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…

Lenski’s new results; Behe’s red herring

Richard Lenski is an evolutionary biologist who studies evolution by analyzing changes in bacterial populations.  Perhaps he is most famous for his long-term experiment where his group identified a population that evolved to use a nutrient (citrate) that E. coli normally can’t use.  This was a very important finding as it provided proof-of-concept that random mutations alone are sufficient to induce new functions.

In a recently published paper in Nature, Lenski takes the above experiment and analyzes the frequency of mutation throughout these populations.  The goal of this paper was not to show which specific mutations led to the ability of the bacteria to use the new nutrient source.  The goal was to look at the level of overall mutation rate during the experiment.  In the authors own words:

The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest.

Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

Of course the Discovery Institute and ID proponents are not going to keep quiet about any work coming from Lenski’s lab as their work provided such an important part of the evolutionary puzzle.  Michael Behe took up the challenge this time and wrote an entry at Evolution News and Views.  Lets address some of Behe’s points.

Behe’s first compliant is that

[Lenski’s group] identified a couple score of mutations which they say are likely beneficial ones. That is almost certainly true, but what they don’t emphasize is that many of the beneficial mutations are degradative — that is, they eliminate a gene or its protein’s function.

First, Behe is attacking the paper for something that is really irrelevant to the point of the paper.  It also doesn’t disprove the original result of that spontaneous mutations that led to a novel attribute.  It is a red herring designed to poke holes in Lenski’s work instead of directly arguing against it.  So why all the degradative mutations?  Well, these experiments were done in a lab under strict conditions (single temperature, no other organisms, defined nutrients) to eliminate other variables. Without these other stimuli, is it any wonder that most changes are degradative?

Behe also criticizes the rise in what is called a mutator line in these experiments.  A mutator strain is one in which mutations arise more frequently than in a normal strain.  Again this doesn’t really address the ideas of the new paper or in the proof-of-concept of Lenski’s original data.

Anyway, who cares that these strains became mutator strains. A mutator just increases the frequency by which mutations arise. Maybe it would have taken 3 times as long for the beneficial mutation to arise if the mutator strain hadn’t evolved. It doesn’t change the fact that the cells evolved into a state where they could use a nutrient that they couldn’t before.   Besides, it is a moot point as one of the original mutation had arose before the 20,000 generation, a time before the mutation that led to mutator strain had occurred.

Finally, Behe closes with the expected tactics that we have grown to love from ID proponents.  The first tactic as illustrated above is to wrongfully criticize valid experiments in favor of evolution.  The second tactic is then to say how this data really proves intelligent design:

Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems. So much for the power of random mutation and natural selection.

First, an ID proponent would not expect the E. coli to ever use the new nutrient.  The “power of random mutation and natural selection” led the bacteria to a whole new attribute.  Don’t forget, this experiment lasted only decades, or 1/100,000,000 the time bacteria are believed to inhabit the earth.  Finally, like I stated above, these were very unnatural conditions that would never be experienced during normal life on earth.

Discovery Institute has no goal (posts)

One thing you have to love about the Discovery Institute is their constant hypocrisy. Take for example, the recent post by Jonathan Wells, entitled Moving the goalpost.

For those of you unfamiliar with the logical fallacy of moving the goalpost, it describes a situation where one party says that if certain specific goals are met, then something is proven.  However, when those goals are met, the group changes the goals or adds qualifiers.

For clarification I will take an example from this particular post.  Many if not all Intelligent Design proponents (IDers) have said that there are no examples of speciation observed in living organisms.  Scientists have pointed to the speciation of different plants by polyploidy as an example.  Not being satisfied with this, Jonathon Wells now says that such examples do “not produce the major changes required for Darwinian evolution.”

Now that I think about it, maybe hypocritical isn’t the best word to use here.  IDers don’t engage in moving the goalposts, because they do not really have goals or specific ideas. In fact, it has been said that ID is not interested in who, what, where, or why of the intelligent designer. Without any such characteristics, it is impossible to test the idea of ID. This lack of goals is exactly what makes ID a pseudoscience.

Getting back to Wells’ current post, it is obvious that he is not paying attention to current evolutionary theory.  First, he says that the theory of evolution “has only one rule: survival of the fittest.”  This is not what the theory of evolution states. Its actually more about reproductive success than fitness.  Besides, there are other factors involved including genetic drift and geographic isolation.

He then goes on to say that evolution is “unguided.”  No, it is guided by survivability. Calling evolution unguided is like saying that a train is unguided.  Sure, there is no steering wheel to control it, but there is no doubt that the train is steered by the rails that it sits upon.  These are central tenets to evolution and it is really surprising that Wells wouldn’t know them.

Wells claims that the Scientific American’s Steve Mirsky is engaging in moving the goalposts.  He takes a recent tongue-in-cheek example by Mirsky of calling each dog breed as its own species:

face it, the only shot a male Chihuahua has with a female Mastiff involves rock climbing or spelunking equipment.  Biologists clearly continue to include the two types of dogs within the same species out of modesty. But with creationists fighting evolution education throughout the country, the time calls for bold action. Let’s reassign the trembling, bug-eyed Chihuahua to its own species. Voilà, humans have observed speciation.

Wells responds:

Voilà, indeed! If we cannot find evidence for the origin of new species, let’s just call dog breeds separate species. If Darwinism is in danger of losing, let’s just move the goalpost!

Is this post a joke? Mirsky was definitely joking. He even says so in his podcast.  Wells presenting this as a true argument put forth by evolution proponents is dishonest and deceitful.

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.

Answering a few intelligent design proponent questions

In a recent Forbes column, Michael Egnor (of Discovery Institute fame) wrote “Why I don’t believe in atheism’s creation myth.”  In the middle of the column, Egnor asks a series of questions concerning evolution and intelligent design.   These random questions are meant to cast doubt in reader’s minds about the validity of evolution without giving any real arguments. He probably doesn’t expect any answers to his questions, but here we go anyway. I have included the questions as written in here along with my own answers.

Why, when the genetic code was unraveled, didn’t scientists question Darwin’s assumption of randomness?

Contrary to Egnor’s insinuation, the unraveling of the genetic code supported randomness. The enzymes that copy DNA are not perfect and allow for random mutations to occur at a low frequency.

Why didn’t Darwinists ask the difficult questions that are posed for their theory by the astonishing complexity of intracellular molecular machinery?

What difficult questions? Scientists ask difficult questions all the time. Does he really think that trying to describe what happens inside a living cell is easy work?

Why do Darwinists claim that intelligent design is untestable, and simultaneously claim that it is wrong?

We already have a highly substantiated theory to explain the diversity of life on earth: evolution.  Therefore, intelligent design is unnecessary.  Why do we need to bring in a baseless idea that is untestable?

Why do Darwinists claim that intelligent design theory isn’t scientific, when both intelligent design and Darwinism are merely the affirmative and negative answers to the same scientific question: Is there evidence for teleology in biology?

What defines science is not what questions it asks, it is in the approach to answering the questions.  In order for something to be scientific, it needs to make predictions that can be tested and be shown to be falsifiable.  Intelligent design does neither.  Science takes into account all evidence.  Intelligent design ignores or denies scientific findings.  Science deals with the natural world.  It does not deal with the supernatural because, by definition, the supernatural does not follow the laws of physics.Intelligent design requires a supernatural being.

Why do Darwinists–scientists–seek recourse in federal courts to silence criticism of their theory in public schools?

We do not want an unscientific viewpoint based on an unscientific set of beliefs determining the direction of science in public schools.  Logic, reason, and evidence have failed to work. Extensive debate doesn’t work. What else do we have? Using the courts is all that is left in many situations.

What is it about the Darwinian understanding of biological origins that is so fragile that it will not withstand scrutiny by schoolchildren?

Scientists are not afraid that school children will be able to disprove evolutionary theory.  We are afraid of having a scientifically illiterate populous.  It is very easy to indoctrinate children.  Their minds have not matured and they do not have the knowledge necessary to fully evaluate a theory such as evolution.

These same questions, or slight variations, seem to arise quite often in Intelligent design proponent’s writings.  They have been answered many times before, but they still keep being asked.  Of course intelligent design proponents are not really interested in the answers, they are more interested in casting doubt on the evolutionary point of view.

Does Ignoring the Designer Make Intelligent Design Real Science?

In a recent episode of the podcast, ID the Future, Casey Luskin argues that Intelligent Design (ID) proponents do not let the question of the identity of the designer enter the discussion.  He believes this avoidance of such a central aspect of the idea of ID allows it to be science.  He reasons that if they do not ever talk about a supernatural designer, then Intelligent Design does not rely on the supernatural.

The first problem with this type of attitude is that ignoring the cause of an effect (the designer is the cause and each living being is the effect) makes it not science.  Imagine if a new disease was discovered and the people studying it decided that they were not going to study the cause of the disease.  All they want to study is its characteristics because the disease could have metaphysical causes.  This group would be harshly criticized and could lose their funding.  Drawing an arbitrary line to separate what can and can’t be included is unscientific.

Luskin is using this attitude as a get-out-of-jail-free card.  He wants to take away the completely valid criticisms that the idea is based on the supernatural.  However, the identity and properties of the designer are paramount to the theory.  Similarly, the mechanisms behind evolution are paramount to the Theory of Evolution.  Without knowing the who, what, when, where, why, and how of the designer, the whole idea of ID is worthless.

Not only is Luskin using this as a get-out-of-jail-free card, but he is having his cake and eating it too (sorry for all the sayings).  He wants all the benefits from having an all-powerful, all-knowing, yet sloppy designer, but doesn’t want to have to deal with the problems  and criticisms associated with the acknowledging the characteristics of the designer.  This method of saying that the designer is off-limits does just that.

Luskin argues that intelligent design is squarely in the realm of science because it deals with the empirical. Yet, the tenets of intelligent design are all based on nonquantifiable characteristics.  Irreducible complexity is not quantifiable or even a cohesive idea.  The same could be said for “apparent design” or Dembski’s use of information theory.  So even if you do ignore the designer, ID is not real science.

The reasons listed above show us that leaving out the identity of the designer is a political move not a scientific one.  It is used to pretend that ID is not religiously motivated so it won’t be subject to the establishment clause of the U.S. constitution.  This goal of the Discovery Institute and other ID proponents is becoming obvious with the constant promoting of “academic freedom” bills and the push to create pro-intelligent design student groups.

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Slim pickings for an Intelligent Designer

If we are to believe the proponents of Intelligent Design, the “designer” could be a number of different beings.  In this post, I am going to go through a thought experiment to determine the characteristics that would be necessary for a designer.  At the end, I will run through a list of possible candidates for the designer.  Please feel free to mention anything that I have missed.

Characteristics of a designer:

Inconceivably powerful – In order for the designer to have accomplished all that is given credit to it, the designer would need the ability to repeatedly create life out of thin air.  This designer would have to create each individual species that has ever lived on earth.  Since their appears to be more than 1.5 million species alive today, the amount of planning, raw materials, energy, and time required would be astronomical.

Sloppy – There are so many design flaws in living organisms that one would have to assume that the designer would have to be not only inconceivably powerful, but also very sloppy.  An efficient designer wouldn’t allow things like a rabbit needing to eat its own poop in order to digest it.  They would also not allow for things like birth defects, prevalence of poor eyesight, or cancer.

Cunning – The designer would have to be extremely secretive about its involvement in the life of the earth.  There are no blueprints lying around for us to examine.  There is no landing strips for the designer.  There are no artifacts of which the designer used to engineer the earth’s organisms.

Practical Joker – How else would you describe something that gives the impression that life arose through evolution?  Somewhere, the designer must think it is really funny to have all organisms to be able to be grouped into a phylogenetic tree that matches the underlying genetic code similarities.

Possible designers:

God – Of course the most obvious designer would be God itself.  Since God by definition is all knowing and all powerful, there is no use in discussing its attributes.  However, I would like to point out that there is no discussion of intelligent design in the bible.  In fact, the bible seems to indicate that all of life was made at once without the intervening organisms that are proposed by intelligent design and seen in the fossil record.

Aliens – In order for a species of aliens to be the designer, they would have to be thousands or millions of years more technologically advanced than humans.  As stated above, they would have to have inconceivable power.  Then where are these aliens today?  Why haven’t we been able to detect any sort of evidence of their existence?  Its not like we haven’t been looking or listening.

It is not clear what motivation such a species would have to be so involved with life on earth.  I guess it could be for their own personal enjoyment, but that seems like a boring way to have fun.  One could also suppose that they wanted to create some sort of companionship to an otherwise cold universe.

Future Humans – Perhaps the designer is actually humans from the future that decided that they would need to go back in time in order to ensure that humans would exist.  In order to accomplish this task, the future humans would use the paleogeographic record as a blueprint.  They would have to painstakingly recreate every known and to be discovered organism that existed on the planet.  Of course this all depends on the ability for humans to be able to repeatedly time travel, which seems to be prohibited by the laws of physics.

Secret society of underground creatures – Yes, I know this is ridiculous, but none of the other ideas for designers seems plausible either.

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