Discussions of Book of Mormon issues and evidences, plus other topics related to The Church of Jesus Christ of Latter-day Saints.

Sunday, September 29, 2019

Stunning Revelation about the Building Blocks of Life, Amino Acids

Foreordained or predestined: complex theological debates have raged around these terms for centuries. Finally science has weighed in, and the correct answer appears to "preordained." Maybe not for the human soul, but at least for the building blocks of mortality, our amino acids. A Sept. 10 news item from the science website, Phys.org, has this intriguing headline: "Scientists find biology's optimal 'molecular alphabet' may be preordained." Here's the story:
An international and interdisciplinary team working at the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology has modeled the evolution of one of biology's most fundamental sets of building blocks and found that it may have special properties that helped bootstrap itself into its modern form.

All life on Earth uses an almost universal set of 20 coded amino acids (CAAs) to construct proteins. This set was likely "canonicalized" or standardized during early evolution; before this, smaller amino acid sets were gradually expanded as organisms developed new synthetic proofreading and coding abilities. The new study, led by Melissa Ilardo, now at the University of Utah, explored how this set evolution might have occurred.

There are millions of possible types of amino acids that could be found on Earth or elsewhere in the universe, each with its own distinctive chemical properties. Indeed, scientists have found these unique chemical properties are what give biological proteins, the large molecules that do much of life's catalysis, their own unique capabilities. The team had previously measured how the CAA set compares to random sets of amino acids and found that only about 1 in a billion random sets had chemical properties as unusually distributed as those of the CAAs.

The team thus set out to ask the question of what earlier, smaller coded sets might have been like in terms of their chemical properties. There are many possible subsets of the modern CAAs or other presently uncoded amino acids that could have comprised the earlier sets. The team calculated the possible ways of making a set of 3-20 amino acids using a special library of 1913 structurally diverse "virtual" amino acids they computed and found there are 1048 ways of making sets of 20 amino acids.

In contrast, there are only ~ 1019 grains of sand on Earth, and only ~ 1024 stars in the entire universe. "There are just so many possible amino acids, and so many ways to make combinations of them, a computational approach was the only comprehensive way to address this question," says team member Jim Cleaves of ELSI. "Efficient implementations of algorithms based on appropriate mathematical models allow us to handle even astronomically huge combinatorial spaces," adds co-author Markus Meringer of the German Center for Air and Space.

As this number is so large that they used statistical methods to compare the adaptive value of the combined physicochemical properties of the modern CAA set with those of billions of random sets of three to 20 amino acids. What they found was that the CAAs may have been selectively conserved during evolution due to their unique adaptive chemical properties, which help them to make optimal proteins, in turn helping organisms that could produce those proteins become more fit.

They found that even hypothetical sets containing only one or a few modern CAAs were especially adaptive. It was difficult to find sets even among a multitude of alternatives that have the unique chemical properties of the modern CAA set. These results suggest that each time a modern CAA was discovered and embedded in biology's toolkit during evolution, it provided an adaptive value unusual among a huge number of alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs, ultimately leading to the modern set.

If true, the researchers speculate, it might mean that even given a large variety of starting points for developing coded amino acid sets, biology might end up converging on a similar set. As this model was based on the invariant physical and chemical properties of the amino acids themselves, this could mean that even life beyond Earth might be very similar to modern Earth life. Co-author Rudrarup Bose, now of the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, further hypothesizes, saying "Life may not be just a set of accidental events. Rather, there may be some universal laws governing the evolution of life."
In other words, our set of 20 coded amino acids, the key toolkit of life, displays uncanny suitability for making complex proteins. They are so wonderfully tuned that we might even be able to expect life elsewhere in the universe to be be using pretty much the same set. As Dr. Rudrarup Bose put it, "Life may not be just a set of accidental events." Our amazing molecular machinery appears to have been beautifully endowed with ideal properties by "some universal laws" or something.

The study referred to by Phys.org is Melissa Ilardo et al., "Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets," Scientific Reports, volume 9, article number 12468 (28 Aug. 2019). The authors focus on only 3 of the most important (among many) properties of amino acids related to solubility, acidity (pKa, the logarithmic acid dissociation constant), and size.  These parameters are viewed as part of a chemical space (think of a 3D chart with axes for each parameter). The goal for a useful amino acid toolkit would be to cover a broad space "smoothly" without heavy clustering. Amino acids that are well dispersed in that 3D space would appear to be more capable of achieving the diverse needs of proteins than ones that gives less ideal distribution in chemical property space. Here is an excerpt regarding the approach:
To describe the properties of the molecules in the computed sets, we used the same descriptors previously reported: van der Waals volume (Vvdw), logarithmic acid dissociation constant (pKa, considered specifically over the range from 2–14 here) and partition coefficient (logP), which were selected based on their ability to characterize the functional chemistry space of α-amino acids (cf. refs3,37). Vvdw is simply a measure of the volume of space occupied by the amino acid, which is expected to play a role in mediating steric interactions. LogP describes the affinity of a molecule to a hydrophilic or hydrophobic solvent. In the context of protein structure, this is an important factor in protein folding, and is essential for the heterogeneous nature of protein surface potentials, which is essential for catalysis. pKa describes the pH at the mid-point of a proton transfer by the amino acid side chain, which influences the charged state of an amino acid residue. This in turn affects a host of interactions within and among proteins and their substrates.

While thousands of additional descriptors exist38, we selected what we considered to be fundamental properties that define molecular interactions. This selection was made to minimize bias introduced by considering instead the properties through which we functionally characterize amino acids in modern biochemical contexts. Additionally, these properties are reliably predicted and quantified through chemical property prediction software, an important consideration given the theoretical and computational nature of our data set. This analysis is exploratory, requiring broad, and simplified, choices of molecular descriptors. A previous publication20 offers a specific investigation that justifies the descriptors relating to size, pKa and hydrophobicity, particularly in the light of older work39 that has been built on productively40,41. It is striking that such simple metrics are able to classify amino acid chemical space so effectively2,3.

We used the definition of optimality that was previously introduced to test the CAA alphabet, as described in Ilardo et al.3, namely that more “optimal” sets are those that have broader range and/or evenness of coverage of chemical space. “Better” or “more optimal” sets are those that cover chemical space in the three descriptor categories (Vvdw, pKa and logP) both more broadly and evenly than a comparison set.

Some Background Thoughts

One of the many mysteries of life on earth is the way DNA encodes directions to create the many complex proteins that create and maintain our bodies. All the mind-boggling complexity of proteins and the bizarre machines they create are achieved using just 20 different building blocks called amino acids. A simple coding system in our DNA relies on different combinations of just four bases, adenine (A), guanine (G), cytosine (C), and thiamine (T), to represent any of the 20 amino acids by a "codon" made from a sequence of three bases. Long sequences of these codons encode the genes, proteins, regulators, etc. in our DNA, and the resulting series of amino acids joined together when proteins are made from our genes create amazing tools that carry out numerous essential functions. The coding of information with four bases to define a series of amino acids seems so simple but gives such incredible complexity in the end. The way a series of amino acids can become twisted, wrapped, and folded layer upon layer into bizarre 3-dimensional shapes is a topic for wonder and much further research, but it all depends on the properties of our 20 basic building blocks. But why those 20 amino acids? Here's a table showing the chemical structure of these 20 coded amino acids from Particle Sciences.

Looking at the list of amino acids, it's easy for pundits to see some slop and inefficiency. Some of the 20 amino acids are very similar. It's easy to think that a smaller set could be used that could make our DNA much more efficient. It's easy to think that the apparent inefficiency is what you can expect when random choices are made in nature that lead to something that works that a hypothetical intelligent designer could have made much more efficient. An example is provided by Stuart Cantril,  "They’d none of them be missed – why 20 amino acids and not 15?," a post on a leading chemistry blog at Nature.com, The Skeptical Chymist, from 2008. Cantril suggests that we don't really need all 20 amino acids and would have a far more efficient set if nature had been smart enough to just use 15. I don't know if the new study changes any of the speculations raised there, but if indeed all 20 amino acids appear to be optimized and cannot readily be improved by swapping them out for others, then it would seem that the subtle differences between some of them must play important functional roles, perhaps like a Phillips head versus a slotted (flat head) screwdriver. A good toolkit needs both (though a screwdriver with many detachable heads is the more intelligent choice).

Cantril argues, for instance, that several amino acids with hydrocarbon side chains of different length seem redundant.  "Do we really need 4 different hydrocarbon side chains (methyl, isopropyl, sec-butyl, isobutyl)? ... Get rid of two of them – probably a long one and a short one." This may have been answered adequately by  Andrew J. Doig in "Frozen, but no accident – why the 20 standard amino acids were selected," FEBS Journal, Volume 284, Issue 9  (May 2017): 1296-1305. Doig discusses the four amino acids with hydrocarbon side chains, Val, Leu, Ile, Phe (valine, leucine, isoleucine and phenylanaline) and explains why they are needed in spite of being similar:
These hydrocarbon side chains are clearly present to drive protein folding by forming hydrophobic cores, yet why exactly these were selected deserves an explanation. Firstly, why are there so many hydrocarbon side chains, rather than just, say, Leu? Multiple hydrocarbon side chains may be used as they are required to fill a protein core with no clashes and no holes. A variety of pieces are required to fit all the gaps within a protein core. Each can adopt a number of rotamers [variants of a molecule that differ in how a portion of the molecule has been rotated] with similar energies, thus giving a range of possible shapes for each side chain. Thus, Leu and Ile are both needed to increase the range of possible hydrocarbon 3D shapes, despite Ile being more costly to synthesise....

Val, Leu, Ile and Phe are striking in that they all have branched carbons, rather than straight chains. Using a branch gives one fewer dihedral angle to be fixed compared to a straight chain. Side chains therefore enter a protein core not just because they are hydrophobic, but also because they do not lose too much conformational entropy when they fold. Similarly, rings are rigid, so Phe has a large hydrocarbon surface and only two bonds to be fixed.

Hydrocarbon side chains larger than Phe, Ile or Leu may not be used, as they would be less soluble as amino acids. A cyclohexane ring is also less soluble than a benzene ring, so Phe is used, rather than cyclohexylalanine.
The point is that achieving the desired 3D shape of the protein and having it be stable, not "mush" that changes shape unpredictably, is vital for protein function, and these related amino acids help give the 3D shape needed of the units within the folded protein to fill up the space inside and do that efficiently without losing other properties such as solubility.

On the other hand, Doig is not impressed with methionine. He  argues that this sulfur-containing amino acid might have been more useful back when the earth lacked an oxygen-rich atmosphere, but now is a non-ideal amino acid that we are "stuck" with.  But in light of Melissa Ilardo et al.'s publication, it would seem to be a unique structure gives some significant benefits that can't be obtained without it. Of methionine specifically, the authors write:
Conversely, Met [methionine] appears to be advantageous in small set sizes compared to the possibilities within the XAAs [xeno amino acids, the set of alternate amino acids considered]. However, it is not until larger set sizes that Met begins to become adaptive when looking at the coded set. This could indicate that Met does not offer an enormous adaptive advantage to the encoded set as a whole, however, there are very few possibilities within the XAA library that have similar chemical properties to Met, and therefore Met is uniquely advantageous to encoded sets.
The authors also point how how leucine and isoleucine play an important cooperative role in their extensive numerical analysis, making it appropriate that the code amino acids would include both, in spite of the tendency of chemists to see them as nearly the same.

Fascinating work, intriguing implications. Thanks be to "universal laws."

Update, Oct. 1, 2019
Andrew Doig's commentary on the role and selection of cysteine (Cys) as a coded amino acid is also noteworthy, especially the second paragraph below:
A key function of proteins is to bind metals. Soft metals, such as copper, zinc and cadmium, bind more tightly to sulfur than to oxygen. Cys may therefore have been selected for its metal binding properties, despite its high biosynthetic cost (Table 1). In particular, Cys is commonly used to bind iron‐sulfur clusters. These cofactors are found in a wide variety of metalloproteins, are playing crucial roles in metabolism and are very ancient [43]. The SH side chain is also an effective nucleophile; it has a lower pKa than OH, readily forming S.

Cys is the only side chain able to perform redox reactions, by forming disulfide bonds to stabilise folded proteins. Cys was selected in an anaerobic environment, however, where disulfide bond formation would have been rare or nonexistent. It is therefore not plausible that Cys was selected for its ability to form disulfides, and its subsequent use for this purpose, starting very approximately 1.5 billion years later after the Great Oxidation Event, is a lucky accident.
Lucky accident, or "preordained" wisdom from a wise universal law or something? Every aspect of life itself, from the miracle of efficient carbon synthesis in stars, the balance between electromagnetic and gravitational forces that allow stars to exist perched on the razor's edge between violent explosion on one hand and gravitational collapse into oblivion on the other, the many wonders of water, the architecture of Earth's core and its protective magnetic field, and the many miracles of amino acids and proteins (not the least of which are the bizarre and intricately organized "lucky beyond imagination" machinery of FTP synthase and the spliceosome), all calling attention to lucky accident after lucky accident in ways that suggest that our cosmos and this planet has been rigged for life.

To me, it's beyond the question of "could this have happened by chance?" The real question, after pondering something like the splicesome that turns our 20,000 genes into over 100,000 useful proteins by cutting and pasting our encoded amino acid sequences into new beneficial and even essential proteins, is this: "How are such incredible designs, such mind-boggling gadgets and solutions, even possible?"

That a universe tuned to allow stars to exist could also be tuned to make stars efficient carbon creators is amazing. That it could also give us atoms that could provide us with a nearly universal solvent so vital for life that has the incredibly rare, even bizarre feature of expanding when it freezes -- so that sinking ice doesn't fill the oceans from the bottom up but stays on top to insulate them -- is fortunate indeed. And after all that, to have amino acids that could not only be so efficient to support all the intricacies of encoding proteins and ensuring that the proteins fold and function properly in their aqueous environment, but could also give us a protein-based cut-and-paste machine (the spliceosome, as discussed here previously) that mixes and matches amino acids from our genes to allow many more proteins to be encoded beyond what are fit into the DNA in the tiny nucleus of the cell, and do this in a way that doesn't destroy needed proteins or create random lethal junk, well, it's just getting lucky beyond belief, or rather, lucky in a way that should strengthen belief for those open to the possibility of the existence of a Creator.

Related reading:
  • "Protein Structure," from Particle Sciences. 2009.  Describes the basics of protein structure, including primary, secondary, teriary, and quaternary structure, with some hints about how the different amino acids affect the highly complex and intricate structure that a protein chain can end up having after assembly.

Monday, September 23, 2019

Keeping Up with the Book of Abraham: The New Pearl of Great Price Central Website

For those interested in the Book of Abraham, a great new website provides regular articles the emerging evidences of ancient origins of that sacred text. Those already using Book of Mormon Central (BookofMormonCentral.org) should be pleased with the efforts underway at Pearl of Great Price Central (PearlofGreatPriceCentral.org). Regarding the Book of Abraham, the website provides useful introductory information, given in part below:=
Since at least the 1960s, Latter-day Saint scholars have explored the text of the Book of Abraham to see what clues might exist that situate it in a plausible ancient setting. They have also argued for the legitimacy of Joseph Smith’s interpretation of the facsimiles as Egyptological knowledge has progressed. These efforts, in conjunction with ongoing progress in the fields of Egyptology and Near Eastern archaeology, have uncovered numerous points of convergence between the text and the ancient world. Evidence for Joseph Smith’s interpretation of the facsimiles has also come to light. These various lines of evidence do not “prove” the Book of Abraham is true, but they do help us situate the text in a plausible ancient environment, inform how we read the text, and positively impact our evaluation of Joseph Smith’s claims to prophetic inspiration.

To aid readers in these endeavors, Book of Mormon Central will be publishing a series of short essays as part of its new Pearl of Great Price Central research initiative. This series will (1) highlight some of the more noteworthy convergences between the Book of Abraham and the ancient world, (2) explore how Joseph Smith’s interpretations of the facsimiles harmonize with modern scholarship, and (3) provide an overview on what is known about the coming forth and translation of the Book of Abraham.

These short articles aim to provide readers with useful insights as they explore this rich and rewarding text and to bolster confidence in Joseph Smith’s claim to have translated the writings of Abraham. The articles have been kept deliberately short so as to not overwhelm readers with sometimes technical and arcane information about ancient languages and cultures. For those wanting to dive deeper into these matters, suggested readings will be provided at the end of each article.

In addition, a non-exhaustive bibliography has been assembled to provide readers with a sense of the scope of research Latter-day Saints have devoted to the Book of Abraham over the span of many years and to make this research readily accessible for interested readers of this book of scripture.

Finally, a newly reformatted study edition of the Book of Abraham has been prepared to help facilitate a close, engaged reading of the text. While paying attention to reliable scholarship is important in approaching the Book of Abraham “by study and also by faith” (Doctrine and Covenants 88:118), it is crucial not to overlook the text itself.

There is still much we do not know when it comes to how precisely Joseph Smith translated the Book of Abraham. There are likewise still remaining questions surrounding Joseph Smith’s interpretations of the facsimiles and the ancient world of Abraham. This project does not presume to answer all the questions people may have about the Book of Abraham, its coming forth, and its contents. Rather, it hopes to equip seekers and honest questioners with the best, most reliable scholarly resources available and provide answers or insights where possible.
Below are the posts on the Book of Abraham offered there so far:

Jews in Ancient Egypt

This post explores the existence of Jews in ancient Egypt and the possible role they may have played in preserving an account related to the Book of Abraham. The papyri Joseph Smith received "were written in a period when Egypt was ruled by a dynasty of Greek rulers who reigned from circa 300–30 BC." But while Abraham would have written his record long before that, "there is plenty of historical evidence to suggest a plausible way in which those writings could have been transmitted into Egypt."

The Blood of the Canaanites

Abraham 1:21–22 mentions a Pharaoh who was Semitic, or rather, was of "of the blood of the Canaanites by birth." Based on what we know today of ancient Egypt and its Fourteenth Dynasty, that little detail is surprisingly plausible.  One issue that is not discussed in the article is this: Was any of the information discussed in this post available to scholars in 1835? From my searching on Google Books, I don't think so, but would appreciate your input. 

Shulem, One of the King’s Principal Waiters

Figure 5 in Facsimile 3 of the Book of Abraham is identified as “Shulem, one of the king’s principal waiters.” This post explores the plausibility of an Egyptian official of this kind having the apparently Semitic name Shulem.

Zeptah and Egyptes

Book of Abraham manuscripts offer two names for women in early Egyptian history, Zeptah and Egyptes, and the significance and plausibility of these names are discussed. 

Relief of the god Sobek

Sobek, The God of Pharaoh

The Book of Abraham identifies “the god of Pharaoh” as being one of the idolatrous gods worshipped by Abraham’s kinsmen (Abraham 1:6, 9, 13, 17), and in Figure 9 of Facsimile 1, that god is depicted as a crocodile. The crocodile god Sobek of ancient Egypt is a surprisingly plausible candidate for "the god of Pharaoh."

The Idolatrous God of Elkenah

The Book of Abraham mentions the pagan god of Elkenah (Abraham 1:6). This non-biblical name could be a plausible fit for one of the pagan gods worshiped by Abraham's kinsmen. It appears that an ancient god of this name has been identified.

Ur of the Chaldees

The Book of Abraham begins “in the land of the Chaldeans” (Abraham 1:1) and makes reference to “Ur of the Chaldees” (Abraham 1:20; 2:1, 4, 15; 3:1). Where was that? "Taken together, the evidence from the Book of Abraham text and external archaeological and inscriptional sources can reasonably point us in the general direction of modern northern Syria and Turkey as the ancient homeland of Abraham. While there are many questions that scholars still grapple with, enough evidence has surfaced over the years that paints a generally reliable picture of the historical and geographical world described in the Book of Abraham."

The Plain of Olishem

The opening chapter of the Book of Abraham mentions a location named “the plain of Olishem” (Abraham 1:10). There is an excellent candidate for this ancient place in a plausible location. A fascinating, recent discovery.

Human Sacrifice

The Book of Abraham tells of Abraham almost being sacrificed to “dumb idols” and “strange gods” (Abraham 1:7–8). The form of sacrifice was said to be “after the manner of the Egyptians” (vv. 9, 11). Was human sacrifice unknown in ancient Egypt as some have claimed? No, there's strong evidence for the plausibility of this practice under some conditions and times.

Abraham by Emily Gordon side-by-side with an image of the statue of Idrimi via the Maxwell Institute.

Abraham and Idrimi

Explores some intriguing parallels between the autobiography of Idrimi and Abraham's account.

As you'll see from reading these articles, the Book of Abraham in many ways appears to have roots in antiquity with an understanding of some aspects of the ancient Egyptian world. Many details, such as the significance of the Jewish colony at Elephantine in ancient Egypt (and their willingness to build their own temple outside of Jerusalem, much like Nephi did in the New World) probably could not have been known to Joseph Smith. If you are aware of sources available in 1835-1842 for any of these potential evidences of antiquity discussed at Pearl of Great Price Central that could have informed Joseph Smith, were he creator and not translator of the Book of Abraham account, please let me know.

Thursday, September 19, 2019

President Nelson Shares Some Background Information for Recent Policy Adjustments

While some within and without the Church will disagree with the Church's position regarding same-sex marriage, President Nelson's comments this week at BYU help give some insight into the motivations behind some recent policy adjustments. For those who have been patient with this process, the perspective and transparency President Nelson offers may be especially appreciated. It also may be helpful for those wondering why the Church would make an adjustment that seems like a retreat. Below is an excerpt from his talk, "The Love and Laws of God," given at a BYU devotional on Sept. 17, 2019. The video and text are available at BYU.edu.
Though we of the First Presidency and Quorum of the Twelve Apostles cannot change the laws of God, we do have the charge to “build up the church, and regulate all the affairs of the same in all nations.” Thus, we can adjust policy when the Lord directs us to do so. You have recently seen such examples. Because the Restoration is ongoing, policy changes will surely continue.

Perhaps I can illustrate this through policy adjustments regarding those who identify themselves as lesbian, gay, bisexual or transgender (LGBT) and their children. (I realize that other initials could be added to this acronym, but LGBT should suffice for the purposes of this message.)

Consider the policy announced in November 2015 related to the advisability of baptism for the children of LGBT parents. Our concern then, and one we discussed at length and prayed about fervently over a long period of time, was to find a way to reduce friction between gay or lesbian parents and their children.

Because parents are the primary exemplars for their children, we did not want to put young children in the position of having to choose between beliefs and behavior they learned at home and what they were taught at Church. We wanted to facilitate harmony in the home and avoid pitting children and parents against each other. Thus in 2015, the policy was made to assist children and their parents in this circumstance, namely that children being raised by LGBT parents would not automatically be eligible for baptism at age eight. Exceptions to this policy would require First Presidency approval.

The First Presidency and Quorum of the Twelve have continued to seek the Lord’s guidance and to plead with Him in behalf of His children who were affected by the 2015 policy. We knew that this policy created concern and confusion for some and heartache for others. That grieved us. Whenever the sons and daughters of God weep—for whatever reasons—we weep. So, our supplications to the Lord continued.

We also took note of LGBT parents who sought permission from the First Presidency for their children to be baptized. In nearly every case where the LGBT parents agreed to teach their children about—and be supportive of—the covenant of baptism, the requested exception was granted.

As a result of our continued supplication, we recently felt directed to adjust the policy such that the baptism of children of LGBT parents may be authorized by bishops without First Presidency approval, if the custodial parents request the baptism and understand that a child will be taught about sacred covenants to be made at baptism.

We also determined that LGBT parents may request that a baby be named and blessed by one who worthily holds the Melchizedek Priesthood. It is important that these parents understand that ward members will contact them periodically, and that when a child who has been blessed reaches eight years of age, local leaders will recommend that the child be baptized.

Finally, we also clarified that homosexual immorality would be treated in the eyes of the Church in the same manner as heterosexual immorality.

Though it may not have looked this way to some, the 2015 and 2019 policy adjustments on this matter were both motivated by love—the love of our Heavenly Father for His children and the love of the Brethren for those whom we serve.

Because we feel the depth of God’s love for His children, we care deeply about every child of God, regardless of age, personal circumstances, gender, sexual orientation, or other unique challenges.
This may be welcome information on a sensitive issue that many of members of the Church care about. Even for those who object to the original policy from 2015, understanding the motives behind it as well as the reasons for the more recent adjustment may be helpful. 

Rethinking Enemies

One of the challenges for me as I gradually prepare to return to the United States, after my eight years in China, is the animosity here. Too many people treat those who disagree with them on some issues as inherently bad people who deserve to be hated and cast out or silenced. When noted figures die, there can be rejoicing over the death if that person was on the unenlightened side of an issue or two. I've seen families divided in animosity over political or moral differences, where activists escalate issues into matters of absolute right and wrong, and feel obliged to denounce those who they think are wrong on some issue, as if their views are self-evident truth with no room for debate.  If you disagree, you're not just wrong or stupid, you're an enemy.

In one unnecessary schism between people who once were close, I saw a reasonable plea for civility in dialog be overtly rejected with the explanation that appeals to civility are how oppressors secure their privilege, silence opposition, and stop "progress." Sigh. It's becoming a difficult country for people that are used to healthy debates on a wide variety of topics. Now the key skill seems to be avoiding conversations on any topic that might be important to someone lest a slip of the tongue or a sincerely expressed dissenting opinion result in outrage and hate. Too many seem to lack the power to imagine that those who disagree might not be demonic puppy slayers, but reasonable people who see things differently. This applies to social issues, politics, religion, and everything else.

Within the Church, it's important for conservative members like myself to remember that those with different views on the Restoration, Joseph Smith, the scriptures, and so forth may not be apostates seeking to lure others onto the road to spiritual oblivion. In many cases, I've found that I was painfully wrong when I assumed bad intentions of someone with strongly different viewpoints or who did things that offended me. I am not saying that it's wrong to defend core principles or to question bad decisions or seemingly errant doctrines, but rather that I'm learning that it's often a mistake to consider those on the other side of an argument to be enemies. Seeing them as brothers and sisters with a reasonable but different (and possibly dead wrong) viewpoint seems like the more reasonable and charitable position, one that is not easy for me to live up to. But I want to overcome that.

If we are going to learn anything from the Book of Mormon, I suggest it should be the message that Christ emphasized right at the beginning of His ministry to the Nephite and Lamanite peoples of the ancient Americas, as recorded in 3 Nephi 11. Here the Savior addressed the issue of baptism, which had been a topic of contention among the Nephites. He explained the doctrine and practice of baptism, and then warned them against the spirit of contention that had been too common in their religious disputes:
[28] And according as I have commanded you thus shall ye baptize. And there shall be no disputations among you, as there have hitherto been; neither shall there be disputations among you concerning the points of my doctrine, as there have hitherto been.
[29] For verily, verily I say unto you, he that hath the spirit of contention is not of me, but is of the devil, who is the father of contention, and he stirreth up the hearts of men to contend with anger, one with another.
[30] Behold, this is not my doctrine, to stir up the hearts of men with anger, one against another; but this is my doctrine, that such things should be done away.
The Book of Mormon illustrates in many ways how the Adversary uses contention as a tool to achieve his ends, including contention among people who fashion themselves as righteous and orthodox.  Seeing those who disagree with us as enemies and feeling anything close to hate or anger toward them may be falling into a trap meant to hurt us all. There are genuine enemies and people against whom we need protection, but too often, our treatment of others as enemies is unjustified and dangerous.

A beautiful story about changing one's feelings toward apparent enemies comes from the October 2018 General Conference talk of M. Joseph Brough, "Lift Up Your Head and Rejoice":
To help us travel and triumph over our hard times with such glimpses of eternity, may I suggest two things. We must face hard things, first, by forgiving others and, second, by giving ourselves to Heavenly Father.

Forgiving those who may have caused our hard thing and reconciling “[our]selves to the will of God”  [2 Nephi 10:24] can be very difficult. It can hurt most when our hard thing is caused by a family member, a close friend, or even ourselves.

As a young bishop, I learned of forgiveness when my stake president, Bruce M. Cook, shared the following story. He explained:

“During the late 1970s, some associates and I started a business. Although we did nothing illegal, some poor decisions, combined with the challenging economic times, resulted in our failure.

“Some investors filed a lawsuit to recover their losses. Their attorney happened to be a counselor in my family’s bishopric. It was very difficult to sustain the man who seemed to be seeking to destroy me. I developed some real animosity toward him and considered him my enemy. After five years of legal battles, we lost everything we owned, including our home.

“In 2002, my wife and I learned that the stake presidency in which I served as a counselor was being reorganized. As we traveled on a short vacation prior to the release, she asked me whom I would choose as my counselors if I were called as the new stake president. I did not want to speak about it, but she persisted. Eventually, one name came to my mind. She then mentioned the name of the attorney we considered to have been at the center of our difficulties 20 years earlier. As she spoke, the Spirit confirmed that he should be the other counselor. Could I forgive the man?

“When Elder David E. Sorensen extended to me the call to serve as stake president, he gave me an hour to select counselors. Through tears, I indicated that the Lord had already provided that revelation. As I spoke the name of the man I had considered my enemy, the anger, animosity, and hate I had harbored disappeared. In that moment, I learned of the peace that comes with forgiveness through the Atonement of Christ.”

In other words, my stake president did “frankly forgive” him, like Nephi of old [1 Nephi 7:21]. I knew President Cook and his counselor as two righteous priesthood leaders who loved one another. I determined to be like them.
I love how the power of the Jesus Christ can help us overcome the natural man's tendency to hate and treat adversaries or opponents as enemies. In some cases, that victory is a true miracle and of the greatest miracles that occur in this life. To love those and forgive those whom we think have wronged us or are dead wrong on a critical issue important to us is a blessing that brings peace and heals relationships. We need more of that in the world these days.

Sunday, September 15, 2019

The Book of Mormon's Interesting Uses of Isaiah 25:8, "Death Swallowed Up"

There's no question that the Book of Mormon has great intertextuality with the Bible, frequently drawing upon its language to convey its stories and concepts in familiar sacred language. The subtle allusions and variations that occur can often lead to significant insights into how we can better understand and apply the text of the Book of Mormon.

An interesting example of such intertexuality (a.k.a. "blatant plagiarism" if your goal is the easy one of finding fault above all) was recently discussed at Book of Mormon Central in the post, "'Swallowing Up' Death in Isaiah, 1 Corinthians, and the Book of Mormon," Sept. 3, 2019. Here the post draws upon an outstanding publication by Dr. David Larsen of BYU, “Death Being Swallowed Up in Netzach in the Bible and the Book of Mormon,” BYU Studies Quarterly, 55/4 (2016):123–134.

The Book of Mormon, like Paul in 1 Corinthians 15, draws upon a beautiful and hopeful Old Testament passage, Isaiah 25:8, where we read that death will be "swallowed up in victory." The interesting thing is the Hebrew word that was translated as victory in the KJV of Isaiah 25:8: netzach (Strong's H5331). This fascinating word can be translated in other ways, and some of these other ways are consistent with subtle variations in the 3 instances of the Book of Mormon that allude to that passage.

Abinadi in Mosiah 16:7–8 speaks of death being swallowed up in Christ, consistent with other times in the Bible where the netzach of Israel is the "strength" of Israel or the “Triumpher” or “Overcomer,” a great title for the grand Victor, Jesus Christ.

Next Aaron in Alma 22:14 teaches that "the sting of death should be swallowed up in the hopes of glory” (Alma 22:14). According to Book of Mormon Central,
It is therefore fascinating that netzach can also mean “splendor, glory.” In addition to the translations of 1 Samuel 15:29 already mentioned, in that passage netzach frequently gets translated as “Glory of Israel” (see, e.g., NRSV, ESV, NIV), and at least one translation even renders it “Hope of Israel.” The term netzach, translated as “strength” in KJV, but more commonly as “glory” in modern translations (e.g., NRSV, LEB), appears closely with “hope” (tohal) in Lamentations 3:18.
Finally, Mormon in describing the willingness of the Anti-Nephi-Lehites to sacrifice their lives states that to them “death was swallowed up … by the victory of Christ” (Alma 27:28).
Here, Mormon, perhaps drawing on language from Alma’s record, brings the expressions of Isaiah and Abinadi together by adding that it was the victory (netzach) of Christ, rather than replacing netzach with Christ. This fuller articulation may have emerged among the Nephites as an effort to harmonize both Isaiah and Abinadi’s teachings and clarify how death is swallowed up both in victory and in Christ
Sometimes there's much to be learned by considering how the Hebrew of Isaiah or other writers may have been applied in the Book of Mormon. These subtleties suggest the Book of Mormon authors were aware of the range of meaning available for netzach. 

Further Notes:

"Swallowed up in Christ" is not unique to the Book of Mormon. The Scottish pastor Samuel Rutherford's writings have it in 1803 on pp. 411-412 of his 739-page tome, Christ Dying and Drawing Sinners to Himself (Glasgow: Samuel and Archibald Gardner, 1803), though his context may have little to do with Isaiah 25:8, but speaks of how our earthly desires can be swallowed up in Christ as we follow him:

Google Books does not show any pre-1830 instances of "swallowed up in hopes of glory," or "swallowed up in hope." But a search of Early English Books Online (EEBO) shows "swallowed up in hope" does occur in some Early Modern English sources such as a 1605 poem that also links "glorious realm" to the word "swallow."

One of many early examples of a discussion of death being swallowed up is from the 1654 book, Thanatoktasía, or, Death disarmed: and the grave swallowed up in victory by Anthony Tuckney.

Sunday, September 08, 2019

Bad Math and the Premature Dismissal of Brian Stubbs' Work on Uto-Aztecan Languages

In my previous post on the negative review by BYU professor Chris Rogers regarding Brian Stubbs' work on ancient connections between Uto-Aztecan languages and three Old World languages, some comments point to Rogers' Table 6 as key evidence for dismissing the correspondences detailed by Stubbs. Table 6 appears to present evidence that chance similarities could account for what Stubbs has found.

As a reminder, the key to establishing genuine connections between ancient languages is not finding a bunch of random words that can appear to be related, but establishing meaningful relationship with many examples of consistent sound changes. Here is an excerpt from Wikipedia's article on the "Comparative Method" describing how to establish legitimate connections:

Step 2, establish correspondence sets

The next step involves determining the regular sound-correspondences exhibited by the lists of potential cognates. For example, in the Polynesian data above, it is apparent that words that contain t in most of the languages listed have cognates in Hawaiian with k in the same position. This is visible in multiple cognate sets: the words glossed as 'one', 'three', 'man', and 'taboo' all show this relationship. This situation is termed a regular correspondence between k in Hawaiian and t in the other Polynesian languages. Similarly, in those data a regular correspondence can be seen between Hawaiian and Rapanui h, Tongan and Samoan f, Maori ɸ, and Rarotongan ʔ.

Mere phonetic similarity, as between English day and Latin dies (both with the same meaning), has no probative value.[31] English initial d- does not regularly match Latin d-[32]—it is not possible to assemble a large set of English and Latin non-borrowed cognates such that English d repeatedly and consistently corresponds to Latin d at the beginning of a word—and whatever sporadic matches can be observed are due either to chance (as in the above example) or to borrowing (for example, Latin diabolus and English devil—both ultimately of Greek origin[33]). English and Latin do exhibit a regular correspondence of t- : d-[32] (where the notation "A : B" means "A corresponds to B"); for example,[34]
 English   ten   two   tow   tongue   tooth 
 Latin   decem   duo   dūco   dingua   dent-  

If there are many regular correspondence sets of this kind (the more the better), then a common origin becomes a virtual certainty, particularly if some of the correspondences are non-trivial or unusual.[21]

This is at the heart of what Stubbs has done, presenting extensive data on widespread, consistent sound changes that link cognates between Uto-Aztecan languages and three Old World languages (that happen to have Book of Mormon ties). Many are non-trivial, detailed, involve lengthy words and sometimes surprising parallels in meanings and multiple meanings. But Rogers seems to treat this work as amateur excitement over chance parallels.

Suppose, for example, that the German had gone completely extinct a couple hundred years ago and only now had scholars recovered and deciphered a handful of texts. Suppose you are working on the language and begin to notice parallels with English, such as "das Buch" = book, "kochen" = to cook, and "suchen" = to seek. These show a consistent relationship between German "ch" and English "k," which is far more meaningful than if book, cook, and seek seemed to align with, say, "ubakr," "kouki," and "zeqqol." With chance finds, of course, it is unlikely that consistent patterns will arise. So even if your list of cognates was still small, the pattern of sound changes could help you realize that perhaps more than chance was at play.

But chance is always a possibility. In fact, false cognates due to chance can be found without too much trouble. In Chinese, "fei" can mean "fee," but there's no evidence that any legitimate relationship is behind this and many other chance parallels. How often can chance lead to a false cognate? Stubbs suggests it is 1% to 3% of the time. OK, but I think it would be very hard to contrive English-Chinese parallels for 1% of either language. But accepting that range, Rogers crunches some numbers to suggest that the 1500+ cognates presented by Stubbs are meaningless. To do this, he considers that the Uto-Aztecan language family has 30 languages and that Stubbs is scanning 3 Old World languages, which greatly increases the potential for finding parallels. Rogers argues that at a 3% rate of chance cognates, we might expect nearly 5,000 chance parallels, making 1,500 completely pathetic. Here's the relevant portion of his paper from pages 255-256 (click to enlarge):

There's clearly something wrong when he reports that 2,598 similarities are expected by chance alone, for that number is the number with a minus sign (i.e., 2,598 less than zero) is the number Table 6 shows remaining after subtracting the actual calculated number of possible false cognates, 4,126, from the number of cognates presented by Stubbs, 1,528. But much more trouble is occurring here than just reporting the wrong sum. This number of over 4,000 false cognates is based on rather spurious math, IMO.

The first additional problem is that Rogers is using the wrong base in calculating potential false cognates. He treats 1,528 as that base, but the base should be the number of words in the language family being considered, which is an even bigger number. But let's assume that Rogers math is correct and that there's a base of only 1,528 Uto-Aztecan words, incorrectly implying that Stubbs is proposing that 100% of the UA vocabulary is related to Egyptian and Semitic. Even in that case, Rogers obliterates any cause for excitement by multiplying the upper limit of 3% chance of a random correspondence by 30 Uto-Aztecan languages and by 3 Old World languages, in other words, 0.03 * 30 * 3 = 2.70, giving 270% of the entire vocabulary being subject to false cognates with Stubb's 3 Old World languages by chance. That's how 1,528 cognates from Stubbs becomes a potential 4,126 false cognates in the crazy math of Table 6. Something is out of touch with reality here.

Part of the problem here is that the 30 languages of Uto-Aztecan are all related, and that Stubbs is not creating an additional entry and claim for each related cognate in each language. Worse than double jeopardy, Rogers would give a false cognate a penalty of 30 * 3 = 90 words to deduct from Stubbs' list. Note that almost each of the 1500+ cognates from Stubbs involve multiple languages and usually involve reconstructed Proto-Uto-Aztecan words; he's not counting a cognate as, say, 15 cognates when half of Uto-Aztecan languages seem to share it, but lists it as one entry.

Further, great weight should be given to cognates that involve Proto-Uto-Aztecan, which would naturally tend to involve multiple modern UA languages. Rogers should consider the high number of cognates that are related to Proto-Uto-Aztecan, where it makes even less sense to conjure up huge numbers of expected false cognates with the multiply-by-30 tactic.

To get a feel for what Stubbs is reporting and how he counts multiple related hits in multiple languages, below is a randomly selected section from Stubbs' more technical book (I scrolled to a random place and then picked a contiguous section that included discussion of the sound change rule under consideration), where you can see for yourself. Many of those two- and three-letter abbreviations in his explanations are abbreviations referring to specific languages, and UACV followed by a word with a leading asterisk refers to a reconstructed Proto-Uto-Aztecan word from his definitive publication on the language, which is used in each of these entries and I believe the majority throughout the book. Here's the excerpt from pages 80-81 of Exploring the Explanatory Power of Semitic and Egyptian in Uto-Aztecan, which can be downloaded at BMSLR.org for free, courtesy of Jerry Grover (click to enlarge):

Sadly, even some highly educated people have jumped on Table 6 and feel that Rogers with his reported gargantuan numbers for expected false cognates (up to 270% of the vocabulary) has provided compelling reasons to dismiss Stubbs' work as meaningless garbage all due to chance alone. You can always find a reason to dismiss something you don't like, but relying on preconceived notions coupled with bad math is not the most accurate way to reinforce your views. These kind of math errors are easy to make, I'll admit, but it's unfortunate that they survived peer review for the Maxwell Institute's publication. What Stubbs gives us requires more thoughtful attention that this. Yes, it's counter to so much that we think we know so it's easy to want to dismiss it, but the data is not readily explained by chance cognates, and the patterns of consistent sound changes add a great deal that Rogers is missing. I hope Rogers will give Stubbs a closer look! I think he missed some significant aspects of the work he criticizes. Hoping for a round 2!

I also have to point out that Rogers' comment on pp. 255-256 about not accounting for the impact of borrowing is quite puzzling. Stubbs is arguing that there was an infusion of ancient languages, not a genetic relationship. Read Stubbs' response on my previous post to get into that issue more fully. But for today, I'm just addressing the issue of Table 6 and its faulty math.

Further Thoughts on John Gee's Article at The Interpreter

John Gee's recent article at The Interpreter on the Joseph Smith Papers volume on the Book of Abraham points to some genuine problems that merit attention. On the other hand, portions of that review strike me as perhaps too harsh, though others could say the same thing of my critical article on the same volume, The Joseph Smith Papers, Revelations and Translations, Volume 4: Book of Abraham and Related Manuscripts, eds. Robin Scott Jensen and Brian M. Hauglid (Salt Lake City: Church Historian’s Press, 2018), hereafter JSPRT4.

It's difficult criticizing a work one feels is seriously flawed without sounding harsh. But let me remind you of the remarkable positives in that work and throughout the Joseph Smith Papers (JSP) series. The fact that I was able to use the book and the JSP Project website to dig into the details regarding the documents related to the Book of Abraham confirms that the JSP Project has clearly delivered on one of their key objectives: making historical documents relevant to Joseph Smith and his work available for others to study in detail. So while I disagree with some of the editorial decisions including explicit statements, implicit suggestions and omissions, the work still stands as a precious resource for which many of us can be grateful. Pointing to the possible errors, as I have done, may be all that is needed or all that can be reasonably hoped for to provide balance for those interested in finding it.

Apart from possible defects in the volume on the Book of Abraham, Dr. Gee makes an important observation about the Kirtland Egyptian Papers that might merit further attention:
The characters in the margins of the Book of Abraham manuscripts come from Papyrus Joseph Smith XI. The characters in the Egyptian Alphabet documents and the Alphabet and Grammar come from Papyrus Joseph Smith I. Because to the editors the characters are meaningless marks on the page, they pay no attention to their origin or the implications of their origins, which explains why they lump different characters from different sources indiscriminately together in their appendix and misplace some of the photographs. If the Egyptian Alphabet documents were the direct source of the Book of Abraham, we would expect that the characters would coincide and have the same source, but they do not. Because the characters do not match, the efforts to match up characters in the Egyptian Alphabet documents and the Book of Abraham manuscripts have to be seen as independent efforts. It also suggests that both efforts are attempts to match a previously existent Book of Abraham with different papyri rather than stumbling attempts to decipher a particular Egyptian text.
As I understand, Papyrus Joseph Smith XI and I, both shown on page 9 of JSPRT4, were originally part of the same scroll that were separated and separately mounted. But whether the two projects Gee refers to (work with Book of Abraham manuscripts with some characters in the margins and work with the Grammar and Alphabet document and the related Egyptian Alphabet documents) involved work with already separated fragments (as I believe could be the case) or with just different portions of the original unseparated papyrus, I think Gee's point merits attention: these two projects don't have the close relationship one would expect if the Kirtland Egyptian Papers are a window into Joseph's translation to product the Book of Abraham. Rather, it looks like two different efforts, with only minor overlap, and in both cases, there is abundant evidence that the Book of Abraham translation came first, as discussed in my article for the Interpreter, with further evidence in my discussion of the twin manuscripts for Meridian Magazine.

Gee's observation is important. Different characters are (generally) used in the Book of Abraham manuscripts and the Grammar and Alphabet plus Egyptian Alphabet documents. I believe that there is a touch of overlap in that 2 characters from Joseph Smith Papyrus XI (the characters are labeled as 5.27 and 5.28 in JSPRT4) were used by Phelps in Book of Abraham Manuscript C and also occur in the GAEL and the Egyptian Alphabet documents, though these characters have fallen off the mounted papyri fragments as shown in the recent photographs for the JSP Project. It does seem plausible that we are seeing not a window into how Joseph created live translation of a particular Egyptian text, but a window into how the scribes worked with bits and pieces of existing revelatory text (surprisingly, including some portions of the Doctrine and Covenants in addition to portions of the Book of Abraham text and perhaps commentary on Facsimile 1 and 2) in attempts to match up various concepts with Egyptian characters from Papyrus Joseph Smith XI and I, as well with non-Egyptian "Egyptian" characters from a variety of sources, apparently including some archaic Greek, a few Masonic ciphers, etc. It's all thoroughly puzzling and certainly doesn't fit the narratives that critics like to offer about how we are seeing Joseph's translation taking place.

What was the purpose of the Egyptian and non-Egyptian characters being matched up to English text in the Book of Abraham manuscripts? As previously pointed out (see "The Twin BOA Manuscripts: A Window into Creation of the Grammar and Alphabet of the Egyptian Language?"), the header of the twin documents gives us a loud declaration that the critics continue to ignore: "Sign of the fifth degree of the Second part" clearly refers to an unfinished section of the largely unfinished  Grammar and Alphabet of the Egyptian Language, a bound book with far more blank pages than written pages in its sparse text. The two scribes preparing Book of Abraham Manuscripts A and B were apparently continuing the work of W.W. Phelps, who already covered Abraham 1:1-3 in Book of Abraham Manuscript C, apparently drawing upon an existing text of the translation, as the other scribes continued to do for Manuscripts A and B. Phelps had become unavailable for the Book of Abraham project due to other demands, necessitating the hiring of a new scribe, Warren Parrish, on October 29, 1835 (this raises serious questions about JSPRT4's dating of manuscripts written by Parrish as a scribe for the Book of Abraham effort -- the editors of JSPTR4 claims that these documents may have been written as early as July 1835, which I feel is unreasonable). Joseph hired Parrish and was clearly interested in this work, but we should know that he did not need and Alphabet and Grammar to receive revelation, but was certainly interested in understanding ancient language, however futile that intellectual that quest was for him and his team as far as Egyptian was concerned.
Parrish and Frederick G. Williams continued where Phelps had left off. Their title of "Sign of the fifth degree of the Second part" means not that they are writing down fresh scripture dictated from Joseph's lips, but were preparing further entries for the section of Phelps' GAEL with that same title, but which was never completed and which never received the additional entries that could have been worked out from the recent attempt at linking characters to the text. We don't know the purpose of the GAEL -- to me there are too many puzzles to fit any one theory comfortably, whether it's reverse engineering the decipherment of Egyptian, creating a reverse cipher to encode English, or compiling the "pure language" of the ancients. Whatever it was, the project behind the Kirtland Egyptian Papers was quickly abandoned and left incomplete. I would say the KEP's purpose certainly wasn't creating the translation of the Book of Abraham from Egyptian characters. That assumption requires ignoring far too much data.

So when Gee writes, "Because the characters do not match, the efforts to match up characters in the Egyptian Alphabet documents and the Book of Abraham manuscripts have to be seen as independent efforts," I think I largely agree. Not completely independent, but perhaps two different aspects of an ongoing and futile project. And I also generally agree with the next sentence:  "It also suggests that both efforts are attempts to match a previously existent Book of Abraham with different papyri [or possibly different sections of a single original papyrus fragment] rather than stumbling attempts to decipher a particular Egyptian text." Overall, his perspective on the relationship between these documents is a valuable one, with the kind of insight that I wish had been provided from time to time in JSPRT4.

To be fair to JSPRT4, I should note that there is some language in there (as quoted in my articles) recognizing that the twin manuscripts might have been created using an existing text, but the additional possibility that is recognized, that they may represent live dictation by Joseph Smith, faces massive problems in light of the textual data and other data and these problems should have been noticed and noted. The failure to consider the implications of the textual evidence is one of many unfortunate omissions and missed opportunities for more accurate understanding of these manuscripts in JSPRT4. But in spite of such flaws, it's still a remarkable book that can help students of the Book of Abraham dig in and learn more about a mysterious adventure in the history of the Church, the story of the Book of Abraham and its related documents.