I've been so busy lately that I forgot to mention the latest Carnival of Evolution. This is doubly embarrassing because it features one of my favorite blogs [Carnival of Evolution #28 - Featuring Sandwalk].
Be sure to answer the survey questions ...
WELCOME to the 28th edition of Carnival of Evolution! This time the carnival has returned home. Not since the first edition back in August 2008 has an edition been posted here. That is cause for celebration, so let's do that with a little survey. I am interested who reads Carnival of Evolution, so please spend the next two minutes tops taking this brief survey about yourself and CoE. Results will then be posted here for the bemusement of all.
The Velvet Underground was a New York rock band in the 1960s. It was never very popular and never made much money but it's said to have influenced many other, more successful, bands.
Chad Orzel asks you to identify The Velvet Underground of Science by which he means an individual who isn't very famous but had a huge impact on science. Naturally, he has an example from physics.
I have an example from molecular biology. Max Delbrück (1906-1981) was one of the founders of the 'phage school (along with Salvador Luria). Delbrück began his science career as a physicist but when he went to the USA he switched to biology and soon became interested in bacteria and bacteriophage.1 During the 40s, 50s, and 60s he had a huge influence on the members of the 'phage group who used to meet regularly at Cold Spring Harbor where Delbrück taught a summer course in 'phage genetics.
Jim Watson, Matt Meselson, Franklin Stahl, Gunther Stent, Seymour Benzer, Edward Kellenberger, and Alfred Hershey are just a few of the scientists who were directly influenced by Delbrück. They all got together to contribute to Phage and the Origins of Molecular Biology in 1966. The book was a Festschrift in honor of Max Delbrück on his 60th birthday.
There were many more second and third generation scientists who grew up in the 'phage group. My own supervisor used to refer frequently to Delbrück's "Principle of Limited Sloppiness" as an effective way of doing science.
Delbrück, Alfred D. Hershey, and Luria won the Nobel Prize in 1969 but he (Delbrück) is still not very well known among today's students. I think that every biochemistry and molecular biology student should have to read The Eighth Day of Creation by Horace Freeland Judson in order to learn the history of their field.
They might discover that much of what they think of as "modern" was actually understood almost half a century ago.
Photo Credits: Top: Delbrück in the early 1940s from Wikipedia. Bottom: Delbrück and Luria at Cold Spring Harbor in 1953.
1. Physics was too easy—he wanted more of a challenge.
The article in question is by Steve Talbott1 and it's published in The New Atlantis: Getting Over the Code Delusion. Here's how the editors introduce the article ...
Editor’s Note: This is the first in a planned set of essays by Mr. Talbott explaining the significance of a revolution in genetics and molecular biology that has only just begun to receive public attention. Although this essay is at times necessarily technical, we trust that our readers will not find it prohibitively so — and we have appended a modest and informal glossary to help smooth the path.
You all know where this is going, don't you?
Talbot sets up his "revolution" by describing several problems.
A number of conundrums have helped to nudge molecular biology toward a more contextualized understanding of the gene. To begin with, the Human Genome Project revised the human gene count downward from 100,000 to 20,000–25,000. What made the figure startling was the fact that much simpler creatures — for example, a tiny, transparent roundworm — were found to have roughly the same number of genes. More recently, researchers have turned up a pea aphid with 34,600 genes and a water flea with 39,000 genes. Not even the "chimps are human" boosters were ready to set themselves on the same scale with a water flea. The difference in gene counts required some sort of shift in understanding.
A second oddity centered on the fact that, upon "deciphering" the genetic Book of Life, we found that our coding scheme made the vast bulk of it read like nonsense. That is, some 95 or 98 percent of human DNA was useless for making proteins. Most of this "noncoding DNA" was at first dismissed as "junk" — meaningless evolutionary detritus accumulated over the ages. At best, it was viewed as a kind of bag of spare parts, borne by cells from one generation to another for possible employment in future genomic innovations. But that’s an awful lot of junk for a cell to have to lug around, duplicate at every cell division, and otherwise manage on a continuing basis.
In this day and age, anyone who equates junk DNA with non-coding DNA isn't worth reading. They've lost all credibility as far as I'm concerned.
Talbott explains the solution later on in his article when he says ...
So what’s going on? These puzzles turn out to be intimately related. As organisms rise on the evolutionary scale, they tend to have more "junk DNA." Noncoding DNA accounts for some 10 percent of the genome in many one-celled organisms, 75 percent in roundworms, and 98 percent in humans. The ironic suspicion became too obvious to ignore: maybe it’s precisely our "junk" that differentiates us from water fleas. Maybe what counts most is not so much the genes themselves as the way they are regulated and expressed. Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.
Anyone who states or implies that there is a significant correlation between total haploid genome size and species complexity is either ignorant or lying.
Larry Moran Genome Size, Complexity, and the C-Value Paradox"Organism rise on the evolutionary scale"? Has Talbott done any research at all for this article? His understanding of evolution is no greater than kindergarten level if he believes that there's an evolutionary scale with us near the top.
The idea that noncoding DNA contains sequences that govern gene expression has been with us for fifty years. That's hardly revolutionary. The idea that the amount of junk DNA in a genome equates to complexity has been soundly disproven. The idea that humans might need a million base pairs of DNA to control expression of every gene is ludicrous and has absolutely no evidence to support it. In fact, nobody I know has ever shown that mammalian genes require more regulatory sequences than insect genes or those of crustaceans (water fleas). What we have here is a perfect example of The Deflated Ego Problem.
What about the third "conundrum"?
Another conundrum — perhaps the most decisive one — has been recognized and wrestled with (or more often just ignored) since the early twentieth century. With few exceptions, every different type of cell in the human body contains the same chromosomes and the same DNA sequence as the original, single-celled zygote. Yet somehow this zygote manages to differentiate into every manner of tissue — liver, skin, muscle, brain, blood, bone, retina, and so on. If genes determine the form and substance of the organism, how is it that such radically different cellular architectures result from the same genes? What directs genes to produce the intricately sculpted and differentiated form of a complex organism, and how can this directing agency be governed by the very genes that it directs?
We've known the basic answer to this "conundrum" for about five decades. Talbott's idea of a revolution is very strange.
Don't bother reading the article in The New Atlantis. There's nothing "new" there and it may make you very angry.
1. Steve Talbott is a Senior Researcher at The Nature Institute. "My primary undertaking right now is a critique of conventional science with a view toward establishing the foundations of a new, qualitative science. The project, which requires an extraordinarily radical assessment of contemporary habits of thought, is headquartered here."
Science and Religion: Confrontation or Accommodation?
How should secular humanists respond to science and religion? If we champion science, must we oppose faith? How best to approach flashpoints like evolution education? A wide-ranging examination featuring a spectrum of distinguished panelists:
* Jennifer Michael Hecht (moderator) * PZ Myers * Eugenie Scott * Chris Mooney * Victor Stenger
This is a technological achievement, one that was based on years of work with other animals.
I do not favor awarding Nobel Prizes for technology. I prefer to give the science prizes to those who have advanced our fundamental understanding of the universe. This prize is for medicine, which is technology, so it doesn't violate any rules. But in the past the prize in Physiology or Medicine has usually been for basic research.
It worries me that there may have been non-scientific motives behind this year's selection. We saw a horrid example of that last year when the Nobel Peace Prize was announced and I hope this isn't a trend.
As well as leading to a host of new treatments for infertility, the work also founded the principles behind stem cell research, cloning and techniques that would allow couples to prevent passing on inheritable diseases to their children.
Christer Höög, professor of molecular biology at the Karolinska Institute in Stockholm, and a member of the Nobel Prize Committee, said the birth represented a "paradigm shift"
"It showed for the first time that it is possible to treat infertility," he said.
Prof Edwards' work was highly controversial at the time and there was strong opposition to what was seen as 'playing God' and the research had to be privately funded.
There are two main problems with Intelligent Design Creationism. The first is that the IDiots never have anything positive to offer by way of explanation. They complain about how evolution can never do this or that but they never give us a better explanation based on their beliefs. The second problem is that the IDiots often get their science wrong when they complain about evolution. Sometimes this is deliberate, but in many cases it's because they just don't understand what they're criticizing.
Their criticisms of evolution are based on the notion of a false dichotomy. They think that there are only two choices: their conception of evolution, or Intelligent Design Creationism. Thus, if they can refute their version of evolution it follows that creationism must be true.
People often make the claim that Intelligent Design Creationism isn't science. That may be true if you only think of it as promoting the idea of an intelligent designer but even there it depends on how you define science. However, much of the Intelligent Design Creationism literature isn't about defending creationism, it's about attacking evolution and those arguments definitely fall within the definition of science. As scientists, we have to deal with all the objections to evolution no matter what the motives of the challengers.
I think it's somewhat simplistic to dismiss all the Intelligent Design Creationist literature on the grounds that it's not science. Some of it has all the earmarks of science, it's just bad science. And bad science isn't limited to IDiots. I think there are many Theistic Evolutionists who are also guilty of promoting bad science and there are many atheist scientists who are just as guilty. The peer-reviewed scientific literature is full of examples.
Although it makes my American friends cringe, I favor teaching the controversy. It's the only way to show students the difference between good science and bad science.
Some of the Intelligent Design Creationists can craft pretty convincing arguments against evolution. It takes a lot of work to refute them. I going to give you an example of such an argument from The Edge of Evolution by Michael Behe. Let's see how you do.
The Two Binding Sites Rule
Behe's version of the history of life requires a God who intervenes quite frequently to create specific mutations that are almost impossible to account for by random mutation. Behe makes a good case for the problems with random mutation. In fact, his arguments are similar to those put forth by the mutationist camp—a group that I'm in sympathy with. Most biologists would not be able to refute Behe's arguments because they would agree with some of his false premises.
Behe's "Two Binding Sites Rule" is a good example. He argues that in order for two proteins to interact, evolution needs to create a small patch on the surface of each protein where five or six amino acid side chains become compatible with binding. Some of these changes could be neutral so they could arise independently but the analysis of hundreds of known binding sites shows that many of the mutations would be detrimental if they occurred by themselves—a single charged amino acid residue on the surface, for example.
It looks like you need to wait for three or four specific mutations to occur simultaneously in order to get a moderate interaction between two proteins that did not originally bind to each other. And these can't be just any proteins, they have to be proteins where there is a selective advantage to forming a complex. The example I've chosen is a bacterial photosynthesis reaction center where four polypeptides (gold, blue, green, purple) interact with each other and with multiple cofactors (space-filling molecules) to form a very complicated structure. Presumably, there was a time in the past when some of these proteins didn't bind to each other or to the cofactors. Over time, evolution favored variants that could form the complex. How could this happen according to evolutionary theory?
Studies on in vitro mutagenesis show that the probability of forming any de novo binding site is very low. For example, it's quite difficult to engineer specific antibodies that will bind to a particular antigen. The data shows us that you need a library of more than one billion antibody molecules in order to get one that will bind. Those one billion mutations are far from random. They are engineered so that they are confined to a small patch on the surface of the antibody where it is known that other proteins can potentially bind.
Behe argues from this evidence that the probability of creating a new binding site by random mutations is exceedingly small. So small, in fact, that such mutations would only arise in very large populations after several hundred million years of evolution. He bases his argument on some experiments he describes in the first few chapters or his book.
Behe points out that it is sometimes very difficult for the malaria-causing parasite, Plasmodium falciparum, to develop resistance to some drugs used to treat malaria. That's because the resistance gene has to acquire two specific mutations in order to become resistant. A single mutation does not confer resistance and, in many cases, the single mutation is actually detrimental. P. falciparum can become resistant because the population of these single-cell organisms is huge and they reproduce rapidly. Thus, even though the probability of a double mutation is low it will still happen.
If the probability of a single mutation is about 10-10 per generation then the probability of a double mutation is 10-20. He refers to this kind of double mutation as CCC, for "chloroquine-complexity cluster," named after mutation to chloroquine resistance in P. falciparum.1 Behe's calculation is correct. If two simultaneous are required then the probability will, indeed, be close to 1 in 1020.
Let's see how this relates to the evolution of protein-protein interactions. Here's how Behe describes it on page 135 of his book.
Now suppose that, in order to acquire some new, useful property, not just one but two new protein-binding sites had to develop. A CCC requires, on average, 1020, a hundred billion billion, organisms—more than the number of mammals that has ever existed on earth. So if other things were equal, the likelihood of getting two new binding sites would be what we called in Chapter 3 a "double CCC"—the square of a CCC, or one in ten to the fortieth power. Since that's more cells than likely have ever existed on earth, such an event would not be expected to have happened by Darwinian processes in the history of the world. Admittedly, statistics are all about averages, so some freak event like this might happen—it's not ruled out by the force of logic. But it's not biologically reasonable to expect it, or less likely events that occurred in the common descent of life on earth. In short, complexes of just three or more different proteins are beyond the edge of evolution. They are lost in shape space.
We're all pretty knowledgeable here but how many of you can immediately refute that argument? If you can't then you have no business accusing Behe of being stupid or silly and of dismissing his book as just another example of creationist ignorance. The correct explanation of the problem will undoubtedly appear soon in the comments. Before peeking, why not try and see how you would answer Behe if you were debating him in front of a large audience of creationists?
1. Behe may have been wrong about the specific chloroquine resistance mutation he used as an example. The two mutations may not have occurred simultaneously. Nevertheless, the principle is sound. If the single mutations are detrimental then you need both to get resistance and the probablity of two such mutations occurring together is 10-20.
Brian Dalton is Mr. Deity. If you haven't been watching all the episodes over the past few years then go to the website and buy the DVD. You won't regret it.
Brian is as funny in person as he is on the videos. He explained how "Mr Deity and the Virgin" was inspired by a debate he saw on TV.
Brian's wife, Amy Rohren, plays "Lucy" (Lucifer, Satan), Sean Douglas plays Jesus, and Jimbo Marshall is God's chief of staff.
One of my personal favorites is "Mr. Deity and the Really Unique Gift."
This brings me to my challenge. I challenge all theists and all their accommodationist friends to post their very best 21st century, sophisticated (or not), arguments for the existence of God. They can put them in the comments section of this posting, or on any of the other atheist blogs, or on their own blogs and websites. Just send me the link.
Try and make it concise and to the point. It would be nice if it's less than 100 years old. Keep in mind that there are over 1000 different gods so it would be helpful to explain just which gods the argument applies to.
There have been over 500 comments on that posting and dozens of attempts to meet the challenge, ranging from the fact that Babylon hasn't been re-built to variations of the old Cosmological and Ontological Arguments that have been around for centuries.
I think it's fair to say that nobody came up with anything that even remotely resembles a modern "sophisticated" argument that the Gnu Atheists are ignoring. Therefore, I declare victory.
From now on, whenever any accommdationist or theist accuses me of not having studied philosophy or theology I'll point them to my post and remind them that the Emperor really doesn't have any clothes. That includes a few people who sent me email messages explaining why they wouldn't lower themselves to post a comment on my blog. They implied that they still had some really good arguments for the existence of God but they aren't going to reveal them to me because I wouldn't understand them.
Seanna Watson, Steve Watson, Sue Strandberg, and a photo bomber.
This photo is from last night after dinner. Today at noon I was witness to the strangest phenomonon—before we could sneak away for lunch, there were no less than 14 people who deliberately took photographs of this man. Sometimes I had to photograph him with various people using their cameras.1 What is it about this guy? He's not particularly photogenic.
Yesterday we were part of a live podcast moderated by three Montreal Atheists; Jacon Fortin, Ryan Harkness, and Jeffrey Jones. They talked about dicks and how to be one. Phil Plait would not have been pleased!
I really don't like Darwin worship. It's true that I think he was the greatest scientist who ever lived, but science has moved on since 1859. Modern scientists respect, but do not worship, the past.
There are a couple of other problems with the lyrics. I'm confused about the reference to "theory" as some kind of "abstraction" and I don't like the implication that we go back and read Darwin to refresh our memory about modern evolutionary theory.
I also don't like the simplistic explanation of how real science is done. It's a common myth that publishing a peer-reviewed paper is the only way to do science. There are two things wrong with this mythology. First are the obvious exceptions, Origin of Species being one of them. Second, there's plenty of bad science papers in the peer-reviewed literature. Publishing in the peer-reviewed literature is neither necessary, nor sufficient, as a measure of good science.
I'll be in Montréal, Québec, Canada this weekend attending the Atheist Alliance International (AAI) convention, Atheists Without Borders (Atheés Sans Frontières).
I'm arriving around 6pm on Thursday and leaving Sunday afternoon. Anyone else going? Contact me by email so we can get together. Maybe food and beverages on Thursday evening? (My address is at the top of the left sidebar.)
Most of Montréal is on a large island in the middle of the St. Lawrence river. The site was occupied by the St. Lawrence Iroquois when the first Europeans arrived in the 1530's. They had established a large village called Hochelaga but this village was largely deserted by the time Europeans constructed the first settlement in 1611.1 My ancestor, Barthélemy Montarras, was a soldier in the Compagnie Froment, Le régiment de Carignan, based in Montréal around 1665.
The dominant feature of the city is Mont Royal (Mount Royal) a group of hills right in the middle of Montréal island. The hills were first scaled by Jacques Cartier in 1535. A wooden cross was erected in 1635. The giant illuminated cross that we see today was built in 1924.
Montréal has several half-decent universities but, more importantly, it has many excellent bistros and cafés. I hope to try several of them this weekend. There are some special dishes that you just can't get in Toronto—or if you can get them, they're not nearly as good. It's sad that some of my friends won't be able to sample the smoked meat or the poutine due to restrictions imposed by their doctor.
1. Quebec City was founded in 1608. Santa Fe, New Mexico in 1608 and the Mayflower arrived in Massachusetts in 1620.
The video below shows Stephen Meyer explaining evolution to the people who attended the Four Nails in Darwin's Coffin event at Southern Medodist University.
I'm posting this for my students in the class I teach on scientific controversies. One of the fundamental principles of any debate is to define your terms in a way that's intellectually honest and consistent. In the case of the creation/evolution debate, if there's actually a scientific controversy (there isn't) then everyone should be using the best scientific definition of evolution.
In his latest book, Signature in the Cell, Meyer refers to "modern" evolutionary theory as "neo-Darwinism." He never defines it but it's clear that he thinks of neo-Darwinism as the idea that mutation and natural selection are all there is to evolution. It's clear that Stephen Meyer has not read any modern textbook on evolution.
Watch the video and see how Meyer explains evolution to his mostly scientifically illiterate audience. At 6 minutes he says, "What we want to address tonight is the question of whether or not the principle neo-Darwinian mechanism of mutation and selection is sufficient to produce the forms of life that we see."
The scientific answer to this question is "no," mutation and selection are not sufficient. You also need random genetic drift, speciation, and geological events such as meteor impacts and ice ages in order to account for life as we see it today. (That's not an exclusive list, see Macroevolution.)
Meyer, and the next speaker, Richard Sternberg, are criticizing the ability of natural selection to explain the evolution of new forms in just a few million years. Most of their criticisms would apply to ALL explanations of evolution and not just those that rely only on mutation and natural selection but their arguments are much weakened by their lack of knowledge of modern evolutionary theory. It seems easy for them to knock down the strawman version of evolution that they don't believe in.
If there's a genuine scientific controversy here, you'll never learn about it by listening to these IDiots. However, it's worth noting that the quality of debate in the evolution/creation wars has improved considerably over the past thirty years. It used to be the case that any college student could instantly recognize the main flaws in the creationist position. Today, the average college biology student would have a great deal of difficulty debating Stephen Meyer, Richard Sternberg, Michael Behe, or Doug Axe. (Jonathan Wells? Not so much.) In part, that's because the average college student doesn't know enough about evolution. We aren't doing a very good job of teaching evolution.
Martin Rees is the President of the Royal Society in the UK. This is a position of enormous influence. When Rees speaks you can assume that he is representing the position of the Royal Society, or at least it's leaders.
He is equally scathing about Hawking's more recent comments about there being no need for God in order to explain creation. "Stephen Hawking is a remarkable person whom I've know for 40 years and for that reason any oracular statement he makes gets exaggerated publicity. I know Stephen Hawking well enough to know that he has read very little philosophy and even less theology, so I don't think we should attach any weight to his views on this topic," he said.
Unlike many of the Fellows of the Royal Society he has presided over in the past five years, Lord Rees is not a militant atheist who goes out of his way to insult people of belief – Richard Dawkins once called him "a compliant quisling" for his tolerance of religion.
"I would support peaceful co-existence between religion and science because they concern different domains," Lord Rees said. "Anyone who takes theology seriously knows that it's not a matter of using it to explain things that scientists are mystified by."
His next popular science book is about these things that science still cannot explain, such as the origin of life on Earth and the scientific nature of human consciousness. This, he insisted, is what science is really about, and why it has the power to touch everyone of every culture.
I don't have time for a detailed explanation of this particular accommodationist position so I'll just note a few points.
Hawking said there's no need for God but his views can be dismissed because (unlike Martin Rees?) he's not an expert on philosophy and theology.
Rees does not go out of his way to insult people of belief. Good for him. Neither do lots of atheists, including Stephen Hawking. What's the point? Sounds to me like Dawkins might have been correct.
Did Martin Rees just go out of his way to insult atheists like Stephen Hawking? I guess atheists don't deserve the same kid-gloves treatment that we owe to theists.
Religion and science concern different domains. So they do. Religion is firmly planted in the domain of mythology and superstition. What does that prove?
Martin Rees is an astronomer. He's writing a book about the origin of life and human consciousness. I wonder if we should bother paying any attention to this book since he's not an expert in biology?
I've been so busy lately that I forgot to mention the latest Carnival of Evolution. This is doubly embarrassing because it features one of my favorite blogs [Carnival of Evolution #28 - Featuring Sandwalk].
