Let's Get Something Straight About Ardi

Last week the journal Science published a raft of papers describing the fossil remains of Ardipithecus ramidus, an ape that lived 4.4 million years ago and that is more closely related to humans than to chimpanzees. The split between the lineages that (in retrospect) lead to humans and chimpanzees is thought to have occurred about 6 million years ago. So Ardi--as the fossil has been nicknamed--lived a million (or two) years after that split.

The common ancestor of humans and chimpanzees remains unknown because of a lack of fossils. In fact, it may surprise you to learn that until a few years ago there were no chimpanzee fossils either--and what has been found is just teeth. Presumably this is because they live in areas that are not conducive to fossilization.

Anyway, in the absence of fossils scientists have only been able to imagine what that common ancestor was like, and at times they have tried to make inferences based on chimpanzees. But it's easy to forget that chimpanzees are the product of 6 million years of evolution just as we are. Ardi gets us closer to that common ancestor, and based on her the discoverers argue that some of the traits of the common ancestor were a little more like humans and less like chimpanzees.

Unfortunately some of the reporting on Ardi contains confusing language--sometimes coming from the scientists that made the discovery. For example, one of the authors (C. Owen Lovejoy) has been quoted as saying that we didn't evolve from apes--apes evolved from us. First of all, humans are apes (just like we are mammals and primates). But more importantly, chimpanzees did not evolve from humans or vice versa. Each came from a common ancestor. Apparently that common ancestor has traditionally been thought to have been much like a chimpanzee. What Lovejoy means is that we can no longer use chimpanzees as a stand-in for the human-chimpanzee common ancestor because some chimpanzee characteristics evolved after the split.

The bottom line is that in light of Ardi, the authors argue that the common ancestor of humans and chimpanzees was a little more like humans, and a little less like chimpanzees, than previously thought.

I hope that helps. See Carl Zimmer's informative post, Ardipithecus: We Meet At Last for more.

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An Evolutionary Prediction with Teeth

I don't think this needs additional comment. From the author summary of a paper published earlier this month:

Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin's theory of descent with modification.

Reference:

Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS. (2009) Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals. PLoS Genet 5(9): e1000634.

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President Uchtdorf's Creation Conundrum

I've been kind of lazy about blogging lately. So here is something quick that I had intended to post on a while ago, but had forgotten about.

Last year at the October 2009 General Relief Society meeting, President Dieter F. Uchtdorf gave a talk that included counsel to exercise individual creativity. That portion of the talk served as the basis for this brief Church video.




Here is an excerpt:

...remember that you are spirit daughters of the most creative Being in the universe. Isn’t it remarkable to think that your very spirits are fashioned by an endlessly creative and eternally compassionate God? Think about it—your spirit body is a masterpiece, created with a beauty, function, and capacity beyond imagination.

It struck me as odd that President Uchtdorf used spirit bodies as examples of masterpieces of creation. First, to say that most people have never seen a spirit body is--I think it's safe to say--an understatement. When I read those words all I can do is imagine that he's right. Why choose something that most people can't directly identify with?

But beyond that, the human (physical) body is often held up as an example of God's marvelous creations. (For examples, see here, here, and here.) Why didn't President Uchtdorf follow suit? Maybe he just wanted his example to correspond to his earlier use of the words "spirit daughters". Or maybe he was being sensitive to the body-conscious among his audience by using a more abstract and idealized example. But I can't help but wonder: Is it possible that he intentionally avoided a traditional example of natural theology? If so, why?

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What Is BYU Doing for Science Education in Utah?

An article in the journal Evolution: Education and Outreach describes an outreach program in Utah for aiding the teaching of evolution in state public schools. The program is called the Utah Evolution Education Program and six of the nine authors of the article are BYU faculty (plus at least one former). From the article, Evolution Education in Utah: A State Office of Education–University Partnership Focuses on Why Evolution Matters:

The Utah Evolution Education Program is a partnership between the Utah State Office of Education, individual school districts throughout the state, and a group of seven university professors with backgrounds in evolutionary biology, genetics, and geology. Our primary goal is to provide resources to teachers as they apply the state science standards in biology and earth systems, both of which rely on knowledge of the theory of evolution. Beyond this, our efforts are focused on creating a forum in which school boards, public school administrators, public school teachers, and our university team can openly discuss concerns and challenges to teaching evolution in each respective school district. Finally, our program is designed to empower public school teachers with recent advances in evolutionary biology that can be integrated into their curricula and that clearly illustrate the value of evolutionary biology as a theory with practical applications to improve the human condition. In short, our approach is to show all members of the public school community—including elected school boards, administrators, public school teachers, and ultimately students—what evolution is and why it matters.

If you would like more detail, go read the whole thing. Oh, and Go Cougars!

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BYU Is Different, But Not So Different

Recently Elder Jan Paulsen had the following to say about teaching evolution in Church schools.

To those who teach at our colleges and universities, let me say that you have a demanding, often difficult, but sacred assignment. It is a ministry you hold in trust. It is understood that to care for your ministry responsibly you have to take your students on many a journey of findings into various disciplines of study. They need to know what they will meet in their profession and in life. As part of that exercise you will also expose them to the elements and concepts of evolution. That is understood.

...however, I appeal to you that when you take your students out on the journey, you bring them safely back home before the day is over. And their home must always be in the world of faith. You owe it to the students, you owe it to God, you owe it to their parents, you owe it to the church, and you owe it to yourself as a believer to safely guide them through difficult moments on their journey.

Before continuing, take a moment and consider whether you agree with Elder Paulsen.

Alright, now I need to fill in some of the context. First of all, I should mention that Elder Jan Paulsen is the current leader of the Seventh-day Adventists (yes, they call him 'Elder'), and the quote above comes from a statement he released in response to a controversy over the teaching of evolution at La Sierra University, a church-owned school.

Seventh-day Adventists take a literal approach to Genesis. As Paulsen put it,

We reaffirm the Seventh-day Adventist understanding of the historicity of Genesis 1-11: that the seven days of the Creation account were literal 24-hour days forming a week identical in time to what we now experience as a week; and that the Flood was global in nature.

In fact a Seventh-day Adventist, George McCready Price, pretty much pioneered "flood geology," which has become a pillar of young-earth creationism. (Speaking of Price, this is the same George McCready Price that Joseph Fielding Smith was fond of, and James E. Talmage sought to discredit. For more, see here. But I digress.)

You can read about the controversy here. It appears that at least some of the science faculty take pride in their work and try to teach science as science. So when a student wrote a paper that one of the professors judged to be shallow on science while containing creationist apologetics, the professor told the student that the paper was unacceptable and he received a lower grade. Emails were exchanged, and before long the controversy moved beyond the university with outsiders upset that the university was teaching evolution as "fact."

It will all probably blow over. For one thing, the university president is on the side of the professor. And as for the professor,

Bradley says he’s felt no pressure to change anything about his course, and says bluntly that he doesn’t plan to turn his class into a theological seminar, or to present evolutionary theory only to then dismantle it for students. While he’s fine with helping students work through struggles of faith, Bradley says he won’t undercut decades of peer reviewed scientific research in the interest of religious consistency.

“I am not OK with getting up in a science course and saying most science is [B.S.],” he said.

For some strange reason this all seems familiar to me. I mean, it's not like this kind of thing would ever happen at BYU. Oh no, never.

I don't know what morale is like among BYU biologists. My sense is that it's pretty good and that the university is more supportive of them now than ever before. But I imagine there are days when they feel misunderstood. On such days perhaps they can take some consolation that faculty at other religious universities face the same problem. And they can count at least one blessing: the leader of our Church has not affirmed a 24/7 creation week.


Discussion question: Do you agree with Jan Paulsen, even though his world of faith may be different from yours?

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Making Hash of Science, Religion, and Politics

In cryptography a "one way hash function" is a mathematical operation or algorithm that is easy to do, but difficult to undo. For example, one can multiply two prime numbers together quite easily. However, given only the result, it is difficult to figure out which two prime numbers were multiplied together, especially when the number is large. In fact if the the number is large enough, supercomputers may take years to figure it out.

Today I was reading a little essay on FactCheck.org, "Health Care and the 'One Way Hash'" that used the concept of a "one way hash" as an analogy for the kind of work they do--trying to get past sound bites to the more complicated reality. Credit for the analogy actually goes to Julian Sanchez at the Cato Institute, whom they quote:

Sanchez: The talking point on one side is just complex enough that it's both intelligible—even somewhat intuitive—to the layman and sounds as though it might qualify as some kind of insight. (If it seems too obvious, perhaps paradoxically, we’ll tend to assume everyone on the other side thought of it themselves and had some good reason to reject it.)[*] The rebuttal, by contrast, may require explaining a whole series of preliminary concepts before it's really possible to explain why the talking point is wrong. So the setup is "snappy, intuitively appealing argument without obvious problems" vs. "rebuttal I probably don't have time to read, let alone analyze closely."

Upon reading this I immediately thought of the many anti-Mormon or creationist arguments I've encountered that are so wrong-headed that I've hardly known where to begin.

Sanchez's original post is about our need to rely on qualified authorities when making judgments about technical issues. He points out that legitimate authorities often have to contend with "one hash arguments," and that lay people are therefore likely to be misled if they ignore the authorities and try to judge the issues for themselves. And it turns out that the paragraph quoted above was about the "one hash arguments" of Intelligent Design proponents.

Anyway, I love the analogy and I think I may start making use of it. FactCheck concludes with advice that applies beyond public policy.

Keep this in mind the next time you see what looks like a knock-down, one-sentence argument for your favorite public policy option. If it looks like a pretty obvious (but not too obvious) argument, there’s a decent chance that you’ve just found yourself a one way hash.

I think that goes for arguments both for and against.


* You would think that some arguments would be too obvious, but apparently not. Skeptics of global warming, for example, say all kinds of things that seem so obvious that, if they were true, you would wonder how mainstream scientists could be so stupid and still survive into adulthood.

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Summer Reading Report

Back in July I posted what books I was reading this summer. Having now finished, I thought I'd write a few words about each of them--my book report, if you will.


The Fabric of the Cosmos: Space, Time, and the Texture of Reality, by Brian Greene.

Relativity, quantum mechanics, entropy, the Big Bang, inflationary cosmology, string theory, and M-theory are all covered in this book. Greene does an admirable job of presenting highly mathematical concepts in a more intuitive way. Unfortunately, there just isn't a way to imagine more dimensions, and quantum mechanics is just not intuitive. Although I enjoyed the book, I gave up toward the end and failed to finish it. The problem is that Greene leads you through so many twists and turns that it is easy to lose sight of the the major concepts. And at the end when he turns to things like time travel and other stuff that ought to be exciting, well I was just tired of trying to keep concepts straight and remember what was covered ten chapters previously.

But don't let me discourage you because if you put in the effort to read most of the book, I think you will probably find your understanding of cosmology to be the best it has ever been (assuming you are not a cosmologist).


Death From The Skies!: These Are the Ways the World Will End . . ., by Phil Plait.

This is a fun book that uses all of the different astronomical ways that life on Earth could be destroyed as a hook for teaching about astronomy and cosmology. Asteroids, supernova, gamma ray bursts, black holes, and even alien attacks are all covered. It's an easy read and makes learning pretty painless. I don't think I'm giving anything away if I tell you that we are toast. It's just a matter of time.

I should also note that Phil Plait has a blog, Bad Astronomy, and is prominent in the skeptical movement.


The Code Book: The Evolution of Secrecy from Mary, Queen of Scots to Quantum Cryptography, by Simon Singh.

For pure enjoyment, I think this was my favorite book of the three. Cryptography is the kind of topic that could really put you to sleep, but Singh keeps it interesting by using history and personal stories while explaining advances in cryptography and cryptanalysis. Medieval intrigue, WWI, and WWII are each tied to cryptography, sometimes in multiple ways. For example, in WWII the Polish and British breaking of German codes generated with their Enigma machine played an important role in winning the battle for the Atlantic. Meanwhile, the U.S. used Navajo speakers as a means of encrypting messages that the Japanese were never able to break. Singh also covers the cracking of Egyptian hieroglyphics and the ancient script of Crete, Linear B.

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Betsy McCaughey Should Probably Never Be Believed Again

[This post is a little off-topic for this blog, but I can't help myself. I have no other outlet.]

Although she did not use the words "death panels" (a term that was introduced by Sarah Palin), the whole ruckus over the allegation that the health care overhaul would encourage euthanasia of seniors was started by Betsy McCaughey. She is a former lieutenant governor of New York and gained national attention when she helped to sink the Clinton health care plan.

As already mentioned, her latest appearance on the national scene came from saying the following on former Senator Fred Thompson's radio show.

And one of the most shocking things I found in this bill, and there were many, is on Page 425, where the Congress would make it mandatory -- absolutely require -- that every five years, people in Medicare have a required counseling session that will tell them how to end their life sooner, how to decline nutrition, how to decline being hydrated, how to go in to hospice care. And by the way, the bill expressly says that if you get sick somewhere in that five-year period -- if you get a cancer diagnosis, for example -- you have to go through that session again. All to do what's in society's best interest or your family's best interest and cut your life short. These are such sacred issues of life and death. Government should have nothing to do with this.

I don't think I need to elaborate on how that claim has played out in the national discussion. It's an absurd claim that has consumed an inordinate amount of attention and scared a lot of people.

This week, McCaughey appeared on The Daily Show to explain herself--and she did not back down. You can read some analysis of the interview, as well as watch it in its entirety (which I have), here. At the end of the interview, McCaughey invoked her Ph.D. and experience reading legislation to bolster her authority on this issue. Either she or I have problems with reading comprehension.

There are problems from the very beginning. In part 1 starting at 1:43, she says regarding advance care planning consultations,

"The government prescribes what must be covered in detail, including foregoing nutrition, hydration, and even antibiotics. . . . But it does prescribe that the medical professional shall, not may, shall--must include all these issues."

Oh really? Well let's have a look at that. The text of the House bill is available here (pdf). The outline format of the bill is a little tough to follow; if you want to see it laid out in a more visually friendly fashion, see here.

OK, page 425 and 426 lay out what elements an advance care planning consultation covered by Medicare "shall" include. The elements are spelled out in paragraphs A-F. It's pretty straightforward stuff--what a living will and power of attorney is, what kind of resources are available for helping patients make decisions, the continuum of end-of-life services, the advantages of planning ahead, and so forth. No mention of foregoing nutrition or hydration, although of course they would fall within the continuum of end-of-life services.

Page 427 appears to be about how this section would apply to States, depending on State law. Anyway, no mention of nutrition or hydration.

Page 428 defines who can provide advance care planning consultation, states that an initial physical examination does not count as a consultation, and gives the circumstances under which such a consultation "may" occur more often than every five years.

Page 429 says that the advance care planning consultation can include the formulation of a "life sustaining treatment or a similar order." It then defines what elements must be included in such an order. It must (i) be signed by a physician or other approved health care provider and be in such a form that it can stay with the patient, (ii) communicate the individual's wishes for treatment, (iii) be uniquely identifiable and in a standard format, and (iv) may include advance directives.

Page 430 is where the scandal is. Remember on page 429 when it said that a life sustaining treatment order should communicate the wishes of the patient about treatment? Well page 430--referring back to page 429--suggests the kinds of things that an individual "may" include in their wishes.

‘(B) The level of treatment indicated under subparagraph (A)(ii) may range from an indication for full treatment to an indication to limit some or all or specified interventions. Such indicated levels of treatment may include indications respecting, among other items--

‘(i) the intensity of medical intervention if the patient is pulse less, apneic, or has serious cardiac or pulmonary problems;

‘(ii) the individual’s desire regarding transfer to a hospital or remaining at the current care setting;

‘(iii) the use of antibiotics;

‘(iv) the use of artificially administered nutrition and hydration.’.

So there you go. That's it. The bill says that in expressing their treatment wishes, a person "may" include such items as where they want to be, whether they want antibiotics, and whether they want artificial nutrition and hydration.

McCaughey goes on to assert that page 432, which basically says that the government will measure "both the creation of and adherence to orders for life-sustaining treatment," means that you will be locked into your life sustaining treatment order. You see, according to her, physicians will be rated, in part, by the percentage of their patients that have treatment orders, and the percentage of those orders that are followed. It's unclear to me whether physicians would actually have a financial incentive to ensure that their patients have treatment orders, but given that its contents are decided on by the patient I don't see the big deal even if that is true--which I doubt. And would you want your doctor to ignore your wishes? I don't think so. But McCaughey envisions a bizarre scenario where lucid patients change their mind about their treatment options but physicians refuse to allow any changes because they have to report whether they followed through on the treatment order.

McCaughey has established a pattern of making false claims. Whatever one thinks of the Clinton health care plan, and whatever one thinks of the current health care plan, and whatever one thinks of McCaughey's motives, I hope we can come to a consensus on this: On matters of health care reform or interpretation of legislation, Betsy McCaughey should not be believed anymore.

[Now that I've had my turn, commenters may also vent their spleen--within reason of course.]

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