Saturday, November 17, 2012

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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Wednesday, October 03, 2012

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 Ln = (Wn2-WN2)/(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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Saturday, September 29, 2012

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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Friday, September 21, 2012

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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Sunday, September 09, 2012

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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Thursday, September 06, 2012

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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Sunday, August 05, 2012

Another Utah Geology Report

Last month our family took a trip to Utah. I always enjoy my visits there--which sadly seem to be increasingly spaced apart. Having been an easterner for most of my life, I love the change in scenery that Utah offers and I try to incorporate learning a little geology each time I visit. This post is my show-and-tell report, focusing on southeastern Utah again. (Previous reports here, here, and here).

Let me pause to highlight two helpful resources for learning about Utah's geological history. The Utah Geological Survey website has lots of good information that can help you get a general feel for the history. Also, I spent a lot of time with Utah's Spectacular Geology: How it Came to Be, by Lehi Hintze, in my hand. Hintze divides the geological history into nine chapters. But the best part of the book is toward the end where 19 areas are given individual treatment, including photographs with labels. (See modest recreation of one image below.) I found the book to be very helpful and informative. Its one defect is the lack of an index (!).

OK, moving on. We spent a day down at Arches National Park (ANP). But first we stopped at Dead Horse Point (DHP), which is near by and a must-see if you've never been there. When you turn west off Highway 191 onto 313 toward DHP, look to the right and you will see this, (but without labels). (Click for larger.)


The labeling is based on a similar image in Hintze's book. The Wingate Sandstone is pretty easily identifiable at both DHP and ANP, and the Chinle Formation is rather distinct with its green coloring. The Chinle Formation contains uranium--too bad I didn't have a Geiger counter to play with.

On this trip I experimented with taking images that could be viewed in 3D. This was easily done by snapping a picture, taking a step to the side, and taking another picture. I've put them side-by-side below. Look between the two pictures and relax your eyes, as though you are looking through your screen. With a little practice, you should be able to bring the two images together such that you see three images. You'll be focused on the one in the middle, which should lock into place and become 3D. Once you are successful, should be able to keep the effect while moving through the pictures. You can see slightly larger versions by clicking on them, but you may have more difficulty bringing them together. I find it helps to back away from the screen a little, and then once I have the image I can look closer.

Dead Horse Point







Arches National Park







This next picture is of the Fiery Furnace at ANP. I didn't realize at the time that my life was in danger, but when I looked at the picture I saw that the Grim Reaper was coming after me.




Book Cliffs

On the east side of the road between Price and Green River are what are known as the Book Cliffs. Some Internet sources say that they get their name because they look like shelves of books. However, I have it on pretty good authority that it's actually because of their appearance from above--they look like pages at the edge of an open book. The grey rocks are Mancos shale, which was laid down over 65 million years ago when the interior of North America was covered by sea (picture the Gulf of Mexico stretching up through Canada) with Utah as the western shoreline.



North of Price is a small town called Helper. Just north of the merger of Highway 6 with 191, Highway 6 cuts through rock. That black strip is a coal seam.



We only spent a day in the Moab area, but those are the geological highlights of our trip. I took a lot of pictures that I would like to share, but they just don't do the area justice! Go see it for yourself; I don't think you'll be disappointed. I can't wait to go back.



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Thursday, July 19, 2012

Surely it is the Earth that Moveth

The Book of Mormon seems to be explicitly heliocentric. In a passage expressing his frustration with mankind, Mormon writes about God (with an apparent allusion to Joshua):

14 Yea, if he say unto the earth—Thou shalt go back, that it lengthen out the day for many hours—it is done;

15 And thus, according to his word the earth goeth back, and it appeareth unto man that the sun standeth still; yea, and behold, this is so; for surely it is the earth that moveth and not the sun. (Helaman 12:14-15)
What is this kind of statement doing in a document that purports to be ancient? Did the Nephites understand the workings of the solar system better than most of the ancients? Is it an anachronism that gives away Joseph as a fraud? Or is it possible that the scientific clarification was a commentary made during the translation process?

In the latest issue of BYU Studies, David Grandy argues that none of the above are correct. In his article, "Why Things Move: A New Look at Helaman 12:15" (subscription required), Grandy draws on the work of John Walton to contend that this is a case of our failure to understand ancient ways of thinking. We are the children of Newton, who think of matter as inanimate and passively following physical laws, like machines. God doesn't need to push the earth around the sun, gravity does that. In contrast, the ancients saw God's hand in all aspects of the world, including motion. If we look at the larger context of Mormon's statement, we see that he emphasizes that everything on earth obeys and moves according to God's command--except man. The verses surrounding 14 and 15 are all about how various parts of the earth (dust, hills, mountains, water) move, shake, part, rock, dry, etc, as commanded.

Grandy writes:
Rather than confirming Copernican cosmology, this verse suggests that Mormon is invoking Joshua’s event, not because Joshua’s account is scientifically inaccurate and therefore in need of correction, but because it reinforces Mormon’s own admonition that humans, being indigenous to the earth (their bodies made of the dust of the earth), should follow the many examples of responsive obedience they witness among things with which they are intimate—dust, hills, mountains, the foundation of the earth, the great deep, and so on.


This is all well and good, but Mormon specifically says, "the earth goeth back, and it appeareth unto man that the sun standeth still...for surely it is the earth that moveth and not the sun." Grandy notes that although this sounds like it assumes axial rotation and orbiting, those are assumptions that we bring to the passage. If he was like other ancients, Mormon did not share our concept of a sphere sitting in space. He would instead have pictured something like the picture to the left [image source]. The focus in these verses is on movements of the earth; it can move back and forth, and thus "goeth back." The contrast drawn with the sun is simply tailoring language to keep focus on the earth.

I'm not sure whether I buy this. I am quite sympathetic to attributing differences between scripture and science to differences in culture and worldview, so when Grandy asserts that Mormon did not share our scientific outlook, I'm on board. My trouble is that verse 15 is so suggestive to me of Copernican motion. If I try to empty my head of orbits and revolutions, does Mormon's statement make sense given the context? I guess it kind of does--maybe I just need to get used to it. I think it helps to keep in mind that Mormon referred to "the earth," not "Earth." That's a subtle but perhaps important difference.

I don't know whether he is right or not, but I think Grandy's argument is at least worth considering.


Continue reading...

Sunday, July 08, 2012

Modern Mormonism: Revisiting the Church's Pragmatic View

A few weeks ago I highlighted a quote from a news article in which a Church spokesman said something to the effect that the Church takes a pragmatic view of science-religion conflicts. That quotation is now contained in a larger commentary, Mormon and Modern, posted on the Church's Newsroom site. I think it's worth quoting at length (footnotes removed).

For Mormons, there need not be a conflict between devotion to one’s faith and meaningful participation in modern society. Faithful Latter-day Saints are currently engaged in education, science, business, the arts and political life. In a pluralistic world, modern sensibilities tend to compartmentalize spheres of human activity. But Mormon thought encourages integration. Individual character, for example, should not be divorced from public character. Elder Richard G. Scott of the Quorum of the Twelve Apostles counseled: “Avoid compartmentalizing your life into segments that apply to profession, to Church, and to family, using different standards in each segment. Your life is a continuum where the same standards of integrity and hard work apply to every aspect of your life.”
Later:
Mormons welcome truth from whatever source and take the pragmatic view that where religion and science seem to clash, it is simply because there is insufficient data to reconcile the two. Latter-day Saints approach such tensions as challenges to learn, not contradictions to avoid.

This productive tension can enrich both mind and heart. All understanding, whether spiritual or rational, is worked out in constant questioning and discovery. The Prophet Joseph Smith said, “By proving contraries, truth is made manifest.” Latter-day Saints do not expect God to simply hand down information. He expects us to wrestle with the complications of life through prayerful searching and sound thinking. “You must study it out in your mind,” Mormon scripture teaches, and then answers will come. This pattern of inquiry opens Mormons to expanding spiritual possibilities.

While the ultimate aims of religious and secular life do not always align, Mormons “follow the admonition of Paul” by seeking after anything that is “virtuous, lovely, or of good report or praiseworthy,” whatever the source may be. Embracing a world full of truth and meaning, Latter-day Saints aspire to heed the call of Joseph Smith to “gather all the good and true principles in the world and treasure them up.” President Boyd K. Packer of the Quorum of the Twelve Apostles has encouraged “a harmonious combining of both the intellect and the spirit.” Mormons, therefore, do not compartmentalize one truth from another.

This is aspirational stuff. It was brought to my attention by Dave's Mormon Inquiry, where Dave notes (emphasis in original):
If there is something to criticize in the essay, it is that it does not, perhaps, represent the actual approach that many Latter-day Saints and LDS teachers of religion have taken or do now take to faith versus science issues....

Wouldn't it be great if essays like this were reprinted in the Ensign? That's such an obvious move it's hard to understand why it isn't just standard practice. Still, this broad-minded essay is another step forward.
Here, here! Dave's broader criticism is that Newsroom statements may not be filtering down to average members. So until the Church starts putting these things on LDS.org, my advice is to become familiar with them and maybe keep a copy in your preferred electronic device. You may then confidently reference them in Sunday School, or wherever.


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Friday, June 29, 2012

The Church Showcases an Evolutionist

This is what is currently highlighted on the I'm a Mormon webpage.



I guess the PR department has gone rogue. ;-)


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Tuesday, June 26, 2012

A Conservative Approach to Environmental Problems

Jonathan Adler is a conservative-leaning law professor, who works on environmental issues. Last month he was invited to do a series of guest-posts at The Atlantic on conservative approaches to environmental issues [1]. I don't usually advocate for particular environmental policies on this blog, nor am I doing so here. However, since most environmental policies have a strong regulatory component administered by the federal government, and are therefore often viewed as 'liberal,' I thought it would be worth highlighting ideas from someone on the more conservative side. Adler argues that

the embrace of limited government principles need not entail the denial of environmental claims and that a concern for environmental protection need not lead to an ever increasing mound of prescriptive regulation.
The core of his argument involves a greater focus on property rights, and I think he makes a number of fine suggestions. I think it would be wonderful if voices like his could gain greater currency in the marketplace of ideas (and politics). This passage nicely encapsulates the bottom line.
Environmental problems are difficult, and typically defy easy solution. Though I believe in property-based solutions to many (if not most) environmental problems, the viability of such approaches should not be oversold. At the same time, the environmental limitations of property rights and markets should not be overstated, particularly in comparison to the viable regulatory alternatives. In environmental policy we rarely have the option of pursuing a clearly identifiable "ideal" approach. Rather, our choice comes from the collection of second-best (and third-best, fourth-best, etc.). The question is not which approach is perfect, but which approach is better (or not as bad) as the others.

Property Rights and the Tragedy of the Commons

Property Rights and Fishery Conservation

How Property Rights Could Help Save the Environment

Is Washington, D.C., Really the Environment's Savior?

A Conservative's Approach to Combating Climate Change


Notes:

1. Honestly, I'm not entirely sure how to define a conservative approach, since this year's conservative idea can be rejected as next year's totalitarianism (see cap-and-trade, individual mandate). As Adler was wrapping up his series of posts the House stopped NOAA from expanding its catch shares program, leading Ronald Bailey (of the libertarian Reason Magazine) to opine, "If it's not the Democrats screwing up policy, it's the Republicans - that's bipartisanship for you!"



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Sunday, June 17, 2012

The Church Takes the Pragmatic View

The Deseret News has a nice article on the teaching of evolution, particularly at BYU. I like this part:

Scott Trotter, spokesman for the LDS Church, offered further clarification:

“Science and religion are not at odds in our faith. We accept truth wherever it is found and take the pragmatic view that where religion and science seem to clash, it is simply because there is insufficient data to reconcile the two.”
There are several ways to interpret that, but it's a whole lot better than it could have been, from my view.

H/T: Gary at NDBF, who shows what the statement could have been.


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Tuesday, June 12, 2012

The Book of Abraham: FARMS Phones It In

The most recent issue of the Maxwell Institute (FARMS) publication Journal of the Book of Mormon and Other Restoration Scripture (21:1) is now available online, and it has an article by LDS Egyptologist John Gee titled, "Formulas and Faith." Here, Gee addresses mathematical attempts to determine the length of the Joseph Smith papyri (which I discussed earlier). I should make clear that I am not any kind of expert on the papyri or the running arguments surrounding them. Nor do I know much about the persons involved. Nevertheless, I'm sorry to say that I was disappointed in this article for reasons that I will explain below.

Gee sets the issue up as follows:

One of the more prominent issues with the Book of Abraham is the relationship of the Book of Abraham to the Joseph Smith Papyri. There are three basic positions here:

1. The text of the Book of Abraham was translated from papyri that we currently have. (Or, from the unbelieving perspective, Joseph Smith thought that the text of the Book of Abraham was on papyri that we currently have.)

2. The text of the Book of Abraham was translated from (or Joseph Smith thought the text of the Book of Abraham was on) papyri that we do not currently have.

3. The text of the Book of Abraham was received by revelation independent of the papyri.
Gee notes that hardly any informed Mormons accept the first proposition. It may come as a surprise that Gee claims that the third option is held by a majority of Church members (something that may be worth some further attention later). From that perspective, the issue of scroll length is moot, but in light of the second theory Gee is willing to discuss the matter anyway (though I think I detect a sigh and roll of the eyes).

The crux of Gee's argument is that the formulas developed by Cook and Smith, and others, have not been tested on papyrus scrolls of known length. But Gee says that he has done so.
In November of 2010, I had the privilege of measuring the interior seventy-three windings of [a scroll at the Royal Ontario Museum] (after that point the scroll is no longer contiguous).

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. I then compared the outcome with the actual interior length of the scroll. The results are shown on the graph.


I have to admit that I'm not entirely clear on how to interpret this graph--I think it shows the predicted remaining length as each additional winding is included in the calculation, with the outermost winding being number 72. Nevertheless, Gee's message is clear: neither formula is perfect, but Cook and Smith's formula is not even close.
On the basis of observations I have made while measuring various scrolls, I am not convinced that these formulas can ever yield anything more than rough approximations. More empirical data is needed to make refinements in the formulas.
Fair enough. It's worth noting, however, that if Cook and Smith's method underestimates true length by up to 75% (as Gee claims), that still puts the Hor scroll length at only 600 cm, less than half of Gee's estimate using the Hoffman formula, and perhaps a little cramped for the Book of Abraham. Nevertheless, Gee's caution is a point well taken. However, if you recall my previous post, Cook and Smith were explicit about their methodology, spelling out measurements, assumptions, and formulas. They wanted others to be able to reproduce their work. Now if you were Cook and Smith (or an interested third party) you might want to know where their formula breaks down, or how to adjust it to make it more accurate. Unfortunately you won't get any help from Gee in this article. Aside from the number of windings and the total length of the scroll, no measurements or details of how the winding locations were identified are given, nor is there any hint that they are forthcoming. All we have to go on is a graph and his assurance that it doesn't work. Nor does Gee address Cook and Smith's different winding length measurements for the Hor papyri. That seems like an insufficient response to me.

Moving on, I think Gee's article mis-characterizes the Cook and Smith article. First let's review the basic argument of Cook and Smith (my paraphrase):

1. Based on our calculations, the Hor scroll is too short to contain the Book of Abraham.
2. There is reason to think that the Hor scroll was the one identified as having the writings of Abraham.
3. Therefore, the Book of Abraham is probably not a direct translation of Egyptian text.

Before we look at Gee's further criticisms, you need to know that one witness described seeing a "long roll" (the apparent source of the Book of Abraham) and "another roll." Now let's look at Gee's criticisms, which are mostly confined to three paragraphs. We'll take them one at a time.
Although the Cook and Smith method of determining scroll length is anything but accurate[,]...even if it had been successful, it would have created other problems. Cook and Smith fail to establish which was the long roll because they applied their formula only to the Horos scroll; they did not apply it to any of the other extant scrolls and thus fail to meet another of the necessary conditions.... They measured only the Horos scroll because they assumed it to be the source of the Book of Abraham. Yet the eyewitnesses identify the long roll as the source. Bent on proving that the Horos scroll was not the long roll, they overlooked the implications of such a view. If the scroll of Horos is not the long roll, it simply cannot be the source of the text of the Book of Abraham (according to the accounts of the eyewitnesses). By endeavoring to prove that the Horus scroll was not the long roll, they would have undermined their own case, which depended on the Horos scroll being the proposed source of the text of the Book of Abraham.
'Long' is a relative term, and it seems to me that Gee is perhaps putting more weight on the distinction between a roll and a long roll than is warranted. (Wouldn't five feet be long to a non-Egyptologist?) Be that as it may, I don't see any evidence that Cook and Smith were "bent" on proving the Hor scroll was not the long roll. They don't frame the question in that way and, in fact, they don't even address the issue of the long roll until the end of their article when, lo and behold, they suggest that the Hor scroll was indeed the long one. But even if Gee is right about Cook and Smith disqualifying the Hor scroll as the long one, does that undermine their case? I guess it depends on what you interpret their case to be. Gee seems to imply that their case is that the Book of Abraham is bogus. But whatever the authors think personally, their article does not argue such a thing. At any rate, their immediate conclusion is that the Hor scroll did not contain the text of the Book of Abraham. If they unwittingly demonstrated that the other scroll was longer, then by Gee's criteria their conclusion is actually stronger.
Cook and Smith would like to minimize the length of the Horos scroll because they believe that finding would eliminate the possibility that the Book of Abraham was translated from a scroll that we do not currently have (theory 2). Even if their calculations had been correct and thus had shown that the scroll of Horos was not the long roll observed by the witnesses, that simply would have meant that another scroll would have been the scroll containing the Book of Abraham. So their attempt to eliminate theory 2 as a possibility would not, in fact, have actually been successful even had their formula correctly predicted a short length for the scroll of Horus.
Here Gee makes a logical leap of his own, which is to assume that if the Hor scroll was too short to contain the Book of Abraham, then another scroll must be longer. What is the justification for that? Gee makes a good point--that it would have been better if Cook and Smith had also evaluated the other fragments for comparison. But if Cook and Smith had determined that another scroll was longer, would that necessarily mean anything? I guess it depends on how much longer. But at the very least, someone would need to explain why the Book of Abraham referred to a vignette (Facsimile 1) on a totally different scroll, which was owned by a different person [1].
Furthermore, their attempt, even if successful, would not have eliminated the most popular theory—that Joseph Smith received the Book of Abraham by revelation unconnected with the papyri (theory 3). It certainly cannot force anyone to accept the theory that the Book of Abraham was translated from the extant fragments of the Joseph Smith Papyri (theory 1) since that theory is excluded by the historical evidence. So for those who care about such matters, there are still two theories (2 and 3) that are not excluded from consideration.
Here we come to the reason I quoted the conclusion of Cook and Smith in my previous post. Having ruled out the scroll of Hor as the source of the text, they listed several alternatives. Here they are again:
(1) the Document of Breathing served as a mnemonic device for the Book of Abraham, (2) the Breathing text served as a catalyst (rather than source text) for the Book of Abraham, (3) the Document of Breathing is a corrupted version of the Book of Abraham, which Smith restored to its pristine state, or (4) the Book of Abraham is simply an imaginative mistranslation of the hieratic script.
Hey, I recognize that second option and it looks a lot like Gee's theory 3. Gee doesn't seem to recognize that Cook and Smith's work supports his preferred theory (at least by popularity--allegedly), by their own admission.

All of this leads me to conclude that Gee's article does not engage Cook and Smith's work in a fair or convincing manner. People who only read Gee's article will get the impression that he has bested bumbling critics who can't construct a coherent argument. However, having read both articles, I get the impression that Gee didn't read theirs very carefully.


Notes:

1. One suggestion that I have seen is that Abraham referred to a figure that was missing from the papyri, so Joseph adapted by using a different illustration.

Further Reading:
A Guide to the Joseph Smith Papyri by John Gee

Eyewitness, Hearsay, and Physical Evidence of the Joseph Smith Papyri by John Gee

Some Puzzles from the Joseph Smith Papyri by John Gee

I Have a Question: Why doesn’t the translation of the Egyptian papyri found in 1967 match the text of the Book of Abraham in the Pearl of Great Price? by Michael D. Rhodes

Criticisms of Joseph Smith and the Book of Abraham, by W. V. Smith

FAIR Wiki: Book of Abraham Papyri


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Saturday, June 09, 2012

Was the Book of Abraham Too Long for its Papyrus?

While the saints were in Kirtland, Joseph Smith acquired some Egyptian mummies and papyri from a traveling showman. Having examined the papyri, he said that they contained the writings of Abraham and Joseph of Egypt. The Book of Abraham, now in the Pearl of Great Price is the product of Joseph's translation work. Because the outermost portions of the scrolls of papyri were fragile, they were separated from the rolls and mounted on paper. Following Joseph's death, the papyri were divided up and some of them ended up at a museum in Chicago, where they were apparently destroyed in the Chicago Fire of 1871. However, at least some of the mounted fragments of papyri eventually made their way to the Metropolitan Museum of Art in New York City in 1918, and were later given to the Church in 1967. One of the fragments of papyri is immediately recognizable as Facsimile 1 in the Book of Abraham.

The re-discovery of the papyri was exciting because it offered an opportunity to check Joseph's translation against that of modern scholars. It quickly became apparent that the surviving fragments did not contain the Book of Abraham. At first glance it appeared that Joseph Smith was proven wrong. However, although one might expect the writing surrounding the vignette that became Facsimile 1 to be the Book of Abraham, defenders have noted that the Egyptians often placed vignettes next to unrelated text. It is therefore possible that the text of the Book of Abraham came from another portion of the papyrus. But how much papyrus was there?

Joseph originally had at least five different documents, with only three of them represented by surviving fragments of papyri. Facsimile 1 comes from a document called the Book of Breathings made by Isis and was owned by a man named Hor. Facsimile 3 also comes from this scroll, but it was destroyed in the fire with the rest of the scroll. Facsimile 2 was an independent document. Given that the Hor scroll contains (or contained) Facsimiles 1 and 3, it is natural to assume that this scroll was the source of the Book of Abraham. This assumption is strengthened by the book itself, which says:

12. And it came to pass that the priests laid violence upon me, that they might slay me also, as they did those virgins upon this altar; and that you may have a knowledge of this altar, I will refer you to the representation at the commencement of this record.

13. It was made after the form of a bedstead, such as was had among the Chaldeans, and it stood before the gods of Elkenah, Libnah, Mahmackrah, Korash, and also a god like unto that of Pharaoh, king of Egypt.

14. That you may have an understanding of these gods, I have given you the fashion of them in the figures at the beginning, which manner of figures is called by the Chaldeans Rahleenos, which signifies hieroglyphics. [Abraham 1:12-14]
So how long was the Hor scroll? The surviving portions of this scroll apparently come from the outer end, as mentioned above. Although its original length is unknown, one can take a couple of approaches to estimating. One way is to compare to similar scrolls of the same period. You can also take a mathematical approach to the question because when the scroll was wrapped up, the outermost portion of the scroll contained the rest within it. With an idea of the winding length and the thickness of the papyri, one can estimate the maximum length of the scroll. (Imagine taking a roll of toilet paper and using a marker to draw a line from the cardboard tube to the outer edge--but just on one side so that the line roughly represents the radius. When unrolled, you would see a repeating pattern of marks at one of the edges. The distance between marks would be the winding length, which shortens as you progress toward the original center.)

LDS Egyptologist (and FARMS associate) John Gee originally went with a generic estimate of 320 cm (10.5 ft). However, after applying a published mathematical formula, he updated his estimate to 1250.5 cm (41 ft).

So far so good.

In the Winter 2010 issue of Dialogue: A Journal of Mormon Thought, independent researchers Andrew W. Cook and Christopher C. Smith published a paper, "The Original Length of the Scroll of Hôr," that took another look at the question [1]. They wrote:
Gee reported 9.7 and 9.5 cm as the lengths of the first and seventh windings, respectively, but offered no details regarding identification of winding locations. When we attempted to replicate Gee’s results, we found that his measurements did not seem to be accurate, and in fact required that the papyrus be impossibly thin.
In the rest of their paper, Cook and Smith described in detail how they attacked the question. Briefly, they traced the original papyri (because they were not permitted to photograph them) and then digitized their tracings to convert them into a grid of measurements. To determine winding locations (i.e. repeating patterns of damage to the upper and lower edges), they used a mathematical autocorrelation formula in order to reduce subjectivity. Let's look at an example. First we have a tracing of the papyri overlaid onto an independently obtained photograph.


Next, the upper portion of the of the tracing has been digitized into a coordinate system that matches the contour of the of papyri (though it is a little vertically stretched). The dotted lines show the same tracing shifted 10.42 cm to the right. Note the general agreement in contour.


Here is the output of the correlation function, which has a peak at 10.42 cm. This is the winding length, and was used in the last figure to determine the winding location.


Cook and Smith applied this method to the top and bottom of each fragment from the Hor roll. A cursory examination of the paper reveals lots of mathematical formulas and figures. The authors wrote:
Our choices are based on a desire to provide all details necessary for others to verify our work and duplicate our results.
In endnote 39 they add:
We are happy to make our data available to anyone interested in verifying our results.
I'm not going to pretend that I fully understand their method. Math is not a strength of mine. But those who do understand should be able to replicate their results.

When it's all put together, Cook and Smith estimate that the Hor scroll was approximately 150 cm (4.9 ft). Their estimate is within 3 cm of that of Klaus Baer (Hugh Nibley's Egyptology tutor). Based on the width of the surviving columns of text, and how it correlates to English translation, Cook and Smith estimate that the Book of Abraham would have required at least 511 cm (16.8 ft). Therefore, they argue that the Hor scroll is too short to have contained the Book of Abraham.

I don't know whether they are right or not, but it's a fun and interesting exercise. Their concluding paragraphs will be important later, so I quote them in full.
In recognition of the unlikelihood that there ever was a Book of Abraham source text on the inner section of the Hôr scroll, several alternative theories have been put forth to the effect that: (1) the Document of Breathing served as a mnemonic device for the Book of Abraham, (2) the Breathing text served as a catalyst (rather than source text) for the Book of Abraham, (3) the Document of Breathing is a corrupted version of the Book of Abraham, which Smith restored to its pristine state, or (4) the Book of Abraham is simply an imaginative mistranslation of the hieratic script. The ultimate success of any existing or future theory will depend on its ability to account for all of the evidence, including the fact that there was simply no room on the papyrus for anything besides the Breathing text.

Irrespective of Joseph’s method of translation, it is clear that he sensed in the Hôr scroll a richness of symbolic and religious potential that contemporary scholars could not see. To the experts who viewed Chandler’s collection in New York and Philadelphia, the Hôr scroll was a cryptic relic of a dead religion from a dusty tomb. Joseph, however, breathed fresh meaning into the crumbling little scroll, giving it new life as powerful scripture for the latter days. Perhaps the Egyptian vision of the afterlife, described in Hôr’s Document of Breathing, is not so far-fetched after all.

In my next post we will look at the FARMS response.

Notes:

1. Cook is a physicist and Smith is a graduate student in religious studies. Smith is not LDS; I don't know about Cook.

Further Reading:
A Guide to the Joseph Smith Papyri by John Gee

Eyewitness, Hearsay, and Physical Evidence of the Joseph Smith Papyri by John Gee

Some Puzzles from the Joseph Smith Papyri by John Gee

I Have a Question: Why doesn’t the translation of the Egyptian papyri found in 1967 match the text of the Book of Abraham in the Pearl of Great Price? by Michael D. Rhodes

Criticisms of Joseph Smith and the Book of Abraham, by W. V. Smith

FAIR Wiki: Book of Abraham Papyri



Continue reading...

Tuesday, June 05, 2012

The Transit of Venus (Life Sucks Edition)

Today is a transit of Venus. Venus's transits across the sun occur in pairs eight years apart. The last one was in 2004 and there will not be another one until 2117. They played an important role in helping astronomers to figure out the size of the solar system. In his book, Coming of Age in the Milky Way (you really should read it if you haven't), Timothy Ferris recounts the trials early astronomers went through in order to push the boundaries of knowledge. My favorite story is as follows:

Guillaume le Gentil...sailed from France on March 26, 1760, planning to observe the transit [of Venus] the following year from the east coast of India. Monsoons blew his ship off course, and transit day found him becalmed in the middle of the Indian Ocean, unable to make any useful observations. Determined to redeem the expedition by observing the second transit, Le Gentil booked passage to India, built an observatory atop an obsolete powder magazine in Pondicherry, and waited. The sky remained marvelously clear throughout May, only to cloud over on June 4, the morning of the transit, then clear again as soon as the transit was over. ...

Worse lay ahead. Stricken with dysentery, Le Gentil remained in India for another nine months, bedridden. He then booked passage home aboard a Spanish warship that was demasted in a hurricane off the Cape of Good Hope and blown off course north of the Azores before finally limping into port at Cadiz. Le Gentil crossed the Pyrenees and at last set foot on French soil, after eleven years, six months, and thirteen days of absence. Upon his return to Paris he learned that he had been declared dead, his estate looted, and its remains divided up among his heirs and creditors.
That story makes me laugh every time I read it.



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Saturday, June 02, 2012

Review of Parallels and Convergences

In March of 2009 a group of LDS engineers (mostly) gathered for a conference at Claremont Graduate University focusing on Mormon perspectives on engineering. Videos of the talks were made available online, and now Kofford Books has published the talks as a collection of essays. It is edited by A. Scott Howe and Richard L. Bushman (yes, the), the principle conference organizers.

Overview

What does Mormonism have to do with engineering? Is there something about the gospel that improves bridges, batteries, or automobiles? Terryl Givens' introduction, "No Small and Cramped Eternities: Parley Pratt and the Foundations of Mormon Cosmology," which was the keynote address at the conference, provides the basic orientation. He describes Pratt's role in systematizing and popularizing Joseph Smith's teachings, particularly with respect to the eternal nature of element and the physical corporeal nature of God. The result can perhaps be summarized with the following sentence.
What this means is that, by naturalizing Deity, the entire universe of God and humankind, heaven and hell, body and spirit, the eternal and the mundane—all are collapsed into one sphere.
With this idea in place it becomes easier to see God as a master engineer, who possesses and uses technologies that seem miraculous to us. Thus the interest of LDS engineers. The rest of the book follows in this vein with speculative excursions into the nature of spirit matter and how human advances in technology may fulfill prophecy and God's purposes. Essays cover the concept of Gaia, how Mormonism dovetails with transhumanism, a novel argument for the existence of God, and more. The book wraps up with a survey of technological advances by David Bailey. It is a credit to the organizers that they were able to attract the involvement of Richard Bushman, Terryl Givens, and David Bailey.

The introduction to the first section of chapters opens with this arresting idea, which also serves as an additional overarching theme:
In the same way that each person should have the privilege of hearing the gospel in his or her own language, it might be important to consider that technical language is another mode of expression into which we ought to translate our most important concepts.
Although the scientific revolution began with figures like Galileo and Newton, most of what is taught in college courses on any scientific topic dates from the late 19th century onward. With two minor exceptions, none of our canonized scripture was written after 1847. Is it any wonder, then, that scripture and science often do not speak the same 'language'? In fact, Givens goes so far as to suggest that the "humanizing and temporalizing" of God by Joseph Smith's King Follett discourse,
does have one virtue, however—one that we will have the boldness perhaps to someday plumb, in that it lends itself to the world’s best hope for a naturalistic theology. Stripped of all invocations of transcendent entities and transcendent eternities, such a universe should be at least potentially appealing to the hardcore materialists currently working the anti-God/anti-religion circuit [1].
After quoting Richard Dawkins--a prominent scientist and atheist--to the effect that god-like extraterrestrials probably exist, a later essay asserts:
“Eternal progression” is what Mormons call that perhaps unfamiliar version of Darwinian evolution. “God” is what Mormons call those god-like extraterrestrials that didn’t start that way. Whether we ever get to know them or not, there are very probably gods. So says Richard Dawkins. So said Joseph Smith.
Translation indeed!

The book has many interesting ideas--sometimes old ideas presented in new ways. For example, chapter 11, "Spiritual Underpinnings for a Space Program," makes an impassioned defense of space exploration, and the authors envision a future day of planet colonization as fulfilling God's purposes.
It should be apparent that the peopling of other worlds will occur according to natural laws and that the recent outpouring of inspiration regarding space technology might be for the purpose of building a foundation of necessary technologies that will allow us to participate in this great work.
In this essay, planetary colonists become futuristic Jaredites.

This is all heady stuff that's fun to think about. Given the speculative nature of the topics discussed, I suppose it was inevitable that I would find some things to object to. Some of the towers of logic are constructed quickly, but perhaps not durably. I am not an engineer; my background is in the biological sciences. Nevertheless, a few problems stood out to me that I would like to briefly tackle.

Criticisms

One essay claimed that:
Inside each cell, ribosomes are a form of enzyme that are highly interconnected with microtubules. They read RNA strands and manufacture proteins that are building blocks for various cell structures. Microtubules function as both scaffolding and as microprocessors for the cell. From an engineer’s perspective, the microtubules (controller) and ribosomes (factory) would be exactly the sorts of functions where we would want to have a capacity for remote control.
Anybody who has taken a cell biology course will be familiar with the scaffolding role of microtubules. But the notion that they are microprocessors that participate in neural networks, and might even be involved in consciousness, was new to me. Granted, I am not a neuroscientist; but my brief look into the scientific literature suggests that these ideas are being promoted by a small handful of theorists who admit that they don't have solid evidence of these functions yet. Thus I believe that any functional role of microtubules in brain function, apart from their structural role in cells, remains hypothetical at best. As to the broader point, I am not aware of a significant interaction between ribosomes and microtubules under normal circumstances, and I don't know that I've ever heard of microtubules playing a role in the regulation of gene expression--they certainly are not among the chief mechanisms.

You might expect me to bring this up, but in the essay arguing for space exploration the authors write:
The Creation story mentions several points at which God and those involved in the preparation of the new world initiate new phases in the Creation sequence. We can imagine advanced celestial engineers periodically visiting the new world to take samples of the atmosphere, water, soil, and variety of organisms and determining that the planet is ready for the next step. We can see in our mind’s eye advanced celestial biologists selectively engineering certain organisms and releasing them into the environment where they take over the older generations, and slowly bring the biosphere up to a new level of readiness.
Indeed, I think this kind of scenario is envisioned by many Mormons. However, the paragraph immediately preceding the one just quoted says:
Perhaps the evidence shows a kinship of all life because the advanced engineers used the same highly adaptive set of programmable building blocks to construct the bodies of each species. Whether the organisms appeared strictly through emergence from a single ancestor or were physically brought and placed in turn as an already developed species, that kinship would be apparent.
This is an argument that is popular with young-earth creationists and intelligent design proponents alike. It seems quite reasonable because it appeals to common sense and experience, but unfortunately it is not well supported by the evidence. Now is not the time to get into the details, but generally speaking, the sequence divergence for the same gene in different species is proportional to their evolutionary separation. Furthermore, our genomes bear the marks of history; approximately half is made up of broken viruses and other self-replicating (or formerly so) DNA elements, much of which we share with other species in patterns that are easy to understand from the perspective of common descent but difficult to justify from a design perspective. With respect to patterns, the same could be said for the fossil record.

The same essay employs quotations from several Church leaders in support of the idea that life on our planet was brought from a previous one, and this is used as implicit support for the idea that we might reach out and colonize other planets. One of the leaders quoted is Joseph Fielding Smith, who said that the universe is peopled with God's children. Although strictly speaking this quote is not misused, it is misleading in the larger context. President Smith is often said to have predicted that man would not go to the moon, with the Apollo landings as an obvious refutation. But this obscures his larger point which, ironically, was that Earth was created as the dwelling place for humans, and that we have no business trying to colonize the moon or any other planet. He might turn out to be wrong on that too, but he clearly would not have agreed with the thesis of the essay.

Chapter 7, "Quantified Morality," sketches out an idea of how morality can be quantified. The basic principle is that moral decisions maintain the greatest number of future possibilities. This interesting idea is then converted into the concept of entropy, which theoretically could be quantified. To put it simply, destructive behaviors are said to increase disorder (entropy) and righteous behaviors minimize disorder, or even create order (i.e. decreasing entropy). The problem with this that any local decrease in entropy is always more than offset by an increase in entropy elsewhere. Yes, your room is more ordered after you clean it, but any drop in entropy is offset by the energy you use and the heat you produce while doing so. Living organisms are great at increasing entropy. So if changes in entropy are the measure of morality, a desolate planet is morally superior to one filled with life. Yet, even though I think this essay is fundamentally flawed, there are gems of interest. Consider this:
As we contemplate the eternal principle of self-replication as a way to combat entropy at all levels [which I dispute], we can speculate that self-replication also applies to planets—that the inhabitants of one world grow and progress until they eventually achieve the ability to replicate their biosphere on another world: “And as one earth shall pass away, and the heavens thereof even so shall another come; and there is no end to my works, neither to my words. For behold, this is my work and my glory—to bring to pass the immortality and eternal life of man” (Moses 1:38–39).
I never thought of that scripture like that before.

Chapter 8 contains a more mundane error.
We have evidence that our ancestors used spears 5 million years ago, but did not fire-harden the points until 500,000 years ago. Over 100,000 years later, we began making complex blades. Roughly 65,000 years after that, we began using the bow and arrow; 14,000 years after that, we began using gunpowder. Less than a thousand years later, we used a nuclear weapon in war.
This appears to assume that spear use by chimpanzees can be extrapolated to the common ancestor of humans and chimpanzees 5-6 million years ago. Be that as it may, the subsequent chronology puts the first nuclear weapon at roughly 320,000 years ago.

Conclusion

The value of this book is not in its explication of science, which I have noted is suspect at times. To me, the value of the book is the new perspectives that it brings to the scriptures and words of Church leaders, emphasizing the exciting and forward-looking side of our theology. I think it would make a nice gift for your scientifically inclined LDS friend or relative. My personal opinion is that if you want this for yourself, a cheaper electronic copy is a better choice, but I may be biased by the fact that I was already broadly familiar with the contents of the book. Then again, there are several engineers in my ward who might enjoy the book and it's too bad I can't easily lend it to them. In my opinion, more Mormons should be thinking along the lines of this book.

Notes:
This review is based on a complementary Kindle copy that I received.

1. Givens elaborated on this somewhat in the Q&A at the conference.


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