Posted by Reed on June 25, 2005 | Comments (10) | TrackBack (0)

We all know the Media is too liberal, so thank God for Deep-Sea News.

Posted by pz on June 24, 2005 | Comments (1) | TrackBack (0)

We mammals haven't been good poisoners. There are a few primitive forms that secrete toxins—the platypus has poison spines, and an unusual insectivore on a few Caribbean islands, Solenodon, has grooved fangs and secretes a salivary toxin, and itty-bitty shrews have toxic saliva—but our class just hasn't had much natural talent for venom. At least, not recently.

New discoveries of some fragmentary fossils in Canada have shown that there were some flourishing species of small, poison-fanged mammals running around in the Palaeocene, 60 million years ago.

Continue reading "Bisonalveus browni, a venomous mammal" (on Pharyngula)

Posted by Tara Smith on June 14, 2005 | Comments (79) | TrackBack (0)

Well, not quite.  I’ve been catching up on my Science reading after a lot of travel, and found this very cool little article.  (“Cultivating the Third Eye,” Science, Vol 308, Issue 5724, 948, 13 May 2005)

Continue reading  “Appearing next in Springfield?”

Posted by Gary S. Hurd on June 02, 2005 | Comments (2) | TrackBack (0)

The Schweitzer/Horner team that we have followed for years has released their newest result today.  They had raised a tremendous clamor among young earth creationists late last March when they announced that they had recovered flexible tissues identifiable as blood vessels, blood cells, and osteocytes from a Tyrannosaur rex femur. (See ”Dino Blood Redux”).  At that time, they made a rather cryptic comment that there was something unusual about the gross architecture of the bone, and that they had a second paper already in review with Science.

The online supplemental data with their March article (Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK (2005) Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex. Science 307(5717):1952-1955) indicated that they had molecular data directly attesting to the evolutionary relationship between dinosaurs and birds.  At that time, I noted the direct contrast between creationist David Menton’s complaint, “Why not compare the histology of the dinosaur bone to that of some living reptile? After all, dinosaurs are reptiles,” (‘Ostrich-osaurus’ discovery?) and Jack Horner’s comment that, “Birds are dinosaurs.” 

Today we learn that the unusual gross anatomy from the interior of the MOR 1125 femur was immediately recognized by Schweitzer as Medullary bone.  Medullary tissue is a calcium-rich layer lining the inside of bird’s bone marrow cavities that develops during the egg-laying process.  The formation of medullary tissue is today uniquely avian and distinct from reptilian egg-laying biology.

The actually paper becomes available Friday, June 3rd.  We will look forward to reading it, and examining the creationist’s reactions in a following item.

Posted by Reed on June 02, 2005 | Comments (6) | TrackBack (1)

The Society for the Study of Evolution, which is ironically based in Kansas, has redone their website: http://www.evolutionsociety.org.  The website contains information about evolution and science education, statements from scientific societies on evolution, a white paper on evolution and society, and many more interesting things.

The objectives of the Society for the Study of Evolution are the promotion of the study of organic evolution and the integration of the various fields of science concerned with evolution.

The Society publishes the scientific journal Evolution and holds annual meetings in which scientific findings on evolutionary biology are presented and discussed.

The Society for the Study of Evolution holds its annual meeting with The Society of Systematic Biolologists and The American Society of Naturalists.  This conference is simply called “Evolution.”  Evolution 2005 is at the University of Alaska, Fairbanks and begin June, 10th.

I will be attending the conference and presenting some of my doctoral research on simulating sequence evolution.  Prof. Steve Steve will be traveling with me to the conference and will be at my talk (early Sunday morning) if anyone wants to meet him.

Posted by pz on May 31, 2005 | Comments (8) | TrackBack (0)

Maybe half of my audience here will be familiar with this problem. You're a man, and you're hauling this massive, ummm, package around in your pants everywhere you go. Other men fear you, while the women worship you…yet at the same time, your e-mail is stuffed to bursting with strange people making friendly offers to help you make it even bigger. It's a dilemma; you think you would be even more godlike if only it were larger, but could there possibly be any downside to it? (There is a bit of folk wisdom that inflating it drains all the blood from the brain, but this is clearly false. Men who are stupid when erect are also just as stupid when limp.)

A couple of recent studies in fish and spiders have shown that penis size is a matter of competing tradeoffs, and that these compromises have evolutionary consequences. Guys, trash that e-mail for penis enlargement services—they can make you less nimble in pursuit of the ladies, or worse, can get you killed.

Continue reading "The burden of bearing a massive penis" (on Pharyngula)

Posted by pz on May 27, 2005 | Comments (0) | TrackBack (0)

The journal BioEssays has a lovely series called "My favorite animal", in which biologists get to wax rhapsodic about their favorite creatures. It's a great idea, since not only does it mean we get some enthusiastic writing, but more exposure is given to organismal biology. I read so many papers that go on and on about some specific molecule and in which the only illustrations are photos of gels and blots that it's nice to see whole animals for a change.

This month, Arthur and Chipman wrote about a centipede, Strigamia maritima, and its development—so not only do I get animals, I get embryos. Oh, happy day!

Continue reading "Strigamia maritima" (on Pharyngula)

Posted by Jim Foley on May 18, 2005 | Comments (74) | TrackBack (0)

Continue reading  “The Dmanisi skulls and creationism”

Posted by pz on May 16, 2005 | Comments (39) | TrackBack (0)

This very strange object was peering out at me from the cover of last week's Nature…and "peer" is exactly the right word. Those are some of the eyes of a cubozoan, a box jelly, of the species Tripedalia cystophora. These eyes have some very peculiar features, and show that once again nature trumps the imaginations of science fiction artists.

Continue reading "Jellyfish eyes" (on Pharyngula)

Posted by Steve on May 12, 2005 | Comments (41) | TrackBack (0)

  The New York Times has an article today about a new rodent discovered in Southeast Asia that’s so different, it’s been placed in its own family.

‘Oddball Rodent’ Is Called New to Science.

They live in the forests and limestone outcrops of Laos. With long whiskers, stubby legs and a long, furry tail, they are rodents but unlike any seen before by wildlife scientists. They are definitely not rats or squirrels, and are only vaguely like a guinea pig or a chinchilla. And they often show up in Laotian outdoor markets being sold as food.

It was in such markets that visiting scientists came upon the animals, and after long study, determined that they represented a rare find: an entire new family of wildlife. The discovery was announced yesterday by the Wildlife Conservation Society and described in a report in the journal Systematics and Biodiversity.

The new species in this previously unknown family is called kha-nyou (pronounced ga-nyou) by local people. Scientists found that differences in the skull and bone structure and in the animal’s DNA revealed it to be a member of a distinct family that diverged from others of the rodent order millions of years ago. “To find something so distinct in this day and age is just extraordinary,” said Dr. Robert J. Timmins of the Wildlife Conservation Society, one of the discoverers. “For all we know, this could be the last remaining mammal family left to be discovered.”

It sure does look delicious.  While I don’t know any details about this new mammal, there are several predictions I can make about it based on our knowledge of evolution:

• It will have red blood cells that lack nuclei.

• It will have three middle ear bones.

• It will have continuously growing incisors.

• It will be endothermic.

And so on.  I can make these predictions based on known synapomorphies within the mammal or rodent lineages.  These are characters inherited from the common ancestors that all mammals (or rodents) share.  If this new species is not related through ancestry with other rodents and mammals, and was perhaps “specially created”, there is no reason to suspect that it would have these characters, especially since they are not relevant to the morphological appearance of the animal.

Posted by Reed on May 03, 2005 | Comments (6) | TrackBack (0)

Law Evolution Science and Junk Science has an interesting post on the fallacy of the appeal to inappropriate authority.

In summary, an appeal to authority is a valid method of argument and of making decisions. It recognizes the obvious fact that we cannot all be experts in everything. It would be a mistake to have your neurosurgeon change the brakes on your car and your car mechanic to operate on your brain tumor. If you see a neurosurgeon for your brain tumors and a car mechanic for your disc brake adjustments and you don’t know much about either, you are essentially betting your life on an appeal to authority.  We all reasonably do that every day.

Analyzing Intelligent Design under the appeal to authority fallacy immediately  presents several problems.

Go Read It.

Posted by Nick Matzke on April 13, 2005 | Comments (66) | TrackBack (0)

Scientific American’s John Rennie has definitely discovered the joy — perhaps “grim pleasure” would be a better word — of blogging about evolution and the silliness of creationists.  Today, he announced that the American Society of Magazine Editors just gave science journalist David Quammen and National Geographic’s editor, William L. Allen, the 2005 National Magazine Award in Essays for the November 2004 National Geographic article that asked and answered the question, “Was Darwin Wrong?”

Continue reading  “Quammen gets award”

Posted by John Wilkins on April 11, 2005 | Comments (6) | TrackBack (0)

A new report in Science has come out firmly in favour of the Homo floresiensis not being a “pathological microcephalic”. Read more here.

Posted by Steve on March 28, 2005 | Comments (7) | TrackBack (0)

Anyone familiar with evolutionary biology will probably have heard of Robert Trivers, the brilliant scientist who made major contributions to evolutionary theory back in the 70s.  Unbeknownst to me, he had been on hiatus for a good while.  Now it appears he’s back.  The Boston Globe has an article about Trivers, his work, his eccentric life, and his impending return to the spotlight:

The evolutionary revolutionary.

It’s a good read.

Posted by perakh on March 06, 2005 | Comments (21) | TrackBack (0)

This essay has been called to life by Steve Reuland’s post to Panda’s Thumb  titled “What good is half an underlying language structure?” ( www.pandasthumb.org/pt-archives/000853.html ) which refers to Carl Zimmer’s posts to Loom (http://www.corante.com/loom/archives/2005/02/25/building_gab_part_one.php and http://www.corante.com/loom/archives/2005/03/01/building_gab_part_two.php ).  One point touched upon in passing by Zimmer and by some comments’ writers, was the question of whether or not natural languages have all evolved from the same proto-language.

Continue reading  “Letter Serial Correlation points to languages evolution”

Posted by Steve on March 01, 2005 | Comments (42) | TrackBack (0)

Zimmer has another two-part series up, this time on the evolution of language.

Building Gab: Part One.

Building Gab: Part Two.

It concerns a long-running debate between linguists about how language was acquired by our species.  Go read it right now.

Posted by Jim Foley on February 28, 2005 | Comments (113) | TrackBack (0)

Continue reading  “Not a German Piltdown”

Posted by Pim van Meurs on February 23, 2005 | Comments (5) | TrackBack (1)

From our friends at the NCSE

Chris Mooney reports in The American Prospect that John H. Marburger III, director of the White House’s Office of Science and Technology Policy, denounced “intelligent design” as unscientific. Mooney writes:

Speaking at the annual conference of the National Association of Science Writers, Marburger fielded an audience question about “Intelligent Design” (ID), the latest supposedly scientific alternative to Charles Darwin’s theory of descent with modification. The White House’s chief scientist stated point blank, “Intelligent Design is not a scientific theory.” And that’s not all — as if to ram the point home, Marburger soon continued, “I don’t regard Intelligent Design as a scientific topic.”

In March 2004, when asked about the Bush administration’s scientific credibility in light of the president’s reported skepticism about evolution, Marburger similarly got it right: “Evolution is a cornerstone of modern biology.”

Posted by Nick Matzke on February 06, 2005 | Comments (4) | TrackBack (0)

Over on the Philosophy of Biology blog Michael Ruse has just written an extensive eulogy of Ernst Mayr.  It includes an excellent summary of the importance of Mayr as well as many entertaining anecdotes. 

I recently expressed the view that I would be proud to be kicked by Ernst Mayr.  It seems that Ruse felt the same way:

But Mayr had many more years of active life.  Even last year he was scrounging one of my books from our shared publisher, Harvard University Press, so that he could put the boot into me one more time before he was done.

(Michael Ruse, Ernst Mayr Eulogy)

I have quoted some of the important points and good bits below, but you should really read the whole thing.

Continue reading  “Michael Ruse on Ernst Mayr”

Posted by Reed on January 19, 2005 | Comments (1) | TrackBack (0)

Massimo Pigliucci, evolutionary biologist at SUNY-Stony Brook, has a blog, (mostly) Rationally Speaking.  Pigliucci is well known for his popular writings about evolution, skepticism, and humanism.

Posted by Pim van Meurs on January 09, 2005 | Comments (59) | TrackBack (0)

New paradigm needed: More intelligent ‘intelligent design’

Richard D. Colling is chairman of the biology department at Olivet Nazarene University and author of “Random Designer — Created from Chaos to Connect with the Creator. His e-mail address is Richard Colling

Dr Colling points out how the debate about evolution and religious faith has been fueled by unsupportable statements by both atheists and creationists.

Fueled by bold, but unsupportable atheistic pronouncements from a few scientists that science and evolution render God superfluous, and reinforced by a continuous barrage of heated anti-evolution rhetoric flowing from scientifically naive creationist voices over many years, this idea of mutual exclusivity has seemingly become entrenched as the prevailing premise in contemporary American culture.

This has caused a tension which is now spreading into issues of public policy and education.

Continue reading  “Richard Colling: New paradigm needed: More intelligent 'intelligent design'”

Posted by jkrebs on January 08, 2005 | Comments (29) | TrackBack (0)

One of the things I am interested in is the common “man in the street” objections to the theory of evolution.  A very common concern is the “micro” vs. “macro” distinction:  many people can accept evolution within a species, but just can not see how one species can ever evolve into something else.  Such people therefore can not accept common descent, which is a central tenet of evolutionary theory.

I’ve recently had two interesting encounters with this: one last week during an appearance on a conservative radio talk show and the other in response to an unsolicited email from a member of Dr. Kent Hovind’s staff.  In both cases I was met with considerable resistance to the obvious question of “if common descent isn’t the means by which new species have came into existence, then what is?”  The obvious answer - the one which was the default historically before the theory of common descent and the one held by many anti-evolutionists today, is special creation: creation ex nihilo, the immediate materialization into existence of new organisms.  However, as the following encounters show, anti-evolutionists are reluctant to put this on the table as an actual “competing hypothesis.”

In order to illustrate, I would like to summarize these two encounters, the first here in this post and the other in a second, separate post.

Continue reading  “Radio talk show discussion on common descent”

Posted by Pim van Meurs on December 31, 2004 | Comments (32) | TrackBack (0)

I have collected an extensive, but hardly exhaustive, list of educators, scientists and religious people supporting evolution and/or speaking out against Intelligent Design.

I will move the list to PandasThumb once I finish the translation from HTML to BBCode and clean up the organization (such as alphabetizing the states and adding an index).

If you are aware of any additional links please add a comment and I will update the list to reflect the latest, most up-to-date list.

Read further at Wedgie World

Posted by Reed on December 31, 2004 | Comments (6) | TrackBack (1)

Carl Zimmer has written another good post on his blog about the evolution of the immune system: The Whale and the Antibody.

You can find this same remarkable system in humans, albatrosses, rattlesnakes, bullfrogs, and all other land vertebrates. You can also find it in most fish, from salmon to hammerhead sharks to sea horses. There are some variations from species to species, but they’ve all got B cells, T cells, antibodies, thymuses, and the other essential components. But you won’t find it in beetles, earthworms, dragonflies, or any other invertebrate on land. Nor will you find it in starfish, squid, lobsters, or lampreys in the water. All these other animals rely instead on rudimentary immune systems that cannot learn.

For those who reject evolution, this sort of pattern tells them nothing. Like everything else in nature, they can only wave their hands and declare it the inscrutable work of a designer (lower case d or upper case D as they are so inclined on a given day). But immunologists and other scientists who actually want to learn something about the immune system find this view useless. Instead, they look at how animals with an antibody-based immune system are related to one another. And what they find is both straightforward and astonishing. All of the living animals with an antibody-based immune system descend from a common ancestor, and none of the descendants of that common ancestor lack it. That means that the antibody-based immune system evolved once, about 470 million years ago.

Posted by Pim van Meurs on December 09, 2004 | Comments (7) | TrackBack (0)

The human parathyroid gland, which regulates the level of calcium in the blood, probably evolved from the gills of fish, according to researchers from King’s College London.
Anthony Graham and Dr Masataka Okabe published their findings in the Proceedings of the National Academy of Sciences.

Continue reading  “Human Gland Probably Evolved From Gills”

Posted by Reed on December 07, 2004 | Comments (5) | TrackBack (0)

Fresh Challenges in the Old Debate Over Evolution

David Jackson’s life straddles all the fault lines in the battle over the teaching of evolution in public schools.

Jackson is a professor of science education at the University of Georgia’s College of Education in Athens. He believes to his core that science has proved valid Charles Darwin’s theory of how life on Earth developed from a common ancestry and why life has such diversity.

About half the students he teaches to become middle school science instructors — and to teach evolution themselves — believe that God created the Earth 6,000 years ago, he said. Scientist friends tell him not to teach those students because anyone with those beliefs “shouldn’t teach.” But he tells them it is his job to make sure that his students understand evolution, not believe it.

Of course the problem with the title is that ID is not actually a fresh argument.

Posted by Dave Thomas on November 19, 2004 | Comments (10) | TrackBack (0)

Creationists and Intelligent Designists have long pointed to bats as problems for evolution, because of the general lack of transitional fossils. 

Here’s a sample of such an argument from the dean of young-earth creationists, Duane Gish of the Institute for Creation Research:

Bats (of the order Chiroptera), the only flying mammal, are especially interesting. Evolutionists assume, of course, that bats must have evolved from a non-flying mammal. There is not one shred of evidence in the fossil record, however, to support such speculations, for, as Romer says, “Bats appear full fledged in both hemispheres in the Middle Eocene …”

And here’s an example from the dean of ID, Phillip Johnson:

It isn’t merely that grand-scale Darwinism can’t be confirmed. The evidence is positively against the theory. For example, if Darwinism is true then the bat, monkey, pig, seal, and whale all evolved in gradual adaptive stages from a primitive rodent-like predecessor. This hypothetical common ancestor must have been connected to its diverse descendants by long linking chains of transitional intermediates which in turn put out innumerable side branches. The intermediate links would have to be adaptively superior to their predecessors, and be in the process of developing the complex integrated organs required for aquatic life, flight, and so on. Fossil evidence that anything of the sort happened is thoroughly missing and in addition it is extremely difficult to imagine how the hypothetical intermediate steps could have been adaptive.

And here’s another from Johnson:

Perhaps one day scientists will be able to test some macroevolutionary mechanism, involving changes in the rate genes or whatever, that will explain how a four-footed mammal can become a whale or a bat without going through impossible intermediate steps. The difficulties should be honestly acknowledged, however.

I’m pleased to report that that “one day” has arrived.

Continue reading  “A Quantum Leap in Bat Evolution”

Posted by Jim Foley on November 17, 2004 | Comments (8) | TrackBack (0)

Guess what? The Fossil Hominids website has just reached the ripe old age of 10 years! The site’s goal is to present the evidence for human evolution, and to address creationist arguments about it. I started it in 1994 because the talk.origins archive had no material on human evolution, despite it being a hot topic in the creation/evolution debate. The first version of the site was not a web page, but a 53K text file available by ftp from the talk.origins archive, which at the time was an ftp site rather than a website. (ftp, or File Transfer Protocol, was a common way of getting files to and from other computers before the web took off). The original page was just a list of descriptions of species and fossils and a brief rebuttal of some creationist arguments. I converted it into a web page in November 95 and added the first illustrations. The page had grown to 151K by April 96, and in October 96, it was split into multiple web pages. The site has been steadily growing since 1994. At the moment, it consists of 170 web pages totalling about 1.8M in size, including a number by other contributors, along with about 230 image files. The home page gets about 400 hits per day. The site is now one of the top resources on human evolution on the web, and (I think) the best source of information about human evolution and creationism on or off the web. I’ve enjoyed building the site and plan to keep improving it. If you’ve never visited, please drop by!

Posted by Jim Foley on November 10, 2004 | Comments (21) | TrackBack (1)

The discovery of Homo floresiensis, the dwarf human species from Flores in Indonesia, has received such massive media attention that creationists have naturally responded to it. Carl Weiland of Answers in Genesis has written an article on Homo floresiensis, and Agape Press has also written an article interviewing AIG's founder, Ken Ham.

AIG basically agrees with the researchers who found the bones (nicknamed 'the Hobbit') that they are a dwarf variety of Homo erectus. However AIG (unlike almost all modern scientists) considers that H. erectus really belongs to H. sapiens, and that the Flores bones should therefore be assigned to H. sapiens too. The human kind, says Wieland, "had a greater range of variation than exhibited today".

That's putting it mildly. If creationists can claim that Homo sapiens and Homo floresiensis belong to the same "kind", on what grounds can they say that australopithecines and H. floresiensis can't also be the same kind, since in its overall body shape floresiensis looks more like an australopithecine than a modern human? In fact, for a while Peter Brown and his team seriously considered placing floresiensis in the genus Australopithecus.

Continue reading  “Homo floresiensis and Answers in Genesis”

Posted by Dave Thomas on October 30, 2004 | Comments (54) | TrackBack (0)

I’ve recently obtained permission from Science and an author of the recent paper “Evolution of Coral Pigments Recreated,” to use the splendid figures in a popular discussion of this important new work.  Permission to post these figures was granted only for the NMSR page, so I can’t post them here, but here’s a link to my new article, “New Work Documents the Evolution of Irreducibly Complex Structures.”

Here’s a snippet:

Recent work on the evolution of pigments in star corals, “Evolution of Coral Pigments Recreated,” by Juan A. Ugalde, Belinda S. W. Chang, and Mikhail V. Matz, (Science 2004 305: 1433 (9/3/2004), Copyright 2004 AAAS) shows conclusively that “irreducibly complex” structures not only can evolve, but that they have evolved. This should lay to rest the “Intelligent Design” assertion that this type of complexity is forbidden to natural evolution.

And Ugalde et. al.’s conclusion:

The more complex red color evolved from green through small incremental transitions (a stepwise accumulation of improvements), each identified in our experiments by ancestral gene reconstruction (Fig 1D). This mode of evolution has been anticipated since Darwin, but has only recently been demonstrated in computer simulation experiments (5, R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami, Nature 423, 139 (2003), “The Evolutionary Origin of Complex Features” )

Continue reading “New Work Documents the Evolution of Irreducibly Complex Structures” (offsite at NMSR)

Posted by Pim van Meurs on October 27, 2004 | Comments (7) | TrackBack (0)

Historically, the central dogma in molecular biology has been that the genetic information in DNA is transcribed into intermediate RNA which are translated into amino acids to form proteins.  Proteins were seen as the primary regulators of the expression of genes. While this picture appears to be correct for prokaryotes, a different picture arises for eukaryotes.

Mathematical considerations have shown that while generating complexity is simple, controlling it isn’t. The amount of regulation needed tends to scale as the quadratic of the number of genes. The genome size of prokaryotes seems to be limited by these considerations.

Continue reading  “Evolvability: RNA and The Gems of "Junk" DNA”

Posted by Pim van Meurs on October 13, 2004 | Comments (6) | TrackBack (0)

While researching the hot topic of ALU repeats for my posting on evolvability, I ran across the following paper

Alu elements and hominid phylogenetics by Abdel-Halim Salem, David A. Ray, Jinchuan Xing, Pauline A. Callinan, Jeremy S. Myers, Dale J. Hedges, Randall K. Garber, David J. Witherspoon, Lynn B. Jorde, and Mark A. Batzer published in PNAS October 28, 2003
vol. 100
no. 22
12787-12791

Let me add a disclaimer that I am a novice when it comes to evolutionary biology. While I am familiar with the term such as ALU repeats, SINE and retroposons, I am not by any means an expert. Nevertheless, I like to share my research and learning with the readers of Panda’s Thumb, in the hope that 1) people like me who are similarly interested in learning more about “what is hot” in evolutionary theory can learn about some of the details 2) others, more capable than me, can add their comments, suggestions and objections.

Continue reading  “Evolvability: ALU repeats and hominid phylogenetics”

Posted by Pim van Meurs on October 04, 2004 | Comments (13) | TrackBack (0)

Testing fundamental evolutionary hypotheses by David Penny, Michael Hendy and Anthony Pool was published in Journal of Theoretical Biology volume 223, pages  377-385 in 2003.
Penny et al show that ‘Intelligent Design’ can be formulated as a testable hypothesis but this requires us to formulate motivation(s), means and/or opportunity to restrain the explanatory power of an ‘intelligent designer’. Additionally, they show why various potential ID hypotheses can be rejected based on the experimental evidence. Until ID proposes other hypotheses, common descent seems to remain the best hypothesis available. Since the Geoscience Research Institute (GRISDA) proposes an alternative theory of ID (multiple independent origins) I will explore this hypothesis and show that again the data do not bode well for ID.

Continue reading  “Testing fundamental evolutionary hypotheses”

Posted by Pim van Meurs on September 26, 2004 | Comments (19) | TrackBack (0)

“A recent Vatican document analyzed evolution in the light of faith, stepping into an area that has long been a religious and scientific minefield. ” Thus starts an article on the recent work by the International Theological Commission.

First, it accepts as likely the prevailing tenets of evolutionary science: the universe erupted 15 billion years ago in a “big bang”; the earth formed about 4.5 billion years ago; all living organisms on earth descended from a first organism; and man emerged some 40,000 years ago with the development of the larger, human brain.

(John Travis Creative tension: omnipotence of God vs. dynamism of a universe )

Noticable quote by U.S. Jesuit Father George Coyne, director of the Vatican Observatory:

“But I think the question itself is wrong. It’s not just necessity or chance, it’s also opportunity. We live in a universe that statistically offers so many opportunities for the life-building processes to work together,” he said.

Continue reading  “Vatican Accepts Evolutionary Science”

Posted by Reed on September 05, 2004 | Comments (15) | TrackBack (0)

In my last post, Common Design Errors, I proposed a problem for biblical creation.  I received one response from a creationist, who cited Inai et al. (2003).  This paper compared the largest set of homologous exons between humans, guinea pigs, and rats.  You see, guinea pigs, like most primates and a few other taxa, lack L-guluno-gamma-lactone oxidase.  Two sections were quoted to me.

Continue reading  “Scurvy, Guinea Pigs, and You”

Posted by Reed on August 29, 2004 | Comments (19) | TrackBack (0)

Biblical creationism offers two explanations for what we see in nature: “God did it” and “the Fall did it.”  Such theology often argues that God created nature perfectly and corruption entered into the world after the Fall.  Such things like blind cave fish are explained as post-Fall degeneration.  Such theology often argues that any similarities observed between “unrelated” organisms are due to common design.  This is often invoked to explain similarities between humans and other creatures, because biblical creationism holds that humans are not related to any other species.  However, these explanations are unable to account for common design flaws, which are features that are clearly biological flaws but are shared between organisms that are supposed to be unrelated.  Unary pseudogenes are an excellent example of this problem for biblical creationism.

Humans, chimps, gorillas, and other primates lack the ability to synthesize ascorbic acid (vitamin C) and must eat a diet that includes it to survive. Other animals are able to synthesize ascorbic acid because they have a complete metabolic pathway. However, humans et al. are missing a key enzyme, L-gulano-gamma-lactone oxidase, which is involved in the synthesis of ascorbic acid. However, we do have the non-functioning remains of this gene still in our DNA, as do other primates which have been studied: chimps, gorillas, orangutans, and macaques. In all five species the gene is broken in the same way (deletion of same exons) and is found in the same place in the genome.

Biology explains this shared flaw by proposing that in an ancestor of all five species, a deletion occurred in the L-gulano-gamma-lactone oxidase, rendering it non functional. This deletion was then passed to its descendents, producing the pattern that we see today. Biblical creationism is unable to explain it because either God would have to have made a flawed creation or humans would have to be related to other species. Neither are options that biblical creationism allows.

I have proposed this problem many times to biblical creationists who insist that humans do not share a common ancestor with any other species.  None of them have yet to account for this interesting fact of nature.

References

1. Nishikimi M et al. (1994) “Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man.” Journal of Biological Chemistry 269: 13685-13688

2. Ohta Y and Nishikimi M (1999) “Random nucleotide substitutions in primate nonfunctional gene for L-gulano-gamma-lactone oxidiase, the missing enzyme in L-ascorbind acid biosynthesis.” Biochimica et Biophysica Acta 1472: 408-411

Posted by jml 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 John 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 Reed 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 Reed on July 05, 2004 | Comments (3) | TrackBack (0)

The eminent evolutionary biologist Ernst Mayr — who is a member of NCSE — celebrated his 100th birthday on July 5. Writing in the July 2 issue of Science, he reflected on his eighty years of “watching the evolutionary scenery,” from his education in Germany through the development of the Modern Synthesis to the discoveries of molecular biology. “[E]volutionary biology is an endless frontier,” he concluded, “and there is still plenty to be discovered.”

The Panda’s Thumb is pleased to join its voice to the chorus of those around the world who have wished Professor Mayr a very happy birthday.

Note: Modified from NCSE’s release.

Posted by Reed on July 05, 2004 | Comments (3) | TrackBack (0)

A while back I was looking through my 1970s Funk & Wagnals’ Wildlife Encyclopedia and read the entry on River Dolphins.  In it a particular passage caught my eye because it was not very parsimonious.

We usually take it for granted that because whales, porpoises and dolphins are so obviously descended from land animals, their ancestors must have returned directly to the sea.  As a result, it is something of a surprise to learn there are such animals as river dolphins, and we suppose they have come up rivers from the sea.  In fact, the ancestors of dolphins could just as easily have left the land fro the rivers, and later invaded the sea.  This is supported by the primitive characters exhibited in the skeletons of the freshwater dolphins.  In most whales, porpoises and dolphins the seven neck vertebrae are squashed together and fused, and the animals have no visible neck.  In freshwater dolphins the vertebrae are separate and there is still some sign of a neck.  Also, the skull of a freshwater dolphin has not undergone the same fundamental changes as the skulls of its marine relatives, and in several ways is more like the skull of the extinct dolphin Squalodon of 15 millions years ago.

The problem of this hypothesis is that it requires the river dolphins of the Amazon, Ganges, Yangtze, etc. to all be autochthonous and essentially unrelated, since those river systems are separated by good span of geography.  So I went digging to see how science has progressed in 30 years, and found this gem.

Hamilton H et al. (2001) Evolution of River Dolphins. The Royal Society Proceedings: Biological Sciences, 268: 549-556.

Continue reading  “River Dolphins and Evolution”

Posted by John Wilkins on June 28, 2004 | Comments (12) | TrackBack (0)

One long-standing question in understanding the origin of life is the so-called “chirality problem”. While this is an unresolved question in our understanding of the origin of life, it is used by anti-evolutionists to beat evolutionary theory over the head. As we never tire of telling folk, the origin and subsequent evolution if life are two distinct issues.

What is the “chirality problem”? Let’s start by briefly discussing what chirality is. Biological molecules of some complexity often come in two forms that while chemically identical, have different three dimensional shapes; a “left-handed” one, and it’s mirror image, a “right-handed” one (see alanine graphic). Of particular importance for living systems are amino acids (levo- or left-handed) and sugars (dextro- or right-handed). Handedness is due to the carbon atom’s bonding capacities. This property of some molecules was discovered in 1847 by none other than Louis Pasteur (the molecule was a form of tartrate) in the dregs of some wine.

[img][*]http://www.pandasthumb.org/pt-archives/L-alanine.jpg…[*]http://www.pandasthumb.org/pt-archives/D-alanine.jpg…[/img]
Chiral forms (enantiomers) of the amino acid alanine. White balls are hydrogen atoms, grey balls are carbon atoms and the red ball is an oxygen atom, The left handed form is not superimposable on the right handed form).

How, it is asked, could this have occurred at the beginning of life? Surely ordinary physical processes should have given us a mix of both left and right handed forms (known as a racemic mixture)?

Well, firstly it turns out that ordinary physical processes do produce an excess of left over right forms. Recently, though, it was discovered that life itself can generate a particular enantiomer or chiral form of a particular molecule.

Continue reading  “The Left Hand of Darwin”

Posted by Steve on June 25, 2004 | Comments (9) | TrackBack (0)

This is the first in an ongoing series about recent discoveries and commentaries concerning aspects of evolution that affect our everyday lives.  On the one hand, it’s a fun way to showcase some of the recent goings-on in the literature, and on the other, it’s a way to rebut the occasional creationist claim that evolution isn’t important to biology or to science at large.  That assertion is false, and would be irrelevant even if true, but in my opinion (and I suspect this is true of most of us here), the aspects of evolution that affect our day-to-day lives are the most fascinating.

Consider the existence of man-made pollutants.  Since the advent of modern chemistry, humans have found ways of making new and useful chemicals that can’t be found in nature.  Unfortunately, part of what makes a chemical useful is its ability to resist breaking-down.  And if it happens that such a chemical gets produced in huge quantities, and that some of this quantity manages to make its way out into our environment, it can be quite a hazard to human and environmental health.  The resistance to degradation becomes a part of the problem, because these chemicals can accumulate over many years to the point where they become toxic.  It’s therefore important for us to understand methods by which these compounds can be eliminated. 

Fortunately, our bacterial friends have evolved ways of dealing with many of the persistent pollutants that have been dumped into the environment.  In a just published review in the Journal of Biological Chemistry, Lawrence Wackett of the University of Minnesota describes some of the enzymes that microbes have evolved to digest these man-made chemicals.  Unlike enzymes that evolved gillions of years ago, many of which have histories that are impossible to reconstruct, these enzymes show signs of having evolved quite recently.  Wackett notes: 

Another lesson being learned from biodegradation studies is that functionally significant enzyme evolution occurs on shorter time scales than previously appreciated; weeks, months and years rather than eons.

Continue reading  “Better Living Through Evolution, pt. 1: Cleaning up a mess/upending the "scientific key" of ID.”