Daniel Wolpert: The Real Reason for Brains

Advertisements

Brain-Computer Implant Has Passed 1000-Day Milestone

Via io9.com

A paralysed woman was still able to control a computer cursor with her thoughts 1000 days after having a tiny electronic device implanted in her brain, say researchers who devised the system. The achievement demonstrates the longevity of brain-machine implants.

The woman, for whom the researchers use the pseudonym S3, had a brainstem stroke in the mid-1990s that caused tetraplegia – paralysis of all four limbs and the vocal cords.

In 2005, researchers from Brown University in Providence, Rhode Island, the Providence VA Medical Center and Massachusetts General Hospital in Boston implanted a tiny silicon electrode array the size of a small aspirin into S3’s brain to help her communicate better with the outside world.

Top image: 2006 Matthew McKee.

The electrode array is part of the team’s BrainGate system, which includes a combination of hardware and software that directly senses the electrical signals produced by neurons in the brain which control the planning of movement.

The electrode decodes these signals to allow people with paralysis to control external devices such as computers, wheelchairs and bionic limbs.

In a study just published, the researchers say that in 2008 – 1000 days after implantation – S3 proved the durability of the device by performing two different “point-and-click” tasks by thinking about moving a cursor with her hand.

Her first task was to move a cursor on a computer screen to targets arranged in a circle and select each one in turn. The second required her to follow and click on a target as it moved around the screen in varying sizes.

Leigh Hochberg, visiting associate professor of neurology at Harvard Medical School and director of the BrainGate trial, told the website Medical News Today:

This proof of concept – that after 1000 days a woman who has no functional use of her limbs and is unable to speak can reliably control a cursor on a computer screen using only the intended movement of her hand – is an important step for the field

However, the device did not perform perfectly – fewer electrodes were recording useful neural signals than they did when tested six months after implantation.

The researchers say there is no evidence of any fundamental incompatibility between the sensor and the brain. Instead, they believe the decreased signal quality over time can largely be attributed to engineering issues. Ongoing research means these issues are now less of a problem than they were when S3 received her implant.

Speaking with Brown University’s news service, lead author John Simeral, assistant professor of engineering at Brown, said that they would like to further improve the sensitivity of the device:

Our objective with the neural interface is to reach the level of performance of a person without a disability using a mouse

Hochberg says that S3’s implant is still working and she is still participating in trials.

This post by Helen Thomson originally appeared in New Scientist.

The ancestor of all life on Earth might have been a gigantic planetary super-organism

Via i09.com

The ancestor of all life on Earth might have been a gigantic planetary super-organism

All life on Earth is related, which means we all must share a single common evolutionary ancestor. And now it appears that this ancestor might have been a single, planet-spanning organism that lived in a time that predates the development of survival of the fittest.

That’s the idea put forward by researchers at the University of Illinois, who believe the last universal common ancestor, or LUCA, was actually a single organism that lived about three billion years ago. This organism was unlike anything we’ve ever seen, and was basically an amorphous conglomeration of cells.

Instead of competing for resources and developing into separate lifeforms, cells spent hundreds of millions of years freely exchanging genetic material with each other, which allowed species to obtain the tools to survive without ever having to compete for anything. That’s maybe not an organism as we would comprehend it today, but that’s the closest term we have for this cooperative arrangement.

All that we know about LUCA is based on conjecture, and the most promising recent research has been in figuring out what proteins and other structures are shared across all three domains of life: the unicellular bacteria and archaea and the multi-celled eukaryotes, which are where all plants and animals evolved from. This isn’t a foolproof method — it’s possible that two extremely similar but not identical structures could evolve independently after LUCA split into the three domains — but it’s a good starting point.

Illinois researcher Gustavo Caetano-Anollés says about five to eleven percent of modern proteins could be traced back to LUCA. Based on the function of these particular proteins, it appears LUCA had the enzymes needed to break down nutrients and get energy from them, and it could also make proteins, but it probably didn’t have the tools necessary to make DNA. This fits with other research that suggests LUCA fed upon many different food sources, and that it had internal structures in its cells known as organelles.

The big difference between LUCA and everything that came after, of course, is DNA. Because LUCA didn’t have the tools to deal with DNA, it probably used RNA instead, and it likely had very little control over the proteins that it made. The research suggests the ability to precisely control protein manufacture only came long after LUCA split apart, which means that protein-making was probably always a big crapshoot.

That’s why LUCA had to be cooperative, with any cells that produced useful proteins able to pass them on throughout the world without competition. This was a weird variation on what we know as natural selections — helpful proteins could go from a single cell to global distribution, while harmful or useless proteins were quickly weeded out and discarded. The result was the equivalent of a planet-spanning organism.

So why did this paradise of cellular cooperation give way to the last three billion years of cutthroat competition? The simple answer is that some cells probably outgrew this arrangement, as they had finally developed all the structures needed to survive without help. We don’t know quite why that happened, but it appears to coincide with the sharp increase of oxygen in the atmosphere. Whatever the cause, cells began eking out their own independent existences, ending the reign of LUCA that had lasted hundreds of millions of years… while beginning a new order that is still going strong 2.9 billion years later.

BMC Evolutionary Biology via New Scientist. Image by fusebulb, via Shutterstock.

LUCA: Last Universal Common Ancestor More Complex Than Previously Thought

Via Science Codex

CHAMPAIGN, Ill. — Scientists call it LUCA, the Last Universal Common Ancestor, but they don’t know much about this great-grandparent of all living things. Many believe LUCA was little more than a crude assemblage of molecular parts, a chemical soup out of which evolution gradually constructed more complex forms. Some scientists still debate whether it was even a cell.

New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report.

The study builds on several years of research into a once-overlooked feature of microbial cells, a region with a high concentration of polyphosphate, a type of energy currency in cells. Researchers report that this polyphosphate storage site actually represents the first known universal organelle, a structure once thought to be absent from bacteria and their distantly related microbial cousins, the archaea. This organelle, the evidence indicates, is present in the three domains of life: bacteria, archaea and eukaryotes (plants, animals, fungi, algae and everything else).

The existence of an organelle in bacteria goes against the traditional definition of these organisms, said University of Illinois crop sciences professor Manfredo Seufferheld, who led the study.

“It was a dogma of microbiology that organelles weren’t present in bacteria,” he said. But in 2003 in a paper in the Journal of Biological Chemistry, Seufferheld and colleagues showed that the polyphosphate storage structure in bacteria (they analyzed an agrobacterium) was physically, chemically and functionally the same as an organelle called an acidocalcisome (uh-SID-oh-KAL-sih-zohm) found in many single-celled eukaryotes.

Their findings, the authors wrote, “suggest that acidocalcisomes arose before the prokaryotic (bacterial) and eukaryotic lineages diverged.” The new study suggests that the origins of the organelle are even more ancient.

A new study suggests the ancestor of all living things had a complex cellular structure. The research team included (from left) University of Illinois entomology professor James Whitfield, with crop sciences professor Gustavo-Caetano Anollés and crop sciences professor Manfredo Seufferheld, also from Illinois. (Photo Credit: L. Brian Stauffer)

The study tracks the evolutionary history of a protein enzyme (called a vacuolar proton pyrophosphatase, or V-H+PPase) that is common in the acidocalcisomes of eukaryotic and bacterial cells. (Archaea also contain the enzyme and a structure with the same physical and chemical properties as an acidocalcisome, the researchers report.)

By comparing the sequences of the V-H+PPase genes from hundreds of organisms representing the three domains of life, the team constructed a “family tree” that showed how different versions of the enzyme in different organisms were related. That tree was similar in broad detail to the universal tree of life created from an analysis of hundreds of genes. This indicates, the researchers said, that the V-H+PPase enzyme and the acidocalcisome it serves are very ancient, dating back to the LUCA, before the three main branches of the tree of life appeared.

“There are many possible scenarios that could explain this, but the best, the most parsimonious, the most likely would be that you had already the enzyme even before diversification started on Earth,” said study co-author Gustavo Caetano-Anollés, a professor of crop sciences and an affiliate of the Institute for Genomic Biology at Illinois. “The protein was there to begin with and was then inherited into all emerging lineages.”

“This is the only organelle to our knowledge now that is common to eukaryotes, that is common to bacteria and that is most likely common to archaea,” Seufferheld said. “It is the only one that is universal.”

The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.

“You can’t assume that the whole story of life is just building and assembling things,” Whitfield said. “Some have argued that the reason that bacteria are so simple is because they have to live in extreme environments and they have to reproduce extremely quickly. So they may actually be reduced versions of what was there originally. According to this view, they’ve become streamlined genetically and structurally from what they originally were like. We may have underestimated how complex this common ancestor actually was.”

Their study appears in the journal Biology Direct.

New Chemical Reagent Turns Biological Tissue Transparent

Via GizMag

The clear mouse embryo on the right was incubated in the Scale reagent for two weeks

Scientists are constantly looking for new and better ways of seeing through biological tissue, in order to see cells within it that have been marked with dyes, proteins or other substances. While recent research has involved using marking materials such as carbon nanotubes and firefly protein, scientists from Japan’s RIKEN Brain Science Institute have taken a different approach – they’ve developed a chemical reagent that causes the tissue surrounding the marked cells to become transparent.

Known as Scale, the reagent was created by a team led by Dr. Atsushi Miyawaki. Already, they have used it to turn mouse brain tissue clear, in order to optically image the fluorescently-labeled cerebral cortex, hippocampus and white matter. They were able to see several millimeters into the tissue (keep in mind how small mouse brains are), allowing them “to visualize the axons connecting left and right hemispheres and blood vessels in the postnatal hippocampus in greater detail than ever before.”

Not only did Scale turn the unmarked tissue transparent, but it also did not decrease the intensity of the fluorescent proteins that the RIKEN team used to mark cells.

While the experiments performed so far have mainly involved brain tissue samples, Miyawaki believes that it should work equally well on other organs, and ultimately in living subjects. “We are currently investigating another, milder candidate reagent which would allow us to study live tissue in the same way, at somewhat lower levels of transparency” he said. “This would open the door to experiments that have simply never been possible before.”