Researching Creation

Special Creation Research Society Discount for Students

JB — Sat, 03 Sep 2011 04:39:00 +0000

For those interested in joining the Creation Research Society, they are running a special membership drive at a steeply discounted price:

See here

The Doctrine of Creation and the Making of Modern Biology

JB — Tue, 28 Jun 2011 04:24:00 +0000

I just posted a new article on the Classical Conversations website - check it out!

On Being an Amateur

JB — Wed, 18 May 2011 12:54:00 +0000

I'm posting this mainly because I was thinking about it today, and it took me over an hour to find it. So I'm saving it here for future reference. Biblo at Telic Thoughts put up some excellent thoughts about being an amateur ID proponent. I also added the following comment:

I think it is dangerous for any discipline to reject the criticisms of amateurs out-of-hand. I have been programming computers for 25 years, have a book on programming that is used at Princeton University, have taught programming, and have numerous papers and articles on programming published by IBM and others.

Nonetheless, I still, often, have customers who come up with ways of doing things that I don't think of – customers who have never programmed a day in their life. I know many people who dismiss their customers ideas out-of-hand because they don't believe that non-programmers have valid input. That is total B.S. The fact is, being a non-programmer gives someone an outside look at the issues that aren't obscured with all the things us programmers normally worry about that, and sometimes that opens their minds up to possibilities that we don't see.

It doesn't mean that I take their ideas without criticism – there are more bad ones than good ones (which is expected, because they are outside the field, and aren't familiar with the issues). But nonetheless, I would be a lesser developer if I used the fact that these people are non-experts as a reason to dismiss what they had to say.

This also often requires translating what the have to say. Non-experts often use terms wrong, have a bad understanding of the way certain concepts work together, and the like. But *my* job is not to use my expertise as a way of beating their ignorance over their heads, but rather to *translate* their conceptualizations of their ideas into full-fledged, implementable ideas. So, rather than using my expertise to knock down, I use it to build up – to find a way to understand the non-experts in the most gracious light, and find a way for them to be right.

Doing so improves us both.

New Book - Sacred Cows in Science

JB — Sun, 20 Feb 2011 04:00:00 +0000

The book Sacred Cows in Science was just released. This book is a compilation of issues from 17 authors in 3 countries which each challenge some aspect of science that normally goes unchallenged. I have a chapter in it, so please take time to purchase a copy! My chapter is on genetic mutations and whether they are accidental or not (or both).

The book covers a lot of territory, including astrophysics, biology, sociology, and other topics. Many of the topics deal directly or indirectly with creation and evolution but not all. Anyway, the chapters are all very different, some lay-oriented and some that are more technical. Anyway, purchase a copy today!

A Theory of Undesign

JB — Tue, 08 Feb 2011 15:51:00 +0000

One thing that is often missing in ID contexts is a theology of "undesign". That is, if we are going to take our design inferences seriously, that means that there needs to be a real category of "undesign". Yet, if we take our faith seriously, then we also need to understand God as the designer of the whole universe.

David Snoke takes a pass at working through this issue in a paper titled "Defining Undesign in a Designed Universe". Well worth your read.

Wooden Ships the Size of Noah's Ark

JB — Mon, 20 Sep 2010 04:30:00 +0000

Ian just pointed me to an excellent link about Chinese Treasure Junks. These are ships built in the 15th century that have approximately the same dimensions as Noah's ark, and built out of wood. Pretty amazing! I wonder what these could teach us about the ark itself, if anything, and if perhaps the technology to build these came from the ark itself.

Please vote for the Little Light House

JB — Tue, 31 Aug 2010 18:26:00 +0000

Please vote for the Little Light House to receive $500,000 from Kohl's Cares. This is a wonderful organization which benefits special needs children without taking any payment whatsoever. They have been a lifesaver to me and my family.

Creation Q&A Day on Facebook

JB — Tue, 31 Aug 2010 12:32:00 +0000

For any of you with questions about creationism, I encourage you to come and ask questions at Creationism Q&A Day on Facebook with Creation Nation X. Our friend Ian hosted the last one, and I'll be hosting this one with a focus on biology.

Random Thought on Diversification

Sat, 28 Aug 2010 03:29:00 +0000

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.

Why Online Conversations Are Hard

JB — Sun, 15 Aug 2010 20:27:00 +0000

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.

The Mind

JB — Wed, 21 Jul 2010 03:30:00 +0000

[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:

BSG/CGS 2010 Meeting Speaker List

Thu, 24 Jun 2010 05:16:00 +0000

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:

Biology

Bartlett - Estimating Active Information in Adaptive Mutagenesis
Bartlett - Developing an Approach to Non-Physical Cognitive Causation in a Creation Perspective
Demme - Grasses and Shrubs or Grain and Thorn-bushes? The Vegetation of Genesis 2.5
Francis - Use of Halobacteria as a Model Research Organism in the Undergraduate Research Laboratory
Sanders - Baraminological Status of the Verbenaceae (Verbena Family)
Wilson - Revisiting the 'Clear Synapomorphy' Criterion
Wise - Dominion: Human raison d’être, Foundation of Bioethics, Foundation of Environmentalism
Wood - Species and Genus Counts for Terrestrial Mammal Families Reveals Evidence for and against Widespread Intrabaraminic Diversification
Wood - A Re-evaluation of the Baraminic Status of Australopithecus sediba Using Cranial and Postcranial Characters

Geology

Austin - Submarine Liquefied Sediment Gravity Currents: Understanding the Mechanics of the Major Sediment Transportation and Deposition Agent during the Global Flood
Cheung, Strom, Whitmore - Persistence of Dolomite in the Coconino Sandstone, Northern and Central Arizona
Garner - Permian Cross-bedded Sandstones and Their Significance for Global Flood Models
Gollmer - Deep Ocean Interaction in a Post-Flood Warm Ocean Scenario
Hutchison - Potential Mechanisms for the Deposition of Halite and Anhydrite in a Near-critical or Supercritical Submarine Environment
Oard - Dinosaur Tracks, Eggs, and Bonebeds Explained Early in the Flood
Ross - YEC Geology in the Classroom: Educational Materials, Challenges and Needs
Snelling - Radiohalos in Multiple, Sequentially-Intruded Phases of the Bathurst Batholith, NSW, Australia: Evidence for Rapid Granite Formation During the Flood
Snelling - Radiocarbon in Permian Coal Beds of the Sydney Basin, Australia
Stansbury - How Does an Underwater Debris Flow End? Flow Transformation Evidences Observed within the Lower Redwall Limestone of Arizona and Nevada
Whitmore, Strom - Clay Content: A Simple Criterion for the Identification of Fossil Desiccation Cracks?
Whitmore - Preliminary Report and Significance of Grain Size Sorting in Modern Eolian Sands
Whitmore, Maithel - Preliminary Report on Sorting and Rounding in the Coconino Sandstone

Sanford Publishes New Bioinformatics Tool

JB — Thu, 17 Jun 2010 02:47:00 +0000

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.

You can download the program from Skittle's website on sourceforge., or find more information about the program at dnaskittle.com.

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 on Owen's Resolution to the Form/Function Debate

JB — Mon, 14 Jun 2010 16:11:00 +0000

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.)

Creation Research Society Conference

JB — Sun, 13 Jun 2010 12:49:00 +0000

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):

Mark Armitage - Some Unusual Tiny Plants
Charles McCombs - Mutations and Natural Selection: A Population Genetics Study using Mendel's Accountant
Douglas A. Harold and Lindsay N. Harold - Origins Research Group Involving Current Students in Creation Research
Joel David Klenck - Genesis Model for the Origin, Variation, and Continuation of Human Populations
Charles McCombs - Reality of Chirality
Jeff Tomkins - Plant Cold Tolerance Research at ICR: An Intriguing Venture in Irreducible Complexity and Intelligent Design
Cheng Yeng Hung - Concurrence between Science and Bible on Our Immediate and Original Ancestors
Raúl E. López - The Paleolithic Archaeology of Palestine: A Biblical View.
James J. S. Johnson and Nathaniel T. Jeanson - What is a created 'kind' (mîn), as that term is used in Genesis, and from where do the 'kinds" we see today originate?
Thomas J. Foltz - The Creationist's Silver Bullet: Information, Origins and the Impossibility of Macro-Evolution
Joel David Klenck - Genesis and the Gardens of God
Joel David Klenck - Geographical Locations of Genesis Gardens
Samuel R. Henderson - A Theoretical Extension to Newtonian Gravitational Theory
Mary Beth De Repentigny - Looking for the "God Particle" at the Large Hadron Collider
Patricia Nason - What "Science" Is Being Taught in Our High Schools?
Don Moeller - Craniofacial / Dental Mutations in Zebrafish and Mice Disprove the Ability of Evolutionary Genetic and Developmental Biologic Models to Substantiate Functional Structural Intermediates in Craniofacial/ Dental Evolution
Ronald C. Marks - Science Worldviews Impacting Science
Eugene Chaffin - The Carbon Isotopes and the Strength of the Nuclear Force
Cheng Yeng Hung - Reevaluation of Earth Age Using Hung's Geochronological Dating Model
S. G. Smith - Men, Memes, and Metaphysics
Richard Overman - Evaluation Of The Ar/Ar Dating Process
Wayne Spencer - Extrasolar Planets and Creation
Keith Davies - The origin of the distinctive patterns of element abundances in the sun
Ronald G. Samec - Astrochronology: Toward a Maximum Apparent Age of the Time Dilated Universe
Danny R. Faulkner - Is the Flood Memorialized in the Constellations?
Michael Oard - Dinosaur Tracks, Eggs, and Bonebeds Explained Early in the Flood
Mark Armitage - The anatomy of light production in Photinus pyralis

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!

A Home Microbiology Lab

JB — Sat, 12 Jun 2010 02:49:00 +0000

Just found this site and thought someone here might find it interesting. Especially interesting is this page, with instructions on how to setup a kitchen microbiology lab.

Here is a virtual lab.

BSG 2010 Conference - Register Today!

JB — Fri, 21 May 2010 12:42:00 +0000

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!

Team Creation Award with Folding @ Home

Wed, 12 May 2010 14:23:00 +0000

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.

So much information!

JB — Wed, 12 May 2010 02:55:00 +0000

There is so much going on, it is difficult to keep track of! Unfortunately, I am, yet again, left without time to make adequate reflection, so I'm just going to give a dump.

New super-small microbes! Apparently, they may be free-living, too! They apparently have comparatively simple genomes. This is going to be an interesting one to watch. What other forms of life await discovery?
Seven wonders of the quantum world
How cells maintain the spatial distribution of proteins
Cornelius Hunter gives a great presentation on the issues surrounding realism, completeness, and method in science
Plants channel messages to different parts of themselves
New genetic sub-code affecting gene expression rates (I think this is the paper it is refering to)
Another genetic sub-code directing tissue-specific splicing activity
Free Will doesn't exist, but we should believe in it anyway in Scientific American (commentary here and here)
Interesting hypothesis about the calendar and the Bible
Someone at UD pointed to a very interesting video on Cichlid fish (and also a paper on them I haven't read but probably should)
Another interesting hypothesis - this one about King Solomon's navy
"Secular Reason" is theologically bound
Video on information processing in the cell
A personal curiosity on how cover crops work
I have been told that this paper in linguistics makes for interesting thoughts regarding consciousness, but haven't had time to read it
An interesting paper on the separation of human families at the time of Babel and the implications for modern genetics
An old-earth group is trying to move the PCA away from young-earth creationism. In the list of theological concerns people might have, they didn't even mention the flood! In fact, when stating what YEC people think about features of the earth's surface, they only mentioned the "appearance of age" and completely left out that most YECs think that the flood was involved! It looks like someone is trying to pull a fast one on the PCA. There are plenty of reasons to doubt YEC, but it looks like these people are trying to ignore the real issues of the flood while doing so! You can't understand young-earth creationism without referring to Noah's flood! My guess is that they realize that if the PCA realizes that the flood hinges on this, they will stay YEC, so they just leave it out. What a joke.
Just for fun

And, with that, my browser windows are much happier now.

The Cognitum, Pt. 1

JB — Wed, 05 May 2010 04:39:00 +0000

The "cognitum" is a concept in creation taxonomy that groups animals according to the perceptions that humans have about those creatures. I have been a fan of the idea of the cognitum since I first heard about it from Sanders and Wise's paper at ICC. The goal is to develop a standard of taxonomy based specifically on human perception, and not at all on other standards such as genetic data or morphology.

I found this idea extremely intuitive. There is obviously the Biblical reason that Adam was given to naming each kind that God created. Therefore, perhaps God gave Adam (and by extension the rest of us) the power to discern important relationships. It is interesting, for instance, that even children can usually tell, from a simple drawing, the difference between a cat and a dog, despite their relatively similar morphology, combined with the simpleness of the drawing. The same child can, at least by Sanders and Wise's paper, look at a more bizarre representative of the cat family and still identify it as a cat.

But, I think there is another point worth looking at. When there is a debate about the phylogeny of a species on whether it should be grouped according to its morphology vs. its DNA sequences, how is such a decision decided (or for that matter, when any two trees are in conflict)? I think few people think about how tough a question this is. No one saw the type of animals who were the current animals' ancestor. Therefore, we must lean on secondary evidence. But if the secondary evidence is in conflict, there seems to be some sort of a faculty in the human mind that makes such discernments. It is neither perfect nor consistent, but nonetheless it is there.

Sanders and Wise's paper has a whole host of interesting points:

Most taxonomies (scientific or folk) have animals which are at a "fuzzy boundary" - that is, they "kind of" belong to one or more other groups, but have features that separate them quite significantly. Paleoherbs, for instance, have a mixture of features from the two main groups of flowering plants - monocots and dicots, and so are in the fuzzy boundary
The idea of the fuzzy boundary allows us to apply fuzzy-set theory to biosystematics
Classification is an important part of human experience
Most lay people can recognize multiple species as belonging to the same general type, even in somewhat more difficult cases
Most societies employ four or five hierarchical levels of taxonomy, utilize only the outermost levels for their naming, and reserve the fifth level of taxonomy for minor variants. This is interesting if one considers the true distinct "kinds" to exist at these levels of naming, and not at the higher ones.
The cat family, for instance, seems to be a holobaramin, yet certain other animals (meercats and hyaenas) elicit a distinct "felid" response from humans. Why is that?
Species probably expanded to fill a pre-defined biological character space, which is one way God communicates His design to humans
The adaptive radiation and refilling of the earth after the flood to fill biological character space probably produced some overlap from different groups
As part of understanding God's design, we should examine how far the parts of God's design can be modified without disrupting the "gestalt" pattern that is recognizable.
We can compare the underlying functions associated with an organism's "gestalt" with the variation of functions present within a cognitum
The cognitum concept lies in continuity with the platonic view of biology which predominated the pre-Darwinian era. Creationists should revisit many of these taxonomical concepts to see which ones we need to incorporate into the modern Creation viewpoint.
With the cognitum concept in mind, we should evaluate the genetic basis of different patterns and identify the genomic constraints that restrict the distribution of patterns
How and why are larger cognita chained together by a fuzzy boundary?
Is there some line after which fuzzy boundaries give way to clear-cut phylogeny? Might this help draw the line for baramins?
Hopefully, as the cognitum concept is studied we will learn to differentiate homoplasy (cross-line similarity) due to separate origins from homoplasy from genetic recombination within the same cognitum.
We need to look into the cognitive neuroscience of gestalt formation in the human mind
Is there a relationship between human memory capacity and the structure of the biological world (i.e. so that humans can comprehend it)
Cognita could be used to identify basic baramins and inclusions for baramins before we have a good breeding/morphological/genetic analysis

Anyway, as you can see, there were a lot of things that jumped out at me.

I also had a thought - I wonder if the "fuzzy boundary" organisms might have originated in locations with a low diversity of species. So, basically, an organism "sensed" the lack of biological character space, and then morphed to fill it.

It is interesting to compare this notion of taxonomy with a study on <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635482/?tool=pubmed">adaptive radiations in cichlid fish</a>. I have not read it in detail (a commenter on UD pointed me to it), but the abstract says, "The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5Myr into a radiation speciation becomes a lot less frequent."

But even more interesting is this statement -- "The available data suggest that the propensity to undergo adaptive radiation in lakes evolved sequentially along one branch in the phylogenetic tree of African cichlids, but is completely absent in other lineages."

This indicates that there might be a "basal-type" species which is presumably more similar to ark-based species than others, from whom adaptive radiations tend to take place. This would be super-awesome if it is true.

Sanders also has a newer paper out on the application of the cognitum, but I haven't had time to read it yet. Wood has a basic overview for those interested. A quote from Wood quoting Sanders:

What is most striking from the results compiled in Appendix A is the high level of support by the molecular data for the circumscription of the core groups of most of the primary cognita identified. ... This suggests that the core groups of primary cognita are units that are generally internally consistent morphologically, as well as genomically. ... The decoupling of molecular similarities from morphological similarities just above the family/order level suggests that the circumscribed core groups of cognita at this level or the subfamily/family level may closely reflect the constitution of holobaramins represented by them. In fact, more precise methods of documenting both the decoupling of morphological and molecular characters and mosaic recombination of these characters, so easily depicted in a cognitum system, may eventually prove to serve as a criterion in delimiting holobaramins.