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Christmas day was the birthday of Isaac Newton. Or maybe it wasn't. Olivia Judson in the New York Times explains why a slowing earth and a change in calendar makes Newton's birth date somewhat uncertain.
Most wards will study "Gaining Knowledge of Eternal Truths" in the Teachings of Presidents of the Church: Joseph Smith manual this month. I found the following quote a rather inspiring ideal:
“Mormonism is truth; and every man who embraces it feels himself at liberty to embrace every truth: consequently the shackles of superstition, bigotry, ignorance, and priestcraft, fall at once from his neck; and his eyes are opened to see the truth, and truth greatly prevails over priestcraft. …
“… Mormonism is truth, in other words the doctrine of the Latter-day Saints, is truth. … The first and fundamental principle of our holy religion is, that we believe that we have a right to embrace all, and every item of truth, without limitation or without being circumscribed or prohibited by the creeds or superstitious notions of men, or by the dominations of one another, when that truth is clearly demonstrated to our minds, and we have the highest degree of evidence of the same.” [bolding added]
Premise #1: God cannot allow the evidence for some religious truths to be too convincing or else it would interfere with agency and thus destroy the plan of salvation.
Premise #2: There are people who think that those religious truths have been more or less proven.
Conclusion: These zealous believers have lost their agency and purpose in the plan of salvation.
Discuss.
"Velikovsky in Collision" (1975) is the title of an article written by Stephen J. Gould that gives a general assessment of Immanuel Velikovsky (1895-1979). You don't hear much of Velikovsky these days, but he was apparently rather popular (and always controversial) in his day. His notoriety came from his publications which attempted to explain Biblical and other historical oddities by invoking catastrophic earthly encounters with other planets. Mainstream scientists derided his ideas, which made him a hero among scientific insurgents.
Gould summarized Velikovsky's methodology.He begins with the working hypothesis that all stories reported as direct observation in the ancient chronicles are strictly true—if the Bible reports that the sun stood still, then it did (as the tug of Venus briefly halted the earth's rotation). He then attempts to find some physical explanation, however bizarre, that would render all these stories both mutually consistent and true. Most scientists would do exactly the opposite in using the limits of physical possibility to judge which of the ancient legends might be literally accurate.... Secondly, Velikovsky is well aware that the laws of Newton's universe, where forces of gravitation rule the motion of large objects, will not allow planets to wander. Thus, he proposes a fundamentally new physics of electromagnetic forces for large bodies. In short, Velikovsky would rebuild the science of celestial mechanics to save the literal accuracy of ancient legends. [italics added]
Gould went on to lay out several general critiques of Velikovsky's treatment of geology. One of them deserves particular note because Velikovsky's name often appears along side the term "catastrophism."Third, the inference of worldwide events from local catastrophes: no geologist has ever denied that local catastrophes occur by flooding, earthquake, or volcanic eruption. But these events have nothing to do, one way or the other, with Velikovsky's notion of global catastrophe caused by sudden shifts in the earth's axis. Nevertheless, most of Velikovsky's "examples" are just such local events combined with an unwarranted extrapolation to global impact. He writes, for example, of the Agate Springs Quarry of Nebraska—a local mammalian "graveyard" containing the bones (according to one estimate) of nearly 20,000 large animals. But, this large aggregation may not record a catastrophic event at all—rivers and oceans can gradually accumulate vast quantities of bone and shell (I have walked on beaches composed entirely of large shells and coral rubble). Also, even if a local flood drowned these animals, we have no evidence that their contemporary brethren on other continents were the least bit bothered.
I wish I had a better handle on the history of catastrophism in geology. Charles Lyell revolutionized geology by popularizing the method of interpreting past changes to the earth using known geological processes, an approach known as uniformitarianism. In contrast, catastrophists appeal to large-scale or global disasters. My sense is that catastrophists tend to have a bad name, not because large-scale catastrophes never happen, but because they are invoked without sufficient evidence in order to save whatever pet theory the catastrophists are pushing. Having said that, uniformitarianists may have been a little too hardened at times in the past. Modern geology is apparently not as rigid. (For what it's worth, doing a Google search on uniformitarianism or catastrophism brings up a lot of creationist websites.)
Gould concludes,The Velikovsky affair raises what is perhaps the most disturbing question about the public impact of science. How is a layman to judge rival claims of supposed experts? Any person with a gift for words can spin a persuasive argument about any subject not in the domain of a reader's personal expertise.... But what it is a person who knows neither astronomy, Egyptology, nor geology to do—especially when faced with a hypothesis so intrinsically exciting and a tendency, shared, I suspect, by all of us, to root for the underdog?
Gould never really answers the question.
For more critique of Velikovsky, see here.
Postscript:
Velikovsky apparently had a fan among the writers of the Church's Old Testament institute manual.Although the majority of geologists, astronomers, and other scientists believe that even this long period is not adequate to explain the physical evidence found in the earth, there are a small number of reputable scholars who disagree. These claim that the geologic clocks are misinterpreted and that tremendous catastrophes in the earth’s history speeded up the processes that normally may take thousands of years. They cite evidence supporting the idea that thirteen thousand years is not an unrealistic time period. Immanuel Velikovsky, for example, wrote three books amassing evidence that worldwide catastrophic upheavals have occurred in recent history, and he argued against uniformitarianism, the idea that the natural processes in evidence now have always prevailed at the same approximate rate of uniformity. These books are Worlds in Collision, Ages in Chaos, and Earth in Upheaval.
[Note: The following is simply an opinion that may or may not have merit. Nobody cares what I think anyway.]
Next year will be the 150th anniversary of the publication of Charles Darwin's On the Origin of Species, and the 200th anniversary of Darwin's birth. Next November (2009) will also mark the centennial of the 1909 First Presidency statement, "The Origin of Man." This anniversary seems like an appropriate opportunity for the Church to take stock of where we stand, both scientifically and doctrinally, on the issue of evolution, including its implication for humans. Drafted by committee and issued by the First Presidency under Joseph F. Smith, "The Origin of Man" primarily re-affirmed the doctrine that man was created in the literal image of God. However, several paragraphs are easily interpreted as anti-evolution. Although Heber J. Grant's administration issued a similar statement lacking the more anti-evolution paragraphs, in practice "The Origin of Man" remains the foundation of the Church's official position.
Considering the state of science in 1909, the continued vindication of evolution should be stunning. So much of what we know today has been discovered since then. For example, when "The Origin of Man" was published, the concept of the gene was still forming. The knowledge that genes were composed of DNA, and understanding of the DNA code and the way it reveals evolutionary relationships lay decades in the future. Likewise, radioisotopes were recent discoveries and the idea that rocks could be dated radiometrically was just being conceived, and the discovery of many impressive and vindicating fossils lay yet in the future. Certain ideas have also been discarded in the last hundred years, and to the extent that "The Origin of Man" appears to respond to them, it is at best irrelevant and at worst misleading.
Throughout the twentieth century, evolution and other aspects of natural history have been the source of considerable controversy within the Church. The year 2009 provides an opportunity for the First Presidency to bring Church discourse on this topic into the twenty-first century. An endorsement of the particulars of evolution is not needed and would be unwise; a simple statement acknowledging that a process of evolution in the creation is evident, or, more conservatively, declaring that the Church has no position on the method of creation, would suffice. Such a statement would leave members free to discuss the issue without questions of allegiance to Church doctrines or authorities entering in. It would also exhibit an ideal also articulated by the same 1909 First Presidency: "That which is demonstrated, we accept with joy."
It is almost a decade old, but I finally read Galileo's Daughter by Dava Sobel. In some ways it is like watching a train wreck--we all know the basic story, but there is something mesmerizing about watching it unfold. Also not insignificant are parallels to our day, of man versus church. Consider the letter below written by Cardinal Roberto Bellarmino, one of the chief Church intellectuals and adviser to the Pope, to a supporter of Galileo in 1614 (before Galileo got into trouble). Change the topic under discussion and it might easily have been a product of a General Authority from our own Church history. What lessons should we draw from it?
Letter:"I have gladly read the letter in Italian and the treatise which Your Reverence sent me, and I thank you for both. And I confess that both are filled with ingenuity and learning, and since you ask for my opinion, I will give it to you very briefly, as you have little time for reading and I for writing:
"First. I say that it seems to me that Your Reverence and Galileo did prudently to content yourself with speaking hypothetically, and not absolutely, as I have always believed that Copernicus spoke. For to say that, assuming the earth moves and the sun stands still, all the appearances are saved better than with eccentrics and epicycles, is to speak well; there is no danger in this, and it is sufficient for mathematicians. But to want to affirm that the sun really is fixed in the center of the heavens and only revolves around itself (i. e., turns upon its axis ) without traveling from east to west, and that the earth is situated in the third sphere and revolves with great speed around the sun, is a very dangerous thing, not only by irritating all the philosophers and scholastic theologians, but also by injuring our holy faith and rendering the Holy Scriptures false. For Your Reverence has demonstrated many ways of explaining Holy Scripture, but you have not applied them in particular, and without a doubt you would have found it most difficult if you had attempted to explain all the passages which you yourself have cited.
"Second. I say that, as you know, the Council [of Trent] prohibits expounding the Scriptures contrary to the common agreement of the holy Fathers. And if Your Reverence would read not only the Fathers but also the commentaries of modern writers on Genesis, Psalms, Ecclesiastes and Josue, you would find that all agree in explaining literally (ad litteram) that the sun is in the heavens and moves swiftly around the earth, and that the earth is far from the heavens and stands immobile in the center of the universe. Now consider whether in all prudence the Church could encourage giving to Scripture a sense contrary to the holy Fathers and all the Latin and Greek commentators. Nor may it be answered that this is not a matter of faith, for if it is not a matter of faith from the point of view of the subject matter, it is on the part of the ones who have spoken. It would be just as heretical to deny that Abraham had two sons and Jacob twelve, as it would be to deny the virgin birth of Christ, for both are declared by the Holy Ghost through the mouths of the prophets and apostles.
"Third. I say that if there were a true demonstration that the sun was in the center of the universe and the earth in the third sphere, and that the sun did not travel around the earth but the earth circled the sun, then it would be necessary to proceed with great caution in explaining the passages of Scripture which seemed contrary, and we would rather have to say that we did not understand them than to say that something was false which has been demonstrated. But I do not believe that there is any such demonstration; none has been shown to me. It is not the same thing to show that the appearances are saved by assuming that the sun really is in the center and the earth in the heavens. I believe that the first demonstration might exist, but I have grave doubts about the second, and in a case of doubt, one may not depart from the Scriptures as explained by the holy Fathers. I add that the words ' the sun also riseth and the sun goeth down, and hasteneth to the place where he ariseth, etc.' were those of Solomon, who not only spoke by divine inspiration but was a man wise above all others and most learned in human sciences and in the knowledge of all created things, and his wisdom was from God. Thus it is not too likely that he would affirm something which was contrary to a truth either already demonstrated, or likely to be demonstrated. And if you tell me that Solomon spoke only according to the appearances, and that it seems to us that the sun goes around when actually it is the earth which moves, as it seems to one on a ship that the beach moves away from the ship, I shall answer that one who departs from the beach, though it looks to him as though the beach moves away, he knows that he is in error and corrects it, seeing clearly that the ship moves and not the beach. But with regard to the sun and the earth, no wise man is needed to correct the error, since he clearly experiences that the earth stands still and that his eye is not deceived when it judges that the moon and stars move. And that is enough for the present. I salute Your Reverence and ask God to grant you every happiness."
In 1988 (then) Elder Packer gave the keynote address at BYU as part of a series of symposia on the Book of Mormon. "The Law and the Light" is notable for its extended attack on evolution--the most significant one by a General Authority since Elder Bruce R. McConkie's "The Seven Deadly Heresies". (Back when it was an active blog, I collected President Packer's statements about evolution and gave some analysis at Mormons and Evolution).
Although the speech was published in, The Book of Mormon: Jacob through Words of Mormon, To learn with joy, along with other papers from the symposium, copies of the talk could be a little difficult to find, possibly due to the introductory statement: "The article may not be reproduced in whole or in part without written permission from the author."
That is no longer a problem because the speech is now available online at BYU's Digital Collections.
Background Note: Although he gave few details, in a Sunstone Symposium presentation Duane Jeffery said that it was originally decided that "The Law and the Light" would not be published. However, since it was the keynote address publication was ultimately permitted, along with a disclaimer as to its non-authoritative status.
[This post is part of a series, What Separates Humans from the Animals?]
Before we look at a difference between us and prosimians (lemurs, bushbabies, etc), we need to briefly touch on three genetic concepts. I've tried to make them as painless as possible.
Concept #1: Stop Codons. DNA is made of 4 basic molecules (nucleotides) that are represented by the letters A, T, G, and C. In a gene, every 3 nucleotides codes for an amino acid (the building blocks of proteins). However, there are several combinations that mean, 'Stop. This is the end of the gene.' These are called 'stop codons' and mutations can do two things with respect to them: (i) a mutation in a gene can create a premature stop codon, thus truncating the protein product, or (ii) a mutation can erase a stop codon, thus extending the coding of the gene until a random stop codon in the downstream sequence is reached.
Concept #2: Introns and Exons. Most of your genes are actually fragmented into pieces called exons. After the DNA is transcribed into RNA--but before the RNA is translated into protein--the extra parts (introns) are cut out and the exons are spliced together. The following image from Wikipedia conveys the idea:
The take-home message here is that the introns (the blue lines) were cut out before the RNA was used to make a protein. Simply put, there are signals in the sequence that tell enzymes where the introns are and where the ends of the exons are that should be joined together.
Concept #3: Transposons. Take a course on bacterial genetics and you will be introduced to transposons. Transposons are selfish-DNA elements that are kind of like viruses, except the don't jump from cell to cell. Rather, they spread copies within the genome. They come in various types and have different mechanisms of replication. Your basic cut-and-paste transposon has a simple structure. It consists of a transposase gene, which does the cutting and pasting of DNA, and flanking inverted repeats, which the transposase recognizes. I've made a diagram illustrating the structure and movement of a simple transposon.
Many organisms other than bacteria have transposons in their genome, including us. However, in our case they seem to be remnants of the past because they have sustained mutations that have rendered them inactive. There are other mobile genetic elements in our genome that are different from transposons, but similar in general concept.
Alright, let's proceed.
The basic background to this story is that a gene was discovered in the human genome that is a chimera of a known gene (SET), and a transposase gene from a transposon called Hsmar1. Humans, other apes, and monkeys all have this chimeric gene, which is called SETMAR. Prosimians and other placental mammals only have the SET part, without the addition of the transposase. So the presence of SETMAR sets us apart from prosimians and all other distantly related mammals. So how did SETMAR come to be?
Cordaux et al looked at it and figured out how to get from SET to SETMAR in a few simple steps. I will be referring to their Figure 1. (Click to enlarge.)
Fig. 1. Milestones leading to the birth of SETMAR. The structure of the SETMAR locus (Right) and a simplified chronology of the divergence time of the species examined relative to hominoid primates (Left) are shown. Pink boxes represent the two SET exons, which are separated by a single intron (interrupted black line) and form a “SET-only” gene whose structure is conserved in all nonanthropoid species examined and terminated with a stop codon (∗) located at a homologous position (except in cow; see Fig. 2 a). The Hsmar1 transposon (event 1) was inserted in the primate lineage, after the split between tarsier and anthropoids, but before the divergence of extant anthropoid lineages. The transposon is shown here with its TIRs (black triangles) and transposase coding sequence (red box). The secondary AluSx insertion within the TIR of Hsmar1 (event 2) is represented as a blue diamond. The position of the deletion removing the stop codon of the “SET-only” gene (event 3) is indicated as a lightning bolt. The de novo conversion from noncoding to exonic sequence is shown in green, the creation of the second intron is represented as a dashed blue line (event 4), and the splice sites are shown as thick blue lines.
We'll start at the bottom and work our way up.
Starting point: Other mammals--up to prosimians, have a SET gene that has two exons. The dashed lines indicate sequence that is spliced out of RNA before a protein is made (see Concept #2 above).
Step 1: An Hsmar1 transposon inserted just downstream of the SET gene.
Step 2: An Alu element inserted into one of the Hsmar1 inverted repeats. (I've written about Alu elements before--see here. Briefly, they are like transposons but do not contain any genes, themselves.) The Hsmar1 transposon is now stuck in place; it cannot cut itself out because one of its inverted repeats has been partially deleted.
Step 3: A small deletion occurred, which removed the stop codon at the end of the SET second exon, thus extending the exon (see concept #1 above).
Step 4: The extended SET exon included sequence that could then act as a signal for RNA splicing following transcription. The Hsmar1 transposon also contained a splice signal, so the end of SET could be spliced to Hsmar1.
Finish: The final protein product consists of the original SET, plus a few amino acids gained from the extension of the second exon, plus the transposase gene from the Hsmar1 transposon. Thus a new chimeric gene, SETMAR is born.
The creation of the new gene occurred after the group of primates that gave rise to monkeys and apes diverged from prosimians. Of course, these steps did not all occur in an individual animal!
What does SETMAR do? The answer to that is not yet clear. The SET portion is known to modify histones, which are proteins that provide structural support to DNA and can help determine whether a gene is expressed or not. Interestingly, although the transposase has two functions, natural selection seems to be selecting only one of them: the ability to bind DNA, especially the inverted repeats. Putting the two together suggests that the protein helps to regulate gene expression at specific places in the genome. However, for our purposes here, the function of SETMAR does not matter.
The the main point is that we, other apes, and monkeys have a novel gene that prosimians and other mammals do not, and that the genetic structure of the gene gives us clues as to how it was created: co-option of naturally occurring genetic processes.
Reference:
Cordaux R, Udit S, Batzer MA, Feschotte C. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A. 2006 May 23;103(21):8101-6.
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