TCS Daily


Debugging the Universe

By Kenneth Silber - March 9, 2006 12:00 AM

Quantum information science is an arcane field that delves into the role of information in the physical world. Among the questions it asks are: What are the ultimate capabilities for storing, transmitting and manipulating information? Can radically new computers be developed by drawing upon quantum mechanics, the physics of the extremely small? And, is the universe itself some kind of computer, and if so what does this mean?

The field's cosmic implications are explored by two new books with similar titles. Programming the Universe: A Quantum Computer Scientist Takes on the Cosmos gives the perspective of Seth Lloyd, an MIT professor of mechanical engineering who has been a pioneer of quantum computing. Decoding the Universe: How the New Science of Information Is Explaining Everything in the Cosmos, from Our Brains to Black Holes is by science journalist Charles Seife.

Both books are wide-ranging, sweeping from classical thermodynamics and information theory to cutting-edge quantum cosmology. Although each book has merit, Lloyd's is the better work, more engaging in its presentation and less likely to cause confusion. Seife sometimes blurs distinctions between speculation and established science, for example when he hypes the many-worlds interpretation of quantum mechanics or darkly warns that "civilization is doomed" when viewed on a cosmological timescale.

Traditional information theory and computing are built upon bits, the answers to yes-or-no questions, expressed as zeroes or ones. Quantum information science, by contrast, makes use of qubits, units that can assume a continuum of values; this reflects the quantum-mechanical property whereby particles can exist in a state of superposition, simultaneously exhibiting multiple values for such variables as speed and location.

Manipulating qubits, a quantum computer could perform vast numbers of calculations simultaneously. Such computers, however, now exist only in rudimentary form, incorporating small numbers of particles. A practical hurdle to quantum computing is that the required superposition state is fragile; environmental influences jostle particles into taking on definite values for speed, location and such. Nonetheless, future quantum computers may be able to perform such feats as breaking now-invincible codes.

Much work in quantum information science, moreover, aims at understanding the physical world better by applying concepts of information processing. Relativity, as Seife points out, is essentially a theory of information. Although some experiments suggest that pulses effectively can travel at faster-than-light speed, relativity's cosmic speed limit remains inviolate because no information is actually transmitted at the higher speed.

Lloyd has performed calculations regarding the physical world's capacity for information processing. He notes, for instance, that "the ultimate laptop" (a collection of matter the size of a laptop computer, but in which every particle is utilized for computing) could store more information than all the hard drives now existing. Moreover, he has run such numbers for the observable universe as a whole. By Lloyd's calculations, this cosmic computational capacity equals 10122 operations on 1092 bits of information.

These figures can be interpreted several ways: as an upper limit to how much computing could have been done in the universe; as a lower limit to what would be required to simulate the universe; or, as an actual description of what the universe has done. Whether one regards a physical system as a computer, Lloyd notes, is somewhat subjective, and in his view it is useful to consider the universe to be a giant quantum computer. Such an approach, he believes, will generate new insights into physics, including on the highly difficult problem of reconciling quantum mechanics and general relativity.

The universe-as-computer concept may also play into the current strife about intelligent design. It might be argued that a computer implies a programmer. However, this may be taking the analogy too far. What the universe is computing, in Lloyd's picture, is not some external output but rather its own behavior. And a very large portion of its computing power seems to be tied up in such behavior as random collisions of atoms.

<>Indeed, Lloyd's argument may be disturbing to intelligent-design proponents, in that it suggests how complexity can arise from an underlying randomness. In Lloyd's favored analogy, monkeys typing on typewriters produce gibberish — but monkeys typing on computers can produce simple code that would generate a wide variety of outputs.

Similarly, random quantum fluctuations allowed galaxies to coalesce, and later shaped the development of complex molecules like DNA. Lloyd sketches out how life may have originated in a rock crevice, with chemical reactions providing the computing power.

Seife, for his part, very briefly discusses intelligent design, noting accurately that some anti-evolution claims are based on a misapplication of the second law of thermodynamics. This law encapsulates the tendency of physical systems to move to more disordered states, but it applies only to closed systems. By contrast, organisms are open systems that receive energy from their environments (and ultimately from the sun).

Elsewhere, Seife uses terminology that is likely to create confusion. He posits a possible "law of conservation of information," without noting that Intelligent Design theorist William Dembski has used the same wording to propose a different law. Seife is referring to how information continues to exist in some form after it has been violently altered; the smoke from a burning newspaper contains data about the newspaper's content, albeit impossible to reconstruct, and even black holes seem not to truly eradicate the information in the matter they consume. All of which has nothing to do with Dembski's claim that organisms contain information that could not have been produced naturally.

Kenneth Silber is a TCS contributing writer focused on science, technology and economics.

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27 Comments

Only ID can save humanity!
"Indeed, Lloyd's argument may be disturbing to intelligent-design proponents, in that it suggests how complexity can arise from an underlying randomness."

Actually, what disturbs the ID proponents the most is the FALSE ASSUMPTION that accepting evolution will beget an immoral, irresponsible, race of human beings.

Origins 101: Worldviews Begin With Beginnings
AFA Journal, March 2006

...What's at stake in the debate? In short, everything. "Whatever a culture adopts as its creation story shapes everything else," Pearcey writes.

If evolution continues as our culture's official orthodoxy, Christians can only expect the complete secularization in all areas from education to entertainment, from philosophy to politics. And with the NATURAL IMPLICATIONS THAT HUMANS ARE NEITHER ACCOUNTABLE NOR RESPONSIBLE, the future is likely to be one in which raw power rules.

But don't give up too quickly. Although it faces an uphill battle, acceptance of Intelligent Design as a viable theory of origins is growing. At a minimum that could result in the re-establishment of the discarded idea that human life has inherent meaning and purpose. And that could change everything.

http://www.afajournal.org/2006/march/306origins.asp

Shal we regress a moment?
"Lloyd sketches out how life may have originated in a rock crevice, with chemical reactions providing the computing power."

And from where did "the Rock" and the chemicals come? And why did the chemicals react this time in the way they did and not every time they reacted?

If one searches for the process of origins of life when, if in fact, origins of life are not a result of a process, then what is the probability that such a search will result in truth?

Ex Nihilo, of course
Everything that is came from nothing, its ordered and it persists autogenically and anybody that can't see that is obviously a ignurunt hayseed without enough fermal larnin'.

No Subject
Well, "The Rock" came from his father (Rocky Johnson) and maternal grandfather (Chief Peter Maivia) were both professional wrestlers in the WWF.


Sorry, being silly...

So, let's just hope...
That the programmer doesn't decide to delete all the cookies and defrag...

Debugging the unverse,
I read this artical with quriosity, but understand very little, can reviewer not write little simple way. Those who are not trained in science for those you must explain more simply.

Thanks, Ken
I'm in Silber's debt for saving me from reading these tomes to nonsense, and the nonsense that is ID. Thanks.
Don V.

Time and Ethics
"Indeed, Lloyd's argument may be disturbing to intelligent-design proponents, in that it suggests how complexity can arise from an underlying randomness. In Lloyd's favored analogy, monkeys typing on typewriters produce gibberish — but monkeys typing on computers can produce simple code that would generate a wide variety of outputs."

Q: What's the difference between the content of Lloyd's typing, my typing, and the monkeys' random typing, given uncertainty (the uncertainty principle of quantum mechanics)?

A: Time expended in production.

Q: What's the difference between the cognitively useful content of Lloyd's typing, my typing, and the monkey's ramdom typing, given uncertainty (the uncertainty principle of quantum mechanics)?

A: Time and ethics.

He cannot write simpler because a lot of it is nonsense
No one has yet to show how complexity and information together have ever been generated out of randomness. It is the wishful science fiction of the material determinists.

So to imply that complex molecules necessary for life can arise from random quantum fluctuations is absolute nonsense and utterly disingenuous.

Maybe Silber should study the enormity of the origin of life problem. His writings indicate he has no conception of the issue but he is given a platform here for his drivel. The origin of life people have done some interesting research but their so called emergence theory sheds no light on how something as complex and information filled as ATP synthase could have appeared let alone how a cell with genetic material and metabolism could have developed on its own. ATP synthase is just one example and is only one of hundreds of proteins that must have come into existence for metabolism to take place in a cell.

If there were one monkey for every atom in the universe typing on their computers from the Big Bang there would not be enough time to create DNA or one of these proteins let alone the hundreds that were necessary for the first cell. And this does not even include the assembly instructions for a cell which puts all these proteins in the right places and the right sequence. That is a separate issue requiring even more complexity and information than the creating of the parts.

Until the those who propose a deterministic solution for the origin of life state the enormity of the problem accurately and deal with it, they can not be taken as serious people.

ATPase
First, ATPase is not necessary for there to be metabolism. But it is an efficient way to have metabolism, so natural selection chose ATPase as the way to go. However, we also now know that RNA enzymes can also synthesize ATP. Incidentally, there are also RNA enzymes that reproduce themselves and others, transfer amino acids onto tRNAs, transfer amino acids from tRNAs onto growing polypeptides, engage in electron transfer, edit, and splice. For this reason, there has been proposed an "RNA World" as predecessor of the life we now know. Also, it is a false assumption to assume that modern-day metabolism is the only form, and the only form that has ever been. Primitive metabolisms would have arisen first, and led to more complex metabolisms that were more efficient. These more complex metabolisms would have been selected for through natural selection. Of course, these early metabolisms would have arisen through self-organization. A few years ago, the journal Science raun an article about how rocks self-organized through water between the rocks and variable temperatures into rings and loops. If you were to see the rocks, you would naturally have wondered who had come out there and organized the rocks into those rings. Rocks organized into connected rings are a sure sign of an intelligent designer, right? Yet it was proven that self-organization was suffient to explain them. Now with this, we are talking about a very simple process. With life, we are talking about much more complex organic chemicals (even the smallest ones have more complex interactions with one another than do rocks), which naturally result in more complex systems arising.

Unfortunately, these forums are insufficient to deal with the enormity of the problem. Don't rely on them for information. Rather, go read people like Stuart Kauffman, who does deal with the enormity of the problem. He, at least, does not create the kinds of maps as do the IDers, which read at certain points: beyond this point lie monsters.

Natural formation of Pyruvic Acid
Something I came across recently while reading up on Pyruvic Acid:

Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate
Science 25 August 2000:
Vol. 289. no. 5483, pp. 1337 - 1340

Experiments exploring the potential catalytic role of iron sulfide at 250°C and elevated pressures (50, 100, and 200 megapascals) revealed a facile, pressure-enhanced synthesis of organometallic phases formed through the reaction of alkyl thiols and carbon monoxide with iron sulfide. A suite of organometallic compounds were characterized with ultraviolet-visible and Raman spectroscopy. The natural synthesis of such compounds is anticipated in present-day and ancient environments wherever reduced hydrothermal fluids pass through iron sulfide-containing crust. Here, pyruvic acid was synthesized in the presence of such organometallic phases. These compounds could have provided the prebiotic Earth with critical biochemical functionality.

http://www.sciencemag.org/cgi/content/abstract/sci;289/5483/1337

Your answer supports my point of view
The absurdity of your reply supports my point of view that there are no serious people supporting the determinist origin of life point of view.

Let me make some points from your reply

1. How can natural selection choose ATP synthase if it doesn't exist? How did this molecule come into existence. It couldn't be by chance since the probability of that makes Susskind's alternative universes look like a small number in comparison. What produced it? In order for the fittest to survive, there has to be a fittest in the first place.

2. It cannot be that an RNA molecule produced it because the probability that this RNA molecule exists by chance is even smaller than the ATP synthase molecule. These things don't just happen because you want them to. They have to exist for a reason other than that they would be convenient for your scientifically bankrupt theory. You cannot just wave your hand like Mickey Mouse and have it appear.

3. You claim there are other metabolic energy pathways. Maybe you should suggest a few so someone can comment on it. No hand waving here either and say they just exist or must have existed.

4. You assume an RNA world but there is no evidence that anything like this ever existed or even could exist. It is another example of wishful science fiction. The only reason the proposition exists is because a DNA or protein world is even more improbable. There is a real cytosine problem and a fairly impressive adenine problem as well as a very serious ribose problem.

Even if you could find some method of creating the bases and the ribosome for the RNA, there is no plausible way they would combine in any way to form a molecule that contained information. Random RNA molecules don't cut it.

By the way the RNA world is going out of favor. You should keep up with the latest propaganda masquerading as science.

5. What does self organizing rocks got to do with anything? You are confusing order and complexity with information. I am sure there are all sorts of self organizing examples in nature but this is not a sign of information formation. Stuart Kauffman has not produced any thing with information content that did not already start with information content. Complex, yes; but nothing that stores information and reproduces itself.

6. You save the best till last. ID peopke create maps which read at certain points beyond which lie monsters. What a silly comment which just reinforces my point about the lack of serious people espousing a deterministic origin of life view. Are the ID people monsters in your imagination?

Thanks for making my point so easily. If you abandon your deterministic view point you might just learn some science.

Origin-of-life probabilities
Some good sources refuting claims that a natural origin of life was too improbable to have occurred:

http://www.talkorigins.org/faqs/abioprob/abioprob.html

http://www.infidels.org/library/modern/richard_carrier/addendaB.html

DOn't MIstake me for what I am not
First of all, I am not a determinist. The world is in part deterministic, but with emergent complexity comes emergent freedom as well. The world is not just ordered and deterministic, but chaotic and free as well.

It is difficult, at best, to deal with these issues in such a forum. There is, after all, only so much time and space. That being said, let respond at least somewhat, point by point.

1. Your first question shows that you have absolutely no idea what evolution is all about. Not even remotely. Please, for the love of God, take some biology classes. Preferably in molecular biology (I have, to say the least -- I have a B.S. in recombinant gene technology, and I have two years of grad school in molecular biology). ATPase is merely a catalyst. There are many, many kinds of catalysts. And there are many kinds of energy molecules. You assume that only ATP can provide energy. Sulfur, phosphates, heat, light -- all of these can and do provide energy through electron transfers. The most primitive of life would have used the most primitive of energy sources. Also, there is good evidence that clays provide a good surface on which biochemicals can attach, interact, and react. As these biochemicals reacted in systems, we would have had increasing complexity in structures. Some polypeptides would have formed, and these would have themselves provided reactive surfaces. Amino acids and other biomolecules have been found in meteors, and the early earth was constantly bombarded by meteors and comets, providing things such as amino acids to the earth's surface, where they could have then interacted. We know there are biomolecules on some of the moons of Jupiter and Saturn, for example, so such molecules are not uncommon. As polypeptides formed, some would have been more active than others. They would have been selected for. As they resulted in the creation of more complex molecules, there would be more selective pressure. Mutations result in changes, so that some molecules would have developed different forms -- including, later, ATPase from a non-ATPase molecule. WHatever early cell developed something like ATPase would have had an advantage over those that had not. By definition, evolution creates new things from things that were not there -- you don't have to have ATPase in order to create it and then select for it.

2. Organic ring structures are very stable. These molecules can be created from the simplest of molecules: water, carbon dioxide, and ammonia. And there were far more complex molecules around, which would have easily provided the building blocks. Your average organic chemist can make all the nucleotides.

3. Photosynthesis is a metabolic pathway. In fact, there are lots of organic cycles that are driven by light. ALso, there is chemisynthesis -- there are organisms that make use of sulfur to provide energy. Metabolism is simply an organic chemical cycle, and there are lots of organic chemical cycles, which are self-organizing, and run by heat and light and chemical interactions.

4. I addressed some of the problems you mention here. I would only point out that randomness precisely does cut it, because there is a correlation between randomness and order. A "random" string of nucleotides is highly ordered and structured. It can interact with itself and other things in many different ways. When, among all the different strings of nucleotides, there arose one that could copy itself, that one had a clear advantage -- as it was making copies of itself, and randomness was no longer an issue. Of course, there would have been mutations, which would have resulted in different forms -- many would not have worked, and a few would have worked better. Other functions would have arisen. Other strings would have arisen with different functions that would have found being in association with the reproducing RNA very beneficial, as they would have been reproduced as well. These "parasites" would have given an advantage when mutations occured that resulted in beneficial functions. There was perhaps not an RNA world as the first metabolizing pathways, but RNA certainly preceeded DNA, and once it arose, it certainly created a beneficial environment for other biomolecules that associated with them.

5. are you really suggesting to me that rocks organized in rings do not have more information content than do randomly distributed rocks? This has everything to do with information -- self-organization results in an increase in information content.

6. Have you never seen those old Medieval maps of the world, that showed all that was known of the world? In the places that were unknown, they put "beyond this point lie monsters." The result was that people for a long time did not search beyond those points. They were told that there was nothing to see here, so they didn't look. Fortunately, Columbus ignored such people. The IDers have the same attitude: that there is a point beyond which we should stop looking. That is the gimick behind "irreducible complexity." They have no idea if such a thing exists, but they go about declaring this and that to be "irreducibly complex," with the intention of shutting down all inquiry. Thus, it is deeply anti-scientific. There is no irreducible complexity. There is emergent complexity. And we are learning more and more about how it works. SOme choose to remain in darkness. I prefer to climb out of the cave and into the light.

It does help if you are educated enough to get my analogies.

Trolling for irrelevant articles
Do you know how to do anything other than to troll the internet for irrelevant articles? This experiment or similar experiments found several other organic compounds besides pyruvate but so what. Whoopie Do.

Try understanding the problem and maybe you will find some meaningful information to discuss.

Do you know what pyruvate is? It is the primary source for energy for most athletic competitions and the output of the glycolytic cycle. It is converted to lactate unless used immediately as fuel for the Krebs cycle to produce aerobic energy. By products from the Krebs cycle break down even more in the electron transfer system to produce a lot more energy, carbon dioxide and water (it is where the sweat comes from if the exercise is intense enough). Pyruvate is also a relatively simple molecule. It is roughly half a glucose molecule which is also rather simple. You should check out ATP synthase if you want to see something complex. Pyruvate compared to ATP synthase is like comparing a lean-to with the Empire State building.

Consult Robert Hazen's book and you will come up with a lot more interesting stuff about origin of life but not anything that comes close to addressing the problem.

Hazen makes a big deal out of the Citrus Acid cycle or Krebs cycle in his theories on the origin of life which is why he spends some time on this experiment that produced pyruvate. However, Hazen fails to deal with the real complexity of the problem. He won't quantify it because he knows how big the numbers are and all he is doing is shooting blanks. If he told the truth his research grants would probably dry up and he would be ostracized from this bogus area.

The research produces some very interesting information but I am not sure if it has any relevance to the origin of life. A lot of the ID people believe that Hazen and like folks should continue their research not because they think they will find something but because they may find something with relevance elsewhere and the more they flounder on the origin of life issue the more it emphasizes the probability of design.

Another Point
Just because science has not given us all the answers to the universe right now, that does not mean that it will not give us the answers, or that it cannot give us the answers. You may be surprised to know that we do not know everything there is to know, that we still have much to learn, that can be learned through the scientific method. We have to develop theories and hypotheses to test to learn more and more about how the world acts. It does not benefit knowledge to declare that some areas are off limits or inherently unknowable. That is what ID does, and why I object to it. Perhaps there are aspects of life that are inherently unknowable in a scientific sense -- but we are nowhere near knowing where such places lie.

From your postings, you would have been one of the people objecting to the work of Galileo. He was discovering things that were not known -- and those things were inconvenient to the religious world view of the time. But did it benefit CHristianity to continue to believe that the Earth was at the center of the universe? Has it truly harmed Christianity one bit that we have learned it is not? I suppose too that, a hundred years ago, you would have ridiculed the people who theorized about there being other planets around other stars -- and yet, we have discovered planets orbiting other stars.

Are we there yet with our knowledge of biology? Hardly. Biology is two magnitudes of complexity above physics. We are very impressed with ourselves for all we have done in physics, for all we have learned about it. And we should be. But we have only begun to scratch the surface of knowledge of biology. The things happening in biology are so complex, it is difficult to imagine. And we are still making profound discoveries in physics -- with information theory, chaos theory and fractal geometry, emergency theory, complexity theory, and self-organization. Just because 99% of biology is unknown, don't write it off as inherently unknowable. We are at the frontier of biological knowledge.

You got to be kidding
You are sending someone to infidels.org for an unbiased scientific analysis? These are the same guys that roam Amazon leaving one star reviews on anything that questions Darwin. I wouldn't dream of sending anyone to a creationist web site for a discussion of this issue. Talkorigins is bad enough but infidels? Next time you write an article why don't you use infidels.org as your reference and watch even the Darwinists cringe.

I will read them both more carefully when I have time to see how these people rationalize their positions so when the next article appears I can relate their points of view in more detail. A quick glance and I noticed several comments on the infidels site that seem rather stupid. Both sites seem to be enamored with a step wise approach which always seems reasonable till you have to produce the steps. Then it is just hand waving and saying the other person is an idiot. Show me the money. Or better yet the science.

They also seem to ascribe to the infinite number of proteins theory and the set we have are only a small set of what could work(again based on a quick glance). Sounds like a modified form of Susskind's logic. I know that people have classified the amino acids by their tendency to attract or repel water and by charge and other characteristics to see which amino acids are interchangeable. This extends the number of possible protein sequences that could be used for a particular function but even with this modification the numbers are still daunting. Especially since amino acids just don't like to form bonds with each other particularly in water. Then there is the left handed problem.

You got to ask why the speculations on these sites are not part of the serious origin of life research. By the way that is all they are is wishful speculations. Go through each and find the hard science. Their speculations and criticisms may fit their worldview but every belief system needs some faith. This particular set of beliefs just needs a lot more faith than most.

You are talking nonsense
I know of no theory or scientific area that ID says it off limits including Darwinism. You are ignorant of what they claim. Before you make statements like you have here you should try to learn what they say and not what others may have told you. You are also making things up about what I believe. You have no idea what I know or believe.

Nothing is out of bounds for scientific enquiry as far as I am concerned. Go where the science leads as long as it is done honestly and reported fairly. I have yet to see one person favoring the determinist point view report information on evolution fairly.

Your comment indicate that you haven't a clue about Galileo and what happened nor what I think about it. Galileo's theories were not proved till a 150 years later in the late 1700's. In the early 1600's they were just hypotheses and the Catholic Church was in conflict with Protestanism over the interpretation of scripture and Galileo's hypotheses seemed to contradict some passages in scripture. Science and religion have generally been congenial. Probably the most prolific group of people in the history of science have been the Jesuits. And a lot of important science was done at Catholic universities. Similarly a lot of Protestants were equally involved in science. Newton was a very religious man. It is only in the last 150 years that science has turned secular.

You make my point for me by admitting that biology is so much more complex than physics. Thank you. Something so complex just does not happen by chance.

I do not believe biology is more complex than physics though. The creation of DNA and the amazing complexity of the cell is a magnificent achievement but it pales in comparison with the fine tuning of the universe and the power and intelligence that was needed to create it. Unless you are like Silber who believes in an infinite number of universes and we are the lucky ones who landed in the one that works. But then that begs the question why does anything exist let alone an infinite number of universes. Existence is the ultimate question.

No Subject
'I will read them both more carefully when I have time...'

Good. That would be better than dismissing them for what they 'sound like' or who they supposedly are.

Complexity
I don't know why I waste my time talking with people who do not udnerstand the simplest of points, and make an argument where there was not one. Don't mistake me for what I am not.

The fact that you don't even understand biology is more complex than physics shows the state of your ignorance on the subject. I suggest a university education strong in science, and especially in complexity. But I doubt you care to get one.

Self-organization explains precisely how complexity arises by chance. And so does chaos theory, and complexity theory, and systems theory, and information theory, and game theory. All of these theories, and if you knew anything about them, you would know this to be the case, explain how complexity arises out of simplicity.

Irreducible Complexity
When someone says that something has "irreducible complexity," they are saying that no matter how much research you do, you won't find out what caused it to be the way it is.

Look more closely at what I actually said about Galileo.

The Catholic church has changed a lot since then. Today it is opposed to creationism and has refered to ID as both unscientific and un-Christian. I side with the Catholkig church on such things. (increasingly, I side with it on most things)

Give examples
I did not bring up false information about ID. You did.

I did not bring up false analogies about Galileo. You did.

I did not bring up monsters on the edge of maps. You did.

I never said that anything was unknowable or any area should not be investigated. You made that up.

I never questioned your education in science but you assumed I lacked it. My undergraduate majors were physics and mathematics and have studied biology on my own. My current job requires that I understand cellular energy metabolism. The cell is a magnificently complex creation.

I have read detailed discussions on origin of life research from both sides. Have you? Not just the tripe that Silber recommends.

I have read James Watson's book on DNA in which he says he was relieved when he and Francis Crick discovered the double helix because it meant that biology followed the laws of physics. Have you?

I did not imply the Catholic Church or Christianity was backward on science. You assumed I did.

I did not mistake the Catholic Church's position on creation. You did. You should look at the ceiling of the sistine chapel as an indication of the position of the Catholic Church on creation. Also read Cardinal Schoenborn's articles on Intelligent Design. He has never denounced it and in fact spoke favorably on it. Cardinal Schoenborn is one of Pope Benedict's closest advisers. Pope Benedict talks about design in the world on several occasions. Both have said that science and religion should never be in conflict.

Look at your responses to my emails and my responses to yours. Do you see a difference? The only thing I assumed was that you held deterministic views. Otherwise you will believe that somethings are not deterministically caused. If you are not a material determinist then indicate an area in which you are not. One of the obvious areas would be the origin of life but there may be others areas where someone suspended the laws of nature which you believe are more pertinent.

By the way if you subscribe to the Catholic Church's view point then you subscribe to prayer and miracles. Both are interferences in the laws of nature.

Connecting the obvious
Without realizing, you have made the point for me.

Pyruvate IS a relatively simple molecule that can arise from geo-chemical reaction, leading to a non-biological metabolism of sorts -- perhaps the very first adopted by life. ATP, however, is part of an advanced metabolic system that evolved from something less complicated.

So if you're argument is that ATP is a "miracle," then say so, otherwise acknowledge that ATP evoloved.

Agreed
At least I appreciate your efforts, zatavu, even if it falls on deaf ears. Self-organization, it seems, is tantamount to the miraculous for some in the ID crowd.

Out of Context
ANd you have taken all those things out of context. I created an analogy with the maps, and you read some pretty bizarre things into it.

I questioned your lack of education in biology precisely because I saw no evidence of an education in biology. It does not surprise me that your education is in math and physics. It shows. Perhaps you know a great deal about math and physics, but, as SOcrates pointed out when he went to the craftsmen to learn if they knew what they were talking about, he found that they did: "they knew things I did not know, and to that extent they were wiser than I. But, gentlemen of the jury, the good craftsmen seemed to me to have the same fault as the poets: each of them, because of his success at his craft, thought himself very wise in other most important pursuits, and this error of theirs overshadowed the wisdom they had" (Apology). I have read Watson's book -- and more, I have studied molecular biology extensively. Yes, it does "follow the laws of physics," but just because the laws of physics are the foundation of biology, that does not mean that is the end-all and be-all of biology. One can certainly reduce everything happening in a cell to physics -- but this will tell you nothing about the outcome of those interactions, which is the complex cell. If one takes only a reductionist view of the world, as you clearly have, then of course one cannot conclude but the things you do. But that is only half the equation. The other half is that of emergent complexity. The complex physical interactions create systems that act as systems, and not merely as individual physical entities. A cell is a set of complex organic chemical systems reacting and interacting to create something with more complex actions than one could predict from the chemical interactions alone.

Let me give an example:

?The following is an extremely shortened and imprecise
explanation of what would happen in the following situation. Suppose we have some mobile bacteria in solution and we put a drop of toxin in the solution on one side of the container. What would happen in purely chemical terms is the following:
The toxin spreads from the point of origin through the liquid. Toxin molecules bind areas on folded polypeptide molecules embedded in a phospholipid bubble to generate a geometrical change in the polypeptide, causing a chemical reaction on the inside of the bubble (let us say the specific chemical reaction is the addition of water to guanosine triphosphate (GTP) – a composite molecule consisting of the purine guanine, attached to the 1'-carbon of a ribose molecule, with a chain of three phosphates attached to its 5'-carbon – to create the molecule cyclic guanosine monophosphate (cGMP), and a diphosphate). The product of this reaction builds up so long as the toxin keeps the polypeptide properly configured, until there is enough cGMP to bind another polypeptide to create another chemical reaction. This reaction culminates in a configuration change in a polypeptide close to the highest concentration of the toxin, so adenosine triphosphate and water can attach to it and react to create adenosine diphosphate and phosphoric acid, along with a change in the polypeptide’s geometry, which makes it rotate a polypeptide connected to a chain of polypeptides. Continued chemical reactions of ATP and water result in more polypeptide chain rotations. This chain of chemical-physical events continues until the toxin is at low enough concentrations to decouple from the initial polypeptide and thus interrupt the cascade at its origin.
And now for a biological explanation:
The bacterium senses the toxin, and swims away to a safe distance.
The purely biological explanation is much simpler than the chemical one. The simple biological explanation is an illusion masking the chemical complexity (and I gave a shortened version of that) underlying what happens biologically. This is also known as emergent complexity.

The Catholic church's most recent comments on ID proclaim ID to be un-scientific: from http://www.msnbc.msn.com/id/10932031 :

The Vatican newspaper has published an article saying “intelligent design” is not science and that teaching it alongside evolutionary theory in school classrooms only creates confusion.

The article in Tuesday’s editions of L’Osservatore Romano was the latest in a series of interventions by Vatican officials — including the pope — on the issue that has dominated headlines in the United States.

The author, Fiorenzo Facchini, a professor of evolutionary biology at the University of Bologna, laid out the scientific rationale for Charles Darwin’s theory of evolution, saying that in the scientific world, biological evolution “represents the interpretative key of the history of life on Earth.”

He lamented that certain American “creationists” had brought the debate back to the “dogmatic” 1800s, and said their arguments weren’t science but ideology.

“This isn’t how science is done,” he wrote. “If the model proposed by Darwin is deemed insufficient, one should look for another, but it’s not correct from a methodological point of view to take oneself away from the scientific field pretending to do science.”

Intelligent design “doesn’t belong to science and the pretext that it be taught as a scientific theory alongside Darwin’s explanation is unjustified,” he wrote.

“It only creates confusion between the scientific and philosophical and religious planes.”
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And, indeed, it does. Incidentally, prayer and miracles are not interferences with the laws of nature -- they are gifts from God that are outside the consideration of the laws of nature. THey are in addition to, not interferences of.

Finally, I am not a materialist. I subscribe to an ontology of information. Determinism is but one half of the story. And not believing in determinism does not mean that someone suspended the laws of nature. It means, in my case, believing in a set of theories that show the world not to be deterministic, but one of emergent complexity and freedom. I happen to believe that God is not such an incompetent creator that he had to continue interfering in the universe to keep things going. But if you really want to see more of what I think of ID and evolution, I recommend you go to http://www.thegreatideas.org/phpBB2/ where I have been carrying on this discussion with others. I develop several of my ideas in greater detail there.

Do you understand anything?
There is no evidence that ATP evolved. Wherever you got your quote from or if you made it up yourself it is a meaningless statement. You can never say that something evolved from something else unless there is evidence on how that evolution took place. It is no more meaningful than saying Mickey Mouse came by and waved his magic wand and the thing changed. As far as evidence for a certain point of view is concerned the use of the expression "it evolved" is the same as saying there is no evidence about how this thing appeared for the first time.

There has never been any evidence for one thing evolving from another except for some examples of micro-evolution. Be the first to present evidence and you will be a Nobel Prize winner. There is nothing but speculation based on wishful thinking. For the statement ATP evolved from something less complicated has no meaning unless you can find a whole host of intermediates between it and something else and evidence that one thing followed another.

You can speculate all you want but do not pass it off as science. Be honest for a change and be the first pro Darwinist in the world who is. Self organization in the world is a common phenomena and to imply that those who accept the ID view point think otherwise is either stupid or dishonest. Take your pick. Which are you?

There are hundreds of examples of self organization, some completely uncontroversial and some speculative. Go to wikipedia and you will find a bunch. When I say uncontroverisal, I mean there is scientific evidence for it and I suspect we will continue to find new ones. When I say speculative, I mean there is no evidence but some people wish it were true. You decide which is which.

Micro-fallacies
"Be honest for a change and be the first pro Darwinist in the world who is. Self organization in the world is a common phenomena and to imply that those who accept the ID view point think otherwise is either stupid or dishonest. Take your pick."

Self-organization is not some bizarre local phenomenoma, it's a universal principle. So if you accept it, then accept it as such. Thus the molecules that comprise ATP or Pyruvate or anything else can arise from simpler structures without Devine Intervention.

And while you think that over, realize that Intelligent Design makes no attempt to describe the origin of Life. Where, when, and how did this intelligent agent act. Did natural evolution do most, some, or none of the work for life to arise? Did this intelligent Agent create ATP, the entire cell, or entire species -- and all at once, or over billions of years?

Just what the hell does Intelligent Design claim to have happened?

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