Researching Creation

January 07, 2009

Biological Change / Contingency Loci and Symbiosis

JB

Caporale's latest work, The Implicit Genome, covers a lot of cool mechanisms for the generation of variability within genomes.  One interesting mechanism is through contingency loci.

A contingency locus is an area of the genome which has a high mutation rate, which is associated with a frequently-changing environment. A typical reason for contingency loci is to get around the immune system.  The contingency loci in many bacteria are for their outer coat proteins, which is what the immune system recognizes.   Bacteria and single-celled eukaryotes can evade the immune system by rapidly mutating their outer coat.

Now, usually the relationship between microbes, hosts, and immune system is discussed in terms of warfare - this fights this, this evades that.  But what if this was instead a mechanism that wasn't nearly as much about warfare as it was about adaptation?

For example, Opa proteins on N. meningitidis are surface proteins that are encoded by contingency loci.  Different versions of these proteins adhere to different types of cells.  So, what I'm wondering is - are mutations in these contingency loci associated with mutations elsewhere, or expression changes elsewhere?  For instance, might certain microbes alter their biochemistry in coordination with their surface proteins so that they assist the right cell type in the correct way?  In other words, instead of "evading the immune system", might it instead be trying to find a biochemistry which is helpful to the organism, and using surface proteins to advertise to the immune system what sort of tissue the organism is best configured for.  The immune system, rather than "combating" the antigen, might be just cleaning up good microbes which are just in the wrong place, or perhaps in the wrong configuration in the wrong place.

Anyway, it's an interesting possibility, but I'm not sure how it might be investigated.  But it might make a good research project for a budding Creation PhD student somewhere.

I'm not quite sure how this question would be investigated, but it's sure worth asking.

January 05, 2009

General / The Personal Cost of Creationism

JB

I myself have not experienced any discrimination based on my belief in Creationism.  However, that is not the case for many in academia.  Jerry Bergman's new book, Slaughter of the Dissidents, reveals in excruciating detail the perils that befall most academics who are Darwin-dissenters of any stripe (Creationists, IDers, or even evolutionists skeptical of the Darwinian mechanism, or honest enough to allow open conversation about the subject or the possibility that they could be wrong).

If you want to learn more, I posted a review of the book on UncommonDescent.

For those of you wanting to do Creation research in an academic setting, I'll just say this: use caution, but stand up for what you believe in.

By the way, here is an inspiring story about someone successfully standing up for Creation in academia.

December 31, 2008

Information Theory / Randomness in Creation Biology

JB

After a year and a half of waiting, my paper on randomness and Creation Biology has finally been published in the current CRSQ!  The paper is titled "Statistical and Philosophical Notions of Chance in Creation Biology".  The main points of the paper follow:

More Than One Meaning for Random

There are different notions of chance and randomness which have very different implications, but we tend to lump them all together.  This causes sloppy thinking and can blind the way we look at things.  This is true in both Creationary and Evolutionary literature.

One type of randomness is statistical randomness.  A process is statistically random if events in that process occur with fixed percentage frequencies over every "normal" infinite subset of those events.  Another type is philosophical randomness.  A process is philosophically random if it occurs outside the constraints of a system.  The state of a slot machine after pulling its lever is the result of statistical randomness.  The state of a slot machine after being hit by a meteor is the result of philosophical randomness.

Statistical randomness is often used in engineering to great benefit.  It offers a way of counteracting unknowns.  I'll probably devote a post to statistical randomness at a later date.

Preadaptation

The Luria/Delbrück and Lederberg experiments (which are normally used to prove the randomness of mutations) are not by themselves evidence of an unplanned process.  Another possibility explored in the paper are that many of these are pre-adaptive mechanisms.

Basically, I think that many "spontaneous" mutations are actually the result of a process to increase a population's future fitness.  Basically, it forces alternate biochemical configurations into the population at a controlled rate, so that a catastrophic environmental change does not wipe out the entire population.  If a cell uses a statistically random process to create these alternate configurations, the population can keep fixed percentages of alternate configurations without any individual cell needing to know how many of each configuration are already in the population.

Therefore, I think that many (but not all) of the "spontaneous" mutations we see are not haphazard just because they occur in the absence of selection, but instead are planned mechanisms to introduce alternate biochemical configurations into the population (which are likely less fit in the current environment) to prepare for extreme changes to the environment in the future.

Testing for Whether Mutational Hot Spots are Planned or Haphazard

Mutational "hot spots" within the genome may be either the result of a planned mutational mechanism or just the happenstance physical interactions of biochemistry.  I proposed that the proper test for this would be whether or not mutations within the hot spot are more or less likely to be biologically meaningful than a statistically random mutation with uniform probability over the entire genome.  Based on Dembski's work, if a hot spot repeatedly gives us biologically meaningful mutations more frequently than statistically random mutations over the whole genome, then this is evidence that the hot spot is part of a designed mechanism.

December 30, 2008

Geology / Ian Juby's Complete Creation Video Series

JB

Ian just finished posting his last video in his Complete Creation series (actually, there are more to come, but this was the last one which was part of his conference presentation).  The series is 18 videos long (approximately 9 hours), with more videos coming with additional explanatory information.

Anyway, the video series is fabulous.  I recommend you watch the whole thing.

Also, I have added Ian to our list of speakers.  If you need a speaker anywhere in the U.S. or Canada, Ian is probably heading your way sometime during the year.  Email speaking@bartlettpublishing.com to book a presentation with your Church or group.  Also be sure to check out Ian's own website.

December 11, 2008

Discussions around the Web / Todd's New Blog and a New Book on Genesis

JB

Todd Wood, author of Understanding the Pattern of Life, and one of the BSG's founders, as well as part of the team which sequenced the rice genome, just started a new blog on Creation.  He has a great article summarizing Jean Lightner's paper on skin color and the generation of diversity.

Also coming is a new book on Genesis and Creation edited by Terry Mortenson.  This books aims to be a seminary-level book for understanding the Creationist perspective on Genesis.  From the table of contents, it looks like it covers:

  • History of exegesis of Genesis
  • The events surrounding the Church's change of position regarding Genesis
  • The relationship of nature to revelation
  • The genre of the text
  • Critiques of other interpretations
  • The relationship between Genesis and other near-eastern documents (this is actually not based on the table of contents but from a marketing announcement)

I hope to read it soon!

 

November 30, 2008

Geology / Russ Humphreys Latest Summary of Helium Work

JB

Russ Humphreys just published a summary of the current debate regarding his Helium dating methods, complete with an index of criticisms and responses.  Of considerable interested is figure 3, which graphs his predicted data based on a young earth, compared to the predicted data for an old earth, compared to experimental values.

November 29, 2008

Biological Change / A Catalogue of Animal and Plant Baramins (Created Kinds)

JB

Todd Wood just release a new monograph containing a whole bunch of data concerning created kinds, called Animal and Plant Baramins.  For those of you new to Creationism, a baramin is the Creationist term for a "created kind".  For those interested in exploring Creation systematics further, I will refer you to Wood and Wise's  A Refined Baramin Concept.

Anyway, this book is significant because it is the first large-scale treatment of what organisms belong with which created kind (again, for those who are new, Creationists believe that Created Kinds are larger than just "species", and usually estimate the Created Kind to be roughly equivalent with the family level of taxonomy).

Now, I have no first-hand information about the book - it just came out so I haven't read any of it yet, but I did talk with Todd about it at this year's BSG.  Based on that conversation, I'm pretty sure that most baramins in the book are defined using statistical baraminic concepts.  I'm not a big fan of statistical baraminology, and prefer hybridization experiments (obviously, however, that data is not available for fossil species).  In any case, this is a great start to our systematics work. 

Another thing that Todd told me is that ark-based animals have much less variability within baramins than non-ark-based animals.  This is quite interesting, since the ark-based animals would have a genetic bottleneck that wouldn't apply to non-ark-based animals.  I believe he also said that the distribution actually follows what would be expected from a Biblical timescale.

Anyway, I plan on purchasing this as soon as I have the funds, and for those into Creation systematics, I would suggest you do, too.

November 28, 2008

Geology / Marine Fossils Preserved in Amber

JB

"New Discoveries" has a writeup of a new PNAS paper, Evidence for marine microfossils from amber.  Remember, amber comes from tree sap, and marine microfossils come from the sea :)  Although the paper was not speaking of the Biblical Flood, New Discoveries quoted the following from their pages to explain their findings:

It is likely that the flood waters first broke trees apart, transported the shattered timber, and then deposited the remaining pieces. These would have extruded large quantities of sap, which would have engulfed nearby creatures and then, at the bottom of the flood waters, hardened into amber. Marine algae trapped in amber ought to finally prove a flood-based interpretation.

I don't have access to the paper at the moment, but this seemed really interesting.

November 26, 2008

Information Theory / Optimality of the Genetic Code

JB

Teleomechanist has a great post up with a literature review about the optimality of the genetic code.

The genetic code seems to be designed with the following features:

  • Error minimization in protein construction on simple genetic mutations
  • Minimizing bad effects of frameshift errors
  • Error detection/correction through parity checking
  • Ability to layer on additional codes (the original paper for this is worthwhile) to the protein sequence

Anyway, Teleomachinist lists a lot of other interesting aspects about the genetic code, but I thought these were the top ones.  I especially like the fact that the genome seems to be optimized for having additional codes layered on.  That is very interesting indeed.

November 26, 2008

General / Creation Research Society Conference

JB

The Creation Research Society is sponsoring a conference this summer at the University of South Carolina Lancaster.  I think this is CRS's first conference.  Anyone can attend, but you have to be a voting member of CRS to author a paper (or have a voting member as a co-author).

Anyway, I'm probably going to be at the BSG conference this year, though at the moment it does not appear that I will have anything myself to present.  Come to think of it, that might actually make it more fun.