the animal world.

Robert Shapiro—LIFE: WHAT A CONCEPT!

An Edge Special Event at Eastover Farm
[5.9.07]

"Life/ Consists of propositions about life." — Wallace Stevens("Men Made out of Words")

I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.

I'm always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn't be functional until it attained a certain length and could copy itself — appearing on the Earth.

ROBERT SHAPIRO is professor emeritus of chemistry and senior research scientist at New York University. He has written four books for the general public: Life Beyond Earth (with Gerald Feinberg); Origins, a Skeptic's Guide to the Creation of Life on Earth; The Human Blueprint (on the effort to read the human genome); and Planetary Dreams (on the search for life in our Solar System).

THE ENCYCLOPEDIA OF LIFE

IMAGINE an electronic for each species of organism on earth available everywhere by single access on command.
[5.7.07]

May 8, 2007
E.O. WILSON: TED PRIZE WISH: HELP BUILD THE ENCYCLOPEDIA OF LIFE

Chris Anderson, TED Curator

Those of us in Monterey this year watched in awe as E O Wilson unveiled his inspiring TED Prize wish to create an Encyclopedia of Life. (If you weren't there, you can see it at the link above). As E.O. Wilson accepts his 2007 TED Prize, he makes a plea on behalf of his constituents, the insects and small creatures, to learn more about our biosphere. We know so little about nature, he says, that we're still discovering tiny organisms indispensable to life; yet we're still steadily destroying nature. Wilson identifies five grave threats to biodiversity (a term he coined), using the acronym HIPPO, and makes his TED wish: that we will work together on the Encyclopedia of Life, a web-based compendium of data from scientists and amateurs on every aspect of the biosphere.

In Washington DC this morning, the first big step in that dream came true. Five major scientific institutions, backed by a $50m funding commitment led by the MacArthur Foundation, announced the launch of a global effort to launch the Encyclopedia. Ed Wilson described today's announcement as a dream come true.

E. O. WILSON: TED PRIZE WISH: HELP BUILD THE ENCYCLOPEDIA OF LIFE

[5.7.07]

Those of us in Monterey this year watched in awe as E O Wilson unveiled his inspiring TED Prize wish to create an Encyclopedia of Life. (If you weren't there, you can see it at the link above). As E.O. Wilson accepts his 2007 TED Prize, he makes a plea on behalf of his constituents, the insects and small creatures, to learn more about our biosphere. We know so little about nature, he says, that we're still discovering tiny organisms indispensable to life; yet we're still steadily destroying nature. Wilson identifies five grave threats to biodiversity (a term he coined), using the acronym HIPPO, and makes his TED wish: that we will work together on the Encyclopedia of Life, a web-based compendium of data from scientists and amateurs on every aspect of the biosphere.

In Washington DC this morning, the first big step in that dream came true. Five major scientific institutions, backed by a $50m funding commitment led by the MacArthur Foundation, announced the launch of a global effort to launch the Encyclopedia. Ed Wilson described today's announcement as a dream come true.

CONSTRUCTIVE BIOLOGY

[6.25.06]

As creative as we become, and as industrious and as good as we are at designing and manufacturing living things, which we've been doing since the stone age — no matter how good we get at that, it's like calling a candle a supernova. A candle is not a super nova; it's not even in the same league. And we, as intelligent designers, are not in the same league as the "Intelligent Design" forces that started the whole shebang. We're not designing sub-atomic particles from scratch; we're not designing galaxies. We're really not even designing the basic idea of life; we're just manipulating it.

Introduction

"Constructive biology?"

Think of the cell as operating system, and engineers taking the place of traditional biologists in retooling stripped down components of cells (bio-bricks) in much the vein as in the late 70s when electrical engineers were working their way to the first personal computer by assembling circuit boards, hard drives, monitors, etc. It's not an accident that the phrase "bio-hackers" is in the conversation, as this new crowd has a lot in common with the computer engineers who were around the homebrew computer club of the '70s leading the development of the personal computer.

Central to this move to engineer biology, to synthesize life, is Harvard researcher George Church.

"Today I am involved in a number of synthesis and sequencing endeavors," he says. "First, the BioFab group works together on 'constructive biology', which has a number of tightly overlapping parts of a Venn diagram."

"There's IGEM, 'International Genetically Engineered Machines' group, which is now in its fourth year , and has 39 universities involved. It's a very interesting social phenomenon; it involves wiki's and a lot of undergraduates, 39 teams of 10 to 20 people each. It's amazingly intense and enjoyable — kind of like the robot competitions, or the DARPA Grand Challenges. They compete to make cool things during the summer, and some go year-round working on those cool things — engineering life.

"Some of the people who started that group are also part of BioBrick Foundation, a non-profit, and a company called Codon Devices. So the founders of the field are defined by the intersection, or union, of those sets, depending how you look at it.

"BioFab group is also a subset of the Codon Devices scientific advisory board. And that's a Cambridge company that does synthetic biology. We're distinct from IGEM and the BioBrick Foundation and other synthetic biology groups that are emerging. "

Church points out that "almost every new thing is a combination of two old things. This is a kind of a union of engineering design principles that might be familiar to people in large-scale integrated circuits, combining that with genetic engineering, metabolic engineering, both of which are older — decades old, not ancient — and systems biology, which itself is a combination of feedback concepts, differential equations and so forth — those could be incorporated as well. There's also some bringing together of the chemistry and automation to make DNA — large highly accurate pieces of DNA — combining in concepts of laboratory evolution, which is relatively new. These things all meet together — kind of all these streams flowing together suddenly, all at once, into synthetic biology. Enough old things brought together into a new package that it consitutes an invention, a new field."

Unlike typical labs, a BioFab "Lab" can make a copy of itself. "Once you have a really great engineered biology system, you can make as many copies of it as you want: you could scale it up… (it does it itself; it's self-assembling). It's a dream of mechanical, electrical, and chemical Fab Labs — if they ever made, say, a milling machine that could make a copy of itself. That would be great. Then they'd have a self-replicating machine; that would be a milestone."

There are inevitable questions surrounding Church and his colleagues about "playing God" and there are also concerns about the kinds of bio-terror, lab accidents, and Frankenstein-like creations that have informed the writings of such thinkers as Bill Joy and Lord (Martin) Rees. These concerns were addressed by researchers in the field last month at SythenticBiology2.0, the second annual conference in this new field, which was convened at US-Berkeley. According to their Web site, "the SB2.0 community is developing a written statement describing some principles for advancing this new field in a safe and effective way, based on the third day of discussions and here."

—JB

GEORGE CHURCH is Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics. His current research focuses on integrating biosystems-modeling with personal genomics & synthetic biology.

George Church's Edge Bio Page 

Quantum Monkeys

[5.23.06]

 

The image of monkeys typing on typewriters is quite old. . . .Some people ascribe it to Thomas Huxley in his debate with Bishop Wilberforce in 1858, after the appearance of The Origin of Species. From eyewitness reports of that debate it is clear that Wilberforce asked Huxley from which side of his family, his mother's or his father's, he was descended from an ape. Huxley said, "I would rather be descended from a humble ape than from a great gentleman who uses considerable intellectual gifts in the service of falsehood. "A woman in the audience fainted when he said that. They didn't have R-rated movies back then.

Seth Lloyd is an Edgy guy. In fact he likes to work "at the very edge of this information processing revolution". He appeared at the Edge event in honor of Robert Trivers at Harvard and talked from his "experience in building quantum computers, computers where you store bits of information on individual atoms."

Ten years ago Lloyd came up with "the first method for physically constructing a computer in which every quantum—every atom, electron, and photon—inside a system stores and processes information...During this meeting, Craig Venter claimed that we're all so theoretical here that we've never seen actual data. I take that personally, because most of what I do on a day-to-day basis is to try to coax little super-conducting circuits to give up their secrets". Below is his talk along with his discussion with Steven Pinker, Martin Nowak, J. Craig Venter, Lee Smolin, and Alan Guth

SETH LLOYD is Professor of Mechanical Engineering at MIT and a principal investigator at the Research Laboratory of Electronics. His seminal work in the fields of quantum computation and quantum communications—including proposing the first technologically feasible design for a quantum computer.

He is the author of the recently published Programming the Universe: A Quantum Computer Scientist Takes On the Cosmos.

SETH LLOYD'S Edge Bio Page

The Reality ClubSteven PinkerMartin NowakJ. Craig VenterLee SmolinAlan GuthRudy Rucker


THE "GREAT" TRANSITION

[5.7.06]

When we look back after 370 million years of evolution, the invasion of land by fish appears special. However, if we could transport ourselves by time machine to this early period, it isn't clear whether we would notice anything extraordinary. We would see a lot of fish, some of them big and some of them small, all of them struggling to survive and reproduce. Only now, 370 million years later, do we see that one of those fish sat at the base of a huge branch of the tree of life—a branch that includes everything from salamanders to humans. It would have taken an uncanny sixth sense for us to have predicted this outcome when our time machine deposited us in the middle of the Devonian.

Introduction

Evolutionary biologist Neil Shubin writes:

"Within each of us — our skeletons, our behavior, and deep within our DNA — lurks our distant past. Make the relevant comparisons and we find that our hands resemble fossil fish fins, our heads are organized like long-extinct jawless fish, and major parts of our genomes look and function like those of worms and bacteria. We unlock our history as we understand more about our DNA, as we compare ourselves to animals living and dead, and as we discover new fossils from around the world. With all of this history in our bodies, we are most definitely not designed 'intelligently.' Our chances of developing certain cancers, hernias, bad backs, injured knees, and even hiccups are the result of the history that we share with fish, worms, and clams."

"We live in an age of discovery where the classic stories of evolution have become the focus of vigorous new approaches from genetics and developmental biology. Breakthroughs in genetics are beginning to tell us how bodies are built, in essence giving insights into the recipe that builds animals from a single celled egg. Couple these breakthroughs with the remarkable fossil discoveries of the past decade, and we have opportunity to present a new worldview of the human body."

Shubin, a leading researcher in fish-to-tetrapod transition, startled the world on March 31 with the announcement in the journal Science of the discovery of Tiktaalik, ''a mosaic of primitive fish and derived amphibian", which led to global headlines. His moment of realization occurred while digging fish bones out of rocks on a snowy July afternoon.

"While studying 380 million year old rocks in Ellesmere Island, at a latitude of 80 North, I was uncovering one of the key transitional stages in the shift from fish to land living animal. Everybody knows that fish swim with fins and animals that walk on land have legs. I was in the Arctic to learn how this shift happened. The fish I was uncovering had a wrist and fingers. A fish with wrists and fingers? I was immediately struck that this fossil reveals a very deep branch of my evolutionary tree. This is the origin of my wrists and fingers. Huddled in the tent during prolonged Arctic storms, it occurred to me that 3.5 billion years in the history of life are embedded in my own body."

Shubin's essay, "The 'Great' Transition", was written after the discovery but prior to the March 31 announcement. It is excerpted from Intelligent Thought: Science Versus the Intelligent Design Movement.

JB

NEIL SHUBIN, an evolutionary biologist, has been one of the major forces behind a new evolutionary synthesis of expeditionary paleontology, developmental genetics, and genomics. He is chair of the Department of Organismal Biology and Anatomy at the University of Chicago. 

Neil Shubin's Edge Bio Page

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