When its good to keep quiet

This post covers the May 27 and 28, 2008 posts entitled: “MSNBC’s Alan Boyle and Sean B. Carroll Argue Scientists Should Keep “Quiet” about Support for Intelligent Design”.  This post is broken down into two parts with the first Luskin’s answer to Carroll’s opinion and the second is Luskin attacking Carroll’s facts.  To be honest, I completely agree with Sean B. Carroll.  We should be teaching our children the best theories of the day, not unsupported ones.  Educators should keep quiet about Intelligent Design and any other unsupported idea. 

Luskin writes (emphasis mine):

The implication is clear: Boyle and Carroll think that there should be no academic freedom for scientists or educators to speak in favor of intelligent design. In Boyle and Carroll’s world, if you have real doubts about evolution, then like Newton, you should just keep “quiet.”

I have to hand it to Luskin here. He shows us what the “academic freedom” bills really are: Intelligent Design bills.  The rest is Luskin rehashing how all ideas should be given equal credence.

In the second part of the post, Luskin tries to poke holes in evolutionary theory by pointing to the unresolved issue of a complete tree of life (TOL). As I have written before, ID proponents love to point to unresolved issues in science (evolution, geology, etc) as somehow giving validity to ID. In this case, Luskin is using the imperfect science of creating phylogenetic trees. These may be imperfect due to mathmatical constraints, lateral gene transfer, high frequency of mutation, etc, but they generally produce a tree that is in agreement with evolutionary theory.  However, problems do arise when trying to work out the details.

The inability to construct robust phylogenetic trees is not due to evolutionists being wrong. If common descent was wrong, then you would never be able to produce trees that match up so well with evolutionary relationships. Luskin is taking small problems in evolutionary biology as reasons to discount it, while ignoring the complete lack of data supporting ID.

Luskin then writes about the relationships between genes of different species: 

“Since their DNA might be similar due to functional requirements and not inheritance from a common ancestor…”

This statement goes a long way to illustrate the lack of understanding that Luskin has in regard to conserved sequences. Genes are quite complex and are made of different regions. Some of these regions are the parts that are critical for the genes function, while other parts are unimportant. The less important parts are still similar between species, but since they are not important for function, they are definitely not similar due to simply functional requirements.

I want to finish by showing a quote of Luskins that illustrates a new technique used by IDers:

If the loss of function by turning off genes, and the usage of the same genes to build organs in vastly diverse organisms—a fact cited by design-proponents as supporting common design—are the best facts [Carroll] can muster against design, then it would appear that ID has very little to fear from the discoveries of evo-devo.

So IDers are now going to take evidence that really supports evolution and say that it supports intelligent design? Although intellectually dishonest, it is a brilliant move to persuade people to a side that has no evidence of its own.

    

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Reason-Free and Proud of it

On May 20, 2008 post entitled “Washington Post Editorial Page on Evolution: Fact-Free and Proud of It,” John West writes about the coverage of various academic freedom bills by a Washington Post writer named Jo-Ann Armao. The editorial is short and I encourage you to read it. Rather than rehash all the points made in the editorial, I will simply ask:

Is there really a need for such a bill? Besides the evolution deniers, who is this really going to help? Scientists should be the ones to challenge scientific theories, not teachers.

Back to the Discovery Institute Blog.  West’s first point is to bring up that there are scientists who are anti-evolution:

The Post also absurdly claims that offering criticisms of Darwinism is tantamount to “question[ing] the existence of gravity or… suggest[ing] that two plus two equals anything but four.” Tell that to the more than 700 Ph.D. scientists at institutions such as Princeton, MIT, Ohio State, and the University of Georgia who have expressed their skepticism of the central tenet of Neo-Darwinism.

This allows me to bring up the funny, yet highly effective, ‘project Steve.’ The idea is to compile a list of scientists who both accept evolution and are named Steve. Steve isn’t the most rare name, but it does represent only a small percentage of scientists. The funny thing is that at current count there are 886 Steves on the list. Compare that to the 700 scientists that John West points to, and the absurdity of pointing to these scientists becomes apparent.

Dismissing evolution isn’t exactly like dismissing the existence of gravity, but it isn’t far from the truth. In order to not accept evolution, you have to ignore the vast abundance of evidence pointing towards evolution. One would also have to ignore the complete lack of real evidence for intelligent design. Finally, you would have to disregard the fact that more and more evidence for evolution is found every day, while none is found for ID. On second thought, it is exactly like questioning the existence of gravity.

West goes on to use a technique often used by IDers:

I gave Ms. Armao an entire list of scientific controversies involving key aspects of biological and chemical evolution, including the origin of the first life, the role of mutations, the limits of natural selection, and the origination of animal body plans during the Cambrian Explosion some 500 million years ago. Such controversies are already discussed in the mainstream scientific literature—but teachers are being forbidden in many places from telling students about them.

The idea here is to point to real scientific controversies and then imply that the controversies somehow show weaknesses in evolution. These are simply details that need to be worked out and are part of the scientific process to understand any theory, including evolution. Lets go back to the theory of gravity for a second. There are controversies in this theory, including whether or not there is a particle that is responsible for gravity (see: graviton). By John West’s logic, we should allow for criticism of the theory of gravity to be taught in school.

Upside down on wombat pouches

In a May 20, 2008 post entitled Billions of Missing Links: Wombat Pouches, Geoffrey Simmons writes:

A design must be considered improbable if it is highly functional and durable yet too complex to have come about spontaneously or by intermediate steps.

This is a simple rewording of irreducible complexity, an idea that is being destroyed with increasing frequency in the fields of paleontology and in molecular biology. IDers proclaim that the species we have today are too complex to have come about by intermediate steps. Who are they to decide what is too complex?  It seems like an arbitrary call to me and set up for future arguments using the moving goalposts fallacy. Besides, systems that once appeared too complex to work without individual parts are now able to be simplified. For example, blood clotting, functional eyes, and the complement system.

The “missing link” brought up in this post is the one of the upside down pouch in wombats:

The wombat has an upside-down pouch. Scientists presume, and it makes sense, that position prevents dirt from entering the pouch when the wombat is digging in the ground. Could there have been transitional species with pouches situated sideways, or did the first wombats have to scoop dirt out of their pouches every day?

The author is using a technique to make evolution sound stupid by bringing up a wombat that would have a sideways pouch or that wombats would have to scoop dirt.  Of course the change from right-side-up to upside-down could have simply been in one step.  When a wombat came along with a mutation that led to an upside-down patch, it would have a strong advantage in being able to raise healthy young.

This characterization of the wombat is laughable, yet convenient for IDers. I suspect the example was brought up because it is going to be hard to find intermediate fossils of wombat pouch evolution due to the pouch being made of soft tissue. Since soft tissues don’t fossilize, it will be hard to trace its evolution.  Unfortunately, there have not been any useful fossils found of wombat ancestors.  But then again, present day-like wombats have not been found either, as would have been predicted by ID.

Pseudogenes and pseuodscience

In the May 9, 2008 post entitled “Another Intelligent Design Prediction Fulfilled: Function for a Pseudogene”, Casey Luskin writes that new findings relating to “junk” DNA not really being junk is evidence against evolution. He argues that a designer makes everything for a purpose, including junk DNA. So finding functions for this “junk” DNA somehow gives credence to intelligent design and evidence against evolution.

It doesn’t.  Evolutionary theory would predict that very little DNA would be “junk.” Extra DNA for no reason goes against one of the main tenets of evolution: If you don’t use it, you lose it.  Also, Luskin fails to mention that there have been predictions of the functionality of “junk” DNA by biologists. These include spacing and regulatory RNAs, among others that do not contradict evolution.  His argument is a strawman and illustrates how IDers either do not understand or are willfully ignorant of evolutionary theory.

The worst part of this post his how blatantly Luskin misquotes the article.  Here is what he wrote:

Like other types of “junk” DNA, Darwinists have almost universally considered pseudogenes to be evolutionary garbage–once-functional genes that were rendered functionless by random mutations. But a recent article in Nature concludes the following:

“Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway.”

The full sentence from the abstract of the article changes its meaning and shows how the authors felt this new data actually helped in the understanding of evolution:

Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals.

Casey ignores this part of the text in typical the IDer way.  He is arguing with the strawman argument that evolutionary theory says that “junk” DNA would have not function, but does not bring up the point that the authors actually make in their paper. Which is that this new data supports evolution.

Finally, little progress in the fight for reality.  Casey admits that loss-of-function (like cavefish losing eyesight) can be explained by natural causes, but “ID is far more interested in explaining GAIN of function?”

Great, we are halfway there, but it is hard to imagine loss without gain (or vice versa). When animals such as Tiktaliik started to lose fins and gain limbs, is that a gain or a loss?

Academic Freedom does not mean freedom from reality

From the May 16, 2008 entry entitled “Evolution Academic Freedom Bill Submitted in South Carolina is Sixth this Year“.

Casey Luskin reminds us that there are currently six proposed “academic freedom” bills in the United States.  As you are probably aware, the new technique used by creationists/IDers is to attack evolutionary theory by using the guise of “academic freedom.”  It is a decent technique because who doesn’t like freedom?  A link to the new bill can be found here.

One of the provisions really caught my eye:

D)Public school educators must be supported in finding effective ways to present controversial science curriculum and must be permitted to help students understand, analyze, critique, and review the scientific strengths and weaknesses of theories of biological and chemical evolution in an objective manner.

The only reason that evolution is “controversial” is because of groups like the Discovery Institute trying to push their religion into science.  Within the scientific community (the people that study science daily) there is no controversy.  What is worse is that the educators must be “supported” in finding ways to undermine evolutionary theory.  Does supported = forced?

Casey ends with quote from Senator Fair:

“The very nature of science is to ask questions and to go where the evidence leads.” If the evidence is on the side of evolution, then the NCSE has nothing to fear from this bill.

The evidence is on the side of evolution.  However, young minds are easily persuaded by a teacher that doesn’t fully understand the preponderance evidence for evolution or one who is going to bring their denialism into the classroom.  The fear of the bill comes from the ability of teachers to indoctrinate students into nonscientific thinking and lead to a noncritical view of the world.

 

Michael Egnor is Missing Links

Today, Dr. Michael Egnor illustrated his spite for Dr. Steven Novella.  Dr. Novella is an academic neurologist that runs the Neurologica blog along with the Skeptic’s Guide podcast and the New England Skeptical Society.  I have followed Steve, through the podcast and blog, for nearly the last three years.  He is highly logical, extremely bright, and intellectually honest when debating others.  Egnor does not outright display his spite, but instead insinuates that Steve is somehow hiding from Egnor by deleting posts from the Neurologica blog.  Here is how Egnor finishes the post:

I emailed Dr. Novella, and asked him:

Steven,I’ve noticed a few missing posts on your blog. The posts were related to our on-going debate. Why are they no longer available? …

Mike

So far, no answer. His blog posts are gone. Like they never even happened. So I publicly ask Dr.Novella this question: what happened to your blog posts? A post on your blog NeuroLogica to answer this question would be helpful.

Now I did a little checking this afternoon.  There are a lot of posts that are no longer available on his blog, not just the ones pertaining to Egnor.  Why not mention that others?  Why publically ask Steve and not wait to see if it is some technical glitch?  Because it is an attack on the character of one of Egnor’s enemies.

Introduction to Evolution News and Views

This blog is essentially a response to the Discovery Institute’s Evolution News and Views Blog.  Here is their description:

The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution. Click here to read more.

The blog has at least 15 contributors, each with their own background.  Several of these have advanced degrees, including PhDs and at least one MD. Now why do I think that I can create a blog to counteract all these writers?  Simple, I have reality on my side.  I will (when time permits) take each entry and simply and succinctly show its fallacies, ignorance, and flagrant personal attacks.The purpose here is not to insult the authors at the Discovery Institute, but to expose their biases (wether conscious or not) and to defend science.