Science Blogs vs Scientific Literature

 
Royce Murray is a highly respected scientist. He doesn't like science blogs, a point he makes in an editorial published in Analytical Chemsitry [Science Blogs and Caveat Emptor].

David Kroll discusses Murray's ignorance of scienc blogs in an article on Terra Sigellata [“The current phenomenon of ‘bloggers’ should be of serious concern to scientists”]. I urge you to read Kroll's article to see why Royce Murray is so wrong about blogs.

I'd like to make another point. Murray begins his editorial with ...

If you are a science scholar, you hope that all scientific articles that you read are grounded in fact. There is a lot of background information to guide you, including statistical data on what professional journals are read widely, with papers therein that produce citations by other subsequent papers and in general, influence the direction of forthcoming new science. As scholars publishing in professional journals, we are schooled in the importance of factual reliability and impact of articles we read in science journals. In terms of impact, we know of various collective valuations of journals through metrics like the so-called “Impact Factor”. By extension, editors and reviewers reinforce the meaningfulness of Impact Factors by explicit attention to the reliability of submitted articles; if the Scientific Method has not been adequately followed, then there should be a downwardly adjusted evaluation of impact. The picture of scientifically grounded innovations feeding progress in science is well established. I firmly believe that this system has served science well and that the scientific literature has provided generally reliable information and vast benefits to society over the centuries to the present and will continue doing so into the future.

I don't disagree with the final conclusion; namely that publication in scientific journals has served science well over the past 150 years. However, I do disagree with the general tone of this paragraph because it fails to recognize the poor quality of many papers that are published in the scientific literature. The focus on "impact factor" is especially disappointing since it caters to "me-too" science and not true innovation and risk-taking.

Royce Murray's criticism of science blogs would be a lot more credible if he were more honest about the limitations of the scientific literature. The lack of credibility in the scientific literature is often responsible for bad journalism and leads to an incorrect view of science among the general public. How many times have you seen an article in the popular press that's based on a bad scientific paper? How many times do we have to read about new cures for cancer before we admit that the scientific literature isn't all it's cracked up to be? And let's not even talk about fields like evolutionary psychology.

Fact is, the peer-reviewed scientific literature hasn't been very successful at weeding out bad science. It's about time we recognized this and tried to find a way to fix it. One of the advantages of blogs is that they frequently highlight the bad papers that make it into the scientific literature—they also point to the good papers.

Before blogs, there was no good way for the scientific community to critique the scientific literature. Some scientists think that papers in the peer-reviewed scientific literature should be immune from such criticism from the outside. They think that the only criticism should come from within the scientific literature. In other words, if you don't like a paper you have to publish another paper refuting the science.

One of the strange things about this attitude is that those very same scientists are very happy about issuing press releases and very happy to have their work praised in the popular press.

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Philosophers, Science, and Creationism

Investigating the boundary between science and religion

Richard Johns is a Sessional Instructor in the Department of Philosophy at the University of British Columbia. He came to my attention because he just posted a note on Uncommon Descent where he points us to a paper he recently published. Here's the link to his posting: The Limits of Self Organization.

You know as well as I do that anyone posting on that blog is a creationist, specifically an Intelligent Design Creationist. Thus, it won't surprise you to read that his work supports that version of creationism even if the paper itself doesn't mention Intelligent Design Creationism. (Where have we heard that before?)

I’m writing to tell people about a paper of mine that was published in Synthese last month, titled: "Self-organisation in dynamical systems: a limiting result". While the paper doesn’t address intelligent design as such, it indirectly establishes strict limits to what such evolutionary mechanisms as natural selection can accomplish. In particular, it shows that physical laws, operating on an initially random arrangement of matter, cannot produce complex objects with any reasonable chance in any reasonable time.

Synthese is "An International Journal for Epistemology, Methodology and Philosophy of Science." It is not a science journal. Please keep that in mind. Here's a link to Richard Johns' article published online last month [Self-organisation in dynamical systems: a limiting result]. Most of you won't be able to see that article so he kindly provided a link to Pre-published version.

The abstract makes you sit up and take notice.

Abstract
There is presently considerable interest in the phenomenon of “self-organisation” in dynamical systems. The rough idea of self-organisation is that a structure appears “by itself” in a dynamical system, with reasonably high probability, in a reasonably short time, with no help from a special initial state, or interaction with an external system. What is often missed, however, is that the standard evolutionary account of the origin of multi-cellular life fits this definition, so that higher living organisms are also products of self-organisation. Very few kinds of object can self-organise, and the question of what such objects are like is a suitable mathematical problem. Extending the familiar notion of algorithmic complexity into the context of dynamical systems, we obtain a notion of “dynamical complexity”. A simple theorem then shows that only objects of very low dynamical complexity can self organise, so that living organisms must be of low dynamical complexity. On the other hand, symmetry considerations suggest that living organisms are highly complex, relative to the dynamical laws, due to their large size and high degree of irregularity. In particular, it is shown that since dynamical laws operate locally, and do not vary across space and time, they cannot produce any specific large and irregular structure with high probability in a short time. These arguments suggest that standard evolutionary theories of the origin of higher organisms are incomplete.

All the code words are there. There's no way the editors of Synthese could be unaware of the implications of this work. It purports to be evidence of the existence of God. We can safely conclude that the discipline of philosophy has admitted the possibility that science could prove the existence of God.

(Don't bother reading the paper. It's one of those complicated lines of argument involving lots of mathematical equations. There probably aren't more than a few dozen people in the entire world who can understand the paper and offer objective criticism. I don't know if any of them reviewed the paper—I suspect not, but what do I know?)

Richard Johns concludes that current evolutionary theory is incomplete.

I have argued that there is an important limitation on the kinds of object that can appear spontaneously in a dynamical system. Such systems, with laws that operate locally and invariantly across space and time, are able to control only the local structure of the state. The state as a whole is therefore uncontrolled, except insofar as it is constrained by the local structure. This led us to the Limitative Theorem, which says that an irregular object, i.e. one that is largely undetermined by its local structure, cannot easily be produced in a dynamical system. Indeed, it was shown that its production is no easier than the appearance of an object of very similar size in a purely random system.

This result, while relevant to biology, does not of course contradict the theory of evolution in its most general form, i.e. that life evolved through a process of descent with modification. This is just as well, since the historical process of phylogeny is very well supported by the evidence. Nevertheless, the Limitative Theorem does suggest that the currently recognised processes driving evolutionary change are incomplete.

Doesn't this create some problems concerning the border between science and philosophy? You betcha, and Richard Johns is fully aware of the implications. Here's what he wrote on his blog [Why should self-organisation be limited?].

My theorem is also pure doom and gloom. Let's be honest: It offers no positive suggestion at all.

Can such negative claims be part of science? It is often said that a scientist must propose hypotheses that are empirically testable. That's not really true, however. While that's a big part of science, a lot of good scientific work is indeed negative. Much useful work is done by experimentalists who show that, while hypothesis H might predict empirical result E, E doesn't actually occur. Also, while most theorists are busily showing that H predicts E, other theorists very helpfully point out that H doesn't really predict E at all, even though we thought it did. A really negative scientist might even show that no hypothesis of a certain type will ever predict E.

I'm afraid I'm one of those really negative scientists. I've shown that no hypothesis in a very broad class predicts the existence of complex living organisms. More precisely, life cannot self organise in any dynamical system whose laws are local and invariant under spatial translation.

This is a very important point. Is it scientific to show that something cannot happen? I think it is.

Let's take a simple case like group selection. George Williams made a name for himself back in the 1960s by presumably showing that group selection could not occur by any known mechanism of evolution. Nobody, as far as I know, suggested that he wasn't being scientific. Lamarckian evolution is anther example. Although it's theoretically possible to pass on acquired characteristics, we discount that possibility because we can show that the connection between phenotypic changes and altering the genome rules out Lamarckian inheritance as a general mechanism of evolution.

If showing that something is theoretically impossible is valid science in some cases then why do we declare that attempts to do the same thing by Intelligent Design Creationists are automatically ruled non-scientific?

Richard Johns faces a special problem because he seems to have bought into methodological naturalism as a limitation on science. Again, from his blog ...

At this point a worrying possibility emerges. This no-go theorem is so broad that it rules out just about any naturalistic theory of the origin of life! It certainly seems to rule out all the naturalistic theories presently proposed. Yet, the whole business of science is to provide natural explanations for phenomena, so this result is unscientific after all. (Even if it is technically correct, take note.)

Well, this is an awkward business! What are we to do?

Indeed. What is he to do? Let's assume, for the sake of argument, that Johns has made a reasonable case for his argument. Let's assume that there may be ways of showing that life is impossible under the known laws of chemistry and physics. Is that science? Does it fit into the restriction of methodological naturalism?

I think the answer to the first question is "yes." It may be bad science, it may even be really bad science, but it's still science to investigate whether completely naturalistic explanations can account for life as we know it.

Let's not pretend to be naive. If there's no naturalistic explanation then there has to be some other kind of explanation.

So I think we have to broaden our horizons, and be open to new kinds of explanation. Perhaps it won't be that bad? And we have no other choice, if we want our explanations to be true.

We know what that means. By ruling out naturalistic causes, we are forced to consider supernatural causes. Is that what makes Richard Johns' work unscientific but not that of George Williams and many other theoreticians of biology? 'Cause if that's what methodological naturalism is all about then it's an ass.

I think everything is fair game for science. Our goal is not to develop rigid rules that make us feel good by ruling our opponents out of bounds just because we don't like their conclusions. Our goal should be to show that they are wrong.

I fully expect that people like Wesley Elsbery and Jeffrey Shallit and will show us why Richard Johns is wrong, just as they did for similar arguments by Bill Dembski. As they do that, Elsbery and Shallit will be practicing science as a way of discovering truth. It would make no sense to declare that Richard Johns has stepped outside the realm of science but Elsbery and Shallit remain inside its boundaries.

The Intelligent Design Creationist attacks on evolution are wrong because they are bad science, not because they are not science.

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The Recurrent Laryngeal Nerve Must Have a Rational Design

 
Casey Luskin is at it again. The Intelligent Design Creationists are trying to argue their way out of the obvious implications of the path taken by the recurrent laryngeal nerve, especially in giraffes.

Now they're saying that, far from being an example of sloppy design, the path of the nerve has to have some selective advantage according to science. Thing is, you need to have a proper understanding of evolution in order to discuss this intelligently.

Enjoy, while keeping in mind why we call them IDiots [Wolf-Ekkehard Lönnig: Under Neo-Darwinism, the Recurrent Laryngeal Nerve Must Have a Rational Design.

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Which Country Has the Best Brains?

 

BBC News has an article on which countries produce the most Nobel Prize winners: Which country has the best brains?.

So, which country has the best brains? I love the answer given by John Wilkins, "Surely not the one that cannot work out per capita rates of Nobel Prizes."

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A Canadian Atheist Accommodationist

 
Canadian Atheist is a blog run by several Canadian atheists (hence the name ). One of them is Brent Kelley, an undergraduate at the University of Alberta in Edmonton, Alberta, Canada.

Here's what Brent said in today's posting: The Atheist Disposition,

Almost everybody I talk to seems to disagree with the “militant” positions that firebrand atheists such as Dawkins and PZ take. They feel they are too extreme and that their outlook too rigid.

I might disagree to some extent, but that’s not the point. The point is that the great atheist leaders that many atheists regard so highly are often viewed by outsiders as extreme, unreasonable, and ridiculous. Even those who agree with our cause often feel this way. Which means that if we’re trying to get the public on-board with our ideas and opinions, we’re failing.

We need to work on our image. I’m not sure where to start, but perhaps approaching the problem from the ground up is a nice way to start tackling the issue. What I would suggest is for atheists everywhere to be a little more friendly to not only one another, but also to others outside their atheist circle of friends. Before you attack a theist’s beliefs, ask yourself if the argument is worth it. You probably wont change their mind anyway. Instead, perhaps you could start up a discussion about science and try to explain the scientific viewpoint on this or that. Slowly and gently introducing them to the worldview of scientific naturalism might make them more receptive to atheism and critical thinking. And be open to their ideas too, you might even learn something. Do whatever, just don’t get into a shouting match and reinforce the stereotype that atheists are argumentative, unfriendly, and annoying. [emphasis in original]

Why not visit their blog and post a comment? I did.

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Teach Your Children Scientific Literacy

 

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[Hat Tip: Greg Laden]

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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The Great Accommodationist Dud: Round 2

 
Point of Inquiry is a series of podcasts financed by the Center for Inquiry. Chris Mooney is one of the people CFI pays to produce the podcasts. He decided to continue the accommodationist debate with PZ Myers and selected the moderator from round 1 to step in for him on the podcast. Unfortunately, Jennifer Hecht doesn't understand the concept of "moderator" so the podcast ends up being Jennifer and Chris against PZ.

PZ does a good job but it's tough defending yourself against two people who are coming at you from very different directions. Jennifer Hecht does not sound very convincing to me. She seems to believe that "a little bit of religion" is perfectly compatible with science and shouldn't be challenged. Towards the end of the podcast, Chris tries to bring up the fact that there are people who find the Gnu Atheists annoying and offensive. PZ replies, very effectively, by pointing out that many people find Chris Mooney annoying, arrogant, and offensive but they aren't telling him to shut up! I would add Jennifer Hecht to the list of people I find arrogant,¹ annoying, and offensive.

Here's the podcast, it's a better utilization of your time than the first round was.

PZ Myers, Jennifer Michael Hecht, and Chris Mooney - New Atheism or Accommodation?

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1. By my definition, you aren't "arrogant" if you are right. You are only arrogant when you are close-minded and wrong.

Is Thanksgiving Day a Religious Holiday?

 
Tomorrow is Thanksgiving Day in Canada. It a holiday marked by good meals and getting together with friends and family. I've never thought of it in any other context. But then, I treat Christmas the same way (except there are presents).

Douglas Todd is a columnist for the Vancouver Sun and he has a very different view of thanksgiving as expressed in his article: At Thanksgiving, do atheists feel grateful?.

Are atheists thankful? And, if so, to whom? Or what?

In the Pacific Northwest, which has the highest proportion of non-religious people in North America, Thanksgiving is not always simple for those who do not believe in a transcendent reality.

How do the almost two out five British Columbians who say they have no religion, and especially the 16 per cent who are atheists, approach a festive day that encourages humans to express a sense of thankfulness, particularly for life itself being a gift?

What is it with people who believe in supernatural beings—especially in those Gods who need to be thanked from time to time? Why are these believers completely incapable of seeing anyone else's point of view? Is there something about believing in "transcendent reality" that affects their brains?

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The Great Accommodationist Dud

 
I watched the whole three hours streamed live on the conference website. It was about as exciting as watching paint dry except that drying paint doesn't make you angry. All four panelists managed to miss the point.

It wasn't until we got to the very last question that anyone grasped the important point; namely, that PZ Myers and Vic Stenger have very different goals than Chris Mooney and Genie Scott.

Chris and Genie want people like PZ and Vic to keep a lid on it because the Gnu Atheists are making their life more difficult. Tough. There's no reason why PZ and Vic (and the rest of us) have to share their goals just because they think they're more important than getting rid of religion.

And why did Vic and PZ allow Genie to get away with defining science as methodological naturalism?

I was very disappointed in everyone on the panel, and in the moderator.

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Carnival of Evolution #28

 
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.

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The Velvet Underground of Molecular Biology

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.

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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.

Three Conundrums

 
Razib Khan over at Gene Expression is discussing a recent article on epigenetics and other "revolutions" in molecular biology. Check out Razib's postings: Arise the vehicle! Arise the cell! and Epigenetics – what revolution?.

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.

I've addressed this before. Knowledgeable experts in the field were predicting 30,000 genes at least as far back as the late 1960s. Their predictions were very close to the mark [False History and the Number of Genes] [Humans Have Only 20,500 Protein-Encoding Genes] [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. Steve Talbot hasn't done his homework. This isn't a very auspicious beginning.

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.

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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."

The Accommodationist Debate

 
I wish I were going to be in Los Angeles next weekend at the Secular Humanism Conference.

I would definitely attend this session ...

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

I sure hope it's going to be on YouTube!

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2010 Nobel Prize in Physiology or Medicine

 
The 2010 Nobel Prize in Physiology or Medicine was given to Robert G. Edwards "for the development of in vitro fertilization". They should have added "in humans."

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.

Here's an example of how the award is being treated in the press [British IVF pioneer Robert Edwards gets Nobel Prize].

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.

The good news is that the Vatican is really, really, pissed! [Vatican official criticises Nobel win for IVF pioneer]. I think it's because the Roman Catholic Church is pro-life.

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