Climate Science: Find Your Own Dang Answers

In my surfing on the internet, and occasionally in personal conversation, I've noticed that some people have strong opinions on climate science despite the fact that they seem to have no familiarity with the subject. Sometimes they think that they have an insight as to why human-induced climate change is bogus--as if their particular insight never occurred to the experts.

The internet is a wonderful tool for accessing information. However, it can also be a confusing world of claims and counter-claims. And it doesn't help that acronyms and unfamiliar words abound. So to assist my fellow non-experts out there, I thought I would list a few resources for getting the mainstream science.

First is the Intergovernmental Panel on Climate Change (IPCC). This is a scientific body established by the United Nations that reviews and synthesizes the state of climate research every five years. Their last report was in 2007 and consists of three parts:

1. The Physical Science Basis

2. Impacts, Adaptation and Vulnerability

3. Mitigation of Climate Change

These reports may look kind of scary, but the IPCC has given you some help. Each part has a "Summary for Policymakers" that gives the key points. And guess what? Each paragraph of the summary contains a reference to the full report so that if you want more detail on a particular point you can quickly find it in the full report. In addition, the Physical Science Basics part has a "Frequently Asked Questions" document that is a collection of FAQs that are scattered throughout the report. It's a nice place to start.

Next up is the U.S. Global Change Research Program (USGCRP).

The USGCRP began as a presidential initiative in 1989 and was mandated by Congress in the Global Change Research Act of 1990 (P.L. 101-606), which called for "a comprehensive and integrated United States research program which will assist the Nation and the world to understand, assess, predict, and respond to human-induced and natural processes of global change."

The USGCRP consists of representatives from a number of federal science agencies and recently released its 2009 U.S. Climate Impacts Report. This report focuses on the basic science and how climate change is expected to impact the U.S. It also has an Executive Summary; however the section that explains the science, Global Climate Change is pretty readable. If you do nothing else, at least look through the figures and sub-headings.

The 2007 IPCC report obviously does not contain more recent developments, and the next report is not due until 2013. Recently a group of climatologists, some of which were authors of the IPCC report, released an update called The Copenhagen Diagnosis. It is quite readable and addresses common questions in separate boxes that are distributed throughout the document.

Finally, there are various other websites where you can find information. There are the various government agency websites such as NOAA, NASA, EPA, USGS, and so forth. Then there is RealClimate.org, a blog maintained by a number of climate scientists, including some high-profile ones. The magazine New Scientist has put together a feature dealing with common climate myths. And of course there is Wikipedia which, although it must be taken with a grain of salt, usually provides simple but good information. After getting a feel for a topic at Wikipedia you can go to one of the other sources I listed for more authoritative information.

So there you go. The next time you find yourself wondering if we are just experiencing a natural warming period, or if the warming can be explained by the sun, or how scientists could possibly know how much CO2 was in the atmosphere in millennia past, go dig into these sources and find the answer. Do you think a particular climate change claim is exaggerated, or have you heard that climate scientists have ignored a particular issue? Go find the topic in these sources and see how it is handled. Whether you believe the information is up to you, but at least you will have authoritative mainstream information.

Metaphorically speaking, you have the dictionary in front of you. Look up the word for yourself to see how it's spelled and what it means.

Updated Recommendations:

America's Climate Choices - May 2010, the National Research Council of the National Academy of Sciences released three reports on climate change.

Climate Change: NASA's Eyes on the Earth - a slick website that explains climate change in a clear and simple way.

EPA Endangerment Findings - The Environmental Protection Agency's explanation of why greenhouse gases pose a danger under the Clean Air Act, with responses to public comments.

The Discovery of Global Warming - an online history maintained by the American Institute of Physics.

Video lectures of a college course at the University of Chicago.

Blogs:
Skeptical Science - a great resource for dealing with common misconceptions.
Climate Progress
Anti-Climate Change Extremism in Utah - the blog of BYU geologist Barry Bickmore.
Open Mind

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AP: No Science Fraud in Climategate Emails

From the AP:

E-mails stolen from climate scientists show they stonewalled skeptics and discussed hiding data — but the messages don't support claims that the science of global warming was faked, according to an exhaustive review by The Associated Press.

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Maybe Reality Really Does Have a Liberal Bias

You may have seen t-shirts or bumper stickers that say, "Reality has a liberal bias." Braggadocio? Apparently not.

A recent poll by the Pew Research Center found that in the U.S. only 6% of scientists identify as Republicans. In contrast, 55% identified as Democrats and 32% as independents. This lopsidedness held regardless of whether the scientists were in academia, government, or industry. Ouch.

This imbalance has important implications for reality: If scientists study the nature of reality, and most scientists are "liberal" (i.e. not conservative Republicans), then "reality" is liberally biased.

Does anybody think like this? Yes. Andy Schlafly is the son of conservative activist and Eagle Forum founder Phyllis Schlafly. He is the man behind Conservapedia--a Wikipedia for conservatives. He is also behind a project to purge the Bible of liberal bias by preparing a "conservative" translation.

A look at some of the Conservapedia article pages (and their associated talk pages) reveals the extent to which Schlafly sees science as liberal bias.

On black holes:

Like most college majors, physics students repeat what they're taught. If they received good grades, then it becomes even harder for them to question it. But keep in mind that the people doing the teaching are the most liberal group in the world, and they almost never encourage the student to open his mind and think critically for himself.
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Black holes are far too popular in science magazines and liberal publications like the New York Times to "go away" that easily.
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There's a broader point here. Why the big push for black holes by liberals, and big protests against any objection to them? If it turned out empirically that promoting black holes tends to cause people to read the Bible less, would you still push this so much? Certainly there is no practical justification to pushing black holes; no one will ever be helped by them in any way.

On the theory of relativity (here and here):

Despite censorship of dissent about relativity, evidence contrary to the theory is discussed outside of liberal universities.
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Look, there's no denying that physics professors are among the most liberal group anywhere, and far more liberal than the Democratic Party as a whole. Within physics departments, the promoters of relativity are particularly liberal, more so than, for example, material science types. Keep in mind that many of the promoters of the phony man-made global warming are physics professors.
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Relativity is an unproductive liberal favorite that wastes taxpayer money, misleads well-intentioned students and pushes the masses toward relativism.

On global warming:

The myth of dangerous man-made global warming is promoted by liberals and socialists seeking greater government control over the production and use of energy, which is a substantial percentage of the economy.

On evolution:

Given that liberalism is so prevalent in academia, it is not entirely surprising that college graduates are indoctrinated into the evolutionary paradigm via evolutionary propaganda.

Despite the aforementioned lack of evidence for the evolutionary position and the aforementioned counter evidential nature of the evolutionary paradigm, atheists and liberals persist in advocating the evolutionary paradigm.

Unfortunately this kind of collection of anti-science attitudes is not limited to Schlafly. Tom Bethell, a senior editor at The American Spectator and author of The Politically Incorrect Guide to Science has contrarian views on evolution, AIDS, the theory of relativity, climate change...and Shakespeare to boot. In addition to evolution, some of the top people at the Discovery Institute--the big pusher of Intelligent Design--also have contrarian views on AIDS and climate change.

More recently, in the wake of the controversy generated by the CRU emails Rush Limbaugh said about climate change:

I've instinctively known this from the get-go 20 years ago. The whole thing's made up. And the reason I know it is because liberals are behind it. When they're pushing something, folks, it's always bogus.

He feels the same way about H1N1 influenza.

We are the targets of lies, damn lies and science and scientists are rapidly becoming as trustworthy as politicians.

In some ways none of this is surprising. (Well, black holes surprised me.) Evolution and global warming have long been sticking points with the Right, and it has been four years since Chris Mooney published The Republican War on Science.

None of this is to deny that elements of the Left have their own problems with science. But I wonder if we may be entering into a positive feedback loop that will increasingly politicize science and draw it into the culture wars: the Right takes positions contrary to mainstream science, science-friendly citizens reject the Right, the Right takes this as evidence that science is liberally biased, repeat. I hope not, and I hope that more Republicans will speak up for science--which is a strange thing for me to say since according to Andy Schlafly I am liberally biased.

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Nature on Climategate

The journal Nature explained its position on the Climategate controversy in an editorial in today's issue. Here are a few highlights.

A fair reading of the e-mails reveals nothing to support the denialists' conspiracy theories. In one of the more controversial exchanges, UEA scientists sharply criticized the quality of two papers that question the uniqueness of recent global warming (S. McIntyre and R. McKitrick Energy Environ. 14, 751–771; 2003 and W. Soon and S. Baliunas Clim. Res. 23, 89–110; 2003) and vowed to keep at least the first paper out of the upcoming Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC). Whatever the e-mail authors may have said to one another in (supposed) privacy, however, what matters is how they acted. And the fact is that, in the end, neither they nor the IPCC suppressed anything: when the assessment report was published in 2007 it referenced and discussed both papers.

As for the papers published by Nature:

The stolen e-mails have prompted queries about whether Nature will investigate some of the researchers' own papers. One e-mail talked of displaying the data using a 'trick' — slang for a clever (and legitimate) technique, but a word that denialists have used to accuse the researchers of fabricating their results. It is Nature's policy to investigate such matters if there are substantive reasons for concern, but nothing we have seen so far in the e-mails qualifies.

It also discusses issues of raw data.

If there are benefits to the e-mail theft, one is to highlight yet again the harassment that denialists inflict on some climate-change researchers, often in the form of endless, time-consuming demands for information under the US and UK Freedom of Information Acts. Governments and institutions need to provide tangible assistance for researchers facing such a burden.

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Climategate: Let's Get Some Things Straight (long)

Last month somebody hacked into a server of the Climatic Research Unit (CRU) of the University of East Anglia (UEA) in the U.K. and obtained thousands of emails and documents that have since been distributed on the internet. The CRU is one of the leading institutes studying climate change, and critics claim to have found evidence that scientists associated with the institute have fraudulently manipulated data to make it look like Earth is warming and have suppressed disagreement. The controversy has been called Climategate (although some call it SwiftHack). There has been a lot of fallout in the press and in the blogosphere, but from my view the ensuing argument has generated more heat than light.

I have yet to see any real evidence of data manipulation or fraud. Evidence of such has been claimed based on a few much-quoted emails but they turn out to have reasonable explanations. Below I review a few of the scientific issues from my non-climate-scientist perspective.

1. One of the most quoted emails was from Phil Jones in 1999. It reads in part:

I've just completed Mike's Nature trick of adding in the real temps to each series for the last 20 years (i. e. from 1981 onwards) and from 1961 for Keith's to hide the decline.

Is this evidence that these scientists were intending to deceive? Many people have already pointed out that the word "trick" was simply a casual synonym for "novel solution". But what about "hide the decline"? In order to understand this we have to back up and talk about Michael Mann and the hockey stick controversy.

Reliable temperature measurements before around 1850 are lacking, so in order to study temperature fluctuations pre-1850 various proxies are used. Proxies are other natural phenomena that are affected by temperature that scientists can study in place of thermometers. One proxy of particular relevance here is tree rings; the growth of at least some trees is altered depending on temperature, and those alterations can be seen in the rings. Using a number of proxies, in the late 1990's Michael Mann published a reconstruction of Northern Hemisphere surface temperatures reaching back 1000 years. His reconstruction was featured in the 2001 IPCC report.


The figure to the left shows the inferred temperatures based on proxies, while the red shows more recent actual temperature measurements for comparison. This reconstruction has been controversial and some statistical criticisms of minor effect on the result were found to have merit. Ultimately Congress asked the National Research Council of the National Academy of Sciences to evaluate Mann's work and in 2006 they issued their report: Surface Temperature Reconstructions for the Last 2,000 Years. It is a non-technical report and is pretty readable. In summary the report found (emphasis added):

The basic conclusion of Mann et al. (1998, 1999) was that the late 20th century warmth in the Northern Hemisphere was unprecedented during at least the last 1,000 years. This conclusion has subsequently been supported by an array of evidence that includes both additional large-scale surface temperature reconstructions and pronounced changes in a variety of local proxy indicators, such as melting on ice caps and the retreat of glaciers around the world, which in many cases appear to be unprecedented during at least the last 2,000 years. Not all individual proxy records indicate that the recent warmth is unprecedented, although a larger fraction of geographically diverse sites experienced exceptional warmth during the late 20th century than during any other extended period from A.D. 900 onward.

Based on the analyses presented in the original papers by Mann et al. and this newer supporting evidence, the committee finds it plausible that the Northern Hemisphere was warmer during the last few decades of the 20th century than during any comparable period over the preceding millennium. The substantial uncertainties currently present in the quantitative assessment of large-scale surface temperature changes prior to about A.D. 1600 lower our confidence in this conclusion compared to the high level of confidence we place in the Little Ice Age cooling and 20th century warming. Even less confidence can be placed in the original conclusions by Mann et al. (1999) that “the 1990s are likely the warmest decade, and 1998 the warmest year, in at least a millennium” because the uncertainties inherent in temperature reconstructions for individual years and decades are larger than those for longer time periods and because not all of the available proxies record temperature information on such short timescales.

In other words, Michael Mann was probably right, though he overstated the case a little. But even if he wasn't, the report did not consider his temperature reconstruction as primary evidence for climate warming.

In the discussion on tree rings the report pointed out that:

Although limiting factors controlled tree ring parameters in the past just as they do today, it is possible that the role of different factors at a single location or over an entire region could change over time. This possibility has been raised to explain the “divergence” (i.e., reduced correlation) between temperature and ring parameters (width and maximum latewood density) during the late 20th century (Jacoby and D’Arrigo 1995, Briffa et al. 1998). ...

Elevational treeline sites in Mongolia (D’Arrigo et al. 2001) and the European Alps (Büntgen et al. 2005) are not affected by “divergence.” This geographic separation was confirmed by Cook et al. (2004), who subdivided long tree ring records for the Northern Hemisphere into latitudinal bands and found not only that “divergence” is unique to areas north of 55°N but also that the difference between northern and southern sites found after about 1950 is unprecedented since at least A.D. 900.

In other words, beginning around 1950 tree rings in some trees in the Northern Hemisphere do not agree with the temperature trends that have been directly measured. That is, some of the most recent tree ring proxies show cooling, but our instruments show warming. The reason for this "divergence" is not known and is an issue of further research. However, it has been known about by climate scientists since at least 1998, and is discussed in the 2007 IPCC report (large pdf) (p. 472-473). Again, this is apparently only an issue in some trees, and otherwise the historical tree ring proxies agree with other proxies as well as instruments. (For a comparison of various proxies and instruments, see this figure.)

So back to the email about hiding the decline: Phil Jones has explained what he meant in his 1999 email.

One particular, illegally obtained, email relates to the preparation of a figure for the WMO [World Meteorological Organization] Statement on the Status of the Global Climate in 1999. This email referred to a “trick” of adding recent instrumental data to the end of temperature reconstructions that were based on proxy data. The requirement for the WMO Statement was for up-to-date evidence showing how temperatures may have changed over the last 1000 years. To produce temperature series that were completely up-to-date (i.e. through to 1999) it was necessary to combine the temperature reconstructions with the instrumental record, because the temperature reconstructions from proxy data ended many years earlier whereas the instrumental record is updated every month. The use of the word “trick” was not intended to imply any deception.

Phil Jones comments further: “One of the three temperature reconstructions was based entirely on a particular set of tree-ring data that shows a strong correlation with temperature from the 19th century through to the mid-20th century, but does not show a realistic trend of temperature after 1960. This is well known and is called the ‘decline’ or ‘divergence’. The use of the term ‘hiding the decline’ was in an email written in haste. CRU has not sought to hide the decline. Indeed, CRU has published a number of articles that both illustrate, and discuss the implications of, this recent tree-ring decline, including the article that is listed in the legend of the WMO Statement figure. It is because of this trend in these tree-ring data that we know does not represent temperature change that I only show this series up to 1960 in the WMO Statement.”

Below are the original figure (top) and an alternate that shows the various proxies separately (bottom) (from here; click to enlage).


You can see in the bottom figure that as measurements approach the year 2000 the tree proxy (green) dips (and more recently has apparently continued its downward trend). Was it misleading for Jones to leave that dip out of the original figure? To the casual observer it would seem so. However, the purpose of the figure was to represent temperature trends. It would therefore also have been misleading to leave it in because it is known--by comparison to instruments--to be wrong.

It seems clear that Phil Jones omitted the decline in the tree ring proxy because to do otherwise would cause confusion rather than represent the state of the science. Even in the past few days I have seen someone claim that the "decline" shows that temperatures have not risen. It does no such thing, as should be clear from what I have explained above. Further, even if we grant that Jones was seeking to deceive, he has clearly failed because the decline has repeatedly been noted in the literature, including the 2007 IPCC report, as mentioned above.

2. In a 2003 email Michael Mann wrote, referring to the medieval warm period, that:

...it would be nice to try to contain the putative "MWP"...

Although the email doesn't elaborate on what that means, we are assured by critics that it was a desire to hide the fact that there was a warm period in the Northern Hemisphere 1000 years ago. Well, if that was the case he failed because there is a whole page-and-a-half discussion of it in the 2007 IPCC report (p. 468, linked above; see also this figure). And anyway, Mann has explained what he meant.

In this email, I was discussing the importance of extending paleoclimate reconstructions far enough back in time that we could determine the onset and duration of the putative "Medieval Warm Period".

Since this describes an interval in time, it has to have both a beginning and end. But reconstructions that only go back 1000 years, as most reconstructions did at the time, didn't reach far enough back to isolate the beginning of this period, i.e. they are not long enough to "contain" the interval in question.

In more recent work, such as the IPCC Fourth Assessment Report published in 2007, the paleoclimate reconstructions stretch nearly 2000 years back in time, which is indeed far enough back in time to "contain" or "isolate" this period in time.

3. There has been some confusion about how much of CRU's data from temperature measurements since 1850 has been publicly available. Not all of it has been, and this combined with a purloined programmer's log that expressed frustration with the poor condition of a database has fueled doubts about CRU's analysis of global temperatures. On New York Times reporter Andrew Revkin's blog, University of Illinois climatologist Michael Schlesinger pointed out that there are multiple organizations from different countries that have done similar analyses, and all get the same basic result, as shown in this figure (see blog post for more details).


Although the vast majority of the raw temperature readings are apparently shared among the groups, they perform their own analysis and make their own decisions about how to translate those temperatures into meaningful data. Obviously the experts think they have produced an accurate picture of temperature trends, however I think it remains possible that there may be problems at both the level of raw data, as well as analysis, that might alter the picture somewhat. We will have to wait and see, but I doubt it will change much.

Conclusion:

Phil Jones and Michael Mann are now under investigation by their respective institutions, and any academic misconduct should be dealt with appropriately. However, so far I have not seen any emails that show dishonest manipulation of data, nor have I seen any reason to fundamentally doubt the state of the science. As stated by the American Meteorological Society in response to this episode:

For climate change research, the body of research in the literature is very large and the dependence on any one set of research results to the comprehensive understanding of the climate system is very, very small. Even if some of the charges of improper behavior in this particular case turn out to be true — which is not yet clearly the case — the impact on the science of climate change would be very limited.

This paragraph from a Sep 30, 2009 post at RealClimate.org, a blog run by climate scientists (some of whom are the subject of this controversy), may prove prophetic.

The timeline for these mini-blogstorms is always similar. An unverified accusation of malfeasance is made based on nothing, and it is instantly ‘telegraphed’ across the denial-o-sphere while being embellished along the way to apply to anything ‘hockey-stick’ shaped and any and all scientists, even those not even tangentially related. The usual suspects become hysterical with glee that finally the ‘hoax’ has been revealed and congratulations are handed out all round. After a while it is clear that no scientific edifice has collapsed and the search goes on for the ‘real’ problem which is no doubt just waiting to be found. Every so often the story pops up again because some columnist or blogger doesn’t want to, or care to, do their homework. Net effect on lay people? Confusion. Net effect on science? Zip.

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Origin of The Origin of Man

Today marks the 150th anniversary of the publication of Charles Darwin's On the Origin of Species. This month also marks the centennial of the 1909 First Presidency statement, "The Origin of Man." To mark the occasion SteveP (of Mormon Organon) and I put together a few posts. Steve's contributions are:

The Origin of Species marks the beginning of the end
Origin, ID and the God of the Gaps
On the Origin of Species is 150 years old!
Your evolution book gift giving guide for Christmas

Also, over at Mormon Insights S. Faux wishes everyone a Happy Mutability Day! (Happy mutability day to you, too.)

My contribution is a guest post at By Common Consent called Reflecting on The Origin of Man. Below I fill in a little more detail.

The end of the 1909 statement drew on an article previously written by Orson F. Whitney and published in the Contributor in 1882. In that article, Whitney discussed the absurdity of both evolution and creation ex nihilo. The end of the article is quite similar to the end of the 1909 statement. Compare below.

Elder Whitney's article (Contributor, vol. 3, June, 1882. No. 9.):

Man is the direct offspring of Deity, of a being who is the Begetter of his spirit in the eternal worlds, and the Architect of his mortal tabernacle in this. God himself is an exalted man, possessing body, parts and passions, refined and developed to the highest state of perfection. He organized the world and all that it contains, from matter; from ever-living spirit and everlasting element, which exist co-eternally with himself. He formed every plant that grows and every animal that breathes, each after the image of its own kind, and determined the fixity of their respective species. He made the tadpole and the ape, the lion and the elephant, but He did not make them in His own image, nor endow them with godlike reason and intelligence. Monkeys are the offspring of monkeys, and have been from time immemorial. Hybrids may appear, but they are without the power to propagate. There is no instance on record where a baboon ever evolved into a human being, and science in attempting to unearth a "missing link" which it is claimed will connect mankind with monkeykind, is like a blind man hunting through a haystack to find a needle which isn't there. For man is the child of God, fashioned in His image and endowed with His attributes, and even as the infant son of an earthly father is capable in due time of becoming a man, so the undeveloped offspring of celestial parentage is capable in due time of becoming a God.

The Origin of Man:

The Church of Jesus Christ of Latter-day Saints, basing its belief on divine revelation, ancient and modern, proclaims man to be the direct and lineal offspring of Deity. God Himself is an exalted man, perfected, enthroned, and supreme. By His almighty power He organized the earth and all that it contains, from spirit and element, which exist coeternally with Himself. He formed every plant that grows and every animal that breathes, each after its own kind, spiritually and temporally—“that which is spiritual being in the likeness of that which is temporal, and that which is temporal in the likeness of that which is spiritual.” He made the tadpole and the ape, the lion and the elephant, but He did not make them in His own image, nor endow them with godlike reason and intelligence. Nevertheless, the whole animal creation will be perfected and perpetuated in the Hereafter, each class in its “distinct order or sphere,” and will enjoy “eternal felicity.” That fact has been made plain in this dispensation (see D&C 77:3).

Man is the child of God, formed in the divine image and endowed with divine attributes, and even as the infant son of an earthly father and mother is capable in due time of becoming a man, so the undeveloped offspring of celestial parentage is capable, by experience through ages and aeons, of evolving into a God.

[This is an edited version of a previous post at Mormons and Evolution.]

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What is Carbon Dating Good For? (Not Much.)

For whatever reason, carbon dating seems to be the main radiometric dating method that people know of. They know it is used for dating ancient things, so they presume that fossils, and even the age of the earth, are dated using carbon dating. Yet in the overall scheme of the earth, carbon dating is pretty much worthless. That's because it is only good for organic material up to about 50,000 years old. In contrast, Earth is about 4.5 billion years old.

I don't begrudge the fact that people don't know this; there are many things I am quite ignorant about. I do get a little annoyed when anti-evolutionists yammer on about the problems with carbon-14 dating (as if scientists are unaware of the problems and limitations) and claim that this represents a problem for determining the age of the earth or of fossils.

Anyway, for fun I decided to make a graph of the usefulness of carbon dating relative to the age of the earth, as well as a few other points of comparison.



The black lines of the y-axis are a little hard to resolve, but they represent 10 million year increments. The values for the comparisons are as follows:

Carbon Dating: 50,000 years
Age of the Earth: 4.5 billion years
Dinosaur Extinction: 65 million years
Life on Earth: 3.7 billion years
"Cambrian Explosion": 530 million years

As you can(not) see, carbon dating doesn't even show up. That's because the maximum usage of carbon dating is represented by 1/200th of the space between two lines. I think I've made my point.

So don't be hard on people who don't realize the vast time disparity between the age of the earth or dinosaurs and carbon dating usefulness. It's a simple and innocent mistake. But if they make that mistake while getting on their high horse about the problems of carbon dating, don't take them seriously either.

Note: if you would like to learn more about radiometric dating, start with Radiometric Dating: A Christian Perspective.

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Animal Joy

Reverend William Buckland (1784-1856) was an English geologist and paleontologist. He was invited to contribute to a series of books "on the power, wisdom and goodness of God, as manifested in the creation." In 1836 his book titled, Geology and Mineralogy considered with reference to Natural Theology was published. In it Buckland explained that carnivores were consistent with a benevolent God, in that they provide swift death to creatures that would otherwise suffer from sickness or injury, thus reducing the aggregate amount of suffering. He concluded,

The appointment of death by the agency of carnivora as the ordinary termination of animal existence, appears therefore in its main results to be a dispensation of benevolence; it deducts much from the aggregate amount of the pain of universal death; it abridges, and almost annihilates, throughout the brute creation, the misery of disease, and accidental injuries, and lingering decay; and impose such salutary restraint upon excessive increase of numbers, that the supply of food maintains perpetually a due ratio to the demand. The result is, that the surface of the land and depths of the waters are ever crowded with myriads of animated beings, the pleasures of whose life are coextensive with its duration; and which throughout the little day of existence that is allotted to them, fulfill with joy the functions for which they were created [emphasis added].

I ran across this quote in The Greatest Show on Earth by Richard Dawkins (and he got it from Nonmoral Nature by Stephen J. Gould). It immediately reminded me of the creation narrative from the temple where, as Hugh Nibley put it,

...it is the privilege of every form of life to multiply in its sphere and element and have joy therein. (Brother Brigham Challenges the Saints, p. 43)

Of course, Buckland published his work before the temple as we know it existed. It is tempting to think that whoever included the sentiment expressed by Nibley into the temple narrative (Joseph? Brigham?) was importing a view of nature already prevalent in the culture. On the other hand, I don't know how prevalent such a view was, and anyway it seems to me that, in the context of the temple, it represents God's creations in a state of paradise rather than in our fallen world.

Natural theology, however, held that nature reveals the character of God, so unseemly features of nature such as carnivores had to be cast in a positive light. Gould wrote,

We may find a certain amusing charm in Buckland's vision today, but such arguments did begin to address "the problem of evil" for many of Buckland's contemporaries — how could a benevolent God create such a world of carnage and bloodshed? Yet this argument could not abolish the problem of evil entirely, for nature includes many phenomena far more horrible in our eyes than simple predation. I suspect nothing evokes greater disgust in most of us than slow destruction of a host by an internal parasite — gradual ingestion, bit by bit, from the inside. In no other way can I explain why Alien, an uninspired, grade-C, formula horror film, should have won such a following. That single scene of Mr. Alien popping forth as a baby parasite from the body of a human host, was both sickening and stunning. Our nineteenth-century forebears maintained similar feelings. The greatest challenge to their concept of a benevolent deity was not simple predation — but slow death by parasitic ingestion. The classic case, treated at length by all great naturalists, invoked the so-called ichneumon fly. Buckland had sidestepped the major issue.

Those flies made an impression on Charles Darwin too. In an 1860 letter Darwin wrote,

I own that I cannot see as plainly as others do, and as I should wish to do, evidence of design and beneficence on all sides of us. There seems to me too much misery in the world. I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of Caterpillars, or that a cat should play with mice.

Alas, the joy of animals notwithstanding, "the problem of evil" remains a difficult one.

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Good Riddance

October of 2002 was a scary time for my wife and I. At that time an unknown person (or persons) was shooting--usually fatally--people at random in the D.C./Maryland/Virginia area. As the days passed, another person would be gunned down and the shooter would vanish into the fall air. One of the murders occurred less than a block from where I often bought gas. Although nobody had been shot in their home, we covered some windows that allowed a view into our living room from the busy street outside, and we watched the nightly press conferences given by local law enforcement. An angel of death that seemed unstoppable roamed the area, and nobody was safe.

Finally on October 24 John Allen Muhammad and Lee Boyd Malvo were captured, and we breathed a sigh of relief. Days later we became parents.

As I write this, John Allen Muhammad has 5 minutes until execution by lethal injection. Having been turned away from the Supreme Court and denied clemency by Virginia Governor Tim Kaine, it is all but certain that Mr. Muhammad will die tonight.

I know that there are problems with the death penalty. I know that innocent people have been put to death, and I support efforts to make the application of the death penalty fair and just. However, I also continue to believe that some people deserve the death penalty, and that justice demands it. And I believe that this is one of those cases.

In the day that all wounds are healed, I hope that John Allen Muhammad will be a new person--fit to live among saints. But for now I say good riddance; let justice be done.

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To read about how the case unfolded, see here.

Update: John Allen Muhammad died at 9:11 pm.

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Doubt Is Their Product

This week I finished reading Doubt is Their Product: How Industry's Assault on Science Threatens Your Health, by David Michaels. Michaels is a professor in the Department of Environmental and Occupational Health, at the George Washington University School of Public Health and Health Services. During the Clinton administration he served in the Department of Energy, and he is President Obama's nominee to head the Occupational Safety and Health Administration (OSHA).

Here is a description of the book from its website:

"Doubt is our product," a cigarette executive once observed, "since it is the best means of competing with the 'body of fact' that exists in the minds of the general public. It is also the means of establishing a controversy."

In this eye-opening exposé, David Michaels reveals how the tobacco industry's duplicitous tactics spawned a multimillion dollar industry that is dismantling public health safeguards. Product defense consultants, he argues, have increasingly skewed the scientific literature, manufactured and magnified scientific uncertainty, and influenced policy decisions to the advantage of polluters and the manufacturers of dangerous products. To keep the public confused about the hazards posed by global warming, second-hand smoke, asbestos, lead, plastics, and many other toxic materials, industry executives have hired unscrupulous scientists and lobbyists to dispute scientific evidence about health risks. In doing so, they have not only delayed action on specific hazards, but they have constructed barriers to make it harder for lawmakers, government agencies, and courts to respond to future threats.

If you don't want to read the whole book, you can get a good feel for it from an article he previously published, "Manufacturing Uncertainty: Contested Science and the Protection of the Public’s Health & Environment [pdf]."

I am not unsympathetic to the desire of industries and companies to avoid excessive regulation and drains on productivity. On the other hand, employees, consumers, and the general public have a right, I think, to be protected from harm (or at least warned of harm). Navigating the conflict between those interests is not easy, and I'm glad it isn't my job. But although government regulation is much maligned in political discourse, a moment's thought reveals what a miserable place this country would be without them. For various reasons, Dr. Michaels argues that the balance of interests is currently tipped in the favor of industry, and gives a number of examples. In some cases, industry and government are (or have been) allied in disregard for human health.

Read the book (or at least the article) and see what you think.

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A Conspiracy of Statisticians, No Doubt

Statisticians reject global cooling

In a blind test, the AP gave temperature data to four independent statisticians and asked them to look for trends, without telling them what the numbers represented. The experts found no true temperature declines over time.
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The AP sent expert statisticians NOAA's year-to-year ground temperature changes over 130 years and the 30 years of satellite-measured temperatures preferred by skeptics and gathered by scientists at the University of Alabama in Huntsville.

Statisticians who analyzed the data found a distinct decades-long upward trend in the numbers, but could not find a significant drop in the past 10 years in either data set. The ups and downs during the last decade repeat random variability in data as far back as 1880.

Saying there's a downward trend since 1998 is not scientifically legitimate, said David Peterson, a retired Duke University statistics professor and one of those analyzing the numbers.

Identifying a downward trend is a case of "people coming at the data with preconceived notions," said Peterson, author of the book "Why Did They Do That? An Introduction to Forensic Decision Analysis."

Let's just remind ourselves what those NOAA data look like.

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Pros and Cons of the H1N1 Vaccine

From The Daily Show (Oct 15):

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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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Death Panels: Universal or Private?

A Daily Show panel weighs in on who should run death panels.




Oh, and since we're at it here is a twist on a classic.

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LDS Guys Talk Physics (and other stuff)

If you like physics, then you may be interested in a blog that popped onto my radar a few weeks ago. It's The Eternal Universe, and it's run by several BYU graduates who majored in physics. At least two All of them have gone on to graduate school.

One of the contributors is planning to explain black holes, quarks, and other fun things with an LDS audience in mind. My understanding of physics can always be improved; I'll be watching.

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Fallible Memories and Prophetic Succession

Our memories are surprisingly unreliable. I say surprisingly because they seem so real and concrete. Of course they are accurate enough for us to get by without major disruption, and most of the time there is no way to prove them wrong anyway. But sometimes they can be wrong in a big way.

Discover Magazine has an article titled "How Much of Your Memory Is True?" that discusses how our understanding of memory is changing. Part of it deals with false memories.

Even harrowing memories—the so-called flashbulb memories that feel as if they have been permanently seared into the brain—are not as accurate as we think. Less than a year after a cargo plane crashed into an Amsterdam apartment building in 1992, 55 percent of the Dutch population said they had watched the plane hit the building on TV. Many of them recalled specifics of the crash, such as the angle of descent, and could report whether or not the plane was on fire before it hit. But the event had not been caught on video. The “memory” shared by the majority was a hallucination, a convincing fiction pieced together out of descriptions and pictures of the event.

Reading this reminded me of the famous story in LDS history of the passing of the prophetic mantle from Joseph Smith to Brigham Young. After Joseph was killed it was unclear who should be in charge. A meeting was held on August 8, 1844 where both Sidney Rigdon (counselor in the First Presidency) and Brigham Young (president of the Quorum of the Twelve Apostles) addressed the congregation and explained why they were entitled to lead the Saints. Many people (including one of my own ancestors) said that while Brigham Young spoke he seemed to sound and/or look like Joseph, and this was taken as evidence of divine approval of Brigham Young. Unfortunately, there are no known contemporaneous written accounts of this manifestation. Even Wilford Woodruff failed to mention anything miraculous in his lengthy journal entry for the day.

Of special interest here are Apostle Orson Hyde and John D. Lee (of Mountain Meadows fame), both of whom left retrospective accounts of their experience. Elder Hyde's accounts are pretty detailed. For example, in 1869 he said,

We went among the congregation and President Young went on the stand. Well, he spoke, and his words went through me like electricity. "Am I mistaken?" said I, "or is it really the voice of Joseph Smith?" This is my testimony; it was not only the voice of Joseph, but there were the features, the gestures and even the stature of Joseph before us in the person of Brigham. And though it may be said that President Young is a complete mimic, and can mimic anybody, I would like to see the man who can mimic another in stature who was about four or five inches higher than himself. Every one in the congregation-every one who was inspired by the Spirit of the Lord-felt it. They knew it. They realized it.

I sat myself down in, the midst of the congregation, with my two wives, whom Joseph had given and sealed to me. When President Young began to speak, one of them said, "It is the voice of Joseph! It is Joseph Smith!" The exclamation of the other was, "I do not see him, where is he?"

The problem is that Wilford Woodruff's journal says that Orson Hyde arrived in Nauvoo on August 13 (he is also missing in History of the Church 7:231) and John D. Lee's own diary says that he arrived August 20--five and twelve days, respectively, after the meeting occurred.

If the written journals are correct, it appears that Hyde and Lee unconsciously created memories of the passing of the mantle based on the stories of others. Or giving them more benefit of the doubt, perhaps they transposed a later spiritual experience onto a false memory of attending the August 8 meeting. Whether the other accounts are of a similar nature is the kind of question historians worry about. My own opinion is that there was at least a core group of people who genuinely had the described experience. They wouldn't be the only ones; decades later several people reported a similar experience when Heber J. Grant followed Joseph F. Smith as Church president.

Nevertheless, the examples of Orson Hyde and John D. Lee (and maybe even Wilford Woodruff) raise questions about the nature of religious testimony and witness. Can we be confident, for example, that the scriptures do not contain any false memories? Whatever the case, these examples suggest that the line between truth and fiction can be blurry. That, and if you have a miraculous experience you should write it down quickly.


[Related post: A Case of First Presidency Amnesia.]


References:

Lynne W. Jorgensen and BYU Studies Staff, The Mantle of the Prophet Joseph Passes to Brother Brigham: A Collective Spiritual Witness. BYU Studies 36, no. 4. (1996-1997)

Richard Van Wagoner, The Making of a Mormon Myth: The 1844 Transfiguration of Brigham Young. Dialogue: A Journal of Mormon Thought, vol. 28 no. 4. (1995)

Reid L. Harper, The Mantle of Joseph: Creation of a Mormon Miracle. Journal of Mormon History vol. 22 issue 2. (1996)

Thomas Alexander, Mormonism in Transition, p. 117

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What Separates Humans from Chimpanzees? (Part 1)

[This post is part of a series, What Separates Humans from the Animals?]

In a previous post in this series I explained that transposons are short stretches of DNA that make copies of themselves and insert back into the genome at a different place. Retrotransposons are very similar; the main difference between them is that regular transposons are directly copied as DNA, but retrotransposons are copied into RNA and then back into DNA, which then integrates into the genome. It may come as a surprise that retrotransposons make up about 42% of the human genome! (Regular transposons contribute another ~3%.)



There are several kinds of retrotransposons. Some are disabled viruses that are distantly related to HIV. Here we will focus on Alu elements, of which there are over 1 million copies in the human genome (or about 10% of the genome). Alu elements are only found in primate genomes, but they don't code for any proteins. A mere ~300 base pairs (i.e. DNA 'letters'), they depend entirely on proteins produced by the cell and other retrotransposons, for their replication. When new Alu copies integrate into the genome of a germline cell, the Alu element becomes part of the DNA that is passed on to that person's descendants. In humans they sometimes cause genetic diseases when they integrate into--and thus disrupt--a functional gene.


Scientists have found that Alu elements make great genetic markers, and the reason is pretty simple: for any stretch of DNA that has an Alu element, the ancestral state can be inferred to be the same stretch without the Alu. As an analogy, consider a document that has been photocopied repeatedly and distributed throughout an office. If you compare two copies--one with a nice big coffee stain, and one without--you know that the clean copy is descended from a copy that pre-dates the coffee-stained one. The same reasoning applies here. Further, the chances of two Alu elements independently inserting into the exact same place are low, and it is rare (but not impossible) for an Alu element to be precisely removed.



When Alu elements are copied, mutations can occur which are then propagated to subsequent copies. For this reason, Alu elements can be grouped into families based on sequence differences [1]. Salem et al. compared Alu elements of a particular family in the genomes of humans, chimpanzees, bonobos (pygmy chimpanzees), orangutans, siamangs, green monkeys, and owl monkeys. More specifically, they looked for Alu elements that were located in the same place in the genome of different species. Their overall finding is summarized in Figure 3 of their paper.

(Click to enlarge.)

Figure 3. Primate relationships reconstructed by using Dollo parsimony analysis of Alu elements. Primate relationships were derived from analysis of 133 Alu loci by using maximum parsimony criteria. The number of insertions observed along each branch of the tree is indicated, and bootstrap support values are placed above each node.

The figure is read similar to a family tree. Each node represents a common ancestor of all species to the right of that node. The numbers underneath the triangles indicate how many Alu elements are contained in identical locations in the genome of each species descended from that node. So, for example, humans, chimpanzees, bonobos, and gorillas all share 33 separate Alu elements at the same place in their DNA. Humans have 7 unique insertions, chimpanzees and bonobos together have 14. So for this family of Alu elements, humans and chimpanzees (including bonobos) are separated by 21 unique insertions. (If we consider all Alu families, humans have about 7,000 lineage-specific Alu insertions and chimpanzees have about 2,300.)

Yet, the unifying nature of the Alu insertions is obvious. As the authors wrote,

The patterns observed clearly indicate a stepwise pattern of insertion reflecting the relative divergence of each group in the hominid lineage.

The clarity is impressive, but there is one minor snag. The authors found one Alu insertion shared between humans and gorillas that is not shared with chimpanzees. If you looked only at that insertion you would conclude that humans are more closely related to gorillas than chimpanzees. Is this a problem? No.

The splitting of the lineages that led to gorillas, chimpanzees, and humans are thought to have occurred within a few million years of each other. This has resulted in the trichotomy problem, which I have explained before (see Understanding Trichotomy). As I wrote then,

Humans, chimpanzees and gorillas each have their roots in a common gene pool. However, the sorting of ancestral polymorphic alleles in the diverging lineages is subject to evolutionary processes such as genetic drift. Thus purely by chance, alleles can become fixed in a way that gives a different picture than the true species-branching pattern.

In other words, as the lineages leading to the different species were branching off from one another, the presence of that particular Alu within each population was in flux. Probably by chance, it was lost from the chimpanzee lineage and retained in the gorilla and human lineages. In support of this, the authors estimated the ages of the conflicting Alu insertions based on mutation rate and found that the anomalous insertion supporting the human-gorilla relationship is 1-4 million years older than those that support the human-chimpanzee relationship.

It is beautifully amazing to me that such short and simple pieces of DNA can provide such a clear picture of evolutionary history.


Notes:

[1] To see how the distribution of Alu families among primates also supports common descent, see Figure 3 in Roy-Engel et al.


References:

Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12787-91.

Roy-Engel, A. M., M. A. Batzer and P. L. Deininger (2008) Evolution of human retrosequences: Alu. In "Encyclopedia of Life Sciences".

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What's the Deal with Cattle and Methane?

On my recent vacation, my dad asked me about the science regarding cattle and methane in connection with global warming. As much as I would like others to think that I know everything, I unfortunately do not, so I could only give a vague answer. I've since done a little poking around on the internet to find out more, and I figured I would post it here for anyone interested.

Here is a two-minute summary:

Methane (CH4), of course, is the main component of natural gas and is produced in a variety of places in nature. Like carbon dioxide, methane is a greenhouse gas because it traps heat in the atmosphere. Before the year 1750, methane levels in the atmosphere averaged around 700 parts per billion; now the level is around 1,700 parts per billion.

Ruminant livestock such as cattle, sheep, and goats have a special digestive system that allows them to break down plant material. Methane is a by-product of their digestion (enteric fermentation), and is released into the atmosphere. Livestock account for around 20-30% of human-related methane production; in the U.S. livestock and landfills are the top two human-related sources of methane.

Efforts at reducing livestock methane emissions are focused on better efficiency, genetics, and nutrition, especially in the beef industry.

For more information, see the following links to the EPA: here, here, and here.

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One Giant Leap for Mankind

40 years ago today, Neil A. Armstrong and Edwin E. "Buzz" Aldrin Jr. became the first humans to set foot on the moon, while Michael Collins orbited as the command module pilot. They left a plaque that said,

Here Men From The Planet Earth First Set Foot Upon the Moon, July 1969 A.D. We Came in Peace For All Mankind.

For more incredible pictures, see The Big Picture.

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Moon Landing Sites Photographed by Satellite

NASA's Lunar Reconnaissance Orbiter (LRO) has photographed five of the six moon landing sites. Equipment, and even a trail through the dust, are visible! Even better images are expected once the LRO is settled into its orbit.

Here is the best one, but go see the rest!

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Alternative Medicine Fails; Not That It Matters

I'm back from vacation, and although I'm not exactly awash in free time, I hope to push out some of the blog material that has been accumulating. First up: alt med.

A June AP news story looked at what has been gained by the government's spending of $2.5 billion on research into alternative medicine, much of it through the National Center for Complementary and Alternative Medicine (NCCAM). The answer: almost nothing. But let's back up.

NCCAM, and its earlier incarnation, the Office of Alternative Medicine, has been the personal project of Senator Tom Harkin (D-IA), who became convinced that bee pollen helped his allergies and that another Congressman had been cured of cancer by alternative medicine.

Last February in a Senate hearing, Harkin complained--I am not making this up--that NCCAM was too negative in that it was casting doubt on many treatments but not validating enough of them.

One of the purposes when we drafted that legislation in 1992 . . . was to investigate and validate alternative approaches. Quite frankly, I must say it's fallen short. I think quite frankly that in this center, and previously in the office before it, most of its focus has been on disproving things, rather than seeking out and proving things.

As if the problem is science!

There is a hierarchy of plausibility in alternative medicine. Toward the top are herbal treatments because they are basically unregulated drugs. It is entirely possible that some of them could be useful. Toward the bottom are homeopathy or treatments that claim to alter some sort of vital energy or life force, because they are essentially supernatural claims and are often rooted in pre-scientific notions about physiology and medicine.

I agree with those who argue that the term 'alternative medicine' is really a misnomer. To begin with, some things that are called alternative medicine are encompassed within mainstream medicine (e.g. nutrition, exercise, relaxation, and other healthy lifestyle activities). But beyond that, treatments that are shown to be effective are incorporated into mainstream medicine; those that remain untested or unproven are not, and don't really deserve to be called 'medicine'. I know which group I want when I get sick.

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