Converging Paths to Truth...and Peace?

A little over a decade ago I purchased my first book on Mormonism and science, The Search for Harmony. It contains a number of classic essays, and it will always have a fond place in my heart. However, as I have revisited it from time to time, I've noticed that it has a somewhat gloomy tone as various authors express their sadness that the Church has betrayed its original openness to truth and marginalized supporters of science. Given that most of the essays were written during the 70's and 80's, this is understandable. After all, it was 1980, for example, when Apostle Bruce R. McConkie included evolution in his talk, "The Seven Deadly Heresies."

As I look back at the essays in that book, I don't share the sense of gloom. Most Church members and leaders are perhaps not as enlightened on scientific topics as I wish they were, or think they ought to be, but more and more I sense a return to the spirit of President Heber J. Grant's admonition to leave science to scientists.

As evidence, I would like to highlight the Summerhays lectures, a series of talks given at Brigham Young University by faculty on science and religion between 2003 and 2008. In 2011 the lectures were published by both the Religious Studies Center (a publishing arm of the BYU religion department) and Deseret Book. The RSC has since made the book available for free on its website. The lectures themselves are not all that remarkable--some are better than others--but I believe that their very existence, combined with the publishers standing behind them, make them important. The book models the attitude expressed in a Church Newsroom commentary last July that,

Mormons welcome truth from whatever source and take the pragmatic view that where religion and science seem to clash, it is simply because there are insufficient data to reconcile the two. Latter-day Saints approach such tensions as challenges to learn, not contradictions to avoid.

Contributors include Terry Ball (dean of Religious Education), Robert Millet, (former dean of Religious Education), and Michael Whiting (evolutionary biologist), and their essays anchor the book (in my opinion). Each contributor presents his own view, but collectively the lectures contain positive comments on the role of BYU in education in the sciences, critique of creationism and defense of Darwin's character, an overview of the BYU Evolution Packet with a link to where it can be found, calls for peacemaking and a "healthy agnosticism," and more.

Below I excerpt parts that I liked, or think important. I also have some criticisms and additional comments, but I'll save those for a separate post.

Ball:

Rather than adding to the tension that some individuals and institutions create between science and religion, a Brigham Young University education should help students increase their understanding and appreciation for both. ...we should not only avoid alienating secular learning from spiritual development but also endeavor to avoid compartmentalizing and departmentalizing the two. Spiritual development can and should occur in all classes taught on the BYU campus, and secular learning may indeed find application in Religious Education classes.

How tragic it would be if a BYU student who had the potential to become a James E. Talmage or a Henry Eyring never reached that potential because some teacher, purposefully or unwittingly, convinced that student that one must abandon faith in God in order to be a credible scientist, or conversely, that one with a testimony of the restored gospel cannot accept the tenets of science. It is imperative that as a community of learners at BYU we work to avoid such a tragedy.

Millet:

More times than I would like to remember, during the decade that I served as dean of Religious Education, I received phone calls from irate parents who simply could not understand why Brigham Young University was allowing organic evolution courses to be taught. They would then ask what I planned to do about it, as though I were the head of the campus thought police. I would always try to be understanding and congenial, but I would inevitably remark that such things were taught at this institution because we happened to be a university; that what was being taught was a significant dimension in the respective discipline; and that we certainly would not be doing our job very well if a science student, for example, were to graduate from Brigham Young University and be ignorant of such matters.

I must admit sadly that when I was a student here at BYU and even in my first years as a faculty member, it was not uncommon for ideological grenades to be flying back and forth between the Joseph Smith Building and the Eyring Science Center. This person was labeled as godless, and that one was categorized as ignorant or naive. This faculty member hustled about to put forward his or her favorite General Authority quote, while that one relied upon a Church leader with a differing perspective. Thereby authorities were pitted against one another. Very little light, if any, was generated, but there was a great deal of heat, including much heartburn for university and college administrators. And of course the real losers during this “war of words and tumult of opinions” were the students. They admired their science teachers and valued their opinions but did not want in any way to be in opposition to what Church leaders believed and taught. They trusted their religion teachers but were not prepared to jettison their field of study. Further, such standoffs did something that for me was even more destructive: they suggested that one could not be both a competent academic and a dedicated disciple—one had to choose. And such a conclusion is tragically false. It defies everything that Brigham Young University stands for.

It is wrong to hide behind our religious heritage and thus neglect our academic responsibilities; there may have been a time when some faculty members at BYU excused professional incompetence in the name of religion, on the basis that BYU is different, that it is a school intent on strengthening the commitment of young Latter-day Saints. This was commendable but insufficient. It is just as myopic, however, to hide behind academics and thus cover our own spiritual incompetence. We can be thoroughly competent disciples and thoroughly competent professionals. We do not hide behind our religion, but rather we come to see all things through the lenses of our religion.

If my Latter-day Saint colleagues and I can enjoy such a sweet brotherhood and sisterhood with a growing number of Evangelical Christians—a group with whom we have been in intense dialogue since 2000—then surely it is possible for men and women of faith who labor in varying avenues of science to enjoy cordial and collegial relationships with those involved in the study and teaching of religion, especially at Brigham Young University, the best of all worlds. Our epistemological thrusts may be different. Our presuppositions may be different. Our tests of validity and reliability may be different. But our hearts can be united as we strive to look beyond the dimensions of our disciplines toward higher goals. Some things we may and should reconcile here and now, while other matters may await further light and truth and additional discovery.

Whiting:

I am not aware of any other scientific idea that has generated as many diverse views in the Church as evolution has, and very often the discussion of this wide range of ideas has resulted in more heat than light. When I teach evolution in the BYU classroom, I must often curtail students who begin selectively quoting their favorite General Authorities and pitting the quotations of one against another, as if one General Authority could beat the other up. While I am grateful that the Church has never expressed the same extreme views about evolution as have other religious denominations, there still persists a belief that evolutionary ideas and Church doctrine are fundamentally hostile to each other and that the full acceptance of one requires the compromise of the other.

I, of course, recognize that there are ideas in evolutionary theory that can be spun in such a way as to be in direct conflict with the doctrines of the Church, and unfortunately some prominent evolutionary biologists have gained great fame by doing so. Likewise, I recognize that there are interpretations of Latter-day Saint scripture that can be formulated in such a way as to contradict current ideas in evolutionary theory. What I would caution against is forcing a Joshua ultimatum here with “Choose you this day whom ye will serve” (Joshua 24:15), as if these are fundamentally and diametrically opposed views of creation with no degree of overlap and no possibility of reconciliation. In my experience, students who continue to think of this as a dichotomy will either have their faith so shaken when they learn the evidence for evolution that they drift away from the Church, or they will simply shut their eyes and their minds to what I consider to be a glorious way to view creation.

Ball:

In recent times, religious scientists not only have had to defend their faith in God and revelation, but also frequently find their commitment to scientific principles unjustly questioned. A Georgia judge, arguing against the teaching of evolution in school, offered an overzealous polemic that illustrates the point well. Making absurd accusations about the effect of Darwin’s theories on society, the judge claimed that the “monkey mythology of Darwin is the cause of permissiveness, promiscuity, pills, prophylactics, perversions, pregnancies, abortions, pornotherapy, pollution, poisoning and proliferation of crimes of all types.” Such pejorative and irrational rhetoric only serves to fan the flames of hostility between science and religion while deepening the dilemma for men and women devoted to both disciplines.

Whiting:

I might mention here that some portray Darwin as a man eager to destroy faith and tear down religion. These people are like the detractors who paint Joseph Smith and the history of the Church with similar brushstrokes. Within the Church, I have occasionally heard members equate Darwin with Korihor, the anti-Christ from the Book of Mormon. But these caricatures are too simplistic and not true to the record. (It seems to me that members of the Church should be particularly sensitive to the misrepresentation of mid-nineteenth-century historical figures in order to push a particular agenda forward.) Certainly the ideas that sprang from Darwin’s work had a profound influence on religious thought and still continue to do so, but by all accounts Darwin was a loving father and a kind man, afraid of confrontation, and someone who would much rather study the mining habits of earthworms than be involved in a debate over science and religion. Darwin was a complex man, and many lengthy biographies have delved into factors in his life that may have influenced his scientific ideas, including his faith, but at his very core, Darwin was simply a scientist trying to explain patterns in the natural world, and the notion that he had a hidden agenda to destroy religion is simply wrong.

There has been a temptation for some members of the Church to place us in the same category as religions that identify themselves as creationists. I tell my students that Mormons are creationists in the same way we are born-again Christians. Does the Church have a doctrine of being “born again”? It certainly does, but it is so radically different from churches that label themselves as born-again Christians that we have not adopted the name because we do not embrace the dogmas associated with being “born again.” Likewise, the Latter-day Saint doctrine of creation is sufficiently distinct from those religious groups that label themselves “creationists” that I am grateful the Church has not adopted this label.

Intelligent design is based on the (flawed) notion that there are certain features in the biological world that are too complex to be explained via evolution and that the probability of evolution giving rise to complexity is so vanishingly small that it is simply not possible. Consequently, they argue, the only scientific explanation for biological complexity is that there must be an intelligent designer working behind the scenes. The attempt to mandate the teaching of intelligent design in public schools led to a lengthy trial centered in Dover, Pennsylvania, in 2004. The overwhelming evidence during the trial established that intelligent design was a mere relabeling of the type of creationism described above and that it [is] not a scientific alternative to evolution. So while the Latter-day Saints do indeed have a doctrine of creation and certainly a belief in a Supremely Intelligent Creator, we are neither creationists nor proponents of intelligent design because both labels come with unwanted and uncomfortable doctrinal baggage.

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Lead Heads

The Guardian's George Monbiot:

At first it seemed preposterous. The hypothesis was so exotic that I laughed. The rise and fall of violent crime during the second half of the 20th century and first years of the 21st were caused, it proposed, not by changes in policing or imprisonment, single parenthood, recession, crack cocaine or the legalisation of abortion, but mainly by … lead.... It's ridiculous – until you see the evidence.

He's talking about the recent cover story for Mother Jones, "America's Real Criminal Element: Lead," by Kevin Drum. The whole article is worth reading, but here are the highlights:

-Lead was added to gasoline in the 1920s to eliminate knocking and pinging in automobile engines.

-Following WWII, the boom in automobile sales resulted in increasing environmental lead levels from auto emissions, particularly in dense population areas.

-Children in these areas were exposed to increasing levels of lead.

-The rise and fall of environmental lead mirrors the rise and fall of violent crime 20 years later.

-The link between lead and crime holds true in different cities, states, and countries.

-Lead is now known to cause damage to the developing brains of children, particularly in areas involved in control of aggression, attention, emotional control, etc. It also lowers IQ. These effects can be seen at blood levels previously thought to be safe.

-In children followed from birth to adulthood, higher blood levels are associated with arrests for violent crime.

-Residual lead in soil and old paint (especially dust produced) continue to cause damage.

-Areas with the highest levels of residual lead also tend to be the areas of highest crime.

When you put the whole puzzle together you get a compelling picture. Drum:

Needless to say, not every child exposed to lead is destined for a life of crime. Everyone over the age of 40 was probably exposed to too much lead during childhood, and most of us suffered nothing more than a few points of IQ loss. But there were plenty of kids already on the margin, and millions of those kids were pushed over the edge from being merely slow or disruptive to becoming part of a nationwide epidemic of violent crime. Once you understand that, it all becomes blindingly obvious. Of course massive lead exposure among children of the postwar era led to larger numbers of violent criminals in the '60s and beyond. And of course when that lead was removed in the '70s and '80s, the children of that generation lost those artificially heightened violent tendencies.

In a follow-up blog post, Drum is clear that lead was, and is not, the sole driver of crime. Without lead there would continue to be violent crime for a variety of reasons. However the evidence suggests that lead is largely responsible for the epidemic of crime.

Okay, so we have taken lead out of gasoline and paint. Existing environmental lead is still a problem, but at least it's not getting worse. Right? Back to Monbiot:

There is only one remaining manufacturer of tetraethyl lead on earth. It's based in Ellesmere Port in Britain, and it's called Innospec. The product has long been banned from general sale in the UK, but the company admits on its website that it's still selling this poison to other countries. Innospec refuses to talk to me, but other reports claim that tetraethyl lead is being exported to Afghanistan, Algeria, Burma, Iraq, North Korea, Sierra Leone and Yemen, countries afflicted either by chaos or by governments who don't give a damn about their people.

In 2010 the company admitted that, under the name Associated Octel, it had paid millions of dollars in bribes to officials in Iraq and Indonesia to be allowed to continue, at immense profit, selling tetratethyl lead. Through an agreement with the British and American courts, Innospec was let off so lightly that Lord Justice Thomas complained that "no such arrangement should be made again". God knows how many lives this firm has ruined.

Is it just me, or does it seem like those countries don't need a lower violence threshold?

Back to Drum:

Not only would solving our lead problem do more than any prison to reduce our crime problem, it would produce smarter, better-adjusted kids in the bargain. There's nothing partisan about this, nothing that should appeal more to one group than another. It's just common sense. Cleaning up the rest of the lead that remains in our environment could turn out to be the cheapest, most effective crime prevention tool we have. And we could start doing it tomorrow.

I find the whole idea striking! To think that so much hand-wringing about the cause of crime has perhaps been entirely beside the point--it makes me wonder what other of our ills have been entirely misdiagnosed. It's also another example where industrial production of a product has real consequences for society. What makes this one especially interesting is that it affects behavior.

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How Joshua's Sun Stood Still While the World Turned

I've been reading John Walton's Ancient Near Eastern Thought and the Old Testament: Introducing the Conceptual World of the Hebrew Bible. It's a little on the dry side, but it gives you a flavor of the world of the Old Testament. One part that caught my attention was Walton's interpretation of the episode of Joshua and the sun standing still.

Then spake Joshua to the LORD in the day when the LORD delivered up the Amorites before the children of Israel, and he said in the sight of Israel, Sun, stand thou still upon Gibeon; and thou, Moon, in the valley of Ajalon.

And the sun stood still, and the moon stayed, until the people had avenged themselves upon their enemies. Is not this written in the book of Jasher? So the sun stood still in the midst of heaven, and hasted not to go down about a whole day. [Joshua 10:12-13]

This story is usually summarized as follows: The Israelites were battling the Amorites but were running out of daylight. So Joshua commanded the sun to stop--which it did by God's concurrence--giving them extended light in order to conquer the Amorites. That requires a bit of inference, however, since the scripture never says what Joshua's motivation was. And one thing that doesn't make sense is that Gibeon is east of Ajalon. If the sun was over Gibeon and the moon over Ajalon, it suggests that Joshua was in between them, and that it was actually morning. Why would Joshua be concerned about daylight in the morning?

The story has been a frequent focal point for battles over the nature of miracles, with defenders asserting the power of God and the need for faith and critics (who might otherwise be believers) pointing out the unlikely nature of such an occurrence. Some, such as John A. Widtsoe, took a middle ground: defending the power of God on the one hand, but recognizing that other means may have been used, or the story may have been poorly transmitted.

John Walton takes a different path that relies on knowledge of ancient Near Eastern culture. The ancients believed that the movements of celestial objects were manifestations of the power of the gods and that they communicated information about the disposition of the gods. Since these cultures used a lunar calendar to establish months, the new moon (beginning) and full moon (middle) were of particular interest to their timekeeping.

The point of full moon was determined when the sun and moon were at opposition, which is to say that the sun and moon were on opposite horizons for a few minutes. If opposition occurred on the fourteenth day of the month, then all of the days were full days (i.e. 1/30 of a month), which was a good omen. If opposition occurred on the wrong day (the fifteenth, for example), then the days of the month were not the right length, which was a bad omen. Mesopotamian omen literature contains various interpretations of celestial happenings, and commonly uses terms like stand, wait, and stop to refer to relationships between celestial objects. Walton:

When the moon and/or sun do not wait, the moon sinks over the horizon before the sun rises and no opposition occurs. When the moon and sun wait or stand, it indicates that the opposition occurs for the determination of the full moon day.

With this as background, Walton translates the Joshua passage as follows:

"O sun, wait over Gibeon and moon over the valley of Aijalon." So the sun waited and the moon stood before the nation took vengeance on its enemies. Is it not written in the book of Jashar, "The sun stood in the midst of the sky and did not hurry to set as on a day of full length?"

The shift in meaning is quite subtle, with most of the change being in the last phrase. "And hasted not to go down about a whole day," becomes "and did not hurry to set as on a day of full length."

I looked at a couple of alternate Bible translations to see what they do with this passage, especially the last phrase. The NIV and NRSV are both consistent with the KJV. However, Young's Literal Translation renders it as follows: "and hath not hasted to go in -- as a perfect day," which supports Walton. Thus, the way this passage is translated seems to hinge on what you think the original authors had in mind. If you didn't know about the surrounding omen literature, you wouldn't have any reason to think anything other than that the length of daylight was significantly extended.

There is still a little uncertainty as to what the exact scenario was. Some have thought that Joshua wanted a good omen for the Israelites. Walton thinks that Joshua wanted opposition to occur on the wrong day so that the Amorites would be demoralized by a bad omen.

Joshua's knowledge of the Amorites' dependence on omens may have led him to ask the Lord for one that he knew would deflate their morale-for the opposition to occur on an unpropitious day. This does not change the general idea that God fought on behalf of Israel, but it does give the interpreter a more accurate picture of the way in which God did so.

Whatever the exact details, a little background on the culture radically transforms this story and renders debate over the size of the miracle mostly moot.

Before ending, let me head off a potential objection. Helaman 12:14-15 does not authenticate the traditional interpretation of the Joshua story. Mormon does not specifically mention Joshua, so it is possible that the parallel is a coincidence. However, even if Mormon did have Joshua in mind, he may have misunderstood the meaning (or we have misunderstood Mormon's meaning) since he was long removed from ancient Near Eastern culture, as are we.

Further Reading:
See also Walton's original essay, "Joshua 10:12-15 and Mesopotamian Celestial Omen Texts," most of which can be read here.

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The Book of Abraham and the Great Toilet Paper Test

In light of the recent controversy over whether and how the length of the original scroll of Hor (the source of Facsimile 1) can be determined, I thought I would have a little fun and try my hand at the problem. (For background see here, here, and here.) However, not having any papyri to measure, I decided to use toilet paper as a model. Below I describe my procedure and present my results.

Methods
I did not want to use a complete roll of toilet paper because that would be a lot of work, so I searched my house for a partially used one. Having located a suitable roll, I located the end of the roll and drew a line along the edge to the cardboard center. I knew that I would not be able to draw a precise line because I needed to use a marker, which bled a little. In order to have a better defined mark along the edge, I used a knife to cut along the line. I then gradually unrolled the roll and measured the length between marks (winding length), rounding to the nearest millimeter (0.1 cm). I found that this particular brand of toilet paper could stretch a few millimeters, so I tried to always measure it while it was relaxed but straight.

The last winding was not directly measured; the circumference of the cardboard tube was used instead. This alternate method was used because it was difficult to obtain an accurate measure of the last winding due to the way the toilet paper was glued to the tube. A small length of paper extended beyond the last mark, but was ignored for convenience. Having completed this series of measurements, I rewound the toilet paper. Anyone who has rewound toilet paper knows that it is never the same as before, with the windings being somewhat more loose. The purpose of this was to simulate thicker toilet paper of the same length. I cut and marked the opposite end of the roll, and measured the new winding lengths. This time I was able to measure the last (innermost) winding length directly.

Exterior windings can be used to calculate the maximum length of missing inner roll using the Hoffmann formula. John Gee has given the formula as Z=((E²-6.25)/2S)-E, where Z = the missing remainder of the roll, E = the length of the last existing winding, and S = the average change in winding length. Andrew Cook has given the Hoffmann formula as Z=(E²–6.25)/(2S)–E+S/2. Not having access to Hoffmann's original publication, I can't say which is correct. However, I found that the two formulas agreed to within a centimeter, so for my purposes the difference is irrelevant. Here I report the form given by Gee.

Cook and Smith expressed their formula as L_n = (W_n²-W_N²)/(4piT). Although it looks different, this formula is almost identical to the Hoffmann formula, which is illustrated to the right where I have colored identical terms. Hoffmann uses 6.25 (i.e. 2.5²) assuming that the missing innermost winding would be no less than 2.5 cm. For the toilet paper, I used the actual last winding measurement in its place. T represents the change in radius, while change in winding length (S) can be thought of as circumference. Thus S = 2(pi)T (i.e. circumference = 2(pi)r), and 2S = 4(pi)T. According to Cook,

Our centered convention for the winding numbers and definition of where the missing section begins removed the factor of –E+S/2 from the right-hand side.

I don't quite understand how that works, so I just went ahead and compared the results of the equations in a straightforward manner. I don't know which is most appropriate, but I found that using Cook's expression yielded a remainder of zero on the last winding, while Hoffmann's (via Gee) gave a negative number, which suggests to me that Cook's expression is better.

Results
The results of my two tests are shown below (click for large). Each graph represents the predicted maximum length of roll remaining at each winding based on the two formulas, compared to the actual remaining length. For each test, S (or T) was calculated from either a running average of change in winding length (i.e. average of all previous windings), or as a sliding window of the average of the three previous windings. (Note that the sliding window begins at winding 4; the running average begins at winding 2.)

The Hoffmann and Cook formulas gave nearly identical results, which is not surprising since the equations are essentially the same. Test 1 using a running average S (or T) tended to overestimate the maximum remaining length, but gave fairly consistent results. In contrast, the sliding window of S (or T) gave predictions that often varied from the true remainder, sometimes dramatically.

Results for the running average S (or T) for Test 2 tended to underestimate the maximum remaining length, while the running average gave more accurate predictions. I believe that this can be accounted for by the fact that I rerolled the toilet paper by hand, which resulted in the outer windings being looser than the inner ones. The initially large changes in winding length (S) of the outer windings--as the winding became tighter--had a large impact on the running average S (and T). The sliding window, in contrast, used only local changes in S (or T) and so calculations for inner windings were not affected by the loose outer windings.

In his rebuttal to Gee, Cook wrote:

Another way of determining a scroll’s original length, which involves less math, is to plot the lengths of the extant windings and fit a straight line to the results. The missing windings will reliably lie along the straight line.

I tested this by doing a linear regression (using the spreadsheet trend function) on either the first (outer) 3 or 10 windings. Using only 3 windings yielded a prediction that was reasonably accurate for Test 1, but clearly inaccurate for Test 2. However, in both cases using 10 windings yielded predictions that agreed well with the actual length.

Cook's rebuttal contains the first seven measured winding lengths of the Hor scroll, as well as 12 remaining interpolated winding lengths. I applied the Cook/Smith formula to the first seven windings using the T value reported in their original article. I then compared that to the length given by linear regression based on the same seven windings. Agreement between the two was quite good. Finally, I compared these results to a linear regression based on only the first three winding lengths, which gave the same result to within 3 cm of the other regression.

Note: Spreadsheet is available here

Conclusions

I undertook this toilet paper test primarily as a fun exercise, and its results are only as good as my competence and accuracy, both of which may be called into question. Nevertheless, based on my exercise I conclude the following:

1. The Hoffmann and Cook/Smith formulas are essentially the same and give very similar results. Why exactly Gee found otherwise will remain unknown until he is more specific about his method. Cook has suggested that Gee mistakenly applied Cook and Smith's derived value of T for the Hor scroll to the Royal Ontario Museum, not understanding that T is unique to each scroll and derived from the winding lengths.

2. Although they may be sound in theory, these formulas can give inaccurate results, which I think can partially be attributed to uneven tightness in winding. Whatever the source of error, I think it is wise to treat the results with caution, as my results in some ways mirror those of Gee's for the Royal Ontario Museum scroll.

3. Linear regression based on as few as 10 windings gave reasonably accurate results in both tests. This may represent a better approach and, at the very least, can serve as a cross-check.

4. In the particular case of the Hor scroll, linear regression based on Cook and Smith's measurements of extant winding lengths agrees well with results obtained from using their formula, even when the regression is done using as few as three windings. I therefore think that their conclusion that the missing inner portion of the scroll was 56 cm is correct to within 10 cm. (Cook has revised the length to 51 cm because of a calculation error. My linear regression using seven windings put the missing portion at 60 cm. However, if we assume that winding lengths could be as small as an unrealistic 0.2 cm, the linear regression puts the missing length at 65 cm.)

In summary, although I believe Gee has legitimate reason to be wary of the application of these formulas, Cook and Smith's estimate of the lost portion of the Hor scroll seems correct. What, if anything, this means for the Book of Abraham depends on other assumptions and considerations.

References:
1. John Gee, Some Puzzles from the Joseph Smith Papyri.

2. Andrew Cook and Chris Smith, The Original Length of the Scroll of Hôr (pdf).

3. John Gee, Formulas and Faith.

4. John Gee, Book of Abraham, I Presume.

5. Andrew Cook, Formulas and Facts: A Response to John Gee.

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The Joseph Smith Papyri: Updating the Length Controversy

Last June I blogged about attempts to determine the original length of a scroll of papyrus that Joseph Smith possessed, and from which he may have derived the Book of Abraham. At the very least we know it is the source of Facsimile 1. Andrew Cook and Chris Smith (neither of which are believing Church members, as I understand) developed a mathematical approach to determining the winding length of the scroll, which is more precise and sophisticated than simply eyeballing the papyri, and then applied a formula to determine the original length of the scroll. Their conclusion was that the scroll of Hor was too short to have contained the Book of Abraham.

John Gee, an Egyptologist associated with FARMS/Maxwell Institute, published an article in which he criticized Cook and Smith's method. According to Gee, their formula gave inaccurate results when applied to an actual complete scroll. However, I noted that I found Gee's article unsatisfactory because it did not engage Cook and Smith's article in the level of detail that it deserved. Further, in laboring to discredit their work, Gee missed or ignored the fact that their conclusion was compatible with what Gee claims to be a popular LDS view: that the Book of Abraham was more a product of revelation than a translation of text.

There have been a couple of additional developments in this little controversy, and so the story needs updating. I will take them in chronological order.

Last month Gee spoke at the annual FAIR conference and his talk touched on this issue. After briefly introducing his own attempts to apply a standard mathematical formula (developed by someone named Hoffmann), Gee said,

Andy Cook developed a slightly different formula and he and Chris Smith applied it to one of the papyri and they’ve been loudly proclaiming that they who have never worked with papyri know more than I who have been working with papyri for a quarter of a century.

Gee then showed his previously published figure that compares a known full scroll with application of Hoffmann's formula compared to Cook and Smith's. Gee claimed to have found 5 errors in Cook and Smith's work, though he did not specify what they were. He then showed the results of fixing one of those unspecified errors, which greatly improved the results (red), compared to the real scroll length (blue) and Cook and Smith's original formula (green). (For some reason, he could not be bothered to label his data series or axes.)

Gee commented:

The errors are therefore something in Cook’s formula and methodology and not something in the papyrus measurements. It shows us that Cook’s methodology is fundamentally flawed.

Now, I attribute Cook’s mistakes to working in a new field, where neither he nor Chris Smith have had any experience working with papyrus before. And there were some math mistakes that for some reason Cook did not catch. As you can see, if he corrected one mistake it would have made a big difference in his results.

Gee concluded by saying that both the Hoffmann and Cook/Smith formulas make some "fallacious assumptions" and that they can, at best, "give a ballpark estimate."

Andrew Cook has responded in the most recent issue of Dialogue. The article, "Formulas and Facts: A Response to John Gee" (subscription required) hits back at Gee on several counts. According to Cook,

1. Gee misunderstands the Cook/Smith equation, not realizing that it is the same as the Hoffmann equation, though expressed slightly differently.

2. As a corollary, Gee's representation of differences of result between the Hoffmann and Cook/Smith formulas is incorrect. They should be exactly the same.

3. Gee erroneously accuses Cook and Smith of estimating the thickness of the papyri in order to derive winding lengths, when in reality Cook and Smith measured winding lengths in order to derive thickness.

4. Differences in the smoothness of the two lines suggest that Gee did not treat the formulas consistently, which had the effect of exaggerating the alleged inferiority of Cook and Smith's formula. Further, it appears that he applied the thickness derived by Cook and Smith for the Hor scroll to the known Royal Ontario Museum (ROM) scroll instead of deriving a new value for the ROM scroll.

5. Cook obtained winding measurements for the same ROM scroll, and applied the Hoffmann and Cook/Smith formulas, and compared the results to the actual scroll length. The results of the two formulas were identical, and both were nearly identical to the actual scroll.

6. The novel contribution of the Cook/Smith paper was the autocorrelation method of identifying the winding lengths, which has been mostly overlooked. Accurate measurement is important for the reliability of the result.

7. Cook concedes that their paper contains a calculation error. However, it is not known whether that was among the errors Gee claimed to find, and anyway it only made a difference of 5 cm in the final result.

I can't adjudicate all of these points, but I think Cook makes a good case. For example, take point #3. In his "Formulas and Faith" article, Gee wrote:

Cook and Smith use the thickness of the papyri (which they did not measure but only estimated) as an indication of the change in diameter to calculate the difference between the lengths of successive windings in the scroll. Hoffmann—knowing that most papyri are already mounted, thus rendering it impossible to measure the thickness—uses the average difference between successive windings for the same purpose....

With the data gleaned from this intact roll in Toronto (that is, the individual winding lengths), I applied each of the mathematical formulas, using the assumptions made by the authors of the formulas concerning papyrus thickness, air-gap size, and size of smallest interior winding.

But as Cook correctly points out, they clearly did not begin by estimating the thickness and air-gap size. Rather, they used a similar method to that of Hoffmann--using winding length to derive effective thickness (i.e. change in radius). "Our primary task therefore, is to determine the effective thickness of the papyrus from the winding lengths." I can't help but conclude that Gee is wrong here.

It appears to me that on the technical merits Cook and Smith really do have the upper hand. Gee may have a quarter of a century experience working with papyri, but it's not obvious to me why that should give him mathematical superiority, particularly when his adversary (Cook) is apparently a theoretical physicist. We are talking about physical dimensions here, after all. If Gee ends up eating humble pie after having trashed Cook and Smith's work, he's only got himself to blame.

However, I do think that Gee's sense of caution is legitimate. I will explain why in my next post.

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Important Experimental Evolution Result Detailed

In 1988 biologist Richard Lenski started 12 identical cultures of E. coli bacteria and began propagating them every day to study their evolution. Along the way, he and his students froze cultures so that they could always go back and study them more closely. A few years ago his lab reported that after about 31,000 generations the bacteria had gained the ability to live on citrate as a food source. The results received a lot of fanfare and attracted the interest of anti-evolutionists. However, the paper describing the result was not fully satisfying because it didn't look into the underlying genetic changes that gave rise to the citrate-eating ability.

This week Lenski's lab published a follow-up paper and we now know what happened....mostly. E. coli already have a gene (citT) for a protein that imports citrate into the bacterial cell, but it isn't turned on in the presence of oxygen. When they looked at the citrate-eating bacteria, they found that the area around that gene had been duplicated, but in a way that put the duplicated gene under a new promoter, which is a section of DNA that regulates when genes are turned on. This is illustrated in Figure 2 of the paper:

The new arrangement allowed citT to be turned on in the presence of oxygen and, lo and behold, citrate-eating bacteria were born. However, they weren't very efficient at first so further tweaks to the new arrangement refined their ability. Some of these tweaks included further duplications of the new arrangement to increase the amount of the importer protein produced.

This would all be interesting enough, but they also found that if they went back and inserted the new gene arrangement into ancestral bacteria from before generation 20,000, it hardly worked. But it did work if they put it in ancestral bacteria after generation 20,000. This fits with their previous results where they found that the ability to eat citrate could re-evolve in cultures started from stocks after generation 20,000. It thus appears that other unspecified mutations elsewhere in the genome set the table for the gene duplication and rearrangement to be useful. Unfortunately we may never know what those other mutations were because even with the genome sequence, figuring out which mutations were important would be an enormous amount of work. Interestingly, when they looked at the genomes of the bacteria from the re-play experiments, they found that the same kind of gene duplication and rearrangement often occurred but that no two were exactly alike. In a few cases the genetic event was quite different while giving the same basic result.

The authors propose that evolution often proceeds in a manner that can be divided into three parts: potentiation, actualization and refinement. First, mutations accumulate that are of little significance on their own. Second, some kind of genetic event occurs that results in a new function or new regulation of the function. This genetic event is able to be accommodated because of the previously unimportant mutations. Third, the new ability is refined by further mutation.

The whole study is quite elegant and was clearly a lot of work, and it will go down as a landmark in experimental evolution. Yet, its results are not surprising. These kinds of genetic events can be inferred to have occurred many times in the genomes of all manner of organisms, including humans. But now we have a detailed record of one that occurred (and re-occurred) in a laboratory. This study is also a clear refutation of the ridiculous but frequent claim by creationists that mutations can only degrade genetic information.


See also Carl Zimmer's summary: The Birth of the New, The Rewiring of the Old

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Genome Junk

A mini scientific controversy has broken out this week, exacerbated by anti-evolutionists, that has to do with how much of the human genome is functional. It may surprise you to learn that only about 1% of the genome codes for proteins. Since proteins are the foundation of all of the building blocks of the body and all of its chemistry, it is reasonable to wonder what the rest of the 99% of the genome is for.

Although it has become common in both popular and scientific publications to claim that the rest was long dismissed as junk, this ahistorical claim is not correct. Biologists have long recognized that other non-coding parts of the genome (i.e. not coding for protein) play important regulatory roles in gene expression. For example, in order for a protein to be made, DNA must first be transcribed into RNA, which is then used as the template for protein synthesis. In order for transcription to occur a collection of proteins must assemble around DNA upstream of the gene, which then proceed along the DNA while copying it into RNA form. Some stretches of DNA are particularly attractive places for the transcription machinery to assemble, and these are known as promoters (because they promote gene transcription; get it?). Over the decades additional methods of regulation have been recognized. More recently it has been recognized that RNA molecules themselves can serve important regulatory functions. But the basic point to be made here is that biologists have long understood that not all non-coding DNA is worthless junk.

However, biologists have also come to understand that over 50% of the genome is made of the remnants of viruses and other self-replicating pieces of DNA. In addition, there are extra broken copies of genes scattered around the genome. Although there are some interesting cases where these elements have taken on a function by helping to turn on/off a particular gene, or something similar, it is hard for many biologists to imagine that all of it has important function. After all, the genome is not static and these are ongoing phenomena. Sometimes a novel insertion of one of these elements can cause disease. Yet there are some biologists who think that most, if not all, of the genome has function because of stringent natural selection.

This debate would probably attract little attention if it weren't for anti-evolutionists. The notion that much of the genome is full of dispensable junk built up over millions of years is offensive to people who think that God created the human genome out of whole cloth. Why would he load it up with useless junk? As the Intelligent Design movement was taking shape, ID proponents made what they claimed was a scientific prediction based on ID: that there is no junk DNA. The reasoning is that if the human genome is designed, then it won't contain lots of non-functional DNA [1]. ID proponents have been pushing this and have trumpeted every report of DNA being moved from the non-functional category to the functional.

This week a high-profile paper was published claiming that 80% of the genome is functional, and most of the reporting has followed along with the narrative that whereas scientists used to think that the genome was mostly junk, it turns out to almost all be functional. However, a lot turns on the meaning of the word functional, and the lead author of the paper has admitted to setting the bar extremely low. For example, if a section of DNA is transcribed into RNA it is deemed functional. But what is missing is evidence that all of that RNA actually does anything important for the cells in question. After all, the basic interactions of DNA with its environment are governed by the laws of chemistry (and the underlying laws of physics), and there is going to be noise. Should we really believe that none of those RNA transcripts are accidental by-products of chemistry? Similar questions can be raised about the other criteria used to judge a piece of DNA functional, like protein binding, etc. Critics suspect, based on comments by the lead author, that the 80% bit was really a gambit to increase the splash of the paper.

Evolutionary biologist T. Ryan Gregory has been writing about the junk DNA issue for years at his blog. Since most vertebrates have about the same number of genes (20,000-30,000), an often unstated assumption is that more complex organisms need more extra DNA to regulate those same number of genes in more complex ways. However, it turns out that genome size does not correlate with organismal complexity, which has led Gregory to propose the onion test.

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

I'm with the critics on this one, and not just because it defies the ID brand. The claim that 80% of the genome is functional just doesn't pass the smell test (or, in my view, the onion test), and it renders the term functional virtually meaningless.

For more on this controversy, see Nature's blog post, Fighting about ENCODE and junk. T. Ryan Gregory and Larry Moran have been blogging about this at a furious pace. You can find entries into their analysis here. For more general background on junk DNA, Gregory has a nice collection of older posts (both his and others').



Notes:
1. Like so much else with ID, lack of junk DNA is not a scientific prediction based on ID. This is because ID proponents also disclaim any knowledge of the designer's motives or identity. That being the case, there is no reason to think that the designer would avoid accumulation of junk DNA. For example, the designer could have started life, or a few lineages of life, and let them evolve from there. If these lineages accumulated junk DNA, they would still be in line with the central claims of ID. You cannot claim that junk DNA is incompatible with design while simultaneously claiming not to know anything about the methods or motives of the designer. Well, actually you can because it's a free country, so you can say anything you want. But we're talking about logical discourse here.

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Arctic Sea Ice is Recovering

The summer of 2007 saw a record in seasonal Arctic sea ice melt. A few years later in an online discussion, I was told that Arctic sea ice was recovering. This was based on the fact that sea ice melt in subsequent years had not reached the low point of 2007. A look at decade-scale trends did not support the assertion, but hey--trends shmends!

This summer is smashing the 2007 record low (source).

We've already passed the previous record, and we probably have not hit bottom quite yet.

But here's the good news: Seasonal Arctic sea ice melt in the next couple of years will probably not reach this year's low. And that means Arctic sea ice is recovering! Yay!

Skeptical Science illustrates how this game is played (note that 2012 is not shown (yet?)):

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