Creation Bits

This blog has been officially superceded

2008-06-01T21:36:00.001-07:00

I just finished transitioning all of my blogs onto my new website. Here is the superceded version of this blog. Also see all of my other blogs.

This video is great!

2008-03-30T11:19:00.000-07:00

Methodological and Philosophical Naturalism

2007-02-25T06:28:00.001-08:00

If by “methodological naturalism” one means something distinct from “philosophical naturalism”, then there are two necessary items:

1) There are things that science cannot deal with. This also means that if science attempts to deal with something outside its scope, then it will likely be wrong. However, given that, is there a way to determine if a phenomena is studyable by science? If there is not a mechanism to determine whether phenomena X is within the boundaries of science, then how do you know that your inquiry and results are reasonable?

2) If methodological naturalism is really distinct from philosophical naturalism, then there should be no problem with a hypothesis that is methodologically naturalistic but has implications against philosophical naturalism.

An example of #2 is irreducible complexity. IC _is_ methodologically naturalistic. It implies philosophical non-naturalism, but there is nothing in IC which requires anything but methodological naturalism to deal with.

Another similar issue is the direction of complexity. Do more complex sequences evolve from less complex sequences or the other way around? If we are not assuming philosophical naturalism, there should be no problem with the hypothesis that previous forms were more complex rather than less, and that evolution is either a “de-evolution” or a working out of previous patterns. Neither of these hypotheses are distinct from methodological naturalism, but they both imply philosophical non-naturalism.

As a practical example, look at the origin-of-life. There is an assumption that this event can occur through physics and chemistry. Methodological naturalism would not assume this. There is absolutely no evidence that this can occur. In fact, there are numerous reasons why life should be an “assumed” of science rather than it be assumed that life can develop from non-life. Under the assumptions of methodological naturalism, there is no reason to assume that life can come from non-life. Yet many only consider origin-of-life scenarios “scientific” and the idea that life only comes from life is non-scientific. The fact that the latter hypothesis is the only one which has evidence (and thus should be preferred in a methodologically naturalistic scenario) the fact that many textbooks talk about the “origin of life” show that they are participating in philosophical naturalism rather than methodological naturalism.

Fantastic Post at Creation Safaris

2007-01-16T11:23:00.000-08:00

Creation Safaris has a FANTASTIC POST about people who lose their faith through science, and the futility of using science as a foundational epistemology. This should be required reading in the crevo debate.

Why Many Distrust Public Schools

2006-11-20T20:45:00.000-08:00

I'm hoping that this is just a teacher being stupid and not reading the actual answers from the curriculum....

Here is a homework assignment on logic. The nicer handwriting is the teacher writing the "right" answers.

I am convinced

2006-08-23T07:49:00.000-07:00

I am convinced that most Darwinists have absolutely no clue about what Intelligent Design is about. This problem is worsened by the fact that many people like to argue for "intelligent design" without having either read anything on the subject nor doing any sort of research into what it is about.

As a good test of your own knowledge of what Intelligent Design is about, see this paper (just the abstract and conclusion are enough to see the content of the paper -- the conclusion is on pgs 65 and 66) and see if you can tell why this paper is considered to be a paper on Intelligent Design (and in my opinion, one of the most important papers on Intelligent Design).

If anyone wants to discuss the paper, or doesn't understand the connection to Intelligent Design, please post in the comments below.

Can we get an apology?

2006-08-21T14:15:00.000-07:00

I've heard SO MANY TIMES from evolutionists who complain that there is no difference between micro- and macro- evolution, and that the distinction is an invention of creationists who have their head in the sand. Now, the micro- macro- distinction is often used in evolutionary peer-reviewed literature (some even adding an in-between level -- meso), but the evolutionists who complain about Creationists not publishing in the peer-reviewed journals seem to not have read it. Now that PZ Myers is officially on record about the micro- macro- distinction, can all of the evolutionists who complained about this being a false distinction created by deceitful Creationists to apologize?

Just to clarify -- I don't think that PZ ever made this accusation. But I have been in a great number of evolutionary debates, and in nearly every one where the topic was discussed, they said that micro/macro was a false distinction created by Creationists.

(just to note, depending on how it's defined, Creationists don't necessarily disagree with macroevolution per se, either)

The Evolution and Design Class at Cornell

2006-08-16T17:22:00.000-07:00

Recently there was a biology class in Cornell dealing with Intelligent Design and Evolution. It was unique in that not only was ID-vs-evolution a topic open for discussion at a major university, but also that it invited participants from all perspectives to the debate on the class's website.

If you are interested, the record of the site/class discussion is archived here and the student papers on evolution and design are here.

I participated fairly heavily in the debate, especially in the opening weeks. Hannah and Salvador were the primary ones holding up the ID position.

Anyway, it was a great time, and a lot of learning by everyone.

Many thanks to Allen McNeil for opening his class to the rest of us.

Intelligent Design Postings

2006-06-27T05:47:00.000-07:00

Over at UncommonDescent, I have a post establishing the link between evolution and abiogenesis and also a parody of the people who complain about a "God of the gaps".

Apparently, reductionism makes you less than sane. At what point of denying reality do we get to call in the people in the white coats?

The Cobb County Sticker

2006-06-13T08:48:00.000-07:00

Edward Sisson has written a great review of the Cobb County case. It makes numerous excellent points, including:

The fact that all available textbooks teach evolution, and that the Cobb County school board chose the most hard-line pro-evolution text, and chose to include that evolution material in the curriculum, clearly communicates to those who endorse evolution that they have become the dominant political insiders, and the Sticker merely shows that they do not have absolute monopoly control – yet.

It is deeply disturbing that the trial court felt that failure to give the pro-evolution side absolute monopoly control was equal to sending a message to the pro-evolution side that they are “political outsiders.” Nonsense. Denying someone monopoly control of an issue is not the same as declaring that person a political outsider on that issue. That the trial court could judge such a record to have such an effect bespeaks an extreme bias.

Interesting Conversations

2006-05-30T23:50:00.000-07:00

Thought you all might find the following conversations interesting:

The argument from incredulity vs. The argument from gullibility

Dennett and Dawkins are “Darwinian Fundamentalists” — Dennett says so himself. This has a great definition of what Darwinian Fundamentalism is, and why there is a controversy:
A Darwinian fundamentalist is one who recognizes that either you shun Darwinian evolution altogether, or you turn the traditional universe upside down and you accept that mind, meaning, and purpose are not the cause but the fairly recent effects of the mechanistic mill of Darwinian algorithms. It is the unexceptioned view that mind, meaning, and purpose are not the original driving engines, but recent effects that marks, I think, the true Darwinian fundamentalist.

Artificial EAM presented as RMNS

Paul Nelson apologizes for misrepresentation after Darwinists throw a hissy. I completely agree that Nelson should make the correction, but isn't this a case of the pot calling the kettle black? If a single misrepresentation of a single email thread from several years ago is enough to be put on Brayton's "bad Creationist" list, what would happen if the same rubric were applied to evolutionists? I think the standard he is holding up is idiotically high, and the fact that there exist creationists who can stand up to it for years on end speaks _highly_ of the ethics of the creation movement, not lowly.

The limits of adaptability -- there were many good conversations. I think that my conversation with Chris Hyland was especially interesting.

Science Magazine Promotes Irreducible Complexity and Genetic Front-Loading

2006-05-19T19:59:00.000-07:00

Did I miss the part of the show where Science magazine started pushing ID? In the May 19th issue, all-of-a-sudden it seems that they've switched sides. Now they are advocating something which sounds an awful lot like front-loading, and using irreducible complexity as the evidence. Crazy stuff.

What this new paper is saying is that Eukaryotes are the ancestors to Prokaryotes, not the other way around. So what's the big deal? Two things. (1) It directly contradicts the slow progression from less complex to more complex idea, and (2) the reasoning behind this is somewhat based on Behe's idea of irreducible complexity, but without the explicit Intelligent Design implications. Obviously there is a lot I would disagree with, but this is a huge, huge, huge step in the right direction. It acknowledges the difficulty in creating complex, integrated cellular machines from an evolutionary framework. It also acknowledge that there are actually limits to evolution's ability. They also fail to point out the difficulty to the origin of life that this brings (if the ancestor is _more_ complex, then you have even more difficulties) and the implicit hat tip to front-loading (front-loading is an ID hypothesis that the universal common ancestor was created pre-loaded with all the information necessary to differentiate into many lesser forms -- the information is "front-loaded" into the universal common ancestor, and then later organisms are all specializations and degredations from that ancestor).

Interestingly, if you use this reasoning to say that eukaryotes can't have evolved from prokaryotes, why couldn't you use this reasoning to say that eukaryotes can't have evolved from nothing?

Let's look at the primary argument:

Genomics and proteomics have greatly increased our awareness of the uniqueness of eukaryote cells. This, together with increased understanding of molecular crowding, as well as the dynamic, often reductive nature of genome evolution, offers a new view of the origin of eukaryote cells. The eukaryotic CSSs [cellular signature structures] define a unique cell type that cannot be deconstructed into features inherited directly from archaea and bacteria. [emphasis mine]

This points out that evolution is primarily in the detrimental direction. In fact, this fact is referred to throughout the paper. Usually, however, they mention the idea that evolution goes both up and down, and the fact that the "down" part has been ignored by many biologists who view evolution as upward-only. However, while they were correct in pointing out the failing of the "upward march" evolutionary argument, they failed to point out that the "up" part is primarily an inference from universal common ancestry, not an empirical observation from the data. In their defence, they were primarily talking about sequence loss and gain, not information. The idea of conservation of information is not dependent on the sequence length. There are indeed beneficial things which increase genome length. But these always occur within a larger semantic framework which governs them.

Anyway, they talk a lot about the potential for genome decay, which is another ID/Creationist idea.

The hat tip to irreducible complexity is in both the title and the last sentence of the quote. There is no step-at-a-time scenario which facilitates going from bacteria and/or archae to eukarya.

Anyway, it is very significant that this paper was published in Science.

Meyer vs Ward VIDEO

2006-05-15T20:08:00.000-07:00

I previously posted audio to this debate. The video is available, now, too.

Traces Preceding Actuals, Fossil Poop as Evidence

2006-05-13T20:57:00.000-07:00

Distribution of Footprints and Body Fossils

When debating flood geology, the lines of evidence that I concentrate on are those that point out that the sorting of the fossil record seems to not be based on time properties, and therefore another set of properties needs to be investigated (obviously the one I think is appropriate is the flood).

For example, when you look at the comparison of fossil footprints with body fossils, you find a massively disproportionate fossil distributions in amphibians, reptiles, and dinosaurs, with footprints concentrating in the lower strata (Triassic and Jurassic), and body fossils concentrating in the upper strata (Cretaceous).

While evolutionists don't seem to think anything of this, Creationists think this is evidence of fleeing behavior from rising floodwaters. After the K/T boundary, which is where many Creationists put the zenith of the flood, there are very, very few footprints found.

Trackways Preceding Body Fossils

It's interesting that in many cases, our earliest evidence of an animal is from its trackways, not body fossils. For instance, this paper in Geology points out that arthropod trackway fossils precede arthropod body fossils by 40 million years according to the geologic timescale. This isn't unique, either.

Dinosaurs Pooped Grass Before it Existed

Really interesting data comes from fossilized poop. This paper makes some interesting points about grass:

Grass is known only in poop in the late Cretaceous

Grass is known only in pollen in the Paleocene

Real grass fossils don't exist until much later in the Paleocene

That's about 50 million years between when grass was pooped out to when it actually became a full-fledged member of the fossil record.

Obviously, evolutionists simply view this as pushing back the time when grass came into being. But creationists think that it should cause pause for people when grass is showing up in poop 50 million years before it shows up anywhere else. If the fossil record for grass is off by 50 million years, what else is off by 50 million years? And what makes us so certain that we simply lack the evidence for its existance well before that? Of course, it could be that time is not the dominant factor in fossil sorting.

The Coelacanth and Others Presumed Dead

Finally, it is interesting to see fossils presumed long-dead are still alive and well. The Coelacanth has not left a fossil in almost a hundred million years according to the geologic record. In fact, it's position in the fossil record is so steady that it was long used as an index fossil. However, the Coelacanth is still alive and with us today. On page 4 of the issue of Creation Matters linked above, it has graphs of three animals long presumed dead which are very much with us. The Neopilina has been missing from the fossil record for 350 million years, and yet still lives.

The evolutionists use terms such as "ghost lineages" and "lazarus taxa" to preserve their suppositions. Obviously, if the fossil record did represent millions of years, it would be imperfect. However, this is more than imperfection. These are systematic problems that occur over and over again. If the fossil record is a record of millions of years, it is so spotty that really nothing of interest can be gleaned from it. However, I believe that it is a record of something much different -- a record of death from the flood.

You have ocean bottom dwellers at the bottom. Amphibians above that. Trackways of amphibians and reptiles (in many places, such as the grand canyon, they are almost all going uphill). Body fossils of reptiles. And then a period of few or no fossil tracks. After that, you start getting a more-or-less modern assortment of land animals. Now, why so few mammals in flood rocks? Because dead mammals and birds float (reptiles suspend and amphibians sink).

I think the facts of the fossil record point to a physical process. While the process of the flood is not fully elucidated yet, I look forward to future research which will do just that.

Meyer vs. Ward

2006-05-02T14:53:00.000-07:00

Stephen Meyer has faced off against Peter Ward twice. Check them out here.

The first match was on the radio (transcript).

The second match was a live event hosted by the Seattle Times.

What is the Intelligent Design Research Program?

2006-04-22T20:05:00.000-07:00

Several times the issue has come up -- what is the Intelligent Design research program? Many people think of Intelligent Design as simply being a negative argument about evolution. If you want the Creationist research program, see my other blog. They overlap to an extent, but they have very different focuses.

Biological Research

Research into informationally-directed changes in the genome. See Molecular Strategies in Biological Evolution (also see my summary of the first paper in this volume), A Biochemical Mechanism for Nonrandom Mutations and Evolution, Adaptive evolution of highly mutable loci in pathogenic bacteria, and Environmental regulation of mutation rates at specific sites (last three summarized here).

Possibly restructuring taxonomy around design patterns instead of incidental historical happenstances. See Sternberg's description of the ID on taxonomy.

Exploring the limits of biological change. See Axe's paper on the sensitivity of proteins to gradualistic mutation and my own article on the subject.

A holistic view of biological systems. For example, Wells sees centrioles as not just having a lot of interactions, but that the point of their interactions being to generate a polar ejection force. And, as pointed out before, irreducible complexity is just an empirical definition of holism, so see Darwin's Black Box.

Genome decay as a real phenomena. See my previous review of this subject.

The Study of Purposeful Action

Most people incorrectly view Intelligent Design as being about biology. Biology is actually just a side-issue of Intelligent Design -- though it is a very, very active side-issue. The fundamental idea of Intelligent Design is the study of purposeful action. It rests on a theory of causation that purposeful action is distinct from material causes. Current science is oriented around material causation. However, if you are to study purposeful action, you will need a very different set of tools. ID is only scratching the surface of what is there. You have a whole host of issues as to how purposeful causation links to material causation. This sort of study will, by necessity, look different than investigations into material causes. It will also not be as predictive as material-based-science, because purposive causes are, pretty much by definition, not completely predictable. That does not mean there is no means of empirical analysis available, only that it will take on a distinctive character. Dembski's primary work in this area is The Design Inference, which examines the nature of intelligent/purposeful causation in order to make an inference whether or not a system has an intelligent cause as its origin.

Other People's Lists

Dembski's List of Design-oriented Research Questions

Dembski's Keynote address at RAPID discussing moving ID to a disciplined science.

There was another list of research topics in ID, but I cannot locate it at the moment. It had several suggestions along the lines of the study of purpose and mind.

Of course, one of the best benefits of Intelligent Design in research isn't even the research program itself, but an end to the endless, needless invoking of evolutionary just-so stories and exaggerations in every biological paper. For two simple examples, see this article and this one. Or just see this site for a near-real-time listing of some of the more funny and eggregious. Here is d’Abrera’s summary of the situation:

No field worker who studies insects, may now freely gaze upon his discoveries of insect morphology, biology or behaviour, without the taint of speculative Darwinism compelling him to colour his conclusions. No more is such a worker allowed to make direct, uncomplicated observations about objective facts about butterflies or moths.... Instead he is now compelled through the pressure of insidious programming by the overlords of the scientific establishment, to subject everything he has objectively observed to the tyranny of subjectivist and useless speculation about butterflies and their hypothetical origins. He must do so for no other reason than being able to collect his grant and acquire his PhD or some other doubtful honour of mutual respectability amongst his peers. The really dangerous part of this global pseudo-scientific cultism is that our worker has unconsciously been made to pass from the intellectual liberty provided within the legitimate realms of distinterested hypothesis, into the cul-de-sac of totalitarian absolutism of unprovable dogma.... Evolutionists thus become roped into the bondage of their own theory. They postulate it as holy writ and then labour ceaselessly to find the ‘evidence’ to fit it. Such tendentious labours only bestow the opprobrium of ‘contrivance’ upon the evidence so gleaned.

Naughty, Naughty

2006-04-10T20:12:00.000-07:00

It seems that MikeGene has inferred teleology from a cell's ability to control its mutation rate and the Darwinists have got their panties in a wad about it. Very funny. Apparently it is a biological faux pa to make teleological comments on research material. Next thing you know we'll be seeing MikeGene wearing white after labor day.

I've also heard he controls the weather and wrote the screenplay to Glitter :)

An editorial

2006-04-07T08:13:00.000-07:00

here

Posts from Friends

2006-04-04T21:31:00.000-07:00

I had a couple of emails I wanted to share with you all. The first one is amusing, from Jean Lightner. We were discussing the Creationary aspects of speciation, and some of the various issues involved. During the conversation, she quipped:

Of course the most rapid speciation seen today is probably when biologists get together to discuss taxonomy. ;)

On a more serious note, George Cooper had the following to say on the philosophical aspects of using Creationary assumptions when doing science:

Should creationists, who believe the Bible, be faulted for behaving in an unscientific way? Thomas Kuhn argues that all of scientific endeavor is guided by beliefs.

"There is no such thing as research in the absence of any paradigm." (Kuhn, p. 79)

"No experiment can be conceived without some sort of theory." (Kuhn, p. 87)

"Each group uses its own paradigm to argue in that paradigm's defense....The status of the circular argument is only that of persuasion. It cannot be made logically or probabilistically compelling for those who refuse to step into the circle." (Kuhn, p. 94)

"Without commitment to a paradigm there could be no normal science." (Kuhn, p. 100)

"The proponents of competing paradigms are always at least slightly at cross-purposes. Neither side will grant all the non-empirical assumptions that the other needs in order to make his case." (Kuhn, p. 148)

If Kuhn is right, then even evolutionists have "non-empirical assumptions."

Lindberg and Numbers, in the introduction to their book, wrote: "When human beings are involved, so are human agendas and interests." (Lindberg and Numbers, 2003, p. 5)

The creationist Ken Hamm had a humorous way of saying it: "We are all biased. The only question is which bias is the better bias to be biased with?

The creationist E. Andrews is in agreement with Kuhn when he writes, "Many of the so-called facts of evolution arise from carefully selected evidence and depend upon preconceived interpretations of the observations." (Andrews, p. 2)

The biased filmstrip "Science Under Attack: Evolution vs Creation," states, "In the end, the choice between creationism and evolution is based on the individual's personal philosophy and on what seems more reasonable." So far, so good. But then the filmstrip veers into false propaganda. "Is it more reasonable to start with the assumption that creation is a fact? Or to start from the assumption that we know nothing, and then see what we can find out?" (AVNA) As we have seen from Thomas Kuhn, no scientist ever starts his research from nothing.

Eisely stated that Darwin made his round-the-world trip on the Beagle looking for evidence to support his theory of evolution. Darwin was not open-minded. Darwin himself wrote that, "All observation must be for or against some view if it is to be of any service!" He also wrote, "Let theory guide your observations, but till your reputation is well established be sparing in publishing theory. It makes persons doubt your observations." He also admitted, "The force of impressions generally depends on preconceived ideas." (last quote from p. 141, Eiseley, 1961)

Eugene Dubois was a convinced Darwinist, and he devoted his life to the search for fossil evidence to support his belief. Pat Shipman wrote a book about this with the title: The Man Who Found the Missing Link: Eugene Dubois and His Lifelong Quest to Prove Darwin Right. (Simon & Schuster, NY, 2001) Ironically by the end of his life, Dubois concluded that Darwin was wrong regarding gradual evolution and survival of the fittest.

If scientists * like Dubois - can believe in evolution and then go out in search of evidence to support evolution, then why can't creationists unabashedly declare their faith in creation and then look for evidence to support creation?

In their introduction to one of Darwin's books, John Tyler Bonner and Robert M. May wrote that Darwin's book The Descent of Man left "no role for the Deity to play." (Darwin, p. xi) They also reported a "disparity between what Darwin actually did, and what he said he did." (Darwin, p. xii) More specifically, "It was an essential part of this 'method' that he worked at all times within the framework of a point of view which gave meaning and coherence to seemingly unrelated facts." (Darwin, DM, p. xiii)

Even Albert Einstein acknowledged, "It is the theory which decides what we can observe."

William James wrote, "Science would be far less advanced than she is if the passionate desires of individuals to get their own faiths confirmed had been kept out of the game."

Regarding the late Stephen Jay Gould, defender of Darwinism, John Caiazza wrote, "Gould assesses the legitimacy of social biology according to an ideological standard." (Caiazza, pp. 575-588) Gould was both an atheist and a Marxist.

(note that he forgot to mention which books he was quoting out of, but one can probably guess)

I think some of the more recent work in the philosophy of science validates Cooper's ideas even further, but you get the gist.

Evolution -- the Propetual Motion Machine

2006-03-29T15:01:00.000-08:00

Robert Marks did a great piece on Evolution being the modern equivalent of a perpetual motion machine here.

Basically, the argument is like this:

The search space for finding a beneficial set of mutations for a changed environment is very, very huge

Bernoulli's principle of insufficient reason states that without knowledge, all changes are on an equal playing field, thus the changes must be a blind search

Blind search even in a small search space with a small target is impossible (i.e. only 500 bits)

Therefore, in order to actually achieve success, one must use information to structure the search space to get results quicker

However, if the search space is optimized for certain sets of problems, it will be unoptimized for others. Search optimizations require problem-specific knowledge to work at all

Therefore, evolution cannot occur unless organisms have been designed with optimizations to find relevant solutions

Darwinists see evolution as some sort of magical problem-solving device. It violates all laws of probability and optimization, yet somehow people still cling to it, because, since they know God doesn't exist, it must be true!

Using a different approach, I have written a short article on the algorithmic issues that make evolution impossible.

Darwinism and the Integration of the Sciences

2006-03-18T20:41:00.000-08:00

UncommonDescent has a great post about the problems that neo-Darwinism is starting to show now that sciences are starting to integrate with each other.

Darwinian evolutionary biologists have enjoyed a privileged position of authority, especially in academia, because anyone who questions their theses, whether on the grounds of theoretical principle or evidence, is immediately labeled an enemy of science. Never mind that the hypotheses are built on a foundation of wishful speculation, and that contradictory evidence is consistently ignored or dismissed with ridicule.

The essence of the Darwinian evolutionary hypothesis can be comprehended with little effort by almost anyone: Vary stuff randomly, and keep the stuff that works the best. The stuff that works the best will make copies of itself. This explains everything!

But an interesting turn of events has occurred in the last 30 or so years.

Scientists in other fields have started to question the “vary stuff” part of the hypothesis. Engineers, mathematicians, computer programmers and information theorists understand the statistical problems presented by the phenomenon of combinatoric explosion, which evolutionary biologists ignore as being surmountable with time and probabilistic resources, with no hard analysis of the probabilities involved.

Great post! Also, you all might want to take a look at Part 2 of Paul Nelson's account of his debate with Sarkar.

Semi-Meiosis and Prescribed Evolution

2006-03-17T21:12:00.000-08:00

John Davison requested that I post an old paper of his on the web for people who are interested. The paper is Semi-Meiosis as an Evolutionary Mechanism from the Journal of Theoretical Biology in 1984. Also, I scanned in his response to comments on his paper (unfortunately, I do not have a copy of the comments themselves).

Davison's hypothesis has been refined over the years, and it has recently emerged as the Prescribed Evolutionary Hypothesis. The idea is that ontogeny (development from an embryo to a full-grown organism) and phylogeny (the diversification of organisms through time) are similar processes. Both follow a planned set of changes, which are self-limitted. In ontogeny, development stops in the adult form. In phylogeny, progress stops when the organisms have finished diversifying. He views obligatory sexual reproduction as the halting event for phylogeny. Semi-meiosis is a form of reproduction that Davison hypothesizes was the norm before obligate sexual reproduction, which enabled major gene reorganizations without having the problems of finding a suitable mate, or diluting the effect of the change.

Anyway, this is more-or-less the quintessential non-Creationist Intelligent Design hypothesis. It has evolution proceeding, but proceeding not by random processes, but according to an orderly, more-or-less predetermined process.

Interestingly, while Davison thinks absolutely that large-scale evolution has occurred in the past, he similarly thinks that it is _not_ happening today. He gives evidence for this in his paper Is Evolution Finished? The reason for the change is that, like ontogeny, phylogeny has a final form that it attains, after which it stops developing -- it self-limits.

Anyway, as a Creationist, I disagree with several of his points, but they are all worth consideration. Kurt Wise has put forward some similar ideas, though in a much more limitted form (see pgs 7-11 of that paper). Davison does not have much tolerance for Creationists such as me, as he puts it "A past evolution is undeniable. A present evolution is undemonstrable."

Also of interest is that I think Davison has come to disagree with monophyly. He does not view man as a separate creation as Creationists do, but I think I remember him mentioning that Primates may in fact be a separate starting point of phylogeny, as well as other taxonomic groups.

Dr. Davison -- if you are reading this and I have misrepresented your ideas in any way, please correct me in the comments below.

The reliance of evolution on theological arguments

2006-03-14T20:41:00.000-08:00

I just finished reading Nelson's The Role of Theology in Current Evolutionary Reasoning. Fantastic paper. It shows how some of the main arguments for evolution are resting on theological assumptions, and even with those theological assumptions, the arguments don't carry the weight they suppose.

[note -- in all quotes, italics are in the original, bold is mine]

Evolutionists use two primary arguments for their position. The argument from imperfection (as in Gould's The Panda's Thumb) and the argument from homology. Nelson's basic point is that the former requires a definition of perfection which is both defensible and measureable, and the latter only qualifies evolution into the race -- it does not set it up as a preferential system unless empirical evidence that such homologies could be the result of common descent are found. His basic point is thus:

If homology provides evidence for descent, it must do so not because homologies are inconsistent with what a rational creator would have done. A rational creator might have done any number of things. Rather, homologies appear to mark out a pathway of natural transformation characterizing a continuous geometry of organic form, i.e., of descent. Is the appearance of natural transformation more than an appearance? Is the geometry of nature profoundly continuous? These questions want empirical answers. Speculations about the freedom of the creator should be seen for what they are, and abandoned.

So, basically, in order to prove the homology argument, it requires someone to show that there is in fact such continuous variation between creatures, not just that such homologies are not consistent with what one person's conception of a creator might do. The ultimate argument is that such a way of designing is fundamentally uncreative. In response, Nelson uses a quote by Lovtrup:

Why not? Even the Creator may use a good device more than once. Yes, why not indeed? Darwin's arguments against this possibility are postulates, unfounded by any evidence.

Nelson also notes that the common objection that an engineer could design better limbs than vertebrate limbs is a wholly unsubstantiated objection. It was made in 1859 by Owen with no support, and has been repeated ever since.

Nelson attacks the arguments from imperfection by two means. The first is to show that optimality depends precisely on (a) knowing precisely what it is that is being optimized, (b) knowing what such an optimization would look like, and (c) being able to compare what exists to what should be. (a) and (b) are wholly untenable. First of all, it presupposes a particular theology, namely one with an omnipotent Creator. While that is fine for debating Creationists (that is in fact what Creationists generally believe), it does not provide support for evolutionary theory over and above other theological outlooks. The dichotomy between Christianity and evolution is a false one, and one on which evolution rests. If the Christian conception of God were to be invalidated, evolution does not follow before a different conception of God. Of course, we do not even have to go there. Viewed individually, an organism may be viewed imperfect, when in fact if it were viewed combined with the rest of the system, the system my be judged perfect. Nelson says:

...the necessary finitude or limits of scientific observation may lead us to infer mistakenly that an organic design (e.g. the panda's thumb) is imperfect, when its imperfection is only apparent, that is, local. On this view, any judgment of perfection or imperfection must be qualified with a proviso that perfection -- defined as divinely created perfection -- can be judged only on the scale of the whole creation. And there is no reason for a creator to optimize one part of the universe at the expense of the whole.

Nelson doesn't mention this, but determining whether a given observation is optimized in relation to some idea of free will makes this determination almost impossible. Since we can't design free will, we don't know what sorts of tradeoffs are involved, and certainly don't know what perfection or imperfection would look like in such systems.

Nelson notes another problem with the imperfection argument. Namely it is that of cooption. Many evolutionists use co-option as evidence against design. If something looks rigged, if it looks like a secondary adaptation of an existing element, then it could not have been designed. However, this supposes that there exists only static theories of creation -- i.e. that all ecosystems are set up as they were from creation. But almost no creationist holds on to this view. Most creationists hold to dynamic theories, where a created kind has had secondary causes affecting their interaction with the environment, including speciation. It is essentially a false dichotomy which is set up. Either one believes in secondary causes in the current natural order, or one believes in divine fiat. Left out is the possibility of multiple, distinct creations which are further diversified by secondary causes.

Nelson makes a convincing case that a large portion of evolutionary theory rests not on empirical evidence, but on theological arguments, and bad theological arguments at that.

Yet many hold that the Darwinian revolution entailed the surrender of theological speculation in biology. Indeed, many scientists and philosophers would argue that natural science and theology view each other across a largely (if not completely) impassable epistemological gulf. Science, on this view, is by its very nature committed to a thoroughgoing methodological naturalism. Hence, the problem which opened this essay: the persistence of Darwinian theological themata in evolutionary theory is inconsistent with the doctrine of methodological naturalism.

But should science necessarily be committed to methodological naturalism? The shortcomings of theological arguments for evolution may be evidence enough that science has no business meddling in theology (or vice versa). I draw a different moral, however. Science will have to deal with theological problems if science is a truth-seeking enterprise; theology must confront the patterns of scientific experience if it hopes to speak to all of reality. What this essay helps to show, I think, is how very easy wit will be to do both theology and science badly. That is not a brief for methodological naturalism, however. It is a tale of caution about how we should go about explaining the origin of the world's creatures.

As for methodological naturalism, I should point out that Nelson has a short but interesting brief out on whether methodological naturalism should be assumed in science. Basically he points out that (a) we cannot know a priori if naturalism is true, therefore (b) using naturalistic assumptions means that we may be unnecessarily limitting ourselves to possible true explanations, and (c) searching for false explanations is not useful.

If the role of theology in biology is of interest to you, I suggest you also check out Hunter's book Darwin's God. It makes a lot of the same points here. However, it has many, many examples, and many more specific questions. Hunter does a better job at the specifics (after all, it's a full book), while Nelson does a better job of isolating the specific theological/philosophical questions that are at issue. Darwin's Proof is Hunter's follow-up work, but I have not read that book yet.

New Baby!

2006-03-02T14:14:00.000-08:00

If anyone is interested, information about my new baby is available here!

Life will find a way... because it's created to!

2006-02-28T12:35:00.000-08:00

I found Pharyngula's most recent blog entry amusing, since, he starts out by saying:

These enzymes are not smart or guided in any way

and later in the essay says:

Even more impressive is a truly maximal pairing that allows all of the homologous portions to be in register, a structure called an octavalent that brings all 4 pairs of chromosomes together in a very specific tangle. This is an optimal arrangement for pairing, but is less likely to have occurred simply because getting that many chromosomes into an ideal arrangement is difficult.

Apparently they are guided. This is precisely the property of created systems. They have backup systems that try to mitigate damage. It is a "very specific" tangle. It is an "optimal arrangement". How many undesigned systems are fault tolerant through modulating themselves into "very specific" or "optimal" arrangements?

I suggest everyone read the article -- it is very fascinating. I imagine that repetitive elements are used by the chromosomes for alignment purposes. So much for "junk" DNA! This paper is going on my Inter-library loan request list!

Monophyly in Biology

2006-02-26T19:45:00.000-08:00

I just finished Malcom Gordon's The Concept of Monophyly: A Speculative Essay.

For those of you not up on terminology, monophyly is a fancy way of saying "Universal Common Ancestry". This means that the variety of life can be viewed as one giant family tree. Polyphyly means that organisms had more than one root. Creationists believe in a polyphyletic system -- each "created kind" represents a uniquely rooted tree. Non-creationists can also believe in a polyphyletic system in two ways. (1) There were multiple starts to life, each resulting in a different branch of life today. This is usually thought of in terms of the three domains of life -- archaea, eukaryota, and bacteria. Another view is that there were numerous starts to life, but that in the past, horizontal transfer was the rule instead of the exception. Life started in many different ways according to many different paradigms, and then merged in different ways to establish the higher levels of taxonomy. The latter approach is the one examined by Gordon in this paper.

First of all, it was nice to see that my previous comments about common ancestry being the result of specific origin-of-life scenarios, not evoolutionary theory itself is backed up in the scientific literature. Even more so, when you remove the requirement that the origin of life must be naturalistic, you remove even the reasons for assuming that certain groups had ancestors in the first place.

Gordon shows the diverse functioning in the genome as essentially being built up from multiple ancestral lines which came together through lateral transfer. He argues his point by showing that very diverse organisms have very interesting patterns of gene sharing that aren't explainable by a monophyletic common descent, but are explainable in a very high lateral transfer scenario. However, this requires that (a) such degrees of lateral transfer is even possible, and (b) that it would have been so widespread. Another way of looking at the data, however, is in terms of design patterns. If you allow an intelligent designer, then I think that common design patterns is the most natural result of following this data. There are no direct evidences of ancestry, the monophyletic view isn't tenable, and the degree of lateral transfer required for Gordon's polyphyletic view has never been observed. However, design patterns are indeed exactly how designing intelligences go about the act of creating.

He distinguishes three levels of evolutionary differentiation:

Micro-evolutionary differentiation (populational changes)

Meso-evolutionary differentiation (genera and families)

Macro-evolutionary differentiation (kingdoms, phyla, and classes)

He points out that monophyly works best for micro- and mesa- levels of evolutionary differentiation. Interestingly, this is exactly what creationists claim! Also note that interbreeding among species can adversely affect monophyletic assumptions in even these cases.

Another interesting thing about the paper is that he notes that the monophyly/polyphyly question affects the "perception of how many different kinds of organisms there are and have been". I hadn't thought of that, but indeed assuming monophyly would require a massive number of unseen transitionals, while for polyphyly these would not be necessary.

Also, he points out to a number of known cases of gene transfer, and that it occurs even between highly diverse groups of organisms -- even between kingdoms. This includes plasmid transfers, viruses incorporating their genomes into hosts, and host DNA into their genomes, and transposons which can be experimentally transferred between organisms in different lineages.

Personally, I think the ability for organisms to be able to incorporate DNA from other sources indicates (a) that life is based on a common, unified plan, and (b) that organisms can transfer DNA as a mechanism to help other organisms in the environment adapt to each other. However, these claims have not been investigated to my knowledge.

Anyway, here are some good quotes from the paper:

There is, however, no doubt that strong circumstantial cases have been made, based largely upon morphological evidence, for polyphyletic origins of a number of major groups of organisms.

Do traceable lines of descent exist that might ultimately permit characterization of the genomes of organisms basal to the clades for the highest categories? The answer to this question increasingly appears to be no. Recent work on genomic structures demonstrate that all living organisms are genetic composites: mosaics and chimeras composed of bits and pieces of multiple genomes derived from multiple sources.

The base of the universal tree of life appears not to have been a single root, but was instead a network of inextricably intertwined branches deriving from many, perhaps 100 or more, genetic sources. The traditional version of the theory of common descent apparently does not apply to kingdoms as presently recognized. It probably does not apply to many, if not all, phyla, and possibly also not to many classes within the phyla.

[about tetrapod evolution] everything we know is circumstantial and indirect, and what actually occurred remains unknown.

[concerning traditional analyses of phylogeny] Possible polyphyletic scenarios were methodologically and philosophically excluded as impossible [emphasis mine]

The crucial role that statistically inadequate sampling of Devonian faunas has played in the development of our perceptions must explicitly be acknowledged...The animals found represent only a small, stochastically selected, possibly quite unrepresentative, sample of the biodiversity that existed in these groups at those times. There is no way of knowing to what extent, if at all, those specific organisms were relevant to later developments, or what their relationships might have been to each other.

Th evidence cited and the arguments made in this essay indicate that the applicability of the concept of monophyly at the macro-scales of evolutionary differentiation increasingly appears to be severely limited. An operational definition of the concept does not seem possible at the macro-level. Indeed, the phenomena of a monophyletic origin for the universal tree of life probably did not occur.

It is also desirable to avoid restricting frameworks for the evaluation of relevant data to only cladistic models.

The author's hope is that this essay may contribute in a small way to the mitigation of the strong trend toward more and more reductionism that pervades much of modern biology. I think biologists should try to avoid what I call "physics envy." The search for the simplest, most inclusive explanations for biological phenomena certainly must continue. However, that search should be tempered with the realization that over-generalization (including efforts to force everything in entire fields of study into single conceptual molds, such as the cladistic mold in evolutionary biology) is also a hazard along the path to understanding of the natural world.

Sorry for the massive quoting. I'm too tired to summarize.

New Baby on the Way

2006-02-17T09:33:00.000-08:00

My wife is dialated to 2 centimeters. If posts suddenly stop for a time, that's because I'm busy :)

Splitting the Difference

2006-02-16T19:03:00.000-08:00

Creationists often object to evolution because of the lack of transitional forms. Evolutionists often claim that finding a fossil C in between species A and B will just create two gaps - A to C and C to B, and therefore creationists will never be satisfied. In a recent post David Woetzel responded to this objection, and his post is below (reproduced by permission):

Now let's consider the evolutionist's argument that finding "in betweens" will just create two more gaps, so creationists will never be satisfied that something is transitional. This is a wrong-headed argument. We can establish an absolute yardstick based on the evidence from the field and lab experiments. There is a certain range of genetic variability within a species. Be generous and take the extremes of that (akin to a biblical "kind") and we have a credible gap measurement. Then if we find a morphological breach in the panorama of life that is much larger than that, the creationists can rightly assert that there are "missing links." If the evidence, on the other hand, is that the record of life is largely "continuous," then evolution becomes MUCH more credible. We might not know HOW it happened, but it sure LOOKS like common descent happened. Unfortunately for the darwinists, that is not the case. This is not merely the assessment of the creationists. The page I cited above links to hundreds of quotes by leading evolutionists buttressing the claim that the primary characteristic of the fossil record is "discontinuity."

For a simplistic graphical presentation of this idea, go to:
http://www.genesispark.com/genpark/audit/pattern4.htm

Genesis Park has lots of other resources on it for anyone interested, as well as a section on transitional forms.

History, Creation, Observables, and Scientific Theories

2006-02-11T23:37:00.000-08:00

In the book Ever Since Darwin, Stephen Jay Gould made the following criticism of Vellikovsky:

As startling as specific claims may be, I am more interested in Velikovsky's unorthodox method of inquiry and physical theory. He begins with the working hypothesis that all stories reported has direct observation in the ancient chronicles are strictly true—if the Bible reports that the sun stood still, then it did (as the tug of Venus briefly halted the earth's rotation). He then attempts to find some physical explanation, however bizarre, that would render all these stories both mutually consistent and true. Most scientists would do exactly the opposite in using the limits of physical possibility to judge which of the ancient legends might be literally accurate.

Now, I'm not here to defend Vellikovsky, but there is something in Gould's crticism that is fundamentally wrong. Gould criticized Vellikovsky for his method of inquiry. Here is the question -- how does science operate? Does it not proceed by observations which are then systematized? When conflicting views of physics were developed by electromagnetics and classical physics, finding a physical explanation that rendered both these observations true was the concept of general relativity, which, last I heard, was still enjoying scientific success, even though at the time many thought that it was outside the limits of physical possibility.

Vellikovsky's method is simply to take observations at face value. Since the writers of these histories were there and we were not, they are the best ones to report what it was that they saw and did. Should we rewrite observations because they don't fit in with current theory, or should we rewrite current theory when it conflicts with recorded observations?

Obviously ancient histories will not be error-free. However, that is not the same as unreliable. A modern false dichotomy is that you must either view scriptural history as 100% accurate without even a single mistake, or you must view it as a fairy tale. But we do not hold any other history or account to such a standard. If the existence of an error or even a set of errors would cause a historical work to be considered fantasy, then the whole of Western history should be discarded at once. But we do trust histories to be reliable, and the existence or possibility of the existence of isolated errors does not keep us from viewing historical accounts as being true and reliable.

It is a complete shame that Vellikovsky's primary idea is seen as some bizarre view of planetary motion. What Vellikovsky brought to the table was not a physical theory of space, but a collection of observations that demanded explanation. The specific explanation that Vellikovsky put forth is interesting but ultimately irrelevant. What Vellikovsky pointed out was that, in these periods of time, there were earth-wide events that are testified to from cultures around the world which had no contact.

Now, I haven't read Vellikovsky's books yet (I have a few sitting on my shelf), so these examples may or may not be representative of his. But bear with me.

What's interesting is not just that the Bible reported that the Earth stood still, but that it was corroborated by many other cultures. Now, on the other side of the world, they did not experience a prolonged day. They experienced a prolonged night! And we find stories there of not a long day but a long night.

And then the flood. Richard Dawkins once compared questioning evolution with questioning the existence of the Roman empire. I assume that his thinking was that while we might not have documentation of every day of the Roman empire, the historical evidence overwhelmingly testifies to it. However, while the Roman empire made its mark in history, there were many cultures that had never heard of it. However, what culture in the whole world does not have testimony to the great flood? The flood is the most widely-testified to event in history. (Well, almost. Actually, the most well-attested idea in history is the seven-day week, which is not only present in a huge number of cultures worldwide, but is also present throughout the biological world, including single-celled organisms, in what is called circaseptan cycles -- however this isn't observation so is only tangential to the present conversation).

Now let's get back to Gould. Scientists rely on observation to build models. While we may have circumstantial evidence of what happened in the past, historical documents provide the only first-hand evidence of what occurred. Should not a scientist conform their theories to observations, rather than the other way around? Do not scientists often rely on the observations of others? Why is it then out-of-bounds to consider the observations of the ancients in consideration of physical theory?

The question is one of trust. Scientists tend to trust each other more than those outside their field. They don't trust ancient documents. However, is this not simply an instance of chronological snobbery? How is the decision to trust another scientist's data set not the same as the decision to trust the written observations of the ancients? Why is one data set necessarily scientific and the other one not?

Ultimately, what sets Creationists apart is that we trust the historical writings of the Hebrews. This is not a blind trust, as many before us have shown how it connects with surrounding histories, including Josephus and Ussher. Ultimately, our physical theories must conform to the observations -- if we trust those that gave us the history, then there is no reason to exclude their observations any more than one should exclude non-confirming data from an experimental data set.

Stegasaurus Just One of the Many Animals Drawn by Ancient Cambodians

2006-02-04T21:34:00.000-08:00

UPDATE -- for more on historical dinosaur reports, see this entry.

GRRRR... -- it appears I am unable to spell. It's not stegasaurus it's stegosaurus.

Dinosaurs in Ancient Cambodian Temple

It appears that the ancient cambodians had drawings of many common creatures in their temples. Creatures they probably saw every day. Including monkeys, deer, water buffalo, parrots, lizards, and ...... a stegasaurus.

DaveScot is Destroying Dembski's Blog [Updated, not anymore]

2006-01-31T05:59:00.000-08:00

UPDATE -- It seems some people have trouble reading comments. My issue with DaveScot has been resolved, and we are on good terms. Original blog entry is kept only because I don't like deleting blog entries -- they generally make a good historical archive.

----------

It seems that DaveScot is trying his best to alienate everyone who disagrees with him in order to be liked better by Darwinists, whom he doesn't like. DaveScot is essentially the new Commander-in-Chief of Dembski's blog, and he seems to be saying that any argument against common ancestry is now verboten because it won't help him win.

It seems to be centering around Davison's Prescribed Evolutionary Hypothesis. I think Davison's Prescribed Evolutionary Hypothesis is fascinating, but I think that the ID community did a much better job when it wasn't about a specific view of origins. Multiple hypotheses were part of ID, including Davison's and also including OEC and YEC. If it now becomes about a specific view of origins, I think it is headed back to the dustbin.

Now, DaveScot doesn't represent the ID community. He isn't even a major player. I'm not really worried about the immediate future of ID, as it is currently in the hands of Dembski, Behe, Meyer, and their likes, who are much more open, and much more focused on the intelligent agency aspects. I like Meyer in particular. While some or all of them may agree with common ancestry (and it is definitely compatible with ID), they aren't exclusionary.

Anyway, hopefully Dembski will either take his blog back or take it down, but leaving it in the hands of DaveScot seems to have turned it to the worst.

Fast-forming stalactites

2006-01-29T18:08:00.000-08:00

How long does it take to form stalactites and stalagmites? Not very long at all.

See the rest of Ian Juby's virtual museum. Ian is currently touring the US with his mobile creation museum, and I got the pleasure to have lunch with him last week. If you are in the US or Canada and are interested in having him come to your location to speak, you can get contact information from his website.

Gitt Info Theory -- A Preliminary Response to T.O

2006-01-28T20:46:00.000-08:00

Rich Baldwin's FAQ Concerning Gitt and Information Theory

I am still reading Gitt, but I think I know enough to at least preliminarily respond to Baldwin's page on T.O about Gitt. His first argument is this:

A striking contradiction is readily apparent in Gitt's thinking- he holds that his view of information is an extension of Shannon, even while he rejects the underpinnings of Shannon's work. Contrast Gitt's words

(4) No information can exist in purely statistical processes.

and

Theorem 3: Since Shannon's definition of information relates exclusively to the statistical relationship of chains of symbols and completely ignores their semantic aspect, this concept of information is wholly unsuitable for the evaluation of chains of symbols conveying a meaning.

with Shannon's statement in his key 1948 paper, "A Mathematical Theory of Communication"

The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point. Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem.

It becomes very difficult to see how he has provided an extension to Shannon, who purposely modeled information sources as producing random sequences of symbols (see the article Classical Information Theory for further information). It would be more proper to state that Gitt offers at best a restriction of Shannon, and at worst, an outright contradiction.

This is a fundamental misunderstanding of what Gitt is trying to do. Gitt does not disagree with Shannon as to what the measure or definition of information is at a statistical level. Gitt is talking about the higher levels of information. In fact, if you read the Shannon quote properly, you will see that it is confirming Gitt's views. Specifically "These semantic aspects of communication are irrelevant to the engineering problem". Gitt is absolutely correct, the "engineering problem" as Shannon refers to it, is wholly inadequate for describing meaning. Gitt and Shannon are in complete agreement with this. The point of Gitt is to extend the concept of information and be able to view it at more than just the statistical level.

It is strange that Baldwin used an issue that Gitt and Shannon agreed upon as a means of saying that Gitt is in contradiction to Shannon.

The next point is about randomness:

Gitt allows himself to make guesses about the intelligence and purpose behind a source of a series of symbols, even though he doesn't know whether the source of the symbols is random. Gitt is trying to have it both ways here. He wants to assert that the genome fits his strictly non-random definition of information, even after acknowledging that randomness cannot be proven.

I think the point that Gitt was making was that a string of symbols following a strict semantics is evidence of it being from an intelligent source. While he did not prove it, I do not know of any counter-examples, nor did Baldwin even attempt to give any.

Now, using the algorithmic information theory definition of randomness, it is very easy to show that a given sequence of symbols is not random. Baldwin completely misses this point, and seems to assume that since randomness is an undecideable problem, then non-randomness is as well. This is simply false. In algorithmic information theory, if you can compress a string of symbols in any fashion then it is non-random.

In addition, I think it is fairly obvious that the genome fits a rather strict semantic, and in fact the existence of a discernable code is evidence of this. The fact that scientists can isolate genes means that the genes are following a specific semantic. Likewise for other structures such as regulatory regions, they likewise follow semantic rules for their operation. I view semantics as direct evidence of apobetics, and if someone wants to provide a counter-example, I would love to hear it.

Gitt describes his principles as "empirical", yet the data is not provided to back this up. Similarly, he proposes fourteen "theorems", yet fails to demonstrate them.

I'm still reading the book, but this is the most accurate claim in the article. However, Baldwin still does not provide a counter-example to even a single one of them, or even mention which ones he disagrees with and why. He accuses Gitt of arm-waving, but himself is not demonstrating the falsity of any of his statements, except for the arguments against theorem 3 as already discussed.

I also agree with Baldwin that these results are not empirical. Perhaps this is Gitt misusing the term (his native language is German, I believe). These are logical deductions, not experimental results. I don't think that Gitt properly proved his theorems, but I think that this is more due to the fact that this is an area that has previously eluded examination. If Gitt's definition of semantic information is inadequate, what is a better one? The only substantive thing I can draw from Baldwin is that research in this field isn't finished, not that there is anything necessarily incorrect about Gitt's work (this isn't to say it is completely correct, either -- but I think that his work is much more interesting than simply saying it is wrong without providing counter-examples or logical reasons for them to be wrong).

Neither do we see a working measure for meaning (a yet-unsolved problem Shannon wisely avoided). Since Gitt can't define what meaning is sufficiently to measure it, his ideas don't amount to much more than arm-waving.

Gitt agrees that this is a qualitative, not quantitative measurement in its current form.

If we use a semantic definition for information, we cannot assume that data found in nature is information. We cannot know a priori that it had an intelligent source. We cannot make the data have semantic meaning or intelligent purpose by simply defining it so.

Perhaps I am missing something, but I perceive the semantic aspects of the genome to be self-evident.

Real soon now

2006-01-22T19:56:00.000-08:00

Sorry for being out so long. I should be back Real Soon Now^™. The company I work for is moving to a newly renovated building and it has been nonstop work trying to get everything ready and going.

Behe on Astrology

2006-01-06T06:57:00.000-08:00

For those of you who want to know more information about what Behe actually said about astrology, Daniel Morgan has posted the relevant passage from the trial transcripts.

Why Non-Scientists are Skeptical of Scientist's Findings on Evolution

2006-01-03T20:57:00.000-08:00

Often times I hear evolutionists become frustrated with the idea that non-scientists are criticizing scientists on a scientific theory. I share with part of their frustration. Honestly, if someone wants to take part in a debate, they should take the time to learn as much as they can on the subject. However, I thought I would also share the basic reasons why non-scientists (especially religious people) are skeptical of scientific claims of evolution.

The first thing to look at is Philip Johnson's examination of this issue in The Unravelling of Scientific Materialism.

When scientists acknowledge the fact that they cannot even consider the idea of God working, and then somehow claim that they have found evidence of God not working, it is obvious to those listening that there is an error in judgment. Any time I write a paper (although I am not in research, I do write technical tutorials) I try to have someone examine it who is not technical, for the simple reason that I am too close to the subject to see my own biases and distortions. In fact, I usually let my Dad read them, who has not done programming since college, to look over them, precisely because he is not part of the whole rigamorole.

And I think this is what has happened with evolutionary science. They get caught up in this whole way of thinking, and then cannot look back in an objective way and examine what they are doing. They don't see that by excluding an entire method of causality (intelligent causation) they have unnecessarily restricted themselves in what kinds of explanations are allowed.

For example, if I have a stone that is on the floor, and I leave for an hour, and come back, and it's on the table. If I don't acknowledge that an intelligent agent may have moved the stone, I have to come up with some sort of idea of wind gusts that moved the stone from the floor to the table. I will then become _convinced_ about these short-acting, high-velocity, spontaneous winds, simply because I _know_ that the rock moved, and I have a priori decided not to include intelligent causation.

In the words of Behe:

Still, some critics claim that science by definition can't accept design, while others argue that science should keep looking for another explanation in case one is out there. But we can't settle questions about reality with definitions, nor does it seem useful to search relentlessly for a non-design explanation of Mount Rushmore. Besides, whatever special restrictions scientists adopt for themselves don't bind the public, which polls show, overwhelmingly, and sensibly, thinks that life was designed. And so do many scientists who see roles for both the messiness of evolution and the elegance of design.

The question is, can God's action be allowed to be considered by science? I don't claim to know the answer to this question definitively, but we should look at the consequences of answering the question either way.

If "yes", then we need to have explanations of why the similarities of organisms are the result of common descent rather than common design. We need to know why the idea of non-interventionistic abiogenesis makes more sense than the nearly global idea that life came from God. We need to have an open dialog as to why happenstance changes make better sense of life than design. In fact, this has happened once in recent history. Of course, the creationists did too well, and since then Dawkins now has a policy of not debating creationists, the AAAS reported inaccurately the outcome of the debate, and the Oxford Union misplaced all records of the debate. The creationists did not win, mind you, but they did very well considering that the debate was held at Oxford, not exactly a bastion of creationism (the vote was 115 to 198 -- the AAAS reported it as 15 to 198). So, if it is "yes", then we need to have more open debates, and there is no reason they shouldn't be nationalized. (by the way, if anyone would like a copy of the audio of the debate, post your email address here and we can arrange it -- I have an agreement with the copyright holder to do this)

Let's now consider the "no" answer. If science has a methodological predisposition saying that it can't consider God, then theologians have a right and responsibility to say that it therefore cannot say anything remotely definitive about what happened in the past. They are flying blind, purposefully ignorant of an entire area of causation, attempting to come up with explanations that simply ignore what theology tells us. It would be the same as trying to construct chemistry without thermodynamics.

This is why the public doesn't trust science in this area. Science is making bold claims resting on unproved presuppositions. Certainly the scientists know more than the public about their area, but the scientists are also claiming to know more about God's actions than the theologians! Why is one alright and not the other? If science wants to methodologically exclude a method of causation, why should anyone take it seriously in how accurately it depicts past events? I can try, as an exercise, to create a view of the past that ignores certain parts of reality, but I can't then take that to be a true history of the earth. It would simply be an interesting, yet counterfactual, view of history.

Advice for ID/Creation researchers

2005-12-23T09:30:00.000-08:00

Found this on Telic Thoughts. Thought it might be helpful to those of you thinking about persuing ID or Creation-oriented research.

How is ID doing in the scientific community?

2005-12-21T18:53:00.000-08:00

Many people say things such as "ID has been refuted by the scientific community". Unfortunately, lay people have very little ability to confirm or refute such pronouncements, and basically have to take them or reject them on authority or faith. The fact is, science journals do not have articles like "is ID true or not" or "lets bury neo-Darwinism". For example, the best anti-neo-Darwinistic paper I've ever read is On the Roles of Repetitive DNA Elements in the Context of A Unified Genomic-Epigenetic System. And the abstract discusses how the paper will analyze the functioning of repetitive DNA in genomes. Of course, if you actually read the paper, it includes about a 6-page destruction of neo-Darwinism buried within it. So, short of reading the scientific journals themselves, there is very little a lay person can do except to take the word of self-appointed science publicizers on how well Darwinism or ID is doing in the scientific field.

Anyway, for you, my reader, I've put together some of the papers that I'm familiar with that deal with some aspect of ID in a favorable way, or is specifically against neo-Darwinism in a way that is open to ID interpretations.

Cell Biology International 2004: Chance and Necessity Do Not Explain the Origin of Life

Theoretical Biology and Medical Modelling 2005: Three subsets of sequence complexity and their relevance to biopolymeric information

Rivista di Biologia 2005: A Prescribed Evolutionary Hypothesis

Rivista di Biologia 2005:Do centrioles generate a polar ejection force? (viewing centriole action as a holistically designed mechanism rather than having arisen through sequential adaptation)

Annals of the New York Academy of Sciences 2002: On the Roles of Repetitive DNA Elements in the Context of A Unified Genomic-Epigenetic System (not quite ID, but very critical of the neo-Darwinian establishment)

Protein Science 2004: Simulating evolution by gene duplication of protein features that require multiple amino acid residues

Annual Review of Genetics 2002: CHROMOSOME REARRANGEMENTS AND TRANSPOSABLE ELEMENTS

Journal of Theoretical Biology 2002: The Protein Folds as Platonic Forms: New Support for the pre-Darwinian Conception of Evolution by Natural Law

Rivista di Biologica 2004: A Survey of Dynamical Genetics

and of course, Proceedings of the Biological Society of Washington 2004: The Origin of Biological Information and the Higher Taxonomic Categories (this was later withdrawn by the publisher, though they did note that it did in fact pass peer review)

In addition, there are a number of papers that are highly suggestive of design, including the ability of microbes to modify their genome intelligently and regulate the process, the ability of animals to sense predators and change the phenotype of their progeny, and the ability of organisms to alter their DNA to turn on specific sets of genes in response to environmental conditions all indicate that there is a system that is designed for environmentally-induced adaptations.

So, ID is alive and well, and is getting more attention in journals, not less. The only thing is that those publishing in those journals tend to keep quiet about actually using the _word_ Intelligent Design for fear of Sternberg-esque backlash. While still a minority viewpoint, it is present and growing, and has not, as many assert, been refuted by science.

Secondhand Lions and Big Fish

2005-12-19T20:41:00.000-08:00

There are two great movies about people who hear fantastic stories as children and don't know what to do with them -- Secondhand Lions and Big Fish. While they both officially come down on the side of "it doesn't really matter if it's true", I think there is a huge lesson to be learned by examining and comparing the two.

[Boy] "Those stories about aftrica, about you, they're true aren't they?"

[Man] "Doesn't matter."

[Boy] "It does, too. Around my mom all I hear is lies, I don't know what to believe."

[Man] "If you want to believe in something, believe in it. Just because something isn't true doesn't mean you can't believe in it. Sometimes the things that may or may not be true are the things that a man needs to believe in the most. That peoplare basically good. That honor, courage, and virtue mean everyhitng. power and money, money and power mean nothing. That good always triumphs over evil. And I want you to remember this that love, true love never dies. Remember that, boy. Doesn't matter if its true or not. A man should believe in those things, because those things are worth believing in."

This is the question that each of us brings to the Bible. Are the stories true? Unfortunately, in this exchange, the final word seems to be that of Stephen Gould's Non-overlapping Magisteria (or NOMA). The problem with NOMA is that it says that, for belief, facts don't matter. But that is in fact the sole purpose of belief -- to believe the facts. It is quite useless to believe something else. So, if what you believe in isn't factual, there isn't much use in believing in it.

The boy in this story, however, is searching for what is true. Having been next to the lie his whole life, he is DESPERATE for the truth. A good morality tale isn't what he is looking for. This is the same drive that was within the man in Big Fish. His Dad had told so many fantastic stories, that he was no longer able to separate the truth from the lie.

In Big Fish, it culminates with the man joining his father in constructing interesting morality stories. Ultimately, it seems that Big Fish concludes that what is truth does not matter, so long as you live the moment to its fullest.

Secondhand Lions, however, shows that knowing what is true really does matter. Ultimately, the question of what is true or false was a pivot of the boy's life. He was being told that his uncle's were bankrobbers, while they had told him that they won their money from a middle-easter shiek in a series of swordfights. The pivotal conversation went like this:

[Boy] They couldn't have robbed any banks, they were in africa!

[Mom] Here Dan's got actual evidence and you believe in that africa crap?

[Boy] Yes, yes I do.

The Mom's boyfriend had fabricated some evidence about where they had been. In that moment the truth really mattered, and the evidence appeared to be on the side of the Mom's boyfriend. But, ultimately, he decided to trust his uncles. While being ridiculed by those in positions of authority and power, he held on to his belief. And, unlike what his uncle said, it did matter greatly which was true.

The ending of Secondhand Lions is fantastic. I will leave you to watch it, but suffice it to say that the boy's trust in his uncles is vindicated.

Of course, it is easy enough to view a movie and pretend that the question is easy.

The problem with Christianity is that there is no option to hedge your bets, as many in the liberal wing of Christianity are trying to do. What Paul said was that if Christ has not risen from the dead, then we Christians should be the most pitied of all people -- he is quite correct! To live your life for something that is a fantasy is the ultimate waste. As Christians, we can't hope for a second savior if Christ isn't the real thing. Some people have represented Christianity as the "safe" option -- you should at least believe in case it is true. But in fact the opposite is true. Christianity is unsafe in the sense that it requires a total commitment. It doesn't work at all as a fallback option. And if it is false, then all of us who have committed our lives to the cause are fools, and should be pitied more than anyone else.

While I don't think that Creationism is a prerequisite for salvation, I think that trusting in God about what He said occurred is a part of being a Christian. We have to trust that Christ really resurrected. Why would we trust Him for that and not on how He said He created the world?

Unfortunately, there are also some who go too far in this. Not in trusting God, but in what trusting God means. Trusting God does not mean giving counterfactual reports on what you observe. It means dealing honestly with the facts as they are presented. When you believe something on faith -- say so. If the facts as you know them contradict what you believe on faith, there is no harm in saying so. In fact we must. We should be as Kurt Wise, who said:

Although there are scientific reasons for accepting a young earth, I am a young-age creationist because that is my understanding of the Scripture. As I shared with my professors years ago when I was in college, if all the evidence in the universe turned against creationism, I would be the first to admit it, but I would still be a creationist because that is what the Word of God seems to indicate.

When we are honest fully with God, ourselves, and others, God will honor that. He will not honor any deceit in His name.

Anyway, I'm sorry for being rambly, but ultimately what I wanted to get across are:

1) Truth does matter. If Christianity is factually incorrect, it is fully incorrect. NOMA need not apply.
2) Truth also involves separating out what we believe by faith and by observation. There is no problem with taking faith over observation, provided one is honest with this. However, as creation research advances, there has been less and less reason to need to do this.
3) See both movies. They are worthwhile. Be warned -- Secondhand Lions contains lots of moderately foul language and Big Fish has some foul language and some brief nudity. Don't view either if these are things you struggle with.

Misreporting and selective facts about Sternberg

2005-12-17T06:04:00.000-08:00

Another blogger has written a set of "facts" about the Sternberg case. I've posted this response in a few other places, but before I do, I do want to make sure two things are clear:

1) It is not clear what Sternberg's religious beliefs are. He may in fact believe in special creation. He has only said that he is not a Young-Earth Creationist. He also may be a young-earth creationist religiously but not scientifically (i.e. -- believing it personally but not thinking that the science currently supports it). Sternberg has been quiet on his religious beliefs. However, shouldn't they be irrelevant in determining his scientific ability? Or should creationists complain every time an atheist makes a publication on evolution or peer-reviews an evolutionary paper? Some creationists are too quick to list Sternberg as being secular, and, while this may be true, we simply do not have the facts.

2) It is not clear what persecution Sternberg was subjected to. Some of Sternberg's claims have been denied, other's have not, but it is not clear from an independent source what happened.

Anyway, here is my response to the article:

It's basically slandering Sternberg on his association with creationists. The underlying assumption of that post is that legitimate scientists cannot be creationists. Therefore, while legitimate scientists can disagree with each other, if the disagreement is over creationism, the creationist cannot be a legitimate scientist by definition.

Most of the numbered facts on that post are fairly irrelevant, and are not disputed by any post I've ever read on the Sternberg issue.

Why does fact 1 end with an exclamation point? Is there anything even remotely interesting in fact 1?

Why is fact 2 interesting?

What do you mean by the paper was "held" in fact 3? That's a pretty normal delay in peer review. It seems the evolutionists have gone from saying it was "rushed through" to it was "held" trying to find something that will stick.

Fact 4 only exists for the purpose of injecting speculation.

Fact 5 is simply a smear by association, pretending that associating with creationists is some sort of biological crime, and that you can't legitimately be a scientists and a creationist.

Is it really illegitimate to have Todd Wood review your paper? Fasting forward to fact 10, first of all, you should be more careful who you quote from. He did not talk about Wood et al on O'Reilly. That was in the acknowledgements of his paper. Second, it is not clear (though it is irrelevant), that these were his peer-reviewers. I don't know what the peer-review policies for tha Annals of the New York Academy of Sciences is (I have tried to look, but to no avail), but I would be highly surprised if you got to pick your own reviewers.

However, how does Todd Wood not qualify as a legitimate reviewer? He is actively published on various issues about the genome, was part of the team that sequenced the rice genome, and has written chapters in two different fairly standard textbooks on genetics. So what, other than labelling, disqualifies him as a legitimate scientist that should not be peer-reviewing?

Since we're on rule #10, there is no real contradiction. First of all, I've read the paper you were referring to, and he was _very_ careful to not criticize neo-Darwinism itself but only its relationship to transposable elements. Second, the existance of a journal or two that doesn't exhibit this problem does not mean that it doesn't exist. But Sternberg was quite careful to avoid criticizing Darwinism in its entirety. Even more so, Sternberg did not suggest a non-material explanation, which is a double-whammy.

Fact 6 is not in dispute. However, you left out two important facts:

1) Sternberg discussed the paper with a member of the council, who agreed it should be published.

2) After-the-fact, the President of the BSW examined the peer-review file, and agreed that, scientifically, the paper was good to publish, but was a bad move politically:

"Finally, I got the [peer] reviews and agree that they are in support of your decision [to publish the article]."

Also, according to Sternberg:

"At no time during my nearly three years as managing editor did I ever ask the Council as a body for its input on any editorial decision regarding any particular paper. Nor did the Council itself or anyone on the Council intimate to me that the Council ought to be in any way involved in editorial decision-making with regard to particular papers."

This "fact" also manages to leave out the important fact that Sternberg HAD IN FACT DONE THIS BEFORE:

"I had previously chosen on several occasions to handle certain papers directly and that was accepted as a normal practice by everyone involved with the Proceedings."

In fact, this fact is counter-factual, implying the opposite:

"he does not say is whether or not that gives the managing editor the right to solely review a paper, without involving the associate editors or anyone else in the journal's editorial board"

He DOES say that (the quote above) and on the SAME WEB PAGE! For "facts" these are getting awfully disingenuous.

Fact 7 is irrelevant. The ISCID is part of the ID movement, but is not solely about Intelligent Design.

Fact 8 simply is a restatement of the fact that the investigation was not allowed to be completed.

I find it interesting that in fact 9 you automatically choose the side of the smithsonian as "fact" over Sternberg's. How is this distinguished as fact, especially when the information from the OSC is considered with much questioning? I don't know the truth, but to say that FACT resides with one or the other indicates that the author has independent knowledge of the situation.

In addition, Fact 10 fails to address many of the accusations Sternberg himself made.

Anyway, the idea that this is a listing of "facts" is rediculous -- it is deceptive and manipulative treatment of the facts to smear Dr. Sternberg.

The truth is, I don't know for sure what the final truth is as far as Sternberg's beliefs or his persecution. But this list of "facts" does the word "facts" a disservice.

Interesting email about religion, science, and evolution

2005-12-09T20:51:00.000-08:00

On an email discussion, a friend of mine made the following post:

"You only want your religion accepted."

No, as I pointed out, I'm not the one who is pushing only one religious view, you are. You are so busy with your crusade, you've become what you fear others are; and you are so proud of yourself that you can't see it.

I'm quite knowledgeable about science (well, more so than the average non-scientist), and especially evolution...What you are talking about, however, is not science itself but the common *philosophy* of science which says scientific investigations can be carried out without regard to the existence of God. This is quite correct when properly applied. No experiment or observation of natural forces does, or even could, limit or define a concept of deity.

However, when schools teach as fact that the universe began with the "Big Bang," that life formed by natural forces alone from inanimate matter, and that all living things, including humans, evolved by random mutations from that first simple form of life -- that is not the sort of science that says nothing about God. It also can't be demonstrated to be true, in contrast with all the practical, reliable aspects of science which have been both frequently demonstrated and commonly applied.

Unlike art, "science" claims to have "proved" that the entire history of the entire universe can be accounted for by nothing more than chance interactions of energy/matter. The only "god" left to believe in if all that is true is a god who apparently is incapable or unwilling to take an active role in our universe.

You can keep lying to yourself and others that you are simply defending science or even freedom of religion, but I hope someday soon you will realize that you are really helping to establish a government-sanctioned limitation of religion based on the philosophy of materialism.

Cell Biology International takes 20 years to catch up with CRSQ

2005-11-28T20:03:00.000-08:00

It's funny how many times I've heard evolutionists shout "where is the peer-reviewed material" and make fun of creationist peer-reviewed journals like TJ and CRSQ. Then, along comes Cell Biology International to make the exact same arguments creationists have made for decades.

I think this is just the beginning. It will take some time for the dam to break, but when it does, you'll see a very different view of biology. The authors in this article are still cowering behind ambiguous phrases such as that science should "press forward with new research approaches which are not obvious at this time". In other words, they think that we should consider an Intelligent Design scenario, but are to afraid of the Darwinists to actually say so. If they actually came out and said it the editors will stop publishing their papers, or be subject to castigation a la Sternberg.

Anyway, I have heard Darwinists over and over again say that all these arguments are invalid, and here now it is peer-reviewed material in 2004.

I suggest that everyone do an inter-library loan request for the paper. It has a _lot_ of arguments against a materialistic origin-of-life scenarios, any one of them are pretty devastating.

A good summary of Creation ideas

2005-11-16T18:16:00.000-08:00

If someone wants a short, brief summary of creation ideas, I've found ICR's summary of Baumgardner's Los Alamos Origins debate very interesting. The full debate can be viewed here. I have not had time to view the whole debate, but I imagine it's quite interesting.

I at least assume they are both referring to the same debate.

Levels of Teleology

2005-11-14T20:29:00.000-08:00

I developed a levelling of teleology in genomic change for a post I made in an debate with an evolutionist, which showed different kinds of genomic change and how much teleology is involved with each event.

Let's say I need a new gene. There are several possible ways that I could acquire this new gene:

I have no idea I need something to change. If a cosmic ray or copying error causes something to change, and its beneficial, great. However, if the change is detrimental or doesn't fix my situation, I'm toast.

I know I need something to change, but have NO IDEA what. Therefore, I can cause increased mutations to occur randomly throughout my genome, and hopefully something good happens before I suffer from error catastrophe.

I know I need something to change, and I know it is this, specific gene. Therefore, I can put my resources to bear on changing this gene until I can sense that I am no longer in need.

I know I need something to change, and I have this part list of things that I know works to make specific things happen. I'm going to rearrange re-usable parts until I get something working.

I know I need something to change, I know what it is that needs changing, and I know exactly what I need to do to change it.

1 & 2 are Darwinism. 3-5 are ID and Creationism. Darwinists like to claim that 3-5 can be the result of 1 & 2. However, Dembski's No Free Lunch and Searching Large Spaces show why complex adaptations cannot occur through blind searches. Intelligence _must_ be put into the equation, or the blind search makes error catastrophe a certainty LONG before adaptations can occur, and Behe's paper covers just how unlikely that is anyway.

Darwinists claim that 3-5 can come from 1&2, yet they never show any data on how this could or does happen. I'm fairly certain it simply isn't possible.

Also note that my "levels of teleology" are just an example. I'm sure there's lots of things I missed in there, but the idea remains the same.

Is the theory of evolution stronger or weaker?

2005-11-02T05:14:00.000-08:00

I recently had someone claim "The theory of evolution has only been improved upon and progressed since its conception."

I thought you all might be interested in my response:

"The theory of evolution has only been improved upon and progressed since its conception."

Mostly by abdigating its original conception (i.e. the one that creationists originally opposed).

The idea of "change" is not counter to creationism, nor is the study of change. Not even Linnaeus believed in fixity of the species. So, if you are talking about creationism contrasted to _any_ theory of change, you are simply debating people who haven't lived for over 300 years.

Now, if you are talking about evolution as a notion of atelic change (i.e. not purposeful), then in fact evolution is somewhat on the ropes these days. While many biologists studying purposeful change in organisms will currently append some sort of Darwinistic mantra to the end (i.e. "we can see how a process of natural selection could lead to such functions") it is wholly without evidence, and fewer and fewer are appending those to their works. And Dembski, in his "Searching Large Spaces" paper, shows why such scenarios (Darwin leading to teleology) are even less credible than the purely Darwinistic approaches they are replacing.

Teleology is back with a vengeance, even in biological papers, it's just that it is politically incorrect to doubt that such teleology came by anything but naturalistic means.

It has been shown, that (a) natural selection does almost nothing except get rid of completely inept creatures. It does not prevent bad mutations from spreading. (b) adaptive change within an organism is NOT undirected. (c) everything within the cell is there serving a purpose. (d) cells are highly complex, with many interdependent parts which cannot change independently. (e) The genetic code is so complicated that the idea of a "gene" is not even really valid anymore, especially when looking at gene conversion, alternative splicing, and other fun that occurs within the genome. (f) horizontal gene transfer indicates that the whole biosphere is made to co-adapt, with specific mechanisms in place to facilitate that adapatation.

All of these point to creation, not a materialistic universal common ancestry. It is "evolution" in the sense that it is a science of change, but it is not evolution in the sense of a purposeless drift through time from one species to another by haphazard processes.

Likewise, Universal Common Ancestry is more of an assumption than a result.

Fantastic Post

2005-10-27T04:13:00.000-07:00

Arguing in the Streets

Check it out.

Sorry I haven't been putting out much. I've got a big project at work that's eating me for the next several weeks.

Stephen Meyer is my hero

2005-10-09T14:18:00.000-07:00

Here is a Nightline interview with Stephen Meyer about Intelligent Design (PDF file).

Absolutely fabulous. His responses to the questions are absolutely perfect, and I suggest anyone debating this subject to read the interview. The following quotes from the interview are arranged topically, not chronologically.

On motives:

I think there’s a tremendous amount of motive-mongering that is detracting from the substance of the debate. And the problem with motive-mongering is that everybody can play that game, everybody has a motive. Richard Dawkins has said that Darwin has made it possible to be an intellectually fulfilled atheist, something he thinks is a good thing. That it would be completely illicit for us to say, “well, Richard Dawkins is wrong about evolutionary biology because he wants to be an atheist.” Motives are properly irrelevant to the assessment of an argument and to the assessment of evidence; and in any case, they are equivalent, there are motives on both sides: many of the leading people on the Darwinist side have motives, people on our side have motives. We want to see the debate settled and discussed on the basis of the evidence, and that’s where we think it should finally reside.

On the identity of the designer:

The question of the identity of the designer is what I would call a second order philosophical question. From the evidence of the information that’s embedded in DNA, from the evidence from the nanotechnology in the cell, we think you can infer that an intelligence played a role. In fact, there are sophisticated statistical methods of design detection that allow scientists to distinguish the effects of an intelligent cause from an undirected natural process. When you apply those statistical measures and criteria to the analysis of the cell, they indicate that the cell was designed by an intelligence. Now, the second question then you want to ask is, “Who was the designer?” The media commonly says, in fact recently it was said that we’re so clever that we don’t say the designer is God. Well, the reason we’re not saying the identity of the designer is not because we’re trying to be clever or get around Supreme Court rulings, or anything of the sort. We’re just trying to be careful about what the scientific evidence does and does not support. It supports the conclusion that there was an intelligence; the second order question of the identity of the intelligence is something that is for philosophical deliberation.
...
...

I think some of the people who hold to the theory of intelligent design think that God is the designer. But as I mentioned, that is not a refutation of the argument. The argument is based on scientific evidence, and the evidence is very clear from the cell that you have very sophisticated nanotechnology and information technology and that has to be explained. And we think intelligence is the best explanation for that.
...
...
People have different answers to the question of who the designer is. The key question for us is how you interpret the observed information that is present in the cell. And we think intelligence provides the best explanation for that. After you have inferred that, then there is a second question that needs to be deliberated upon, and that is who is the designer?
...
...
I think the designer is God, but, look, it’s not like we are trying to make a scandal of where the evidence might lead. We think that the evidence leads first to intelligence, and then from there, there is a second question, which is the identity of the designer, and there are some people who think it’s God, and there are some people, like Fred Hoyle, who think that maybe it is some sort of imminent intelligence within the universe. Francis Crick speculated that some other intelligence may have been involved. But we are insisting that from the scientific evidence, from the presence of digital code in the cell, you can tell that an intelligence played a role in the origin of life.

This was both (a) completely honest about his own beliefs, and (b) completely direct about where the evidence lies.

On the "wedge document":

The statement in the Wedge says to replace it with a theory which is consonant with a theistic worldview. That doesn’t mean that you can prove theism from the evidence, it means that it is consonant or consistent with it. And one of our main concerns at the Center for Science and Culture has been to challenge the materialistic worldview that has been erected atop the science of the 19 th century, which we now think is outdated and won’t stand the challenge of the information age – especially the information technology that’s being discovered in biology.

On information:

Intelligent design is the theory that there are certain features of living systems that are best explained by reference to an intelligent cause rather than an undirected natural process. In the 19 th century, when Darwin was first concocting his theory, the cell was thought to be something very simple. But in the last 30 to 40 years, we’ve learned that the cell is chalk full of nanotechnology; there are turbines and pumps and ? machines, rotary engines. And most impressive of all, there are reams and reams of digital code stored along the spine of the DNA molecule. And if you think about that reflectively, and realize what we’re looking at, we’re looking at things that we think bear the distinctive hallmark of an intelligence. Bill Gates has said DNA is like a software program; Richard Dawkins said that it’s like a machine code. We know from experience that intelligence always produces software, programmers produce software programs. We know more generally that intelligence always produced information, whether we find it in a hieroglyphic inscription or in the text of a written document. So when we find information embedded in DNA, in living cells, we think that we are looking at strong evidence for a prior intelligent source. So the theory of intelligent design is the idea that that appearance of design, that nanotechnology or that information that’s embedded in a living organism, is not just an appearance, is not illusory as the Darwinists assert, but instead is evidence of real design, actual design. And so we contrast our theory with the Darwinian idea that things look designed–

On ID being an "argument from ignorance":

Well, Chris, all scientific theories are based on inferences from evidence. If we could see everything directly, we wouldn’t need to theorize. And Darwin’s theory is in fact an inference from a number of different classes of evidence. And Darwin justified the theory not because he could make observable predictions in the laboratory – after all he was trying to reconstruct the distant past – instead he justified it because it provided a better explanation of the evidenced than the main competitor hypothesis, and that’s precisely how the theory of intelligent design is formed, framed, and justified. We argue that our theory provides a better explanation of some of the critical pieces of evidence of biology, namely the irreducibly complex molecular machines and circuits that we seen in cells and the presence of this informational software that drives everything in the cell as it’s embedded in the DNA molecule.
...
...
Well, what you’re getting at is that our argument is an argument from ignorance, but it’s not an argument from ignorance, it’s based on the evidence that has been discovered of the complexity in the cell, the information-bearing properties in particular, but it’s also based on what we know about it takes to build informational systems. That in our experience, our repeated and uniform experience, intelligence is always involved in the production of information. So when we find information in the living system, the most natural inference to draw is that there was an intelligent source. Now that form of reasoning happens to be precisely the form of reasoning that is always used in the historical sciences, where our present knowledge of the cause and effect structure of the world guides our judgment as to what is the most likely explanation of what happened in the past.

He covers a lot of other topics, too. I like how he manages to distinguish between ID and creationism without disparaging creationism. In fact, he is at least somewhat friendly to research-oriented YECs, though not necessarily the polemic ones.

Lots of news items

2005-10-06T16:48:00.000-07:00

Scientists (or journalists) stoop to new low in search for life on other planets

Origin-of-life articles tend to be, well, bordering on the inane and rediculous.

I came across this one today, and, well, it should really win an award:

Test Equipment Finds Life in Mars-like Conditions

Now, it could be that the actual research was much more on-the-ground than the article makes it appear, and perhaps it is the journalists trying to make headlines from little bits of research that look juicy. I've seen it happen. In this case, it could be that there was a press release about testing equipment to be used in future studies _on_ mars, but some journalist wanted to make it sound a little juicier.

But anyway, somehow, someone, somewhere thinks that by finding a place on earth with similar geology to mars, we have somehow gotten closer to the discovery of life on other planets.

It boggles the mind.

Three from Creation-Evolution Headlines

Several interesting articles today from crev.info, all of which are worth looking at:

Science Writer Advocates Debate with Creationists

Creation-Evolution Contest in Grand Canyon: New York Times Prints Eyewitness Repor

Can Networks Design Themselves?

A random discombobulated thought

2005-10-03T19:02:00.000-07:00

I had this thought the other day. It's probably just malarky, but since most blogs are just a bunch of malarky, I thought it would fit in pretty well in the blogosphere.

This idea came to me while thinking about the created kinds and diversity, and while watching the video for Dennet's "Darwin's Dangerous Idea". It occurred to me that:

a) there is a wide variability within created kinds, as has been fully documented by creationists since Linnaeus
b) within certain environments, there are very tightly coupled dependencies at play
c) these tightly coupled dependencies defy both traditional forms of creation and evolution
* they defy evolution because many of these dependencies show signs of being irreducibly complex
* they defy traditional creationist models because they are part of a created kind whose other members do not display such traits
d) some of the strangest species are island species

(c) has had me curious for a while. But I had this idea: what if in biology we are looking too zoomed in? What if we needed to zoom out to get a better picture? A fellow member of the CreationTalk mailing list has often pointed out the many ways that species within an environment seem to communicate with each other. Because of evolutionary predispositions and because of the existence of carnivory, we often assume that nature is in a violent struggle within itself for resources. But what if instead it was working in (at least somewhat) of a cooperation to produce resources?

The idea I'd like to offer up is this -- the created kinds are designed to sense their environment, and adapt to the complete ecological niche. Not only looking out for their survival, but looking out for the survival of the biosystem. Therefore, when certain parts of an ecology are missing, then existing animals can adapt to fill the role. They communicate biochemically to figure out a good stasis, and then change themselves to it.

On islands, you have a very limitted set of created kinds initially arrive, and somewhat haphazardly. Therefore, they have to do quite a bit of adapting to the new environment, to establish a stable ecosystem.

Anyway, it's a thought -- that the environment as a whole comes together to form an ecosystem, and that looking at animals as complete independent, autonomous units is missing the big picture.

Evolution in the news

2005-09-29T20:48:00.000-07:00

It's strange that evolution has all-of-the-sudden made it to a highlight of the national news. I think that the influence of creationists has really frightened the Darwin establishment. It has now degenerated to name-calling and near-slander. Oh well. The creationists are not completely clean in that regard either.

Anyway, I thought I'd point you to a few articles I found interesting:

An interesting read on why the ACLU is so adamant about evolution

A very interesting reply to the evolutionist's open letter to 50 state governors

[UPDATE]A very good reply to the Elie Wiesel open letter

On another note, I recently read Eugenie Scott's new book "Evolution or Creationism". I didn't read every word, but what I found really amusing was that she presented young earth creationism fairly correctly, while completely misrepresenting the Intelligent Design movement. She also did a pretty good job of covering the facts of the scopes trial, though she left out one important one -- Bryan only took the stand under the condition that Darrow would do the same, but Darrow backed out of the deal so he wouldn't have to be questioned.

Anyway, what I take from this is that Eugenie thinks that young-earth creationists don't have a chance, so they can be fairly represented. This wins points from AiG and the rest for being fair and balanced to their side. Apparently she does see ID as a threat because of the gross misrepresentation of it. Eugenie basically admitted the reason that the ID'ers kept their articles out was because Eugenie would pick the worst ones, and would give the ID'ers no editorial input (this already happened to Dembski once with "Intelligent Design Creationists and Their Critics"). You know, it's funny, if you were to publish my thoughts in your books for you to rip apart, I would at least want to have some control over which specific papers were included, too.

Anyway, it's clear that Eugenie feels the need to misrepresent ID, but feels no need to misrepresent young-earth creationists.

Personally, I think that this is going to blow up in her face for several reasons:

* The distortions of ID are fairly obvious
* Her book will not have any real impact to the ID movement -- it's not anything anyone hasn't heard before
* Creationists are going to come from behind and take the ball while noone is looking. It's already happening. Over the next 10-20 years, creationists are going to make huge strides in building a sensible model which makes sense both physically and historically
* Once that happens, the boat will have already passed

The election of the next president and congress is fairly critical, because I can see the other side getting desparate once they start losing in the scientific culture as well. Already they are playing games with the schools (as pointed out in the "open letter" response above), they may soon start playing games with the government. We'll see.

Invoking Darwin an Afterthought in Most Research

2005-09-17T20:32:00.000-07:00

Philip Skell has an excellent editorial in The Scientist as to why biologists invoke Darwin. As he points out, Darwin is very rarely useful to experimental science, but almost all research is given some sort of Darwinian speculation. Anyway, I've pointed this out before to Darwinists who say that all biology rests on Darwinism. Perhaps now they will at least listen rather than write such arguments off a priori.

Honestly, read some biology papers, and you'll almost always see in the conclusion some sort of Darwinian myth being foisted upon the evidence, where it wasn't really even in play for the experimentation itself.

Anyway, you can read the editorial for yourself here.

Are Christians Lacking in Abstract Logic Skills?

2005-09-16T22:11:00.000-07:00

I recently made the following post on FreeRepublic, and thought I'd reproduce it for you here. Basically, the author was charging Christians as being illogical. I have included my entire response, but the final paragraph is what I consider most important for answering this question. Some parts may be hard to follow based on lack of context, but I'm sure you'll be able to follow the basic argument.

Again, you are confusing issues. Your original claim was:

"Because if God did everything that we can't explain, then where's the motivation to find out what we don't know?"

You still did not support your claim of "everything". Behe's criticism is not that evolution has not occurred -- in fact he specifically thinks it did. Instead, Behe's claim of Irreducible Complexity is that the Darwinian process is incapable of producing such structures, not that no theory of evolution can produce such structures. Behe's main point is that science is stuck defending a dead mechanism that has no explanatory power, and it should get off its duff and explore other options.

In addition to that, Irreducibly complex systems match very closely with what designers normally design. Therefore, looking for design in biology is a valid preliminary inference, precisely because Irreducible Complexity matches what we know about how designers do design.

"The research on flagellum evolution has since explained away Behe's argument"

(1) Making up stories is not equivalent to an explanation. (2) Saying the small parts have other uses is likewise not an explanation, just as having a screw being part of a computer does not mean that a computer evolved from screws.

"but like typical ideologues, the ID and creationism advocates don't recognize that they've lost that fight"

If scientists can show experimentally how the flagellum developed, then you can call the case closed. Or, instead, show mathematically how such a feature is likely.

"Behe was satisfied that he had the answer, based on a lack of knowledge. That provides motivation to halt further science."

No, it halted further exploration of a Darwinian mechanism. It did not halt inquiry altogether. I'm all for abandoning dead theories. I don't think we should stick to bad theories just because someone will think that I'm "halting progress" on it. Bad theories should be halted, and replaced by better ones.

You seem to be arguing against design a priori as a bad argument for anything. Does design exist at all? If not, then we should fire our artists and programmers and just write a master program to do it. If it does, then you are excluding an entire mode of operation that is EXTREMELY COMMON in everyday life simply because of personal preference.

"Very true. But religion has abandoned acceptance of most of science"

Most of science? Are you serious? Please name the scientific law that Churches are explicitly against that is experimentally verifiable. (note that I indicated "law" because laws are mathematical, thus eliminating both fudge factors and speculation).

"My particular theory is that faith has acted as a filter, dividing people between those who can understand abstract logic, vs. those who operate emotionally."

This ultimately gives you away -- abstract logic can only lead from premises to conclusions. It appears that it is you who do not understand abstract logic. My favorite Star-Trek quote is, "logic is the beginning of wisdom, not the end of it". Abstract logic only works if you have correct assumptions, but logic cannot tell you whether or not your assumptions are correct. If you have bad assumptions, logic will lead you the wrong way. My own theory is that Darwinists are people who _only_ have abstract logic, and not any other facet of wisdom. Therefore, they are unable to analyze their own assumptions, because logic is their only tool, which is completely inadequate to the task. It is true that there are some in the Church without logic, but I think you are confusing what you see as a "lack of logic" with what is really a "broader wisdom than logic alone can provide".

Materialism and Theism

2005-08-23T06:46:00.000-07:00

I thought I'd post what I posted in Dembski's blog in response to a post by "Dan S." (see the link for full context -- it's the second comment if the link doesn't take you there directly).

The writer dramatically overstates mainstream acceptance of ID research.

Mainstream where? Mainstream science? Maybe. Mainstream America, the acceptance is probably understated. While science itself cannot be determined by popular vote, what belongs in publicly-funded governmental education science programs certainly should be, unless we believe in rule by a "priestly class". As Philip Johnson points out, the public thinks that it may have been hoodwinked on this one, and is now demanding an open, public audit of the books.

To talk about an atheistic, materialistic worldview conflates methodological and metaphysical naturalism, and suggests that science - at least mainstream science - is in some way “atheistic,”

It depends. There are two things here:

When you deal with the ordinary events that occur ordinarily on any given day, you are discussing things that can be empirically determined. However, when you get into specifics - that X or Y did or did not happen in history - then you are espousing beyond strictly empirical science. As Stephen Hawking said, no cosmology is independent of philosophy. So to present a cosmology IS EXACTLY to present a specific philosophy. If science is the study of the "normal rules", to say that a given past event or set of past events must have occurred exactly according to the "normal rules" is to make a philosophical statement that the "normal rules" can never be broken. This is beyond the bounds of empirical science and stretch into philosophy, and is precisely the pretext on which the inference of unguided design and universal common ancestry are based.

Second, there is the question of whether or not even the "normal rules" can entirely be determined in terms of material causes. If humans have free will, then the will cannot entirely be determined in terms of material causes. That is not to say that there are no material causes involved in someone's will -- noone doubts that material causes do come into play. However, to say that there are _only_ material causes is to reach beyond the available evidence and to posit something that is both unsupported and philosophical, not empirical.

The question that Intelligent Design asks, is "are there only material causes", and "are there ways of identifying features that have been set by non-material causes". Intelligent Design says that intelligences (including our own) are not wholly subject to material causes, and in fact such non-material causes leave a distinctive ordering on material matter. This ordering can be measured, and the existence of a designer can be inferred based on the organizing characteristics of what is being examined.

Here's a question I like to ask:

If a science teacher says that "everything is the result of material causes", is that teacher in violation of separation of Church and State?

If a science teacher says that "the description of reality is incomplete without God" (or any other non-material cause), is that teacher in violation of separation of Church and State?

Both of these are equally unprovable (science, if it is to be regarded as the study of material causes, cannot therefore proclaim that material is all there is), philosophical (relies on the assumption that material causes are all that exist), and even theological (necessitates what God can or cannot do -- if God exists, it assumes that He does not participate in non-material causes -- not a proven statement, simply a theological one). Likewise take these two statements:

"The evolution of life on Earth was an unguided process."

"The evolution of life on Earth was guided by life's creator." (or some alternate intelligence).

Both of these are equally unprovable (noone saw this specific event occur), philosophical (proclaims that science is the limit of knowledge), and even theological (because it establishes as a factual basis what God is or is not doing). Yet in both sets of statements, the first would be allowed in the science classroom, and the second would be called "religious".

The point is that we actually do have a de-facto state religion -- secular humanism. The modern mantra of "Separation of Church and State" simply means that non-secular religions are not allowed in schools, while secular ones are allowed.

The fact is that science continually speaks to philosophy and theology, and the claim of those who are against Intelligent Design is that philosophy and theology cannot speak back in any way, even just to say that there are more than non-material causes in the world.

Amusing

2005-08-20T17:55:00.000-07:00

I found this little quote amusing, called the Harvard law:

Under the most rigorously controlled conditions of
pressure, temperature, volume, humidity, and other
variables, the organism will do as it damn well pleases.

Sorry I haven't been active much. Been busy with work and also been looking into some of Dembski's newer work.

I'll post more as I get the chance.

The Creationist Model

2005-08-06T05:47:00.000-07:00

I spent a considerable amount of time writing this post on FreeRepublic, so I thought I would post it here as well for future keeping. It was in response for someone asking me how I thought biodiversity occurred:

"Really? Let's see it, in your own words. What is your ID hypothesis?"

It's actually fairly simple. There are three basic mechanisms for biodiversity for a creationist:

* heterozygous fractionation -- basic mendellian speciation
* darwinism -- this is usually deleterious
* genomic modularity -- this is the innate ability of a genome to reconfigure itself in response to environmental stress.

The first has been fairly well proved. It was found by a creationist (Mendel) and no one doubts that it occurs. The second is also fairly standard, the difference being that creationists do not think that Darwinism has any significant creative power.

For example, if you set off fireworks, the direction of the fireworks is set mostly by the direction you aim the firework, and the explosive properties of it. The wind can modify the course a little bit, but it would be silly for someone viewing the interplay of a spark with the wind to say that the wind was the ultimate cause for the direction of the spark. The primary direction was set by other factors. I've also related it to breaking in a shoe. Breaking in a shoe changes the shoe itself, and sometimes even gives a better fit. But it would be futile to try and view the creation process for the shoe as a continuous breaking-in process -- it just doesn't work.

The final mechanism proposed by creationists is genomic modularity -- the ability of genomes to modify themselves. This goes under quite a few names, including natural genetic engineering, altruistic genetic elements, the AGE-ing process, and genomic modularity. Basically, it says that the cell and the genome can work together to reconfigure the genome in response to the environment. In fact, this is the primary role of transposons. There are several ways that this can happen:

1) some genes remain inactive in the genome until they are needed, these are pre-coded adaptations that simply get switched on
2) organisms can create new genes in response to specific environmental stresses
3) organisms can exchange DNA with their environment to better adapt to the organisms living in the area
4) probably some other ways people haven't thought of yet.

An example of (1) is in photosynthesis. There are two primary types of photosynthesis - C3 and C4. Evolutionary trees would have C4 photosynthesis being developed 16 different times! However, in many genuses examined within families that have C4 photosynthesis, it is found that even the genuses that do not have C4 photosynthesis still contain all of the genes necessary to pull it off. The difference being the promoter regions of the C3 and C4 genes. So, not only did C4 photosynthesis evolve 16 times, some of the plants have all of the genes necessary to do C4 photosynthesis and yet do not. C4 is quite a complicated pathway, needing an entire new set of organnelles to perform. The creationist explanation is that these families (or technically, holobaramins, but I will use family since its a more familiar term and is roughly correct) were created with both sets of genes, and the cell is able to activate different types of photosynthesis under environmental stress (likely related to a drop in available C02 gases).

Evidence of (2) is available in looking at pseudomonas. This has a highly adaptable genome, and in fact is able to manufacture _systems_ of genes for adapting to new food sources in less than 9 days. You might wonder, "if genomes can manufacture their own genes, then why would one even need to make a polyphyletic hypothesis?" As I explain in http://crevobits.blogspot.com/2005/08/genetic-algorithms.html the only way to make variation algorithms work is to have a significant portion of the algorithm be non-varying. In fact, it is the constraints imposed by the non-varying part of the algorithm that is most important to the algorithms function, even for those algorithms which rely on codal change to work. In fact, they would in fact be functionless if _everything_ could change. Error catastrophe would occur in just a few generations. In fact, not only can pseudomonas manufacture genes for food production in new environments, it will place these newly manufactured genes onto plasmids for transmission to the rest of the population. Likewise, there is a general mechanism in many bacteria called the SOS mechanism, which induces such change in times of extreme stress for the population, much like the bacteria is performing a full search of its variable capacity in order to find a pattern that works in the environment. As evidence that process does not change the basic patterns of the organism, note that pseudomonas was discovered in the 1800's and STILL is readily identifiable by the same description as it was then, despite its ability to manufacture new gene _sets_ in less than 9 days.

3) This one is not as fully fleshed out yet (none of them are very much, due to the very limitted amount of money available for creationist research), but Orchids are able to adapt morphologically to the insects that are nearby. There are several organisms that appear to "know" how to adapt to the local environment. One mechanism of this is likely interspecies gene transfer along mechanized lines. Viruses are thought to be genetic carriers designed to help this process along faster.

In the young-earth creationist model, the general trend of life is downward, because since the fall we no longer have God sustaining us as He once did. Therefore, random mutations have a generally deleterious effect on the harmony that these systems have. Viruses have gone from being beneficial components to harmful because they have lost the specificity they once had -- whether site specificity, organismal specificity, or lost their ability to constrain reproduction. For example, a virus which may be beneficial in one family may be harmful to another. If the mechanisms for keeping family specificity is broken, then the virus goes from being beneficial to harmful. Likewise, mutations on the transposons or on other components that deal with activation/deactivation of genes or with the natural genetic engineering have caused these mechanisms to not be quite as able as they have been in the past. While it is possible for an "unexpected" mutation to confer an advantage in some cases, in most cases it is deleterious, but not deleterious enought to affect propogation. Especially mutations within an adaptive mechanism, since that would not directly affect the organism's fitness within an existing environment, and thus could easily spread throughout the population.

Anyway, I discuss how one might weigh the benefits of each approach here:

http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html

Also, the link I pointed out earlier in this post is also relevant in such a discussion.

Genetic Algorithms

2005-08-03T06:26:00.000-07:00

I think its amusing how much evolutionists think that genetic algorithsm are their salvation. The funny thing about genetic algorithms is that they _rely_ on a stable, semantic base for their operation. Creationists don't have any problems with non-deterministic operations happening within populations or even individual organisms. It's that these operations have specific boundaries past which the organism or population falls into error catastrophe. You can't pass gradually from one system to another without hitting error catastrophe.

I always hear "but genetic algorithms produce information". This is one of the dumbest comments I have ever heard, and it pains me that it comes from people who actually program computers! Genetic algorithms are explicitly designed, and include both changing and non-changing parts. It's the non-changing parts that are most important and make the algorithm useful at all!. Evolutionists would have a point if they could point me to a system where all parts of the algorithm change, and have the program, through any sort of non-codal selection (i.e. the selectors cannot simply view the current coding -- that's looking ahead), and the system fundamentally changes what its doing without going through error catastrophe. It simply cannot be done.

Avida is an interesting concept, but it actually shows the weakness of Darwinism. First of all, Avida is incapable of error catastrophe. Second of all, most of the functions of Avida are NOT susceptible to the genetic algorithm. While in evolutionary theory, all parts of the organism are susceptible to evolutionary change, in Avida only a VERY SHORT part of it is. The non-existance of error catastrophe should be enough to disqualify Avida anyway, but even more in order to get it to produce even the smallest, tiniest algorithm, not only to you have to provide HUGE incentives for the algorithm, you have to provide HUGE incentives for ALL of the operations leading up to the algorithm. This is basically forcing a path. It is itself a form of programming. In addition, it is nothing like what happens on earth -- the "benefits" from "beneficial evolution" are not as large, and small deviations are not as costly.

I know someone will say, "but that's what we think happened -- the earth (the environment) programmed the genes". First of all, its funny that to salvage anything, they simply move the design argument to the earth. The earth contains the design is what they are actually arguing, whether they think so or not. So, they are denying creation by explicitly affirming theistic evolution. You see, in order for the environment to serve as a sufficient program, it has to be specifically designed to get you to specific stages! In the Avida example, ALL of the intermediates were PRE-PROGRAMMED into the environment. When the environment did not contain justification for ALL the intermediates PLANNED OUT (remember, evolution requires NO PLANNING), evolution simply did not occur. Programming depends on a plan. If the plan is not in the algorithm, it is in the environment, which would be simply another embodiment for the algorithm. But without design neither one works. However, we know that the plan was not encoded in the environment based on the fact that the environment does not work in the way needed to form drastic semantic change. Therefore, it is reasonable to conclude that the design lies in the organism, or at least that is one of the locations where design is present.

For justification of this, when experiments on Avida were carried out using conditions similar to those in real life, nothing managed to evolve, even given the all of the unrealistically-favorable pieces inherent in the Avida system. For details see here and here.

A funnier reply is here.

The actual Avida software can be found here. I haven't personally used it yet, but plan to shortly. I tried awhile ago and couldn't get it to compile on my Linux box. It has since moved sites, so hopefully they've updated the platform to work with modern compilers.

The bar for entry

2005-08-02T20:48:00.000-07:00

There seems to be some disconnect between creationists and evolutionists in what level of proof creationists should come up with in order to include openly creationists conclusions in their work, as opposed to simply referring to them as "unsolved problems in theoretical biology" as Lambert did or other such walks around the issue. Evolutionists always say that the problem with creationism is that their ideas aren't good enough. After all, evolution is all the rage in peer-reviewed literature.

Anyway, my guess is that this is the bar set for creationists. I could be wrong, but from conversations with evolutionists I'm pretty sure its something like this:

1) since we all know that evolution happened, anything that says it didn't happen must be scientifically flawed
2) we are willing to rethink #1 if you can prove in your experiment evolution to be false. It has to be proof, however, not just doubts about evolution.
3) any external references used in #2 must be to peer-reviewed sources, which have had to go through this same process, therefore eliminating any previous work done by creationists
4) any reference to existing work done by evolutionary biologists cannot be used for support of creationism no matter what the data says or we will accuse you of quote mining.

Is this a valid bar to set for new ideas? That an idea must, without reference to any other work, be provable with a single experiment to the exclusion of any other possibility? Anyway, just thought I'd point that out.

Literature Links

2005-07-26T20:24:00.000-07:00

I've come across some good secular literature worth the read. I have not myself read all of this, but it all comes across well-recommended from various sources:

Two steps forward, one step back: the pleiotropic effects of favoured alleles - describes how much pleiotropy limits the ability of genes to mutate. Pleiotropy is when one gene is involved in multiple different functions. What may be a beneficial change to one function is often deleterious to the rest.

Gene Duplication and the Origin of Novel Proteins - why everything evolutionists thought they knew about gene duplication's role in evolution is wrong.

Simulating evolution by gene duplication of protein features that require multiple amino acid residues - computing the difficulty in obtaining novel, useful proteins with gene duplication.

Evolution at Two Levels: On Genes and Form - a good overview of the modern hypotheses of evolutionary change and benefits and problems of each.

A 21st Century View of Evolution - the genome was not nearly as static as we thought. And hey, those transposons really are useful for something! While Shapiro admits no design, it is hard to read his work and not come away with thinking that there is more than natural law at play here.

These last two freely available on the web, while the others you have to pay for (if anyone finds free links, let me know).

Catholics Clearing Up Their Beliefs

2005-07-09T13:36:00.000-07:00

Thank goodness, a high-ranking Catholic has finally cleared up in public what the Catholic Church thinks about evolution:

Finding Design in Nature (linking to the FR page because it has a large excerpt, and the full article requires login)

Basically, while I wish that they would go further in endorsing the Biblical account, they have clarified that they are not materialists, and that a purely material theory of origins is unacceptable.

While this is not an "official" word from the Church, much of it is simply restating and clarifying the things the Church has said over the last 50 years. And he apparently has the blessing of the pope to write the article.

Philosophical Predispositions

2005-07-01T20:45:00.000-07:00

I haven't had much time to post, although there is a whole lot I've wanted to say. Hopefully I'll have time to catch up soon.

The question I want to address today is what is the status, scientifically, of philosophical presuppositions?

Evolutionists and long-agers are always adamant that they deal only with facts and data and that it's only those creation-looneys who use philosophical presuppositions in their work, and that those presuppositions invalidate everything they do.

A bigger question to ask, which I am not ready to address yet, is the general role of philosophical presuppositions in science. For today, we will look at a subtopic of when are presuppositions considered "science" and when are they considered "religious nuttery".

Some think that philosophical presuppositions are only when creationists try to invoke miracles as explanations. However, evolutionists and long-agers have their own philosophical presuppositions that they bring in.

The one I want to focus on most of all is that of the Big Bang. Hawking, in The Large Scale Structure of Space-Time, is quite candid about the philosophical assumptions of the Big Bang model. First of all, he makes an admission that creationists have long pointed out which many long-agers fight tooth-and-nail about:

However we are not able to make cosmological models without some admixture of ideology.

This is something I've long pointed out to others, and which other organizations have been doing a lot longer than me -- how you interpret the data depends on the assumptions that you bring to the data -- that's the admixture of ideology that Hawking is talking about.

What's really interesting is that Hawking goes on to say that a simple interpretation of the available data would lead one to conclude that our galaxy is in the center of the universe. Since then, further red-shift data shows itself to be quantized in a way that would indicate a center. So what is the ideology that Hawking brings into cosmology? It is this:

Since the time of Copernicus we have been steadily demoted to a medium sized planet going round a medium sized star on the outer edge of a fairly average galaxy, which is itself simply one of a local group of galaxies. Indeed we are now so democratic that we would not claim that our position in space is specially distinguished in any way. We shall, following Bondi (1960), call this assumption the Copernican principle

If you read this carefully, he is saying that they are bringing in an assumption that we are NOT in a spatially distinguished position in the galaxy. Note that this is imposed on the evidence, not brought out from it.

So how do you meld the concept of our position appearing to be significant while they presuppose that it is not?

Ordinarily, we would interpret our observations to mean that we are located near a very special point in the galaxy. Therefore, we must simply assume that the universe appears this way for everyone.

so we shall interpret the Copernican principle as stating that the universe is approximately spherically symmetric about every point (since it is approximately spherically symmetric around us).’

If you read the language carefully, he is simply asserting that it must be spherically symmetric everywhere, because otherwise we would have to admit that we are in a special place.

Now, if a creationist uses a philosophical presupposition to show why something that is apparently long-age can be interpretted as a young age artifact, it is called quackery, but what do they call it when a secular scientist does the same thing with atheism? They call it the standard model.

If anyone thinks I'm reading too much into this, I encourage them to use Amazon.com's SearchInside feature and look up these quotes and read them in context. If it means something different to you, please correct me. But I think you will find this to be true.

Likewise, in geology you have the same sort of thing happening. Over a decade ago, Berthault showed that layered sedimentation does not imply a gradual succession. Likewise, recently geologists have shown that a process formerly thought to take millions of years can actually happen in a decade. This quote is nice:

Conventional wisdom says that changes to crustal rocks pushed down deep when continents collide develop over millions of years. But it seems that some metamorphism may be caused by tectonic events lasting only a decade

It appears that what is driving many of the former interpretations of these events were not experiment and data, but rather interpretation based on assumptions. When long ages are assumed, everything looks like it takes millions of years. Then, when you know the process, you see it only takes a decade.

Anyway, I get irritated when evolutionists pretend that they have no philosophical predispositions but are merely "interpretting the data as it is" when in fact everyone has an ideology they bring to the table -- evolutionists just have a hard time admitting it. Creationists, on the other hand, readily admit their philosophical predispositions, and for being honest they are ridiculed. It might be fair to ridicule them if everyone else is free from such supposing. However, it seems that when you assume atheistic, humanistic, or materialistic philosophy it is called science, but when you assume any sort of theistic philosophy you are considered a religious nut who is a danger to science.

(NOTE -- this article relies heavily on this AiG article by Russell Humphreys. While I'm not copying him directly, the impetus for writing this sprang from reading that article. I had previously assumed that the structure of the universe defined by Hawking was based on empirical observation. I had no idea that Hawking had simply pulled it from his assumptions, and the data led in the other direction. I wonder what other surprising atheistic interpretations we mind find if we look under enough rocks. Perhaps publishing such a compendium might be useful....)

My Favorite T.O Quote Mine Entry

2005-06-23T21:07:00.000-07:00

UPDATE - There is an update below.

I wanted to write a response to my favorite T.O. quote mine project entry. This one the T.O. guys thought was so good that they made an entire page devoted to it. The funny thing is that the page they made gives more credence to the creationist interpretation than even the creationists did!

It is obvious what Lionel's (the quote mine refuter) error was -- it was he was assuming that the creationist quote was saying something it didn't say. This happens quite a bit in my experience. Evolutionists assume that creationists are stupid, backward, disingenuous people, and therefore attribute all sorts of not only bad motives to creationists, but also stupid theories. For example, so many evolutionists believe that creationists believe that there is no species change. This is so obviously ludicrous to anyone who has ever read, listened, or watched anything by any reputable creationist organization, that it's strange that such a myth continues. However, evolutionists seem to always assume they know what creationists think, even without reading what they actually say, or thinking about it. They just assume that it must be stupid, and therefore read it in such a way as to disregard it out-of-hand.

I should assume that most creationists can understand what I find so amusing just by reading the entry. For those of you who take T.O as the carrier of the official evolutionary gospel, I'll explain myself a little more.

Here is the quote:

I fully agree with your comments on the lack of direct illustration of evolutionary transitions in my book. If I knew of any, fossil or living, I would certainly have included them. . .I will lay it on the line, There is not one such fossil for which one might make a watertight argument.

So what is the point of including this? I have not read the book in question, but it seems fairly obvious that the focus on the part that there is no fossil that makes a watertight argument for evolutionary transitions. If the context is different, I hope someone points it out to me so I can correct or retract this page.

Lionel seemed to regard the thrust of the argument being that Colin Patterson didn't believe in transitional fossils. That is just stupid. Of course evolutionists believe that there were transitions, and that some of the fossils are those. Noone is saying that they don't believe such things. What the quote points out is that unlike what evolutionists say, this is not a bulletproof case. In fact, as the quote points out, there is not one such fossil for which one might make a watertight argument.

What's even more amusing is that when Lionel includes the rest of the quote, it does more damage to the dogmatic evolutionary position than the original, abbreviated quote. Here is the continuation of the quote:

... a watertight argument. The reason is that statements about ancestry and descent are not applicable in the fossil record. Is Archaeopteryx the ancestor of all birds? Perhaps yes, perhaps no: there is no way of answering the question. It is easy enough to make up stories of how one form gave rise to another, and to find reasons why the stages should be favoured by natural selection. But such stories are not part of science, for there is no way to put them to the test.

So, not only is the fossil sequence not a watertight argument, it isn't even testable. And, as creationists have always pointed out, It is easy enough to make up stories of how one form gave rise to another, and to find reasons why the stages should be favoured by natural selection. But such stories are not part of science.

But isn't that what evolutionists do all the time? Make up untestable stories, call them "science", and then claim it as an evidence that evolution is right and everyone else is stupid? Here, Colin is being very honest and pointing out that creationists are correct when we criticize how scientific any sort of dogmatic position on origins is. The public part of science just can't say this, it is more based on presuppositions and philosophy than testable hypotheses.

Now, Patterson does add, I think the continuation of the passage shows clearly that your interpretation (at the end of your letter) is correct, and the creationists' is false. I assume this is due to Lionel's having stated to Patterson his own interpretation of the creationist argument.

He then talks about how evolution has done more harm than good to biosystematics, and somehow the fact that a creationist recorded it was problematic. If a creationist had said something damaging about creationism at a creationist conference, would the T.O crowd ignore it if we waved it away as something only addressing serious, concerned creationists?

It is a complete enigma to me how Lionel thinks that this is a win for evolution, and how it shows that creationists are lying. All of Lionel's own research confirms the validity and the context of the quotes. The only thing is that when Lionel uses the creationist negative innuendo, and the professor says, "oh no, I certainly don't want to be considered a friend of them". The only thing the T.O post has is innuendo. Period. He simply attributes negative motives to creationists, and then calls his hypothesis valid even though his own research confirms the creationists, simply because he assumes that creationists must be lying and stupid.

It also points out once again that T.O considers anything a creationist says as "refuted" simply because they post a page about it. It also echoes the theme of "certainly science should be open to criticism, just not from them."

UPDATE

I just noticed that in the top right corner the entry has a now-defunct link to a letter from Patterson to the person I _think_ was the original person who recorded the quote. The site is no longer there, but thanks to The Wayback Machine, I was able to scrounge up the original letter. Here it is:

British Museum (Natural History)
Cromwell Road London SW7 5Bd
Telephone 01-589 6323 ext

Department Of Paleontology

Luther Sunderland
5 Griffin Drive
Apalachin, NY 13732
USA

Date: 10th April 1979

Dear Mr. Sunderland:

Thanks for your letter of 5th March, and your kind words about the museum and my book. I held off answering you for a couple of weeks, in case the artwork you mention in your letter should turn up, but it hasn't.

I fully agree with your comments on the lack of direct illustration of evolutionary transitions in my book. If I knew of any, fossil or living, I would certainly have included them. You suggest that an artist should be asked to visualize such transformations, but where would he get the information from? I could not, honestly, provide it, and if I were to leave it to artistic licence, would that not mislead the reader?

I wrote the text of my book four years ago. If I were to write it now, I think the book would be rather different. Gradualism is a concept I believe in, not just because of Darwin's authority, but because my understanding of genetics seems to demand it. Yet Gould and the American Museum people are hard to contradict when they say that there are no transitional fossils. As a paleontologist myself, I am much occupied with the philosophical problems of identfying ancestral forms in the fossil record. You say that I should at least ‘show a photo of the fossil from which each type organism was derived.' I will lay it on the line - there is not one such fossil for which one could make a watertight argument. The reason is that statements about ancestry and descent are not applicable in the fossil record. Is Archeopteryx the ancestor of all birds? Perhaps yes, perhaps no: there is no way of answering the question. It is easy enough to make up stories of how one form gave rise to another, and to find reasons why the stages should be favored by natural selection. But such stories are not part of science, for there is no way of putting them to the test. So, much as I should like to oblige you by jumping to the defence of gradualism, and fleshing out the transitions betweeen the major types of animals and plants, I find myself a bit short of the intellectual justification necessary for the job.
Thanks again for the writing.

Yours Sincerely,

Colin Patterson

Philosophy of Science Part 1

2005-06-20T18:20:00.000-07:00

I'm planning on posting more about science, the scientific method, science's relationship to truth, and other topics about the philosophy of science, but more research is required, first. However, in the meantime, let me give you this excellent quote from Fester Chugabrew from FR on the relationship between faith and science:

Previous comment:

One system requires no proof and accepts things on faith [regarding faith]. The other system accepts nothing on faith and requires proof for all it's beliefs [regarding science].

Fester's Reply:

My understanding of good science it that it is not only able to make use of inference, conjecture, and leaps of faith, but must do so in order to reach out into the unknown. My understanding of faith is that is rests on evidence and is not merely a fabrication of the imagination.

Book Review: Icons of Evolution

2005-06-19T12:53:00.000-07:00

Icons of Evolution is a good book, but it really does not address the creation/evolution issue per se. It actually has one central thesis: that the icons that represent evolutionary theory in many textbooks and science presentations are not nearly as conclusive as they seam, and often have either been debunked, highly questioned, or simply are not conclusive to what they purport to say.

It is not a book about whether or not evolution is true or not, but whether the presentation of evolution as normally done is more propoganda than reality. If you read the book with this in mind, it does an excellent job of proving its point. If you read it as an anti-evolution book (which it isn't, really), then it fails.

What I appreciated in the book was how it showed how many of the controversies within science over certain experiments are largely smoothed over in textbooks and presentations to make the appearance that everything is thought of and agreed upon, when in fact it isn't.

The chapters on the tree of life and vertebrate homology were my favorite, though I don't think he went as far with the homology argument as he could have (perhaps because he is writing for a non-science audience).

The NCSE has criticized his work and Wells has responded. However, I do think the NCSE is correct in criticizing Well's giving of a D for using photographs instead of Haeckel's embryo drawings. Since the main problem with the evidence was that it was a faked drawing, using real photographs should rate you much higher than a D (this probably comes from Wells being an embryologist, and knowing the problems of embryonic recapitulation better than others).

The book looks like it was put together fairly rushed. It needed a better editor, and occasionally Wells needed to put some more time into rounding out his arguments a little more thoroughly. They were mostly correct, but you can usually find them stated in a much better fashion on the web.

Anyway, it's worth the read, but only if you do so in the context it is offered in, and not as a creation-vs-evolution book.

Book Review: Origins: Linking Science and Scripture

2005-06-19T12:01:00.000-07:00

I've read several well-known and lesser-known creationist books in the past two years while trying to sort out my own beliefs on the subject, so I thought I'd share with you some thoughts I've had on some of them.

I especially like books written by practicing scientists, as they generally do much better justice to the opposing side. Reading a book that has not respect at all for the evolutionary position is a waste of time, as the writer rarely sees the need to justify claims that seem evident to him/her, but perhaps not to the audience.

On recommendation from someone else, I purchased a copy of Origins: Linking Scienceand Scripture. This is a really good book for the fact that it treats origins as it should -- as a unified research proposition, rather than a lot of independent lines of research. Therefore, Roth follows a path of a holistic view of origins issues, and tries to weigh the matter as honestly as he can from the position of scripture or secular science. He is very honest with his preconceptions, as well as the fact that his preconceptions may cause him to draw different conclusions than his reader.

As I mentioned, Roth is a practicing scientist, including research into the effects of light and pigment on the rate of coral reef growth, as mentioned in the about the author section. He is published both secularly and in the journal Origins, whose character I was unable to ascertain.

Roth begins his book with an excellent list of paradigms that have shaped certain sciences which eventually were discarded entirely. He shows that because of this, we should not discard a theory simply because current science is founded on a different principle.

The first section is on biology, and, while it is well worth reading and has many additional insights you might not otherwise know, it is basically the same types of arguments as other creationists give. However, his attention to the complexity of the cells complexity in regards to error correction is very good, as well as his list of books by non-creationists who are questioning the validity of current origin-of-life research.

He has a chapter on fossils, but its way too short. On the other hand, it does give a good overview of the geologic column from an evolutionary view for those who don't have secular science books available.

He continues on in other chapters to talk of the geologic column, and this is where his book does a really good job. It is difficult to grasp the main creationist positions about the flood and its impact on the geologic column from most creation/evolution books. He does an excellent job of summarizing them. Some of the points from these chapter include:

The fossil sequence is too orderly to not demand an explanation. Therefore, no creationist account of the fossils is sufficient unless it accounts for the fossil sequence.

The fossil record is much more complete than many say, given that 98% of terrestrial vertebrates are present within that record (most are not as well-represented as terrestrial vertebrates, but still well-represented). Therefore, any evolutionary account must take this into consideration when discussing transitional forms.

For the flood he gives the three major models of why the fossil sequence is ordered: motility, ecologic zonation, and buyancy. He clearly favors ecologic zonation. For the evolutionists, he points to both the gradualistic and punctuated equilibrium models of evolutions as the mechanisms for producing the fossil succession.

He also points to evidences for a worldwide flood, including:

abundant underwater activity on the continents

widespread sedimentary deposits -- evidences of a vast sea covering vast expanses of land

incomplete ecosystem fossilization -- animals are often found fossilized separate from any vegetation for them to live off of

gaps in the sedimentary layers -- specifically he mentions that where there are hundreds of millions of years of "gaps", there is virtually no evidence for millions of years of erosion

He then mentions several other things about rocks, but I must have slept through that part, because looking back over the book I really don't remember reading it.

He then proposes several questions about geologic time, showing that any number of geologic processes can lead to any number of ideas for the age of the earth and specific rock formations, and that saying that we definitively know the age of the earth only means that we are selective in what evidences we are choosing to include.

He ends with a pretty good discussion of science and scripture and their interplay, and ultimately sums up what he believes the evidence points to (I'll let you guess where that is :] ).

Just for the record, as some people I've talked to have been confused, Ariel Roth's conception of a young-earth creationist does not rely on a specific age for the physical rock that is the earth, but for the geologic column, which is the record of life on earth. It is the age of the geologic column which he finds important.

I was a little disappointed that the book had nothing on astronomy, which could be linked to either (a) the author thinking that astronomy is a winning argument for evolutionists, (b) that the author, being a biologist, is not qualified to write on astronomy, or (c) the author does not believe that the age of the universe is a worthwhile question to ask. He points to (c) within the book, but I was still a little sad that he decided not to go down that road.

Anyway, all-in-all it was a great book. While it did not give as thorough of a treatment as I'd wished to several subjects (understandable due to the length and subjects covered), it was very good.

Double Standards

2005-06-17T05:39:00.000-07:00

I find it amusing when talking with evolutionist friends that whenever a difficulty in the science of evolution comes up, they regard it as a research issue, but whenever a difficulty of the science of creation comes up, they regard it as an a priori insurmountable difficulty, which automatically disproves creationism once and for all.

Likewise, whenever creationists revise the mechanism (not the basic biblically-recorded historical facts of creation), evolutionists call foul, even though they themselves believe that for science to be valid it must be revisable with future evidence.

On the whole, I see three major problems:

1) People unable to see their own presuppositions, or even recognize the role of presuppositions in logic, reason, and science, and therefore assuming they do not have any
2) A gigantic double-standard for how much and what kind of evidence must be used for creation to be a plausible theory.
3) A misunderstanding of the nature of historical inquiry, and how it differs from observational/experimental science.

One of the funniest things I've seen said is this:

1) because creationism includes an all-powerful God, it cannot be tested, and is therefore not scientific
2) everywhere that creationism has been tested it has been proven wrong

Not only are both of these extremely inaccurate, the sequence of thought is nothing short of hilarious.

(1) is untrue because (a) we have a historical document, and therefore cannot propose anything we want, (b) our historical document says that the heavens declare that there is a God, and (c) it is reasonable to assume that the events recorded in the Bible left its mark on creation.
(2) is untrue because there are many areas where creation has been tested and proven right. It is only proven wrong on the _assumption_ of long ages of evolution. Just a few places where science shows theology off the top of my head:

The pre-adaptation of many organisms to environments they have not been in yet (they often have dormant genes that are available for alternate environments)

The existence of continental-wide evidence of water flow

The ability to definitely prove heredity to the levels of biblical kinds where supposed, and the difficulty of proving it beyond that.

The fact that much of recorded ancient history, even through pagan countries, trace their lineages back to Noah, and that there are many cultures whose date of creation and the flood are almost exactly what the Bible suggests.

The fossil record is ordered _beyond_ what it should be given known natural history, indicated that the ordering process is physical, not biological. For example, there are many "living fossils" that are alive today, but whose last appearance in the fossil record is, by evolutionary timescales, hundreds of millions of years old. Is it reasonable to have a so-ordered fossil record if natural history itself is not so ordered? I think that this shows that the ordering of much of the fossil record is based on a physical ordering process, not a historical one.

The existence of DNA, and the fact that it is a carrier for an independent message is one of the most revealing proofs of a creator. Nowhere else except by creative agency is there such a coding system.

The fact that most dangerous aspects of life are simply good things out-of-control is evidence of a good world followed by a fall (many venoms, for example, also have healing and other good properties in lower concentrations, and many pathogenic viruses and bacteria are actually degenerate adaptations of otherwise helpful organisms).

The existence of both perfect and imperfect adaptations is also evidence of a good world followed by a fall.

Anyway, the funniest part of all of it is not just the fact that both of these points are wrong, but that they are completely logically meaningless when combined.

Interesting Article on Physics Myopathy

2005-06-03T05:19:00.000-07:00

Physics principles too myopic, Nobel winner says

In the April lecture, he explained that Newton’s law of gravity is considered to be a fundamental law, but it is impossible to observe this force in objects on a nanoscale.

“When you get up close and take it apart to see how the law works, you discover it’s not there,” he said.

Heat laws are also thought to be fundamental, he explained, but the smallest particles do not obey them.

“Heat, conceptually, is like a painting of Monet; when you get up close to see its parts, to see how the parts work, you discover nothing but a lot of meaningless dots,” he said.

The distinction between fundamental and emergent laws then becomes nonexistent and even basic assumptions become mysterious. Because laws like those regulating heat and gravity are only true for some matter, the foundations of physics are becoming weak, he said.

“Physics is now in the midst of a crisis, an ideological battle,” he said. “The most fundamental things you know may not be fundamental.”

Laughlin also argued that, for mysteries like why atoms are so uniform throughout the galaxy, physicists form creation myths to explain away these quandaries. Inflationary cosmology, he said, is the “myth” created to solve this problem by saying that during the expansion after the big bang, matter became uniform.

“That, on the face of it, is a pretty far-fetched theory, but the reason we take this theory so seriously is the depth of the crisis. In other words, we really need to have an explanation for why this stuff is so uniform, and we don’t have it,” he said. “I like to say that the emergentist nature of the theories of the universe are really an act of desperation.”

The best chance at solving some of these mysteries of the universe, Laughlin suggests in A Different Universe, is to avoid the reductionist approach of studying particles too minute to measure, and to look at the basic realities of the natural world.

(emphasis mine)

I'm very excited that physicists have figured out that reductionism isn't all it's cracked up to be. I'm not against reductionism, but I do think that the trend toward reductionism to the exclusion of other principles is damaging both to science and to other human endeavors. Specifically, the trend toward reductionism is damaging towards morality, because ultimately you can reduce bad actions to non-bad parts. "I didn't kill him with a gun, I just moved my finger a little toward my body. It's not normally illegal for me to move my finger in this way, is it?" Reductionism doesn't work in life, nor does it really work in science. There is validity in searching for reductionism, because some things in fact can be reduced. However, every once in a while, you need to back up, take a breath, and say "is this really right?"

I'm very glad such a prominent physicist is doing this. Very encouraging.

The Nike Metaphor and Other Thoughts

2005-06-03T05:01:00.000-07:00

The Nike Metaphor

Is macro evolution just micro-evolution carried out for 3.5 billion years? Personally, I don't like using terms like micro- and macro-evolution, because there's some much confusion about what they mean. I prefer using things just as gaining complex information or just lateral or downward change. Gaining complex information in the creationist perspective is the result of creation, and lateral or downward change is the result of evolution. I like to illustrate this with an example from Nike:

It's like buying a shoe at the shoestore. If I buy a shoe, when I first get it is fairly stiff and rigid. However, as I walk in my shoe, it will "break in" and become more comfortable. However, the breaking-in process tells me nothing about how my shoe originally got here nor why there are differences between a Reebok and a Nike. It won't get me air pumps in a shoe that doesn't have them, and it won't generate new kinds of material.

Likewise, creationists believe that complex systems do not originate by chance alone. There are small changes, but they are more akin to "breaking in" (whether good or bad changes -- note that good changes are not increases in complexity) than to creating. Now, creationists believe that the "breaking in" process is much more complicated than my description of shoes (which includes modular genomic elements that can rearrange as a result of environment), but ultimately, complex systems are not built from the result of chance and law, but need a designing agent. ID'ers call this the Law of Conservation of Information.

Exercising Proverbs 26:4

2005-05-31T19:29:00.000-07:00

Sometimes it's amusing what people come up with for responses to posts. It's sad when people on your own side start making inane comments, but it's amusing to watch others do it. I have a policy of specifically letting such posts stand, because I think they do a much better job of refuting their own stance than I ever could.

Some of my favorite verses are:

Answer not a fool according to his folly, lest thou also be like unto him.
Answer a fool according to his folly, lest he be wise in his own conceit.

(Proverbs 26:4-5)

Once you know that these are your two options, deciding whether or not to post a response is simple. If posting just makes you part of the "argumentation game" then just shut up, but if you have a point of contention that the other person truly isn't aware of, then speak up.

This is an amusing response I got today. It's from someone who normally speaks intelligently:

There is a creationist model and not just a grab-bag of talking points!!?? Er, no. You mean, "One of the talkiing points is 'All mutations are bad, bad, bad!'"

Have you read the lead article of this thread? Your talking point is wrong, wrong, wrong.

Apparently he was frustrated that creationists actually think and do not just shout off talking points like he wanted them to. He made up a talking point that he wanted me to be spouting off, and then refuted his made-up talking point.

The Catholic Evolution of Evolution

2005-05-24T06:17:00.000-07:00

Here's another good post worth quoting from FreeRepublic (from Tantumergo):

"But even if it's true does it necessarily mean God doesn't exist or He isn't the God we've all been sure he was?"

No, it doesn't mean that, even though it is a theory concocted and promoted by atheists in order to provide a materialist explanation for the existence of life.

However, whether it is true or not as a scientific theory is of great importance, because it fundamentally affects the paradigm or worldview within which people operate. Not least, from the moral perspective, if you keep telling people for long enough that they are simply monkeys with big brains, then we should not be surprised if they eventually start acting like monkeys with big brains, and before you know it you will have a world filled with Hillary Clintons!!!

It has also been the bane of Catholic theology for the last 70 years. Once "theologians" such as Pierre Teilhard de Chardin SJ got it into their heads that evolutionism was the way that the world worked then modernism received a massive boost. No longer was the deposit of faith something that had been delivered once to the saints in a world of fixed and immutable truth, but now everything was involved in a process of development - a process of becoming rather than being. Everything that had gone before could be discarded or re-interpreted to fit with a process of updating and adaptation to the world in which we lived. All history was caught up in an evolutionary flow of progress of the advancement of man, headed towards that point in the future where mankind would evolve into the cosmic Christ. Teilhard de Chardin was roundly condemned by Pius XII, but the Jesuits are still trying to rehabilitate him to this day.

The theory has also been used very effectively by heretical theologians to undermine the doctrine of Original Sin and consequently the need of mankind for a Redeemer.

Obviously Genesis is not meant to be a science textbook which gives detailed how-to's of the creation. God could have created by a process of evolution if he had wanted to, however, he gives us no indication in Revelation that He did and there is no evidence from science that he did either.

Great discussion on the age of the Earth

2005-05-23T21:47:00.000-07:00

I found this wonderful link today:

How to Decide Between Sides on Difficult Issues

It specifically talks about the age of the earth. I thought it did a fair treatment to both sides of the argument (though it is not recent enough to have all of the recent arguments), but I would be interested if a long-ager could give an assessment of it, too.

Gould and Dawkins

2005-05-17T21:44:00.000-07:00

I'm reading Gould's "The Panda's Thumb" right now. Let me just say -- in comparison w/ Dawkins, Gould is amazing. Honestly I can't figure out why people like Dawkins so much -- his books are boring and his analogies are horrendously flawed.

Gould, on the other hand, is much better all the way around. Thankfully, Gould was also a prolific writer, so, while we no longer have Gould around, he's left us much to remember him by.

To compare, I started Dawkin's "Climbing Mount Improbable" two months ago. I have started and completed three other books in their entirety in the meantime. I still can't bring myself to read more than a few paragraphs of Dawkins at a time. It just feels like wasting my time. Gould, on the other hand, I bought The Panda's Thumb three days ago, and am already on essay #4.

Anyway, pretty much the only argument I have w/ Gould is that he, like many evolutionists, seems to misunderstand creationism. He still wants to equate creationism with Aristotelian creationism. In the first three essays, he talks a lot about two different kinds of design within animals -- near-perfect design and cobbled-together-from-whatevers-handy design. He says that the first isn't good evidence for evolution because, while natural selection can do that, so can a creator. He thinks that the real evidence for evolution is the "cobbled-together" part.

The funny thing is that he's absolutely right. And, for the most part, creationists AGREE with evolutionists that the parts of organisms which are half-functional and seem to be cobbled together from other uses or simply arisen from adaptation probably ARE the result of evolution. See, the evolutionists see only one source of biological innovation -- evolution. Creationists see two -- design and evolution. And I think Gould has inadvertantly pointed out a general way to distinguish them.

More Replies to T.O's Creationism Claims Index

2005-05-13T21:16:00.000-07:00

CD103: The entire geologic column is based on the assumption of evolution.

The responses are these:

"The geologic column was outlined by creationist geologists."

This is an exageration at best, and direct misrepresentation at worst. Let's look at their example:

"For example, Adam Sedgwick, who described and named the Cambrian era, referred to the theory of evolution as "no better than a phrensied dream" (Ritland 1982)."

Based on this link, Sedgwick is a theistic evolutionist. His problem with Darwin was the part of leaving a purely naturalistic view of evolution.

Here's some relevant paragraphs from that link:

Sedgwick also did not object to evolution, or "development" as such theories were called then, in the broad sense -- to the fact that the life on Earth had changed over time. Nor was he a young-Earth creationist; he believed that the Earth must be extremely old. As Darwin wrote of Sedgwick's lectures, "What a capital hand is Sedgewick [sic] for drawing large cheques upon the Bank of Time!"

However, Sedgwick believed in the Divine creation of life over long periods of time, by "a power I cannot imitate or comprehend -- but in which I believe, by a legitimate conclusion of sound reason drawn from the laws of harmonies of nature." What Sedgwick objected to was the apparent amoral and materialist nature of Darwin's proposed mechanism, natural selection, which he thought degrading to humanity's spiritual aspirations. His letter of November 24 went on to state:

This view of nature you have stated admirably; tho' admitted by all naturalists & denied by no one of common sense. We all admit development as a fact of history; but how came it about? Here, in language, & still more in logic, we are point blank at issue-- There is a moral or metaphysical part of nature as well as a physical. A man who denies this is deep in the mire of folly. Tis the crown & glory of organic science that it does thro' final cause, link material to moral. . . You have ignored this link; &, if I do not mistake your meaning, you have done your best in one or two pregnant cases to break it. Were it possible (which thank God it is not) to break it, humanity in my mind, would suffer a damage that might brutalize it--& sink the human race into a lower grade of degradation than any into which it has fallen since its written records tell us of its history.

It seems that T.O is just as bad at quote mining as they claim creationists are. They also entirely leave out the Scriptural Geologists, who objected to the evolutionary geologists of the period.

One thing to point out is that "evolution" had been around long before Darwin -- Darwin simply provided a naturalistic mechanism. Many naturalists even back to the Greeks (and before) believed in a gradual evolution.

Also to note, is that creationists don't object to the idea of a column of geologic rock per se, but of the specific interpretation given it by evolutionists.

"The geologic column is validated in great detail by radiometric dating, which is based on principles of physics, not evolution. Furthermore, different dating techniques are consistent, and they are consistent with the order established by the early pioneers of stratigraphy."

This is only true if you completely gloss over the aberrant dates. Aberrant dates are often not reported. Here are some aberrant dates to think about:

Diamonds found at the bottom of the geologic column are fairly consistently dated to 50,000 to 70,000 years on equipment that can accurately detected up to 90,000 years.

Dating by the speed of helium escape from Zircons usually shows around 5,000 years on rocks that otherwise date to millions of years (this is controversial, so you can see the ICR claim, Talk.Origin's response, and Russel Humphrey's reply)

Woodmorappe has given a number of accounts of known cases where dates are discarded. T.O has replied (see their "other links" section to see Woodmorappe's and other's reply to T.O's reply). In fact, you should probably take the time to read Woodmorappe's reply.

The fact is that aberrant dates ARE thrown out. If they get data back which conflicts wildly with "known" ages for things, they probably wouldn't even bother publishing it. Why would they? This is not an accusation of lying, but rather human nature. "It was probably a bad sample -- I must have overlooked something."

Anyway, the RATE group this November, 2005, is going to be giving the results of their multi-year study into radiometric dating for determining earth ages. It should be interesting.

Just to note, we've hit some other T.O claims in here, such as CD015 and to a lesser extent CD010 and its sub-claims.

Also, I _think_ in the RATE group data to be presented in November, the RATE group is going to present evidence that certain types of radioactive decay has had other rates in the past. This should be interesting, if true.

Talk.Origins "Index to Creationist Claims" pt1

2005-05-12T21:26:00.000-07:00

It's fun to browse Talk.Origins. Sometimes they have good points, and sometimes they only think they have good points. It is an assumption of most evolutionists on the web today that Talk.Origins rebuttals are foolproof, which is quite amusing to watch. Anyway, occasionally as I get the impetus, I'll respond to parts of T.O's website.

CB040: Left-handed amino acids

Claim: life uses only left-handed amino acids, which couldn't have arisen naturally.

T.O's talking points are mainly hand-waving:

"The amino acids that are used in life, like most other aspects of living things, are very likely not the product of chance. Instead, they likely resulted from a selection process."

Oh, the unobserved _chemical_ selection process. I hate to break it to you, but natural selection requires life, and chemical selection is a contradiction in terms. Chemical reactions move TOWARD equilibrium, not away from it.

"A simple peptide replicator can amplify the proportion of a single handedness in an initially random mixture of left- and right-handed fragments"

Amplification isn't good enough. We need 100%.

"Serine forms stable clusters of a single handedness which can select other amino acids of like handedness by subtituting them for serine; these clusters also incorporate other biologically important molecules such as glyceraldehyde, glucose, and phosphoric acid"

From Creation Safaris:

"The serine cluster is not a chain, but a ring. Further, it does not attract other amino acids to form peptide-bonded chains. The Cooks crew only tested eight amino acids for like-handedness joining the serine clusters."

So, not much help there.

"An excess of handedness in one kind of amino acid catalyzes the handedness of other organic products, such as threose, which may have figured prominently in proto-life"

Wild speculation doesn't count as evidence.

"Amino acids found in meteorites from space, which must have formed abiotically, also show significantly more of the left-handed variety, perhaps from circularly polarized UV light in the early solar system"

We're looking for 100% here.

"The first self-replicator may have had eight or fewer types of amino acids"

Speculation unless we can actually build a self-replicator.

"It is not all that unlikely that the same handedness might occur so few times by chance, especially if one of the amino acids was glycine, which has no handedness."

It depends on the length, and we've tried thousands of different combinations and have not been able to even force one in the lab.

"Some bacteria use right-handed amino acids, too"

This sounds like a big claim, but really is a bunch of crap. It's a bluff that you won't do the research yourself. Do you know WHY some bacteria use right-handed amino acids? They use it as a COATING to DEFEND THEMSELVES (i.e. screw up the functioning of would-be predators). It is not just a "plug-n-play" system. I'm not 100% sure, but I think that the cases where right-handers are used, again, it's 100% right-handers.

For all known enzymes, if you have EVEN ONE amino acid of the wrong hand, the entire enzyme will be rendered useless.

Here's a good AiG article on the subject.

Also, other molecules (like DNA) are all right-handed.

CB015 : DNA needs certain proteins in order to replicate. Proteins need DNA to form. Neither could have formed naturally without the other already in existence.

"DNA could have evolved gradually from a simpler replicator;"

Complete bluff. We have no idea if this could have happened.

"RNA is a likely candidate, since it can catalyze its own duplication"

Another bluff. While RNA has enzymatic properties, we have never found an RNA molecule that could self-sufficiently catalyze its own duplication. We've tried thousands of combinations and haven't gotten it to work. We still need those enzymes to do the very tricky copying procedures for us.

"The RNA itself could have had simpler precursors, such as peptide nucleic acids (Böhler et al. 1995). A deoxyribozyme can both catalyze its own replication and function to cleave RNA -- all without any protein enzymes (Levy and Ellington 2003)."

I have not looked into this work, but my guess is that this is more bluffing. I know that other works (Huber et al., A Possible Primordial Peptide Cycle, Science 2003) contain nearly all bluffs and no real data. Just a lot of suppositions, what ifs, and maybes. For a full response, see this.

CB035: lots of stuff about Miller-Urey

There's not a whole lot wrong with their criticisms of creationist criticisms, except that they leave out a REAL BIG CLAIM -- it doesn't matter. Edward Peltzer first noticed this years ago. The Miller-Urey experiment was thought to be useful because it matched the examination of a meteorite believed to be billions of years old. Here's what Peltzer had to say:

I asked myself, "Why is a meteorite that is 4.5 billion years old, with processes that went on for perhaps millions, if not billions, of years, so similar to an experiment that a graduate student can do over the weekend?" Something else is happening here, and we are missing it.

...

Sure, in Miller's experiment we make that first step. But in the meteorite, there's so much more time there. Shouldn't there be some evidence of going the second step, or the third step? And it suddenly hit me. Why should the two look anything alike at all? The Miller experiment was stopped after a week or ten days. Nobody stopped the meteorite. It had ample opportunity to go much further. Yet the two are virtually the same.

CB010.1: Even the simplest, most primitive forms of life -- bacteria -- are incredibly complex, much too complex to have arisen by chance.

Here is their response:

"There is no reason to think that the life around today is comparable in complexity to the earliest life. All of the simplest life would almost certainly be extinct by now, outcompeted by more complex forms."

Eukaryotes ate my evidence. But you have to take my word for it anyway.

"Self-replicators can be incredibly simple, as simple as a strand of six DNA nucleotides (Sievers and von Kiedrowski 1994). This is simple enough to form via prebiotic chemistry. Self-replication sets the stage for evolution to begin, whether or not you call the molecules "life.""

This one is new to me, but I'm going to call a pre-emptive BS. DNA doesn't self-replicate -- that's the whole reason for proposing RNA world, which still hasn't found a self-replicating RNA strand.

"Nobody claims the first life arose by chance. To jump from the fact that the origin is unknown to the conclusion that it could not have happened naturally is the argument from incredulity."

To say that it did happen naturally is not shown by ANY EVIDENCE WHATSOEVER, but instead by a whole lot of bluffing about might-have's and could-have's, when we still haven't gotten chirality figured out.

We still don't have evidence that the fountain of youth doesn't exist, but most of us have grown up and stopped searching for it. The argument against the fountain of youth is likewise an argument from incredulity.

If you have no weapon, no motive, no body, and no circumstantial evidence, you can't make a case at trial. Likewise with the origin of life. All indications is that life comes from life, and information from intelligent beings. If someone has another mechanism, that's great. But so far it's just a lot of hand-waving.

Initial Conclusions

Notice how much T.O assumes that you aren't going to look into their claims and just assume that they've done proper research, and that claims from evolutionary scientists don't need to be checked and validated against a BS detector. It's a giant confidence game.

Anyway, that was fun, though it took more time than I wanted. Hopefully I'll have time to do it again soon.

The Fireworks Metaphor

2005-05-11T05:07:00.000-07:00

An excellent metaphor used in Understanding the Pattern of Life is relating organism diversification to fireworks. The baraminologists think that the majority of diversification occurred just after the flood, with the harshness of the postflood world inducing a large amount of unprecedented diversification (the mechanism thought to be genomic modularity). Since then, the environment has been relatively stable, and so diversification does not proceed as rapidly, and the mechanism doesn't work as well due to mutational loads.

Baraminologists agree w/ evolutionists that neo-darwinism accounts for some amount of change, and for perhaps much of modern change. However, what they disagree about is if neo-darwinism accounts for the majority of diversity.

They liken it to a firecracker. When a firecracker explodes, sparks are sent out everywhere. However, after the explosions, the paths of the sparks are modified by wind, producing slight variations. However, the main direction of the sparks is set by the firecracker explosion, not the wind. They equate neo-darwinism to be more of a "wind-like" factor in the diversification of animals. Sure, it accounts for some things that we are presently seeing, but in the course of history, it is not the wind that set the major directions, but instead (1) creation and (2) post-flood diversification.

Understanding the Pattern of Life Book Review

2005-05-09T20:29:00.000-07:00

I just finished reading Understanding the Pattern of Life by Todd Wood and Megan Murray. This book is a creationist introduction to biosystematics, known as baraminology (baramin coming from Hebrew for created kinds). This review is a review of (1) the book, (2) the methods, and (3) the terminology.

In general, this is a very excellent first effort of modern creationists to put out a constructive book on biology from a creationist perspective. This IS NOT a creation/evolution controversy book. There are some definite shortcomings both as a book and as a methodology, but I think it is exceptional given how few resources are currently put into the topic at this point. If you read the book, be warned that it starts out really slow and kind of boring, but really, really, really picks up towards the middle and end with very fascinating looks at creation biology.

The book is organized into three sections -- foundations, methodology, and applications.

In foundations, the first chapter deals with the importance of naming, specifically from a biblical perspective. It's a good, introspective chapter as to why we bother with all of this, as well as some history on it. It emphasizes the holistic approach of baraminology, as apposed to the reductionist view of, say, cladistics. The second chapter introduces the terminology, and this is my main sticking point.

Baramins originally referred to the original created kinds. This is an unusual word as it is. However, it was complicated by the fact that it is nearly impossible to be certain that what you find in nature is, in fact, an original created kind. Therefore, this method of biosystematics is more inspired by the biblical kinds, and hopefully approximate to them, but not exactly. Therefore, they came up with the concept of holobaramin to be an empirically determined approximation of the original baramin. The goal is to find the holobaramins.

Then, to add more confusion, they added the words monobaramin for any kind of inclusive group -- anything that adds members to a group, such as the ability to cross-breed, and apobaramin for any kind of exclusive or subtractive evidence, such as having a radically different genome. You theoretically arrive at the holobaramin when your exclusions and your inclusions hit the same group of animals.

At its core, what they are trying to do is to find and measure continuities (monobaramins) and discontinuities (apobaramins) in nature. I agree wholeheartedly with the approach and with most of the methods. However, I wish a better terminology could have been thought of. Perhaps, to help gain new audiences, using simpler terms such as simply "continuous" and "discontinuous" would have been more helpful. Reading entire chapters of "baramin"-based words is extremely annoying.

One thing that I think was missing, however, was mentioning that not every useful classification system would relate to monobaramins and apobaramins. Sometimes in classification, there comes times when other naming / classification systems are more appropriate. It would have been nice for the book to touch on those things.

The history of baramins is a concise view of biblical history in specific relationship to ecological events affecting animal populations.

In the methodology section, the "gathering and interpretting biblical data" chapter should have been left out, and simply mentioned in the introduction. This is a far bigger field than to cover in one chapter (the book admits as much), and instead of attempting it, there should have been one or two paragraphs about animals in the bible and translation issues, and then give the reader a reference to other works on the subject. I understand the desire to include such a chapter in a creation-based biosystematics book, but it is really an entirely different subject altogether.

The "successive approximations" chapter really needed to be reworked. I kept on feeling like they were arguing in a circle, and then merely stating "we're not arguing in a circle." I agree in general with the direction they are going, but I think they need to approach it in a different manner so that it doesn't sound like it's being argued in a circle.

The next three chapters, however, were great. It talks in-depth about discontinuity, followed by an in-depth chapter on breeding/hybridization. This is excellent material. The one issue that I have is that it seems on occasion that the ability for two species to hybridize is given as conclusive evidence of monobaraminic relationship. While I agree that it is strong evidence, I don't think that it is conclusive evidence, especially as Leviticus outlaws breeding between kinds. I emailed Wood about this, and he said that (1) baramins were not directly equivalent with the "min" of Genesis, but rather a human concept justified on a scriptural basis, (2) breeding was not used as 100% conclusive proof of monobaraminic relationship, but he was not aware of places where it was ever contradicted by the statistical evidence, and (3) the word translated into "kinds" in Leviticus is not the same "min" found in Genesis anyway.

While hybridization is a fascinating subject, the chapter on statistical baraminology is even more interesting. They give two methods for this: BDIST (for biological distance) and ANOPA (for analysis of patterns). BDIST is the more easily explainable. To compare species with BDIST, each basic trait for each species considered is quantified between 0 and 1. Each pairing of species is then plotted together with all of their traits. If the trait plots give a generally ascending line, then that is evidence of continuity. A descending line is evidence of discontinuity. I have not yet fully grasped ANOPA yet, but here's what I _think_ it is: you take a dimension for every character trait, and plot each species being examined within this n-dimensional matrix, and then calculate a 1D, 2D, or 3D projection of this n-dimensional space for easy viewing.

Even better than the baraminology methods is the applications. Each of these chapters is wonderful, although I wish that they were longer. These topics are covered, and great things are said about each:

Design, including design for non-function (like beauty)

Biological imperfection, including contemplations of the origins of pathogenic diseases (although True Origin has a better, more extensive review of this topic)

Diversification was probably the book's absolutely best chapter. Covered rates of diversification, reasons for diversification, and different means of diversification. The means are: heterozygous fractionality (from Mendel), Genomic modularity (the ability of a genome to modify itself in response to the environment) as well as participate in lateral genetic transfers, and neo-darwinistic theory. Baraminologies uses all of these to one degree or another, but denies the neo-darwinistic mechanism as having the ability to create new biological systems. They had a great analogy to fireworks which I will hopefully touch on in a later post.

Biogeography was good, with information I was unaware of. Unfortunately, the chapter was too short to consider biogeography in general, and instead considered only the areas where creationist biogeography differs from traditional biogeography.

Anyway, I would recommend this book to anyone, if only for the diversification chapter. I'm hoping for future releases of this book with expanded chapters.

A few nits:

Very few of the experiments mentioned were talked about in detail. I kind of felt like I needed to have a copy of Following Form and Function just to get the details. In fact, that will probably be my next book purchase.

It definitely could have been longer. I would want a biosystematics book to go into more detail into what many more of the major baramins are thought to be.

Successive approximation should have followed the statistical methods -- it would have given it a bigger punch. On the other hand, statistical methods, in requiring "outgroups", is somewhat reliant on the concept of successive approximation.

The terminology. Sadly, I doubt this will be changing.

MORE RESEARCH. I kept on feeling like I was getting the same sources over and over. I probably was. This is a new field, but there needs to be more research done on it, or at least with these methodologies that can be co-opted.

There's probably more I could say, but you're probably bored reading by now. If you want a constructive view of creationist biology, buy the book. Also, see the Baraminology Study Group website. I think they're having a conference soon, which, unfortunately I can't attend :(

Another Great Post

2005-05-09T20:25:00.000-07:00

Hit upon this post as well, thought I'd share. This post is about the informational content of DNA.

The Shannon-Weaver General Model of Communication (1947) proposed that all communication must include six elements:

* a source
* an encoder
* a message
* a channel
* a decoder
* a receiver

According to in Warren Weaver's introduction to Shannon's paper:

The word information, in this theory, is used in a special sense that must not be confused with its ordinary usage. In particular information must not be confused with meaning.

In fact, two messages, one of which is heavily loaded with meaning and the other of which is pure nonsense, can be exactly equivalent, from the present viewpoint, as regards information.

You tap on a membrane suspended above a steadily flowing jet of water. The air under the membrane causes slight deflections in the jet of water. A laser is aimed at a receiver. The jet of water flows through the laser beam, deflecting it from its target. Every time the water jet is deflected by the movement of the air, the laser beam hits its target. The laser receiver is connected to a computer which takes each 'hit' and turns it into a 1 and each miss and turns it into a 0. The computer sends these etc. etc......

You get the idea: the air waves, the jet of water and so on are all channels. The words channel and medium are often used interchangeably, if slightly inaccurately. The choice (a pretty stupid one above) of the appropriate channel is a vitally important choice in communication. It's obvious that you don't use the visual channel to communicate with the blind or the auditory channel with the deaf, but there are more subtle considerations to be taken into account as well. A colleague of mine was clearly much more responsive to visual communication than I. To elucidate his arguments he would inevitably grab a pencil and a piece of paper and sketch out complex diagrams of his arguments. Though they may have help him to clarify his ideas, they merely served to confuse me, who would have preferred a verbal exposition. But that argument deteriorates into one of semantics and differentiating meaning from signal concerning the definition of information. According to the Shannon-Weaver model of communication, meaning is divorced from that of the existance of a signal for a message to exist.

Genes are sections of DNA that code for a defined biochemical function, usually the production of a protein. The structure of a protein determines its function. The sequence of bases in a given gene determines the structure of a protein. Thus the genetic code determines what proteins an organism can make and what those proteins can do.

mRNA (Messenger RNA) is used to relay information from a gene to the protein synthesis machinery in cells. mRNA is made by copying the sequence of a gene, with one subtle difference: thymine (T) in DNA is substituted by uracil (U) in mRNA. This allows cells to differentiate mRNA from DNA so that mRNA can be selectively degraded without destroying DNA.

Genetic code is a language that is used by living cells to convert information found in DNA into information needed to make proteins. A protein's structure, and therefore function, is determined by the sequence of amino acid subunits. The amino acid sequence of a protein is determined by the sequence of the gene encoding that protein. The "words" of the genetic code are called codons. Each codon consists of three adjacent bases in an mRNA molecule. Using combinations of A, U, C and G, there can be sixty four different three-base codons. There are only twenty amino acids that need to be coded for by these sixty four codons. This excess of codons is known as the redundancy of the genetic code. By allowing more than one codon to specify each amino acid, mutations can occur in the sequence of a gene without affecting the resulting protein.

To refer to a particular piece of DNA, a person in Detroit might write: AATTGCCTTTTAAAAA. This is a perfectly acceptable way of describing a piece of DNA. That code can then be sent via the internet to somebody in Tokyo, where someone with a machine called a DNA synthesizer could actually synthesize DNA from the information specified by AATTGCCTTTTAAAAA alone. Subsequently that specific DNA can be spliced into a gene of some bacteria and a particular protein can be manufactured. Your premise is demonstrably false.

Furthermore, your statement There is no more information in DNA than there is in a snowflake is woefully ignorant. You confuse information with entropy. Clearly the degree of randomness within that of a snowflake is less than that of liquid water. Suggesting that the entropy of DNA is equivalent to that of a snowflake is ridiculous. DNA in inert form can be crystalized and may have similar entropy to that of a snowflake, and if I vaporize that DNA crystal and then re-crystalize it, its entropy essentially remains unchanged (it will be no more or less ordered than its previous crystalized from). But you will never be able to synthesize a protein from that form of crystalized DNA material (as from its orginal deconstructed form), while the deconstructed fundamental components of the snowflake can recreate another, albeit disimiliar snowflake it still will be a snowflake. The former has to do with a fundamental degree of randomness, the latter has to do with the fundemental physical properties of its components. What differentiates functional DNA from its inert form is that of its organization. What evolution has not done is provide a suitable answer to whether or not random chance, time and natural processes are sufficient for the origin of the organization inherent in biological DNA.

Finally, using your syllogism, and one of the examples you cite in support of your positin, I can stipulate that there's no more information on that CD-ROM you say contains War & Peace, than that of a grain of salt. That's perfectly sound logic (Modus Tollens) but invalid.

A Great Post

2005-05-08T19:46:00.000-07:00

With permission, I am reposting this post from CharlesWayneCT on FreeRepublic.com. He does not believe in creation, but I think the way he frames the debate is very interesting and worthy of consideration:

You are correct in that science cannot abide such a lame explanation as "God just made it that way".

But if he DID just make it that way, it wouldn't really matter that it isn't a satisfying scientific explanation.

Creation is by its very nature an extra-scientific event. But it doesn't claim to be anything else. Evolution on the other hand makes the scientific claim, and therefore must be measured on that basis.

There are those who argue for "scientific creationism", but they don't mean that the act of creation is scientific (which really confuses the issue). They mean that the evidence of history which is discovered through observation is not inconsistant with whatever view of creation they are peddling.

But the detective work of divining history through observation is not the same "science" as the "scientific theory" of evolution. Which in fact is a theory with widespread evidence,observable and repeatable. It's just that the "scientific theory of evolution" describes a natural process, not an historical event. Historical events are not scientific theories.

If we could distinguish between history and science, and teach stuff in the proper context, I imagine most "creationists" would crawl back into their spiritual worlds and leave the rest of you alone. They have a point -- no matter how well you can 'explain' observations by the evolutionary model, and no matter if you can find fossils which fit a historical hypothesis that is consistant with an evolutionary model, you simply cannot prove the manner in which we reached our current state of affairs.

Part of the problem is that those who wanted to be free from religion co-opted the science of evolution to use it as a hammer to smash the pillars of religion. The "God is Dead" crowd made a religion out of the science of Evolution, and it was inevitable that those who held to other doctrine would fight back. Science simply was caught in the crossfire.

Apologetics and Christianity

2005-05-04T18:51:00.000-07:00

Often people misunderstand the role of apologetics in Christianity. Sadly, this is often misunderstood by the apologists themselves!

Many people think that the role of an apologist is to win an argument to convince people that Christ is true. I honestly cannot think of a worse result for apologetics. Let's take a look at how this plays out, even if you win the argument:

You argue with a non-believer. You win, they admit it, and because of your argument the believe in Christ.

They run into another person tomorrow, who is an atheist. The atheist brings up an issue that you had not addressed. New believer asks you about it.

You either (a) hadn't heard this argument before, and don't have an answer for it, or (b) your answer isn't as convincing to the person as your other arguments, or (c) they can't find you.

Therefore, since the new believer has found someone with a temporarily better argument, they believe the atheist now.

What's wrong with this picture? They believed the argument, not Christ! The fact is that being a Christian means REPLACING our current method of epistemology (epistemology == way of knowing) with that of knowing and believing Christ first and above all else. In the case of the argument, the person still placed their own reasoning above that of knowing Christ. Therefore, when their reasoning said "turn to Christ", they did, and when it said "turn away", it did that, too. Christ was never Lord -- their mind was.

Likewise Paul said that he didn't come with crafty arguments, but came to declare the power of Christ crucified. Indeed, it is only the power of the cross which causes a change in Lordship, not a good argument. This is why prayer is your most important weapon, NOT YOUR ARGUMENT! (Note that I fail in this area all the time)

So what's the use of apologetics? Well, apologetics has several very good uses:

To Encourage Existing Believers

Apologetics can be an encouragement to existing believers. As mentioned, believers believe because we have set Christ to be our source. However, being fallen people, we are easily led astray. Apologetics helps believers back to Christ when the world tries to paint Christ as a fairy-tale.

To Remove Issues from Non-believers

While apologetics in and of itself should not be the basis of a conversion, it can remove stumbling blocks on the path. Jesus is not deceitful, and knowing that reality is consistent with the sayings of Jesus (even if we only know that consistency in part) can help unbelievers turn to Jesus. If the Holy Spirit is working on them, and they are saying "yes, but....", apologetics can help remove the "yes, but..."s. Also, since Christianity is historically rooted, apologetics can help show that the history of the Bible is true, so the Holy Spirit can work on showing that the claims are likewise true. This is the method used by Paul in Acts 17 -- he showed them where God had been working in the history of man to lead to Christ.

To Help Establish Good Doctrine

Apologetics can help the development of doctrine by sorting out the what is the apparent problems in scripture and the apparent problems in the world/scripture relationship, and showing in which ways scripture answers the world, in which ways it is consistent with the world, and which areas the scripture is silent on. This is the job of most theologians as well, but it has heavy overlap with that of apologetics.

A Warning

While I have mentioned removing stumbling blocks, I want to point out that we should not remove all stumbling blocks. There are many necessary stumbling blocks, especially as Christ has referred to himself as a stumbling block. We should be careful to remove only the unnecessary stumbling blocks, and leave the necessary ones in. Jesus Himself would sometimes give reasons for people NOT to follow Him. In the evangelical culture, we often forget that the road to Christianity can involve some necessary stumbling blocks, and those are inherent in Christianity and should not be removed. Specifically is the Lordship issue. As I've mentioned, Lordship means that Jesus is your primary source. You should not be modifying your view of Jesus to accomodate your other views. You should be modifying your other views to accomodate Jesus. If a person is not ready to relinquish Lordship of their lives over to Jesus, they should be counselled, with love, in the same way that Jesus counselled: "Warning! This is only for people who will follow Me to the end!"

How to Talk to Your Biology Teacher

2005-05-03T22:19:00.000-07:00

Nothing bothers me more than creationists who have not looked at the creation/evolution debate seriously thinking that they can just jump in and be useful. The fact is that honest people have looked at the facts and decided that evolution is right. Therefore, you are going to need more than just a cursory knowledge of it to successfully debate it.

Likewise, debate is not always the answer. What does the Bible say to wives whose husbands are not saved? Does it say to nag them into the kingdom? No, it says to show great respect, so that by your example they may come to know Christ. When in a teacher/student setting, the teacher is in the position of authority, and likewise it is your job to show respect, not disrespect. By being honest, open, and most of all, respectful, you can win a lot more people than being aggressive or passive-aggressive (note that neither of these are Christ-like attitudes).

I recently found this story of a student who successfully converted her teacher, which can act as a model for Christians who want to spread Christ in the biology classroom:

One day, he heard that Louisiana had passed a law requiring equal time for creation with evolution, and he was flabbergasted– how stupid, he thought, and how evil! He used the opportunity to launch into a tirade against creationism in class, and to give them his best eloquence in support of Darwinism. Little did he know he had a formidable opponent in class that day. No, not a silver-tongued orator to engage him in a battle of wits; that would have been too easy. This time it was a gentle, polite, young female student.

This student went up to him after class and cheerfully exclaimed, “Great lecture, Doc! Say, I wonder if I could make an appointment with you; I have some questions about what you said, and just want to get my facts straight.” Dr. Lumsden, flattered with this student’s positive approach, agreed on a time they could meet in his office. On the appointed day, the student thanked him for his time, and started in. She did not argue with anything he had said about evolution in class, but just began asking a series of questions: “How did life arise? . . . Isn’t DNA too complex to form by chance? . . . Why are there gaps in the fossil record between major kinds? . . . .What are the missing links between apes and man?” She didn’t act judgmental or provocative; she just wanted to know. Lumsden, unabashed, gave the standard evolutionary answers to the questions. But something about this interchange began making him very uneasy. He was prepared for a fight, but not for a gentle, honest set of questions. As he listened to himself spouting the typical evolutionary responses, he thought to himself, This does not make any sense. What I know about biology is contrary to what I’m saying. When the time came to go, the student picked up her books and smiled, “Thanks, Doc!” and left. On the outside, Dr. Lumsden appeared confident; but on the inside, he was devastated. He knew that everything he had told this student was wrong.

So, let's see what happened:

Allowed the professor to vent in front of the class about Creationists and listened attentively

Did not pose embarrassing questions in front of the class

Did not even claim that the professor was wrong

Asked questions respectfully

Listened carefully to answers

Did not feel the need to rebut every point (or even any point) the professor made

After listening to the answers, said "thank you" and left the issue at that.

The professor knew himself that what he was saying was wrong, and because it was a non-confrontational situation, was able to have some perspective and think clearly on the subject. Backing people into a corner makes them defensive. Behaving like Christ allows God to work in them, and I can guarantee you that He is more effective than you.

This is in great contrast to how the Discovery Institute and Jonathan Wells wants you to ask your teacher embarrassing, confrontational questions to spark a controversy. While there's nothing wrong with being honest about evolution's shortcomings, there is both a way and a time to do it, and many ways and times where it is inappropriate.

There's nothing wrong with debate, but let's be like Christ when we do so, especially when it involves people who are in authority over us. Remember, if you are a Christian, you are always on display for being Christ in the world. The world should know Christians by their humbleness, meekness, love, giving, and respect, not for being annoying in biology class.

Dawkins Doesn't Debate Creationists

2005-05-03T16:27:00.000-07:00

Why doesn't Dawkins debate creationists? Dawkins gives his own reasons. I don't know for sure, but I imagine that it might at least also include what happened at the 1986 Oxford Union Debate. Dawkins was debating A.E. Wilder-Smith. Also on Dawkin's side was John Maynard-Smith, and likewise Wilder-Smith had Edgar Andrews on his side.

So what were the results?

Since scientists repeatedly say that creation is as debunked as a flat earth, you'd think that there would be noone voting that Wilder-Smith had won the debate. You'd be quite wrong. The result?

198 to 150 in favor of the evolutionists.

This is not sometime in the 1800's or in the early 1900's, this is 1986. Since then, Dawkins has refused to debate creationists. Also note that it was Dawkins and Maynard Smith who brought up religion, which seems to validate Hunter's conclusion that the ultimate reasoning behind evolutionary theory is not science, but religion.

If you want a copy of the debate, see this site to order.

At the end, Dawkins made an impassioned plea for a "0" vote for the creation side. I would guess that the fact that the creationists made such an impression on their audience has been in part responsible for his unwillingness to do it again. Dawkins claims that he doesn't do it because the creationists get respect by the debate even happening at all. I don't believe that he is so confident in winning, based on the results of the Oxford Union debate.

What Scientific Advances Have Resulted From Creationism? GENETICS

2005-05-01T20:56:00.000-07:00

All the time people say that creationism has never lead to scientific advances. I find that highly amusing. The fact is that most of the greats of the history of science are creationists. The standard response is that those people were not researching creationism, did not have the data, were motivated by religion, or that creationism, while they believed it, did not contribute anything to what they learned. Some have also thought that the reason they were creationists was simply beause of the Church's power.

These are all very valid arguments for many of history's scientists (although some will argue that Christianity, while not necessarily creationism, is what led to science in the first place).

However, there is at least one scientist, and one very influential theory, that is likely the result of using creation as a starting point for scientific inquiry. What is it?

Mendel, and the field of Genetics.

What? Isn't genetics the foundation of evolution? No. In fact, it took 70 years for evolutionists to manage to modify evolution enough to fit genetics in. In fact, Mendel's genetics was a direct rebuttal of the evolutionary ideas of his day.

Although Darwin's specific theory of evolution (i.e. natural selection) had not occurred when Mendel was doing his experiments, the general idea of transformism (a soft form of universal common ancestry) was a popular concept. Lamarck had already come up with his ideas of evolution, though his theory was rejected in favor of Darwin's. Transformism was a popular and powerful concept which was taking root in biology. However, Mendel's experiments were a rebuttal to transformism. The general argument was like this: breeders are able to create new species, therefore, we should expect that all of the species we see today are the result of permanent transforms over time.

Mendel's rebuttal is th at heritable characteristics are available as discrete units. He was able to show that these transformations by breeders were not permanent, because the original species could always be brought back in by rebreeding with animals in the original population. Because these traits are discrete, there can be no permanent transforming of one species into another.

Here is the relevant section from Mendel's paper:

Gärtner, by the results of these transformation experiments, was led to oppose the opinion of those naturalists who dispute the stability of plant species and believe in a continuous evolution of vegetation. He perceives in the complete transformation of one species into another an indubitable proof that species are fixed with limits beyond which they cannot change. Although this opinion cannot be unconditionally accepted we find on the other hand in Gärtner's experiments a noteworthy confirmation of that supposition regarding variability of cultivated plants which has already been expressed.

So, (1) we can change one species into another and back, (2) many traits are discrete characteristics, therefore there are limits to the amount of transformation possible (since all hybrids come from a cross of discrete characteristics already present in animals that are able to hybridize).

While genetics has advanced beyond just mendellian genetics, and mutations show that the genes can be modified, neither of these has been able to get past Mendel's conclusions. Why?

* The original idea of mutations from which the integration of genetics and evolution suggested was that these mutations could happen rather quickly. Now that we know just how many change it takes to modify one gene coding for a protein into another, this becomes much more difficult than originally proposed, and we have few if any examples of this happening (a possible exception is the nylon bug which I will hopefully have time to address soon).
* We have much evidence that for most vertebrates, hybridization is possible within the family level, but not outside. There are clear discontinuities past that point. This indicates that most change in the past has been bounded.
* Mutation loads are usually dangerous, not helpful. Otherwise, we wouldn't see so many birth defects from incestual relationships.

Anyway, so what does this have to do with creationism?

The fact is that Mendel was a Catholic monk. Specifically, he was a Catholic monk arguing against evolution. Would that not put him in the creationist camp? What his specific motivations were are subject to speculation (yes, we are speculating to a degree here, but I don't think that any of this is unreasonable). There are reports that there is a copy of Origin of the Species in his monestary with margin notes in his handwriting. However, I haven't found any reports as to what these notes actually say.

Here is another good essay regarding Mendel and creationism.

AiG's One Blood: The Biblical Answer to Racism video has some excellent material on this. In fact, I can't hardly keep the video on my shelf I have so many requests to watch it. The book is available online, and chapter 2 discusses speciation with Mendellian Genetics (though it doesn't say much about Mendel himself).

An A-Priori Commitment to Millions of Years?

2005-04-29T19:55:00.000-07:00

Many people rightly claim that Creationists have an a priori commitment to a young earth. We in fact do (at least to some extent -- the biosphere). However, I have been wondering of late whether or not the other side has similar commitments, even though they claim not to. The reason for that is that many of the original reasons for belief in "millions of years" have been long refuted. However, when you look at projections for the age of the earth or the universe, they get progressively longer, but the reasons for projecting this have been shown to be wrong.

This indicates to me that perhaps they had an a priori commitment to long ages, probably based on Greek philosophy (which had been revived during the renaissance). The geologists of the 19th century talked about getting out from under the Abrahamic
(or was it Mosaic -- can't remember the actual terminology) system. Anyway, the dates go slowly outward from Mosaic dates -- starting out at about 80,000 years, and progressing steadily upward until we are at the 4 billion mark for the earth today, and the 20 million mark for the universe.

Anyway, nothing explicit, it is certainly very likely that they did not have an a priori commitment, but it just made me wonder, and I might look into it more at a later date.

Evolution and Alchemy

2005-04-28T20:05:00.000-07:00

It occurred to me the other day that evolution is a lot like alchemy. Alchemy arose during the early days chemistry. It made sense in that time -- there were a number of transformations that were known to be available between materials, why shouldn't there be transformations available between lead and gold?

That general idea, coupled with a few fraudulent examples of it happening, kept the fires of alchemy burning for long after it should have died out. But, again, it made sense -- they had no reason to think that the changes available by chemical means were limitted.

This is almost the same situation in biology. Change has been observed in living beings (and in fact had been observed LONG before evolution or even aristotelian biology), but not the kinds of change required to fully rewrite the way an organism works. While there is quite a lot of variation available even within a single population, ultimately there is not the ability for transformations between life forms no matter how much time you had.

Mendel's work actually showed this experimentally (and his paper said as much), but this has been widely ignored. It was assumed that mutations solved this dilemma, but the kinds of mutations normally observed do not add up to the power needed to do the necessary transformations in any amount of time.

Naturalism, Science, Theology, Polkinghorne, and Dembski

2005-04-27T21:37:00.000-07:00

I wanted to post about two great articles regarding naturalism, science, and theology. While I am not an ID'er, I very much respect Dembski, and the first article is his. The other, by Polkinghorne, is very interesting, though I find myself at odds with him a lot more often than Dembski.

The first article is Intelligent Design: Yesterday’s Orthodoxy, Today’s Heresy. There are several interesting things within the article. The ones I found most interesting is:

The fact that bad theology in the 19th century is what led to Darwinism. Specifically, he contrasted William Paley's theology of a watch built by a watchmaker with the Church Father's theology of a master flutist who both created a flute and loved to play it. Paley leaves God distant from creation, instead of intimately involved. This distance eventually led to evolution (in fact, when Darwin was still a Christian, Paley was one of his favorite reads).

The fact that you can't have a completely self-contained interpretive framework. Ultimately, you have to involve ideas and thoughts from other disciplines, based on (or at least inspired by) Godel's incompleteness theorems.

The problems with current Christian education of its pastors.

It points out that evolutionary ideas have been around for a looong time, and Creation is in direct opposition to them.

Here are some quotes:

“Enuma elish” are the first words of the poem. They mean “when on high.” The poem is talking about the origin of the world, and it ultimately tries to vindicate Marduk as the head god of the Babylonians. The poem starts out with Tiamat and Apsu, who are the salt and fresh waters. Notice that this starts with natural, material forces. As the salt and fresh waters mingle, there is a sort of cohabitation, and out of this comes a first generation of gods. As the gods go on, they kill each other and do various things. For generation upon generation you get new gods, and as you read along, you find that these gods are becoming more and more conscious and intelligent, until you finally get to the head god, Marduk.

Notice what is happening. It is not that you are starting out, as in Genesis, with “In the beginning God created the heavens and the earth;” that God speaks the world into existence; that God, a conscious, intelligent, personal agent, is the source of all being, and then everything is created as a result of this intelligence. Rather, intelligence is emerging as a byproduct of natural forces working themselves out. So we see an evolutionary story in the Enuma Elish. I am not just imposing it; it is there.

And more:

Paley was a theist, but it is easy to see why with Paley’s natural theology it was a very short step from theism to deism. But now push it a little further: If a perfect watch is one that never needs winding, would an even more perfect watch be one that constructs itself? A watch is just an object in motion. Material objects move. So why not just set it up so that material objects build the watch and then allow the watch to continue indefinitely? There was a fellow named Kingsley who described evolution as the result of God, but he said, “God makes a world which makes itself.”

I think you see where this is going. You go from theism to deism, but once you have a perfect watch that does not need God except at the beginning stages, why not just take it further and just have a watch that constructs itself? I think that is where the logic of science went. By the time you get to Darwin you have a world in which everything makes itself. And what Darwin brings to the party, as it were, is an account of how you get biological organization and complexity.

And then:

Let me just say where I believe we are now. I think we are finding that this concept of a world that creates itself is no longer adequate. For the idea that the world created itself to be convincing, you are going to have to argue that material processes are adequate to explain everything in the world. To do that, there has to be a reduction to natural law. Basically, what you have to say is that for anything that happens, there is an antecedent circumstance and some law-like relationship that takes you from one thing to the other. You have this in Newtonian mechanics. For example, if you have a certain orbit, then there were some initial conditions, some properties of the matter which led to that. Or if you are trying to explain some instance of biological complexity, then there must be some background conditions, some natural selection pressures, or certain properties of variation that could account for that.
...
It is not that the principle of sufficient reason breaks down. It is just that when intelligence is a sufficient reason, there is no reduction possible. If God in his wisdom creates the world, it makes no sense to ask: What is behind that wisdom? Who designed that wisdom? There is nothing behind it. That is how intelligence works. Intelligence is creative. Intelligence is not an open book; intelligences write books. They create novel information. You cannot reduce them to these material mechanisms.

If I had to characterize in a nutshell what is happening within the Intelligent Design (ID) movement, I would say this: We in ID are saying that this picture of a materialistic world, entirely controlled and capable of being explained by mechanisms is no longer adequate, and we have good solid reasons for showing the insufficiency of that worldview on scientific grounds.

A similar thing happened in the 1930s in mathematics, when a mathematician named Kurt Gödel showed that there were true mathematical statements that could not be proven. The things that are proven in science are those things that you can explain in terms of material mechanisms. Gödel’s result is called “the incompleteness theorem” because it is saying that there are truths that are not susceptible to this sort of mechanization of mathematics. Likewise, the mechanization of science is incomplete—it does not account for everything.

And that brings us to the second article: Religion in an Age of Science. It's a very interesting article. However, Polkinghorne does not hold that scripture is in authority over science, and that where scripture and science disagree, we should look to scripture. He believes the other way around. However, the arguments against naturalism and science are excellent. Especially this paragraph:

There is a second thing I want to say, and it's this: many people have a picture of the physical world which is very outdated. The great triumphs of the science in the eighteenth century, and the further discoveries of the nineteenth century, encouraged a view of the physical world as if it were in some sense mechanical, a rather rigid and deterministic world. Actually, we've always known that can't be right, because we've always known as an absolutely basic fact of human nature that we have the experience of choice and responsibility. In the twentieth century we have made further scientific gains and twentieth-century science has seen the death of a merely mechanical view of the world. In part, that is due to the cloudy fitfulness of quantum theory lurking at the atomic and sub-atomic roots of the world. But I think, more importantly still, it is also due to another unexpected insight of science gained in the last thirty - forty years. Even the physics of the everyday world, even the physics of Newton, is not as mechanical as Sir Isaac and his followers would have thought it to be. That's a very surprising discovery. Those of us who learned classical physics, learned the subject by thinking about certain tame, predictable systems, like a steadily ticking pendulum. That's a very simple robust system. If you take a pendulum and slightly disturb it, or you are slightly ignorant about how it is moving, the slight disturbance only produces slight consequences, the slight ignorance only produces slight errors in your estimation of how it will behave. We thought the everyday Physical world was all like that. It was tame, it was predictable, it was controllable - in a word, it was mechanical. Now, we've discovered that, in fact, almost all the everyday physical world is not like that at all. Almost all of the everyday physical world is so exquisitely sensitive that the smallest disturbance produces quite uncontrollable and unpredictable consequences. There are very many more clouds than clocks around. This is the insight that is rather ineptly named chaotic dynamics. It came as a very great surprise to us. It is not altogether astonishing that the discovery was first made in relation to attempts to make models of the earth's weather systems. In the trade it is sometimes called the butterfly effect: that the great weather systems of the earth are so sensitive to individual circumstance that a butterfly stirring the air with its wings in Beijing today will have consequences for the storm systems over London in a month's time. Now, that world - that exquisitely sensitive world - is an intrinsically unpredictable world. We can't know about all those butterflies in Beijing. So we've learned that the physical world, whatever it is, it certainly isn't mechanical, even at the everyday level. It is something more subtle and more supple than that. To do justice to the full development of the argument, I'd need to say a good many more things, but I think already one can see the beginnings of a picture of the physical world that is unpredictable in detail and open to the future. That is a gain for science. Science begins to describe a world which is sufficiently flexible in its development, a world of true becoming, of which we can consider ourselves as inhabitants. The future is genuinely new, not just a rearrangement of what was there in the past. In such a world of true becoming, with its open future, we can begin to understand our own powers of agency, our own powers to act and bring things about. I would want to say also that such a physical world is one which, in my view, is capable also of being open to God's providential interaction and his agency in the world. So that whole picture of the physical world has been loosened up. It is much more hospitable to the presence of both humanity and divine providence than would have seemed conceivable a hundred years ago.

Complaining that a Scale is not a Microscope

2005-04-27T21:28:00.000-07:00

If anyone is reading my blogs, you probably know already that while I am not an ID'er, I don't mind defending them from idiotic attacks. One recent one that I keep coming across is this:

"ID sucks because it can't tell us who the designer is"

Or, more generally,

"ID sucks because it does not give a complete account of origins and doesn't resolve the theological debate entirely"

The issue is that ID isn't meant or designed to do that. ID answers ONE QUESTION and ONE QUESTION ONLY -- was X designed? That can only have three answers -- yes, no, and I don't know (actually, ID can only answers that question two ways -- yes and I don't know). ID is simply a TOOL. To complain about ID because it doesn't answer every question about life, the universe, and everything is just as silly as complaining that a scale doesn't have the same features that a microscope does. A scale only weighs things. It won't tell you why it weighs that amount. It won't tell you what color something is. It will only answer the question WHAT DOES IT WEIGH. Likewise, ID only answers the question IS X DESIGNED?

I find it odd that scientists would reject a tool on the grounds that it has a very specific purpose, and answers a very specific question.

Another attack on ID (this one from theologians) complains that ID gives the false impression that the way life exists on the earth was the way that it was created, which is biblically false. Again, this is another misunderstanding of what ID is -- ID does not say that everything was created as it is. ID allows for both designed and undesigned biological systems, and for designed systems to falter. The ONLY QUESTION THAT ID ANSWERS is WAS X DESIGNED?

I think that a lot of these "misunderstandings" of ID arise because of one of two reasons: (a) people don't want ID to be true, and therefore purposefully have a false impression of what it is or does, or (b) some creationists are overly-pushing ID as being the answer to all of their ills in the science/religion conflicts. I think both answers are true.

Starlight and Time

2005-04-27T20:58:00.000-07:00

Russel Humphreys did a talk on starlight and time, which makes me want to break out both the astronomy and physics books. However, what was more interesting is that the starlight problem is just as problematic in Big Bang theory as it is in creationism. In the Big Bang theory, the problem is termed Horizon Problem.

This brings me to think about one of the problems in origins research -- to come up with a properly suitable comprehensive theory of origins, it would require knowledge of a vast array of sciences, most of which people study their entire lives. Therefore, once a paradigm is established, it would take an exceptionally long time for it to be disestablished, since the disestablishers would have to have answered all of the questions from all areas of science.

AiG Conference

2005-04-27T20:08:00.000-07:00

I went to an AiG conference last weekend. It was a great conference, but not for the reasons I expected.

First of all, I have a lot of respect for Russel Humphreys. I didn't before the conference. I appreciated the fact that he was humble about his own findings, and, specifically regarding his speed of light study, was very tentative about them. Reading Hugh Ross's assessment of the situation had led me to believe that AiG did not put any disclaimers on the material, but in fact they do. In addition, in a personal conversation with Russel after the conference, I asked him how many evidences he had collected for a young earth. He told me he had collected around 200, but only wished to disclose the ones that had been well-researched, which he publishes on ICR's web site.

Second of all, my favorite talk was on racism. I had thought about skipping that topic, because I thought it was going to be very boring. But instead, I learned many fascinating things. One of which was that the reason my parent's generation is so bigotted is probably because bigotry was taught as a fact of biology. Now, neither I nor AiG think that evolution is the source of racism. The existence of racism in biology textbooks simply tells me why its so engrained in them that they can't seem to let it go. So what was AiG's point? It was that the Bible contained the truth all along. When the Church abondoned God's word to follow secular science, when secular science changed, the Church was left holding the bag, and was no longer a light to the culture. It wasn't about racism per se, but about the Church compromising to contemporary culture. When people try to rectify the Bible with personal beliefs and modern science, it is always the Bible which winds up changed. As believers, we are to put the Bible first, not last.

The third thing, which is mostly trivia, is that the Ice Age ended around the time of Abraham. Job, which was written roughly at the same time, takes place in the middle east, but has an unusually high number of references to cold, ice, and snow. I thought that was interesting.

I also bought some videos there, which is unusual for me, since I usually buy books. Anyway, I've really enjoyed the Creation Astronomy video, and look forward to the research Jason Lisle will be doing with AiG. I also enjoyed Tas Walker's biblical geology video, and am doing some more research on my own in that area.

Welcome to CrevoBits

2005-04-26T20:54:00.000-07:00

In my other blog, crevo.blogspot.com, I try to post fairly well-formulated thoughts about the Creation and Evolution controversy. In it, I try to make the case for Creation, while being fair to evolution. However, I often have a lot of things floating around in my head, interesting sites that I visit, and half-formed thoughts that I want to ponder some more. This blog will be the little bits and pieces of thought that don't fit on my other blog.

Anyway, you'll probably find a lot wrong with the blog -- that's its whole point. Please help me out by posting how stupid I am in the comments. However, please help me out by being specific and including links if you can. I'm also always looking out for good books to read!