Intelligent Design does not make predictions and is not science.

Since it has been so long since I last wrote a blog post, I thought that I ease back into blogging by attacking the lowest of the low hanging fruit from the Discovery Institute. Namely, the argument that Intelligent Design (ID) is real science.

Recently, Casey Luskin wrote a post discussing how ID proponents test their theory in real world situations.  Luskin provides a short list of four items (is that the most he could come up with?) that are supposed predictions of ID.  Lets take them one at a time:

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

This is not a prediction. Life has already been seen to have “intricate patterns that perform specific functions.”  In fact, isn’t the complexity of life what made people believe ID in the first place?

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

It is rare to find any facet of an organism that doesn’t already have a precursor, let alone “large amounts of novel information.”  The prediction of ID should state that there will only be the instant appearance of new structures. Any evidence for a slow, gradual development of a structure would refute ID and prove evolution.  For example, you might see a fully formed tetrapod without any precursors if ID was true.  However, we see in the fossil record myriad examples of transitional forms from fish to tetrapod (Tiktaalik, Panderichthys, etc.).

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

This prediction seems odd to me. Convergence is a prediction of evolution. Take for example the convergence of the ability to fly. Evolution would predict that different organisms would gain the ability to fly, but they would achieve this ability by slightly different methods.  Luskin is predicting that structures would be re-used by different organisms.  Why do all wings look so different? Does a fly’s wing resemble a bird’s or a bat’s? Not at all.

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

4) “Much?” Luskin should have said “all.” if we are to believe in intelligent design.  Why waste even a single nucleotide if you were to design an organism’s DNA? This sort of ambiguity is what makes these predictions worthless.

I think it is clear to see that the predictions put forth by Luskin are basically worthless for providing support that ID is real science.  What do you expect when you can give the “designer” any attribute, power, or foresight that you desire?

Another point against Intelligent Design: blurry lines of design

In reading some of the older posts from the Evolution News and Views blog, I came across a short post by Casey Luskin explaining that there is some wiggle room to what was and wasn’t designed in the Intelligent Design (ID) theory.

Luskin writes:

Of course anyone with a cursory knowledge of ID would be aware that ID fully allows for the action of natural processes, and design is only invoked when we find tell-tale signs of intelligent action, such as high levels of complex and specified information.

At the surface, this seems like a perfectly reasonable statement that makes ID sound as though it is a well-defined theory.  However, this view of intelligent design leaves a lot of leeway.  How complex and specified does it really have to be to be considered ‘designed’?  Since these are arbitrary values, one could never really separate two objects or organisms and say one is designed and one isn’t.  This sort non-measurable attributes makes ID not science.  However, it does give an ID proponent a way out when something is demonstrably nature driven.   All they have to say is that the designer didn’t design that, but now look over here…

The Discovery Institute engages in censorship

Many from the Discovery Institute have argued against censorship in any form.  Yet, when someone criticizes Discovery Institute fellow, Casey Luskin, they fully engage in censorship.  Recently, Luskin appeared on Fox News to discuss the recent battle of how evolution should be taught in Texas schools.   DonExodus posted a point-by-point video rebuttal to Luskin:

The Discovery Institute responds by sending a copyright claim and demanding the video be taken down.   Below is DonExodus describing the situation in his own words:

This example of censorship is shocking in light of what they have written on the subject.  Take for example the whole idea of academic freedom.  The supposed impetus for needing academic freedom is that some scientists were being censored due to their beliefs.  In regard to academic freedom day celebrations:

we want students everywhere to speak out against censorship and stand up for free speech by defending the right to debate the evidence for and against evolution

Then there is this blog post that says Censorship is Wrong.

I do realize that their are a variety of opinions at the Discovery Institute, and that not everyone there agreed that this action was appropriate.  However, enough people did agree for this action to move forward illustrating, yet again, that the DI is not interested in a full and eqqual intellectual debbate/

Luskin can’t see the reality of evolution for the trees (part 3)

Part 3 – Analysis and rebuttal (cont)

This post is the third part of a three-post series aimed at clearing up the misinformation written by the Discovery Institute’s Casey Luskin in regard to phylogenetic trees and  the idea of a complete tree of life (TOL).  In parts 3, 4, and 5 of Luskin’s series, he continues his bastardization of the evidence for evolution.

In part 3, Luskin discusses what he calls “extreme genetic convergence.”  The problem is that he confuses genetic convergence with heredity.

One data-point that might suggest common design rather than common descent is the gene “pax-6.” Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes.

Having the same gene controlling eye development in different organisms is completely compatible with evolutionary theory.  This gene (pax-6) could have controlled the development of a very simple eye, perhaps a patch of photosensitive cells, in a common ancestor.  Subsequent organisms would use the foundation laid by pax-6 and add their own specific modifications to yield different eye types.  Luskin’s assertion here that pax-6 argues against evolution makes no sense, except for someone who is actively looking to twist data to their preconceived notion.

Luskin is also outright wrong when he says that pax-6 is used to “control development of their very distinct types of eyes.”  Pax-6 is necessary for eye development, but it does not influence the type of eye made.  For example, if you take the mouse pax-6 gene and put it into a fruit fly, the fruit fly makes fly eyes, not mouse eyes.  It is clear Luskin is either confused or is misrepresenting the facts.

Homology is evidence against evolution?

In part 4, he argues that homology between animals, both at the molecular level and at the physiological level, is a problem for evolution.  Luskin doesn’t really do any of his own work, but instead quotes from the Explore Evolution “textbook”:

To summarize, biologists have made two discoveries that challenge the argument from anatomical homology. The first is that the development of homologous structures can be governed by different genes and can follow different developmental pathways. The second discovery, conversely, is that sometimes the same gene plays a role in producing different adult structures. Both of these discoveries seem to contradict neo-Darwinian expectations

Neither discovery contradicts the theory of evolution.  It doesn’t matter the path that a gene or structure takes to be effective, it just matters that it is effective.  Explore Evolution is trying to take an interesting facet of biology and say it disproves evolution without really showing how common descent precludes these features.

Let’s turn the tables and ask what do these two discoveries mean for intelligent design? Well it means that here is another example of stupid design. I say stupid because what designer would use “different genes” and “different pathways” to come up with the same structure. That would be a monumental waste of time and effort for the designer. How about using the same gene for different functions? Well, that is better design, but it goes completely against the first point.

Morphological vs. phlyogenetic trees

In part 5 of Luskin’s series of posts, he claims that morphological data does not correlate with phylogenetic trees.   Maybe they don’t fit exactly, but the similarities are so common that it is ridiculous to think they are not due to common ancestry.  Like I mentioned in part 1, there is a lot of problems associated with the creation of mathematical models used to predict phylogenetic trees. Likewise, trees based on morphology are subject to their own problems.

To make his point, Luskin actually refers to the gene (cytochrome B) that I had picked in part 1 of my series of posts.  Using the sequence of this gene from different ape species,  I was able to produce the exact same phylogenetic tree as had been done using endogenous retroviruses.   What does Luskin say about cytochrome B?

pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny.

I didn’t look throughout all of “classical animal phylogeny,” but I was able to create evidence for common ancestry using cytochrome B that matched both morphological and molecular evidence.  Without common ancestry, this should not have been possible.

One final point. Whenever someone looks up scientific articles, it is best to look at the newest articles for obvious reasons. Yet Luskin did the exact opposite.  To help make his point here, Luskin quotes from several scientific papers that were published around the turn of the century.  One is even from 1993.  These papers came before the genomics era and before automated sequencing was common.  They do not really belong in this discussion.

Conclusion

Through his series of posts, Casey Luskin tries to portray the state of phylogenetic analysis as being counter to the theory of evolution.  I hope that I have showed that the opposite is true.  While we don’t have and may never have a complete tree of life, the data that we obtain creating trees or bushes is points squarely to common descent.

Luskin can’t see the reality of evolution for the trees (part 2)

This post is the second part of a three-post series aimed at clearing up the misinformation written by the Discovery Institute’s Casey Luskin.  In his recent posts, Luskin tries to persuade his readers that the idea of a tree of life (TOL) and the very idea of phylogenetic trees is erroneous and not evidence of common descent.  These trees are created by looking at genetic similarities between organisms to arrange them in terms of relatedness and common ancestry.  In my series of posts, I will expose the weaknesses in the arguments put forth by Luskin.

Part 2 – Analysis and rebuttal

In this second part of my three-part series on the realities of the TOL, I will provide rebuttals to Luskin’s points.  These points were written in Luskin’s part 1 and part 2.

One of Luskin’s points in his post is to question the motives and biases of scientists.  Here, Casey Luskin claims that scientists assume there is a tree of life so their findings will support their preconceived notions:

the first assumption that goes into tree-building is the basic assumption that similarity between different organisms is the result of inheritance from a common ancestor

Of course this is a ridiculous proposition.  I guess Luskin has completely forgotten all about Charles Darwin and all the study into evolution since that time.  Prior to Darwin, common ancestry was not an idea that had any credence.  Sine the time of Darwin, more and more evidence keeps adding to Darwin’s idea basic ideas of common descent.  Basing ideas on evidence is not the same thing as assuming.

Luskin also contents that scientists engage in ad hoc reasoning:

whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified

No. What scientists do is to take this new information and form new hypothesis and alter the details of evolution. Science is always changing.  Finding unexpected things is what makes science interesting and nothing is gained in science by keeping ideas that have been proven wrong.

As far as saving “common descent from being falsified,” evolution is easily falsifiable.  Find a rabbit in the precambrian and all of evolution will fall apart.  Find genes in humans that more resemble cockroach genes than any mammal.  However, one result like this would need to be critically analyzed to go against years of research and thousands of experiments.

I find it hilarious that he uses the idea of “ad hoc reasoning” to criticize evolution. The whole idea of intelligent design (ID) is ad hoc reasoning. Any result or any piece of data can be simply said to have been designed that way. There are no predictions or testable hypothesis in ID.

In his second post, Luskin draws heavily on the false idea that scientists are abandoning the tree of life.  A lot of his all comes from the dreaded New Scientist article, “Darwin was wrong.”  I am not going to go into the details as many others have shown that the article was inaccurate to say the least here, here, here , and here.

In addition to heavily quoting the New Scientist article, Luskin “quote mines” from several different scientific papers.  One of the more egregious examples comes from a 2005 science paper by Rokas et al.  Luskin says:

Other scientists agree with the conclusions of the New Scientist article. Looking higher up the tree, a recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”

Luskin neglects to mention that the next couple sentences:

In contrast, the same genes robustly resolved phylogenetic relationships within a major clade of Fungi of approximately the same age as the Metazoa. The differences in resolution within the two kingdoms suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences.

Luskin fails to mention a few critical points in the article.  He ignores the fact that a well constructed tree based on Fungi can be made.  Also missing is the fact that the authors came up with a hypothesis to explain the previous data. Finally, Luskin fails to mention that the authors provide for a better way to look create phylogenetic trees when problems arise, rare genomic changes.

Luskin continues the quote mining throughout the post, but he never really says anything favors an intelligent design perspective.  He is just using the tried and true method of ID proponents, namely to find the currently unresolved issues in the scientific literature and omit the overwhelming number of successful findings.

Luskin can’t find a fact to support intelligent design (Part 2)

In the first part of my two part blog post addressing Casey Luskin’s assertion of the existence of facts that support intelligent design(ID), I analyzed Luskin’s overview of the framework for ID.  In that post, I concluded that the very ideas that intelligent design are grounded on are completely arbitrary and baseless.  In my second part, I was hoping to analyze real data that ID proponents bring forth when arguing for ID.  Unfortunately, I did not find anything that resembles a scientific argument from Luskin.

The purpose of Luskin’s post was as a response to students seeking to “find a fact” that supports ID.  However,  Luskin does not give any “facts” He gives generalities and provides post hoc explanations.  Phrases like “ID explains why” and “ID encourages” are in places where facts should have been.  References are included, but he never states one solid fact that came from these studies.

Facts would have been something like this:

  • The fossils of Tiktaalik show bone structures that are a hybrid of water living and land living animals. They were found in a geological place and time that corresponds to a time shortly before fossils of land animals can be found.
  • Genes between closely related species have a high degree of homology.  Less related species have less homology.

How hard would it have been to provide equivalent facts? Not very, provided there are real facts to back up intelligent design.  Since Luskin never provided any real information, I am not going to devote any more time to Luskin’s “facts.”

Luskin can’t find a fact to support intelligent design (Part 1)

Casey Luskin of The Discovery Institute wrote a series of posts where he attempts in vain to help students “find a fact” that supports intelligent design (ID).  Apparently, several students sent letters to the Discovery Institute in response to their professor’s challenge for them to find a fact that supports ID.  Luskin came up with what amounts to be crap (unsurprisingly).

In the first part of my response to Luskin, I am going to analyze his premise that “ID provides a framework for developing novel hypotheses.”  In other words, how ID is relevant in any way.  He first starts by discussing several points that he believes shows how intelligent agents act when they design something:

(1) Intelligent agents think with an “end goal” in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function (e.g. complex and specified information).

Already I see a problem with Luskin reasoning.  He believes that the more complex something is, the more it is designed.  This is demonstrably false.  Take for example a sidewalk.  Made of almost pure cement, a sidewalk is anything but complex and contains little “information.”  Yet, it is clearly designed.

(2) Intelligent agents can rapidly infuse large amounts of information into systems:

Ok, but intelligent agents can also remove large amounts of information, like in my sidewalk example.

(3) Intelligent agents ‘re-use’ functional components that work over and over in different systems (e.g., wheels for cars and airplanes).

When humans make things, they reuse the same parts over and over.  Screws, nuts, etc. are often the exact same size even in products that are made in different parts of the world.  In nature, we see as many different sized “screws” as we do organisms.  Designing something like this doesn’t make sense.

(4) Intelligent agents typically create functional things.

Fair enough (at least for the things that don’t end up in the garbage).

Luskin then goes on to say that these observations (as flawed as they are) can be used to generate hypotheses that lead to predictions. (well, Luskin said “generate hypotheses based upon testable predictions,” but I think we know what he meant).  Here are his four general predictions:

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

This is not a prediction.  This is a centuries old observation of the workings of the world.  Retrodiction does not equal prediction so this one fails.

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

Again this is not really a prediction as much as it is an observation of current paleontology.  However, I would say that you are hard pressed to find good examples of this.  If ID were true, you should expect to see hundreds of examples in the literature. I am having a real hard time thinking of even one.

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

Ok, finally something we can really address.  Yes, we already knew about convergance before the birth of Intelligent design, but lets ignore that for now.  One example that comes to mind is the convergance of flight.  Let’s compare wings and see if we see those same screws, nuts, etc. between organisms.  Do we see the same type of wing between birds and bats? obviously we don’t.  How about birds and insects, or bats and insects?  Nope, not very similar at all.  I guess we can say they all flap in their own way, but is that enough to satisfy an ID propoent? Apparantly..

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

This prediction could have been made by evolution also.  Like the old saying goes, use it or lose it.  Besides, what does he mean by “much”? This is a typical vague prediction that is easy to fulfill without really having any meaning.

So far, I am not impressed with Luskin’s answer to the professor’s challenge.  If this is all that the Discovery Institute has to offer the students, they are in for a failing grade.  In part 2, I will examine Luskin’s “facts” in detail.