Their guiding philosophy, of course, is that the scriptures and statements by various Church leaders (many of which are quoted) can be taken at face value as accurate in their description of natural history. In contrast to many young-earth creationists, WeaverResearch does not attribute most of the fossil record to Noah’s flood. Evolution is right out, so how does one explain the principle of faunal succession? The answer at WeaverResearch is that the order of fossilization corresponds to reproductive fecundity. At the fall of Adam and Eve (and presumably again after Noah’s flood), all of the existing organisms began to reproduce and fill the earth. However, the rates of reproduction differed and so less complex organisms filled the earth and were fossilized before more complex organisms.

A foundational scripture for WeaverResearch is Doctrine and Covenants 121:12

And also that God hath set his hand and seal to change the times and seasons, and to blind their minds, that they may not understand his marvelous workings; that he may prove them also and take them in their own craftiness; [emphasis added]

Using other scriptures the term ‘times and seasons’ is interpreted to refer to the orbit, tilt and rotation of the earth. According to WeaverResearch, changing the ‘times and seasons’ is not a poetic way of saying that God controls the destiny of the earth (as Daniel 2:21 suggests), rather the letter from Liberty Jail is an explicit acknowledgment that God has subjected the earth to catastrophies such that scientific methods of determining time are skewed. Apparently God has done this on purpose, and yet, paradoxically, the confusion can be overcome by anybody with a Bible.

Perhaps the centerpiece of the website is a geological and archeological correlation with the scriptures. This chart shows carbon-14 dates and where they really line up with scriptural dates, with the same done for major geological events. The Permian extinction correlates with Noah’s flood, of course the continents separate with Peleg, and a few other events are shown correlated to Abraham, Moses and Christ. Thus, according to the chart, you can find the actual scriptural date on which events, otherwise thought to be ancient, occurred.

Although interesting, this approach leaves a lot of questions unanswered; here are a few of mine:

1. C-14 dating has been used on ancient Egypitian artifacts to obtain dates in agreement with those derived from other historical sources. Yet according to the correction curve for carbon dating, this should be impossible for anything older than about 2,000 years ago. How can this be?

2. Some radiometric dating techniques can be used over a very wide time range. Argon-argon dating, for example, has been used for some of the most ancient rocks (eg. 4.5 billion years ago), and yet under optimal conditions it can also be used for much more recent dates, such as the Mt. Vesuvius eruption of 79 AD. Imagine a geologist dates the lava from a volcanic explosion using argon-argon and gets a date of 15,000 years ago. The remains of a tree that was burned and covered by the lava are found and C-14 dated to 15,000 years ago as well. According to WeaverResearch, this correlates to about 3,750 years ago (between Abraham and Moses). The problem is that rocks dated by argon-argon to 50 million years ago would also correlate to 3,750 years ago. If the correlation chart is right, then given the right outcrop, dating could give you younger rocks laid down before older ones–an obvious problem. Why would rocks formed at the same time give such different (correlated) ages when measured by the same method? Or stated another way, what governs whether isotopes in a rock formed between Abraham and Moses decay super-fast to appear 50 million years old versus 15,000 years old–a difference of over two orders of magnitude?

3. If the order of fossilization is a function of relative rate of reproduction, why does it also happen to correlate with the order of morphological transitions, like for tetrapods moving onto land or mammals moving back into water?

4. Were dinosaurs really that much more fertile than rodents or birds?

5. When different dating methods that use different assumptions agree (isotopes, tree rings, varves, sediment layers, ice core layers), isn’t that pretty good evidence of their reliability? Would catastrophies that throw up mountain ranges overnight, cause isotopes to decay at rates never observed by humans, and wipe out species also be expected to add layers to seasonal records in accordance with isotope decay rates?

In regard to evolution, I will just point out that faunal succession is only one line of evidence. Others include biogeography, anatomy, and genetics. They each tell a pretty consistent story.

Despite the problems, those who think that the standard of true belief does not allow for concessions to the natural sciences may find WeaverResearch a breath of fresh air. Others will wish for winds of change.

[Comments–both pro and con–on WeaverResearch are welcome. I just ask that they remain respectful; good people will be found on both sides.]

Topics covered include: the origin of life, constructing the tree of life, placing humans in the tree, history and philosophy of science, science and theology, basics of how evolution works, and practical applications.

You can download the whole book, or individual chapters, as pdf files. Did I mention it’s free? So go get it, and then you can print out chapters to read at your leisure. Once again, here is the link.

I don’t think Mark characterizes science fairly here, or even BYU for that matter. Science must deal with evidence that is public and theory that is precise. God has, to all appearances, deemed that spiritual evidence be private; and while canonized revelation is in a sense public, it is not very precise. (And to the rather limited extent evidence of religious matters has been public and its theoretical interpretations precise, the track record in confrontation with science/history/empiricism has not been particularly kind to religion, in my opinion.)

So if anyone is declaring separation between science and religion, it seems to be God, not scientists. I think scientists are happy to address any publicly shareable evidence related to precisely formulated theories. God simply does not seem interested in playing that game.

As for BYU, its value seems to be to teach students to maintain a robust personal spiritual epistemology while learning to successfully use scientific and other modern and postmodern methodologies only as tools—and not as the basis of an entire worldview—where useful in temporal endeavors. Students learn to keep the application of these worldly approaches limited in scope and subordinate in general to personal spiritual epistemology. The philosophical meld Mark seeks seems to simply not be on the table—and it’s God and his BYU trustees (read prophets, seers, and revelators), not scientists, that keep it off the table.

(This will sound harsh, but from what I can tell from Mark’s diatribes about biologists’ and physicists’ dismal understanding of information, entropy, and the intimate relation of these to libertarian free will, I can only imagine that implementation of his vision would turn science at BYU into a tragically unfruitful laughingstock. I think there’s little danger of it ever being remotely considered.)

Based on the slides the talk looks fine and nice, touching on a number of the general sorts of points one would expect a mainstream scientist who is also a loyal Mormon to make. In fact, despite the title, only about a third of the talk (in slides; I of course don’t know how it went down time-wise) directly addresses Intelligent Design, with the rest devoted to more general observations on the relationship between science and religion in general and Mormonism in particular.

He is critical of Intelligent Design—not only as a scientific endeavor, as I expect most working scientists would be—but also as a handmaiden to a Mormon worldview. His bottom lines, which I agree are the right positions for a Mormon to have, are that “I do not recommend ID (meaning the present-day movement and literature) as a foundation for religious belief” and “Ultimately we must find God the old-fashioned way: on our knees, in service to the less fortunate and in good, honest, Christian living.”

His overall approach is like that Stephen J. Gould labeled “nonoverlapping magisteria” (NOMA), an outlook described in a Wikipedia article as “science and religion deal with fundamentally separate aspects of human experience and so, when each stays within its own domain, they co-exist peacefully.” Bailey’s clever rendering of this idea, a play on Matthew 22:21, is “Render unto science the things which belong to science; and unto God the things which belong to God.”

It’s the expected and comfortable outcome of such a talk, and could ultimately be viable, but I am not sure the absence of conflict is quite as facile as presented. Some specific critiques in this respect:

1. 1. He names several prominent scientists of other denominations who are deeply religious, yet have no problem with mainstream science, including evolution. But what they do not face—and what are left unaddressed in this talk—are difficulties with evolution that are peculiar to Mormonism, which stem from literal conceptions of mankind’s being in God’s image, being children of God, and the definition of divinity in D&C 132 as the capacity for eternal procreation.
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3. 2. He says “The LDS Church takes no official stance on scientific issues.” Surely this is too sweeping. Being both wise and shrewd, I seriously doubt you could get any General Authority to make this specific statement, particularly if “evolution” were substituted for “scientific issues.” It is also a statement that is belied by several examples of material more in line with creationist than scientific perspectives in very recent correlated Church publications (to his credit, Bailey points out several of these).
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5. 3. I worry that many difficulties are too easily swept under the rug with statements along the lines of: The LDS God is “a rational, comprehensible God who works within natural law.” I struggle in vain to understand what is meant by the common saying that God “works within natural law.” Is it the same sense that humans work within natural law—that is, God is using engineering and technology? Advanced alien technology, to be sure, but technology nonetheless? Do we imagine that when God created the earth he used cosmic cranes and backhoes of some sort? Or that in guiding evolution he sent agents to set up microbiology laboratories, alter specimens, and put them back into nature? Or that in turning water to wine he somehow managed to do real chemical engineering with some sort of remote-controlled hidden laboratory? Or that when he heals the sick in response to a priesthood blessing he somehow invisibly administers real drugs or performs microsurgery? The difficulty is to understand how such divine technology could be simultaneously (a) invisible to us, (b) nevertheless have effects visible to us, and yet (c) be compatible with the laws of nature of which we already are aware.
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7. 4. He includes a slide on free will, noting that quantum mechanics and chaos release the respective strangleholds of microscopic determinism and practical predictability (practical, that is, in terms of limitations on measurement precision and computational resources). Regrettably, however, the randomness and unpredictability thus introduced do nothing whatsoever to provide the kind of ’self-caused’ ‘control’ on which proponents of libertarian free will insist.

Nevertheless, on balance it is an interesting and eminently worthwhile talk. I commend the Miller-Eccles Study Group for their interest the subject, and Brother Bailey for providing a nice discussion.

A recent paper in Proceedings of the National Academy of Sciences provides a good example of an approach to resolving relationships that has been developed over the last 15 years or so. The central players are mobile genetic elements. These are pieces of DNA that, through various methods, can be copied and inserted into another part of the genome. These insertions represent unique events that are unlikely to occur independently, and the ancestral state can be confidently assumed to be the lack of the insertion. Thus, two genomes sharing the insertion are very likely to be related by descent, and any genome not containing the insertion (with no evidence for a deletion) represents a branching off before the insertion event occured. This should be clearer in a moment.

The authors of this paper used a family of long interspersed elements (LINEs) called L1 to investigate mammalian relationships. L1s are like retroviruses in that they use reverse transcription to insert into the genome. They only contain two or three gene genes which are used for their propegation, however they are not viruses–they remain in their cell of origin. L1s constitute 16% of the human genome and are present in a wide range of mammals. Here, the authors looked for L1s that are present in the same genomic location in a variety of animals. The following figure summarizes their findings.

This phylogeny is read similar to a genealogical chart. Moving left to right, each “T” intersection represents a split and if L1s are indicated, then all animals encompassed at that point share those L1s in the same genomic location. (Note: that doesn’t mean on the same chromosome, it means in the equivalent gene context.) The INT labels designate a particular L1. We can see that everything from bats to rabbits share 10 L1s (INT1068, INT1098, etc.), but only animal groups represented by bats, horses, and dogs and cats share four certain L1s (INT165, INT265, etc). It doesn’t take much time to see that there is a nested hierarchy. That two groups of animals would independently have an L1 insert into the same place is possible but unlikely; that it would happen several times over is even more unlikely. Thus the sharing of L1s–especially multiple L1s–is a good indicator of common descent.

This paper is also good because it presents an anomaly: INT283 makes it look like dogs and horses are more closely related to cows and whales than to bats. The authors rule out an independent insertion event, so how can this be? The answer that the authors favor is called incomplete lineage sorting. Each L1 insertion examined here occured in an individual some time in the distant past and spread through the population until it became fixed (ie. not polymorphic–or in other words–present in all individuals). If the L1 was neither harmful nor helpful (ie. neutral), it might take millions of years to become fixed. If the time to fixation encompassed speciation events, it is possible that the L1 would not be present (or would die out) in some lineages but ultimately become fixed in others, thus giving an incongruent picture. So what probably happened is that an ancestor of cows, dogs, horses, and bats had an L1 insertion that spread into the population. Some members of the population that split off and ultimately gave rise to cows and whales had the insertion and it became fixed. The same holds for the groups that gave rise to dogs or horses. However the L1 insertion failed to become fixed in the ancestors of bats and died out.

Similar studies have been done to resolve closer relationships. For example a type of mobile element that only occurs in primates has been used to help solidify primate relationships and it should come as no suprise that humans remain most closely related to chimpanzees. Because of their abundance and known mechanism of spread, mobile genetic elements such as L1s are powerful tools for determining evolutionary relationships. They also seem to strongly cut against the argument that similarity in DNA sequence between animal groups is merely a reflection of God’s economy of design.

I’ve got a DNA that’s specifically mine, a blood type that’s specifically mine. Those formulas are written in every cell of my body. No doubt those are on file in that great, heavenly filing cabinet. It’s much easier for me to believe that the same individual can be created again with those formulas and elements available.

Elder Nelson seems to be saying that if every part of his body were obliterated, perhaps a record of his genetic code could be used to create an equivalent and unique body. Let us further speculate that the code would be refurbished to eliminate problems or unneeded code and to add any improvements or corrections needed.

In trying to understand the relationship of organisms to one another, scientists face an important question: is a characteristic identical by state or descent? The simplest way to illustrate the question is to consider DNA sequence. Whether you are comparing species or individuals within a species you will find groups that share unique DNA sequences. That sequence may indicate that all individuals sharing it are closely related, but not necessarily. Mutations can occur independently in different individuals who do not share a close relationship. In this case, the characteristic is identical by state (IBS). In contrast, a mutation that originates in an individual and spreads to his/her progeny–each inheriting the characteristic from their ancestor–results in groups that are identical by descent (IBD) (and also by state). In order to avoid being misled into thinking that a DNA sequence is identical by descent when it is really just by state, scientists try to pick more complex characteristics that would be less likely to happen independently.

A central LDS doctrine is that man is created in the image of God, but the details of the creation have not been revealed. Are we in His image by descent or state? Some LDS attacks on evolution seem based in defending the proposition that we are literal descendants of God, with an unknown fudge-factor introduced by the Fall. We could call this “in God’s image by descent.” For those who hold to a theistic evolution scenario, humans have been formed in the image of God to unknown precision by natural processes (perhaps with some divine intervention)–something we could call “in God’s image by state.”

This brings me back to Elder Nelson’s speculation on the resurrection. What meaning does biological descent have when refracted through the Fall, and then the Resurrection? If we are in God’s image by descent, the perfection of that image will apparently be by state. But if that is so, is the thought that the original creation was one of mere(!) state so terrible? I think that any path to God’s image is good enough for me.

Elder Packer’s version of evolution is not one that any biologist would recognize.

(hat tip to a commenter at NDBF)

Perhaps the primary reason for denying any sense of progress is that none is detectable without overlaying the data with unverifiable assumptions. When the fossil record is examined with its large parade of life-forms that have come and gone over enormous expanses of time, how can we say with any certainty (leaving religion aside) that we, or any other life-form, were the intended outcome? How do we know that we are not just precursors to other life-forms to come? Without appeals to religion such questions are unanswerable. In the popular literature some scientists debate whether something like us would inevitably turn up sooner or later. Such arguments are interesting but nothing more than intellectual gymnastics for now. (I’ve discussed before that these types of issues are a problem for any kind of historical study and for other branches of science. He specifically denied it was the case, but hypothetically speaking, if Pres. Hinckley said that hurricane Katrina was sent by God to destroy New Orleans, no objective evidence could be marshalled to discount that the destruction of New Orleans was just a chance–though not unlikely–event.)

In the late nineteenth century and the early part of the twentieth century, the idea that evolution entailed some kind of progress did exist. I don’t think such views had any kind of cosmic destination in mind, but ideas put forth by Darwin mixed with those of Lamark served as a basis for a sense of human progress through evolution. These ideas were used to justify such ugly things as racism (including German superiority), downtrodding the poor, eugenics, and even war. This, in turn, fueled William Jennings Bryan’s opposition to evolution which culminated in the Scopes Monkey Trial. When the notion is adopted that human progress occurs by biologic means, it is an easy step to conclude that some groups of people should be perpetuated and others should not.

A sense of progress can also have consequences on the environment. Afterall, worrying about this or that endangered species can be viewed as an impediment to a kind of human manifest destiny. Using a sense of unfolding purpose in evolution, some may conclude that the inability of various life-forms to persist in the face of human expansion is “nature’s way.” I remember a conservative political commentator once ridiculing environmental advocates as being in conflict with evolutionary principles–as though extinction is part of evolution’s “divine” plan.

So I, for one, am glad that evolutionary theory has divested itself of any sense of unfolding progress. Aside from being unverifiable from a scientific standpoint, it is easily used to justify brutal treatment of other people as well as the rest of nature. The sciences describe the world; they do not tell us how the world ought to be.

–Begin Quotes–

In 1979 President Kimball met with the Presiding Bishopric…and Elder McConkie to discuss a proposal that on the Church’s sequicentennial the First Presidency publish an official statement on the creation and evolution. But after extended discussion, they decided in 1980 not to issue any such official statement. According to Elder Ezra Taft Benson’s grandson Stephen, Elder Benson had strong personal anti-evolution views but “acknowledged that ‘the Lord may not have revealed enough to create unanimity among the Brethren.’” Elder Benson reportedly said any statement would be “unwise” and serve only to “widen differences…” (pg. 96-97)

President Kimball was not a doctrinaire, and he felt a need to intervene in doctrinal matters only when he saw strong statements of personal opinion as being divisive. Elder McConkie’s talk at BYU on “The Seven Deadly Heresies” implied he had authority to define heresy…President Kimball responded to the uproar by calling Elder McConkie in to discuss the talk. As a consequence, Elder McConkie revised the talk for publication so as to clarify that he was stating personal views…But there was no corrective public criticism of the talk… (pg. 101)

These statements [such as Elder McConkie’s in the speech referenced above], without any public expression of a different view by other leaders, gave the mistaken impression that the Church had a position on the issue, despite the continuing hands-off position of the First Presidency and the Twelve. (pg. 97)

–End Quotes–

According to Edward Kimball, President Kimball said little about the issue in public and was noncommittal in family discussions, viewing it as a distracting issue. (pg. 97)

First let’s get some things straight: DNA is not simply a code. Yes it codes for proteins, but it has physical/chemical properties of its own. Some proteins recognize and can bind to specific sequences of DNA–a fact that is routinely used in laboratories to manipulate DNA by cutting it in specific places. Proteins are composed of amino acids, which each have physical/chemical properties. It is these properities that give a protein its overall shape and function. So altering the sequence of DNA can change how proteins interact with it, or if the change is in a stretch that codes for a protein, it can change the sequence of amino acids which in turn can alter the properties of the protein.

Sometimes letters composing words and sentences are used to illustrate changes in DNA or amino acid sequence. It is a useful analogy but it does have limitations. Words have meaning because we assign the meaning to them whereas proteins act on other proteins and molecules as a result of physical and chemical properties. Their “meaning” is dependent on context.

There are several ways that new genes can be created.

1. Gene Duplication: There are a couple of ways that genes can be duplicated–for our purposes we’ll just say that copying errors or recombination can each lead to duplication of genes. With duplicate genes there are several potential outcomes. Two simple scenarios involve the duplicate copy either mutating into useless sequence, or mutating and taking on a different function–either way the original copy is able to carry out the original function. There are numerous families of genes in our genome–families of genes that are a result of gene duplication and modification. Examples include the globin genes (including myoglobin and hemoglobin) as well as Hox genes which control developmental processes.

2. Exon Shuffling: In eukaryotes (like us) many genes are broken up into units called exons, while the sequence between the exons are called introns. Introns are spliced out before translation into protein occurs. Through various mechanisms, an exon of one gene can be tacked on to (or into) another gene leading to a novel chimeric gene.

3. Mobile Elements: These can be thought of as stretches of selfish DNA that copy and paste themselves throughout the genome. If they land in the middle of a gene they can alter the way the sequence is spliced, thus altering the amino acid sequence of the protein. Alternatively, if they land near a gene they may alter how, when, or where the gene is turned on or off (see amylase below).

4. Lateral Gene Transfer: This is not as common in us, but genes can be moved from one organism to another (by a virus, for example).

5. Sequence Coding: Also less common, sometimes sequence in or adjacent to a gene can change such that the gene is extended by a number of amino acids.

6. Gene Fusion/Fission: Two genes can be fused into one, or one gene split into two.

In addition to the creation of new genes, the regulators of gene expression can be altered. For example, in a previous post I dealt with the amylase enzyme and how it came to be expressed in the mouth (in addition to the pancreas). In that case, a gene duplication occured followed by the insertion of “junk” DNA in front of one of the genes. That “junk” DNA acts like a switch and is responsible for the expression of amylase in the mouth. It is a case of an apparently accidental occurance that happens to be useful.

Thus we see that new information can be generated in the genome. Whether it has all happened strictly by natural processes is another question–and one that is probably ultimately unanswerable by scientific means. Nevertheless, we should not underestimate the creative processes that already exist within the genome.