2010
March 03, 2010
Discussions around the Web / Stuff I Would Read and Comment On If I Had the Time
JB
I get information from a number of sources, and often times wind up with more things to read and write about than there is time in the day. So, in order to get my browser back down to its normal size, I’m just going to share with you a link list (note that I have not even read most of these):
· A new approach to evaluating genetic information by looking for corollaries in modern information processing published in tbiomed (this seems to go hand-in-hand with my earlier work on metaprogramming and genomics)
· Testing Common Descent via the Continuity Between Biogeography and Evolution
· A Marxist critique of evolution
· Project Creation looks interesting
· A Gutenberg book by Descartes on scientific reasoning
· A high-quality version of the “Beware the Believers” parody video used for Expelled promotion
· An old post of Hubert Yockey where he reviews his reviewers
· This looks like a great genomics tool if I ever get a chance to mess with it
· I am told that this journal issue has some interesting papers of interest to ID’ers
· Michael Behe defends himself
· Salvador has an interesting post on quantum cosmologies
· A comparative review between Intelligent Design and emergent evolutionary perspectives on origins
Ah! Good! Now I can close my browser windows.
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February 27, 2010
Information Theory / Information Theory, Physics, and Free Will
JB
I just finished reading a paper that is both fantastically interesting, and a little disheartening. It is disheartening only because I thought that my senior paper for seminary was going to be freshly novel, but it turns out that someone else already made 90% of my arguments 11 years ago, and actually made most of them better than I could. The paper is “Algorithmic Information Theory, Free Will, and the Turing Test” by Douglas Robertson (Complexity 4(3): 25-34).
Here are some quotes from the paper (note that AIT is “Algorithmic Information Theory”):
“…free will appears to create new information in precisely the manner that is forbidden to mathematics and to computers by AIT” (26)
“There would be no reason to prosecute a criminal, discipline a child, or applaud a work of genius if free will did not exist. As Kant put it: “There is no ‘ought’ without a ‘can'” (26)
“A ‘free will’ whose decisions are determined by a random coin toss is just as illusory as one that may appear to exist in a deterministic universe” (26)
“AIT appears to forbid free will not just in a Newtonian universe, or in a quantum mechanical universe, but in every universe that can be modeled with any mathematical theory whatsoever. AIT forbids free will to mathematics itself, and to any process that is accurately modeled by mathematics, because AIT shows that formal mathematics lacks the ability to create new information.” (26)
“The fundamental secret of inspired mathematical practice lies in knowing what information should be destroyed or discarded, and what rearrangement of available information will prove to be most useful.” (30)
“The very phrase “to make a decision” strongly suggests that the information is created on the spot.” (31)
“If…we do accept this definition of free will, then an immediate corollary from AIT is that no combination of computer hardware and sofware can exercise free will, because no computer can create information.” (31)
“There is perhaps no clearer demonstration of the ability of free will to create new information than the fact that mathematicians are able to devise/invent/discover new axioms for mathematics. This is the one thing that a computer cannot do. The new axioms produced by mathematicians contain new information, and they cannot be derived from other axioms. If they could, they would be theorems rather than axioms.” (31)
“it has long been accepted that free will is impossible in a Newtonian deterministic universe. But now the impossibility is seen to carry over into all possible physical theories, not just Newtonian theories, because it is inherent in mathematics itself. According to AIT, no physical model (i.e. no mathematical model for a physical process) can allow the creation of information. In other words, free will is impossible in any physical universe whose behavior can be accurately modeled by a computer simulation.” (33)
“All theory is against the freedom of the will; all experience for it” (33 citing Samuel Johnson)
“The idea that all physical processes can be modeled is an assumption that is so deeply ingrained in physics that it is seldom questioned, seldom even noticed.” (33)
“It may be that physicists since the time of Newton have been exercising a careful (but generally unconscious) selection proess. Physicists may have studied only those physical processes that happen to be susceptible of mathematical modeling. This would immediately explain the reason behind Eugene Wigner’s famous remark about the “unreasonable effectiveness of mathematics.” But if it should turn out that many physical processes are not susceptible to mathematical modeling, just as nearly all numbers cannot be expressed with any mathematical formula, this would represent as deep a shock to physics as Godel’s theorem was to mathematics, and one that is far greater than the shock that resulted from the loss of Newtonian determinism when quantum mechanics was developed or the loss of Euclidean geometry when general relativity was discovered.” (34)
“The possibility that phenomena exist that cannot be modeled with mathematics may throw an interesting light on Weinberg’s famous comment: “The more the universe seems comprehensible, the more it seems pointless.” It might turn out that only that portion of the universe that happens to be comprehensible is also pointless” (34)
“The existence of free will and the associated ability of mathematicians to devise new axioms strongly suggest that the ability of both physics and mathematics to model the physical universe may be more sharply limited than anyone has believed since the time of Newton.” (34)
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February 16, 2010
Dinosaurs / In Pursuit of Mokele-Mbembe
JB
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February 11, 2010
General / New Creation Museum Being Built in the Ozarks
JB
A friend of mine sent me a link to a Creation museum that is currently being built.
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February 10, 2010
Biological Change / Randomness in Creation
JB
About two years ago I got my first major paper published in the Creation Research Society Quarterly. You can read a summary of it here. Today, I received permission to post the paper publicly on my website! Yay! If you are interested, check out the paper:
Statistical and Philosophical Notions of Randomness in Creation Biology
Let me know what you think!
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May 21, 2010
General / BSG 2010 Conference – Register Today!
JB
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!
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May 12, 2010
General / Team Creation Award with Folding @ Home
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.
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May 12, 2010
Discussions around the Web / So much information!
JB
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.
Seven wonders of the quantum world
How cells maintain the spatial distribution of proteins
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
And, with that, my browser windows are much happier now.
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May 05, 2010
Biological Change / The Cognitum, Pt. 1
JB
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.
June 24, 2010
General / BSG/CGS 2010 Meeting Speaker List
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
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June 17, 2010
Information Theory / Sanford Publishes New Bioinformatics Tool
JB
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!
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June 14, 2010
Discussions around the Web / Todd Wood on Owen’s Resolution to the Form/Function Debate
JB
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.)
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June 13, 2010
General / Creation Research Society Conference
JB
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
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!
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June 12, 2010
Biological Change / A Home Microbiology Lab
JB
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.
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July 21, 2010
General / The Mind
JB
[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]
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.
Some interesting and related papers I found in Google Scholar:
The Modalized Gödelian Argument Against Computationalism
Creativity, the Turing Test, and the (Better) Lovelace Test
The modal argument for hypercomputing minds
Computation, Hypercomputation, and Physical Science
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August 31, 2010
General / Please vote for the Little Light House
JB
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August 31, 2010
Discussions around the Web / Creation Q&A Day on Facebook
JB
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August 28, 2010
Biological Change / Random Thought on Diversification
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.
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August 15, 2010
Discussions around the Web / Why Online Conversations Are Hard
JB
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.
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April 08, 2010
Activism / Help Ian Win a New Car!
JB
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April 07, 2010
Discussions around the Web / Future Directions of CORE Research and More
JB
Sorry for the lack of posting. This is my last semester in seminary, and I’m focusing on that. Anyway, here’s some stuff that I found rather interesting:
Richard Sternberg has an excellent series of articles detailing signs (and SINEs) in the genome.
Roger Sanders published a paper on his cognitum studies. I will blog about the cognitum later when I have more time. In the meantime, here’s Todd’s take on it.
Todd Wood discussed some anticipated research at Bryan’s Center for Origins Research
Paul also talks about Pitcher plant symbioses in relation to natural evil. It turns out they may be natural toilets. Todd follows up on this here and here.
Andrew Snelling published several papers dealing with discordant radioisotope ages found by dating different isotypes (paper 1; paper 2)
Phil Vischer (creator of veggietales) held an engaging and respectful conversation about origins on his blog (followup post here).
Jay Richards tells us when to doubt a scientific consensus
Unlocking the Mystery of Life and Privileged Planet are now available on YouTube
The Dembski/Marks Evolutionary Informatics lab website just got a facelift, and it includes a scaled-down, graphical version of Avida that runs in your browser!
Creation Safaris makes the case against physicalism
There was a lot more if you count Journal of Creation papers and CRSQ papers, but I don’t have time to get into them now. Hopefully this will keep you busy for a while!
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September 20, 2010
General / Wooden Ships the Size of Noah’s Ark
JB
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