Thursday, May 31, 2007
There are few books which I find both reinforcing and clarifying my views, but Chalmers has certainly done this. Chalmers is trained as a physicist and uses examples near and dear to my heart given my mechanics specialty in Engineering Science. Historical examples are the framework that is used in an attempt to look at the patterns of science and especially the interaction between science and experiment. In my 25 years of experience with experiment and theory, but especially due to my specialization in scientific/engineering computing where I can rapidly contrive both experiment and theory, the various observations that Chalmers documents are invariably things that I have experienced first hand. Is the problem with the theory or the experiment? Does the theory really match the experiment, or am I merely deluding myself? If my theory predicts a novel experiment, is this really useful? Or is there some conflicting theory which also predicts the novel experiment and is better in general? On and on it goes.
It seems that all of the theories of science mentioned and the reasons for their refutation have all passed through my head before. The effort to systematically sort through the theories, carefully define them and give them names that can be used to communicate between people, however, is extraordinarily useful and something that I haven't seen before. The reading of this book may or may not be useful for science practitioners, but as a framework for discussion about science it is invaluable. The need for a balance between respect of science and skepticism is extremely important to me. Chalmers undoubtedly has a different balance than I do, but overall, the analysis is something nearly identical to what I have been using.
Here are some of the routine science topics that come up and how they would be addressed from this framework:
0) Science is based on Facts + Logical deductions. Usually, only a creationist is suicidal enough to challenge this, but Chalmers trashes this in the first few pages. I doubt that he is a creationist. What we see as facts is affected by our education and upbringing. The tools of logic are insufficient to get any kind of science off the ground. The real situation of science is vastly more complex and chaotic than what we are taught as children in school.
1) Sherlock Holmes: "when you have excluded the impossible, whatever remains, however improbable, must be the truth". Sorry, Sherlock (and Dawkins), but this wasn't a paradigm that was even considered for refutation purposes. Induction was a paradigm, but Dawkins version is: sonar uses echo location, radar uses echo location, bats use echo location, therefore bats are designed by evolution. This deserves nothing more than a "huh?".
2) Faith vs. Science. I have argued many times in the past that science without faith is impossible. Don Quixote had more success against the windmills. Now we are treated to Beyesian theory where belief (i.e. faith) is assigned a numerical value between 0 and 1! We have interlocking webs and paradigms with Kuhn where the truth of what we see is based on the truth that others see and we are stuck with faith in the community.
3) Evolution. Chalmers studiously avoids bringing evolution into the discussion. The falsification methods of Popper arose due to the problems of Marxism and astrology. How can these be distinguished from true science? The primary complaint was that both Marxism and astrology were "vague and multifarious". In terms of both "vague" and "multifarious", evolution exceeds both Marxism and astrology! Given the multi-million year time frames needed to conduct macro-evolution experiments, a large portion of the theory is in the category of "unfalsifiable". Dawkins, however, mentions a "falsification" item where two widely separated organisms per evolution theory have a nearly identical gene. Immediately an ad hoc modification is employed where it is assumed that a virus moved the gene from one organism to the other. All of the elements of bad science are exhibited here. Why is it even a candidate for science?
4) Intelligent Design. As with evolution, creation science would fail misreable. ID is a different matter. Chalmers has little to suggest regarding "what new theory should we try?" or "what new experiment should we perform?" or even "what new theory of science should we ponder?". Intelligence is what answers these. We bring together pattern recognition, analogies, induction, logic and experience in an unkown process within our heads and answer these questions. Clearly ID is the paradigm that is above both the scientist and the science philosopher. Given that engineering = science+ID, the notion that ID doesn't exist or isn't real is incomprehensible.
5) Does a theory of science exist? The answer from this book is that there are multiple theories with pros and cons, but no general theory that applies to all science throughout history. Chalmers goes further to note that there may be different scientific methodologies in different disciplines.
6) Galileo. If only fundamentalists could discuss science without hearing about flat earths, stupid church leaders and inquisitions! It is soooo refreshing to have a discussion of Galileo and his conflict with the Aristotelians that doesn't require one year of remedial history instruction for the non-fundamentalists!
7) Complexity. Experiments depend on theories and theories on experiments. This is acknowledged throughout the book. What isn't mentioned is that things are becoming exponentially more complex: Experiments depend on more and more theories and assumptions as well as sub-experiments, while theories also take more and more experiments to be confirmed. Does our confidence remain the same in an era of "big science" where some fusion experiments cost more than $1 billion? There is much more to this which affects are political choices.
In conclusion, I loved this book and would strongly recommend it to anyone who wants to actually think and discuss science rather than ignorantly rant about it. Thanks again to Byron for recommending this.
Wednesday, May 30, 2007
This book is rather delightful and something that I am looking at due to a challenge from Byron at Nothing New Under the Sun. My claim to Byron was that there is no theory of science, hence, requiring theology to comply with science is a silly endeavor. He responded by pointing me to this book. At this point, it seems that we both are wrong and both right. Chalmers seems to be quite highly respected in this endeavor and I so far have every reason to agree. More importantly, he has had 20 years to have his ideas presented, challenged, fixed, edited and re-challenged, so there is some maturity in this presentation. The other fact, however, is that scientists don't take philosophy of science classes. They are thrown into the laboratory and generally pick up skills and habits from others who have gone before.
My problem is that I both respect and despise science, because there is clearly much that can be done, but also clearly many abuses and many errors. So far, Chalmers has done an excellent job to diss the version(s) of science that is taught to children in high school or earlier. On the other hand, it seems that there are some consistent concepts which we use and he is slowly working to identify them. I will hold off on any review until I have completed the book, since how the plot ends is not yet clear to me and I am anxious to see how all the pieces fit together when it is done.
Tuesday, May 29, 2007
I bought this at the same time as The Blind Watchmaker with the intent of reading and reviewing it also. A key error of The Blind Watchmaker was the notion that a design space always has an uphill direction. Looking at the title and the first illustration in this book, we again see one mountain, one summit, and there is always an uphill direction. From my engineering experience, I can only rank this as utterly naive. What is clear is that we will be treated to another mountain of errors hidden in a fog of non sequiturs. The book went onto the shelf to gather dust because I have more important things to do.
This was part of yesterday's 30 miler. The summer is starting to arrive, although it won't get really hot for another month. Up on the ridges it was a bit cooler and there was enough wind to keep things comfortable - and the flies away. The grass is mostly brown now and there probably won't be any more rains until November.
Monday, May 28, 2007
I am not quite sure what the point of this chapter was. Microevolution remains non-contentious, but apparently some have protested this. Macroevolution remains the issue, but the key problems that designers face every day aren't mentioned at all, so they were not even honored with a hand wave dismissal.
Dawkins gave an analogy of the horrific battle at Passchendaele during World War I. To hear someone who experienced that battle would certainly be an unforgettable experience. My impression is that Dawkins has never been in the trenches of design, but merely read about them in some history book. Maybe he will find time in the future to write another book and tell us about the blind watchmaker and how he did his design, but I hope he will spend some time with a watchmaker first.
"Nothing in Biology Makes Sense Except in the Light of Evolution" - Dobzhansky, 1973.
In chapter 9, Dawkins noted the dilemma of "punctuated equilibrium" which is compelled by the fossil data. Like it or not, this pretty much precludes any hope of a fossil based verification of macro-evolution ever. Chapter 10 is about taxonomy and is a bit of a rant against some of the practitioners. Taxonomy sets out to identify the "tree of life", which to the Darwinist is an evolutionary tree, but to the Creationist, it is a design tree. How these two would be distinguished is apparently irrelevant.
What is more interesting is that the "tree of life" isn't agreed upon. Now I really don't know much of what has happened in the last 21 years since this was published, by I included Dobzhansky's to put things in context: It was clearly impossible for Dobzhansky to verify macro evolution from fossils, taxonomy, or molecular biology, but that didn't stop him from proclaiming that Darwinism is absolutely mandatory to understand everything in biology.
For the last 140 years, we have been told by theologians that we must believe evolution because the evidence compels it. The overall structure of Dawkins book is now clear however. His first 8 chapters are dedicated to proving that we must believe evolution because the theory compels it, not the data or evidence - exactly the opposite of what I learned in school. Dawkins remains oblivious that all his theoretical proofs would also require that things such as sonar have evolved without the benefit of a designer. In chapter 9, we finally get to the fossil data and he admits that the fossil data will never verify macro evolution. In chapter 10, he admits that taxonomy is a mess. And now, on to the exciting conclusion ...
Links: Chapter 1 & 2, Chapter 3, Chapter 4, Chapter 4b, Chapter 5, Chapter 6, Chapter 7, Chapter 8, Chapter 9,
This chapter takes a completely different tone from what has gone before that gives me a feeling of some humanity behind the author. It is about the theory of "punctured equilibrium", but it still talks around many of the key issues.
In the middle of the chapter, we have this honest admission: "Both schools of thought despise so-called scientific creationists equally". That is a harsh statement. I may not be the least impressed by Dawkins ability to form a rational argument, but that doesn't mean I need to despise him as a person. Unfortunately, this statement is true and also extends to many theologians who despise creationists. Near the end of the chapter, Dawkins says "Whatever the motive, the consequence is that if a reputable scholar breathes so much as a hint of criticism of some detail of current Darwinian theory, the fact is eagerly seized on and blown up out of all proportion." Dawkins mentioned control system theory in the previous chapter. Take his two statements together and we have a feedback loop that is guaranteed not only to lock out creationists, but to silence anyone who would dare report data that conflicted with the theory of evolution. This is indeed the current situation in the Ivory Tower.
Punctuated Equilibrium is a theory that arose due to a conflict between the data (fossils) as interpreted by paleontologists and the perceived theory of evolution being one of more or less constant change. In 1972, it was formally acknowledged that most of the major animal groups show up suddenly in the fossil record. This was neither compatible with creation nor with evolution, if I recall correctly from what I was taught about evolution when I was a child. Dawkins tries to show that evolutionists had always believed in the possibility of wide variations in evolution rates so that none of this should have been the least surprising.
What is more important here is that Dawkins notes a gap between the thinking of the molecular biology community (constant evolution rates), the paleontology community (evolution singularities) and the biology community (something in between). The engineering optimization viewpoint has something to contribute to this discussion. The molecular biology community does an excellent job of looking at current mutation rates. This is a very important contribution for immunology. What isn't possible for them to do is to relate genes to fitness. Optimization is also coupled and we are forever looking at derivatives of fitness functions with respect to design variables. Because it is impossible for molecular biologists to relate mutations directly to fitness, they are forced to abandon the survival of the fittest concept in its entirety and look at mutations alone. Constant evolution rate is the only thing left, but it is completely wrong at a macro evolution level. More importantly, peaks and valleys of fitness are irrelevant by the necessarily simplistic presuppositions of current molecular biology, so the "saltation" issues disappear with a hand wave.
A suggested theory is that most of the macro evolution took place in isolated communities before moving back to larger communities and taking over. The problem here is that we actually do have data. When isolated populations from Hawaii, Australia and New Zealand where brought into contact with Africa, Eurasia and America, the result was the exotic species of the isolated communities suffering, not the other way around.
A final point that Dawkins notes is that selective breeding allows for changes to be made quickly (as in dogs), but eventually there is a point where additional change becomes increasingly difficult. His explanation is that these perturbed states of the species need to build up a sufficiently varied gene pool before evolution can be pushed further and that takes large amounts of time. Optimization theory gives us a different explanation: At the peak or valley, the fitness gradients are near zero, so that perturbations are quite easy. Moving further, however, we eventually hit regions of very large fitness gradients so that it is impossible to keep pushing. If we no longer artificially push the species out of equilibrium, then it will revert back to near its original state. Unfortunately for Darwinism, this is indeed the situation and the reason that "saltation" cannot be explained away without telling science to go to hell.
In spite of these comments, I would commend Dawkins for being much more forthright in this chapter than he has been in any of the previous ones.
Links: Chapter 1 & 2, Chapter 3, Chapter 4, Chapter 4b, Chapter 5, Chapter 6, Chapter 7, Chapter 8,
Sunday, May 27, 2007
First, an excerpt from the book, African Grey Parrots, by Paul R. Paradise.
"Finding a true pair of Greys has always made breeding difficult. Even dealers who import hundreds of Greys and have an eye for what is a male and what is a female are often misled. When they do postmortems on birds that die, they frequently find that a bird supposed to be a female was a male and vice-versa."
In this chapter, Dawkins invokes feedback concepts from control system theory to try to explain the exaggerated tails of the males of certain bird species such as peacocks. Being a perpetual grouch, I will grouch at this on two levels.
Level 1: Dawkins did not mention in this chapter that some bird have drastically different characteristics between the males and females and some have nearly identical characteristics. How is it that the same theory of evolution explains both sets of results? In fact, unlike all other scientific theories which have limited scope, evolution has unlimited scope in being applicable to any data.
Level 2: It is not the least bit nitpicky to note that Dawkins began this chapter by putting the theory of evolution back in it's cage. Next he takes control systems theory out of a separate cage and makes the latter
Like it or not, control system theory and evolution theory are entirely distinct. The former is rigorous and highly mathematical. The later is merely hand waving. I will go on and assert that the theory of evolution really does not have any concrete existence at all. Picking up a book on molecular biology you will always see a similar pattern: Evolution is put on the shelf, a distinct theory of physics or chemistry is used for awhile, and then evolution is recovered afterwards and credited with whatever achievements were due to the physics or chemistry. I would hope that eventually, even atheists would be offended by this silly shell game.
Links: Chapter 1 & 2, Chapter 3, Chapter 4, Chapter 4b, Chapter 5, Chapter 6, Chapter 7,
Saturday, May 26, 2007
This chapter starts with a misrepresentation of a common creationist argument: "People sometimes think that natural selection is a purely negative force ... ". The real issue isn't the natural selection, but the mutation. We don't try to induce mutations into our offspring for obvious reasons: We assume that they are overwhelmingly bad. As I mentioned earlier, Dawkins presumes a monotonic property to the fitness design space which is actually built into evolution theory. Given a constant slope and an equal number of uphill and downhill directions, evolution is guaranteed to head the direction of maximum fitness almost no matter how you work the survival statistics out. The problem here is that there aren't an equal number of uphill and downhill directions. At a summit, all directions are downhill. From the Dead Sea, all directions are uphill. In general, as you approach an optimum the number of increasing fitness directions decreases and the number of decreasing fitness directions increases. Eventually the bad mutations swamp the good ones. Evolution isn't all that efficient, so there is a basic problem that remains glossed over. Moving into X-dimensional design space where X is a large number, this problem is compounded with each new significant design degree-of-freedom. In the multi-objective problem, some of the objectives won't show up every generation. How often is there a plague? Again, the key issue has been completely evaded by the one who presumably has the superior knowledge and can address the issue head on.
The next few pages are appear to be an intron, because I don't know why this matters to the subject at hand. Then we get to a discussion of exon and introns which is worthy of some attention. The assertion is that there are unused portions of the genome - introns - and useful portions - exons. Dawkins claims that this is evidence against design, because it shows that random perturbations acted on the genes. Unfortunately for Dawkins, he explained this using an analogy of the text for The Blind Watchmaker. Various drafts together with the nature of DOS acting on a floppy left fragments all over the disk. So do we conclude that The Blind Watchmaker and/or the various fragments weren't intelligently designed? Perhaps we have evidence that Richard Dawkins doesn't exist!
Of course I am being a little unfair. Dawkins' point is that God wouldn't have been so untidy. This, however, is one of those little points where it is nice to bring out what biologists know, but won't tell you. The floppy disk, for example, is most cost effectively produced in sizes that exceed a majority of the programs out there. What is most efficient for DNA? What is the biological/fitness cost of keeping around a huge DNA molecule that is 90% junk in every cell of an organism? I am not a biology expert, but anyone who picks up a molecular biology text will immediately see that this junk is going to have a big impact on the rate that individual genes are transcribed and many other cell processes, even if the code is completely junk. My software development experience also tells me that unless you know 100% of what a program does, it is foolhardy to declare a portion as junk. Another issue (which might be quite naive) is that these junk portions might be quite useful in some sense related to disease. Some sort of decoy code? Regardless, I have exactly zero confidence in biologists honestly discussing this issue at a college level.
Most of the rest of the chapter is devoted to the notion of a biological arms race. This is the predator-prey paradigm, but again, Dawkins compares this to an arms race such as occurred between the Soviet Union and the US. Is this evidence that neither the Soviet Union nor the US employed Intelligent Designers? A key problem in evolution theory is that technology and intelligent design exist.
Links: Chapter 1 & 2, Chapter 3, Chapter 4, Chapter 4b, Chapter 5, Chapter 6,
Friday, May 25, 2007
The fussing and posturing over Iraq continues. First, as far as I am concerned, Arabs, Jews and Europeans for the most part probably go back to Abraham at one point or another. It is rumored that 16 million Americans trace their descent to the Pilgrims after 4 centuries. How many would be descended from one person after 4 millenia? In a certain sense, we are all cousins, so I intellectually reject all racism and try to purge the emotions that are part of my makeup. That is who I am.
Not too long ago, however, that would not have been the attitude of the West. One group would have said, "Who cares if a bunch of towel heads kill each other? We shouldn't sacrifice our people and resources for them.". Another group would have cynically manipulated the parties to maximize the killing. A version of this was implemented as we tried to keep a balance between Iran and Iraq. They were trying to kill each other, and we made sure that neither got the upper hand.
Today, the honest, racist emotion of "let the towel heads and camel jocks kill each other and we will get some popcorn and beer and sit in the bleachers watching" is reduced to the politically correct, but utterly dishonest "we need to stop the war now, stop the killing, and repent for all of our psychopathic, murderous ways". Both reactions are morally repulsive, but I would rank the later as being lower on the morality scale.
As I said earlier, the question of "Where did the first DNA replicating machine come from?" is just as intractable as "Where did God come from?". In this chapter, Dawkins sets out to disprove this statement by completely evading the issue. Instead, he focuses on how big the universe is and whether or not there might be some unknown (and probably unknowable) chemistry that was the true precursor. The behavior of crystals is alluded to, but I don't see where this leads to anything useful. Did the first microprocessor wash up on a beach due to waves rearranging silicon crystals in sand? Or was it designed? Oh, I forgot - design is impossible, in spite of the neighbor who works at Intel!
In the earlier chapter, Dawkins notes that the Histone H4 protein is common to both peas and humans. We can deduce that the sequence (or something very close) of amino acids is vital to Eukaryotes. This protein has 102 amino acids. If only one 102 amino acid sequence is needed, then the chances of this occuring are one in 5x10132, which is 5x1021 times greater than our absolute upper bound for the number "astronomical" as derived earlier. What is the minimum set of proteins for the first replicating machine? What else is required, since the only replicating machines we know of include proteins, RNA and DNA? Even if all the pieces do happen to exist, what is the chance of them actually being assembled correctly? How many other problems are there that I didn't consider that are the minimum requirements for life? Not only does this chapter not provide any answers, but it doesn't even begin to acknowledge the size of the problem. Again, the only thing that can be said on behalf of the theory of evolution here is that no competitors are permitted, so it is guaranteed to come in first! Survival of the fittest?
Links: Chapter 1 & 2, Chapter 3, Chapter 4, Chapter 4b, Chapter 5,
Thursday, May 24, 2007
Galileo sparked a frenzy when he wrote his book, Dialogue Concerning the Two Chief World Systems. Both the Copernican and Ptolemaic systems are presented together, although Galileo's character who presents the Ptolemaic system is named Simplicio, which roughly means simpleton. If we have a discussion of capitalism vs. socialism, democracy vs. monarchy, free-will vs. predestination, cable vs. DSL, we expect at least to be treated to a caricature of the competing viewpoint.
At almost half-way through the book, Dawkins has yet to formally acknowledge the competing viewpoint: The one of design. What are the strengths and weaknesses of the design argument? I am left with the impression that Dawkins is only comfortable participating in a competition of one.
This chapter focuses on DNA, but as usual, ID analogies are everywhere: Computers, programs, floppy discs, compact disks, ROM, RAM, machines, blueprints. Similar to molecular biology textbooks, ID paradigms are fundamental to understanding what is going on. Then with a sudden wave of the hand, all is evidence for evolution! This is not at all like quantum mechanics. In quantum mechanics, we are compelled to accept a non-intuitive paradigm because none of the evidence can be related to anything familiar and intuitive. Dawkins tries to argue that we should accept a non-intuitive paradigm because everything can be related to things we are familiar with. The fact that these familiar things all run according to the conflicting, ID paradigm is completely ignored. Probably this is the reason that 1/3 of college graduates consistently reject the theory of evolution.
One thing that Dawkins notes is that the DNA vision of biology is new. When we were children, it was all about protoplasm. A hundred years before The Blind Watchmaker was written, however, evolution was proclaimed to be just as obvious, just as firmly established by science and just as compelling based on the evidence, in spite of a completely erroneous understanding of how life worked. Not only was evolution universally accepted in secular environments, but even religious institutions were purging recalcitrants who refused to accept. By the end of the 19th century, evolution was triumphant. The point here is that there is no correlation between the conviction of the Darwinist and the strength and/or availability of his data.
Links: Chapter 1 & 2, Chapter 3, Chapter 4, Chapter 4b,
I remember watching a Addams Family episode where Gomez was returning from parachuting. He explained that each time he does this, he snips a little bit out of the parachute so that eventually he will need no parachute at all! The core of chapter 4 is a synthesis of Paley's wonder together with the idea of evolution. What holds it together is the Gomez logic: We can imagine a small change. The cumulative effect of the small changes allows for big change. It is something that we instinctively know to be false, but virtually impossible to prove false. Just because I can walk increasingly large distances from my home near San Francisco, I really have no expectation of being able to walk to Australia. I can jump a millimeter high one day, and a centimeter the next. Does this mean that I can jump over the moon if I keep at it?
These days, complex systems are never designed from scratch. My several hundred thousand lines of software morphs from one state to another driven both by intelligent design and evolution. When my customers come to me and ask what is possible, there is usually two initial expectations. One is that the effort is incredibly difficult, but usually with a belief that it is much easier than it really is. The other is the opposite of the first. An experienced cost estimator for software or some other engineering project must then visualize an evolutionary sequence that produces the required design. This cost estimator's estimate is invariably quite different from the initial expectations of the customer, unless the customer is also quite familiar with the project. Negotiations are done to bring expectations, costs and risks into some kind of balance. Once the estimate is put into practice, the budget is invariably blown and schedules slip. What was visualized is invariably vastly more difficult when put into practice, no matter what the experience of the cost estimator. Portions of this topic are discussed in The Mythical Man Month by Brooks.
Once the project is finally completed, however, it suddenly seems trivial again. All of the design dilemmas are forgotten and the design increments that produced the final result are trivial to visualize. Suddenly it seems unfair that the costs included dead end design variations and mistakes that needed correction. Again, I am giving all of this in the context of Intelligent Design realities that I live. Not Ivory Tower speculations. There is a huge difference between visualization (imagination) and reality. Yes, Dawkins can visualize all kinds of things, but the gap between imagination and reality is mind boggling.
Wednesday, May 23, 2007
Of course, Christianity considers 'tradition' to be worthless. Tradition is basically man-made and has nothing to do with God's laws and instructions which are universal. As Jesus said, "You have let go of the commands of God and are holding on to the traditions of men".
The priests of depravity know this and always use language such as "human rights" which imply universal validity. As Thomas Jefferson claimed that "all men ... are endowed by their Creator with certain inalienable rights ...". Thus, those who love depravity and hate God invoke the absolute nature of God in their Jihad against morality, while those who would hold to God's laws denounce God in the title of their organization. It is no wonder they are losing.
A proposal I heard awhile back is that all ballots should have a "None of the above" who could be voted for in place of the existing candidates. If "None of the above" wins, then the election would need to be held again with all new candidates. The immigration reform package brought this back to my mind.
Having successfully ignored the elephants in the room for chapter 3, Dawkins proceeds to make some more collosal blunders: He begins by using the eye example and pretending that evolution will do a single objective optimization of a single component. Here, he is projecting a classic ID technique onto the eye. In ID, we work on single components at a time because this is astronomically easier than working on the entire system when optimizing. Either increasing the number of objectives or increasing the number of variables will cause this astronomical explosion in difficulty. Moving from a biological component to a biological system requires both.
Dawkins also introduces us to the X-dimensional design space. Since I work in X-dimensions daily, this is quite familiar to me. What is different about Dawkins X-dimensional space is that all differential increments within this space produce an increase in fitness. There are no peaks, no valleys, no saddle points, no singularities, no non-viable points, no ill-conditioning. All the real problems of design are postulated out of the evolutionary design space. No wonder it is so easy for evolution to do design! If the real world were like this, I too could design anything.
Tuesday, May 22, 2007
This one has been talked about much due to the "me thinks it is like a weasel" example. Dawkins begins by setting up a straw man argument: Evolution is implausible, therefore it is impossible. This is trivially defeated because too many implausible things have become reality. He then sets out to imply the opposite: Evolution must be true because it is plausible. Everything from snake oil salesmen to Star Trek suddenly comes to mind.
The core of his case is the "me thinks it is like a weasel" example where he shows how a genetic algorithm using random letters can be rearranged in just a few generations. Creationists have principally objected that his algorithm chooses the best of each generation and this greatly exaggerates the convergence rate. Of course, if we have a large enough population together with some of the other properties of the problem, this kind of convergence is guaranteed, so this isn't the problem.
The real problem with the example is that it is a single objective, monotonic, constant slope function that is being optimized in a highly restricted design space. The constant slope guarantees that convergence will proceed at maximum speed while the other problem restrictions guarantee that the exponential blowups of probabilities won't be apparent in this case. In the class room, constant slope optimization is a rarity and a key reason that calculus is part of the curriculum.
Even this, however, is trivial compared to the single objective monotonicity of the problem. Mount McKinley is lower than Mount Everest, but it isn't all down hill from Everest to McKinley. A downhill only algorithm will leave you at the bottom of the ocean. Similarly, as we go from one viable software design to another viable software design, the number of non-viable intermediate states is frequently greater than astronomical. For evolution to be plausible, there must be a continuous, monotonic, viable path of fitness that connects from the simplest organism to the most complex. If even one step is missing, then the entire theory collapses. The experience of engineering design is that such a path sometimes exists between two nearly identical designs, but never in general. This is one of the elephants that Dawkins is trying to sweep under the rug.
The other elephant is that before Dawkins could do any of his computational experiments with a genetic algorithm, he needed to have a fully functioning, Intelligently Designed computer. Next, he needed to write a few dozen lines of software with each character being critical to the function of the whole. There are no points for "almost works" unlike the "me thinks it is like a weasel" example. The biologist knows that a certain minimum amount of design complexity is mandatory to represent a genome, preserve it, grow its host, and replicate it. He also knows that this minimum level of complexity is beyond his comprehension and a perfect solution is needed before Darwinian evolution can do anything at all. The Miller-Urey experiment in a way acknowledges the existence of this problem. What isn't acknowledged is that evolution is entirely silent on this issue. "Where did the first genetic replication machine come from?" remains just as intractable as "Where did God come from?".
Consider this CNN article on Palestinians in Lebanon:
"The camp was established by the League of Red Cross Societies in 1949 to Accommodate Palestinian refugees ..."
"Palestinian refugees in Lebanon face specific problems. They have no social and civil rights, and limited access to the government's public health or educational facilities and no access to public social services."
"Most rely entirely on the UNRWA as the sole provider of education, health and relief and social services. Considered as foreigners, Palestinian refugees are prohibited by law from working in more than 70 trades and professions. This has led to a high rate of unemployment among the refugee population."After 58 years, most Palestinians are probably born in Lebanon, but are citizens of nowhere. In Jordan, only 1 in 5 refugees were born in the territory of Israel. Children of illegal aliens born in the US are automatically citizens of the US, but the children of these Palestinians have no legal standing within Lebanon or the other host countries. Like illegal aliens in the US, Palestinians are banned from most jobs. Unlike the Palestinians, illegals usually find a job in the US because this law isn't enforced. In fact, it is the promise of generous benefits plus jobs that draws the illegals here in the first place. Finally, illegal aliens in the US have unlimited access to public health and education.
Much of the problem is that the Arab world maintains petty distinctions related to tribalism that were reinforced with arbitrary borders created in the 20th century. I can't imagine Canadians being displaced into the US and us setting up refugee camps for them and refusing them all services and rights for half a century.
My definition of astronomical is a number that is big enough to account for the size of the universe. It is something that reflects the number of possible events throughout time and space that could have occured from the postulated big bang until now. How big is this number?
If we poke around the net, we find that the age of the universe is guestimated at 15ish billion years. A nice number. Using computer notation, we have 15e9. There are 31,536,000 seconds in a year, giving 4.7e14 seconds since the big bang. If a computer were operating at 1 billion operations per second during this entire time, we would have 4.7e23 operations since the beginning of time.
This is just the beginning. Now what if each particle of the universe were a computer? How many operations could have been performed throughout all time? A "solar mass" is definied as 1.98892e33 kilograms and there are billions of stars in each of billions of galaxies. Astronomers have multiplied this all out and come to a range from 1e72 to 1e87. Taking the upper limit and multiplying by the number of operations, we have our upper bound: 4.5e110, which is 4.5 times 10 billion times a google. Wow! The mother of all computers could do a lot of arithmetic.
Now consider a sequence of 111 base-10 digits. What is the chance of picking a particular sequence? The answer is 1 in 1e111, which is more than the above definition for astronomical. In fact, for those who work in science, engineering and math, 1e110 isn't a particularly big number. A sequence of 111 digits is about as much information as 10 lines of software. If 10 lines have an error, a big chunk of the program will typically fail completely. A typical software product these days has on the order of 1 million lines of software which must be carefully engineered. Still more complex is a biological genome, which typically has 3 billion based pairs to encode the information.
The reason for this discussion is that I picked up "The Blind Watch Maker" to see if Richard Dawkins could form a rational argument. Having read the first 50 pages, I can't answer this yet because he hasn't argued anything. He has mentioned Paley and his awe at the designs of life. He has talked about how engineers do abstract reasoning and described some of the complexities of bats and eyes. He mentioned probabilitiess and billions of years, but only at an elementary school level.
Probabilities come in three forms. First there are the ordinary ones that we face everyday, like the chance of being struck by lightning or being abducted by space aliens(!). Second, there are the probabilities of statistical mechanics which do such an elegant job at describing the behavior of gases such as the air that we breathe. The third is design probabilities requiring specific sequences of characters or words. The probabilities of design problems having occured without a designer tend to be in a class that is completely different where astronomical is a very tiny number for expressing things. Dawkins has graped design. Reading up to this point, however, I am not sure that he has grasped numbers.
Monday, May 21, 2007
Just a review: Evolution and Change are synonyms. If something evolved, it changed. If it changed, it evolved. So what is the Theory of Change? Actually, there are millions of theories of change ranging from Newton's laws of motion to Douglas Adams novels to old wives tales. For some, our confidence is extremely high. Others are pure garbage. The majority are either garbage or uncertain speculation.
So how does Evolution explain things? Evolution, like Change, is a superset of millions of theories. So when the Theory of Evolution explains something, it actually means that sub-theory number 4,332,817 explains the phenomenon, but theory 347,211 might have done just as well. The Evolutionist, having explained something with sub-theory 4,332,817 then observes that Evolution is validated per his observation. The next deduction is that sub-theory 8,543,063 must also be correct because Evolution has been validated per his previous work. This is the core fallacy and where Evolution starts looking more like a Ponzy scheme than a legitimate scientific theory. This is also why the molecular biology text books must alternate reference frames between the macroscopic Evolution concept and the individual sub-theories of physics and chemistry that actually drive change. The connection between the individual sub-theories and the overall Evolution Theory is merely one of grouping and bundling.
Sunday, May 20, 2007
Saturday, May 19, 2007
This article claims that in 5 years the global warming mania will go the way of polyester leisure suits. The reason is that 95% of the greenhouse effect is water vapor while carbon dioxide was only 3.6%. Of the carbon dioxide, man's contribution is only 3.2%, which means that man's total effect on the greenhouse gases is only .12%. What isn't quantified is what we do to effect the water vapor. On the one hand, we chop the rain forest. On the other hand, we make reservoirs in the desert and irrigate a big chunk of the planet which puts moisture back in the air. This might all add up to almost nothing compared to the amount of vapor produced by the oceans.
The reason this is a blessing is that intellectuals are forever taking their inane politics or religion, wrapping them in a "this is science" package, and treating anyone who objects as an imbecile or worse. The growing backlash will hopefully make it more difficult for these highbrow scammers to ply their trade. Darwinists and Intelligent Design deniers, you are next!
Friday, May 18, 2007
A big chunk went to Indian owned companies. The list is loaded with universities. Now I am aware that most engineering professors (and graduate students) are foreign born, but why does Wayne State University need 146 H1b's in one year? Why does the New York City Public Schools need 642 visas (#22), but the Los Angeles Unified School District doesn't show up on the list at all? Maybe there are good explanations, but it would be fun to hear them.
Immigration issues are something very close to me. I have both been an immigrant and sponsored many relatives. Thus, my opinions won't be those of the backwoods bigot, but I presume that won't stop someone from characterizing me as such.
My main gripe is that the border remains a joke, drug prices are heading down due to increasing supply and lawlessness is actively encouraged by our political and religious leaders. So if our government couldn't care less about enforcing the existing laws, why should they care about the new one? In fact, the usual culprits will merely take what they like in the new law and discard anything they don't like. Liberty and Lawlessness for all.
Wednesday, May 16, 2007
Here in the greenest corner of the universe, people are angry about rising fuel prices. For the average 100 mile bay area commute, the current prices still don't hurt much unless you are earning minimum wage. Unfortunately, prices need to be closer to $10 per gallon before people are going to start rearranging their lives around less carbon usage. Before that happens, however, our democracy would probably be overthrown due to hysteria. This is the real reason that global warming shouldn't be taken seriously.
Health costs continue to sore at double digit rates so that California companies have been cutting back on benefits or eliminating benefits altogether. Schwarzenegger and the Democrats are negotiating over plans to fund a universal system. Part of it would come from taxing business and part by fees on doctors and hospitals.
Of course, the problem is almost certainly runaway regulation and litigation combined with caps on numbers of doctors. Another issue is that health users have almost zero incentive to shop based on price and hypochondriacs are invariably fully funded to pursue their hobby. Nothing that is proposed will do anything about this. Kim Jong Il should be proud of our leaders.
Tuesday, May 15, 2007
Jerry was one of the most vocal people on the right for Christian morality for about two decades. Being a public figure who stepped on the raw nerves of the Left, it was guaranteed that every awkward point of his character would be put on display with the good. We all have our faults.
Since he started the Moral Majority in the 1970's, America has continued its march to establish depravity as America's national religion. One shudders to think where we would be today if there had not been leaders who stood up against the theologians and intellectuals who relentlessly push Christian morality out of as many lives as possible, while steadfastly insisting they are the representatives of Christian morality.
Falwell re-branded himself as an Evangelical later on, while sticking to solid Christian values.
The Left too is trying to re-brand as Evangelicals, leading for quite a wide spectrum of opinions within the scope of Evangelical. It will be interesting to see how things develop in the future as this group is not likely to remain harmonious.
This morning, I deleted perhaps 20 spam e-mails from my account. Usually I can detect at a glance what is or isn't spam. Automatic deletion, however, is out of the question because there is about one or two important e-mails per week that the Artificial Intelligence engines mark as spam. Deleting these would be disasterous, so I continue to delete by hand. There are still a number of viagra and other related spams that do get through.
The failure of Artificial Intelligence to handle such an easy task is well known. The fact is that man's intelligence is so complex that only the most trivial tasks can be implemented in AI and rarely to the same degree of proficiency. Does man understand intelligence? No. Does he understand how Intelligent Design is accomplished? Of course not. So why do intellectuals persist in pronouncing ID as a stupid concept when a) it undeniable exists and b) intellectuals don't even understand it? The answer is that if you loathe God, then you are compelled to denounce ID in spite of all the evidence that God piles up in front of your face.
Monday, May 14, 2007
"Many federal judges seem intent on eliminating God from the public schools and the public square in ways that would astound our founding fathers. ... They ignore the fact that the founders were protecting the church from the state and not the other way around."
"However, if judges continue to act like politicians they will get the respect currently given to politicians."
It is almost enough to give hope to this cynic.
Software patents are wonderful things that empower the strong to terrorize the weak and are incredibly efficient at stamping out innovation. The reason that patents stamp out innovation is that they typically cover only one tiny aspect of software that involves thousands of linked algorithms. Frivolous bickering over a few of the algorithms can quickly render the entire product non-competitive. Then there is the bigger issue that while patent enforcement can keep law abiding competitors from making a profit, it does nothing to stop intellectual property theft in some other countries.
Saturday, May 12, 2007
Ooops. I did 6 miles of pavement training on Thursday, which probably caused me to develop the shin splint. The first 14.5 miles to Capehorn pass went well with a 2 hour 35 minute time. That was 10 minutes better than the training run from two weeks earlier, but the pains were starting to develop in the shin area and this was forcing me to run downhill a bit tenderly. The long 4 mile downhill after the summit beyond the pass resulted in the pain slowly increasing. Going up hill was generally preferred since a walk didn't hurt it as much.
About 2 miles from the 50k end point I saw Chiping heading back from the finish for the out-and-back section of the 50 miler. Hopefully he had a good run. The remainder for me became an increasing struggle as every attempt to run was painful and even walking got more and more painful. I reached the 50k endpoint with 6 hours and 35 minutes. Without the shin pain, I could probably have done a bit faster, but I was also fading too. It was certainly enough for the day. This was actually my first time to cover 50k in an organized run, so it still represents a milestone for me. Many other 50 miles gave up before me or finished afterwards. One of them apparently finished the 50k in about 4 hours. Wow!
An interesting feature of this race was that it was the first time that I used an altimeter to check my progress. By memorizing the elevations of the summits and valleys, you can get a good idea of your position on the course using an altimeter. The next two weeks will probably require bicycle training so the shin can heal.
Friday, May 11, 2007
This will be my longest ever "run" that I attempt. The term "run" is used loosely since there will be a lot of walking. Training has gone well and I am quite rested. As always, the completion of this kind of event is in the hands of the Lord. There are simply too many things that can go wrong. I am looking forward to getting up at 4:00am for a long day. Tomorrow is supposed to be fairly cool, which will help me considerably.
My main goal is to finish within 11 hours so that I can qualify for the Western States 100 mile run lottery.
Thursday, May 10, 2007
It took me two hours to get back from San Francisco. The traffic was incredible and the car pool lanes were missing at the major jams. How blessed I am to be able to work from home!
California traffic congestion is a major triumph of NIMBY environmentalism.
Wednesday, May 09, 2007
The statue is of Joseph Strauss, the chief Intelligent Designer of the Golden Gate Bridge. Of course, scientists have proven that Intelligent Design is impossible, therefore, Joseph Strauss never existed. This is a "proven" fact and the existence of the bridge is easily explained by the theory of evolution. The Golden Gate Bridge formed over hundreds of millions of years due to cosmic rays rearranging molecules of iron into crystalline structures. Carbon from the atmosphere was slowly absorbed into the crystal lattice to produce steel. The result was this glorious masterpiece of evolution called the Golden Gate Bridge. See how powerful evolution is at explaining things?
Tuesday, May 08, 2007
I ran a simple test case due to my annoyance with the prophets of evolution proclaiming that evolution was a superior paradigm to ID. The basic problem is of the form: a1^m+a2^m+...an^m -> minimum subject to the constraint a1+a2+...+an=1. This is a trivial optimization problem with the solution: a1=a2=...=an=1/n. We can start it off with a random number generator to make initial values for the a's. Using values of m ranging from 0.5 to 3.5, and values of n=30, a sequential quadratic programming (SQP) method nails the solution to 6 significant digits in about 10 to 20 iterations. The only parameter that I tweaked was the convergence tolerance.
Attempting the same solution with a genetic algorithm requires about 4 million function evaluation and gives me something barely accurate to 2 significant digits. In this case, I needed to tweak the number of parents, the number of children, the mutation rate, the mutation size, the cross-over rates, ... In the end, more ID was required for the genetic algorithm than the ID algorithm! A book I picked up recently, "Evolutionary Computation for Modeling and Optimization" has a chapter on optimization of real valued systems. What is sad is that they do not inform the student that GA methods are hopelessly pathetic when compared to state-of-the-art optimization algorithms. The book does allude to the inefficient of GA, but instead encourages the reader to try IDing the GA methods to emulate aspects of ID methods. Thus, we have a GA implementation of a "line search" algorithm which is a key ID method. In the end, this merely diverts even more ID resources into the effort to prove that ID isn't necessary! Anything to appease the ghost of Darwin.
One final thing to note on this problem is that 99% of the ID goes into the problem definition. Simply by writing down the mathematical description clearly, I have invoked millenia of ID concepts in real numbers, integers, algebra, geometry and calculus. By the time I am ready to solve the problem, countless optimization techniques would work. The fact that a genetic algorithm also works is a no-brainer. This isn't due to the power of GA at all, but rather due to my ID prowess at defining a tractable problem in the first place. The evolution paradigm is worthless in its entirety.
| You scored as Fundamentalist. Fundamentalism represents a movement in opposition to Modernism, stressing the highest importance on foundational religious tradition. Science has brought on corruption of society. God is real and is watching. Scripture leaves little room for interpretation; man is God’s creation. About a quarter of the population in the U.S. is classified as Fundamentalist.|
What is Your World View?
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Monday, May 07, 2007
This is a fun book to read. Fortunately, it doesn't reflect the reality at my local church, but the statistics show that men are leaving the church in the West which seems to be a symptom of a more systematic decline. In contrast, men are doing quite well in Islam making Islam the world's fastest growing religion.
The fundamentalist Christian viewpoint has always been that men and women have equal status and value, although fairly distinct roles. We should first contrast this to the Islamic view, where women exist solely to serve the men. The western secular feminist viewpoint is almost a polar opposite: Men exist to serve the women, or at least men should try to behave more like women.
This viewpoint has moved into the seminaries and pulpits so even the preachers have their personalities modified from the classic John Wayne / Clint Eastwood grouch. OK, they are extreme and I don't like men to be so grouchy. Still, the need for manhood in the church should be obvious. Today a typical Bible study or sermon will frequently focus on subtleties and nuances which are oooed and aaahed over for how profound they are. And just what kind of subtlety and nuances did Elijah or John the Baptist employ? Enough of this nonsense! Christianity needs real men!
Sunday, May 06, 2007
Normally, I consider it foolhardy to start out with a new pair of shoes for a long run, but that is what I did yesterday. REI had a sale so I picked up a new pair on Friday. The retail price of this shoe is $85 and it is advertised as a "cross-trainer" rather than a trail runner, but much of the construction is similar. It is cut lower around the ankle than the regular trail runners which helps me minimize blisters in the ankle area. The price is that they give a little less twist support to my ankles and it makes it easier to collect rocks in the shoe, but I can live with these problems. This shoe also doesn't include Gortex, which saves gobs of money and results in a more breathable shoe (yeah!).
My standard shoes have been Asics for quite awhile due to their comfort, but the softness takes its toll when going over more than 20 miles of rocks. The North Face shoe doesn't have the internal comfort, but does have the harder sole which makes running over rocks relatively painless. The outbound trip from Sunol to Del Valle (19? miles with 4,500 feet of elevation gain) went relatively smoothly. The shoes were good for running regardless of the trail. The real test, however, was on the way back. The last steep grade at the Backpack Area went quite quickly as the rocks still didn't make much of an impression. I was able to run the last several miles of gravel road back to the car. The feet were painful after all of that, but at least the pain was more uniform and there wasn't anything locally severe that would take more than a day to heal. The biggest surprise was finishing up the entire run without a single blister. Another problem that I have periodically is bruised toes, but not this time. What more could I ask for in a trail running shoe?
So why should these shoes be called "Prophecy"? The only thing I can think of is that they would be excellent trail runners to get Jonah from the Mediterranean coast to Ninevah.
UPDATE: Congratulations to Sarkozy.
Saturday, May 05, 2007
This is the first time I went out this far on the Ohlone Wilderness Trail. The picture is looking down on lake Del Valle at the final descent. The road in the distance is one that I have biked many times years ago when I worked at Livermore. The 8 hour 52 minute round trip time is about as good as I could have hoped for. 4 hours 15 minutes was required for the outbound and the remainder coming back. This will be my last long run before the Quicksilver 50 mile run.
Friday, May 04, 2007
In the Ohlone Wilderness, it is usually just me, the vultures, snakes, squirrels and cows, but not much more. Oh, and the Lord, who is always with me and talking to me. I have the greatest pacer of all.
Registration for next year's Miwok 100 begins on January 6th, 2008 at 8:00 am. Don't forget.
In software development, we are usually spending most of our energies meeting deadlines. Everyone is constantly inventing, perhaps discarding and reinventing algorithms. When something works, new deadlines compel the developer to move on immediately to get the next problem solved. So who has time for patents? Typically the developer who files patents is the one with too much time on his hands. Software patents should be done away in their entirety.
The Supreme Court has made it easier to challenge frivolous patents. This is definitely helpful, but for the small business, a frivolous patent means potentially a frivolous lawsuit that can put a company into bankruptcy.
Thursday, May 03, 2007
UPDATE: I finally found the name for this type of bird: Yellow-billed Magpie.
Wednesday, May 02, 2007
This is my thought when the illegal immigration riots heat up: Relax immigration rules, but give vouchers to everyone to send their children to the school of their choice, whether religious or secular. The Left should eat some nasty medicine along with the Right.
I am thankful that I don't drive much. What bugs me is that much of the profits will go to madmen like Chavez or to fund madrassas to promote Islam via Aramco and Saudi Arabia. Iran will use oil wealth to send missiles to Hezbollah, sniper rifles to Iraq, and buy uranium centrifuges. The greens tell us we need to use less oil, which is most easily accomplished through higher prices. In the end, western intellectuals will only find the moral courage to curse western oil companies for increasing their much smaller profits.
This article is a study that shows lesbians are 2.47 times more likely to be obese than average and 2.69 times more likely to be overweight. With GLBT theologians touting GLBT's as model citizens and couples, I thought it would be good to highlight some of the data points that deviate from this script. The article notes that obese people have much higher medical problems. Of course it is always legitimate to make fun of obese people like Rush Limbaugh or Christian leaders who spend too much time eating while they manage their flocks. The authors of the article, however, have discovered something else: "The results of these studies indicate that lesbian women have a better body image than do heterosexual woman". Right.