Ancient Oxygen Levels Correlate With Animal Evolution

A paper in this week's Science correlates rise in atmospheric oxygen with the evolution of large placental animals.

The concluding paragraph of the paper states:

Continue Reading

The data presented here provide evidence of a secular increase in atmospheric oxygen over the past 205 My that broadly corresponds with three main aspects of vertebrate evolution, namely endothermy, placentation, and size. Particularly notable are high stable O2 levels during the time of placental mammal origins and diversification and a close correspondence between marked increases in both atmospheric oxygen levels and mammalian body size during the early to middle Eocene. Although increases in mammalian body size, morphological disparity, and inferred ecological heterogeneity during this interval may have been influenced as well by other environmental factors such as warm global temperatures and the spread of tropical and subtropical habitats, the correlation between evolutionary changes in mammalian body size and increased atmospheric O2 has a physiological basis related to placental mammal reproduction. The changes in oxygen appear to have been driven by tectonics and increased burial efficiency of organic matter on continental margins.

The correlations are represented in this accompanying figure (click to enlarge):



Here are a few more details from news@nature.com:

They have found that the amount of oxygen in the Earth's atmosphere 200 million years ago was only about half what it is today. And the appearance of large placental mammals, around 50 million years ago, happened at the same time as the oxygen level more or less doubled.

This is also about the same time that the Atlantic Ocean opened up: a supercontinent split into the Americas, Africa and Eurasia, creating the ocean between them.

This continental movement created thousands of kilometres of coastline that helped to wash organic carbon into the sea, locking it away from the process of decay. Because such carbon escapes chemical processes that would turn it into carbon dioxide, the more carbon is washed away, the more oxygen remains in the atmosphere...

Placental mammals began to appear at the end of the Cretaceous, but they were small, rodent-sized creatures. "We don't really see large mammals until the Eocene," says Falkowski.

This, he suggests, was made possible by the sudden oxygen rise at that time. Large mammals have a lower density of capillaries than small mammals, so they can only distribute oxygen around their bodies efficiently if there is a lot of oxygen in the air. Placental reproduction also needs a lot of ambient oxygen, because only a small proportion of that in the mother's blood reaches the fetus.

Continue reading...

Philosopher of Science: Robert Pennock

Robert Pennock is a philosopher of science and has also been a prominent critic of the intelligent design movement. He is the author of Tower of Babel: The Evidence Against the New Creationism, and testified as an expert witness in the Dover trial.

His website is one you may want to check out. He has done work on modeling evolution using digital organisms and his site provides the original Nature paper, as well as Carl Zimmer's article in Discover Magazine describing the work. He has a number of his other publications available as well--including "Creationism and Intelligent Design," which was published in the 2003 Annual Review of Genomics and Human Genetics.

Continue reading...

Biologist: Kenneth Miller

Kenneth Miller is a professor of biology at Brown University. He is a prominent defender of evolution and critic of intelligent design. As a vocal defender of evolution, Brown in somewhat unique in that he is also a believing Catholic--which combination is the impetus for his book, Finding Darwin's God. (I have not read the book, but Jeff summarized some of it at Mormons and Evolution.) Brown has a website that you may want to look through.

Here is a partial transcript of Miller's testimony in the Dover, PA trial:

Continue Reading

Q. (By Witold Walczak) The School District argues, you know, it takes a minute to read this statement. I haven't timed it. It takes about a minute to read this statement. What's the big deal? What's the harm in reading this to Dover School District students?

A. (By Kenneth R. Miller) That's a very interesting point. And if they raised the issue, what is the harm in reading it, one might well turn around and say, well then why read it in the first place, if it makes so little difference, if it is of so little consequence? Then why have you insisted on doing this and why are you in court today? The only thing I can infer from turning that question around is that the Dover School Board must think this is enormously important to compose this, to instruct administrators to read it, to be willing to fight all the way to the court. They must think that this performs a very important function.

Now turning it around back to my side of the table, do I think this is important? You bet I think this is important for a couple of reasons. One of which, first of all, as I mentioned earlier, it falsely undermines the scientific status of evolutionary theory and gives students a false understanding of what theory actually means. Now that's damaging enough. The second thing is, it is really the first attempt or the first movement to try to drive a wedge between students and the practice of science, because what this really tells students is, you know what, you can't trust the scientific process. You can't trust scientists. They're pushing this theory. And there are gaps in the theory. It's on shaky evidence. You really can't believe them. You should be enormously skeptical. What that tells students basically is, science is not to be relied upon and certainly not the kind of profession that you might like to go into. And thirdly, that third paragraph that we haven't talked about very much right now points out that intelligent design, which has implicit endorsement in this statement, because we don't hear that it's just a theory, we don't hear that it's being tested, it sounds like it's a pretty good explanation. It's available. It's good stuff. And students will understand immediately, as anybody does who reads Pandas, that the argument is made on virtually every page of Pandas for the existence of a supernatural creator designer. And by holding this up as an alternative to evolution, students will get the message in a flash. And the message is, over here, kids. You got your God consistent theory, your theistic theory, your Bible friendly theory, and over on the other side, you got your atheist theory, which is evolution. It produces a false duality. And it tells students basically, and this statement tells them, I think, quite explicitly, choose God on the side of intelligent design or choose atheism on the side of science.

What it does is to provide religious conflict into every science classroom in Dover High School. And I think that kind of religious conflict is very dangerous. I say that as a person of faith who was blessed with two daughters, who raised both of my daughters in the church, and had they been given an education in which they were explicitly or implicitly forced to choose between God and science, I would have been furious, because I want my children to keep their religious faith. I also want my students to love, understand, respect, and appreciate science. And I'm very proud of the fact that one of my daughters has actually gone on to become a scientist. So by promoting this, I think, this is a tremendously dangerous statement in terms of its educational effect, in terms of its religious effect, and in terms of impeding the educational process in the classrooms in Dover.

Continue reading...

ID Prediction Is Malarky

The Washington Post has an article explaining the strength of evolutionary theory. I want to focus on this portion:

Asked to provide examples of non-obvious, testable predictions made by the theory of Intelligent Design, John West, an associate director of the Discovery Institute, a Seattle-based ID think tank, offered one: In 1998, he said, an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the "junk" DNA in animals' genomes -- long seen as the detritus of evolutionary processes -- will someday be found to have a function.

(In fact, some "junk" DNA has indeed been found to be functional in recent years, though more than 90 percent of human DNA still appears to be the flotsam of biological history.)

Continue Reading

This is malarky. That prediction does not follow from intelligent design (at least the type the DI pushes) any more than evolution predicts that "junk DNA" should exist. All evolution predicts is that if "junk DNA" exists, unless there is a mechanism to remove it, it should be found in organisms in a pattern consistent with common descent. (As an aside, I should point out that to the extent that "junk DNA" has been found to have function, it is not the ID folks who have made the discoveries.) Now let's turn back to intelligent design.

ID proponents have repeated over and over again that intelligent design is about identifying features of the universe where design can be inferred because of their complexity. When scientists point out the many design flaws (or oddities) in nature--and even in the human body--ID proponents respond that the motivations of the designer are not relevant to the discussion about whether something is designed or not. They argue that we can infer design from the thing itself--questions about who the designer is or what his/her/its motivations were are not relevant. Further, although they do not repeat it much, they claim that ID can be compatible with much of evolutionary theory.

If they were sticking to their rules, they would say that intelligent design is silent on the issue of "junk DNA". Now West is trotting out a prediction that is clearly rooted in assumptions about what a designer would or would not do. He cannot have it both ways. Either issues of poor, inefficent, or malevolent design are legitimate in this debate or they are not.

Continue reading...

Evo-ID Smackdown Begins

Kitzmiller et al. v. Dover Area School District goes to trial today in Pennsylvania. Most of the major news sources have stories--here is one from MSNBC.com.

Why the court battle?

Continue Reading

It all stems from a science policy that the Dover, PA school district adpoted that required the following statement to be read to students:

The Pennsylvania Academic Standards require students to learn about Darwin’s theory of evolution and eventually to take a standardized test of which evolution is a part.
Because Darwin’s theory is a theory, it continues to be tested as new evidence is discovered. The theory is not a fact. Gaps in the theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

Intelligent design is an explanation of the origin of life that differs from Darwin’s view. The reference book, “Of Pandas and People,” is available for students who might be interested in gaining an understanding of what intelligent design actually involves.

With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the origins of life to individual students and their families. As a standards-driven district, class instruction focuses upon preparing students to achieve proficiency on standards-based assessments.

As I understand it, many science teachers refused to read the statement so administrators did it for them.

The NCSE has a website that is tracking the case. It has background information and copies of court documents. The book "Of Pandas and People" was published in the late '80s. The NCSE has many reviews of the book. The Panda's Thumb also has links to various information sources, including previous posts relevant to the case.

The Foundation for Thought and Ethics, the publisher of the book, sought to intervene in the lawsuit. Their request was denied, but what is interesting is some of the information that came out in the process. Althought the FTE claimed not to be a religious organization, tax documents said otherwise. Also, early drafts of the book used forms of the word "creation" where "intelligent design" ultimately appeared. The publisher claimed that "creation" was only used as a placeholder term.

Continue reading...

Whales: From Land to Sea

A couple of months ago I read Carl Zimmer's book, At The Water's Edge, which deals with the transition of aquatic life to land and back again. The "back again" part concerns the evolution of cetaceans (whales, dolphins, etc.) If you are interested in these two steps in evolution then you should read the book.

Now Zimmer has a post dealing with whale evolution and the creationist attack thereon. Here are a few links to go along with it.

Continue Reading

The webpage of the Thewissen lab is definately worth exploring. (Thewissen is a major player in the discovery of transitional whale fossils.)

This article, originally from the NCSE has some good background information, although it looks slightly out of date. One of Thewissen's important papers was published in Nature about a month after the above article was posted on talk.origins.

And then there is this illustration of whale transition--and this too.

Although not a scholarly source, Wikipedia seems to have a pretty good page.

On a final note, a reminder of why gap arguments are a bad idea:

"Finally, and most glaringly obvious, if random evolution is true there must have been a large number of transitional forms between the mesonychid and the ancient whale: Where are they? It seems like quite a coincidence that of all the intermediate species that must have existed between the mesonychid and whale, only species that are very similar to the end species have been found."

- Michael J. Behe

Anti-Darwinian, Intelligent Design conjecturist,
writing against the validity of evolution less than a year before three transitional species between whales and land-dwelling Eocene Mesonychids were found.

P.S. I forgot to include this. Note that not all relationships are set in stone.

Continue reading...

David H. Bailey on Science and Mormonism

I happened to come across an old Times and Seasons post today that contains a link to papers of David H. Bailey. Bailey has written a number of essays on Mormonism and science, some of which have been published in Dialogue: A Journal of Mormon Thought. His website makes these essays available, as well as some that have not been published. One essay, "Mormonism and the New Creationism," was published in Dialogue but is not otherwise freely available.

I am adding Bailey's site to the sidebar.

Continue reading...

General Authority Family Size

Just for the heck of it, I decided to graph up the number of children that General Authorities have. I got my information from the 2005 Church Almanac. I used frequency histograms, which means that it shows the frequency of a particular number of children.

Continue Reading

Here are the First Presidency and Quorum of the Twelve.


Here is the breakdown:

10 - Packer, Nelson
8 - Wirthlin
7 - Ballard, Scott
6 - Oaks, Eyring
5 - Hinckley, Faust
3 - Monson, Perry, Holland, Bednar
2 - Hales, Uchtdorf


Next are the Presidency of the Seventy, as well the First and Second Quorums--all General Authorities. (Remember, the rest of the quorums are Area Authorities.)



I will leave any analysis or conclusions to the reader.

Continue reading...

Finding Inspiration in Marching Penguins

An article from yesterday's New York Times explains how some religious-conservatives are drawing inspiration and life-lessons from the film "March of the Penguins." This has raised a few eyebrows.

George Will, quoted in the article, asks,

"March of the Penguins" raises this question: If an Intelligent Designer designed nature, why did it decide to make breeding so tedious for those penguins?

and concludes,

Reality's swirling complexity is sometimes lovely, sometimes brutal; its laws propel the comings and goings of life forms in processes as impersonal as Antarctica is to the penguins...

It is so grand that nothing is gained by dragging an Intelligent Designer into the picture for praise. Or blame.

PZ Myers, scientist and partisan, provides a reminder and observation:

Let's just remember that it is a seasonal monogamy—[penguins] get different breeding partners in different breeding seasons. This apparently justifies the practice of the Republican leadership in cashing in their old wives for new trophies.

Carl Zimmer reports from the future on some additional movies with family values. For example,

Harem of the Elephant Seals: Meet Dad: a male northern elephant seal who spends his days in bloody battles with rivals who would challenge his right to copulate with a band of females—but doesn’t life a finger (or a flipper) to help raise their kids.

For my part, I will just observe the irony that some who criticise evolution as promoting animalistic behavior apparently are looking to animals for lessons on life. Of course, the model animals must be carefully chosen.

Continue reading...

Sex-Ed: No Child Left Behind

Sometimes it is easy to take education for granted. When I see TV commercials warn that an oral contraceptive does not protect against sexually transmitted diseases, I have to remind myself that not everyone has had the benefit of learning that I have. Unfortunately, some of this seems to be by design.

I've come across several news stories about abstinence-only sex education over the past year. Several notable ones include:

1. "Abstinence-only sex education programs, a major plank in President George W. Bush's education plan, have had no impact on teenagers' behavior in his home state of Texas, according to a new study."

2. "A leading group of pediatricians says teenagers need access to birth control and emergency contraception, not the abstinence-only approach to sex education favored by religious groups and President Bush."

3. "The U.S. government's emphasis on abstinence-only programs to prevent AIDS is hobbling Africa's battle against the pandemic by downplaying the role of condoms, a senior U.N. official said on Monday."

Continue Reading

I'm all for encouraging abstinence, but not at the expense of the basic issues concerning sexual health. In terms of high school education, I think kids ought to be taught the basics about reproductive biology, sexually transmitted diseases, and contraception. Yes, teach about abstinence and warn that contraceptive methods are not foolproof, but give them a viable plan B. (But be careful about disparaging plan B, otherwise it seems pointless.) I think the same would basically apply for international efforts as well.

Disclaimers about oral contraceptives not protecting against STDs should be provided for the ignorant, not the intentionally uninformed.

(For basic information about sexually transmitted diseases see here.)

Continue reading...

Thermodynamics, Relativity, and Evolution

I recently heard someone pull out the classic "evolution contradicts the second law of thermodynamics" argument (I'm not sure whether they were just throwing it out, or actually believed it), and it got me thinking. I'm not going to deal with rebuttals to the argument (for those see here or here), I want to go in a little bit of a different direction. (I will state at the outset that I am weak in physics. I encourage comments those of you who are strong.)

Continue Reading

Just out of curiosity I had a look through some of my college textbooks. I think that the first time I encountered the laws of thermodynamics in any substantive way was in basic inorganic chemistry. I still have my textbook and thermodynamics is explained. I looked through several other textbooks--biochemistry, biology, and cell biology. All of these books explain the second law of thermodynamics and most also explain how complex biological structures can exist in the face of it. None of them describe any problem for evolution.

Now let's step back for a moment. The field of biology is broad--some specialties are deeply rooted in mathematics, physics, or chemistry. All of these people have been through basic college courses where the second law of thermodynamics was taught. If it was really a silver bullet fatal for evolution, shouldn't some of these people have noticed and made an issue of it within the scientific arena? Unless you posit a vast cover up, that should be a clue that the argument is actually baseless. On the contrary, I did a quick search and found this paper applying issues of thermodynamics and information theory to evoltuion.

This got me thinking even further. The first law of thermodynamics states that the total energy in the universe is constant--it can be converted into different forms, but it cannot be created or destroyed. Then I remembered the central equation of relativity, e=mc^2. This equation reveals that energy and matter can be converted into one another. With this little bit of knowledge, I might accuse phyicists: "The theory of relativity can't be true because it contradicts the first law of thermodynamics."

I found this PBS site where you can listen to a number of leading physicists explain the meaning of Einstein's equation. Sheldon Glashow actually says that the concept of conservation of energy (by which I understand him to mean the first law of thermodynamics) is wrong. Perhaps what he means is that the law could be generalized a little more to state that the amount of energy and mass in the universe is constant.

I recognize it is not a scholary reasouce, but Wikipedia actually says that the laws of thermodynamics break down in quantum mechanics.

I think there are several lessons here.

1. A little knowledge can be dangerous. Just on an intuitive level it seems ridiculous to me that a concept introduced to all science undergraduates would secretly mean the downfall of the central principle of biology. Yet some people seem to really believe it--you can easily find the claim in creationist literature.

2. It is a mistake to get caught up in the titles of scientific principles. Some people make a lot out of titles like "law" and "theory." Laws are not invincible and theories are not inherently weak. You have to look past the titles to the actual evidence and data.

3. Scientist are sometimes not sure how two concepts relate to each other. For them this represents a challenge to do additional research. For critics, such as creationists, this is taken as evidence that whichever concept they dislike is false.

4. In connection with #2 and #3, it is useful to remember that "unto every law there are certain bounds also and conditions" (D&C 88:38). Science is about discovering those laws, their bounds, and their conditions. Additional information may require a revision of the bounds and conditions. Sometimes this represents an expasion of the law; sometimes it is a contraction.

Continue reading...

Recent Brain Evolution

Science published two papers today that deal with two different genes (ASPM and Microcephalin) involved in brain development. Both genes have variants that show evidence of positive selection in the recent past--one as recent as about 6,000 years ago. Not all people have these variants though. For more information see commentary by John Hawks and Dienekes. Both are worth reading.

The bottom line is that it appears that the human brain is still evolving (which shouldn't be all that shocking, but we do tend to think of ourselves as a "finished" product). However nobody yet knows what effect that these gene variants have on the brain (if any).

Continue reading...

Utah Board of Education Defies Buttars

The Utah state Board of Education has adopted a position that fully supports the teaching of evolution.

From the NCSE:

Continue Reading

About a dozen scientists in attendance endorsed the statement, telling the board that "intelligent design" is not good science. Duane Jeffrey, a professor of biology at Brigham Young (and NCSE board member) compared "intelligent design" to astrology and pyramid power, while Gregory Clark, a professor of bioengineering at the University of Utah, told the board, "Intelligent design fails as science because it does exactly that -- it posits that life is too complex to have arisen from natural causes, and instead requires the intervention of an intelligent designer who is beyond natural explanation. Invoking the supernatural can explain anything, and hence explains nothing."

At the meeting, Buttars told the board that he intended either to introduce legislation calling for the teaching of "intelligent design" or arrange for there to be a referendum on next year's ballot. He told the Deseret Morning News that his "Academic Freedom Act" would "enhance the effectiveness of science education while at the same time ensuring that students are given credible alternative explanations for the origin of life on earth"; the newspaper quoted the act as saying, "We believe that excluding recent scientific discoveries simply because they run counter to the Darwinian model of origins is not good educational policy." [What discoveries? Calling something "complex" is not much of a discovery - LDS-SR.]

Gov. Jon Huntsman Jr. has also expressed support for science and the exclusion of intelligent design from science classes.

The board of education's statement is also available here. (Scroll down.)

Way to go Utah! ...so far.

Continue reading...

Church Gives $3 Million to Fight Measles

From the American Red Cross:

“Put Your Shoulder to the Wheel” – the common hymn in The Church of Jesus Christ of Latter-day Saints beckons people to not stand idly by and watch as conditions deteriorate, but to get involved and work to make the world a better place. The challenge is one the Church itself is living up to, exemplified most recently by its $3 million donation to the Measles Initiative.

Continue reading...

BYU Evolution Packet - Link Fixed

A post from a few days ago dealt with the BYU Evolution packet. Little did I know that the link on my sidebar had become invalid. I'm not sure who put the pdf file together, but it was posted on a BYU server for a zoology class. That internet address has disappeared, perhaps because of reorganization that eliminated the zoology department.

Luckily I had saved the file so I sent it over to Gary at No Death Before the Fall, and he is kindly hosting it. My link (on the sidebar) has been updated appropriately.

The packet is available elsewhere on the internet, but I prefer the pdf file, which also has an explanatory article from the Daily Universe with it.

Continue reading...

Chimpanzee Genome Published

The draft sequence of the chimpanzee genome has been published in Nature this week. A news summary is available at Scientific American.com. Carl Zimmer has a little more analysis here. (And while you're at it, read this other article by Zimmer on chromosome structure.)

Continue reading...