Life 2.0

From the article "Life 2.0" (MSNBC):

So far, researchers have fabricated individual biological building blocks, but they have yet to create an entirely new synthetic self-replicating organism. "Chemical synthesis of life has been a standing challenge to synthetic organic chemistry," says Venter (with palpable impatience). But SynBio researchers see no reason to wait until whole organisms can be created from scratch. They are happy to stitch together lab-designed biological components, or "biodevices," with parts of natural cells to construct hybrid organisms. The SynBio enterprise is not some ivory-tower exercise but a pragmatic field that could soon produce results. Church, who at 53 is an elder SynBio guru, thinks it could happen as soon as two years from now if funding is ramped up and scientists don't run into major snags.

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In a first, scientists develop tiny implantable biocomputers

In a first, scientists develop tiny implantable biocomputers from PhysOrg.com

Researchers at Harvard University and Princeton University have made a crucial step toward building biological computers, tiny implantable devices that can monitor the activities and characteristics of human cells. The information provided by these "molecular doctors," constructed entirely of DNA, RNA, and proteins, could eventually revolutionize medicine by directing therapies only to diseased cells or tissues.

[Continued]

After my first reading of Engines of Creation (December 1987,) I knew that eventually advancements such as this would be made. But I wasn't expecting to see it announced until the middle of the next decade.

Wow.

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The Mathematical Universe

In the paper The Mathematical Universe (PDF,) cosmologist Max Tegmark takes the (epistemological) position that the External Reality Hypothesis (ERH) strongly implies the Mathematical Universe Hypothesis (MUH.) MUH holds that reality isn't just described (modeled) by mathematics, but that mathematics and reality are actually deeply equivalent.

The abstract of the paper says "I explore physics implications of the External Reality Hypothesis (ERH) that there exists an external physical reality completely independent of us humans. I argue that with a sufficiently broad definition of mathematics, it implies the Mathematical Universe Hypothesis (MUH) that our physical world is an abstract mathematical structure. I discuss various implications of the ERH and MUH, ranging from standard physics topics like symmetries, irreducible representations, units, free parameters and initial conditions to broader issues like consciousness, parallel universes and Gödel incompleteness. I hypothesize that only computable and decidable (in Gödel's sense) structures exist, which alleviates the cosmological measure problem and help explain why our physical laws appear so simple. I also comment on the intimate relation between mathematical structures, computations, simulations and physical systems."

In another paper, Parallel Universes, Tegmark defines a taxonomy of different types of Universes (reminiscent of Georg Cantor's taxonomy of different types of infinities.) The existence of Type IV Universes would be a probable consequence of the Mathematical Universe Hypothesis.



In addition to making me think more deeply, and more outside the box, than anything I've read since encountering Eliezer Yudkowsky's essay Staring into the Singularity, these two papers by Tegmark strongly remind me of several things that may be deeply related:

• Gödel's incompleteness theorems


• General semantics


• Pan-critical Rationalism


• The Laws of Form

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End of the Universe as we know it?

The article "Is the evidence for 'alien' universes all around us?" (New Scientist) discusses the possibility that the cosmic microwave background (CMB) left over from the big bang shows evidence that our universe must have collided with others during it's initial period of space-time inflation.

As intriguing as that sounds, it raises yet another issue that just might be of more importance. Apparently, this would mean that there is yet another way for our Universe to end--without warning, and with no known way to prevent it. If you were thinking that the Big Crunch or the Heat Death of the Universe were the only two options, think again:

If universes really are crashing into us willy-nilly, should we be worrying about a fatal collision? "It's true, there is always a chance we will be hit by a lethal bubble, which would come without warning," says Vilenkin. "But since we'll just evaporate in an instant and there's nothing we can do to stop it, there's really no use in worrying."

Life is a major cause of death.

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Diamonds tell tale of comet that killed off the cavemen

From the article Diamonds tell tale of comet that killed off the cavemen:

Scientists will outline dramatic evidence this week that suggests a comet exploded over the Earth nearly 13,000 years ago, creating a hail of fireballs that set fire to most of the northern hemisphere.

Primitive Stone Age cultures were destroyed and populations of mammoths and other large land animals, such as the mastodon, were wiped out. The blast also caused a major bout of climatic cooling that lasted 1,000 years and seriously disrupted the development of the early human civilisations that were emerging in Europe and Asia.

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Researchers Put 'Spin' in Silicon, Advance New Age of Electronics

Researchers Put 'Spin' in Silicon, Advance New Age of Electronics from PhysOrg.com

Electrical engineers from the University of Delaware and Cambridge NanoTech have demonstrated for the first time how the spin properties of electrons in silicon--the world's most dominant semiconductor, used in electronics ranging from computers to cell phones--can be measured and controlled.

[Continued]

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Welcom to the Next Level: Graduating from Genomic To Poteomic Modeling

Normally, if a sci/tech story has already been published on Slashdot before I can post it here, I don't post it here (that happens a lot, by the way--and even more often, Slashdot posts on a story after I have done the same.) However, in some cases, the story is simply too important to ignore. For example, there's this article:

Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development, which presents research results that indicate we're now "going to the next level" in our ability to model biology computationally. We've been modeling biology at the level of genes and amino acids for quite some time now. The next level above that would be the ability to model proteins and protein-based biochemical messaging pathways as a system of inter-operating machines. That's what the above-referenced article is about. Quoting the abstract:

Here, we have developed a dynamic computational model incorporating the current mechanistic understanding of gene interactions during this patterning process. A key feature of our model is the inclusion of multiple modes of crosstalk between the epidermal growth factor receptor (EGFR) and LIN-12/Notch signaling pathways, which together determine the fates of the six vulval precursor cells (VPCs). Computational analysis, using the model-checking technique, provides new biological insights into the regulatory network governing VPC fate specification and predicts novel negative feedback loops. In addition, our analysis shows that most mutations affecting vulval development lead to stable fate patterns in spite of variations in synchronicity between VPCs.

Welcome to the next level.

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From ink to optics, study of particle mixtures yields fundamental insights

From ink to optics, study of particle mixtures yields fundamental insights from PhysOrg.com

Since the invention of ink over 3,000 years ago, people have exploited the unique properties of colloids, in which particles of one substance are suspended in another. Now, Princeton University chemical engineers have answered a fundamental question about these mixtures in work that may have wide-ranging practical applications, including the manufacturing of medicines and optical fibers.

[Continued]

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Do fruit flies have free will?

Do fruit flies have free will? from PhysOrg.com

Free will and true spontaneity exist … in fruit flies. This is what scientists report in a groundbreaking study in the May 16, 2007 issue of the open-access journal PLoS ONE.

[Continued]

My comment: The article says "The term 'will' would not apply if our actions were completely random and it would not be 'free' if they were entirely determined." That's not quite correct. The fundamental issue is this: Our behavior must be fully determined by who and what we are--otherwise, it is not "our" behavior. To put it another way, "free will" and determinism are not, as is commonly believed, mutually exclusive. In fact, "free will" requires that our actions must be a deterministic function of our selves.

The key idea behind free will is neither randomness nor independence of its operation from deterministic law, past history or present stimuli. Free will does not imply any such conditions—and if it did, those conditions would argue against the idea that it is justified to assign moral significance to a person’s conduct.

If a person’s free will were truly random, truly non-deterministic, then that would completely exonerate the conduct of that person. Why should a person bear any moral responsibility for conduct that is intrinsically unpredictable, uncontrolled, random and not determined by anything whatsoever?

Free will requires only that a person’s conduct be determined as a function of who he is, and that he be capable of modifying his conduct in response to events. Strict determinism in no way prevents either of these requirements from being met—as artificial intelligence research clearly shows.

The only illusion connected with free will is the illusion that free will is incompatible with determinism, when in fact free will requires determinism. Just because your response to stimuli is strictly determined in no way denies you free will. Your response to stimuli must be determined by something. With no determinant to your choices, you would have no will at all. What better and more appropriate determinant of your behavior could there be, other than you yourself—your own state of being? The fact that your ‘outputs’ (responses to stimuli) are completely determined by your ‘inputs’ (incoming stimuli) does not change the fact that there must be a function that maps your inputs to your outputs: and that function is you, your essence, your brain, your mind, your personality, your soul.

You have free will precisely and only because you are able to map inputs to outputs, stimuli to responses, goals to actions and information to concepts and beliefs. What makes your will free is the fact that you have a transcendent, invariant goal: the meta-goal to acquire and achieve goals. It is you that must decide how best to achieve your meta-goal, based solely on who you are, what you know, how you feel and what you experience—independent of the will of any other creature. What more could one ask of free will?

Your will is free because it is independently yours, because it is a function of both external stimuli and your state of being, and does not depend on the will of anyone else. Is that not what freedom really is: independence from the will of others? Therefore, strict physical determinism does not mean that free will is an illusion. Free will does not require some random, non-deterministic or supernatural mechanism in order to exist

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How to market a dynamic programming language

The Ruby on Rails community has provided us with a canonical "how to" for marketing a dynamic programming language: Ruby on Rails vs Java.

Where's the Smalltalk version?

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A Two-Time Universe? Physicist Explores How Second Dimension of Time Could Unify Physics Laws

A Two-Time Universe? Physicist Explores How Second Dimension of Time Could Unify Physics Laws from PhysOrg.com

For a long time, Itzhak Bars has been studying time. More than a decade ago, the USC College physicist began pondering the role time plays in the basic laws of physics — the equations describing matter, gravity and the other forces of nature.

[...]

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Common genetic variation is linked to substantial risk for heart attack

Researchers at the Icelandic genomics company deCODE Genetics, along with U.S. researchers at Emory University School of Medicine, Duke University, and the University of Pennsylvania, published an article in Science today announcing the discovery of a common genetic variation on the 9p21 chromosomal region that significantly raises the risk of developing heart disease independent of other recognized risk factors, such as weight, diet or cholesterol levels.

The stretch of DNA (called 9p21) that carries the mutation is in an area of the chromosome that had not previously been identified as a gene. The 9p21 region is not associated with inherited tendencies to have high cholesterol or high blood pressure. But 9p21 is found near two genes called CDKN2A and CDKN2B, which four international teams of researchers last week reported they had identified in their own genome-wide association study looking for genetic causes of diabetes.

The researchers found that, were the gene variant not present, there would be 21 percent fewer heart attacks overall in the population and 31 percent fewer early onset heart attacks.

The medical establishment is slowly coming to the realization that cholesterol does not cause heart disease. Inflammation causes heart disease (which is why statin drugs prevent heart attacks: because they inhibit arterial inflammation.) And lots of things cause inflammation (such as homecysteine.) Perhaps the mutation in the 9p21 chromosomal region either causes inflammation, or makes an individual more susceptible to inflammation-induced arterial blockage.

References:

[1] Common genetic variation is linked to substantial risk for heart attack | PhysOrg.com

[2] DNA mutation causes heart disease in whites | Yahoo | Reuters

[3] The Cholesterol Myths

[4] Inflammation and atherosclerosis

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Web Services 'Wizard' May Help Computers Do People's Work, Scientist Says

In the article Web Services 'Wizard' May Help Computers Do People's Work, Scientist Says, ScienceDaily reports:

Many web services exist today to allow people to find information on websites. But machines can't negotiate with other machines or engage in rudimentary deductive reasoning, as Petrie envisions. Computers use the standard Web Services Description Language (WSDL) put forth by W3C, a consortium established by web inventor Tim Berners-Lee, to understand input messages and deliver output messages in the same language.

But even if a standard way of describing computer services exists on the web, each description uses different terms. A person planning a trip can go to an airline website and find flight information. But machines charged with the same task fail. "Flight" may be abbreviated as "flt" on one carrier's website but as "flite" on another's.

"A human can look at those two words and know that must be the same thing, but a machine has no idea," Petrie says. That makes it difficult for web services to search multiple sites, retrieve desired information and present a menu of options.

Existing web services lack a common understanding of terms. The way to fix this, Petrie says, is to develop formal semantics, or logical expressions from which meaning can be inferred. The challenge is that some formalisms are expressive but too hard to compute, while others are easy to compute but insufficiently expressive.

Full article

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NEC, JST and RIKEN demonstrate world's first controllably coupled qubits

NEC, JST and RIKEN demonstrate world's first controllably coupled qubits from PhysOrg.com

NEC Corp., Japan Science and Technology Agency (JST) and the Institute of Physical and Chemical Research (RIKEN) have together successfully demonstrated the world's first quantum bit (qubit) circuit that can control the strength of coupling between qubits. Technology achieving control of the coupling strength between qubits is vital to the realization of a practical quantum computer, and has been long awaited in the scientific field.

[Continued]

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Cheap source of energy: Cell splits water via sunlight to produce hydrogen

It has often been argued that hydrogen-based power could not be economical, due to the fact that the amount of energy required to produce unbound hydrogen was greater than the energy to be obtained by using unbound hydrogen as a fuel. The problem with that argument is that there was no proof that the situation was anything other than a transient technological limitation. For all anyone knew, a net-positive-energy pathway for using hydrogen as fuel might be discovered at any time. And that's just what Physorg.com now reports has in fact happened:

Cheap source of energy: Cell splits water via sunlight to produce hydrogen from PhysOrg.com

Engineers at Washington University in St. Louis have developed a unique photocatalytic cell that splits water to produce hydrogen and oxygen in water using sunlight and the power of a nanostructured catalyst.

[Continued]

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To Treat the Dead

In the article To Treat the Dead, Newsweek highlights the implications of research that shows that cells don't die after a mere 5 minutes without oxygen. Cells will continue to live for hours without oxygen. The reason that 5-minutes (approximately) of oxygen deprivation usually leads to cell death is that, after about 5 minutes, oxygen actually becomes toxic to the cells.

It's the reperfusion with oxygen-carrying blood that causes cell death, not the 5-minute lack of oxygen itself.

One implication is that it may be possible to develop drugs and/or treatment protocols that will allow the revival of heart attack, stroke or trauma patients after an hour or more without blood flow, instead of the current 5-minute limit. Another implication is that cryonic suspension is far more likely to work than most would have believed.

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Astronomers Deal Blow To Quantum Theories Of Time, Space, Gravity

From the article Astronomers Deal Blow To Quantum Theories Of Time, Space, Gravity:

That theoretical upper limit was then used to set theoretical limits on time. One cycle of a photon carrying that much energy would last 5 x 10-44 seconds, an interval called Planck time. As the shortest potentially-measurable interval of time, theorists speculated that time moves [in] Planck time-sized quantum bits.
...
If time is made up of quantum bits, that would also mean space and gravity should also be composed of quantum units.

Since the expected blurring "signature" of quantum space time isn't seen, however, it might mean that time isn't made of quantum bits, and neither are space or gravity.

Full Article

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