David Klinghoffer recognizes the problems with authorities and quote mining

We all know the drill by now. Intelligent design Creationists attempt to discredit evolution and science by pointing out what they see as flaws in basic theory. They also spend a considerable amount of time attempting to discredit individual scientists using guilt by association or direct character assaults.

One of their favorite tricks is to lift quotations out of context and present them in a way that makes it look like famous scientists are supporting Intelligent Design Creationism—or, at least, supporting the idea that evolution is flawed.

The tactic is so widespread and despicable that it led to formation of The Quote Mine Project
Or, Lies, Damned Lies and Quote Mines. That project ran out of steam about eight years ago because the authors just couldn't keep up with all the misinformation coming out of books, lectures, and articles from leading members of the Discovery Institute.

Stephen Meyer is a expert at this. Here are a couple of examples from his book Darwin's Doubt (2013).

Eugene Koonin and the Biological Big Bang Model of Major Transitions in Evolution

 
Eugene Koonin runs a large laboratory at the National Center for Biothechnology Information (NCBI) in Bethesda, MD. (USA) [Evolutionary Genomics ResearchGroup]. His group tends to focus on new ways of analyzing sequences databases and on interesting findings from database mining expeditions.

Koonin and his coworkers are strong supporters of the Three Domain Hypothesis and they usually interpret their data in terms of three domains of life (Bacteria, Archaea, Eukaryotes) with eukaryotes being derived from archaea. As for other evolutonary relationships, Koonin tends to be a "lumper" rather than a "splitter." He will sometimes conclude that two genes or proteins are homologous based on evidence that others find inconclusive.

Creationist Link

Darwin Doubting Heretic Reveals Himself at National Center for Biotechnology
Evolution News & Views
According to Koonin, proteins with similar architecture (folds) are related by common descent even if there's no significant sequence similarity. This is not an uncommon position but it's controversial. Some scientists are not willing to accept that structural similarity alone is sufficient to establish homology. There are too many cases where this assumption leads to awkward and unreasonable implications. Convergence is a possibility that must be entertained.

Koonin has recently published a paper in Biology Direct where he attempts to explain a number of real—or imagined— problems in evolution. In case you're not familiar with this journal, it's a new "open access" journal with an unusual policy. The reviewers must identify themselves and their comments are posted at the end of the paper along with responses from the author(s). Koonin is one of the editors of this journal and he explains the basic philosophy in an editorial [A community experiment with fully open and published peer review].

In Biology Direct, we seek to live by the realities of the 21st century while addressing the issue of information overflow in a constructive fashion and offering a remedy for the ills of anonymous peer review. The journal will publish "essentially anything", even papers that receive three unanimously negative reviews, the only conditions being that three Editorial Board members agree to review (or solicit a review for) the manuscript and that the work qualifies as scientific (not pseudoscientific as is the case for intelligent design or creationism) – and, of course, that the author wants his/her paper published alongside the reviews it receives. Everything in Biology Direct will be completely in the open: the author will invite the referees without any mediation by the Editors or Publisher, and the reviews will be signed and published together with the article. The idea is that any manuscript, even a seriously flawed one, that is interesting enough for three respected scientists to invest their time in reading and reviewing will do more good than harm if published – along with candid reviews written by those scientists. Under the Biology Direct rules, an author is free to solicit as many members of the Editorial Board as s/he has patience for. The philosophy behind this approach is that what really matters is not how many scientists are uninterested in a paper (or even assess it negatively, which could be the underlying reason for declining to review) but that there are some qualified members of the scientific community who do find it worthy of attention. A manuscript will be, effectively, rejected only after the author gives up on finding three reviewers or exhausts the entire Editorial Board. We believe this is fair under the rationale that work that fails, after a reasonable effort from the author, to attract three reviewers is probably of no substantial interest, even if technically solid.

The paper that concerns me here is Koonin (2007) The Biological Big Bang model for the major transitions in evolution. In all cases, the "problems" that Koonin addresses seem to be the rapid and unexplained appearance of novel characteristics, especially those that count as major transitions in evolution. Examples are the origin of cells and the Cambrian explosion.

These events can all be explained by the Biological Big Bang (BBB) model of evolution as Koonin describes in his paper. The concept of the Biological Big Bang is explained in the abstract ...

I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on.

The BBB model is clearly not gradualistic. Koonin attempts to ally himself with other advocates of episodic change such as Niles Eldredge and Stephen J. Gould. (Where necessary, I have converted Koonin's number references to ones in which the author and date is displayed.)

However, the evolution of life is, obviously, a non-uniform process as described, e.g., in Simpson's classic book [3,4], and captured, more formally, in the punctuated equilibrium concept of Gould and Eldredge [Eldredge and Gould, 1997; Gould and Eldredge, 1993]. Lengthy intervals of gradualist modification are punctuated by brief bursts of innovation that are often called transitions, to emphasize the fact that they culminate in the emergence of new levels of organizational and functional complexity [Maynard Smith and Szathmáry, 1997]

I take issue with Koonin's description of punctuated equilibria (PE). PE is a pattern of evolution that describes speciation events. The morphological changes that characterize a new species are locked in place rapidly during cladogenesis (speciation by splitting). For the most part, these morphological changes are subtle and it often takes an expert to recognize them in the best documented cases. Furthermore, these small changes occur repeatedly in a number of distinct cladogenesis events spread out over tens of millions of years. The result is a very distinctive and well-defined phylogenetic tree that defines the punctuated equilibrium pattern. .

Science Link

Examine macroevolutionary concepts carefully
Nick MatzkePE has nothing to do with the major transitions that Maynard Smith and Szathmáry discuss in their books (The Major Transitions in Evolution, The Origins of Life). Nor is PE related in any way to the big bang problems that Koonin is addressing in this paper. It's difficult to decide whether Koonin misunderstands punctuated equilibria or whether he is just stretching an analogy. I suspect the former.

It is no coincidence that the Biological Big Bang model borrows terminology from cosmology. Koonin is very explicit about the similarities between his evolutionary model and the cosmological model for the origin of the universe. As a matter of fact, he explicitly addresses this issue in response to one of the reviewers (William Martin) who challenges the comparison. To me, the comparison between biology and cosmology seems forced and I think he weakens his case considerably by comparing the origin of the universe to the Cambrian explosion. Comparisons like that—and the false analogy with punctuated equilibria—contribute to the sense of unease that I had on finishing the paper. One has the distinct impression that Koonin is grasping at straws in order to knock down a strawman.

What are the major problem with evoluton according to Koonin? Are they strawmen? He identifies six major problems and claims that they can all be explained by a model where "evolutionary transitions follow a general principle that is distinct from regular cladogenesis." The BBB is characterized by a phase of rapid evolution with extensive exchange of genetic information between organisms. This phase is followed by a slow phase of evolution of the sort that generates the typical tree pattern.

Before describing the six examples, we need to address the differences, if any, between Koonin's Biological Big Bang and the "net of life" model that is replacing the traditional tree of life at the deepest levels [The Three Domain Hypothesis (Part 5, Part 6)]. The similarities are obvious. In the net of life model the early stages of evolution involved massive exchanges of genetic information such that it is now impossible to construct a traditional tree relating the major groups of species such as prokaryotes and eukaryotes. What Koonin is doing is to generalize this event "by proposing that a phase of rapid, promiscuous evolution might underlie many, if not most of the major transitions in the history of life."

The six transitions are listed below. Each one is followed by a brief comment where I attempt to evaluate its significance.

1. Origin of protein folds
There seem to exist ~1,000 or, by other estimates, a few thousand distinct structural folds the relationships between which (if existent) are unclear.

There is no reason to postulate that all proteins sharing a common fold will share a common ancestor. Some of these proteins might well have arisen entirely independently and evolved to a common fold by convergence. In other words, the underlying assumption that the origin of protein folds represents evolution of some sort may be false. Furthermore, there is even less reason to think that groups with different folds have an evolutionary relationship. In order for this to be true there would have to have been a primordial protein with one kind of fold that gave rise to a protein with another kind of fold. Instead different polypeptides with little three-dimensional structure (random coils) may have independently evolved into proteins with particular folds.

2. Origins of Viruses
For several major classes of viruses, notably, positive-strand RNA viruses and nucleo-cytoplasmic large DNA viruses (NCLDV) of eukaryotes, substantial evidence of monophyletic origin has been obtained. However, there is no evidence of a common ancestry for all viruses.

The reason why there's no evidence of a common ancestor for all viruses may be because there is no common ancestor for all viruses.

3. Origin of Cells
The two principal cell types (the two prokaryotic domains of life), archaea and bacteria, have chemically distinct membranes, largely, non-homologous enzymes of membrane biogenesis, and also, non-homologous core DNA replication enzymes. This severely complicates the reconstruction of a cellular ancestor of archaea and bacteria and suggests alternative solutions.

The existence of distinct bacterial and archaeal domains is hotly disputed. Many groups of bacteria have distinctive features that distinguish them from other groups. There is no need to postulate a radically new mechanism of evolution that accounts for bacteria and archaea if they really aren't much different than the major branches described below.

4. Origin of the major branches (phyla) of bacteria and archaea
Although both bacteria and archaea show a much greater degree of molecular coherence within a domain than is seen between the domains (in particular, the membranes and the replication machineries are homologous throughout each domain), the topology of the deep branches in the archaeal and, especially, bacterial phylogenetic trees remains elusive. The trees conspicuously lack robustness with respect to the gene(s) analyzed and methods employed, and despite the considerable effort to delineate higher taxa of bacteria, a consensus is not even on the horizon. The division of the archaea into two branches, euryarchaeota and crenarchaeota is better established but even this split is not necessarily reproduced in trees, and further divisions in the archaeal domain remain murky.

In addition to eurarchaeote and crenarchaeota there are other groups of prokaryotes that are easily resolved by current techniques (e.g., cyanobacteria, proteobacteria). It may be difficult to resolve the base of the tree because of extensive horizontal gene transfer as postulated in the "net of life" scenarios. This is the one case, along with #3, where the concept of an unusual type of evolution may be correct. I still don't like the term Biological Big Bang to describe it.

5. Origin of the major branches (supergroups) of eukaryotes
Despite many ingenious attempts to decipher the branching order near the root of the phylogenetic tree of eukaryotes, there has been little progress, and an objective depiction of the state of affairs seems to be a "star" phylogeny, with the 5 or 6 supergroups established with reasonable confidence but the relationship between them remaining unresolved.

Substantial progress has been made but the problem is very difficult because of the lack of reliable phylogenetic markers. That, plus the fact that we are trying to sort out events that took place more than one billion years ago. It is too early to conclude that our inability to reach consensus means that something strange must have been going on. That's a cop-out at this time.

6. Origin of the animal phyla
The Cambrian explosion in animal evolution during which all the diverse body plans appear to have emerged almost in a geological instant is a highly publicized enigma [32-35]. Although molecular clock analysis has been invoked to propose that the Cambrian explosion is an artifact of the fossil record whereas the actual divergence occurred much earlier [36,37], the reliability of these estimates appears to be questionable [38]. In an already familiar pattern, the relationship between the animal phyla remains controversial and elusive.

Actually, the relationships between animal phyla are quite well understood at the molecular level. The lineages do not appear to be scrambled by excessive recombination between species as Koonin's hypothesis would require.

The Cambrian explosion is an interesting example of fairly rapid morphological evolution. It may be true that dozens of independent animal lineages simultaneously acquired a new mechanism of evolution during the Cambrian but this does not seem to be the most parsimonious explanation of the data.

To sum up, I don't think that Koonin's examples cry out for explanation in the way he thinks they do. Some of them may not even be examples of evolution. It seems reasonable to attribute the origins of the major groups of bacteria, and the first eukaryotic cells, to a rapid exchange of genes in the beginning phase of life on Earth, but there's no need to postulate that this promiscuous phase was ever repeated at other stages and certainly no reason to assume that there were repeated waves of promiscuity followed by quiescent phases of stabilizaton.

The Biological Big Bang is not so much wrong as it is unnecessary.

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Koonin, E. (2007) The Biological Big Bang model for the major transitions in evolution. Biology Direct 2:21doi:10.1186/1745-6150-2-21.

[Photo Credit: The Tree of life is from Ford Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American.]

Five questions for Intelligent Design Creationists

A few Intelligent Design Creationists are beginning to learn about evolution. A few days ago, I speculated about what would happen if they really did start to understand modern evolutionary theory and the massive amount of data that supports the basic facts of evolution [What would happen if Intelligent Design Creationists understood evolution?].

Vincent Torley has responded. He illustrates the problems they will face and reveals some of the rationalizations that they might use to avoid the most severe symptoms of cognitive dissonance [see Professor Larry Moran poses five questions for the ID movement].

Let's take a look at what has to say. Remember that Vincent Torley doesn't speak for all Intelligent Design Creationists but he does have posting privileges on Uncommon Descent and he is frequently praised by some of the ID leaders who post there. I think we can assume that his views are typical.

Here's his response to each of the five questions.

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).

Intelligent Design Creationists reveal their top story of 2016

Yesterday I posted an article on: Creationists list the top ten stories of 2016 . Some of you may have noticed that there were only nine stories. That's because Evolution News & Views didn't post their top story until today. I was pretty sure what it would be.

Let me remind you of the main point I made yesterday. Intelligent Design Creationists claim to have scientific evidence of intelligent design. They claim their movement is focused on demonstrating intelligent design but not on proving anything about who the designer might be.

But that's not what the movement is all about. Most of their writings and speeches are focused on attacking evolution. They hope that by discrediting evolution and science they will, by default, support the case for gods (false dichotomy). They also hope that by promoting gaps in our knowledge they will lend support to those who want to insert gods into the gaps.

You don't need to take my word for it. Just look at what they think are the top stories of 2016. Most of their top nine stories were critiques of science in one way or another. There wasn't a single top story that advanced the case for intelligent design.

So, what about the #1 story? Is it going to be different?

Of mice and Michael

Michael Behe has published a book containing most of his previously published responses to critics. I was anxious to see how he dealt with my criticisms of The Edge of Evolution but I was disappointed to see that, for the most part, he has just copied excerpts from his 2014 blog posts (pp. 335-355).

I think it might be worthwhile to review the main issues so you can see for yourself whether Michael Behe really answered his critics as the title of his most recent book claims. You can check out the dueling blog posts at the end of this summary to see how the discussion evolved in real time more than four years ago.

Many Sandwalk readers participated in the debate back then and some of them are quoted in Behe's book although he usually just identifies them as commentators.

My Summary

Michael Behe has correctly indentified an extremely improbably evolution event; namely, the development of chloroquine resistance in the malaria parasite. This is an event that is close to the edge of evolution, meaning that more complex events of this type are beyond the edge of evolution and cannot occur naturally. However, several of us have pointed out that his explanation of how that event occurred is incorrect. This is important because he relies on his flawed interpretation of chloroquine resistance to postulate that many observed events in evolution could not possibly have occurred by natural means. Therefore, god(s) must have created them.

In his response to this criticism, he completely misses the point and fails to understand that what is being challenged is his misinterpretation of the mechanisms of evolution and his understanding of mutations.

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The main point of The Edge of Evolution is that many of the beneficial features we see could only have evolved by selecting for a number of different mutations where none of the individual mutations confer a benefit by themselves. Behe claims that these mutations had to occur simultaneously or at least close together in time. He argues that this is possible in some cases but in most cases the (relatively) simultaneous occurrence of multiple mutations is beyond the edge of evolution. The only explanation for the creation of these beneficial features is god(s).

Evolution Is Irrelevant to Michael Egnor

The title of this post suggest a story that's about as interesting as the proverbial "Dog Bites Man" story [see Man Bites Dog]. Nevertheless, from time to time it is amusing to see how the creationist mind works.

Michael Egnor is upset about the fact that the American Society for Biochemistry and Moleclar Biology (ASBMB) picked "evolution" as an important concept that should be covered in a biochemistry or molecular biology course. He doesn't like my post: ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution. He decided that he better convince his fellow creationists than biochemists don't know what they are talking about [Is Darwinian Evolution "Indispensable" to Biology?].

Here are some excerpts for your amusement.

The creationism continuum

Intelligent Design Creationists often get upset when I refer to them as creationists. They think that the word "creationist" has only one meaning; namely, a person who believes in the literal truth of Genesis in the Judeo-Christian Bible. The fact that this definition applies to many (most?) intelligent design advocates is irrelevant to them since they like to point out that many ID proponents are not biblical literalists.

There's another definition of "creationist" that's quite different and just as common throughout the world. We've been describing this other definition to ID proponents for over two decades but they refuse to listen. We've been explaining why it's quite legitimate to refer to them as Intelligent Design Creationists but there's hardly any evidence that they are paying attention. This isn't really a surprise.

Press release hyperbole and the "duon" delusion

I recently described a really bad paper published in Science by Stergachis et al. (2013). The principle investigator is John Stamatoyannopoulos of ENCODE notoriety [see The "duon" delusion and why transcription factors MUST bind non-functionally to exon sequences].

The group mapped millions of transcription factor binding sites in the human genome and discovered that 1.8% of them were in exons (coding regions). They assumed that these were functional—they play a role in regulating gene expression. Thus the nucleotide binding sites are also codons meaning that the sequence specifies two different kinds of information. The workers named these sequences "duons."

Do Graduate Students Understand Evolution?

 
The other day I was discussing how to teach evolution with one of my colleagues and the discussion turned to the presumed distinction between students who were really interested in science and everyone else. My colleague claimed that students who were science oriented probably managed to acquire a good understanding of evolution in spite of the fact that some undergraduate courses weren't doing a very good job of teaching the subject.

I pointed out that my impression was different. I suggested that most Professors in our department don't have a firm grasp of one of the most fundamental concepts in biology (evolution), and neither do our graduate students. I reminded my colleague of the times when we cringe at graduate student presentations when the topic of evolution comes up.

Ryan Gregory must have felt the same way since he was prompted to do a survey of graduate students in science departments at Guelph University. The result is published in BioScience. You can read about it on Ryan's blog: How well do grad students grasp evolution?.
Here's the press release...

Science Students Could Brush Up On Darwin, U of G Study Finds

October 01, 2009 - News Release

Even students pursuing advanced degrees in science could brush up on their knowledge of evolution, according to a new study by University of Guelph researchers.

The finding reveals that there is room for improvement in how evolution is taught from elementary school up, said Ryan Gregory, a professor in Guelph’s Department of Integrative Biology, who conducted the research with former student Cameron Ellis.

The study was published today in BioScience. It’s particularly timely, given that this year is the bicentennial of Charles Darwin’s birth and the 150th anniversary of publication of On the Origin of Species, which underpins understanding of the diversity of Earth’s organisms and their interrelations.

“Misconceptions about natural selection may still exist, even at the most advanced level,” Gregory said.

“We’re looking at a subset of people who have spent at least four years, sometimes even six or seven years, in science and still don’t necessarily have a full working understanding of basic evolutionary principles or scientific terms like ‘theories.’”

Many previous studies have assessed how evolution is understood and accepted by elementary, high school and undergraduate students, as well as by teachers and the general public, Gregory said. But this was the first to focus solely on students seeking graduate science degrees.

The study involved nearly 200 graduate students at a mid-sized Canadian university who were studying biological, physical, agricultural or animal sciences. About half of the students had never taken an evolutionary biology course, which is often not a prerequisite.

The researchers found that the vast majority of the students recognized the importance of evolution as a central part of biology. Overall, they also had a better understanding of evolutionary concepts than most people.

“That was encouraging, especially because it was across several colleges — it wasn’t just the biology students,” Gregory said.

But when the students were asked to apply basic evolutionary principles, only 20 to 30 per cent could do so correctly, and many didn’t even try to answer such questions. Of particular interest to Gregory is the finding that many students seem less than clear about the nature of scientific theories.

“This is telling us that traditional instruction methods, while leading to some basic understanding of evolution, are not producing a strong working knowledge that can be easily applied to real biological phenomena.”

Gregory has studied evolution-related topics for years and recently co-organized a workshop designed to improve how the subject is taught in public schools. He is also associate editor of Evolution: Education and Outreach, a journal written for science teachers, students and scientists. He recently created Evolver Zone, a free online resource for anyone interested in evolutionary biology.
He is also helping bring an evolution-inspired art exhibit to U of G this month. “This View of Life: Evolutionary Art in the Year of Darwin, 2009” highlights diverse artists’ views of Darwin’s ideas and evolution in general. It runs Oct. 9 to 30 in the science complex atrium.

Some of us know what the problem is. What are we going to do about it? How are we going to convince professors that evolution education has to change when most of them don't even recognize there's a problem because their own views of evolution are flawed?

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When will they ever learn?

On most days I'm an optimist. I think that eventually the truth will win out and all you have to do is convince people that they are misguided. That's why I spend so much time discussing the view of Intelligent Design Creationists. On the good days, I firmly believe that if I can show them what science is all about then they will come around to accepting evolution.

I cherish a few modest successes over the years. For example, a few months ago I tried to teach David Klinghoffer and his friends about modern concepts of evolution and genetics. The example I used was the 98% sequence similarity between the human and chimp genomes. I showed him that the similarity is quite consistent with our understanding of Neutral Theory and random genetic drift [Why are the human and chimpanzee/bonobo genomes so similar?].

A remarkable thing happened. Some of the Intelligent Design Creationists on Evolution News & Views (sic) and Uncommon Descent actually agreed with me! They tried to explain to their fanatical friends that chimps and humans really do share a common ancestor and that the differences between them are explained by evolutionary theory. (I've included links to all the posts at the bottom of this post.)

Just when you think you are making some progress, the IDiots prove you wrong. Yesterday on Uncommom Descent there was a post on the topic of the similarity between chimps and humans [At last, a proposed answer re 98% human-chimpanzee similarity claim]. The author was probably Barry Arrington posting as "News." Here's the relevant part of that post ...

From this comment (by Gordon Davisson, in response to this post):

In other words, I’m agreeing with Denyse here:

BUT claimed 98% similarity due to a common ancestor (a claim that hundreds of science writers regularly make, in support of common descent) *undermines anything else they have to say on the subject.*

I do not know how to put the matter more simply than this: A person who does not see the problem is not a credible source of information.

He responds:

…just disagreeing about which side is not credible. Take the 98% similarity figure as an example: one of the basic principles of science is that you must follow the evidence. If the evidence supports the 98% figure, and that conflicts with your intuition, then you either have to throw that intuition into the trash bin, or stop claiming to be doing science.

No. Absolutely not.

One should never discard intuitions formed from experience, especially about vast claims. Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.

This is called, among other things, wanting to have your cake an eat it too. The IDiots want you to believe that they accept all of modern science and that their "theory" is consistent with the evidence.

On the other hand, if the science of genetics leads to conclusions that contradict your "intuition" then the science must be wrong.

We've known for decades that this is how the IDiots really think but it's interesting to see someone like Barry Arrington express it so openly.

Now all we have to do is sit back and wait for the more intelligent IDiots to point out that we've been through all that a few months ago and Barry's intuition is wrong. Instead, what we're seeing is Barry Arrington doubling down [Sun orbits Earth vs. Chimps are people too – the differences].

This is not a good day. It's hard for me to remain optimistic.

An Intelligent Design Creationist explains why chimpanzees and humans are so similar
IDiots respond to the evidence for evolution of chimpanzees and humans
A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory
Breaking news: Creationist Vincent Torley lies and moves goalposts
Vincent Torley apologizes and claims that he is not a liar
Vincent Torley tries to understand fixation
On the frustration of trying to educate IDiots
Why creationists think they are more open-minded than scientists
What would happen if Intelligent Design Creationists understood evolution?
Branko Kozulic has questions about fixation
Branko Kozulic responds
Branko Kozulic responds: Part II

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Why does Stephen H. Webb use the word "Darwinism"?

We know why the IDiots use the words "Darwinist" and "Darwinism" to describe evolutionary biologists and modern evolutionary theory. There are three main reasons.

1. They want their flocks to believe that modern scientists worship Charles Darwin and his 150 year-old theory so that when they discredit him—as they are constantly trying to do—it reflects on evolution.
2. They want to link modern evolutionary biology to social Darwinism and it's easier to do so if they refer to evolutionary biologists as Darwinists.
3. They are too stupid to realize that there's a lot more to modern evolutionary biology than natural selection.

Every time you challenge creationists on this point they find some way to defend their use of Darwinism rather than just say "evolutionary biology" or "modern evolutionary theory." There's a reason for this (see above).

Stephen H. Webb is the latest example. Apparently his use of "Darwinism" was challenged so he wrote a blog post on Evolution News & Views (sic) defending it The Strange Mental World of Darwinian Fundamentalists. I hope you appreciate the irony in the title.

John G. West Speaks Out Against Using Derogatory Labels to Describe Your Opponents

John G. West is Vice President for Public Policy and Legal Affairs of the Center for Science and Culture (CSC)—the most important Intelligent Design Creationism propaganda organization. He is upset because some reporters describe Intelligent Design Creationism as a form of creationism. I've taken an excerpt from his post at Attempting to Win the Debate over Intelligent Design through Stereotyping and changed just a few words so you can get the gist of his argument.

The really discouraging thing here is not that some reporters are critical of evolution. It is that so many of them apparently see nothing wrong with preventing evolutionary biologists from defining their own position. This is a very strange way to do journalism, and if journalists started to apply their approach to evolution to other topics, I think it would become manifestly clear how unfair it is. Imagine, for example, a journalist deciding to use "Marxist" as a neutral label for President Obama based on the views of certain right-wing academics and political activists. Would that be regarded as fair or impartial by most journalists? Of course not. What if a reporter redefined Marxist to mean anyone who supports more active government? Would that make applying the term to Obama in a news story more defensible? Hardly. Yet when reporters label evolutionary biologists as "Darwinists," they are essentially doing the same thing.

What is really going on here is censorship. When reporters use as a "neutral" description of evolution a polemical smear invented by its critics, they are effectively silencing evolutionary biologists by not allowing them to speak for themselves. They are poisoning the well so no one will be willing to listen to the actual views expressed by evolutionary biologists. Journalists who write about evolution should re-read the Society of Professional Journalists' Code of Ethics, especially the provisions calling for them to "Support the open exchange of views, even views they find repugnant" and to "Give voice to the voiceless...."

Whatever a news reporter's views on evolution, he or she has a professional duty not to simply spread stereotypes and caricatures. That duty means nothing if it only applies to news coverage of groups and positions with which the reporter agrees. The real test of fairness for reporters is how they treat those with whom they disagree. When it comes to evolution, sadly, many reporters are failing the test.

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Michael Behe and the edge of evolution

Michael Behe's book, The Edge of Evolution, is very interesting. His main thesis is that there are some genotypes that are beyond the reach of evolution. His examples include genotypes where two or three mutations have to occur simultaneously in order to achieve an effect. The probability to this happening is extremely remote but it could happen in some populations with very large effective population sizes.

The reason why mutations have to happen simultaneously in the same organism, according to Michael Behe, is because any one of them, by itself, is detrimental. This defines the edge of evolution because it's a result that cannot be achieved by mutation and selection (or by drift).

Behe is correct. If a given phenotype absolutely requires that two mutations happen simultaneously then this is going to be almost impossible in most species.

A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory

I know I've said this before, but I continue to be astonished at the ignorance of creationists. Those who oppose evolution most vehemently don't understand it in spite of the fact that they are convinced it has to be wrong.

This is most obvious with the Intelligent Design Creationists because they like to use science-sounding jargon to convince us that they know what they are talking about. They claim that they can refute evolutionary biology using scientific evidence. Instead they just reveal their ignorance.

They've been doing it for decades in spite of the fact that many people have tried to educate them. I don't get it.

Recently, I tried to explain how the difference between the chimpanzee and human genomes is consistent with what we know about population genetics, mutation rates, and Neutral Theory. I was aware of the fact that this stuff would all be news to most Intelligent Design Creationists but it was still an opportunity to try, once again, to teach them about modern evolutionary theory.

How can she go wrong?—let us count the ways ...

There's a very good reason why the creationist website Evolution News & Views (sic) doesn't allow comments but that won't stop us from making comments on Sandwalk. Check out Ann Gauger's latest offering at: Waiting for Mutations: Why Darwinism Won't Work.

There are a few errors in that post. How many? Let us count the ways.¹

Theme
Mutation
-definition
-mutation types
-mutation rates
-phylogeny
-controversies
What's interesting about that post is that we've been over the data many times in an attempt to explain mutation to the creationists. Last year I tried to explain why humans and chimpanzees have accumulated about 22 million point mutations since the time they evolved from a common ancestor about 6 million years ago. I thought it would be helpful if they understood why these numbers are perfectly reasonable according to population genetics.

What happened was that the vast majority of commenters on Uncommon Descent called me names and told me I was wrong. A few creationists, Sal Cordova, Vincent Torley, and Branko Kozulic took up the challenge and, for a short while I thought they understood.

A Challenge to Jonathan Wells

 
On February 29th Jonathan Wells published a short review of a scientific paper by Maurice et al. (2008). You can read the original Wells posting at: The Irrelevance of Darwinian Evolution to Antibiotic Resistance.

Wells was trying to make a point. Concerning the work from Dardel's lab (Maurice et al, 2008), Wells claimed ...

Yet Darwinian evolution had nothing to do with it.

First, some bacteria happen to have a very complex enzyme (acetyltransferase), the origin of which Darwinism hasn’t really explained. Come to think of it, most cases of antibiotic resistance (including resistance to penicillin) involve complex enzymes, and the only “explanations” for them put forward by Darwinists are untestable just-so stories about imaginary mutations over unimaginable time scales.

Second, the acetyltransferase story is about minor changes in an existing species of bacteria. But Darwin’s theory isn’t really about how existing species change over time. People had been observing those long before 1859, and most of the new insights we’ve gained since then have come from genetics, not Darwinism. Yet Mendel’s theory of genetics contradicted Darwin’s, and Darwinists rejected Mendelian genetics for half a century. And although an understanding of genetics is important when dealing with antibiotic resistance, Darwin’s theory of the origin of species by natural selection is not.

Third, Dardel and his colleagues made their discovery using protein crystallography. They were not guided by Darwinian evolutionary theory; in fact, they had no need of that hypothesis.

We all know how creationists use the word "Darwinism." Most of the time, it's a synonym for evolution. All of the time, it's an attempt to obfuscate and confuse their audience. What Wells is saying is that evolution had nothing to do with the paper. All that happened was a bit of genetics. According to Wells, "Darwin's theory of the origin of species by natural selection" was not involved.

The senior author of the paper posted a comment on Pharyngula saying, "Actually, we did indeed use darwinian evolution within this work (something unusual in structural biology)." [see Why the Right People Hate IDiots, and links within that posting].

Michael Egnor gallops to the defense of his hero. Today he posted a rebuttal to my criticism of him and Wells [Dr. Larry Moran, Darwinism, and Vicious Personal Invective]. Here's what Egnor says,

Dr. Wells pointed out that research on antibiotic resistance wasn’t guided by Darwinian evolutionary theory. That evolution occurred — that is, that the population of bacteria changed over time — is obviously true, and obviously was relevant to the antibiotic resistance research. Dr. Wells made the observation that the research owed little to Darwin’s theory that all biological complexity arose by natural selection without teleology.

This is an incredible admission from a creationist. Egnor admits that the bacteria evolved. He then goes on to define some bizarre version of "Darwin's theory."¹ But the cat is out of the bag. What we see here folks, is the recognition that there is a distinction between Darwinism and evolution by natural selection. We're still not clear about the difference but it seems that bacteria can evolve resistance to antibiotics.

Egnor admits that the paper used evolution but it just wasn't Darwinism.

Now let's see if Jonathan Wells agrees. I'll apologize to Wells if he will post a comment here, or on Evolution News & Views, agreeing to the following ..

I, Jonathan Wells, agree that Maurice et al. (2006) employed evolution by natural selection in their methodology. My position is that evolution by natural selection is not what I mean when I use the word Darwinian.

Note that I'm not asking him to agree that "Darwinism" was involved in the paper. All he has to do is admit that evolution by natural selection is not what he means when he uses the word "Darwinian."

Michael Egnor has indicated that this is what Wells actually means. Now let's see if Wells himself will admit it.

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1. The standard version of Darwin's Theory of Evolution by Natural Selection is that populations evolve due to the differential survival of individuals with a fitter genotype.

Maurice, F., Broutin, I., Podglajen, I., Benas, P., Collatz, E. and Dardel, F. (2008) Enzyme structural plasticity and the emergence of broad-spectrum antibiotic resistance. EMBO Rep. 2008 Feb 22 [Epub ahead of print] [PubMed]

David Klinghoffer Wants Clear Definitions

A few days ago I mentioned that definitions were important and I asked my students to look at twenty definitions of "evolution" [The Many Definitions of Evolution]. I was surprised to discover that some of you don't think it's very important to agree on how we define important terms and concepts.

David Klinghoffer agrees with me. He recently posted an article on Evolution News & Views (sic) where he called for clear definitions [Terry Mattingly: In the Evolution Debate, Clear Definitions Are Among the Casualties]. Let's see what he has to say ...

The point cannot be hammered home too often: In media coverage of the evolution debate, a standard trick, the one that stands out the most for slipperiness, is the refusal to define common terms. What is "evolution," or "creationism," or "intelligent design"? Readers may think they know. The reporter may think he knows. Usually, the shades of meaning get blurred, with the suspiciously consistent effect of casting evolution skeptics into a bad light.

Oh dear. Klinghoffer thinks that we are guilty of using definitions that make creationists look bad. He quotes from an article by Terry Mattingly who says ....

[T]he committee that produces the Associated Press Stylebook needs to urge mainstream journalists to be more careful when using the words "evolution" and "creationism." Each of those terms has a half dozen or so finely tuned definitions, depending on who is using them at any given moment.

For example, a person who accepts a creation narrative with a "young earth" and a timeline with seven 24-hour days will certainly embrace the creationist label. But what about a person who believes that creation unfolded over billions of years, involved slow change over time, a common tree of descent for species and ages of micro-evolutionary change?

That's simple. Both are creationists [On Describing IDiots as Creationists] [Creationism Continuum] [What Is Creationism?] (The last two posts attempt to deal with some Sandwalk readers who think that their preferred definition is the only correct definition.)

Mattingly then tackles a more difficult definition ....

Similar things happen with the term evolution, which as the Blessed Pope John Paul II once observed, is best discussed in terms of different schools of evolutionary thought, some of which are compatible with Christian faith and some of which are not...

The word "evolutionist" certainly applies to someone who believes life emerged from a natural, materialistic, random process that was without design or purpose. But what about someone who accepts that theory on the biological front, but believes that there is scientific evidence that our universe was finely tuned to produce life? What about someone who says that creation contains evidence best thought of as the signature of its creator (Carl Sagan, for example). What about people who insist they are doctrinaire Darwinists, but still see cracks in the old neo-Darwinian creeds? Are "theistic evolutionists" really believers in "evolution" in the eyes of the truly secular academic powers that be? And so forth and so on.

This is definitely a problem. As we see, Mattingly is terribly confused about the meaning of "evolution" and the difference between it and "evolutionary theory." I agree that we need to be clear about what we mean and I've tried to do that [What Is Evolution?]. (BTW, "theistic evolutionist" is just a euphemism for a particular kind of "creationist.")

Mattingly doesn't give us an answer. I guess he was too busy complaining.

Let's see what Klinghoffer has to say since he's convinced that this is an important issue. How do the IDiots define "evolution" and "Darwinism" and what do they have to say about modern evolutionary theory? How do they define "creationist"?

Waiting .........

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This is what a strawman looks like

This is another post about the stupidity of Intelligent Design Creationists. Stop reading if you don't need any more convincing.

Today is Darwin Day. It's the anniversary of the birth of Charles Darwin (Feb. 12, 1809 - April 19, 1882).

This is not a happy day for the Discovery Institute so they've put up a series of posts on Evolution News & Views (sic) to discredit Darwin and "Darwinism."

One of them is by the newly rejuvenated poster boy, Michael Denton: On Darwin Day, Darwinism Is Well Past Its "Sell By" Date. Here's the part I want you to see,

To understand the core weakness of the Darwinian worldview, it is important to understand what Darwinian natural selection requires. The process will work its magic, building up functional structures in organisms, only when two very strict conditions are met: First, the structure must be adaptive—that is, helpful to the organism in flourishing in its environment—and second, there must be a continuum of structures, functional all along the way, leading from an ancestor species to the descendent.

That is, the thing we are trying to explain must in some way help the creature survive, and between the creature and the creature's ancestor there must be a gradual change, each step of which is stable and enhances fitness, or success in reproduction.

Strictly speaking, that's a reasonable explanation of Darwinism as most evolutionary biologists understand it. But here's the problem. There aren't very many evolutionary biologists who are strict Darwinists these days even though there are many who tilt strongly in that direction.

The Casey Luskin Lesson Plan on Teaching the Controversy

 
I often criticize the Intelligent Design Creationists for not coming up with anything other than criticism of evolution. That criticism is perfectly justified as we can see in Casey Luskin's latest posting on Evolution News & Views: Back to School Lesson Plans That Actually Help Students Understand Evolution. He's even gone as far as proposing a lesson plan on evolution for grades 4-7. One of the important parts of that lesson plan is the challenges to evolution.

It's Monday, and it's Thanksgiving Day in Canada, so I'm taking a bit of a break. Let's have some fun with Luskin's lesson plan. I'll quote each of his points with a brief response.

Step 3: Learn About the Case against Evolution (1.5 hours). Now students will learn about some of the science that challenges evolution. Watch the DVD Icons of Evolution.
- Ask students to explain the difference between microevolution and macroevolution.

This is far too complicated for public school students. The simple answer is that microevolution describes changes occurring within populations and macroevolution describes the history of life. Macroevolution includes things such as speciation that are not part of microevolution and it also includes things like asteroid impacts, ice ages, and drifting continents in order to explain the history of life. There's an important part of evolutionary theory called "Hierarchical Theory" where proponents argue for higher-level mechanisms of evolution such as species selection. They aren't part of microevolutionary explanations. Thus, microevolution is necessary but not sufficient to explain macroevolution [Macroevolution].

-The video mentions the Galápagos finches. Do the finches represent an example of microevolution or macroevolution?

It's on the border between microevolution and macroevolution. The value of the work on the Galapogos finches is that the results suggest how new species are formed. They formed from a combination of physical isolation events (different islands) plus microevoutionary events involving natural selection, and random genetic drift. Such speciation events occurred repeatedly in the history of life and these studies show how they can be explained by purely natural causes.

-The video mentions mutations in fruit flies which gave fruit flies an extra pair of wings. Were these fruit flies able to fly better and survive with the extra wings?

No.

-Are mutations helpful or harmful? Ask for examples of harmful mutations? How about helpful ones?

A harmful mutation is one that decreases fitness. There are hundreds of examples of genetic diseases in humans. A beneficial mutation is one that increases fitness. Antibiotic resistance in bacteria is a classic example but so is HIV resistance in humans. Dozens of field studies have shown that beneficial mutations can arise fairly quickly in populations that are challenged by environmental change. Molecular data documents thousand of beneficial changes to genes and enzymes over time.

-What was the Cambrian explosion?

The Cambrian Explosion was a period in the history of life where we see the appearance of new types of animals. The dates are approximately 500 million years ago and the time frame for the visible appearance of these groups ranges from 10-50 million years. It's important to note that the fossils of the Cambrian don't look like any species that are alive today and they don't contain any examples of land life. It's also important to note that the Cambrian explosion doesn't apply to plants, fungus, protozoa, and bacteria.

What caused the appearance of primitive animal groups 500 million yeas ago, over a period of tens of millions of years? Scientists don't really know but there are lots of ideas on the table. One thing that's very clear from molecular evolution is that the origin of the various lineages (phyla) goes back several hundred million years.

-Does the fossil evidence show that species have evolved by small gradual changes, or large sudden changes? Do fossils support Darwin’s theory? Why or why not?

The are many examples of slow gradual changes over millions of year but there are also examples of patterns called Punctuated Equilibria. In these examples you see very small changes—such as the speciation events in the Galapagos finches—happening at the time of speciation. In other words, the fossil record mimics the sort of thing you see in the Galapagos islands where the small changes occurring at speciation are quickly fixed in the population within ten or twenty thousand years. There's hardly any fossil record of the intermediates showing the transition between these closely related species.

There's nothing in the fossil record suggesting that large sudden changes can occur rapidly. That's a lie propagated by creationists who don't understand evolution and who have a religious agenda that interferes with their ability to do science.

-The video also mentions the origin of life. Does the evidence support the claim that the building blocks of life were present on the early earth? Why or why not?

The origin of life is an interesting scientific problem that hasn't been solved. Although it has nothing to do with evolution, it's clearly related. Some scientists think that life arose in a primordial soup containing abundant supplies of all the necessary building blocks we see today. There is plenty of scientific evidence that some of these building blocks—such as simple sugars and amino acids—can arise spontaneously. In fact, many of them have been detected in outer space. Other scientists prefer scenarios where life began much more simply with very small, highly abundant, chemicals that are still around today in the oceans. It will be interesting to watch for new discoveries as you grow up because science is poised to make significant advances in these areas.

You should keep an open mind on this question and watch for new discoveries from religious leaders that will help you understand the origin of life. It's possible—alghough not very likely—that religious organizations such as The Discovery Institute will come up with a scientific explanation of how, and when, God created life on Earth.

-Compared to humans, was the first life simple or complex? How about compared to a calculator, computer, or cell phone? Are living organisms more or less complicated than human technology? What do students think?

All available scientific evidence points to a common ancestor that was much more simple than humans, or most other species that are living today. Those primitive ancestors are much less complex than a modern computer because, in addition to having only a few hundred genes (at most), the internal cell biology and biochemistry was undoubtedly sloppy and inefficient. No modern machine is anything like that.

We are at the stage in technology development where it is possible to build better life forms than those that evolved naturally and you should look forward to learning about these new artificial forms of life in the next few years. You might even want to think about a future career in science so you can learn this technology.

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