Wednesday, January 30, 2008

Nothing Much Going On

I'm been silent for awhile. There just hasn't been anything really newsworthy or significant to write about. Hamilton Smith has synthesized the first whole bacterial genome. This is the next to last step in creating a tailer made microbe. The news touts it as creating synthetic life, but that's hype. It's just an expensive and fancy way to genetically engineer a microbe. There are simpler and cheaper ways to genetically engineer a bacterium. That isn't the hurdle though. The hurdle is getting the organism approved for environmental release. We've had genetically engineered organisms that could eat oil spills, but those organisms won't be used in the creators' lifetimes because of fear. Still, what Hamilton Smith and his team have done is quite a feat. They have already proved they can transform a whole genome into a bacterium and then select for the segregants (those bacteria carrying the new genome). So, likely, they've already transformed the new genome into Mycoplasma. I'd be more impressed if they heavily modified a genome and put it into something like E. coli or Streptomycetes.


Tuesday, January 15, 2008

Problems with Double Extended Precision on YDL for the PS3

My gcc compiler version is gcc version 4.1.1 20060525 (Yellow Dog 4.1.1-1).

This isn't the best C++ program (modified from PSC):

#include iostream

float FloatMachineEps();
double DoubleMachineEps();
long double LongDoubleMachineEps();
int main(int * argc, char ** argv[]){
float fep;
double dep;
long double ldep;
using namespace std;
fep = FloatMachineEps();
dep = DoubleMachineEps();
ldep = LongDoubleMachineEps();
cout << "Machine epsilon for single precision is: ";
cout << fep << endl;

cout << "Machine epsilon for double precision is: ";
cout << dep << endl;

cout << "Machine epsilon for double extended precision is: ";
cout << ldep << endl;
float FloatMachineEps(){
float fmachine_e, ftest;
fmachine_e = 1.0;

ftest = 1.0 + fmachine_e;
while (1.0 != ftest){
fmachine_e = fmachine_e/2.0;
ftest = 1.0 + fmachine_e;
return fmachine_e;

double DoubleMachineEps(){
double dmachine_e, dtest;
dmachine_e = 1.0;

dtest = 1.0 + dmachine_e;
while (1.0 != dtest){
dmachine_e = dmachine_e/2.0;
dtest = 1.0 + dmachine_e;
return dmachine_e;

long double LongDoubleMachineEps(){
long double ldmachine_e, ldtest;
ldmachine_e = 1.0;

ldtest = 1.0 + ldmachine_e;
while (1.0 != ldtest){
ldmachine_e = ldmachine_e/2.0;
ldtest = 1.0 + ldmachine_e;
return ldmachine_e;

but when I compile and run it on my old 32-bit AMD uniprocessor I get:

Machine epsilon for single precision is: 5.96046e-08
Machine epsilon for double precision is: 1.11022e-16
Machine epsilon for double extended precision is: 5.42101e-20


Machine epsilon for single precision is: 5.96046e-08
Machine epsilon for double precision is: 1.11022e-16
Machine epsilon for double extended precision is: 0

on my PS3 running Yellow Dog Linux. Uh-oh!



"The limits of the possible can only be defined by going beyond them into the impossible"
Arthur C. Clarke

"Science may set limits to knowledge, but should not set limits to imagination."
Bertrand Russel


Tuesday, January 08, 2008

Disturbed by Stories about the Future of Mankind

I watched the third season of Doctor Who last week. There were some really decent episodes from a science fiction perspective. Another episode showed how good an actor David Tennant really is. However, the last stories are deeply disturbing, perhaps because they are based on some sort of false belief that Homo sapiens sapiens is the ultimate survivor even at the end of the Universe 150 trillion years from now. While at my Mom's house over Christmas, I chanced upon her current book collection. In Illium, Dan Simmons creates an epic yarn of a far future Earth populated by Homo sapiens, while post-humans play God on Mount Olympos on Mars and reenact the Trojan War. AI machines live and explore the environs of the outer solar system. Both stories bothered me. They share at their core, the belief that H. sapiens is a survivor, and possibly superior to whatever species of Homo comes next. This is not how evolution works. Evolution is not static, ever. The changes may not be seen outwardly, called a phenotype, but they are there. It is just that mutations affecting outward appearance are easiest to spot and manipulate by breeding. Many a dog breed has been ruined because of bad breeding practices as people selected for looks over health. Likewise, whatever species we evolve into will be better than we are. It will have an advantage over us enabling it to outbreed and outcompete us. The changes may be neurological, affecting behavior or psychology, or they may be physical such as resistance to a plague germ or virus. Who knows what the future is, but I know what it is not.

Our species is fairly young, perhaps 250,000-100,000 years old. We coexisted with H. sapiens neanderthalis and perhaps caused their demise, if not directly, then indirectly. One could argue that it was direct since humans are so good at killing other humans perceived as different. The Neanderthals would be different since they preceded us into Europe and other parts of the world in a previous migration from Africa, and they liked natural shelters like caves rather than building their own (as far as we can tell).

Genetic studies suggest that the genus Homo split from the genus Pan around 4 million years ago, yet, there is about a 98% similarity between us and chimps. What a difference a few genes and their expressions make! White skin and red hair color within Europeans could have occurred within the last 10,000 years, making those mutations quite recent. Dogs evolved from wolves around 100,000 years ago. Cats are almost as old a species it turns out, yet they easily revert to their feral ancestors without humans. Modern Homo sapiens will be lucky to exist another 100 years. Chances are if progress continues that some form of augmentation and genetic manipulation will render our species quaint and archaic in many ways. If we colonize Mars or the Moon, the positive selection of a weaker gravity and no radiation protection of those environments will cause speciations to occur, just as living in a zero-g environment would.

If Buddhism, the New Testament, and Tolle are to be believed, then the next evolutionary step is psychological and neurological, the "humble" inheriting the Earth - those humans without egos. This is in contrast to Dan Simmons' post-human, nano-equipped, egocentric "Gods", his resurrected humans, their illiterate descendants, or Doctor Who's humans surviving unchanged 150 trillion years into the far future watching the stars dwindle and die. I think that the idea of consciousness evolving and no longer being asleep in the dream of form is a much more vivid and realistic vision of evolution than the stories I've seen or read thus far.


Sunday, January 06, 2008

Hold No Thought Closely

From today's Daily Zen
Sitting in Meditation

Sitting in meditation does not primarily
Mean that the mind should be grasped,
That the idea of purity should be clung to,
Nor that it should be motionless.
When you talk of grasping the mind,
Remember that the mind is fundamentally
Unreal and is known to be illusory.
Therefore, there is nothing that can be grasped
When you talk of clinging to the idea
Of purity, remember that the self-nature
Is essentially pure. It is only due to false
Thoughts that the absolute is concealed.
If there is no thinking, the self-nature will
Appear pure and clean.

- Bodhisattvasila Sutra


Friday, January 04, 2008

Be Seeing You!

I purchased the DVD set of The Prisoner. The Prisoner has many themes familiar to us today - constant surveillance, mind control, psychological torture, but it was written almost 40 years ago. It's overarching theme is the role of the individual in a dehumanizing, perverse society that treats people as numbers. It seems to have become a cult classic. I remember watching it almost 20 years ago, and the scary thing is that it's even more relevant today than then. As the US, Britain, China, Russia, and India grow, they will seek more and more to control their populations. Their solutions will likely be the same, from constant camera surveillance, to benign and active mind control, to some form of Identification Number given to every individual (REAL ID in the US). From Patrick McGoohan:

I think progress is the biggest enemy on earth, apart from oneself… I think we're gonna take good care of this planet shortly ... there's never been a weapon created yet on the face of the Earth that hadn't been used...

...We're run by the Pentagon, we're run by Madison Avenue, we're run by television, and as long as we accept those things and don't revolt we'll have to go along with the stream to the eventual avalanche... As long as we go out and buy stuff, we're at their mercy. We're at the mercy of the advertiser and of course there are certain things that we need, but a lot of the stuff that is bought is not needed...

...We all live in a little Village… Your village may be different from other people's villages but we are all prisoners."

Number Two:
What in fact has been created? An international community. A perfect blueprint for world order. When the sides facing each other suddenly realize that they're looking into a mirror, they'll see that this is the pattern for the future.

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