Monday, November 28, 2005
Origin of Life and Shannon Information Systems
For information on the Shannon Information model, see Shannon's original paper on the subject or this summary. Note that Shannon's theory was primarily a theory of communication, but it also included a concept of information that has been foundational for information theory.
The paper basically described the operation of a cell as being similar to a computer system, consisting of programming instructions (genes), written to a specific coded language (DNA/RNA translational mechanism), running on an operating system/hardware platform (the cellular structure).
It also points out that the cell operates as a Shannon communication system.
The points they made were that:
- Determinism does not have enough shannon uncertainty to be a communication mechanism. The amount of shannon information a channel contain is based on the amount of uncertainty available within the channel. If the organization of the genome is based on determinism (where a probability approaches 1.0), there is not enough variability to allow information to come through.
- Chance does not give itself to generating highly organized networks of enzymes. They pointed out that a cell is not merely a bag of enzymes, but a highly structured set of pathways. Such structure does not arise by chance processes.
- The cell consists of many translational, encryption, and decryption pathways, all of which must be in place along with the cellular structure all at once for anything to occur at all. In order to go from prebiotic to biotic there exists a need for integration management, to get all of the parts to work together.
A good quote from the paper:
No amount of time proposed thus far, can explain this type of conceptual communication system. It is not just complex. It is conceptually complex. First, the ribosome/tRNA/aminoacyl tRNA sythetase/amino acid holistic translative system would have had to pre-exist any messages. Then we have to explain how the DNA and mRNA sequence provided the codon-encrypted instructions for the correct proteins to be synthesized. Only then could the receiver and destination have known what those instructions meant.
The appearance of genetic control does not seem possible unless the transmitted message and the decoded outcome were pre-arranged.
So what does all of this mean? I think that what creationists need to be attacking is the age-old question of where information exists -- is it outside of matter in platonic forms, or is it in the matter itself? I think the answer that Christians bring is that intelligent agents impose information onto matter. The information comes from something marginally platonic-like (not that the forms are necessarily pre-existing and eternal, but that ideas are essentially non-material), but is imposed in matter separate from the idea itself.
Basically, this paper provides many of the theoretical justifications for including teleology in biology. Namely, it is the only thing, as Demski says, with enough causitive force to produce what is seen. Then, with a teleological view, we can view biology with fundamentally new glasses that ask, specifically, "for what purpose?"
I think studying informational systems and entities and relating them to biology is one of those areas that are fundamentally tied to Creationist principles (or ID at minimum), even if many of those engaged in researching it don't see the connection.
Ultimately, the whole idea of information and purposeful action needs to be put under a microscope and examined to the greatest degree possible. That is the goal of the ID movement.
Werner Gitt has proposed some extensions to information theory that include semantics. It is quite a good beginnning. Unfortunately, I think some creationists see Gitt's work as an end, rather than a beginning. This needs to be examined, re-examined, pushed, molded, and extended. This is fundamental to what we are saying and doing, and therefore our models of information of all types (semantic, algorithmic, etc.) need to be rock-solid.
Sunday, November 27, 2005
Creationist Paleontologists Unearth Great Allosaurus Skull
Also, they have an article about another dinosaur fossil they have unearthed. Quite interesting stuff. I'd love to be a part of a fossil dig. Ohhh.... the things we could do if time were not an issue!
Thanks to Globe Lens for providing the link.
Sorry I haven't been posting much. I've been reading.
Monday, November 14, 2005
DNA Polymerase for Genetic Change
- Escherichia coli DNA Polymerase IV Mutator Activity: Genetic Requirements and Mutational Specificity by Wagner and Nohmi.
- General Stress Response Regulator RpoS in Adaptive Mutation and Amplification in Escherichia coli by Lombardo, Aponyi, and Rosenberg.
These are both fascinating articles. What they are showing is that, in stress situations, E. Coli is actively modifying its genome on a specific plasmid. This means that the cell can (a) sense trouble, and (b) activate specific change mechanisms to accomplish changes. It has a high degree of specificity as to both the activation of the mutations as well as where the mutations occur. This is natural genetic engineering at work.
As per the creation model, the cell is not a passive bystander of happenstance changes and "hoping for the best", but is in control of the changes that occur.
Basically, what these articles are saying is that a specific stress response factor, called RpoS, is produced when E. Coli cells are in trouble. This causes the cell to switch from using its standard DNA Polymerase (the enzyme which copies the DNA) to using a new type called DNA Polymerase IV (or DNA PolIV for short) when copying a specific plasmid. This polymerase is used to induce mutations within the strand -- both point mutations and frame-shifts.
Note that while this may seem like random mutation it is in fact not -- it includes random factors, but is not entirely random. It seems to be a non-deterministic computation (i.e. - randomized within specified limits). This information shows that the cell acts as a "database administrator" over its genome, and can induce changes when needed, in the specific place that they are needed.
Note that the authors of the articles are very likely not creationists, though their data is very interesting and beneficial to creationists and others who use a telic approach to biology.
UPDATE: Upon closer reading of the second article, it seems that the authors do not feel that the mutation is directed, just a rate increase. The only reason for suspecting this listed in the article itself is that there were mutations on other genes. However, I don't see how that means that the mutation rate was globally changed. I think perhaps they are excluding the possibility of adaptive mutagenesis too early, based on data that is not necessarily in conflict with the idea. Rosenberg herself seems to be trying to push the hypermutation model past the adaptive mutation model, but I don't think the data supports that conclusion (see also here). It seems that their requirement for being "adaptive mutations" is that the mutation must be in exactly one gene. This is an absurd requirement. There is no reason that adaptive mutagenesis cannot be applied to a _set_ of genes. In fact, the F plasmid would be perfect for this to occur, as the plasmid does not even need to exist for the cell to function under normal circumstances.
Sunday, November 13, 2005
The Flores Skeleton and Human Baraminology
First of all, he classifies the bones as human. This is due to several factors:
- Stone tools or artifacts in the same cave
- Charred animal bones nearby, indicating fire
- Many similarities to Homo Erectus and Homo Sapien
He did note that it had the same body size and relative brain size as Australopithecus. The skeleton was very small, but available evidence indicated that it was a healthy adult, and did not have any known pathologies that occur with short stature. So the short stature seemed to be a distinctive morphology of humans in the post-Babel world (Flores is dated later than many Erectine fossils, which seemed to be the main human morphology in Babel and post-Babel times.
Wise notes that human morphology used to be significantly more varied than it is today. He has several hypotheses about what accounts for this. I find them interesting, but not all of them entirely convincing. His primary argument is that there is a programmed set of human morphologies which were triggered by the flood, which all converged on Homo Sapien as part of the plan. This is kind of a wierd idea. Wise explains it by pointing out that frogs have multiple possible ontogenies (development pathways) which all result in the same adult form. The reason for this is in case there is some environmental stress which blocks one particular pathway, there are others that can be taken. This is ontogenic redundancy. Wise proposes a similar thing for humans, but instead thinks that there was a larger-scale diversification, which he called phylogenic redundancy. Basically, for survival or other purposes, the human kind split into several different morphologies, which all separately converged to Homo Sapien. The convergence to Homo Sapien was part of a larger plan.
That was his most interesting claim. Some other claims include:
- The onset of human diversification is not mentioned in the Bible, but archaeologically it seems to occur at the same time as the change in lifespan.
- Heterochrony (change in development rates) is responsible for a large degree of human variability post-flood
- The founder effect is responsible for most of the variation of Homo Erectus
- The divergence of human morphologies _preceded_ their dispersion. I have seen this claim elsewhere, but do not know what the justification is for this. Dispersion often came from a divergent morphology finding a home that suited them, not from a particular morphologic change in response to the environment. This seems backwards, and I hesitate to accept it without further evidence of the claim.
- As noted above, the modern Homo Sapien morphology was derived multiple times independently from numerous Homo morphologies.
Anyway, it was an interesting read. One paper which was highly referenced which I have not read yet is Wise and Croxton's "Rafting: a post-flood biogeographic dispersal mechanism."
Throughout the article, Wise downplays some more common conceptions of the origin of variation. Specifically, he doesn't think that degenerative mutation had much if anything to do with the variation. Likewise, he discounts the effects of heterozygous fractionation. However, he does note the founder effect several times, and I fail to see the difference between the founder effect and heterozygous fractionation. It seems like two names for the same process to me. Perhaps I misunderstood him here.
Anyway, lots of food for thought.
Friday, November 11, 2005
Using multiple lines of evidence, Austin et al. showed that:
- The Earthquake referenced by Amos and other biblical writers occurred in 750 B.C.
- The earthquake appears to have been an 8.2 on the richter scale, affecting from an epicenter near lebanon all the way to Tel Sheva.
- The earthquake became a standard way to discuss widespread panic in Hebrew literature, and was referred to as "The Earthquake" for a long time afterward
- Such an earthquake could explain what is called the "missing earthquake" in tectonic theory (NOTE: I could not find reference to a "missing earthquake" in geologic literature, but if someone could post me a link, I'll add it in)
- Knowing the date of the Earthquake helps authenticate certain chronologies. He shows that it shows that Thiele's chronology (summarized here) works better with the seismic data (NOTE -- I don't know much about this area of chronology -- just reporting what I found on the web).
- The Earthquake seemed to cement the tradition of the writing prophets, starting with Amos. Many of the prophets afterwards referred to the same event.
Anyway, it's exciting to see Austin published in a journal, specifically writing on biblical topics.
NOTE - This post has been updated to reflect the current location of Steve Austin's paper.
Sunday, November 06, 2005
RATE Posters at the American Geophysical Union
UPDATE: In case you're curious, the abstracts are listed here (the full poster is at the link above)
RATE Group Presents Their Findings
I've read parts of Thousands not Billions (they lay book about the RATE results) vcat the bookstore, and I must say it is _excellent_. I'll present the results later when I actually own a copy and have more time (and once I read their new technical book).
Anyway, the conference at which they presented just finished, and therefore the new official RATE book will be available shortly. Let me summarize for you the basic lines of evidence they were working on:
- Helium retention in zircons indicate that nuclear decay has been accelerated. Basically, if you look at the radioisotope decay rates, the zircons look old. But this radioactive decay produces helium. If you look at the helium diffusion rates, they look young. This indicates that there was a time when the nuclear decay was greatly accelerated.
- Polonium halos -- I'm not all that clear on this one. I'll have to look into it more and get back with you.
- Carbon 14 is ubiquitous in "ancient" carbon, and even in diamonds. Carbon-14 should be completely gone after 100,000 years.
- Steven Austin did some work on radiometric dating that is very interesting. He showed some interesting features of radiometric dating that indicate that they aren't showing "dates" at all. First of all, he showed that not only do different methods of dating disagree, they often disagree in reliable ways. This indicates that there was some other process than aging in effect. I don't remember everything that Austin pointed out, but one of the things he pointed out was that the methods with longer half-lives always show longer dates. Anyway, I'll probably report more on all of this after I get the new RATE book.
This doesn't mean that the case is completely solid, nor that there aren't major problems. There are. They are planning a lot of follow-up research.
I'm not familiar with all of the problems, but the biggest problem is the heat problem -- all of this accelerated radioactive decay would produce a lot of heat, and it is unknown how such heat would have been managed. This is a big and significant problem, but I don't see it as insurmountable. There are many suggestions around, but the research remains to be done.
Anyway, this is a very exciting time. Creation Safaris has their own summary of the conference. Note that I was unfortunately not at the conference, but have been following the RATE group's activities for some time now.