Sunday, March 25, 2007
Dealing with Tough Parts of Scripture
Sometimes we try to take the easy road in reading the Bible and not ask the tough questions. I appreciate Oyarsa's honesty with himself and scripture when reading through such a passage. It's a good example for all of us.
Team Creation for Folding@Home and Ideas for Creation@Home
Anyway, the Folding@Home client made it into the PS3's Online Network main menu. I downloaded it, and started team creation. If anyone else wants to boost the Creationist contribution to Folding@Home, download the Folding@Home client, and configure it to be on team 59478.
So this got me thinking... wouldn't it be cool to have something like Creation@Home? So that Creation researchers who want access to clustered machines for numerical calculations could simply use the home computing power of Creationists running Creation@Home. Now, this actually has a whole slew of different technical issues than something like Folding@Home. F@H is based on a small set of special-purpose algorithms. However, something general like Creation@Home would require that any arbitrarily-constructed algorithm be runnable on the systems. This might mean that different researchers might have different libraries they need to load, which means that the Creation@Home client would need fuller access to the system. In addition, to get the full benefit of the different platforms (like the PS3), the algorithms would have to be compiled for each platform on the network, and, in the case of the PS3, it would have to be not only re-compiled, but re-written. Also, it would likely be that we would need everyone running the same operating system (like Linux). However, running Linux on the PS3, while doable, is not something that people who have a PS3 for gaming would be willing or able to do.
Anyway, there is a lot of stuff to consider, and the architecture might be something like that of Planet Lab (a description of the architecture is available in this talk (the PlanetLab software is apparently available here).
Anyway, I'm curious to hear from my readers -- who here would run Creation@Home if it were created? How many have a PS3 that they would consider installing something like Creation@Home? Is there anyone here with a numerical simulation they would like to run on Creation@Home?
In any case, if you have a computer (especially a Playstation 3) that sits idle a lot, consider downloading Folding@Home and sign up for "team creation", team 59478.
Friday, March 23, 2007
Fast Formation of Gold Deposits
Tuesday, March 20, 2007
Interesting Book on Natural Design
According to the product description:
Physiologist Scott Turner argues eloquently and convincingly that the apparent design we see in the living world only makes sense when we add to Darwin's towering achievement the dimension that much modern molecular biology has left on the gene-splicing floor: the dynamic interaction between living organisms and their environment. Only when we add environmental physiology to natural selection can we begin to understand the beautiful fit between the form life takes and how life works.
Monday, March 19, 2007
More from Margulis - Pointers to Additional Symbiotic Research
In “symbiotic planet” you seemed to indicate that symbioses might be the driving factor behind speciation and novelty in life history. However, in many cases, you seem to restrict your arguments to the origin of eukaryotes and other microorganisms. I’m personally more curious in the application of these ideas in present biology. Do we know the mechanisms of symbiotic establishments in the wild? What interesting symbioses have we observed, and what mechanisms were involved? Scott Gilbert has done some interesting reviews of biological phenomena in predator/prey relationships, where, during development, a prey can detect its predator in the environment and develop accordingly. Has any such mechanism been established for symbiotic relationships?In response, Dr. Margulis gives us several interesting things to read. I've added in links to her response to help locate the materials should my readers be interested (post is also slightly edited for spelling and formatting):
Jonathan BartlettI never say anything “is interesting”..except to me or a colleague, family member or friend, but I love your question anyway.
Do we know the mechanisms of symbiotic establishments in the wild? What interesting symbioses have we observed, and what mechanisms were involved?
First: Bacteria, including archabacteria, can mate either by cell to cell contact or by dropping one’s DNA into the wetness to be taken up by the other. All bacteria will rather mate than die when that is the choice. Since you can put them in the refrigerator in the evening and make them be another species by morning I agree with Sorin Sonea (book: Prokaryotology, Universite Montreal Press) that they have no species in the sense nucleated organisms have..Then we work with speciated protists that have no sexual life histories but surely that have species identity.
Jonathan, there is a fine literature dating back to the mid 19th Century that has been summarized in several books: Evolution by Association: a History of Symbiosis research (Jan Sapp) our book Acquiring Genomes: A Theory of the origins (s, plural) of species (Margulis and Sagan, 2002 Basic Books) and now we found that most of the classical well studied cases were known to Boris Kozo-Polyanski in his book A new Principle of Biology [no link found] (he meant evolution by symbiogenesis) in 1926. This book is nearly all translated by Victor Fet, a biol. prof at Marshall univ in Huntington W V.
By no means are these ideas only in the microcosm. What is a cow (or a bison) unable to eat grass? A starved cow. What is a subterranean termite unable to eat and digest wood? A dead termite. Both these types of animals owe their existence to great communities of highly specific symbionts that digest their foodstuffs, make them change their bodies (over time, of course). The rumen, the hindgut. The literature is vast and so detailed that in 1924-26 K-P wrote a book explaining this..he united Darwin's “natural selection (which only ELIMINATES life forms, does not create them) with SYMBIOGENESIS that does create new species in the same genus. Other modes of species change include: polyploidy in plants, hybridization in marine larvae, karyotypic fissioning (centromere reproduction) in mammals and several other modes [emphases mine]. All are far more significant for the generation of new species than “random mutation”. Of course random mutations hone and refine the bigger hereditary processes but there is no evidence I know of that proves that random mutation GENERATES evolutionary novelty..i.e. new species. All this is detailed in the books I mentioned and see the ISS (International Symbiosis Society) and its journal called Symbiosis.
Tuesday, March 13, 2007
Platonic Forms and Front Loading
I’m currently working through Robustness and Evolvability in Living Systems, and came across the following information which seems to be right in line with Denton’s evolution by natural law ideas:
A final, especially counterintuitive feature of RNA sequence space is that all frequent structures are near each other in sequence space. Consider a randomly chosen sequence that folds into a frequent structure and ask how far one has to step away from the original sequence to find a sequence that folds into this second structure…For instance, for RNAs of length n = 100 nucleotides, a sphere of r = 15 mutational steps contains with probability one a sequence for any common structure. This implies that one has to search a vanishingly small fraction of sequence space…to find all common structures.
One of the issues that came up was this -- just how much does this really have to do with intelligent design? If the evolutionary space itself is set up to evolve, does this really have anything to do with Intelligent Design?
Anyway, this is a very good question, and to begin to understand it we need to understand two distinct (but not mutually exclusive hypotheses) in the Intelligent Design world -- front-loading and platonic forms. Just to note, however, not everyone uses these terms equivalently. Especially front-loading, which has a different meaning for nearly every individual who uses it. Anyway, I will attempt to define these two positions, talk about how they relate to each other, and finally, how they relate to this quote from Wagner.
Front-loading is the hypothesis that at some point in the past (usually at the origin of life), organisms were given a rather large deposit of information. The history of life from that point onward has been primarily governed by that information, specializing into the different species we have today. In this view, the original organisms potentially had _more_ information in them than individual organisms do today. The original organisms contained the major patterns and building blocks for all of the major evolutionary themes. Biological patterns may have been stochastically mixed and distributed throughout life (i.e. there was necessarily not _one_ preset destination in mind, just a set of biologically-meaningful patterns from which organisms could choose), but ultimately, the main driver for life patterns comes from this deposit of information.
Now, information, in order to be information, is essentially physics-independent. For example, when you install software on a computer, while the physics of the computer are very much applicable for running the software, you cannot use the physics of the computer to create the software. Intelligent agents use creativity to create the software in a manner that is wholly independent of the physics of computers. Front-loading focuses on the informational aspect of biology -- the physics-independent deposit of information given to the original organism or organisms. Most people who hold to this view think that there is at least some of that original deposit left hanging around in "junk DNA".
The person most active in this area of thinking (if I understand him correctly) is MikeGene and others at TelicThoughts.
Platonic forms is the idea that physics is set up so that there are only a small set of possible configurations that life could have. The reason that life keeps coming up with the same type of solutions over and over again is that these are the forms allowed by physics itself. Therefore, biological forms are time-independent and almost completely non-contingent since they are mandated by physics (in the front-loading scenario, they were completely contingent on the information given in the front-loading act).
Michael Denton is the primary proponent of this view, contained in his papers The Protein Folds as Platonic Forms, Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian, and The Laws for Form Revisited. I believe that this is similar to Conway-Morris's claim in Life's Solution, but I have not read it.
Benton's main point is that physics only allows certain biological motifs. And thus, while there are untold numbers of protein sequences, there are only a small number of folds available to them. Therefore, life, even life as we know it, is not contingent on accidents, but instead is the planned outcome of physics.
Comparing the Theories
Both theories are at least somewhat related to Intelligent Design, though platonic forms is more difficult to examine as a hypothesis. Front-loading puts the infusion of information into biological systems as a process that happens essentially within-time, while platonic forms has the design process occurring pre-time or outside of time.
Note that, on a detail level, the two are mutually exclusive. Information requires freedom of choice for the agent, while platonic forms is specifically about excluding freedom of choice through time. That doesn't mean there aren't both mechanisms in play, only that a single mechanisms cannot be simultaneously part of both (though there can be aspects of each -- the point is that one is the result of a limitting process and the other the result of a freeing process).
My own opinion is that there is a platonic-defined set of biological forms, but that they are fundamentally unreachable without an infusion of information. Both processes are active, with platonic forms being the part that keeps system perterbations from becoming catastrophic, but that the preloaded information is what helps adapt to new situations.
Theologically, I think that God did this in order to show both His transcendence and His immanence. He is transcendent, and made physics according to a specific biological plan. However, so that we would know that God is active (and required) in Creation, he made it so that the platonic forms were unreachable except through design (front-loading). That way, we know that biology is not necessary, but instead chosen.
So, in reference to the above-posted Wagner reference, the existence of a clustered functional space in RNA is clearly platonic, while the ability to find that space initially in the original organisms smacks of front-loading. I was going to include another instance of front-loading in this section of Wagner in this post, but it's already too late and I need to study for a test tomorrow and get some sleep.
Sunday, March 11, 2007
Randomness and Casinos
Think of slot machines. The actual result that a given machine will give on any particular pull of the handle is random in many ways. But it is a designed randomness - whether or not a casino will make money on the slot machine is NOT something left up to chance. The individual pulls are randomized, but the effect is not. The individual events are randomized, but the long-range outcome (that the casino winds up winning in the long term) is not.
Saturday, March 10, 2007
Large Water Stores Under the Earth's Mantle
An increasingly popular method, which Wysession used, is to analyze the way waves damp out from their source...Attenuation data tell seismologists how stiff a region is, which is a function of how hot it is and how much water it contains. Looking at the seismic wave speeds and attenuation at the same time can tell whether an anomaly is due to temperature or water.
What was Found:
Beneath Asia, the fallen Pacific sea floor piles up at the base of the mantle. Right above that he observed an "incredibly highly attenuating region, that is both very damping and slightly slow," he said. "Water slows the speed of waves a little. Lots of damping and a little slowing match the predictions for water very well."
If you combine the volume of this anomaly with the fact that the rock can hold up to about 0.1 percent of water, that works out to be about an Arctic Ocean's worth of water.
Where to Find More:
The research is described in a forthcoming monograph, Earth's Deep Water Cycle, which is in press to be published by the American Geophysical Union.
This work might be of interest to Creationists.
Wednesday, March 07, 2007
Apparently I need to pay more attention to American Idol
New Conference and New Blog
I picked up this tidbit from a new blog on creation and evolution. Note that despite "Crevo Press" as the name of the blogger, this blog has nothing to do with this one (I actually found out about it from my referrer log).