Researching Creation

January 30, 2010

Discussions around the Web / Dr. Faulk's Example of Randomness

As mentioned earlier, Dr. Faulk and Stephen Meyer are having a real debate on the merits of ID.  Dr. Faulk gave what he believes to be a disconfirming example of ID's arguments.  My response, which is also in the comments is below.  In addition, some earlier comments of mine on randomness might be interesting, including:


Dr. Faulk -

I take issue with your description of the processes of antibody diversity generation.  While there is some statistical randomness at play, I would say that the specificity in the process is huge.  The parts of the antibody gene are segregated into matchable parts (V, D, J, and C), which are rearranged in specified ways, whose rearrangments are managed by the RSS signal between each part.  In addition, after recombination, the cell can generate DNA which are needed to make the final protein fold better (Sanz and Capra PNAS 84(4)).

During the mutation afterwards, the mutations are focused on that gene only, and, for that gene, it focuses on the complementary-determining region and skip the C region (which attaches to the B cell, and thus would be counterproductive to mutate) (Papavasiliou and Schatz Cell 109(2 supplement 1)).

To call this orchestration "random" just because it isn't 100% deterministic is an abuse of the term.  It has never been the position of ID that nothing can find a solution within a search space which _utilizes_ randomness.  But rather that this only works when the search space has already been narrowed by information.  This process works only because, rather than mutations happening at random throughout the cell's DNA, they only happen within a well-defined scope - a scope that _matches_ the environment problem that it is trying to solve.

This is the focus of Dembski's work on Active Information, started with his No Free Lunch book and continuing in the papers he has done with Dr. Marks.

If the process were not so constrained, it would not work.  This is the results of not only the work on the immune system, but also those of bacteria - when you mess up the genes in the SOS pathway, evolution does not occur.  The evolutionary definition of randomness is that "one of the central tenets of Darwinian evolution is that mutations are random with respect to the needs of the organism in coping with its environment" (Templeton, "Population Genetics and Microevolutionary Theory", 2006, pg 3). 

Well, your example is actually one that contradicts this statement - the gene which is modified is not random with respect to the needs of the organism, and neither is the are of the gene which is mutated.  This is excluded well over 99.99% of the genome.  How a mutation directed to the correct 0.01% of the genome is considered "random with respect to the needs of the organism" just because, within that 0.01% there is some variability, is completely beyond me.



January 29, 2010

Activism / Bravo to BioLogos


I am not a huge fan of BioLogos, primarily because they don't seem to have a firm grasp of the philosophical and theological impact of their ideas.  However, they did something remarkable today in the world of evolutionary advocates - they let Stephen Meyer have his full say, unedited, on their blog, to respond to criticisms they have made of him.


If only the rest of the scientific establishment would be so intellectually honest.  Most ID'ers are roundly criticized in academic journals without being given adequate (usually not any) space for response.  It is good to know that fellow Christians, even those whom we vehemently disagree with, can operate honestly with each other even when the rest of society frowns upon such activity.



January 27, 2010

General / God's Call to the Scientist in Faithfulness and Rebellion


The gospel is basically a love story.  In fact, in many ways, the scriptures directly make the comparison.  In Revelation, the Church is the bride of Christ. God is continually seeking after his people.  But, unfortunately, our hearts are often hard.

As a Creationist, my heart is God's.  Paul Garner's heart is probably more in the right place than my own, when he says,

I’m not at all interested in trying “to defend a literal reading of Genesis with scientific principles”. Rather, I accept the truth of creation by faith and investigate the world scientifically with that presuppositional basis. That’s not to say that I’m uninterested in evidence, just that my aim in scientific investigation is not “defending Genesis” or “proving Scripture”. I don’t think the Bible needs that kind of help. (see here in the comments)

The goal for Paul is to live faithfully.  And part of that living faithfully is finding new things in God's creation, and using God's scripture as a starting point for all things.

This used to be a common theme in science.  Newton, for instance, was foremost a theologian.  Kepler wanted to enter the ministry, but could not.  But he said, "God is the beginning and end of scientific research and striving".  

Sadly, this thought has been lost.  But God, now like before, still seeks us.  I have been realizing more and more that God often seeks scientists - and, I believe, leads them to discoveries which show God's handiwork - whether or not the scientists are willing to follow.

A case in point is Francis Crick.  Crick said that the reason he went into science was to disprove religion.  But God cared for Crick too much.  God, I belive, helped Crick in his scientific search, to see His creation for what it is.  And that's when Crick discovered DNA.  DNA was certainly a stumbling block for Crick's atheism.  The implications of Crick's discovery, while possibly not immediately obvious to the rest of us, was in fact immediately obvious to Crick - the naturalistic story of its origin just doesn't measure up.  In his book, Life Itself, Crick says, "An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle."  So what was Crick's solution?  Sadly, it was not to turn to God in any way.  Instead, he proposed that the aliens did it.  And, thus, he was freed from looking too deeply into the evidence that God had shown him.

Hoyle's view seems to be similar to Crick's, though I have not done as much research into it.  Hoyle, though he did not believe in God, remarked that "the Universe is a put-up job!"  Meaning, there is just too much intricacy to the design of the laws of the universe.  Likewise, for life, Hoyle thought that we were created by another intelligence within the universe.

Stephen Jay Gould had this happen to him, too.  Here is how he describes the arthropods of the Burgess Shale:

Imagine an organism built of a hundred basic features, with twenty possible forms per feature.  The grabbag contains a hundred compartments, with twenty different tokens in each. To make a new Burgess creature, the Great Token-Stringer takes one token at random from each compartment and strings them all together.  Viola, the creature works - and you have nearly as many successful experiments as a musical scale can build catchy tunes.  The world has not operated this way since Burgess times.

Now, obviously, Gould put an evolutionary spin on this.  Nonetheless, it appears that Gould was looking on in amazement at the way in which the creatures of the Burgess were put together.  It is almost as if he was seeing creation, but not being able to quite admit to it.

What I'm saying is that, when you look at the major discoveries in science by the ones who research them, what you find is God searching for the scientists.  That doesn't often come out in media reports or even in reviews of scientific literature or textbooks.  Few textbooks report that Crick viewed DNA as a stumbling block to the origin of life, or that Gould saw a menagerie of form in the Burgess shale too wonderful to describe, and a pattern unlike anything which is thought to evolve today. 

But, I believe, God is seeking each one of us.  I only hope that the current generation of scientists are faithful to the call that God gives to them, and that they can be humble enough to reject the pride which plagued the science of the 19th and 20th centuries.

And, hopefully, my own work will reflect faithfulness instead of pride.  But I'm still working on that.















January 19, 2010

Physics and Cosmology / Granville Sewell on the 2nd Law of Thermodynamics


Granville Sewell just posted an excellent video which summarizes his mathematical work on the 2nd law of thermodynamics and its relationship to origins debates (Hat tip to UD).

January 18, 2010

Geology / Earth's Catastrophic Past is Available!


Snelling has just released a new two-volume set called Earth's Catastrophic Past.  I've been waiting for this for well over a year, and I know some have known about it for even longer.  Anyway, it is now available for order from ICR!

This book is supposed to contain a summation of the incredible amounts of geological research that has been done by creation geologists over the past half-century, and provide a framework for understanding geology in the context of the Biblical flood.

Thanks to Paul Garner for letting us know!

January 18, 2010

Information Theory / My New Paper on Irreducible Complexity


January 6th was a big day for me.  Huge, actually.  I had finally gotten a paper published (titled "Irreducible Complexity and Relative Irreducible Complexity: Foundations and Applications") that I had been working on for the last 3.5 years.  You might be wondering why it took me so long to come out and announce it.  The reason is simple - most people who have read it misunderstood what I was trying to say.  Therefore, I wanted to take the time to explain the points I am trying to get at in the paper, and a little personal history on how it came about.

In the 2006 BSG meeting, I was a complete unknown.  I knew absolutely no one from before the meeting.  I had come to do a presentation over some interesting overlaps between computer metaprogramming and the way that antibody genes rearrange themselves.

At the meeting was a reporter, who was doing a book on the intersection between fundamentalism and science.  Between meetings the reporter would ask various people questions about their beliefs, and what followed was usually a stimulating conversation.  At one of these conversations, we were talking about evolution, and I (perhaps naively) stated, “it is impossible for new information to be generated by evolution”.  One of the other creationists in the conversation quickly retorted, saying that I was absolutely wrong, and strongly implying that I was foolish for even saying so.  Those of you who are in creation research could probably guess who this was.

I thought this was odd (both the idea that natural selection might offer a way to create information by itself and that I was so roughly thrown under the bus by a fellow creationist).  And pondered it in the back of my mind for awhile.  Did I know for sure that information could not be created?  How did I know this?  The idea that information could not be created by natural selection seemed correct to the engineer in me, but was this really correct?

Another event hit upon the same question.  I had recently purchased a copy of the 1984 Oxford Union debate between Arthur Anderson, A. E. Wilder-Smith, John Maynard-Smith, and Richard Dawkins.  I thought that the creation side (Anderson and Wilder-Smith) was well-argued, save for one detail.  Dawkins (I think) came up with an example of information being created (I forget what it was), and Wilder-Smith (I think) argued that this was not an instance of information being created, but rather of already-existing information being merely “shuffled around”.  Dawkins retorted that since there were only four nucleotides available, all information in the genome arose through “shuffling around” of genetic information.  While my intuition sided with Wilder-Smith, I realized that his argument hinged on a separation between the creation of information and the rearrangement of information.

Again, I intuitively agree with Wilder-Smith’s assessment.  Similar things happen in the rearrangement of antibody gene parts for the creation of novel antibodies.  About 90% of the work comes from shuffling well-defined pieces of information around, and about 10% of the work comes from a series of focused rounds of mutations.  It seemed that most of the information was already existing, and merely being shuffled around.  However, the problem was that there was no objective way of making the assessment between something being created and something being rearranged.

This reminded me of an old friend of mine from my days at Wolfram Research, Chris Knight.  Chris was a computer genius.  I met him when I had just graduated from college and he was just turning 16 -- and he was light years ahead of me in computer programming skills.  One thing that enamored Chris (which enamors a lot of computer science types) is the idea that there is not a clean separation between computer code and computer data.  Computer data can be treated like a code.  And computer code can be represented as data for manipulation.  There are even some languages, such as Scheme and LISP, which elevate such intertwinings of code and data into an art form.

The distinction between “information shuffling” versus “information creation” is similar to the distinction between “code” and “data”.  No person doubts that data can be created without intelligence, but can code?  The idea that code and data can be intertwined so much easily leads a person to conclude that there is no such divide.  But yet, the ability to apply this usefully seems limited to only cases where the code/data is very simple.  But yet, I could not yet see the dividing line between the two.

When I was at Wolfram Research, Stephen Wolfram was just about to finish his magnum opus, A New Kind of Science (hereafter referred to as NKS).  At the time, I was uninterested.  His work in cellular automata did not seem to have any impact on my life and work, so I basically ignored NKS for the time I worked there.  But later, I picked up a copy from the library.  And in those pages, I found the answer to my dilemma.

For the gory details, you can see my paper.  But here’s what I want you to think about.  Imagine a computer program.  There is a difference between these levels of customizability within a program:

  1. The program has no customizations, you just have to go with what the package offers.
  2. The program has a range of customization settings open to the user, and they can set these to a variety of interesting settings appropriate for their business.
  3. The program makes itself available for a programmer to customize it using a general-purpose programming language.

What you see here is not just a rising level of configurability, but also a rising level of intelligence required for making the configurations.  #1 can be configured by an idiot.  #2 can be configured by trial-and-error, and #3 can be configured only by a professional (or perhaps it would be more exact to say that there are aspects of the configuration which can only be used by a professional).

It turns out that there is a type of programming system called a Universal computer.  What makes a Universal computer interesting is that it can, given the right program, compute any computable function.  So it is open-ended.  Here’s the other interesting insight -- Universal computation only arises in chaotic environments.  What makes this so interesting is that a chaotic system, in general, does not give gradual output changes to gradual changes in its programming.  Therefore, to have something “evolve” on a Universal computer it would, by necessity, have to make several leaps to work.  In order to get smooth output changes, which are required by natural selection, one would have to propose a coordinated system of changing the code - something not allowed by naturalistic scenarios, because the changes would have to be coordinated to match the desired gradualistic output.

This provides an answer to my question about information creation versus information shuffling.  If the input domain is open-ended - that is, it is flexible enough to hold the solution to any problem given the right code - then the solution cannot be reached by gradual configurational changes alone, because that is the nature of the way Universal computers behave.  Now, you can design a programming systems where gradual changes to the code lead to gradual changes in the output, and as such would be open to natural selection.  However, these are not Universal computers, and therefore the potential range of results is not open-ended.

Thus, the dichotomy is not necessarily between code and data, but between parameterized programming systems and open-ended programming systems.  If the system is parameterized, then change only happens within the specified parameters.  There may be genuinely new things happening there, but the parameters for their occurrence were specified in advance.  Thus, you can see that the common ID and Creationist claim that “information cannot be created by natural selection” is both true and false.  It is true that open-ended information cannot be created, but if the solution domain is appropriately parameterized, then information can arise within those parameters.

Obviously, this is not a rigorous proof, and if you want a more nuanced version, you should refer to the paper.  But nonetheless, I think that this should give you an idea of the questions that I was attempting to answer and the approach that I took.

There’s a lot more to say about this, but I think this is enough for now.  See the paper for a lot more information, as well as numerous applications.  I especially liked how this related to the evolutionary software Avida in section 3.4.  In any case, this background should help you make sense of what the paper is about and where I am going with it, should you decide to read it.




January 15, 2010

General / BSG 2010 Conference


The BSG (Creation Biology Study Group) just announced this summer's conference, and opened up for abstract submissions.  Here is the announcement and instructions for abstract submissions.  Abstracts are due April 2.

January 08, 2010

General / Creation Research Society Conference This Summer


The planning for the next Creation Research Society conference is underway.  The current plan is the following:

  • Location: University of South Carolina Lancaster
  • Cook-out planned for evening of July 22nd
  • Main conference July 23-24
  • Optional field trip July 25 to Wood's Bay, with possible aerial viewing option in a small plane
  • Transportation can be arranged from the Charlotte, NC airport
  • Price has not been finalized, but will probably be around $60 for pre-registered attendees

The request for papers has not yet been announced.  I will share it when it happens.


January 07, 2010

Biological Change / Tiktaalik - a journey from evolutionary to creationary points of view


Tiktaalik has dominated a lot of the media discussion about evolution in the last few years.  For those who don't know, Tiktaalik is a fossil "fish-o-pod" found in Canada, that is claimed to be an "intermediate form" between fish and early tetrapods (tetrapods are four-limbed creatures).  In addition, it was claimed that it was in the evolutionary-correct position in the fossil record for the fish-tetrapod transition (late Devonian). 

Now, the basic problem in Tiktaalik is that it isn't "transitional" so much as mosaic - that is, it has features of "earlier" and "later" creatures, but no features that might be considered "in transition".  Each feature that it has, it has fully. This indicates that, if it did "evolve", it did so non-Darwinistically - that is, the information seems to have already been in the gene pool, and was merely activated.  On the other hand, in absense of a mechanism of macroevolution, there is no reason to think that it evolved at all.  And from a flood geology perspective it gets even more interesting, but I'll leave that for the moment.

In addition to all this, there is a certain kind of criticism that emerges from lay people that you don't tend to find among experts.  That criticism is of the form of "is this really all the information there is?  Does it really add up the way you say it does?  Is it not possible that there is other evidence out there that you just haven't found yet - perhaps because you weren't looking for it?"

Now, this kind of criticism is usually just ignored by experts, but I personally think that it is epistemologically valid, and an important part of public discourse.  The fact is, every discipline needs to be confident in its own ability to find truth.  However, equally important, is that the public should not grant each discipline the same amount of credulity that it grants for itself.  A discipline can't go anywhere if it has to spend all its days proving its assumptions.  On the other hand, if you can't prove your assumptions fully, then your findings are not binding on others.  If someone has a larger worldview, then different aspects may be in competition.  Why should a person give up belief X which is important to them and which they believe they hold validly, when they don't agree with the assumptions of contradictory belief Y, especially if it is relatively unimportant to their daily lives?

The reason I say all of this is that, in the case of Tiktaalik, it is the lay criticism that wound up being correct.  Let's look at a new article that came out in Nature.  For those of you who are not nature subscribers, here is a short news article on the subject.

What they found is, according to evolutionary timescales, a full-fledged tetrapod existed about 20 MILLION years prior to Tiktaalik.  While Tiktaalik was a transitional, this thing was fully-tetrapod. So, this blows any story about Tiktaalik and evolution completely out of the water.  Tiktaalik has nothing to do with the evolution of tetrapods, because, if evolution is correct, full-blown tetrapods predated the transitional species by about 20 million years.

It's dangerous to put your faith in circumstantial evidence, because the facts can change that quickly.  Yesterday it was an open-and-shut case for Tiktaalik being found right where it was supposed to be in evolutionary transition.  Today, it is more than 20 million years out-of-date.  I say "more than" because, according to evolutionary theory, the tetrapods would have still required time to evolve before this creature existed.

So here's where it gets really interesting - the new find is footprints.  Here's a few things that don't usually get a large mention in introductory textbooks:

  1. There are large gaps (sometimes a hundred million years) in the fossil record where a given species must have existed but did not leave any fossils.  Two examples are the Wollemi pine and the Coelacanth.  These were last seen in the fossil record 150 and 65 million years ago, respectively, yet they still live today.
  2. Many measures of the fossil record show that it is relatively complete
  3. Most creatures are first known from trace fossils (i.e. footprints or other types of trackways) long before we ever see their body fossils.

The interesting implication of #1 is that there is NO WAY AT ALL to infer from the fossil record how long something has been in existence.  If we can verify that the fossil record can be off 100 million years in one direction, if we assume that the same thing can happen in the other direction, then that means that you have a possible margin of error of about half of the phanerozoic era (the phanerozoic is the complete fossil-bearing section of the fossil record).  How can you possibly have a detailed evolutionary progression when you can have this kind of discrepancy between fossil evidence and reality?  If the best you can do is establish which half of the geologic column they existed in, how good is your data, and how are you going to derive evolutionary expectations from it?

Let's look at the second idea - that the fossil record actually seems complete.  There are many ways of measuring completeness.  The interesting thing is that most of them point to the fossil record being essentially complete, at least to the biological "family" level.  That doesn't mean that we won't find anything new, just that we've probably found more than we haven't.  So, this makes an interesting corrective to the preceding paragraph.  Maybe the completeness of the fossil record gives us confidence that most of the extents of organisms are well-represented in the fossil record, and these two (and some others) are merely anomalies.  That could almost work, except...

Why on earth do trace fossils precede body fossils?  As the Nature article on Tiktaalik points out:

Trace fossils — footprints, trackways or trails — are fascinating but often frustrating sources of information. Body fossils of the track makers almost never occur in the same rock beds, so complicating interpretation.

It is much harder to preserve a trackway than a bone.  So why do we know most organisms by trace fossils before we know them as body fossils, and why are the two rarely found in the same rock beds?

The answer, perhaps, is contained in an old Creation-oriented paper titled Stratigraphic Distribution of Vertebrate Fossil Footprints Compared with Body Fossils

In this paper, Brand and Florence argue that the reason for this is that it evidences fleeing behavior.  The flood didn't happen all at once.  It waxed and waned until it covered the earth, which didn't happen until day 150.  Until then, the increasing floods would still have had tides from the moon, and gone in and out over increasing landmasses.  Therefore, if there is a footprint, it is probably of a living creature, not a drowning one.  If there is a body fossil, it is probably a drowned creature.  So if the waters had temporarily receded, new trackways could be lain.  When the waters come back and deposit a new layer, they are killing off organisms into a different rock bed.

Also, as Kurt Wise has pointed out recently, if the fossil record is of a global flood, we should expect much more completeness than the evolutionists.

In any case, this is getting to be rambling.  My main point is that this new fossil find has very interesting implications for both creationists and evolutionists, and tends to validate thought-patterns of lay critics of evolution.


I wrote this last night but forgot to publish it.   In the meantime, several other people have chimed in on the new tracks:

  • Todd Wood points to another recent article by Kurt Wise in Answers Magazine which visits the ground as Brand and Florence.
  • David Coppedge gives nice pull-quotes from several news sources, and points out that the researchers noted that many tracks in even older sediments may have been misinterpreted, and may be tetrapods as well. One thing that is interesting to note is that these older tracks have been with us the whole time, and the reason they were not interpreted as tetrapods is that tetrapods weren't expected to have been alive at that time.  It is always fascinating the ways that our minds work - in many cases only by believing in the credibility of something beforehand are we able to find the evidence that supports that.
  • Finally, Casey Luskin points out that Neil Shubin has made a whole lot of hoopla about Tiktaalik being in just the right place at just the right time.  This blows Neil's whole theory out of the water, completely.  This whole incident reminds me of a line out of Ocean's 11.  Right after Rusty reveals that Benedict's video surveillance of his own vault is rigged, and he is actually in the middle of being robbed, he says "In this town, your luck can change just that quickly."







January 06, 2010

Geology / Archaeology of Sodom and Gomorrah and Other Videos from Recent Conference Available


The Northwest Creation Network recently published the videos from their 2009 conference on their home page.  There are many good videos in there.  One in particular was Steven Austin's discussion of the archaeology of what he believes to be Sodom and Gomorrah.  I'm going to have to rewatch the video, since I missed a lot while cooking breakfast this morning, but it was fascinating.  Steve has done a lot of work with archaeology of Biblical events, and we reported here on an earlier paper he did on the archaeology/geology of Amos's earthquake. Anyway, all the videos are great and worth watching.