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Showing posts sorted by date for query "Evolution News and Views". Sort by relevance Show all posts

Wednesday, May 23, 2012

Flunk the IDiots

Casey Luskin recently offered advice on the The Top Three Flaws in Darwinian Evolution. [see The Top Three Flaws In Evolutionary Theory ] At the end of that post he referred readers to The College Student's Back-to-School Guide to Intelligent Design. This is a remarkable document. It's designed to teach students how to debate their professors and/or disguise their true beliefs in order to pass a class.

Why do the IDiots need such advice? It's because Intelligent Design Creationism is under attack from dogmatic professors who can't think critically and who don't have open minds. The opening section lists examples, such as ...
A professor of biochemistry and leading biochemistry textbook author at the University of Toronto stated that a major public research university “should never have admitted” students who support ID, and should “just flunk the lot of them and make room for smart students.”

Monday, May 21, 2012

The Top Three Flaws In Evolutionary Theory

Casey Luskin is one of the leading IDiots of the Discovery Institute. He posts frequently on Evolution News & Views. Here's one of his recent posts where he lets us in one the The Top Three Flaws in Evolutionary Theory.

If you've ever wondered why I call them IDiots, this will help you understand.
Unfortunately most public schools do NOT teach about the flaws in evolutionary theory. Instead, they censor this information, hiding from students all of the science that challenges Darwinian evolution. But in a perfect world, if the evidence against Darwinian theory were taught, these would be my top three choices:
  1. Tell students that the fossil record often lacks transitional forms and that there are "explosions" of new life forms, a pattern of radiations that challenges Darwinian evolutionary theory.
  2. Tell students that many scientists have challenged the ability of random mutation and natural selection to produce complex biological features.
  3. Tell students that many lines of evidence for Darwinian evolution and common descent are weak:
    a. Vertebrate embryos start out developing very differently, in contrast with the drawings of embryos often found in textbooks which mostly appear similar.
    b. DNA evidence paints conflicting pictures of the "tree of life". There is no such single "tree."
    c. Evidence of small-scale changes, such as the modest changes in the size of finch-beaks or slight changes in the color frequencies in the wings of "peppered moths", shows microevolution, NOT macroevolution.


Thursday, May 17, 2012

David Klinghoffer Will Bust Your Mark VIII Irony Meter

Back in the days of newsgroups (last century) the howlers in talk.origins developed a running joke about irony meters.

The lastest version (Mark VIII) is pretty sturdy but from time to time the IDiots come up with a real challenge. You might want to turn off your irony meter before reading any further and especially before following the link.

Here's David Klinghoffer's latest posting on the "prestigious" IDiot site, Evolution News & Views [What Is It about Professors and Reading Comprehension?].

How is it that many professors in the humanities and the sciences seem unable to read an opinion they don't like and then accurately relate the argument -- say it back to their interlocutor -- before trying to rebut it? This is a basic skill in communication that comes in handy in many areas of life, including personal relationships


Sunday, February 26, 2012

A "Simple" Argument for Intelligent Design Creationism

 
Once again, it's time to remind people of a famous quotation by Isaac Asimov—a biochemist— from his 1981 essay, The “Threat” of Creationism [see Bill Dembski, Isaac Asimov, and The Second Law of Thermodynamics].
Creationists have learned enough scientific terminology to use it in their attempts to disprove evolution. They do this in numerous ways, but the most common example, at least in the mail I receive is the repeated assertion that the second law of thermodynamics demonstrates the evolutionary process to be impossible.

In kindergarten terms, the second law of thermodynamics says that all spontaneous change is in the direction of increasing disorder—that is, in a "downhill" direction. There can be no spontaneous buildup of the complex from the simple, therefore, because that would be moving "uphill." According to the creationists argument, since, by the evolutionary process, complex forms of life evolve from simple forms, that process defies the second law, so creationism must be true.

Such an argument implies that this clearly visible fallacy is somehow invisible to scientists, who must therefore be flying in the face of the second law through sheer perversity. Scientists, however, do know about the second law and they are not blind. It's just that an argument based on kindergarten terms is suitable only for kindergartens. [my emphasis - LAM]
Now, let's look at this video from: Are You Looking for the Simplest and Clearest Argument for Intelligent Design?]. Keep in mind that one definition of a "simple" argument is one that is suitable for kindergarten students (and IDiots).



This video was posted on the leading IDiot blog Evolution News & Views. It tells us a lot about the quality of their science and their commitment to truth.


Thursday, January 19, 2012

James Shapiro Publishes on Evolution News & Views

James A. Shapiro, author of Evolution: a View from the 21st Century has been criticized for being an Intelligent Design Creationist, or at least a sympathizer. He denies it but his denials sound very much like someone who protests too much.

Shapiro has now been allowed to post an article on the main IDiot blog, Evolution News & Views [A Response to Ann Gauger's and Douglas Axe's Comments. I don't agree with his response but that's not the point. Do you know any respectable evolution supporter who would post on a creationist blog?

Can you imagine his University of Chicago Colleague, Jerry Coyne, posting an article on the flagship blog of the Discovery Institute?


Wednesday, January 18, 2012

False Dichotomy

 
A false dichotomy is when you are presented with two choices and told that if one is wrong then the other must be correct but there are actually other choices.

Intelligent Design Creationists are very fond of this argument. They tell you that there are only two choices when it comes to explaining biology: either Darwinism or Intelligent Design Creationism. If a given feature of the biological world cannot possibly be explained by Darwinism, then God must exist and he must have designed the feature.

Here's Douglas Axe illustrating the false dichotomy on Evolution News & views [Let Science Be the Arbiter: A Reply to James Shapiro].
As an ID proponent, I've put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

There is no crutch here. The aspects of protein structure that appear to preclude a naturalistic origin have been described in detail. If Shapiro or anyone else were to show in detail how these are overcome by a naturalistic mechanism, then my argument would fall and I would let it fall. But the reverse needs to be true as well. Scientists who personally side with naturalism have to be willing to let naturalism fall, as otherwise they would be guilty of using a crutch to prop it up.
This is actually an attempt to get around the charge of false dichotomy by extrapolating from a rejection of Darwinian explanations to any naturalistic explanation. If Axe is truly able to demonstrate that his "data" cannot possibly be explained by any naturalistic means then it follows logically that the only other type of explanation has to be supernatural. But what Axe is really arguing against is a Darwinian explanation and it's only his lack of imagination and arrogance that allows him to claim that no other naturalistic explanation is possible.

As we have seen time after time, the Intelligent Design Creationists do not have a scientific theory or any kind of scientific explanation for biological phenomena. All they have is criticisms of science—criticisms that are usually based on a lack of knowledge. When will we see an ID explanation of protein folding and function?


Monday, January 16, 2012

The Mind of James Shapiro

I recently read Evolution: a View from the 21st Century by James Shapiro. It was a very annoying and frustrating experience. I do not recommend this book. I've already posted a rebuttal of his silly claim that the Central Dogma of Molecular Biology needs to be revised [Revisiting the Central Dogma in the 21st Century ]

The really frustrating part was trying to figure out Shapiro's agenda. He clearly has one. Is it just that he's against "conventional evolutionary theory"—whatever that is? Or, is he laying the groundwork for introducing God and intelligent design?

Shapiro denies that he's a supporter of intelligent design yet he published several papers with Richard Sternberg, one of the darlings of Intelligent Design Creationism. Furthermore, he (Shapiro) uses many of the same anti-evolution arguments used by Intelligent Design Creationists.

This prompted Bill Dembski to accuse James Shapiro of "dancing in the DMZ between Darwin and design" [Is James Shapiro a Design Theorist?].
For proponents of intelligent design, James Shapiro's constant dancing in the DMZ between Darwin and design can be frustrating. On the one hand, Shapiro is as dismissive of Darwinism as any ID proponent. On the other, he constantly gives public notice that he is not on the side of ID. And yet, methinks he protests too much.
This got a response from Shapiro that has now been posted on Evolution News & Views ["Is James Shapiro a Design Theorist?": James Shapiro Replies]. Here's what Shapiro says ...

What is wrong with "dancing in the DMZ" between intelligent design (as articulated by Michael Behe and others) and neo-Darwinism? Are these two positions the only alternatives? I doubt it. That is why my 1997 article in Boston Review on evolution debates was called "A Third Way." What Dembski calls the "DMZ" (i.e. a zone free of futile conflict) is the place where the real evolutionary science is taking place. I am proud to be there, and I see that an increasing number of people are joining me when they realize that natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis provide solutions to problems recognized to be intractable under the limitations of conventional evolutionary thinking.
Clear as mud. There's one thing I know for sure: horizontal DNA transfer etc. are perfectly compatible with today's evolutionary thinking. If Shapiro is wrong about this—and he is— then maybe he's also misleading us about his belief in intelligent design creationism.

Wednesday, January 11, 2012

Weep for the Poor Persecuted IDiots

 
The Intelligent Design Creationists at Evolution News & Views and Uncommon Descent have been pushing the idea that acceptance of evolution is associated with moral decay and the rise of Adolph Hitler. Recently, an IDiot going by the pseudonym of "kairosfocus" posted a similar attack on his blog: Visually exposing the Anti-Christ spirit of Nazism (and correcting the New Atheist "Hitler was a Christian" smear often used in retort to exposing* the Social Darwinist history of ideas roots of Hitler's thought.

The goal, obviously, is to link the scientific fact of evolution to the evils of social Darwinism and eugenics.

Somebody posted as comment on that blog (or a related blog) saying ...
xxx, the religious wacko who owns and runs this site, blames all the world’s ills, including Hitler and the nazis, on Darwin, atheists, and material evolutionists.

To see the truth about Hitler and the nazis, see these XXXXXXX:

XXXXXX is a LYING, arrogant, bloviating, sanctimonious, ignorant, uneducated, abusive, delusional god zombie.

See this site for a lot more about XXXXX:
The comment has been removed.

Now "kairosfocus" has complained on Uncommon Descent that such "vandalism" is outrageous and misguided [FOR RECORD: What we are dealing with . . . an example of web stalking and vandalism].
Now, this vandalism of a site wholly unrelated to the matters debated at UD (and tied onwards to a hate site that exploits Google’s freedom of comment policies), was evidently in response to my having posted here at UD, matters linked to the well-known history of ideas roots of Hitler’s thought. I therefore suggest that onlookers examine the Weikart lecture and a discussion of a key clip from Mein Kampf that demonstrated the Darwinist-Haeckelian frame of thought, that beyond reasonable doubt strongly shaped Hitler’s thinking, speech and behaviour. (Those needing documentation on Hitler’s actual attitude to and intentions for the Christian Churches, can look at the recently released Nuremberg investigatory documents here. If after seeing these documents and the like, someone still insists on trying to claim Hitler was a Christian etc etc, s/he is delusional and/or willfully deceitful.)
Furthermore, the behavior of this "vandal" is exactly what "kairosfocus" expects.
As they say, a tree is known by its fruits, and draws sustenance from its roots . . .

(In addition, a note on “blaming the world’s ills.” The likes of this hate-driven commenter will not appreciate or accept that a Bible-believing Christian will hold that much of what ails our world traces to our common challenge of being finite, fallible, morally fallen and too often ill-willed. Hence, our common need for recognition of our moral plight, repentance, forgiveness and moral-spiritual transformation through the gospel. Slander-laced strawmen and scapegoats are ever so much more easy to set up and ignite through irresponsible rhetoric that then clouds, polarises and poisons the atmosphere.)

That refusal to be responsible over a moral hazard closely tied to the Darwinist, evolutionary materialist frame of thought, and that refusal to acknowledge well-established historical facts that are inconvenient to the new atheist agenda are tellingly informative.

The pattern of obsessive, self-justifying, nihilistic hate, stalking, slander, Internet vandalism and abuse is even more informative about an unfortunately significant subset of the New Atheist movement and the danger its patent extremism poses. (After this sort of web vandalism, and worse, can any reasonable person doubt why moderation is necessary to maintain a reasonable tone at UD and elsewhere?)

Ironically, the very conscience benumbed self-justifying by smearing scapegoats that this sort of behaviour demonstrates on the small scale, is what — when such attitudes attained state power — led to the utter breakdown of morality on the grand scale that over 100 million ghosts from the past century tell us never to forget.

Can any reasonable person doubt that had a commentator like the above the power to do as he wished and get away with it, he would do me and my family further harm?

It is time for the New Atheist advocates of evolutionary materialism to take a serious look at what they have been enabling by their intemperate writings and attitudes.
Every atheist blogger gets far worse comments from Christians on a regular basis. Most of us get harassing emails every single day and the authors usually identify themselves as devout Christians doing God's work. These same Christians don't hesitate to send threatening messages to our colleagues and family members in an effort to silence us. Some of the Christian kooks are so dangerous that they have been arrested by police and are currently under forcible confinement in a mental health institution.

Don't weep for the IDiots. They need to examine their own beliefs since it's the creationists who are the biggest threat on these blogs. There must be something wrong with Christianity if that's the kind of activity it promotes. It is time for the Christian opponents of science to take a serious look at what they have been enabling by their intemperate writings and attitudes.


Thursday, December 22, 2011

Do the IDiots Understand Biochemistry and Molecular Biology?

 
We've been discussing whether Intelligent Design Creationists understand enough about biochemistry, molecular biology, and evolution to warrant their criticisms of these fields. The answer is clearly "no" as they demonstrate time and time again.

This time it's an anonymous posting on the premier IDC website, Evolution News & Views [Long Non-coding RNA Punches Another Hole in "Junk Genome" Myth]. The anonymous poster links to a recent paper in Genes & Development that shows a function for a particular long non-coding (lnc) RNA. The paper implies that many of these lncRNAs (up to 400) are expressed in mouse erythroid cells.

Regulatory RNA have been known and studied for at least four decades and various lncRNAs have been characterized over the past twenty years. The IDiot at Evolution News & Views seems to think that this is a new discovery proving that there's no junk in our genome. The facts are quite different.

As I pointed out in my review of The Myth of Junk DNA, the amount of the genome devoted to producing lncRNAs is about 0.1% [Junk & Jonathan: Part 6—Chapter 3]. So, not only have we known about regulatory RNAs for many years, we also know that their genes don't account for very much of the genome, I figure it can't be more than 2% even when you include all of the most optimistic estimates of regulatory RNAs [see What's in Your Genome?].

But the ignorance of the IDiots is much more profound than just being incapable of calculating percentages. The latest posting reveals the depth of their ignorance.
These findings have two important implications. First, non-coding regions of the genome were assumed to be leftover evolutionary relics that no longer play a functional role. The assumption was not due to extensive studies of non-coding regions of the genome, but rather to a commitment to what is known as the central dogma of molecular biology: DNA is transcribed into RNA and RNA is translated into amino acids to make proteins. This was considered the primary purpose of DNA. The non-coding regions were assumed to have no function, and were dismissed as the natural consequence of genetic "junk" accumulating over time. This paper is one among an accumulating corpus of papers discussing new and interesting functions of the non-coding regions of the genome. (See The Myth of Junk DNA by Jonathan Wells for a history of "junk" DNA and additional references describing the function of so-called "junk" DNA. See here for a discussion on the regulatory role of introns.)
There was never a time in the past fifty years when knowledgeable biochemists and molecular biologists thought that all non-coding DNA was nonfunctional junk. This was never an assumption of the Central Dogma of Molecular Biology which states that "... once (sequential) information has passed into protein it cannot get out again" [Basic Concepts: The Central Dogma of Molecular Biology]. There are many scientists who have misconceptions about the Central Dogma [The Central Dogma Strawman] but the IDiots go one step farther by misunderstanding the misconception!

We've known about functions in non-coding DNA since the early 1960s as anyone who has ever glanced at a textbook would know. It's hard to tell whether the IDiots are just butt-ignorant of basic science or whether they are lying. This is an especially tricky problem when the silly strawman argument is popularized by Jonathan Wells because he's supposed to know the science [Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

We know that most of our genome is junk because we know a great deal about genomes, genes, biochemistry, molecular biology, and evolution. We know which parts are likely to be functional and which parts are likely to be broken genes and other kinds of junk. We know this because we understand the subject, not because we are covering up our ignorance.

The IDiots are ignorant of the science and they assume that everyone else is as well. That's a very bad assumption.


Wednesday, December 07, 2011

Fishing for Creationists

Fishing for creationists is not a sport. All you need to do is dangle a bit of bait and dozens of creationists will fight for the right to impale themselves on the hook. The latest victim is Jonathan McLatchie who responded to criticism of Phillip Johnson [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance]. I'm sure the other bloggers on Evolution News & Views don't see him as a fishy victim, they probably think of him as the designated hitter. (You could use "sacrificial lamb" if you want a Biblical metaphor.)

Jonathan M, as he prefers to be known, is studying in Scotland for a Master's degree in evolutionary biology. He's upset with Jeffrey Shallit for criticizing Phillip Johnson's 1993 video (see This Video Should Be Shown to all Biology Students). He's also upset with my critiques of the same video (see Phillip Johnson, One of the Very Best Intelligent Design Creationists).

Monday, December 05, 2011

Earth to Rick: The Debate Is Over and You Lost!

 
Rick Santorum is a former United States Senator. He is running for the Republican nomination for President of the United States. In this video he is explaining why creationism should be taught in schools.

The Discover Institute blog, Evolution News & Views, posted this video [Santorum on Evolution: "It's Worth a Debate." Yeah, It is]. It obvious that the IDiots consider Santorum to be a credible supporter of Intelligent Design Creationism.

I suppose that's understandable given the quality of their other supportersl




Tuesday, November 29, 2011

IDiots and Incivility

 
This is just a heads-up to let you know that Casey Luskin is about to post a series of examples of bad behavior by ID critics [The Uncivil Style of Intelligent Design Critics]. Apparently it's going to be a long series ....
I'm going to let ENV readers in on a little secret: When many of us in the intelligent design (ID) movement read the arguments coming from our critics, we're surprised at their low quality and style. We don't rejoice at this -- we'd much rather see a robust, civil, and fruitful scientific debate over the relevant questions. But the incivility, basic inaccuracy, and unserious tone characteristic of so many criticisms of ID all make you wonder: If the critics had stronger rebuttals to offer, wouldn't we be hearing them?

...

There are so many examples of incivility among ID-critics that it's hard to know where to start. And I'm not just talking about the usual Internet suspects, like PZ Myers, Jerry Coyne, or Larry Moran.
On a completely unrelated topic that has nothing to do with Darwinist incivility ...

While you're checking out Evolution News & Views you might want to read a fascinating article by Richard Weikart defending his books From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany and Hitler's Ethic: The Nazi Pursuit of Evolutionary Progress [Robert J. Richards and the Historical Record]. It even has a photo to illustrate the point about Darwin (see below).


This is a follow-up to a very civil article posted last month: Can Darwinists Condemn Hitler and Remain Consistent with Their Darwinism?.
I threw down the gauntlet to many of my Darwinian opponents by telling her that if Darwinism is indeed a purposeless, non-teleological process, as many evolutionists and biology textbooks proclaim, and if morality is the product of these mindless evolutionary processes, as Darwin and many other prominent Darwinists maintain, then "I don't think [they] have any grounds to criticize Hitler."

According to Flam, these are "fighting words." However, I have spoken with intelligent Darwinists who admit point-blank that they do not have any grounds to condemn Hitler, so I am not just making this up. Many evolutionists believe that since evolution explains the origin of morality -- as Darwin himself argued -- then there is no objective morality. The famous evolutionary biologist and founder of sociobiology, E. O. Wilson, and the prominent philosopher of science Michael Ruse co-authored an article on evolutionary ethics in which they asserted, "Ethics as we understand it is an illusion fobbed off on us by our genes to get us to co-operate."
Anyway, let's not forget the important point and that's Casey Luskin's upcoming series on the incivility of ID critics.


David Berlinksi Prays for Me!!!!

 
Over at Evolution News & Views, Casey Luskin is ranting again about not getting no respect [The Uncivil Style of Intelligent Design Critics]. While checking out recent postings on that site to see whether the evil Darwinists were being treated respectfully, I came across a post by David Berlinski on Phillip Johnson. Imagine my surprise when I read this ....
At the Discovery Institute we often offer an inter-faith Prayer of Thanksgiving to the Almighty for the likes of P.Z. Myers, Larry Moran, Barbara Forrest, Rob Pennock and Jeffrey Shallit.
Thank-you to all the inmates at the institute. I really appreciate your thoughts and prayers.

Next time, could you ask him to send money?


Sunday, November 13, 2011

Jonathan Wells Sends His Regrets

Paulmc visited Uncommon Descent in order to defend junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. Now Wells has responded to several of paulmc's points [Jonathan Wells on Darwinism, Science, and Junk DNA].

We'll get to those issues in another post but right now I want to take note of something Wells said at the end of his article.
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
I can understand why Wells might decline to post a comment on Sandwalk. Many of us know what it's like to try and argue with the readers of the intelligent design blogs. Wells would meet the same reception here that we get over there.

But that doesn't preclude Wells from posting on Uncommon Descent or Evolution News & Views. If he really believes that my review of his book is an example of "confused thinking and malicious misrepresentations of my work"1 then why not back up such a statement with a thoughtful response on a friendly blog? Evolution News & Views would be ideal since comments are banned.


1. Wells has accused other scientists of misrepresentation. It's a common theme in The Myth of Junk DNA and in Icons of Evolution. I quoted this passage in Junk & Jonathan: Part 13—Chapter 10.
Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence. In fact, one of Coyne's colleagues at the University of Chicago is James Shapiro, co-author of the 2005 article cited in Chapter 6 that listed over 80 known functions for non-protein-coding repetitive DNA. [The other author is Richard (von) Sternberg ... LAM] But if Coyne and Avise were not ignorant of the evidence, then they misrepresented it—and they continue to do so. Like Dawkins, Shermer and Kitcher they have forfeited any claim they might have to be speaking for science.
I can understand why Wells is reluctant to defend such statements. It's because they are indefensible.

Monday, November 07, 2011

Two Kinds of Atheists

 
Let me remind you that Evolution News & Views is the Discovery Institute website. When it comes to defending Intelligent Design Creationism, this is as good as it gets.

Let me also remind you that David Klinghoffer is a Senior Fellow at the Discovery Institute. When you see an article by a Senior Fellow on the Discovery Institute website, you just know it's got to be good.

That's why I was so excited to see The Two Types of Atheists on Nov. 3, 2011.
I meant to say that broadly there are two types of people who call themselves atheists but only one really deserves the dignity of the term. The first category -- the peasant, clod, village atheist, am ha'aretz -- is the person like Jerry Coyne with a cartoon version in his head of some one religion or all religions. He rejects the cartoon, figuring that as far as faith goes in general, he's got it all figured out and it's all nonsense. This type of person typifies the New Atheist movement. He has very little of interest to say.

There's a second much rarer type, however, the person who has not only investigated at least one serious faith seriously but also experienced it, known believers, ideally was a believer himself at some adult stage of life. This person, in rejecting God, merits a real hearing.
Aren't you glad that you can get the best of the best by just reading David Klinghoffer on Evolution News & Views?

It amuses me to think of David Klinghoffer as an atheist in training.


Monday, October 31, 2011

Introducing the Scientific Theory of Redemptive Suffering

 
Before introducing you to this new scientific theory we need to remind ourselves of the difference between intelligent design and creationism. This is from the Evolution News & Views website [Is intelligent design the same as creationism?]
Is intelligent design the same as creationism?

No. The theory of intelligent design is simply an effort to empirically detect whether the "apparent design" in nature acknowledged by virtually all biologists is genuine design (the product of an intelligent cause) or is simply the product of an undirected process such as natural selection acting on random variations. Creationism typically starts with a religious text and tries to see how the findings of science can be reconciled to it. Intelligent design starts with the empirical evidence of nature and seeks to ascertain what inferences can be drawn from that evidence. Unlike creationism, the scientific theory of intelligent design does not claim that modern biology can identify whether the intelligent cause detected through science is supernatural.

Honest critics of intelligent design acknowledge the difference between intelligent design and creationism. University of Wisconsin historian of science Ronald Numbers is critical of intelligent design, yet according to the Associated Press, he "agrees the creationist label is inaccurate when it comes to the ID [intelligent design] movement." Why, then, do some Darwinists keep trying to conflate intelligent design with creationism? According to Dr. Numbers, it is because they think such claims are "the easiest way to discredit intelligent design." In other words, the charge that intelligent design is "creationism" is a rhetorical strategy on the part of Darwinists who wish to delegitimize design theory without actually addressing the merits of its case.
John Blumenthal wrote a piece at Huffington Post where he tried to apply this approach [Intelligent Design? Not If You're Over 50]. He noted that, "If you're over 50 and your body is starting to fall apart, it's pretty obvious that the design is anything but intelligent." I'm told that Blumenthal used to be an editor at Playboy magazine.

An anonymous correspondent at the Discovery Institute's blog, Evolution News & Views, decided to set Blumenthal straight by giving us the scientific, non-creationist, intelligent design, explanation [My Back Hurts Therefore It Wasn't Designed].
For some reason, the former Playboy magazine editor has never heard of redemptive suffering and assumes that any Designer worth his salt would have created a universe where everyone has a rollicking orgy in his own Playboy Mansion until one day, he has a painless death. How cruel of the Designer not to have taken Hugh Hefner's plan for a fulfilling life as a model.
Redemptive Suffering? I try to keep up with the scientific literature but that's a new one on me. It can't have anything to do with trying to deduce the motives of the Christian God of the Bible, can it?


Friday, October 28, 2011

The Core Genome

Hundreds of genomes have been sequenced. It should be relatively easy to search all these genomes to identify those genes that are found in every single species. This small class of genes should represent the core genome—the genes that were probably present in the first living cell.

Turns out it's not that easy. For one thing, you have to remove parasitic bacteria from your set of genomes because these species could easily be getting by without some essential genes that are supplied by their hosts. Next you have to make sure you have a huge variety of different species that cover all possible forms of life. In practice, this means that you need about 300 different genomes, mostly bacteria.

I'm reading The Logic of Chance: The Nature and Origin of Biological Evolution, by Eugene Koonin. This is just one of many books that are critical of the most popular views of evolution. Most of these books are written by kooks or religious nutters but some of them are valid scientific critiques of modern evolutionary theory. Koonin's book is one of those and I agree with most of what he has to say. One of his topics is genome evolution.

As Koonin describes it, the first genome comparisons looked at Haemophilus influenzae and Mycoplasma genitalium, two species of bacteria that aren't distantly related. There were about 240 orthologous genes found in both species.1 The first surprise was that this core set was missing some very important members that should have been there.

Some essential metabolic reactions must have been catalyzed by enzymes in the very first cells but the Haemophilus enzyme isn't present in Mycoplasma and vice versa. It took a bit of digging but eventually the problem was solved with the discovery of different enzymes that carried out the same reaction. The genes for these enzymes are completely unrelated.

As more and and more genomes were sequenced, the size of the core genome set shrunk until today it comprises fewer than 100 genes. Most of these genes are genes for the three ribosomal RNAs, about 30 tRNAs, and a few other essential RNA molecules. There are only about 33 protein-encoding genes in the universal core set. They include genes for the three large RNA polymerase subunits and 30 proteins required for translation (mostly ribosomal proteins).

DNA polymerase isn't in the core set because some species of bacteria have unusual DNA polymerases that replicate DNA just fine but are unrelated to the enzymes found in most cells. There are multiple, unrelated, versions of the aminoacyl tRNA synthetases—the enzyme that attaches an amino acid to its cognate tRNA. Some species have one version and other species have the second version. Some species have both. In any case, no single synthetase gene is found in every species so it's not part of the core set.

Koonin refers to this observation as non-orthologous gene displacement (NOGD). He envisages a scenario where a cell with gene X takes up a copy of a non-orthologous gene (gene Y) that catalzyes the same reaction. Over time the newly acquired gene displaces the original version. In this way a non-orthologous version (e.g. gene Y) could have arisen after the formation of the first cell and spread to a variety of different species by horizontal gene transfer. The scenario doesn't rule out the possibility that the two non-orthologous versions could have arisen independently in two separate origins of life but this seems less likely.

Let's look at a couple of examples. Biochemistry textbook writers have known for decades that there are different versions of some common metabolic genes 2 The aldolase enzyme in gluconeogenesis & glucolysis is a classic. Some species have the class I enzyme/gene while others have the class II enzyme/gene. Some species have both.

This is an example of convergent evolution. The enzymes have different mechanisms and, as you can see from the figure, completely different structures. It doesn't seem to matter if a species has a class I enzyme or a class II enzyme since both enzymes are very good at catalyzing the fusion of two three-carbon molecules into a six-carbon fructose molecule or cleaving the six-carbon molecule in the reverse reaction.

The pyruvate dehydrogenase complex (PDC) is a huge enzyme that catalyzes an important metabolic reaction making acetyl-CoA—the substrate for the citric acid cycle. It seemed likely that every single species would have the genes for all of the PDC subunits but many species of bacteria were missing the entire complex. They have a different enzyme, pyruvate:ferredoxin oxidoreducatase that catalyzes a similar reaction. The enzymes have completely different mechanisms and are unrelated.

In this case, we have reason to believe that the enzyme requiring ferredoxin is more primitive and the more common pyruvate dehydrogenase complex evolved later. The PDC genes displaced the gene for pyruvate:ferredoxin oxidoreductase in many, but not all, species. That's why the genes for neither enzyme are part of the core set.

We don't know whether the existing core set of 100 genes truly represents genes that were present in the first living cell or whether they completely displaced the original versions. The fact that many of these genes are part of large operons might have made it easier for them to be transferred by horizontal gene transfer. (The selfish operon model.)

The bottom line is that attempts to reconstruct the genome of the first cell have failed because of NOGD and we now have to incorporate that concept into our way of thinking about early evolution. The good news is that the evolution of completely new genes seems to be much easier than we first imagined. We even have examples of three or four completely different enzymes carrying out the same reaction.3


1. Koonin refers to conserved genes as Clusters of Orthologous Genes or COGs. It actually counts conserved domains rather than entire genes but the differences aren't great so I'll just refer to them as genes.

2. That is, those textbook writers that emphasize comparative biochemistry or an evolutionary approach to biochemistry. Some textbooks just cover human (mammalian) biochemistry so they won't even mention whether bacteria do biochemistry.

3. I'm not sure how the Intelligent Design Creationists explain these observations. Maybe there were several different designers who each came up with their ideal solution to the problem? Maybe there was only one designer who just got a kick out of making different versions of the same enzyme activity but got bored at only two or three?

Tuesday, October 25, 2011

Is Creationism Anti-Science?

 
It's very hard to define science—it's the demarcation problem and, in spite of what you've been told, philosophers don't agree on how to define science.

A lot of the activities of Intelligent Design Creationists qualify as science, as far as I'm concerned. That's why I spend so much time arguing against their attacks on evolution. Many of the IDiots accept common descent. Their attacks on other aspects of evolution aren't much different than similar attacks from legitimate, non-theistic scientists (e.g. objecting to junk DNA, questioning the Cambrian explosion, challenging strict Darwinism). It counts as "science" but it's very bad science and it's wrong.

All IDiots are anti-evolution but some go farther than others. If you are a Young Earth Creationist who believes that the universe was created less than 10,000 years ago, then you are not just anti-evolution, you are anti-physics, anti-chemistry, anti-geology, anti-astronomy, and anti-biology. I think it's fair to say that Young Earth Creationists are anti-science. This includes most (all?) of the Republican Presidential candidates in the United States and more than half the citizens of that country.

The only way YECs can possibly justify their strange beliefs is to assume that all the experts in all those fields are completely wrong about the fundamental concepts in their discipline. How could they possibly trust anything else those scientists have to say about their areas of expertise?

Let me introduce you to a "new voice" in the Intelligent Design Creationist world. Here's what Evolution News & Views says about him [A New Voice in the Debate Over Evolution and Intelligent Design].
There is literally a new voice in the debate over evolution and intelligent design. If you're a regular listener to the Center for Science & Culture's very popular and thrice weekly podcast, ID The Future, you have probably come to recognize familiar personalities, like ENV's Casey Luskin. (If you're not yet a listener, then you should be.) Now you will be hearing more often from radio broadcaster David Boze of Seattle's KTTH.
I assume David Boze is a heavy-weight and it's okay to criticize him.

Listen to the Discovery Institute podcast where Boze defends Young Earth Creationism against the charge that it's anti-science ["Anti-Science": Unpacking a Vague & Distorted Label]. (You can click on the embedded copy below.) Note the sleight of hand where he lumps together the Young Earth Creationists with all other IDiots. His point is that just because you're opposed to "atheistic Darwinian evolution" does not mean you're anti-science.

Perhaps not. But if you believe in the literal truth of the Bible then you are definitely anti-science. You are a genuine idiot. Does David Boze do a good job of defending Republican Presidential candidates against the charge of being anti-science? Will a YEC President harm the reputation of the United States? You be the judge.

Personally, I don't think the new kid on the block is much of a threat. Is this the best they can do?




Friday, October 14, 2011

Is Intelligent Design Creationism a Scientific Theory?

You should recall that Casey Luskin is one of those "serious science bloggers" who strikes fear into the hearts of evolutionary biologists. In fact, we are so afraid of people like Casey Luskin and Jonathan M that we go out of our way to avoid responding to their posts [see: A Reason to Doubt the IDiots].

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...
ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

The scientific method is commonly described as a four-step process involving observations, hypothesis, experiments, and conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesize that if a natural object was designed, it will contain high levels of CSI. Scientists then perform experimental tests upon natural objects to determine if they contain complex and specified information. One easily testable form of CSI is irreducible complexity, which can be tested for by reverse-engineering biological structures through genetic knockout experiments to determine if they require all of their parts to function. When scientists experimentally uncover irreducible complexity in a biological structure, they conclude that it was designed.

Tuesday, October 11, 2011

A Reason to Doubt the IDiots

 

David Klinghoffer is one of the most entertaining bloggers at Evolution News & Views. His version of logic never fails to bring a smile to my face.

Klinghoffer's latest posting is: A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates.
Much of the debate about Darwinian evolution is conducted in public online forums. If interpreted with some care, these give a convenient way of measuring the real confidence of leading spokesmen on the Darwin side. I don't mean the level of bluster -- they're all full of bluster -- but rather what they really must feel at some level deep down.

If you follow the top Darwin blogs you'll notice how eagerly and often they go in for mocking extremely marginal and daffy creationists. PZ Myers specializes in this. So too, in his books, does Richard Dawkins. How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?

Uh, no, thank you!

It's quite a contrast with intelligent-design advocates who, like them or not, wrestle with the top scientists and thinkers on the other side, while ignoring the small timers.
I really don't think this merits further comment by me.1 I'll let the words stand for themselves. I hope you were as amused as I am.


1. I assume those "serious scientists" don't read Sandwalk, Why Evolution Is True, Panda;s Thumb, Thoughts from Kansas, or dozens of other blogs and books that refute the nonsense spouted by those "serious scientists."

Image Credit: conservababes