Posted by PZ Myers on July 17, 2004 | Comments (0) | TrackBack (0)

When you get immersed in the Drosophila literature, it's easy to lose sight of an important fact: flies are weird. Honestly, every species has unique properties, so it's not that we wouldn't be saying exactly the same thing about some other species if it had become the dominant experimental model system, but it's good to constantly remind ourselves of the diversity we see in biology.

One of the most noticeable properties of early fly development is the existence of an extensive maternal contribution to the embryo's organization. Mother Fly goes to a fair amount of effort to stamp her eggs with molecular labels that say, "This End Up". Is this a common strategy? Well, yes—lots of animals give their progeny a boost in reliability of development by incorporating an asymmetric distribution of informational macromolecules. There seem to be some exceptions, though, and they happen to be of particular interest to us, because they are us: mammals. Mammalian ova lack any overt asymmetries, and their early cleavages are simple and equal, producing a clump of cells called a morula with no discernible up, down, left, right, back, or front. So how does a young mammalian zygote figure out which end is supposed to be the head and which the tail?

Continue reading "Polarity in the mammalian egg" (on Pharyngula)

Posted by Reed A. Cartwright on July 17, 2004 | Comments (13) | TrackBack (0)

It’s and oldie, but a goodie.

Mo Rocca interviews Carl Baugh for the Daily Show

Clip Description: “There is no conflict between true science and the Bible.”

I won’t say more, or I will spoil it for you.

(Thanks to Nightshade on IIDB for the link.)

Posted by Steve Reuland on July 16, 2004 | Comments (11) | TrackBack (0)

Two new reviews about books critiquing the ID movement: 

The first is a short dual review of Why Intelligent Design Fails and The Cultures of Creationism, appearing in New Scientist magazine.  PT’s own Matt Young is coeditor of the first. 

The second is a review of Creationism’s Trojan Horse: The Wedge of Intelligent Design, appearing in Science and Theology News.  Our own Paul Gross is coauthor of this book. 

Thanks to Glenn Branch for the heads-up.

Posted by PZ Myers on July 16, 2004 | Comments (0) | TrackBack (0)

Here's a refinement in the story of early pattern formation in the Drosophila embryo. Just to recap a little bit, I've told you that in flies there is a molecule, bicoid, that is expressed in a gradient and that is a transcription factor that regulates the expression of other genes. In particular, there is a set of gap genes, Hunchback and Krüppel and Knirps and Giant and Tailless that read the gradient of the bicoid morphogen and are turned on in specific bands along the length of the embryo.

All of this is more or less accurate, but I have to tell you now that it is also a great simplification. Development is much, much more complicated than that. From that description, you'd think that the bulk of the work in specifying identities along the longitudinal axis is done once the bicoid gradient is set up—everything from that point could require nothing but passive obedience from the downstream genes to what bicoid tells them to do. There are also a great many interactions between different downstream genes that are important in shaping the distribution of gene expression, however, and one thing developmental biologists can't do is get trapped into simple linear thinking.

Continue reading "Dynamic control of gap genes" (on Pharyngula)

Posted by PZ Myers on July 15, 2004 | Comments (12) | TrackBack (0)

Oh, boy. Next week is time for the...

Society for Developmental Biology 63^rd Annual Meeting
University of Calgary, Canada
July 24 - 28, 2004

It's going to be glorious—check out the program. Expect me to come back inspired and all charged up about SCIENCE!

• I'll be leaving next Thursday with my son as batman/factotum/chauffeur, so Pharyngula might be a bit quiet for a while. Maybe. Depends on whether they have the internet up there in Canada. (OK, they probably do. It's going to depend more on how much time I have.)
• Are there any Calgarians or DB geeks out there who want to get together some evening and babble or drink that potent Canadian beer? Let me know.
• I'd also be willing to temporarily loan one or a few people the keys to the Pharyngula soapbox. If you're interested in being a guest weblogger, drop me a line. (Creationists, right-wingers, and evangelical fundamentalists need not apply.)

I'll be taking lots of notes. Expect them to appear online sometime during or after the meeting.

Posted by John M. Lynch on July 15, 2004 | Comments (0) | TrackBack (0)

From ScienceDaily:

Comparing primate genomes is an approach that can help scientists understand the genetic basis of the physical and biochemical traits that distinguish primate species. James Sikela and colleagues, for example, collected DNA from humans, chimpanzees, bonobos, gorillas, and orangutans to identify variations in the number of copies of individual genes among the different species. Their work is published in this month’s issue of the open-access journal, PLoS Biology.

Overall, Sikela and colleagues found more than 1,000 genes with changes in copy number in specific primate lineages. All the great ape species showed more increases than decreases in gene copy numbers, but humans showed the highest number of genes with increased copy numbers, at 134, and many of these duplicated human genes are implicated in brain structure and function.

Because some of these gene changes were unique to each of the species examined, they will likely account for some of the physiological and morphological characteristics that are unique to each species. One cluster of genes that amplified only in humans was mapped to a genomic area that appears prone to instability in human, chimp, bonobo, and gorilla. This region has undergone modifications in each of the other descendent primate species, suggesting an evolutionary role. In humans, gene mutations in this region are also associated with the inherited disorder spinal muscular atrophy. This fact, along with the observation that there are human-specific gene duplications in this region, suggests a link between genome instability, disease processes, and evolutionary adaptation.

The research paper is available at the Public Library of Science - abstract is below:

Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.

Posted by Reed A. Cartwright on July 15, 2004 | Comments (21) | TrackBack (3)

The Get Fuzzy for July 15th.

If your paper doesn’t have Get Fuzzy, you can get it delivered to you via email by signing up to Comics Basic at Comics.com.

Posted by John S. Wilkins on July 14, 2004 | Comments (2) | TrackBack (0)

A new blog “dedicated to the history and philosophy of biology, including Darwinism, evolutionary ethics and game theory” has been started by the philosophy department at Florida State University, Michael Ruse’s home department.

It’s early days yet, with a couple of posts about rational behavior and economic evolution. Keep an eye out - they are seeking contributors, and yours truly has offered.

Posted by Jack Krebs on July 14, 2004 | Comments (100) | TrackBack (0)

A common comment by IDists concerns “junk DNA”: they will claim that it is only “evolutionists” who would have thought that so much of the genome was “junk,” but that an IDist would assume that what looked like junk was in fact there for a purpose.  Therefore, as scientists start to learn about previously unknown functions for some of that “junk DNA,” some of the IDists are crowing “We told you so - if you just wouldn’t have been so dogmatically attached to your theory of blind, purposeless evolutionary processes, you wouldn’t have set research back by dismissing so much of the genome as “junk.”  (I could go find quotes to this effect, but I will assume that those of you who keep up with the IDists know what I am talking about.)

Now in November of last year, Scientific American had an article, “The Unseen Genome: Gems Among the Junk,” in which writer W. Wayt Gibbs (not an IDist)summarized some of the new research on what has been considered the junk part of the genome, and in the process made some similar comments about how “dogmatism” has misled biologists into mislabeling and thus ignoring the “junk.”

However, in March of this year Scientific American published a letter by Harold Brown, a member of the philosophy department of Northern Illinois University, responding to this charge of dogmatism with some very pertinent points.  I’d like to discuss what Brown had to say.

Continue reading  “"Junk DNA"”

Posted by PZ Myers on July 14, 2004 | Comments (0) | TrackBack (0)

Tangled Bank #7 is online at Rhosgobel! The next edition will be in two weeks, at reagank.com.

Posted by Reed A. Cartwright on July 13, 2004 | Comments (54) | TrackBack (1)

Former Vermont Governor Howard Dean M.D.  became a household name earlier this year when he was running for president.  After dropping out of the race, Dean used the network he established to start Democracy for America, “a grassroots organization that supports socially progressive and fiscally responsible political candidates.”  On July 5, Dean wrote an editorial on Bush’s war on science in The Daily Camera (Boulder, CO).

The Bush administration has declared war on science. In the Orwellian world of 21st century America, two plus two no longer equals four where public policy is concerned, and science is no exception. When a right-wing theory is contradicted by an inconvenient scientific fact, the science is not refuted; it is simply discarded or ignored.

Presidential scientific commissions have long enjoyed relative immunity from politics. Presidents of both parties have depended on impartial, rational advice from such groups for decades. Yet under the Bush administration, there has been a concerted effort, led by Karl Rove and other political ideologues based in the White House, to stack these commissions with Republican loyalists, especially those who espouse fundamentalist views on scientific issues.

Will it be long before a prominent panel of fundamentalist theologians, conservative columnists and a few token scientists take up the question of whether the theory of evolution should be banned from the nation’s classrooms? Stay tuned. In George Bush’s America, ignorance is strength.

Posted by Jason Rosenhouse on July 13, 2004 | Comments (26) | TrackBack (0)

William Dembski's latest offering is an anthology entitled Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing. The publisher is the Intercollegiate Studies Institute, a right-wing think-tank.

When I first noticed this book at Amazon I was vaguely optimistic. I didn't expect to agree with many of the essays, but it seemed like an attempt, rare among creationists, to produce something serious. I was hoping that the tone would be respectful, and that I would be given some plausible reason for why the evidence for evolution, so convincing to me, is not convincing to other thoughtful people.

Sadly, it seems that I was expecting too much. I have already done several entries over at EvolutionBlog addressing the book.

In this post I discuss the qualifications of the contributors to the volume and find them, for the most part, wanting.

I have also written a series of lengthy entries about the opening essay in the volume, written by philosopher Robert Koons.

Part One is available here.
Part Two is available here.
Part Three is available here.

I expect to be writing replies to the other essays in the volume as I read them. Here, let me make a few comments about William Dembski's long introduction to the volume.

Continue reading  “Uncommon Dissent”

Posted by PvM on July 13, 2004 | Comments (4) | TrackBack (0)

This is the second installment in my postings on Circadian Rhythms. After having introduced the IC argument for Circadian rhythms, I intend to explain in general terms how the Circadian clock works.

Let me repeat Behe’s definition of Irreducible Complexity

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly… “

Michael Behe in Darwin’s Black Box

On the Application of Irreducible Complexity by  Joshua A. Smart

Knockout Experiments

The best tool thus far in determining whether a gene product is indispensable has been the knockout experiment. In a knockout experiment, mutagenesis is used to produce a null mutant, a gene that exhibits no phenotype whatsoever. The use of knockout experiments in determining an irreducible core is obvious.

Continue reading  “Icons of ID: Circadian Rythms II”

Posted by John S. Wilkins on July 12, 2004 | Comments (15) | TrackBack (0)

A common riff on the role of medical and technological advances is that they have somehow insulated humanity from evolution, or the ordinary course of evolution. This is an old canard - it goes back to the days before Darwin, and is a basic justification of eugenics programs (not just the Nazi horrors, but the more “positive” programs of encouraging the “better” kind of humans to interbreed).

It is thought that if medicine has interfered with the selective pressures we faced in the past, we will face degeneration, or be in control of our own evolution, or something, that will interfere with the “normal” course of evolution.

A very nice article by Gabrielle Walker in Prospect Magazine, a UK publication of The Independent, discusses this in some detail.

Continue reading  “Are humans beyond evolution? No!”

Posted by John M. Lynch on July 12, 2004 | Comments (0) | TrackBack (0)

Over at stranger fruit, I discuss the expertise of the Fellows of the Center for Science and Culture and their ability to examine evolution. All welcome!

Posted by Reed A. Cartwright on July 12, 2004 | Comments (29) | TrackBack (0)

The Pulitzer Prize winning Edward J. Larson has a new book,  Evolution: The Remarkable History of a Scientific Theory.  He teaches both history and law at the University of Georgia.  His background is in the history of science, specifically biology.

”Everyone will agree, whether you like it or not, the theory of evolution is one of the most important concepts of the last 200 years,” Larson said. ”Whether you like it or not, it influences what we think about the world, even for people who don’t accept the theory or all of the theory of evolution. It still influences society, the culture in which they operate and influences a lot of other people, and therefore it impacts our society. And yet, I couldn’t find a book that told the story of its history, full of its controversies, full of the objections, full of the implications as a story that normal people like you and I could read, rather than a technical work of science that is really dry.”

Read the rest at the Athens Banner-Herald newspaper.  (Use username ‘tricky’ and password ‘marymary’ if you don’t have an account.)

Posted by PvM on July 12, 2004 | Comments (16) | TrackBack (0)

Francisco J. Ayala, Teaching Science in the Schools  American Scientist, Volume 92, Number 4 July-August 2004

… It is often argued that the American tradition of fairness and “equal time” beckons that these alternative theories be taught. But these theories are not scientific and therefore have no place in the science curriculum. Not all scientific knowledge is equally certain. When there is uncertainty, alternative hypotheses should be taught in science classes, but only those grounded on naturalistic explanations subject to refutation by empirical observation and experiment. Schools should not teach astrology as an alternative to astronomy, alchemy as an alternative to the periodic table or witchcraft as an alternative to medicine.

The theory of evolution needs to be taught in the schools because nothing in biology makes sense without it. Modern biology has broken the genetic code, deciphered the human genome, opened up the fast-moving field of biotechnology and provided the knowledge to improve health care. Students need to be properly trained in science in order to improve their chances for gainful employment and to enjoy a meaningful life in a technological world.

Continue reading at American Scientist Online

Posted by John M. Lynch on July 12, 2004 | Comments (2) | TrackBack (0)

From EurekAlert:

A butterfly’s wing is a uniquely visual exhibition, not only of the aesthetics of nature, but of the machinery of evolution. Biologists have long appreciated that butterfly wing patterns dramatically exemplify the intricate interplay between genes and the environment — as the patterns evolve to give butterflies advantages in evading predators and attracting mates.

In a paper in the July 13, 2004, issue of Current Biology, biologists Robert Reed and Michael Serfas add a new piece to the evolutionary puzzle of the butterfly wing. By comparing among species the molecular machinery that controls wing development, the researchers are revealing how the regulation of two key genes has evolved in association with specific color patterns. The color patterns they studied vary among species, existing in a continuum including simple lines, teardrops and rounded spots.

Robert D. Reed and Michael S. Serfas (2004) “Butterfly Wing Pattern Evolution Is Associated with Changes in a Notch/Distal-less Temporal Pattern Formation Process” Current Biology 14(13): 1159-1166. doi:10.1016/j.cub.2004.06.046

I’ll leave it to PZ to perhaps comment on this :), but below is the abstract of the paper.

Abstract:: In butterflies there is a class of “intervein” wing patterns that have lines of symmetry halfway between wing veins. These patterns occur in a range of shapes, including eyespots, ellipses, and midlines, and were proposed to have evolved through developmental shifts along a midline-to-eyespot continuum. Here we show that Notch (N) upregulation, followed by activation of the transcription factor Distal-less (Dll), is an early event in the development of eyespot and intervein midline patterns across multiple species of butterflies. A relationship between eyespot phenotype and N and Dll expression is demonstrated in a loss-of-eyespot mutant in which N and Dll expression is reduced at missing eyespot sites. A phylogenetic comparison of expression time series from eight moth and butterfly species suggests that intervein N and Dll patterns are a derived characteristic of the butterfly lineage. Furthermore, prior to eyespot determination in eyespot-bearing butterflies, N and Dll are transiently expressed in a pattern that resembles ancestral intervein midline patterns. In this study we establish N upregulation as the earliest known event in eyespot determination, demonstrate gene expression associated with intervein midline color patterns, and provide molecular evidence that wing patterns evolved through addition to and truncation of a conserved midline-to-eyespot pattern formation sequence.

Posted by PZ Myers on July 12, 2004 | Comments (0) | TrackBack (0)

It's in an unexpected place—O'Reilly's Macintosh developers pages— but here's a useful and brief tutorial in getting started with Bioinformatics and Comparative Genomics.

(via nodalpoint.org)

Posted by PvM on July 11, 2004 | Comments (22) | TrackBack (0)

NSCE reports

Alberts and Labov on teaching evolution

Bruce Alberts, president of the National Academies, and Jay Labov of the Center for Education at the National Research Council have written an article on “Teaching the Science of Evolution,” which appears in the current issue of the journal Cell Biology Education.

Alberts and Labov write, “Cell and molecular biologists have provided some of the most compelling evidence to support the theory of evolution and should therefore be among those who raise their voices the loudest to support science curricula that help students understand the processes of evolution. As scientists, we also should make it our responsibility to present the evidence for biological evolution to all of our students, especially in introductory courses. Most students who enroll in our introductory courses will use them as their terminal courses in science. At least some of those students will go on to careers as teachers or as public servants who will be asked to make decisions about whether to allow nonscientific approaches to teaching evolution to appear in science curricula. It is our responsibility to equip them with the knowledge and understanding of science that they will need to confront such challenges.”

From the National Academies:

Bruce Alberts and Jay B. Labov Teaching the Science of Evolution  Cell Biology Education  Volume 3 Summer 2004, 75-80

More at Cell Biology Education

Posted by John M. Lynch on July 11, 2004 | Comments (51) | TrackBack (0)

Yesterday Pim noted that the Discovery Institute prevented Eugenie Scott from quoting from online material, stating that the material did “not do justice to the complexity of ID”. Now - somewhat ironically - the DIs Center for Science and Culture has had a make-over and the very articles Scott was using are filed under “Scientific Research and Scholarship”. Hard to know what to say really. If the DI/CSCs “scientific research and scholarship” does “not do justice to the complexity of ID” where are we to go to get the truth about ID? Well, the Thumb, of course :)

Posted by PvM on July 11, 2004 | Comments (0) | TrackBack (0)

Intelligent design proponents have raised a myriad of criticisms against the Avida experiments, most of these criticisms miss the point. For instance, the claim that Avida does not accurately model biological evolution. But there are some claims that deserve a closer look. Since I am very interested in these issues, I will address a few of them.

Statistically insignificant sequence space distances are assumed between novel, more complex functions. This is an artefact of logic functions and not protein sequence.

Continue reading  “Icons of ID: Avida”

Posted by PvM on July 11, 2004 | Comments (8) | TrackBack (0)

Another example of a system that could not have evolved via Darwinian pathways is discussed at ISCID.

It is hard to imagine how such a character could have evolved by a Darwinian mechanism. Darwinism requires an environment wherein an organism gradually evolves. For organism to evolve they require some sort of selective constraint. Darwinian theory explains traits according to the best adapted in a particular environment, but a highly radioactive environment has simpley never been present on earth. This must certainly mystified Darwinists.

Luckily science is not constrained by one’s lack in imagination and has found some interesting clues as to plausible scenarios.

Continue reading  “Icons of ID: Deinococcus, ID's appeal to ignorance”

Posted by PZ Myers on July 11, 2004 | Comments (0) | TrackBack (0)

Another Tangled Bank is coming up this week. Send your links to good science and medicine writing to Radagast, who will be hosting it at Rhosgobel. (The usual e-mail address for submissions is still messed up, so send it direct to the host, or to me).