#90: Life/Brain Origins./Evolution: 0. Interstellar/Artificial Origins. 1. Within Cells. 2. Evolution Start. 08.6.23=1 - 09.1.16=5 11pm.

#90: Life/Brain Origins & Evolution. 08.6.23=1 - 09.1.16=5 11pm:

0. Interstellar/Artificial Origins
1. Within Cells: Signaling, Bonds
2. Start of Evolution
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0. Interstellar/Artificial Origins:----------
0-1. Interstellar Origins:-------------------
0-1-1. 'Interstellar 'slowball' could have carried seeds of life' http://tinyurl.com/645z9k
0-1-2. 'More Ingredients For Life Found In Outer Space' http://tinyurl.com/3ffalp

0-2. Artificial Origins: Protocell:---------
'Biologists on the Verge of Creating New Form of Life' http://tinyurl.com/5dge98
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1. Within Cells:-----------------------------
1-1. Signaling in a Cell:
'New probe may help untangle cells' signaling pathways' http://tinyurl.com/4hkj3t
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1-2. Bonds within a Cell:
'Using a light touch to measure protein bonds' http://tinyurl.com/5s6um7
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1-3. 'Smart amoebas reveal origins of primitive intelligence' http://tinyurl.com/58r8yc
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1-4. Cell Images: Inside Cells: http://tinyurl.com/InCells

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2. Start of Evolution;-----------------------
2-1. 'Did evolution come before life?' Bob Holmes: http://tinyurl.com/4p8tuh

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0. Interstellar/Artificial Origins:----------

0-1. Interstellar Origins:-------------------

0-1-1'Interstellar 'slowball' could have carried seeds of life' NewScientist.com news service: NewScientistSpace, Sept4,08: http://tinyurl.com/645z9k

: "" COULD a star in a distant solar system have thrown the life's building blocks our way?

Previous studies into whether material could travel between solar systems predicted that such an exchange would be unlikely, because the speed matter would need to be travelling at to escape one star would mean it was moving too fast to be caught by another.

Now Edward Belbruno and colleagues at Princeton University have shown that planetary systems in young, densely packed star clusters could throw out rocks at a slower pace. They showed that for rocks in certain orbital positions, the gravitational pull of the central star is equal to the pull of other stars in the cluster. This sends the rocks into chaotic orbits that eventually allow them to wander off at about 0.1 kilometres per second - slow enough for other stars to catch them (http://arxiv.org/abs/0808.3268).

The team estimates that up to 1018 individual rocks could leave such a system in the first 100 million years of a cluster's life, before the stars drifted too far apart. They believe these rocks could have carried basic biological components like amino acids. ""


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0-1-2. 'More Ingredients For Life Found In Outer Space' Posted by Adam Korbitz at 6:00AM Sep20,08: http://tinyurl.com/3ffalp

: "" A team of researchers led by Spanish scientists has published their discovery of the complex molecule naphthalene in an interstellar star-forming cloud, indicating many prebiotic organic molecules necessary for life as we know it could have been present when our own solar system formed.

According to the new research -- published in The Astrophysical Journal Letters -- the naphthalene molecules were discovered 700 light-years from Earth in a star-forming region of the constellation Perseus, in the direction of the star Cernis 52.

When napthalene is mixed with water and ammonium -- both also common in the interstellar medium -- and subjected to ultraviolet light, these molecules react to form a variety of compounds essential to the development of life as we know it on Earth, including amino acids and several precursor molecules to vitamins. ""


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0-2. Artificial Origins: Protocell:---------

'Biologists on the Verge of Creating New Form of Life' Alexis Madrigal, Sep8,08: WIRED Science: http://tinyurl.com/5dge98

: "" A team of biologists and chemists is closing in on bringing non-living matter to life.

It's not as Frankensteinian as it sounds. Instead, a lab led by Jack Szostak, a molecular biologist at Harvard Medical School, is building simple cell models that can almost be called life.

Szostak's protocells are built from fatty molecules that can trap bits of nucleic acids that contain the source code for replication. Combined with a process that harnesses external energy from the sun or chemical reactions, they could form a self-replicating, evolving system that satisfies the conditions of life, but isn't anything like life on earth now, but might represent life as it began or could exist elsewhere in the universe.

While his latest work remains unpublished, Szostak described preliminary new success in getting protocells with genetic information inside them to replicate at the XV International Conference on the Origin of Life in Florence, Italy, last week. The replication isn't wholly autonomous, so it's not quite artificial life yet, but it is as close as anyone has ever come to turning chemicals into biological organisms.

"We've made more progress on how the membrane of a protocell could grow and divide," Szostak said in a phone interview. "What we can do now is copy a limited set of simple [genetic] sequences, but we need to be able to copy arbitrary sequences so that sequences could evolve that do something useful."

By doing "something useful" for the cell, these genes would launch the new form of life down the Darwinian evolutionary path similar to the one that our oldest living ancestors must have traveled. Though where selective pressure will lead the new form of life is impossible to know.

"Once we can get a replicating environment, we're hoping to experimentally determine what can evolve under those conditions," said Sheref Mansy, a former member of Szostak's lab and now a chemist at Denver University.

Protocellular work is even more radical than the other field trying to create artifical life: synthetic biology. Even J. Craig Venter's work to build an artificial bacterium with the smallest number of genes necessary to live takes current life forms as a template. Protocell researchers are trying to design a completely novel form of life that humans have never seen and that may never have existed.

Over the summer, Szostak's team published major papers in the journals Nature and the Proceedings of the National Academy of Sciences that go a long way towards showing that this isn't just an idea and that his lab will be the first to create artificial life -- and that it will happen soon.

"His hope is that he'll have a complete self-replicating system in his lab in the near future," said Jeffrey Bada, a University of California San Diego chemist who helped organize the Origin of Life conference.

Modern life is far more complex than the simple systems that Szostak and others are working on, so the protocells don't look anything like the cells that we have in our bodies or Venter's genetically-modified E. coli.

"What we're looking at is the origin of life in one aspect, and the other aspect is life as a small nanomachine on a single cell level," said Hans Ziock, a protocellular researcher at Los Alamos National Laboratory.

Life's function, as a simple nanomachine, is just to use energy to marshal chemicals into making more copies of itself.

"You need to organize yourself in a specific way to be useful," Ziock said. "You take energy from one place and move it to a place where it usually doesn't want to go, so you can actually organize things."

Modern cells accomplish this feat with an immense amount of molecular machinery. In fact, some of the chemical syntheses that simple plants and algae can accomplish far outstrip human technologies. Even the most primitive forms of life possess protein machines that allow them to import nutrients across their complex cell membranes and build the molecules that then carry out the cell's bidding.

Those specialized components would have taken many, many generations to evolve, said Ziock, so the first life would have been much simpler.

What form that simplicity would have taken has been a subject of intense debate among origin of life scientists stretching back to the pioneering work of David Deamer, a professor emeritus at UC-Santa Cruz.

What most researchers agree on is that the very first functioning life would have had three basic components: a container, a way to harvest energy and an information carrier like RNA or another nucleic acid.

Szostak's earlier work has shown that the container probably took the form of a layer of fatty acids that could self-assemble based on their reaction to water (see video). One tip of the acid is hydrophilic, meaning it's attracted to water, while the other tip is hydrophobic. When researchers put a lot of these molecules together, they circle the wagons against the water and create a closed loop.

These membranes, with the right mix of chemicals, can allow nucleic acids in under some conditions and keep them trapped inside in others.



That opens the possibility that one day, in the distant past, an RNA-like molecule wandered into a fatty acid and started replicating. That random event, through billions of evolutionary iterations, researchers believe, created life as we know it.

In a paper released this month in the Proceedings of the National Academy of Sciences, Mansy and Szostak showed that the special membranes, fat bubbles essentially, were stable under a variety of temperatures and could have manipulated molecules like DNA through simple thermal cycling, just like scientists do in PCR machines.

The entire line of research, though, begs the question: where would DNA, or any other material carrying instructions for replication, have come from?

Many researchers have tried to tackle this problem of how RNA- or DNA-like molecules could have developed from the amino acids present on the early Earth. John Sutherland, a chemist at the University of Manchester, published a paper last year demonstrating one plausible way that RNA could have spontaneously been created in the prebiotic world.

Once such molecules existed, Szostak's lab's demonstrated in a Nature paper earlier this summer that nucleic acids could replicate inside a protocell (pdf).

But while many scientists agree the protocell work is impressive, not every scientist is convinced that it contributes to a reasonable explanation for the origin of life.

"Their work is wonderful inasmuch as what they are doing can be," said Mike Russell, a geochemist with the Jet Propulsion Laboratory in Pasadena, California. "It's just that I'm uneasy about the significance of it to the origin of life."

Russell argues that the very first life-like molecules on Earth would have been based on inorganic compounds. Instead of a fatty acid membrane, Russell argues that iron sulfide could have provided the necessary container for early cells.

But UCSD's Bada pointed out that it as unlikely we will ever know how life actually began.

"[Szostak's] point, and how we all view it, is that it's a nice model, but it doesn't necessarily mean that it happened that way," he said.

Szostak suggested that even if life could theoretically or did begin some other way, his lab's hypothesis was (at least) experimentally plausible.

"We're now pretty much convinced that growth and division could occur under perfectly reasonable prebiotic conditions in a way that is not some artificial laboratory construction," he said.

And actually, the most intriguing possibility of all may be that the protocells in Szostak's lab do not closely model earthly life's origins. If that's true, human beings, ourselves the product of evolution from the most primitive organisms, would have created an alternative path to imbuing matter with the properties of life.

"What we have in biology is just one of many, many possibilities," Szostack said. "One of the things that always comes up when people talk about life and universal qualities is water. But is water really necessary? What if we could design a system that works in something else?"

See Also:

* Gandhi Pills? Psychiatrist Argues for Moral Performance Enhancers
* Looking for Love in All the Right Alleles
* Invertebrate Astronauts Make Space History
* NASA: Mars Soil Could Support Extreme Life Forms, Maybe
* Phoenix Lander Searches for Martian Microbial Oases
* Saharan Snapshot of Stone Age Life

Illustrations by Janet Iwasa. 1. A model of a protocell. 2. A movie of a vesicle, or fatty acid membrane, forming.

WiSci 2.0: Alexis Madrigal's Twitter , Google Reader feed, and webpage; Wired Science on Facebook. ""
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1. Within Cells:-----------------------------

1-1. Signaling in a Cell:

'New probe may help untangle cells' signaling pathways' KurzweilAI.net, Jun30,08:
http://tinyurl.com/4hkj3t

: "" MIT researchers have designed a new type of probe that can image thousands of interactions between proteins inside a living cell, giving them a tool to untangle the web of signaling pathways that control most of a cell's activities.

To create the probes, the researchers used the enzyme biotin ligase and its target, a 12-amino-acid peptide.

MIT News ""


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1-2. Bonds within a Cell:

'Using a light touch to measure protein bonds' Anne Trafton, MIT News Office
June 30, 2008: http://tinyurl.com/5s6um7

MIT researchers tug at molecules with optical tweezers

[[ http://tinyurl.com/6b7psl
Image courtesy / Hyungsuk Lee, Jorge M. Ferrer, and Matthew J. Lang
The strength of actin binding protein interactions cross-linking a surface bound and bead tethered actin filament are probed using force from an optical trap. Filamin in green which forms networks of actin filaments shown as a confocal image on the right and alpha-actinin in blue which bundles actin filaments, shown as an image on the left, were probed using this assay configuration. Enlarge image ]]

: "" MIT researchers have developed a novel technique to measure the strength of the bonds between two protein molecules important in cell machinery: Gently tugging them apart with light beams.

"It's really giving us a molecular-level picture of what's going on," said Matthew Lang, an assistant professor of biological and mechanical engineering and senior author of a paper on the work appearing in the June 30 advanced online issue of the Proceedings of the National Academy of Science.

Last fall, Lang and others demonstrated that light beams could be used to pick up and move individual cells around the surface of a microchip.

Now they have applied the optical tweezers to measuring protein microarchitectures, allowing them to study the forces that give cells their structure and the ability to move.

The researchers focused on proteins that bind to actin filaments, an important component of the cytoskeleton. Depending on the arrangement and interaction of actin filaments, they can provide structural support, help the cell crawl across a surface or sustain a load (in muscle cells).

"We're trying to understand how nature engineered these molecular linkages to use in different ways," said Lang.

Actin filaments are most commonly found either bonded or crosslinked by a much smaller actin binding protein.

The researchers studied the interactions between the proteins by pinning one actin filament to a surface and controlling the motion of the second one with a beam of light. As the researchers tug on a bead attached to the second filament, the bond mediated by the actin-binding protein eventually breaks.

With this technique, the researchers can get a precise measurement of the force holding the proteins together, which is on the order of piconewtons (10^-12 newtons).

The same technique could be used to investigate many of the other hundreds of protein interactions that occur in the cytoskeleton, said Lang.

Lead author of the paper is Jorge Ferrer, a recent PhD recipient in biological engineering. Other MIT authors of the paper are Hyungsuk Lee and Benjamin Pelz, graduate students in mechanical engineering; and Roger Kamm, the Germeshausen Professor of Mechanical Engineering and Biological Engineering.

Jiong Chen of Stony Brook University and Fumihiko Nakamura of Harvard Medical School are also authors of the paper. ""


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1-3. 'Smart amoebas reveal origins of primitive intelligence' Colin Barras: NewScientist.com news service, Oct29,08: http://tinyurl.com/58r8yc

Related Articles
* Tiny organisms remember the way to food: 17 March 2007
* Engineers find 'missing link' of electronics: 30 April 2008

* Toshiyuki Nakagaki at Hokkaido University
* Di Ventra's paper on the arXiv
* Massimiliano Di Ventra at the University of California, San Diego

: "" Amoebas are smarter than they look, and a team of US physicists think they know why. The group has built a simple electronic circuit that is capable of the same “intelligent” behaviour as Physarum, a unicellular organism – and say this could help us understand the origins of primitive intelligence.

In recent years, the humble amoeba has surprised researchers with its ability to behave in an “intelligent” way. Last year, Liang Li and Edward Cox at Princeton University reported that the Dictyostelium amoeba is twice as likely to turn left if its last turn was to the right and vice versa, which suggests the cells have a rudimentary memory.

This year, Toshiyuki Nakagaki at Hokkaido University in Sapporo, Japan, won an Ig Nobel prize for his work on amoeba intelligence after his team found further evidence of the amoeba memory effect. They exposed Physarum amoeba to temperatures fluctuating regularly between cold and warm. It was already known that the cells become sluggish during cold snaps, but Nakagaki's team found that the amoeba slowed down in anticipation of cold conditions, even when the temperature changes had stopped (Physical Review Letters, DOI: 10.1103/PhysRevLett.100.018101). "
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1-4. Cell Images:------------------

Inside Cells: http://tinyurl.com/InCells


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2. Start of Evolution;-------------

2-1. 'Did evolution come before life?' Bob Holmes: NewScientist.com news service, Sep15,08: http://tinyurl.com/4p8tuh

: "" A rudimentary form of natural selection likely existed in the primordial soup even before life arose on Earth. If so, the complex "ecosystem" of prebiotic molecules may have made the eventual arrival of life much more probable.

Most experts presume that life arose from complex molecules such as nucleic acids and proteins, which were assembled from a mix of simpler units strung together with chemical bonds.

To examine how this might occur, Martin Nowak and Hisashi Ohtsuki, mathematical biologists at Harvard University, used simple equations to model the growth of such chains of building-blocks.

The model shows that because longer chains require more assembly reactions, they should be much less common than short chains. And if some assembly reactions run faster than others, then chains built from these fast-assembling sequences of building blocks grow to be most abundant. "


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