LIFE

Rethinking "Out of Africa"

Topic: 

  • LIFE
http://vimeo.com/79899367

"I'm thinking a lot about species concepts as applied to humans, about the "Out of Africa" model, and also looking back into Africa itself. I think the idea that modern humans originated in Africa is still a sound concept. Behaviorally and physically, we began our story there, but I've come around to thinking that it wasn't a simple origin. Twenty years ago, I would have argued that our species evolved in one place, maybe in East Africa or South Africa. There was a period of time in just one place where a small population of humans became modern, physically and behaviourally.

RETHINKING "OUT OF AFRICA"

[11.12.11]

I'm thinking a lot about species concepts as applied to humans, about the "Out of Africa" model, and also looking back into Africa itself. I think the idea that modern humans originated in Africa is still a sound concept. Behaviorally and physically, we began our story there, but I've come around to thinking that it wasn't a simple origin. Twenty years ago, I would have argued that our species evolved in one place, maybe in East Africa or South Africa. There was a period of time in just one place where a small population of humans became modern, physically and behaviourally. Isolated and perhaps stressed by climate change, this drove a rapid and punctuational origin for our species. Now I don’t think it was that simple, either within or outside of Africa. 

CHRISTOPHER STRINGER is one of the world's foremost paleoanthropologists. He is a founder and most powerful advocate of the leading theory concerning our evolution: Recent African Origin or "Out of Africa". He has worked at The Natural History Museum, London since 1973,  is a Fellow of the Royal Society, and currently leads the large and successful Ancient Human Occupation of Britain project (AHOB),  His most recent book is The Origin of Our Species (titled Lone Survivors in the US). 

Christopher Stringer's Edge Bio Page


Rethinking "Out of Africa" from Edge Foundation on Vimeo.


Rethinking "Out of Africa"

[CHRISTOPHER STRINGER:] At the moment, I'm looking again at the whole question of a recent African origin for modern humans—the leading idea over the last 20 years. This argues  that we had a recent African origin, that we came out of Africa, and that we replaced all of the other human forms that were outside of Africa. But we're having to re-evaluate that now because genetic data suggest that the modern humans who came out of Africa about 60,000 years ago probably interbred with Neanderthals, first of all, and then some of them later on interbred with another group of people called the Denisovans, over in south eastern Asia.

If this is so, then we are not purely of recent African origin. We're mostly of recent African origin, but there was contact with these other so-called species. We're having to re-evaluate the Out-of-Africa theory, and we're having to re-evaluate the species concepts we apply, because in one view of thinking, species should be self-contained units. They don't interbreed with other species. However, for me, the whole idea of Neanderthals as a different species is really a recognition of their separate evolutionary history—the fact that we can show that they evolved through time in a particular direction, distinct from modern humans, and they separated maybe 400,000 years ago from our lineage. And morphologically we can distinguish a relatively complete Neanderthal fossil from any recent human.

 

The Evolution of Cooperation Edge Master Class 2011

[9.19.11]

Why has cooperation, not competition, always been the key to the evolution of complexity?

MARTIN NOWAK is a Mathematical Biologist, Game Theorist; Professor of Biology and Mathematics, Director, Center for Evolutionary Dynamics, Harvard University; Coauthor (with Roger Highfield), SuperCooperators: Altruism, Evolution, and Why We Need Each Other to Succeed.

Martin Nowak's Edge Bio Page


In July, Edge held its annual Master Class in Napa, California on the theme: "The Science of Human Nature".  In the six week period that began September 12th, we are publishing the complete video, audio, and texts:  Princeton psychologist Daniel Kahneman on the marvels and the flaws of intuitive thinking; Harvard mathematical biologist Martin Nowak on the evolution of cooperation; Harvard psychologist Steven Pinker on the history of violence; UC-Santa Barbara evolutionary psychologist Leda Cosmides on the architecture of motivation; UC-Santa Barbara neuroscientist Michael Gazzaniga on neuroscience and the law; and Princeton religious historian Elaine Pagels on The Book of Revelation.

For publication schedule and details, go to Edge Master Class 2011: The Science of Human Nature.



The Evolution of Cooperation

I would like to talk about the evolution of cooperation. And if I see one person in the room who hasn't heard my joke, for the benefit of this person and to the detriment of all others, I want to tell my joke, because this is what defines me.

I'm a mathematical biologist. What is a mathematical biologist?  A mathematical biologist is best described by the following story:  There's a shepherd and a flock of sheep. A man comes by and says, "If I guess the correct number of sheep in your flock, can I have one?" The shepherd says, "All right, try."  So the man looks and says, "Eighty-three."  And the shepherd is completely amazed because it's right.  So the man picks up a sheep and starts to walk away and the shepherd says, "Hang on, if I guess your profession, can I have my sheep back?"  And he says, "Please, try."  "You must be a mathematical biologist."  "How did you know?"  "Because you picked up my dog." If you really think about it, the important essence of our field is to get the numbers right. 

To Err Is Primate

[7.27.11]

Why do house sellers, professional golfers, experienced investors, and the rest of us succumb to strategies that make us systematically go wrong?

 

INTRODUCTION

People are fascinated by research into the mental lives of monkeys and apes—but not always for the right reasons. What they usually want to know is whether these animals share certain important traits with humans, such as syntax, social reasoning, or altruism. Just how special are we? This question is irresistible, and isn’t going to go away. But the best work in this area is a lot more subtle than this.

This brings me to my colleague Laurie Santos, one of best young scientists in the field of psychology. She does experiments with non-human primates—including capuchins in her laboratory at Yale and rhesus macaques at a field site in Cayo Santiago—as a way to develop and test subtle theories of the nature and evolution of certain central human capacities. Much of her recent research focuses on biases in reasoning and decision-making; she is one of the founders of the exciting new field of comparative behavioral economics.

Santos asks hard questions and makes important discoveries. Her writing and thinking display an easy facility with a range of literatures; she is living proof of a comment once made by Jerry Fodor, that the best interdisciplinary conversations are those that occur inside a single head.

— Paul Bloom
 

LAURIE R. SANTOS is an associate professor of psychology at Yale University and the director of its Comparative Cognition Laboratory. She received her BA (1997) in psychology and biology and her PhD (2003) in psychology from Harvard University. She has investigated a number of topics in comparative cognition, including the evolutionary origins of irrational decision making and prosocial behavior. She is the recipient of Harvard’s Goethals Award for Teaching Excellence, Yale’s Greer Memorial Prize for Outstanding Junior Faculty, and the Stanton Prize from the Society for Philosophy and Psychology for outstanding contributions to interdisciplinary research.

PAUL BLOOM is the Brooks and Suzanne Ragen Professor of Psychology at Yale University. His most recent book is How Pleasure Works.

Excerpted from Future Science: Essays From The Cutting Edge, Edited by Max Brockman (Vintage Books, 2011)


TO ERR IS PRIMATE

[LAURIE SANTOS:]  It was the final shot of the tournament for the world’s number one player. After three tense rounds in the 2009 Barclays Tournament, Tiger Woods was now one putt away from another tournament win. His fairway shot was nearly perfect—his ball had landed just seven feet from the hole. Making this putt would earn him a birdie on the last hole and a hefty payoff. He practically beamed as he stepped up to a putt he had sunk thousands of times before. After the tournament, he would be asked if he had approached this particular shot any differently. “Absolutely not,” he would emphasize. “Every putt you hit is the same process. Go up there. Be committed to what you’re going to do. Hopefully it goes in.” Only this time it didn’t. A stunned crowd watched in disbelief as the ball skimmed past the hole. Tiger’s shot was just a bit off, but it cost him the lead. He took another putt, made par, and lost nearly a million dollars in winnings.

For professional golfers, every putt is a risky decision, one that can have big financial consequences. A putt is reasonably simple goal-directed action, yet each stroke requires more than just motor skill. Good golfers sink putts because they’re also good decision makers. Every putt requires a host of tough choices. Besides having to estimate how the ball will break, a player must choose between playing it safe—going with a softer stroke that will mean an easier following shot if things go badly—or going for the hole at the risk of overshooting. As the above example illustrates, even the best golfer in the world can make errors.

Those of us who aren’t golfers are not immune to the difficulty of making risky decisions. Though we (usually) play for smaller stakes than Tiger, we too spend our days navigating risky choices that can have significant consequences for our health, bank account, and overall well being. The question of how to best make decisions has fascinated humankind for centuries. For economists, the answer has always been relatively simple: making good decisions is a simple act of comparison shopping. A smart decision maker should start by listing all the possible choices for a given decision and then estimate the average payoff of each individual choice. Once the decision maker has all this information handy, he just needs to pick the choice with the highest expected payoff. Simple, right? Unfortunately, in practice the strategy of maximizing your expected return runs into a number of thorny issues.

Molecular Cut and Paste

The New Generation of Molecular Tools
[7.21.11]

INTRODUCTION
by Nathan Wolfe

I spend much of my life studying deadly viruses and central to my work has been the creation of a number of systems for keeping potentially devastating epidemics in check–from microbial field stations in far-flung places to computer platforms that crunch big data to detect outbreaks before they spread. This is exciting and important work, but the truth is that my joy comes from having a profound respect and certain love for microbes.

Since Antonie van Leeuwenhoek first saw the microbial world in the 17th century through his diminutive early microscopes, we have discovered that bacteria, archaea and viruses make up the majority of life on our planet. Far from a world of harmful bugs, our microbial planet is incredibly rich and deep – in fact the overwhelming majority of it completely unconcerned with vertebrates, let alone humans.

While the focus on the deadly microbes represents low hanging fruit for contemporary microbiologists like myself, it was refreshing to see William McEwan articulate the wider potential of bugs in his smart chapter in the welcomed 2nd volume of Max Brockman’s essay series highlighting young researchers – Future Science: Essays from the Cutting Edge.

McEwan begins and ends his essay with personal musings about his fabrication of a novel synthetic virus to accomplish his lab goals. He points out the irony that retroviruses, the family of viruses to which HIV belongs, may be some of most important tools in fighting AIDS—and that altering other viruses has the potential for potent targeted cancer chemotherapy.

The microbial world holds huge potential not just to harm but to help. As we learn more about the vast invisible biological world around us we'll find things that will amaze and enlighten us. Perhaps even save us.   

— Nathan Wolfe
 

WILLIAM MCEWAN is a virologist working on intracellular immunity to viruses. His research focuses on specific mechanisms in mammalian cells that actively overcome viral infection. He graduated with a BSc in genetics from University College London in 2005 and did a master’s degree and PhD at the University of Glasgow, researching immunity to lentiviruses in cats and lions. He is currently a postdoctoral researcher at the MRC Laboratory of Molecular Biology, Cambridge, U.K., where he continues to probe the biology of antiviral immunity.

NATHAN WOLFE is Lorry Lokey Visiting Professor of Human Biology at Stanford University and directs the Global Viral Forecasting Initiative. He is the author of The Viral Storm: The Dawn of a New Pandemic Age.

Excerpted from Future Science: Essays From The Cutting Edge, Edited by Max Brockman (Vintage Books, 2011)


MOLECULAR CUT AND PASTE

[WILLIAM MCEWAN:] This afternoon I received in the post a slim FedEx envelope containing four small vials of DNA. The DNA had been synthesized according to my instructions in under three weeks, at a cost of 39 U.S. cents per base pair (the rungs adenine-thymine or guanine-cytosine in the DNA ladder). The 10 micrograms I ordered are dried, flaky, and barely visible to the naked eye, yet once I have restored them in water and made an RNA copy of this template, they will encode a virus I have designed.

My virus will be self-replicating, but only in certain tissue-culture cells; it will cause any cell it infects to glow bright green and will serve as a research tool to help me answer questions concerning antiviral immunity. I have designed my virus out of parts—some standard and often used, some particular to this virus—using sequences that hail from bacteria, bacteriophages, jellyfish, and the common cold virus. By simply putting these parts together, I have infinitely increased their usefulness. What is extraordinary is that if I had done this experiment a mere eight years ago, it would have been a world first and unthinkable on a standard research grant. A combination of cheap DNA synthesis, freely accessible databases, and our ever expanding knowledge of protein science is conspiring to permit a revolution in creating powerful molecular tools.

WHO IS THE GREATEST BIOLOGIST OF ALL TIME?

[3.11.11]
"So who is the greatest biologist of all time? Good question. For most people it's got to be Darwin. I mean, Darwin is top dog, numero uno. He told us about evolution, he convinced us that evolution happened, and he gave us an explanation for it. I mean, there just wouldn't seem to be any competition. Okay, fine, well you might then say: Mendel. Mendel discovers transmission genetics, and that was pretty good. And I suppose then you have to go pretty far down the list to come to people like Watson and Crick, who just discovered the structure of DNA, which is just a bit of structural biology, really, a bit of biochemistry."
 
"Okay, but who is the real top dog? For me, the answer is absolutely clear. It's Aristotle. And it's a surprising answer because even though I suppose some biologists might know, should they happen to remember their first year textbooks, that Aristotle was the Father of Biology, they would still say, "well, yes, but he got everything wrong." And that, I think, is a canard. The thing about Aristotle - and this is why I love him - is that his thought was is so systematic, so penetrating, so vast, so strange – and yet he's undeniably a scientist."
— Armand Leroi

Leroi

ARMAND LEROI is a Professor of Evolutionary Developmental Biology at Imperial College London, and the author of Mutants: On Genetic Variatey and The Human Body

Arman Leroi's Edge Bio Page

Map

(Click Image to Enlarge)

An 1817 British Admiralty map of Kolpos Kallonis, the lagoon in Greece where Aristotle began the study of the biological world. Aristotle proposed that organisms were formed and maintained by their "souls," by which he meant the topography of their metabolic and regulatory networks. Superimposed within the lagoon, therefore, is a map of the regulatory network of a yeast cell: Aristotle’s vision realized in the 21st C.

 

WHO IS THE GREATEST BIOLOGIST OF ALL TIME?

Topic: 

  • LIFE
http://vimeo.com/79329040

"So who is the greatest biologist of all time? Good question. For most people it's got to be Darwin. I mean, Darwin is top dog, numero uno. He told us about evolution, he convinced us that evolution happened, and he gave us an explanation for it. I mean, there just wouldn't seem to be any competition. Okay, fine, well you might then say: Mendel. Mendel discovers transmission genetics, and that was pretty good.

CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME

Genetics: Life From a Synthetic Genome
[5.18.10]

I feel sure of only one conclusion. The ability to design and create new forms of life marks a turning-point in the history of our species and our planet. — Freeman Dyson

Introduction
By John Brockman

On May 20th, J. Craig Venter and his team at J.C Venter Institute announced the creation of a cell controlled by a synthetic genome in a paper published in SCIENCE. As science historian George Dyson points out, "from the point of view of technology, a code generated within a digital computer is now self-replicating as the genome of a line of living cells. From the point of view of biology, a code generated by a living organism has been translated into a digital representation for replication, editing, and transmission to other cells."

This new development is all about operating on a large scale. "Reading the genetic code of a wide range of species," the paper says, "has increased exponentially from these early studies.  Our ability to rapidly digitize genomic information has increased by more than eight orders of magnitude over the past 25 years." This is a big scaling up in our technological abilities. Physicist Freeman Dyson, commenting on the paper, notes that "the sequencing and synthesizing of DNA give us all the tools we need to create new forms of life." But it remains to be seen how it will serve in practice.

One question is whether or not a DNA sequence alone is enough to generate a living creature. One way of reading the paper suggests this doesn't seem to be the case because of the use of old microplasma cells into which the DNA was inserted — that this is not about "creating life" since the new life requires an existing living recipient cell. If this is the case, what is the chance of producing something de novo? The paper might appear to be about a somewhat banal technological feat. The new techniques build on existing capabilities. What else is being added, what is qualitatively new?

While it is correct to say that the individual cell was not created, a new line of cells (dare one say species?) was generated. This is new life that is self-propagating, i.e. "the cells with only the synthetic genome are self replicating and capable of logarithmic growth."

The paper concludes with the following:

"If the methods described here can be generalized, design, synthesis, assembly, and transplantation of synthetic chromosomes will no longer be a barrier to the progress of synthetic biology.  We expect that the cost of DNA synthesis will follow what has happened with DNA sequencing and continue to exponentially decrease. Lower synthesis costs combined with automation will enable broad applications for synthetic genomics."

Will the new techniques described in the paper allow us to bring extinct species back to life? Here are three examples of three possible stages after the production of a bacterial cell: 1. generating a human, i.e. a Neanderthal; 2. generating a woolly mammoth; 3. generating a tasmanian wolf.

Generating a Neanderthal, given the recent mapping of the Neanderthal genome by Svante Pääbo, seems to be feasible, but it will raise ethical hackles. Don't hold your breath waiting for someone to try it. Generating a woolly mammoth will not be an ethical problem but it also seems feasible by using an elephant's placenta: inject mammoth DNA into a modern elephant egg from which elephant DNA has been removed, then import the elephant egg into an elephant. A real challenge will be to generate a truly extinct species such as a Tasmanian wolf for which no host cells exist.

What does this mean? We don't know yet, and we may not know for years. For now, all we can do is speculate responsibly. As Freeman Dyson notes:

"I feel sure of only one conclusion. The ability to design and create new forms of life marks a turning-point in the history of our species and our planet."

Life goes on.. but it won't be the same.

To provide context, we have put together a retrospective of Edge events, transcripts, and videos featuring the pioneers in this area who are among the key players in what we are calling "A New Age of Wonder" [click here]

The Edge Reality Club discussion on the paper, "Creation Of A Bacterial Cell Controlled By A Chemically Synthesized Genome," is below.

Reality Club: Rodney Brooks, PZ Myers, Richard Dawkins, George Church, Nassim N. Taleb, Daniel C. Dennett, Dimitar Sasselov, Antony Hegarty, George Dyson, Kevin Kelly, Freeman Dyson

EAT ME BEFORE I EAT YOU! A NEW FOE FOR BAD BUGS

Topic: 

  • LIFE
https://vimeo.com/82232759

"Now we are starting to work with organisms that are more likely to appear in a hospital, like staph and influenza, and we have our sights on Clostridia difficile, Pneumococcus aeruginosa, Acetinobacter baumanii and an alarming number of other bacteria that are resistant to antibiotics. We are also working on influenza, which has a convenient little feature called M2e."

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