Is antibiotic resistance evidence for Darwinian evolution?

 
Here's a short video where the IDiots discuss antibiotic resistance in bacteria. This is part of the new attack on evolution. It's the main point of Michael Behe's new book, The Edge of Evolution. The idea is that random mutation and natural selection can only break things but they can't make new structures.

I suspect that very few people can scientifically refute the arguments in this video. It can be done, but it's going to take a bit of effort.

An Interview with Michael Behe

 
I'm reading The Edge of Evolution, the new book by Michael Behe. I'm not finished but I can tell you it's going to be a challenge to refute Behe's main claims. That's not because he's correct—far from it—but because he has done a clever job of picking out scientific data to support his case. The idea is that random mutation and natural selection are simply not capable of doing the things they have to do in order for large scale changes to accumulate. His probability arguments are more sophisticated than those of the average IDiot and I think we owe it to Behe to address them rather than just dismiss them out-of-hand because we don't like the conclusion. I'm looking forward to the challenge.

Here's a short interview with Behe (#5) where he explains his views. Behe says that antibiotic resistance is an example of breaking things rather than creating new things. As you listen to him make this claim, think about the evolution of β-lactamase activity from a transpeptidase enzyme [Penicillin Resistance in Bacteria: Before 1960].


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Denyse O'Leary Asks a Question about Evolutionary Psychology

 
It never ceases to amaze me that the IDiots know so very little about the science they criticize. They have this myopic view of "Darwinism" and they refuse to adjust it no matter how many time they're told that it isn't true.

So when one of them shows the beginning of understanding, it's time to sit up and take notice. Denyse O'Leary has recently shown just a tiny glimmer on Uncommon Descent [Okay: So evolutionary biologist Larry Moran does NOT believe in evolutionary psychology].

Responding to something I wrote at the Post-Darwinist about the popularity of evlutionary psychology among atheists, Moran (a textbook co-author you may well have suffered though in school), responds:

Just for the record, Denyse, I’m one of those evil atheists that you like to rant about but I’m totally opposed to evolutionary psychology.

But you already knew that many evolutionary biologist were against evolutionary psychology, didn’t you?

No, I didn’t, Larry, and if that’s true, it’s high time more of them voiced their objections. The only sustained critiques I have seen are Hilary and Steven Rose’s unjustly neglected Alas, Poor Darwin and David Buller’s also unjustly neglected Adapting Minds. Steven Rose is a neurobiologist, but Hilary Rose is a social scientist, and David J. Buller a philosopher.

No doubt, there are many critiques out there that I haven’t seen, but I wonder what proportion comes from evolutionary biologists, as opposed to social scientists who know the difference between research and speculation.

I'm not allowed to post on Uncommon Descent—apparently they don't want to learn about evolution. I imagine that many Sandwalk readers have also been banned so here's your chance to educate Denyse.

The most prominent opponents of evolutionary psychology are Richard Lewinton, Steven Rose, and the late Stephen J. Gould. I find it hard to believe that the IDiots have never heard of Gould and aren't aware of the debate in the New York Review of Books back in the mid-90's.

Denyse, here are some recent comments about evolutionary psychology [The Central Failure of Evolutionary Psychology]. I've listed some references below.

I don't know what proportion of evolutionary biologists are opposed to evolutionary psychology but I imagine it's significant. Opposition to evolutionary psychology comes from the same people who call themselves pluralists and who don't like to be called Darwinists. (You do recall, don't you, that many evolutionary biologists have moved well beyond Darwinism? You've been told more than once.)

---

Gould, S.J. (1997) Darwinian Fundamentalism The New York Review of Books Volume 44, Number 10 · June 12, 1997

Gould, S.J. (1997) Evolution: The Pleasures of Pluralism The New York Review of Books Volume 44, Number 11 · June 26, 1997

Rose, S., Lewontin, R.C. and Kamin, L.J. (1984) Not in Our Genes. Penguin Books, New York.

John Dennehy's Citation Classic for this Week

 
Check out The Evilutionary Biologist for This Week's Citation Classic. This paper is one of the most important papers in molecular biology. For most people it was the proof that DNA is the genetic material.

Hershey, A.D. and Chase, M. (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36:39-56.

Sandwalk Rating

 

Toronto City Council Approves Yellow Ribbons.

 
Yesterday's report of the deaths of three Canadian soldiers in Afghanistan stampeded Toronto City Council into approving the yellow ribbon decals on fire trucks and ambulances [What Does the "Support Our Troops" Ribbon mean to You?].

The press release from City Council says it all [Statement by the City of Toronto “Support Our Troops” ribbons to remain on Fire, EMS vehicles]. There's talk on the radio that the decals will also be placed on police cars. That's insane—I hope it's a false rumour.

Toronto City Council today voted unanimously to continue the ribbon campaign on Toronto Fire and EMS vehicles for an indefinite period of time as a show of support for the Canadian Forces Personnel Support Agency.

In recommending that City Council unanimously endorse the continuation of the ribbon campaign, Mayor David Miller said that all of Canada’s men and women serving in the military have the unwavering support of all Torontonians.

Toronto’s emergency services train and work closely with the Canadian Armed Forces. They share the common thread of personal sacrifice, dedication and professionalism with Canadian forces and the two services will continue to support and work with Canada’s military.

Circular University of Toronto

 
The main front campus of the University of Toronto is a popular place these days as parades of graduating students walk across it on their way to Convocation Hall.

This photograph was taken by Sam Javanrouh at daily dose of imagery [King's College Circle]. My building (Medical Sciences Building) is at 1 o'clock. The science library is at 10 o'clock and Convocation Hall is at 3 o'clock.

Evolution Ad Wins Award

 
No, unfortunately it's not that kind of evolution. This famous commercial produced by Ogilvy & Mather of Toronto, won the Grand Prix for viral marketing at Cannes as reported in today's Toronto Star [Dove's `Evolution' ad wins at Cannes]. It may not be biological evolution but the commercial sends a powerful message anyway.

Canadians Not So Sure About Evolution

 
A recent Angus Reid poll shows that only 59% of Canadians accept evolution [What does that Darwin know anyway?]. In Ontario that number drops to only 51%.

While the influence of Young Earth Creationism remains low (~25%), there are some surprising differences among the various regions in Canada. Only 9% of the people in Quebec are creationists but that number rises to 33% on the Prairies.

	Evolution: Human beings evolved from less advanced life forms over millions of years	Creation: God created human beings in their present form within the last 10,000 years	Not sure
British Columbia	65%	21%	15%
Alberta	58%	28%	14%
Manitoba/Saskatchewan	56%	33%	11%
Ontario	51%	26%	23%
Quebec	71%	9%	20%
Atlantic	53%	26%	21%
Canada	59%	22%	19%
United States*	53%	66%	3%

*USA Today/Gallup Poll (separate questions)

It's clear we have our work cut out for us if we are to convince Canadians that evolution is the correct view. We need to work on converting that 19% who still aren't sure.

[Hat Tip: a gloating John Pieret]

Tangled Bank #82

 
The latest version of Tangled Bank has been posted on Greg Laden's blog.

This is a review by Derwin Darwin II with the title: Various Proofs of the Theory of Evolution presented in original form by my uncle, the honorable Charles Darwin in the year 1859 and in subsequent years.

Very entertaining. Thanks Greg.

Evolutionary Biologists Flunk Religion Poll

 
In a follow-up to previous studies, Gregory W. Graffin and William B. Provine surveyed prominent evolutionary biologists to find out what they thought about religion. The results are summarized in the latest issue of American Scientst [Evolution, Religion and Free Will]. (Click on the figure to see a larger version where you can read the fine print.)

Our study was the first poll to focus solely on eminent evolutionists and their views of religion. As a dissertation project, one of us (Graffin) prepared and sent a detailed questionnaire on evolution and religion to 271 professional evolutionary scientists elected to membership in 28 honorific national academies around the world, and 149 (55 percent) answered the questionnaire. All of them listed evolution (specifically organismic), phylogenetics, population biology/genetics, paleontology/paleoecology/paleobiology, systematics, organismal adaptation or fitness as at least one of their research interests. Graffin also interviewed 12 prestigious evolutionists from the sample group on the relation between modern evolutionary biology and religion.

A primary complaint of scientists who answered the earlier polls was that the concept of God was limited to a "personal God." Leuba considered an impersonal God as equivalent to pure naturalism and classified advocates of deism as nonbelievers. We designed the current study to distinguish theism from deism—that is to day a "personal God" (theism) versus an "impersonal God" who created the universe, all forces and matter, but does not intervene in daily events (deism). An evolutionist can be considered religious, in our poll, if he calls himself a deist. ...

Perhaps the most revealing question in the poll asked the respondent to choose the letter that most closely represented where her views belonged on a ternary diagram. The great majority of the evolutionists polled (78 percent) chose A, billing themselves as pure naturalists. Only two out of 149 described themselves as full theists (F), two as more theist than naturalist (D) and three as theistic naturalists (B). Taken together, the advocacy of any degree of theism is the lowest percentage measured in any poll of biologists' beliefs so far (4.7 percent).

No evolutionary scientists in this study chose pure deism (I), but the deistic side of the diagram is heavy compared to the theistic side. Eleven respondents chose C, and 10 chose other regions on the right side of the diagram (E, H or J). Most evolutionary scientists who billed themselves as believers in God were deists (21) rather than theists (7).

When asked directly whether they believe in God, almost 80% said no. I wonder how many of them think of themselves as atheists as opposed to agnostics?

Here's the bad news. 79% of these eminent evolutionary biologists say they believe in free will (option A on the question). Even the authors of the study were surprised by that one.

We anticipated a much higher percentage for option B and a low percentage for A, but got just the opposite result. One of us (Provine) has been thinking about human free will for almost 40 years, has read most of the philosophical literature on the subject and polls his undergraduate evolution class (200-plus students) each year on belief in free will. Year after year, 90 percent or more favor the idea of human free will for a very specific reason: They think that if people make choices, they have free will. The professional debate about free will has moved far from this position, because what counts is whether the choice is free or determined, not whether human beings make choices. People and animals both certainly choose constantly. Comments from the evolutionists suggest that they were equating human choice and human free will. In other words, although eminent, our respondents had not thought about free will much beyond the students in introductory evolution classes. Evolutionary biology is increasingly applied to psychology. Belief in free will adds nothing to the science of human behavior.

There's one other surprise. 72% think that religion is part of evolution—it's an adaptation. One can only wonder what these evolutionary biologists think of themselves. Are they able to overcome their deterministic predisposition to God or are they mutants who lack the gene(s)? Maybe it explains why they believe in free will?

[Hat Tip: Denyse O'Leary]

Denyse O'Leary Has Advice for the Fans of Francis Collins

 
From Me?: Something against Francis Collins? No!.

On the other hand, I admit to deep disappointment in the intellectual substance of Collins’ arguments, which I unpack in the multipart review at Access Research Network.

Note to all, especially Collins fans: C. S. Lewis is not a security blanket, and the debate over the origin of free will, morality, altruism, and consciousness has moved on from his day. Today's atheist is not usually a genial, classical God-denier; he is a radical materialist who honestly believes that we are all just robots replicating our selfish genes. And he cannot wait to get his gospel onto the curriculum of publicly funded schools, as "evolutionary psychology," forcing everyone's nose into his nonsense.

Hmmm ... I don't know of very many radical materialist atheists who fall for evolutionary psychology. I wonder who she could be talking about? Maybe it's PZ?

Nobel Laureates: Richard Roberts and Phillip Sharp

 
The Nobel Prize in Physiology or Medicine 1993.

"for their discoveries of split genes"

Richard J. Roberts (1943 - ) and Phillip A. Sharp (1944 - ) received the Nobel Prize in Physiology or Medicine for their discovery of interrupted genes and splicing in eukaryotes [see RNA Splicing: Introns and Exons and Monday's Molecule #31].

Roberts and Sharp discovered that the genes in adenovirus were split into various segments that were combined during RNA processing. The results started to become widely known in 1975-76 and the key papers were published in 1977. Later this gene organization was found to be common in chromosomal eukaryotic genes. Unlike many Nobel Prize discoveries, this one really was revolutionary. Here's the presentation speech by Professor Bertil Daneholt of the Nobel Assembly of the Karolinska Institute.

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

Why do children resemble their parents? This question has probably always fascinated humans, but not until the advent of natural science have we arrived at an increasingly satisfactory answer.

In the middle of the last century, the Austrian monk Gregor Mendel conducted his famous breeding experiments with the garden pea. He concluded that every trait of an individual plant is determined by a set of two genes, one obtained from each parental plant. To Mendel a gene was an abstract concept, which he used to interpret his breeding experiments. He had no idea of the physical properties of genes.

Only in the mid-1940s could it be established that in terms of chemistry, genetic material is composed of the nucleic acid DNA. About ten years later the double helical structure of DNA was revealed. Ever since then, progress within the field of molecular biology has been very rapid, and several Nobel prizes have been awarded in this area of research.

Initially, genetic material was studied mainly in simple organisms, particularly in bacteria and bacterial viruses. It was shown that a gene occurs in the form of a single continuous segment of the long, thread-like DNA, and it was generally assumed that the genes in all organisms looked this way. Therefore, it was a scientific sensation when this year's Nobel Laureates, Richard Roberts and Phillip Sharp, in 1977, independently of each other, observed that a gene in higher organisms could be present in the genetic material as several distinct and separate segments. Such a gene resembles a mosaic. Both Roberts and Sharp analyzed an upper respiratory virus, which is particularly suitable for studies of the genetic material in complex organisms. It soon became apparent that most genes in higher organisms, including ourselves, exhibited this mosaic structure.

Roberts' and Sharp's discovery opened up a new perspective on evolution, that is, on how simple organisms develop into more complex ones. Earlier it was believed that genes evolve mainly through the accumulation of small discrete changes in the genetic material. But their mosaic gene structure also permits higher organisms to restructure genes in another, more efficient way. This is because during the course of evolution, gene segments - the individual pieces of the mosaic - are regrouped in the genetic material, which creates new mosaic patterns and hence new genes. This reshuffling process presumably explains the rapid evolution of higher organisms.

Roberts and Sharp also predicted that a specific genetic mechanism is required to enable split genes to direct the synthesis of proteins and thereby to determine the properties of the cell. Researchers had known for many years that a gene contains detailed instructions on how to build a protein. This instruction is first copied from DNA to another type of nucleic acid, known as messenger RNA. Subsequently, the RNA instruction is read, and the protein is synthesized. What Roberts and Sharp were now stating was that the messenger RNA in higher organisms has to be edited. The required process, called splicing, resembles the work that a film editor performs: the unedited film is scrutinized, the superfluous parts are cut out and the remaining ones are joined to form the completed film. Messenger RNA treated in this manner contains only those parts that match the gene segments. It later turned out that the same parts of the original messenger RNA are not always saved during the editing- there are choices. This implies that splicing can regulate the function of the genetic material in a previously unknown way.

Roberts' and Sharp's discovery also helps us understand how diseases arise. One example is a form of anemia called thalassemia, which is due to inherited defects in the genetic material. Several of these defects cause errors in the editing process during splicing; thus, an abnormal messenger RNA is formed and subsequently also a protein that functions poorly or not at all.

The discovery of split genes was revolutionary, triggering an explosion of new scientific contributions. Today this discovery is of fundamental importance for research in biology as well as in medicine.

Dr. Richard Roberts and Dr. Phillip Sharp,

Your discovery of split genes led to the prediction of a new genetic process, that of RNA splicing. The discovery also changed our view of how genes in higher organisms develop during evolution. On behalf of the Nobel Assembly of the Karolinska Institute I wish to convey to you our warmest congratulations, and I now ask you to step forward to receive the Nobel Prize from the hands of His Majesty the King.

What Does the "Support Our Troops" Ribbon mean to You?

 
Since last October emergency vehicles in Toronto have been displaying a decal in support of our troops in Afghanistan. The decals were placed on the vehicles at the request of firefighters and paramedics, whose unions are strong supporters of the soldiers. The original deal was that the decals would stay on for one year and then be removed when the vehicles came in for routine maintenance this Fall.

The issue has turned into a hot political fight that will be decided today at a City Council meeting [Time limit for 'Support Our Troops' ribbons is up].

As you might imagine, there are some city councilors who want the decals to stay on the ambulances and fire trucks.

Some councilors believe the decision to remove the decals is a black mark on the city.

"I was stunned this morning to hear on the radio that some official at the city had ordered emergency services, particularly ambulances, to take off the decal that supports our troops in Afghanistan," city councilor Brian Aston told CTV News on Tuesday.

"These decals are on there and it makes a very strong statement. To take them off, Toronto is the largest city, would just be an outrage. It would be a black eye on the reputation of our city," Ashton said.

It should also come as no surprise that some councilors want to stick to the original agreement and remove the decals in September.

Coun. Janet Davis said just as many councillors want to see the decals removed as those who support their presence on emergency vehicles.

Mayor David Miller said while emergency crews should continue to support Canadian troops, the one-year time limit for the decals was enough time.

"It's controversial on both sides. There are people who see it as support for the troops and there are people who see it as support for war," Miller said.

I'm one of those who believe that the "Support the Troops" ribbon is a political statement. I don't know very many people who are opposed to the war but have this sticker on their car. On the surface it seems like a no-brainer to offer support to our troops while opposing the mission. But, in fact, the term "no-brainer" is quite appropriate in this case. By blindly advertising support for the military you obscure the true difficulty in making rational decisions about how to deploy our army. It's no secret that most people who "support our troops" are also conservatives who are in favour of the war.

The idea that the "Support Our Troops" yellow ribbons are politically neutral is something that only a supporter of the war would say. It's ridiculous. It would be like putting peace symbols on the trucks on the grounds that surely everyone supports peace.

I am very supportive of individual soldiers who are posted to Afghanistan. It's not their fault that our government is insane. They have to follow orders. But that does not mean that I "support our troops" in the way that the decal signifies. As a matter of fact, I do not support our mission in Afghanistan and I would withdraw the troops tomorrow if I could. Every soldier who dies in Afghanistan will have died in vain. That's hardly a way to offer support to our troops.

Having those decals on city vehicles sends the wrong message. For those of us who oppose the war it signifies that the fire fighters and paramedics are on the other side of the issue. That makes me uncomfortable since these are people who deserve my respect and admiration but they're not going to get it if they push a political agenda through advertising on their vehicles.

Take the decals off. It's no place for politics.

RNA Splicing: Introns and Exons

Most eukaryotic protein-encoding genes are interrupted. The coding regions are divided into numerous blocks called "exons" and the exons are separated by "introns."

An example is shown below. The triose phosphate isomerase (TPI) gene from maize is composed of 9 exons and 8 introns. (Triose phosphate isomerase is one of the enzymes in the glycolysis/gluconeogenesis pathway.)


The top line is a cartoon representation of the TPI gene with each exon in a different color. The thick gray lines between them represent the introns. The gene is transcribed from left (5′) to right (3′) beginning at the promoter (P). The long primary RNA transcript contains both intron and exon sequences. Subsequent processing of this primary transcript results in modification of the 5′ end by addition of an m⁷ GTP cap and modification of the 3′ end by addition of adenylate (A) residues to form the poly A tail. More importantly, the introns are spliced out and the exon sequences are fused to form the mature mRNA. This mRNA is then transported to the cytoplasm where it is translated into protein.

Note that all the coding regions in the exons (hatched) are contiguous in the mature mRNA. The relationship between the exons and the structure of the protein is shown on the right where the color of each segment of the protein corresponds to the color of the exons in the upper figure. There is no correlation between the exons and any protein domains or motifs. (It used to be thought that exons corresponded to domains in the protein.)

The splicing reaction is complicated. The cell must cleave the primary transcript at each end of the intron while holding on to the flanking exons so the chopped RNA transcript does not come apart. Then the two exons have to be joined together. For protein-encoding genes the splicing reactions are catalyzed by an RNA/protein complex called a spliceosome. In some cases, the introns can be thousands of nucleotides long—much longer than the exons.

Let's look at a simplified version of this reaction. The various components of the spliceosome have to assemble at the 5′ (left) end of an intron and at the 3′ end. There's a third site in the middle called the branch site. All three sites are identified by specific short sequences in the primary transcript as shown below.


These are the consensus sequences for vertebrates, including us. The splice site and branch site sequences in other species are similar but not identical.

In the first step of the splicing reaction, the various components of the spliceosome bind to the 5′ splice site, the 3′ splice site, and the branch site. Then the three complexes interact with each other to draw together the ends of the intron and position them near the branch site. This forms the spliceosome.

The first reaction involves an attack of the 2′ -OH group of the branch point adenylate residue on the 5′ splice site. This forms an intermediate where the branch site A residue is attached to three different ends of the primary transcript. The structure resembles a lariat or lasso. This is the structure depicted in Monday's Molecule #31.

Meanwhile, the 5′ end of the transcript is still bound to the spliceosome. This is important because it's about to be joined to the next exon and the reaction wouldn't work if the 5′ end were released following the first cleavage reaction.

In the next step, the spliceosome catalyzes the attack of the -OH group at the end of the 5′ exon on the 3′ splice site. This results in cleavage of the 3′ intron/exon junction and joining of the 5′ exon to the 3′ exon. The intron sequence (dark brown) is released as a lariat (looped) structure.

The two reactions are known as transesterification reactions because they require the breaking of one strand of RNA and formation of a new ester linkage. The details are not very important. What's important is to recognize that splicing depends on the correct interaction between the components of the spliceosome and the 5′ and 3′ splice site sequences (and the branch site).

These interactions are mediated by small RNAs that are bound to the spliceosome proteins. These RNAs are called small nuclear RNAs (snRNAs) and they're one example of a host of small RNAs produced by non-protein encoding genes. The snRNA/protein complexes are called small nuclear ribonuclear proteins or snRNPs (snurps).

The snRNAs are complimentary to the splice sites and branch sites and that's how the various snRNPs recognize them. This interaction is very weak since it depends on only three or four base pairs. It can be even less since there are many slice sites that are not perfect matches to the consensus sequences shown above. The relative lack of significant sequence similarity makes splicing a very error-prone reaction.

U1 snRNP recognizes 5′ splice sites, U2 snRNP binds to the branch site, and U5 snRNP binds to the 3′ splice site. A more detailed description of the formation of the splicesome is shown below.