Tuesday, August 23, 2005
Materialism and Theism
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.
Saturday, August 20, 2005
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.
Saturday, August 06, 2005
The Creationist Model
"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:
Also, the link I pointed out earlier in this post is also relevant in such a discussion.
Wednesday, August 03, 2005
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.
Tuesday, August 02, 2005
The bar for entry
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.