OK, Enough Politics and Back to Having Fun with the Discovery Institute

First off, let me remind you of something we have spoken about a number of times, the Sternberg Peer Review Controversy, where the outgoing editor of a small scientific journal published a paper by the Discovery Institute's Stephen C. Meyer that was later retracted with this comment [I added the emphasis]:

"The paper by Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," in vol. 117, no. 2, pp. 213-239 of the Proceedings of the Biological Society of Washington, was published at the discretion of the former editor, Richard v. Sternberg. Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The Council, which includes officers, elected councilors, and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history. For the same reason, the journal will not publish a rebuttal to the thesis of the paper, the superiority of intelligent design (ID) over evolution as an explanation of the emergence of Cambrian body-plan diversity. The Council endorses a resolution on ID published by the American Association for the Advancement of Science (http://www.aaas.org/news/releases/2002/1106id2.shtml), which observes that there is no credible scientific evidence supporting ID as a testable hypothesis to explain the origin of organic diversity. Accordingly, the Meyer paper does not meet the scientific standards of the Proceedings." (Wayback Machine link)

Why am I reminding you of this?  Well today the DI mentioned it as well, only they forgot a few things.  They actually quoted the paper as if it was never retracted:

"Stephen Meyer explains in "The origin of biological information and the higher taxonomic categories," published in the Proceedings of the Biological Society of Washington:" (To Practice Science, We Must Philosophize)

Do they mention anything about the peer review controversy?  Or how the paper was published without proper peer-review?  Or even the simple fact that it was retracted?  No, they make it sound as if this paper was published and is an accepted part of actual scientific peer-review publications.

What do you think would happen if a real scientist referenced a retracted paper after the retraction?  Exactly . . . most likely unemployment, and deservedly so!  As for what happened after Sternberg violated the peer review process and published his friend's paper?  Ever wonder where is Sternberg working now?  The Discovery Institute's internal lab, the Biologics Institute.

The rest of the article in which the DI tries to pass off Meyer's retracted paper is pretty useless and much the same typical ID nonsense.  For example:

"Intelligent design employs this method of reasoning by observing what humans produce in the present -- namely, complex (unlikely) and specified (matching a pattern) information -- or CSI. This type of information is found, among other places, in computer code and machines. When we find the same properties of complexity and specification in nature, such as in DNA code and molecular machines like the bacterial flagellum, we make an inference to the best explanation: design by intelligence"

Note that Sarah Chaffee, the author of this particular post, uses 'Complex Specified Information (CSI) as if it means something.  CSI is a concept, an unsupported idea.  Did you notice the use of parentheses to change the definition of the terms.  The DI interchanges 'complexity' with 'likelihood of occurrence', but no one else uses that way of defining complexity.  There have been many criticisms of this idea and no one, particularly at the DI has bothered to offer any support other than pushing their idea as if it was reality, just as Sarah does here.  If you are interested in more criticisms of CSI, you can check this out.

I am not going to argue the use of Philosophy in Science, but I do have to argue that while assuming the actions of a deity/designer is philosophical, it has no support in the reality of science.  For example Scientific Philosophers argue the validity of the scientific method and scientific theories, but do they insert the actions of a deity doing inexplicable things into the conversation in an obvious effort to formalize one specific set of religious beliefs?  No!  Just look at:

"For instance, philosopher Jay Richards and astronomer Guillermo Gonzalez argue in The Privileged Planet that the same conditions on earth that make scientific discovery possible also make habitability possible, and this points to design. They note, "Our situation is complex, certainly, but it is also exhibits a specification, a telling pattern, in which the rare conditions for habitability and measurability correlate." In other words, they are reasoning on the basis of CSI"

Aside from Richards and Gonzalez being Senior Fellows at the DI-- something Sarah fails to mention -- like Sarah, they assume complexity and specification in an unsupported way.  You can probably see why I refer to ID as nothing more than wishful thinking and conjecture!

I think we have a handle of the pseudo-scientific methodology of the DI:

• Create a concept with no supporting evidence at all.
• Make up some science-y sounding stuff about it.
• Then just treat it like it means something.

Disagree?  OK, but then how do you explain everything we have seen from the DI since they were formed 20 years ago?  Have they deviated from this little three-step process?  Intelligent Design, CSI, Irreducible Complexity, Dembski's Design Filter, and Nelson's ontogenetic depth all fit perfectly.  Concepts that sound like real science and treated seriously only by the DI and their proponents.  The rest of us seem to be able to philosophize without the need for a deity to be involved.  The DI can't seem to do much without bending a knee.

Dembski's Design Filter Does It Again . . . Sort of

Back a while ago I posted this: "Dembski Design Filter . . . Success?". It was about how the Discovery Institute (DI) took their 'design filter' and 'used it' to come to a conclusion that archaeologists had already come to using real science. Afterwards, the DI claimed some sort of victory . . . for what I am still confused about.

So let's think about this for a minute.  Wild Bill Dembski draws a line in the sand and claims that things on one side of the line are designed and things on the other side of the line are natural.  He claims that the line represents some arbitrary level of complexity and that nothing above a certain 'level of complexity' can be the product of a natural process.  However, he forgot to finish the job before departing the DI, because other mathematicians who looked at what he wrote have pretty much said that it's junk.  While I am paraphrasing, Dembski's response was actually more childish. His response was that pretty much every other mathematician on the planet wasn't smart enough to understand.  Yea, like Wild Bill is the smartest man on the planet.  Well he might be smart, because he's left the DI, but he failed to take his 'crap' with him.

You see, one of his problems is that he has no viable evidence supporting his assumption that natural processes cannot create complexity to any varying degree.  So that makes his 'line' one that cannot be determined with any degree of accuracy.  How can you determine 'complexity' when the very idea basically an opinion.  Look up complexity in the dictionary and you will see what I mean.  It's one of the most circular definitions I have seen.  Here's one:

"the quality or state of not being simple, the quality or state of being complex, a part of something that is complicated or hard to understand" (Merriam-Webster: Complexity)

Well, the DI is doing it again, "A Design False Positive? Applying the Design Filter in Archaeology" claiming some sort of success because they have determined something that archaeologists have already determined . . . again.  Seriously, does anyone believe the design filter is (1) a tool in use by archaeologists or (2) that there is anyone capable of using a tool that is as well defined as smoke?

I also disagree with the title.  Wouldn't a 'False Positive' be the case if their tool determined that the objects under archaeologist discussion had been found to be designed, when they weren't?  That would be a false positive.  A false positive is more like a positive results for the flu when you really don't have it.  Coming to the conclusion that the objects were not designed is a negative not a positive.  And the DI came the same conclusion the archaeologists came too after doing actual scientific work, doesn't sound like a false positive, does it?

Hmmm, so let's see.  How about an analogy.  Let's also keep it pretty simple, for the benefit of the DI.  You are a mechanic and you have a nut you need to tighten.  You grab the appropriate wrench and tighten the nut.  After you are done, along comes a DI marketeer who sees the tightened nut and claims the mechanic tightened it using his tool, a tool no one has ever seen.  The DI comes around after the fact and tries to use your work to bolster their nonsensical claims.  Isn't that what they are doing when they claim things like:

"Archaeology is intelligent design in action"

Are the archaeologists using Dembski's design filter?  Do they use any part of Intelligent Design 'theory'?  Does anyone?  Is there any part of design 'theory' that is capable of being 'used'?  I bet the archaeologists would be surprised if they bothered to read the DI's press release.  Of course the reality is nothing of the sort.  What this is, is an example of using intelligence, well that plus actual measurements, instruments, and analysis . . . you know the science-y stuff the DI seems to be allergic too.  Using intelligence is not the same thing as Intelligent Design, they just keep trying to make that sort of connection in hopes they can convince some folks that ID is something other than conjecture and wishful thinking.  What Dembski's filter has to do with intelligence is a bit beyond . . . well . . . everyone.

So the DI claims another victory for a tool that only seems to come out of the toolbox after all the work is done, but . . . it's a success!  Let's use toast them for yet another meaningless and unsupportable victory!

Trying to grasp 'Information'

The most recent argument against evolution involves 'information', but they [ID proponents] never seem to explain it in a way that makes any sense.  So I have been searching for an analogy that works, but I keep coming up blank.  Not sure if I am going to reach a conclusion, but a couple of things did strike me.  Let's start with Denyse O'Leary's recent definition of Evolution:

"The mere process of eliminating unfit examples of a type in a given environment builds up information over time, resulting in huge new layers of complexity."

So, according to Denyse - Evolution is a build up of complexity.  That really doesn't ring true for me.  I don't see anything that mandates increases in complexity.  What can be, and has been documented, is that as species evolve, genetic information (genome) changes.  Whether those changes increase, decrease, or don't change the amount of genetic information seems more a matter of measurement than a matter of importance.  There is my first problem, by what standard are they measuring changes in genetic information?  I can't seem to find anything specific on such a measurement.

They offer opinion, calling 'information' complex, but what does that really mean?  Just like 'information, how do you measure complexity?  That's my second problem.  Complexity, recently sort of defined by Wild Bill Dembski, and repeated ad nauseum by little casey luskin, is this:

"something is complex if it is unlikely to occur by chance" (Wikipedia: Specified Complexity)

Now when I went looking for a definition of 'Complexity', I couldn't find a real definition, all I really found was that complexity is a characterization and often an opinion.  For example something might be complex to me may not be complex for someone else.  The most common dictionary definition is:

"the quality or state of not being simple, the quality or state of being complex, a part of something that is complicated or hard to understand" (Merriam-Webster: Complexity)

Of course you can't stop there, you then have to define 'complex':

"a whole made up of complicated or interrelated parts" (Merriam-Webster: Complex)

The problem with 'characteristic' definitions like this is they tend to run you in circles, Complexity leads you to Complex which leads you to Complicated.  Complicated is defined in a way that leads back to Complexity:

"hard to understand, explain, or deal with : having many parts or steps" (Merriam-Webster: Complicated)

I am sure something that doesn't surprise anyone, is that Complexity is defined by the rest of the world considerably different than Dembski's definition.  Just because something is complex, as in a whole made up of interrelated parts and maybe hard to understand, does not mean it is unlikely to occur through a natural process!  The formation of an object that may be defined as complex is not determined by its eventual level of complexity.  That's the opinion part of a characteristic definition.  Dembski, luskin, and the rest of the DI claim that complexity is a measure of unlikelihood, but by what measure?  Is a mountain complex?  Maybe it is or maybe it isn't.  To someone looking at one at a distance and the answer might be 'no', but ask a mountain climber or a geologist and you will get a very different answer.  Even Biblical Literalists like kennie ham agree the Grand Canyon formed by a natural process, he just thinks it happened due to an imaginary flood very quickly rather than millions of years of much smaller changes.  See what I mean by a characterization and opinion?

You might have noticed that I am not using Dembski's term 'Chance'.  I don't like that term mainly because it bring to mind something much more random.  Evolution isn't random, it's more unpredictable, which is not the same thing as being random.  But I've posted about that many times.  Although Darwin used the term 'Random Mutation', when you look at mutations within the context of evolution, any randomness is a very small piece.  Mutations themselves aren't particularly random, often they can be traced back to the genes that changed and resulted in the mutation and unless those genes were present, that specific mutation would not have occurred.  If random mutation was completely random, then anything could happen, regardless of the involved genes.  That isn't the case, unpredictable more than random.

I understand why Dembski uses 'chance', because he wants people to think Evolution is completely random and based on the luck of the draw, so to speak.  It's how he sells his argument of the impossibility of evolution. 

But, back to the discussion at hand, the reality is there is nothing anyone has published says complexities in nature cannot occur through a natural process.  They [ID proponents] feel that complexity is unlikely to occur, but that's an unsupported opinion, not based on facts.  Yes, they can call up examples of complex things that occur rarely, but by the same token there are a great many things considered complex that happen often through natural means.  What I think happened here is Dembski made up his own definition of 'complexity' and then started using it as if the world would automatically buy into it.  Is a tree complex?  And yet they grow everywhere and plant evolution is well supported.

While I was in the middle of my mental meanderings, little casey luskin, you know the 'lawyer' tasked with handing out press releases during the Dover Trial.  Well it seems he took a stab at the information argument and he really just muddied up the waters more than provided any clarification.  Here is a link to his post: "A Taxonomy of Information".  The main reason I read it is he started something potentially intriguing . . . and to be honest I usually don't make it past a few lines of most of casey's posts.  I've commented on him many times, but much less often than he posts himself.  But this time he said:

"What are some common definitions of information, and which definition is most useful for making the design inference?"

As you can imagine, I was hoping that the DI would actually pin down the definition of information that might bring some sense to their whole information argument. But, they didn't.  All little casey really did was pile on a bunch of nonsense and then use such nonsense in an effort to justify their shared religious belief.  They jump from a poor series of 'information' explanations right into their favorite topic 'Complex Specified Information' without making any connection.  From there little case' repeats stuff from Dembski on 'complexity' and he's off and running down a winding path that doesn't lead to anything resembling a conclusion.  At one point he says:

"It's important to understand that the idea of complex and specified information is NOT an invention of ID proponents."

Which isn't totally true.  Yes, the term did not originate with the DI, but Dembski's use of the term is certainly did!  To quote Wikipedia again:

" . . .whereas Orgel used the term [specified complexity] for biological features which are considered in science to have arisen through a process of evolution, Dembski says that it describes features which cannot form through "undirected" evolution—and concludes that it allows one to infer intelligent design. While Orgel employed the concept in a qualitative way, Dembski's use is intended to be quantitative." (Wikipedia: Specified Complexity)

OK, you can read Casey's little diatribe on your own time.  I think I've given him more than enough attention here.  Let's go back to the 'information' argument and try and sum up where my thinking has been going.  First let's add in the basic definition of Intelligent Design:

"The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."

The phrase that sticks with me is "best explained".  What they seem to be saying is their explanation is best because the genome is complex and complexity can only come from intelligence and not natural processes.  The only point of agreement is that the genome is complex, that is it has a great many pieces and parts.  But the fact of complexity in no way requires an intelligence.  Inventing things like specified complexity to 'explain' things fails if they cannot back it up with reality instead of wishful thinking.  The whole 'information argument' is rapidly turning into a re-statement of the old 'odds argument'.

You might remember the odds argument.  It was personified when Fred Hoyle made an analogy comparing Evolution to a tornado through a junk yard building a 747.  It was further compounded with some folks claiming to have calculated the odds of the human genome being in existence.  Yet the odds argument doesn't work.  It's like the lottery.  Before you buy a ticket, you can calculate the odds of winning because you know the parameters you are operating within.  Do we know the parameters for the formation of life?  No, and any claims to the contrary are selling one version of snake oil or another.

Let me repeat my favorite analogy about the odds argument.  Take a plain deck of playing cards and shuffle them up.  Deal them out face-up so you can see them all.  Do you see the order they are in?  What are the odds of them being in that order? 52! (52 factorial).  Pretty damn astronomical.  Now the question is did you beat the odds?  Be honest!

The answer, of course, is no.  Unless you predicted that exact order before you started dealing them out, you haven't beaten the odds at all.  Now, what are the odds of those cards being in some order?  Right, 100%.  Without the prediction, the odds are meaningless. 

Let's try one more analogy, start with the number 1 and add 1, you get 2, then add another 1, and you get 3 . . . adding one to a number is a very simple process.  Is there a limit?  Of course not.  We have frequently stated that numbers simply keep going, toward a fairly esoteric idea called 'infinity'.  But that number will pretty quickly reach a level where it is literally incomprehensible to us human beings.  Oh, in the abstract, we can deal with such large numbers by changing the way we express them in various ways to bring them down to a comprehensible level, but something like 1.0 x 10¹⁰⁰ is given the name 'googol', another impossibly large number, a googolplex is equivalent to 1.0 x 10^googol.  The estimate of counting up to a googol would take an estimated 5 x 10⁹⁰ centuries (at 2 numbers per second).  Can you even imagine how long it would take to count up to a googolplex? Based on that, wouldn't such a number be 'hard to understand'?  So it meets one of the common definitions for 'complex'. 

So here we have something created through a simple process that eventually reaches a point where it is barely comprehensible without some esoteric methods of reference, like scientific notation or categorizing with a cute name. I know this isn't a complete analogy, but then what analogy completely represents anything anyway?  But look at how a simple process can eventually add up to levels of complexity that require us to take significant steps to be able to comprehend.  Even then, do most folks really understand numbers that large?

To use this analogy on Intelligent Design, it seems that we start with 1, and add 1, then add another 1 . . . and we reach a point of comprehensibility where we cannot add another number.  To make the jump to a larger number some external factor (intelligence . . . or to be honest, a Deity) must be added because of our inability to comprehend such complex things.  And yet for this to be true, there has to be some barrier that cannot be breached.  Have ID proponents offered up anything resembling a barrier?  Not yet and not for a lack of trying. 

Life evolved and continues to evolve without any evidence of the actions of a capricious deity.  The information argument doesn't really seem to mean much of anything.

Anyone else remember the name Emile Zuckerkandl? A reminder from Larry Moran

Larry Moran has a great post over on Sandwalk, "Emile Zuckerkandl and the 50th anniversary of the birth of molecular evolution".  He tells a little of the story of Emile Zuckerkandl, a name I had heard of many years ago but unlike one of his publishing partners, Linus Pauling, his wasn't a name I had heard of much at all.  Luckily for me, Larry not only reminded me of the name, but some of the things Zuckerkandl did, especially when it came to Intelligent Design.

Yes, I am sure folks at the Discovery Institute didn't like anything he said, but to me it was a nice lesson.  Thanks Larry!

Here's a few quotes, but I really recommend you head over and read the whole post.  [I added a little]

• "To give themselves an edge, the “creationists"—the dominant stripe of anti-evolutionists in the United States—have decided some years ago (Pennock, 2003) to dress up in academic gear and to present themselves as scholars who rise in defense of a legitimate alternative scientific theory, intelligent design. "  [I usually refer to their 'gear' as an ill-fitting lab coat.]
• "The two biased characterizations [Evolution is just a theory and equating the theory of evolution as nothing but a philosophy, an 'ism'] are cherished by nearly every proponent of intelligent design, because desirably one of the points, evolution as a theory, reduces science to incertitude, and the other, evolution as an "ism," reduces it in practice to an unscientific belief. " [Love it]
• "The basis of an established scientific field is not questionable: too many competent, critically minded people working in a number of subfields and analyzing phenomena at a number of levels have contributed to it, with their results supporting one another within a large body of scientific knowledge. A field would have collapsed long since, were it not based on extant phenomena. The flood of creationist references to a particular scientist rather than to a field of science conveniently tends to hide this fact from view. "  [How many times, especially recently, have we been subjected to posts that attempt to denigrate Darwin and his accomplishments.  Here are a few: DI's Denyse O'Leary sounds puzzled!, Discovery Institute upset that Darwin didn't have a Crystal Ball, and Sorry Darwin, it isn't your Evolution anymore? Are you kidding?.]

The one quote you really need to read take a different view of Intelligent Design vs Natural processes, and it deals with complexity.  One of the issues frequently raised when anyone objectively looks at ID is the fact the so-called designer was pretty bad at his job.  Seriously, look at the human body, tell me how that is optimal?  We can barely stand upright and anyone who gets back pain knows what I mean.  How about the number one source of germs (the nose) positioned right above the main air intake (the mouth), or one poster put rather indelicately, the playground located between two sewers (think about it :-)) It's not just humans, but life in general, how many different flight mechanisms exist in nature?   Three that I know of: birds, bats, and insects . . . why?  Why would a 'designer' need three different mechanisms to perform the same task?

Zuckerkandl raised an interesting point.  When you look at things actually intelligently designed, you know the type of things folks at the DI like to point to an say "See, we can recognize design, so biology must be designed."  Simplicity is the hallmark of design, not complexity.  Think about it, the best design is usually the simplest design.  Over time simplicity increases, not complexity.  But what do we find in nature?  Increases in complexity over and over again.  Here is the quote:

"Consider something designed by an intelligence: what would its general distinctive character be, as contrasted with products of nature? Would it be increased complexity? No, it would on the contrary be increased simplicity! This pertinent remark, made and discussed by Glenn Ross (2005), removes a basic misunderstanding that is traditionally cultivated by creationists and intelligent designers. Though relative simplicity does occur in nature at certain levels (e.g., in crystals)—if we consider the hierarchical plane of phenomena encountered in every day life it is simplicity that is much of the time a hallmark of actual intelligent design....What should surprise us is not the universally present complexity of natural structures and processes; it is the fact that the human mind can cut through extremely high interaction complexities by showing that they conform to relatively simple relationships, which the connoisseurs experience as “beautiful”."

Can't argue much with that.  Like I said earlier, I am sure the folks at the DI don't like any of this, but then they don't like much of anything that doesn't start and end with an appropriate 'deitification'.