I was reading Gene Conversion in the Rice Genome, and noticed this:
Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes.
While arabidopsis is probably a different created kind than rice, it got me wondering - what if, when two species enter into symbiosis, one species transfers pseudogenes to another, which are then used in gene conversion to set up the biochemical pathways for the symbiosis?
Thus, pseudogenes might act like a symbiosis integration script, giving a template for interacting with it. The other organism then takes that template, and, through gene conversion, uses pieces out of it to alter its own genome to match the symbiosis?
Anyway, that might be an interesting path to look down.
I was having a conversation with someone about fitness functions, who asked how someone could sneak information into a fitness function. I responded. Of course, someone else then asked about how evolution worked in cases where information wasn't snuck into the fitness function - the answer - it is usually snuck into the parameters of evolution! But I hope you can see why online discussions are hard (for any issue). People take the answer to a single *aspect* of the issue to be a universal answer to the whole deal. They mistake the fact that you are having a conversation with a specific person about a specific thing to be a general public service announcement. We can't spend our lives speaking in qualified statements, but we do need to be aware that people listening in aren't familiar with the full context of the conversation.
[WARNING - this post may not make any sense until I give my BSG talk - sorry - I'll refer back to it later after I describe that talk]
In preparation for my BSG talk on creationary cognition models, I was digging through some papers, and ran into a whole collection of papers on the Gödelian argument against the physicalism of the brain. Would someone please take these papers to the theology departments? Anyone?
This whole area of research seems completely unknown outside of a few specialists (though Penn State seemed to have a lot of contributions, or at least a lot of archived papers that Google Scholar pointed to).
Anyway, when I had started my research in seminary, I thought that my Gödelian argument for the soul was at least somewhat unique. I had read Voie's use of Gödel, but did not realize that there was an actual literature on the subject. I have to say I was a little disappointed when I found Robertson's paper on free will. I realized my argument wasn't brand-new.
Anyway, I found one paper that comes at least a little close to what my BSG presentation will be on - Copeland's Turing's o-machines, Searle, Penrose, and the Brain. On the one hand, even if I didn't add anything to the conversation, I think just popularizing these ideas is worthwhile. However, my goal is to begin a research program to systematize these ideas as part of a general cognitive studies program. I think one reason why these ideas aren't getting as much play is because they are being relegated to philosophy. What we need to do is to start experimenting - then we can put them into practice.
Some interesting and related papers I found in Google Scholar:
Todd just posted the talk list for the BSG/CGS meeting. It looks to be a really exciting time, and I have no idea how they are going to fit so many talks into a day and a half - probably switching to a multiple-track format. Anyone who wants to interact with creation research should come here. Here's the link to register. After this week the registration price goes up.
Here is the list of talks:
John Sanford, a young-earth creationist biology professor at Cornell, just published a bioinformatics paper describing his new genomics tool, called skittle with a bioinformatics graduate student Josiah Seaman. You can read the paper here. The tools allows you to color the genome and experiment with alignments to visualize patterns that are not detectable by other methods.
It runs on Mac, Windows, and Linux.
This tool allows us to detect a number of new patterns in the genome. Not only does it help to find tandem repeats, it also helps to find structured variations in those repeats.
This holistic approach to genome analysis is precisely the sort of research that IDers and creationists are interested in. The reductionist approaches of the last century were useful for digging deeper, but they often blinded researchers to the larger-scale activities of what was happening.
From the paper:
As we have been able to better visualize tandem repeats using Skittle, we have seen a surprising amount of internal complexity. Some of this complexity seems to be easily understood in terms of point mutations and indels, but a great deal of the complexity appears to provide an intriguing array of "puzzles" which invite further study. These puzzling patterns include co-varying deviations from a repeating theme, and internal patterns that are not simply "repeats within repeats". For lack of a better term we are referring to these patterns as structured variation.
If tandem repeats have any function, the "structured variation"
described above could conceivably carry information. A perfect repeat cannot contain any information beyond the base sequence and copy number. However, a repeat with variation can contain considerably more information. Each of the three types of observable variation (substitutions, indels, and alternating repeats) has a direct analog in electronic information technology (amplitude modulation, phase modulation, and frequency modulation, respectively).
And then later, he mentions something interesting about the alignments:
Interestingly, the self-adjusting cylinder alignment, which was designed to simply optimize local alignment as would be expected in vivo, causes a marked increase in the visual coherence of all complex tandem repeats. This suggests to us that such coherence might reflect a minimal energy state, and may reflect actual structure in vivo, and might even reflect an unknown biological function. Logically, such coils could change circumference in multiples of the repeat length and so might modulate local genomic architecture.
Anyway, I am really excited about this, and hope to dig more into this as I have time.
Thanks to Sal for pointing this out to us!
Todd Wood has an excellent introduction to the form-vs-function debate, focusing on the ideas of Richard Owen. From his post:
Owen's eclectic embracing of functionalism and structuralism were answers to different questions: 1. Why are organisms so well-adapted? and 2. Why are there homologies?....Organismal similarity was to Owen based a [sic] natural law of the archetype. The differences Owen attributed to functional requirements. (Thus he saw two answers for two different questions.)
It's the conferencing time of year! The Creation Research Society is putting on their conference this year at University of South Carolina Lancaster July 23-24. Here is a preliminary list of the talks that are going on (i'll post again as this is updated):
Quite a list! I wish I had time to go to both this and the BSG conference, but funds are limited this year. Hopefully next year I can go to both, and maybe a a secular conference or two.
In any case, you can register for the conference here ($55 for CRS members, $90 for non-members).
In addition to all this, Danny Faulkner will be hosting a free field trip on Sunday, July 25 to Wood's Bay State Park, one of the Carolina bays.
Sounds like a lot of fun! As I mentioned, I'll update this when I get a finalized list of speakers, and I will also post the BSG schedule when it is available. You should come to one (or both) of the summer conferences!
Here is a virtual lab.
Registration for the 2010 BSG Conference is now open! I'm excited - Creation research is not a very hot topic in my city, so I rarely have people to talk about new ideas with. So I get excited when the BSG conference rolls around, because I get to spend some time listening, thinking, and talking about God's creation with other interested researchers. I'm giving either one or two talks this year (one has been accepted, the other is still in review).
If any of you are interested, please come! I love meeting readers. In addition, the conference will be at Truett-McConnell college, where Kurt Wise is setting up a Creation research center. It should be fun!
Register Here -- it's only $90 for students ($120 for everyone else), and includes a room!
For those of you who don't know, Stanford has a research project called "Folding@Home" which utilizes extra computing power on people's computers to make a massively parallel computer for doing research on protein folding. Back when I owned a PS3, I used to run this all the time, and started "team creation" for keeping score. Now, however, Dan Watts has been leading team creation, and has just generated a score of 1,000,000 points! Click here to view the team information, and click here to view the certificate.
If you want to be involved in this project, download the software, and then put in team number 59478 to be a part of our team.