Monday, December 31, 2007

Massimo Pigliucci

 

Massimo Pigliucci

This debate on Intelligent Design vx. Evolution is at good starting point in the debate. Several other presentations are given on the page which will add to the discussion.

Wednesday, December 19, 2007

YouTube - What The #$*! Do We Know!? - Part 1 of 10

 

YouTube - What The #$*! Do We Know!? - Part 1 of 10



This is the anchor of a study based on this film. Thanks to work by others, the other parts of this film are on YouTube.




This is part 2 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 3 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 4 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 5 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 6 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 7 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 8 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 9 of this film. Thanks to work by others, the other parts of this film are on YouTube.

This is part 10 of this film. Thanks to work by others, the other parts of this film are on YouTube.

Synthetic DNA on the Brink of Yielding New Life Forms



Scientists in Maryland have already built the world's first entirely handcrafted chromosome -- a large looping strand of DNA made from scratch in a laboratory, containing all the instructions a microbe needs to live and reproduce.


In the coming year, they hope to transplant it into a cell, where it is expected to "boot itself up," like software downloaded from the Internet, and cajole the waiting cell to do its bidding.
Some experts are worried that a few maverick companies are already gaining monopoly control over the core "operating system" for artificial life and are poised to become the Microsofts of synthetic biology. That could stifle competition, they say, and place enormous power in a few people's hands


At the core of synthetic biology's new ascendance are high-speed DNA synthesizers that can produce very long strands of genetic material from basic chemical building blocks: sugars, nitrogen-based compounds and phosphates.


"I see a cell as a chassis and power supply for the artificial systems we are putting together," said Tom Knight of MIT, who likes to compare the state of cell biology today to that of mechanical engineering in 1864. That is when the United States began to adopt standardized thread sizes for nuts and bolts, an advance that allowed the construction of complex devices from simple, interchangeable parts.


If biology is to morph into an engineering discipline, it is going to need similarly standardized parts, Knight said. So he and colleagues have started a collection of hundreds of interchangeable genetic components they call BioBricks, which students and others are already popping into cells like Lego pieces.




J. Craig Venter, chief executive of Synthetic Genomics in Rockville, knows what he wants his cells to make: ethanol, hydrogen and other exotic fuels for vehicles, to fill a market that has been estimated to be worth $1 trillion.




In a big step toward that goal, Venter has now built the first fully artificial chromosome, a strand of DNA many times longer than anything made by others and laden with all the genetic components a microbe needs to get by.



LS9 Inc., a company in San Carlos, Calif., is already using E. coli bacteria that have been reprogrammed with synthetic DNA to produce a fuel alternative from a diet of corn syrup and sugar cane. So efficient are the bugs' synthetic metabolisms that LS9 predicts it will be able to sell the fuel for just $1.25 a gallon.

At a DuPont plant in Tennessee, other semi-synthetic bacteria are living on cornstarch and making the chemical 1,3 propanediol, or PDO. Millions of pounds of the stuff are being spun and woven into high-tech fabrics (DuPont's chief executive wears a pinstripe suit made of it), putting the bug-begotten chemical on track to become the first $1 billion biotech product that is not a pharmaceutical.


Yet another application is in medicine, where synthetic DNA is allowing bacteria and yeast to produce the malaria drug artemisinin far more efficiently than it is made in plants, its natural source.


In the past year, the U.S. Patent and Trademark Office has been flooded with aggressive synthetic-biology claims. Some of Venter's applications, in particular, "are breathtaking in their scope," said Knight. And with Venter's company openly hoping to develop "an operating system for biologically-based software," some fear it is seeking synthetic hegemony.


In fact, government controls on trade in dangerous microbes do not apply to the bits of DNA that can be used to create them. And while some industry groups have talked about policing the field themselves, the technology is quickly becoming so simple, experts say, that it will not be long before "bio hackers" working in garages will be downloading genetic programs and making them into novel life forms.






Andrew Light, an environmental ethicist at the University of Washington in Seattle, said synthetic biology poses a conundrum because of its double-edged ability to both wreak biological havoc and perhaps wean civilization from dirty 20th-century technologies and petroleum-based fuels.



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It appears that synthetic biology is about to have practical applications. 



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Wednesday, October 3, 2007

Mouse brain simulated on computer



Half a real mouse brain is thought to have about eight million neurons each one of which can have up to 8,000 synapses, or connections, with other nerve fibres.


Modelling such a system, the trio wrote, puts "tremendous constraints on computation, communication and memory capacity of any computing platform".


The team, from the IBM Almaden Research Lab and the University of Nevada, ran the simulation on a BlueGene L supercomputer that had 4,096 processors, each one of which used 256MB of memory.


Using this machine the researchers created half a virtual mouse brain that had 8,000,000 neurons that had up to 6,300 synapses.




This article describes some of the work being done to simulate brain function.  I'm adding it here because it is a different way to learn about biology and the new methods being used in it.


Link


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IBM's BlueGene L supercomputer simulates half a mouse brain



Efforts to model the human brain (on IBM's Blue Gene, ironically) haven't reached the point of finality just yet, but it looks like the supercomputer has already tackled a smaller, albeit similar task at the University of Nevada. The research team, which collaborated with gurus from the IBM Almaden Research Lab, have ran a "cortical simulator that was as big and as complex as half of a mouse's brain on the BlueGene L," and considering that it took about 8,000 neurons and 6,3000 synapses into consideration without totally crashing, it remains a fairly impressive achievement. Notably, the process was so intensive that it was only ran for ten seconds at a speed "ten times slower than real-time," and while the team is already looking forward to speeding things up and taking the whole mind into account, it was noted that the simulation (expectedly) "lacked some structures seen in an actual brain." Now, if only these guys could figure out how to mimic the brain and offer up external storage to aid our failing memories.




The Singularity is nearer it seems. 


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Sunday, September 9, 2007

Deepak Chopra

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Deepak Chopra clearly states what I have believed for many years. Death is the loose of personal consciousness. Good cannot exist without bad. Sin is its own punishment.


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Friday, August 24, 2007

Monday, August 20, 2007


Online Videos by Veoh.com

The New Biology - Where Mind and Matter Meet 1of2

Bruce H. Lipton. Ph.D., cellular biologist, author, and former Associate Professor at the University of Wisconsin's School of Medicine. His pioneering research on cloned human cells at Wisconsin and Stanford University's School of Medicine presaged the revolutionary field of epigenetics, the new science of how environment and perception control genes.



A New Blog Begins

For many months, I have enjoyed following stem cell research on http://stemcellreport.blogspot.com/ . I kept finding general biology information that I wanted to report on that was outside of the scope of stem cell work. The result is the creation of this blog which will be wider in scope and will cover those interests