Mobile Genetic Elements and Animal Relationships
by Jared* on July 16th, 2006In the years before DNA sequencing scientists relied on morphology in order to determine the relationships of animals to one another. Tracking changes of anatomy in the fossil record as well as surveying the anatomy of living organisms was the best they could do. The discovery of DNA and the technology to cheaply sequence it helped scientists to resolve relationships that were ambiguous by looking at morphology alone. No method is foolproof, however, and the comparison of gene sequences has its own set of limitations and complexities. For example, point mutations can occur independently or revert to the original state, potentially obscuring true relationships.
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.
Nishihara, Hasegawa, and Okada. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. PNAS vol. 103 no. 26 pp.9929-9934. (This article is freely available here.)
Ah, lovely data! Beautiful Data!! IRRESISTIBLE DATA!!!
This, along with your amylase post, are two of my favorites here. People who see this stuff and deny common descent are truly walking in darkness at noonday.
Thanks, Christian.
There’s more where this came from, though I don’t want to bore people. Unfortunately most people don’t see this kind of stuff–it doesn’t make it into mainstream discussions very often.
As I said at my blog, this is where the discussion gets down to brass tacks.
One of the things I think blogs can in principle do well is exhibit a few concrete examples, chosen with an expert’s eye for key principles, and explained from an expert’s ‘feel’ for the subject, in order to help John Q. Public understand why scientists believe the things they do.
For the purposes of argument, how do such phylo-genetic patterns necessitate common viviparous descent instead of common engineering?
Anyone with a reasonable familiarity with the engineering practice, particularly open source software engineering practice, recognizes this pattern in engineering development. In software, every time a new code base is formed from a previously existing code base, modified sufficiently so that change sets cannot trivially be copied back and forth with the original code base, and maintained independently from there on, is considered a “fork”.
A software engineering fork, exhibits features very similar to a phylum or genus, sometimes completely changing function, most often just gradually diverging in internal engineering such that the forked code base gradually loses a resemblance with the original “branch”, which of course is generally being developed independently, and gradually losing resemblance with its former self.
First, a few general comments on that argument. (None of this is about you personally, this is for the sake of argument.)
1. The intervention (or engineering) of God ultimately cannot be ruled out. That should be self-evident.
2. That mobile elements (MEs) are found in a phylogenetic pattern consistent with evolution is remarkable, given that MEs and DNA did not exist when the theory of evolution was proposed.
3. It strikes me somewhat as parasitism that when further evidence supporting evolution is discovered, naysayers come in and act like such evidence was consistent with their interpretation of creation all along–as though they were expecting such a discovery.
4. The engineering scenario you propose would probably still be unacceptable to many LDS. Either way, our physical bodies were built from the ground up, not top-down.
5. Such an argument is also similar to ones ID folks make. That is, when humans hit upon doing something similar to the way nature operates, we can therefore infer that intelligence designed nature’s process in the first place. eg. Molecules are like motors. Intelligent agents make motors. Therefore intelligent agents made molecules.
6. Such evidence does not stand alone. There is still other genetic and fossil evidence.
Now more specifically:
1. ME’s are sometimes associated with deletions, some of which resulted in pseudogenes. Why primates should have a broken gene necessary for vitamin C synthesis–and the part that exists has TE’s in it (that are presumably shared, though I don’t think that has been addressed thoroughly)–makes little sense to me from an engineering perspective.
2. Certain classes of MEs are still active today and they are pretty well understood. The insertion of many ME’s results in a taget site duplication. That is, the process is such that a few nucleotides of the target site are duplicated and subsequently found on either side of the inserted ME. ME’s can take on function (as I’ve mentioned before.) If an engineer needed the sequence of an ME to serve a function, why include the target site duplication other than to fool us into thinking it was a product of an ordinary natural process?
In short, ancient MEs aren’t really much different from one’s we observe today, and their distribution is largely consistent with common descent. Furthermore, they are associated with features that seem to make little sense from an engineering or design perspective.
Jared, in order for a theory to be regarded as having explanatory power, it must predict things *before* they are discovered. Neither theory did that in this case, so the discovery of MEs is not differential evidence for one theory or the other.
I would say, by the way, that in some cases, divine action can be ruled out, or at least be shown to be superfluous. This is not one of those cases. One of the reasons why most scientists are at a loss is they think of God as an absolute being who could snap his fingers and pop the world into existence. Any comprehensible Mormon theory of divinity is much different, because natural law comes into play.
My argument on the other thread (q.v.) is not so trivial as the ones you describe however - the idea is to establish statistical necessity of a teleological explanation, then under that umbrella various forms of libertarian action - interventionist, hylozoist, two stage design, etc - can be considered.
I believe that the first part (the umbrella) is provable, the second part largely hypothetical. The problem is that most scientists, being ignorant of the power of statistical mechanics, deny the plausibility of any argument to establish the umbrella. Paul Davies and Stuart Kauffman, world experts both, are not among them - that is why they posit new information creatings physical laws - what I call the “secret sauce”.
I believe that intelligences are natural, may be immanent in the the physical and spiritual world, so self design is not out of the question. But whatever it is, no net algorithmic complexity creating process is “law like”. All known natural laws either preserve information, or occasionally, lose it, for reasons I have discussed.
Neither theory did that in this case, so the discovery of MEs is not differential evidence for one theory or the other.
Oh, come on. Are you seriously saying that neither common descent nor engineering should have a privileged position here? Common descent has been around since at least 1859, and although it did not predict the existence of MEs, it certainly has ramifications as to how they are distributed. I have not said anything about proving God did not intervene somehow, but given how far the general predictions of common descent have been borne out, it seems to me that an engineering hypothesis will need to be validated in some stunning predictions before it can be taken as anything other than an attempt to create a gap in which to put God.
the idea is to establish statistical necessity of a teleological explanation, then under that umbrella various forms of libertarian action - interventionist, hylozoist, two stage design, etc - can be considered.
You and I think about very different things.
Technical note: In comment 5 above I wrote: “…MEs and DNA did not exist…” Obviously I meant that they were unknown, not that they did not exist.
Not on that basis, no. Divine engineering has been around a few thousand years longer than that, by the way.
I do not create gaps to put God in. I know that God exists, and is immanent in the world, that spirit is strictly speaking a natural (i.e. real) phenomena, and that intelligence is not deterministic nor stochastic.
Given those axioms, my approach is to address the economy of creation, i.e. given the goal of developing a body for everlasting habitation, what are the most economic means available for God to go about doing that, and what does the evidence imply about the way he actually went about doing so.
The idea that you have to prove something before it is worthy of believing is the hallmark of stupidity. So stupid in fact, that not even scientists follow it - instead they just fudge the line between empirically established science and natural philosophy - and pretend that their dogma is founded on a sound foundation and God himself is up in the night.
“strictly determinist nor strictly stochastic”
By the way, engineering and reproductive common descent are not incompatible. I am convinced of logical common descent - whether that common descent was reproductive in all cases I am not convinced of, given the possibility of the equivalent of resurrection, as well as the possibility of up to three, probabably overlapping (e.g. design build like I-15 if you are familiar with that) creative phases - intellectual, spirit material, and “physical” material).
Mark (#8): given the goal of developing a body for everlasting habitation, what are the most economic means available for God to go about doing that
The obvious answer—promoted by Brigham, probably received from Joseph, endorsed by B. H. Roberts, and not contradicted by any General Authority of which I am aware: an infinite regression of physical procreation. Regrettably, it seems highly unlikely in light of the sorts of evidence Jared has presented.
[I apologize for the short repeated messages.]
No one who believes in Neo-Darwinism has yet been able to explain to me how we live after death. How is it that we have a spirit body that runs on different principles than are putatively responsible for natural selection?
On a Neo-Darwinist account isn’t it rather ridiculous to believe that there is life after death or before birth at all? Or in in the eternality of souls? Or what about the resurrection? What about divine judgment? What about the purposes God has in the human body, e.g. the establishment and eternal preservation of the human family?
To listen to many talk over at T&S, God is an impotent weakling who has to deal with the brute facts of human physiology as if they were a fait accompli and not established by divine design.
As doctrinaire Neo-Darwinism rules out design or teleology of any sort, at least beyond a small handful of fundamental natural laws, after which God vacates the premises, it effectively either rules out God or turns him into the impotent abstraction of the Deists.
Why in the world should I pay homage to the law of gravity or nuclear fusion? Will the law of gravity love me back? Does gravity seek to obtain my everlasting salvation? Or even worse, why should I worship at the eternal casino table? Is Lady Luck a god worthy of worship? On the contrary she is not even a lady. She is a devil - chaos writ large - an effective enemy of all righteousness. A primary purpose of the plan of salvation is to overcome the vagaries and infidelity of circumstance and contingency - the law of the jungle, and establish a proper order according to mercy, justice, and design; and not a haphazard artifact of chance, circumstance, and dice throws.
So tell me, how does the plan of salvation fit into doctrinaire Neo-Darwinism? Is God himself an accident of nature?
Christian (#11), Infinite backward recursion doesn’t solve the problem in the slightest. It effectively asserts that the human body was not designed in any way, rather that it is a law of nature. Practically indistinguishable from Platonism, and pretty strongly contrary to the very idea of creation or design or divine intent as so strongly taught in the scriptures. A world where the future is practically indistinguishable from the past.
Brigham Young didn’t like it, but his teaching on that point naturally leads to the stranger ideas of Orson Pratt - worship of divine attributes, the one true God, the god of Aristotle and Plato, of whom actual divine persons were merely participatory shadows of, just like the Protestant idea of glorification with a few names changed.
I am convinced, on a variety of bases, that there was a date before which the Most High himself did not have a human form as we know it. i.e. that he and others had to get together and decide that we should have two eyes and ten fingers, that they using some means at their disposal created the first human spirit body and then that one of them entered in.
Now this is all in the world of spirits. It is conceivable that there was a process of spiritual common descent. It is also conceivable (horror of horrors) that the Most High occupied a different sort of body for a time while he guided the development of a better one. But none of that squares with doctrinaire Neo-Darwinism of this world.
The only remote possibility is that an intelligence can effectively accomplish such without a body of any kind and then this world was the first world on which the human form, both spiritual body and ‘physical’ body was developed in parallel, such that they could be separated.
I have mentioned elsewhere that it is my opinion that at birth an intelligence discards any previous spirit body, causing loss of memory, upon entering a new hybrid physical / spirit body, but that at death the spirit body is preserved, preserving memory until it is re-clothed with a physical tabernacle at resurrection.
That means that it is at least conceiveable, to me, that many of the souls born on earth did not have bodies of spirit before their advent here, just intelligences. However, for various reasons, I cannot believe that of God and most of the members of the divine council (cf. Ether 3). The biggest reason, is that I think an intelligence needs a body of some type to accomplish higher order mental function.
An intelligence without a body to me has the bare minimum of will and perception, that it might have been a virtual eternity between the time intelligences first started leveraging other (inanimate) material particles as tabernacles, and the advent of the sort of spiritual body with two eyes and ten fingers that spirits have today. The only way to believe otherwise is to assert that the human body is a Platonic form, and I think that is ridiculous.
Mark,
I think we are talking past each other. Many of your comments are directed toward Mr. Determinist Atheist. That is not me. My approach to this issue is roughly as follows: Since its inception, evolution has been derided as a stupid philosophy that is only believed because those evil scientists don’t want to believe in God. I’ve become convinced otherwise–that there is much truth to it and it has a lot going for it, even if it is not the whole picture. I’m fine with God having intervened from time to time, but I want honest evidence and arguments if such intervention is claimed to have a basis in science rather than faith (which is why the current incarnation of ID drives me nuts). And while evolution may have its limits, I dislike marking them purely out of theological comfort.
For my part, I see that you have your own departures from orthodoxy, some of which I find interesting.
I don’t think we are really that different.
Mark, you may not like infinite backward divine procreative regression and its affinity to Platonic forms, but as far as I can tell it is on the basis of philosophical taste and not revelatory or empirical evidence.
I don’t know what your basis is for saying Brigham didn’t like it. He did of course have a conflict with O. Pratt as you mention, but not about an infinite backward regression of divine procreation. B. H. Roberts considered it—what he called ‘eternalism’—to be a central feature and philosophical contribution of Mormonism.
Now I don’t like it either, in my case because it seems to conflict with secular evidence for evolution. I acknowledge this gives me a strong shove towards secularism because (a) I have difficulty continuing to trust Mormonism if traditionally central ideas have to be jettisoned and (b) because of the kinds of questions you raise in #12 (I didn’t take on the label ‘Spinozist’ for nuthin’, though I also respect Jared’s view; he seems to have a greater tolerance for (a) than I do). Unfortunately, I also think the kind of speculation you do in #13 is so far Out There—in terms of being untethered from either empirical evidence or authorized prophetic revelation—that I just don’t think it’s profitable to get into.
Christian (#15), You have misreferred one of my pronouns. “it” was a forward reference to Orson Pratt’s stranger ideas, not a backward reference to infinite backward recursion. My point is there is an inevitable association between the two modes of thought, Young’s and Pratt’s that is and that inevitable Platonism, explicit in Orson Pratt’s system and implicit in Brigham Young’s is that very association.
Now this particular variety of Platonism is notably un-Christian. It is the first principle of virtually any Christian Platonism that God is the author of all the forms, all Christian Platonisms except Pratt’s and Young’s of course.
Now I am a hard Platonist of sorts with regard to natural law, but definitely not with regard to anything that God creates. The problem with Young’s and Pratt’s system is that God never really creates anything, not intellectually at any rate. He just steps into a path authored by no one, sort of like a philosophical version of Calvinism, with the Platonic forms exalted to be God, and God reduced into a mere shadow. That was Orson Pratt’s system and it is a pretty inevitable consequence of infinite backward recursion of anthropoform divine persons.
All I can say is that B.H. Roberts conception of eternalism is not unique to Mormonism at all, it is a warmed over version of Platonism, indeed a step *backwards* from what the Hellenistic Christians believed in a large number of critical respects. It makes a large percentage of the scriptures literally incomprehensible, among other things.
Salvation comes in and only through the name of Jesus Christ. Is Christianity a Platonic form? Does Christ’s name have some sort of metaphysical power?
The scriptures also teach that salvation only comes through a suffering At-one-ment. Suffering is required to acheive that which is un-natural, not that which is natural. Everything about salvation is rather un-natural, as in it requires enormous service, suffering, and sacrifice and cooperation between heaven and earth to acheive. Hardly a Platonic form at all.
Since when did any person ever grow up without sin unto salvation without God’s help or their parents help. On the contrary, they grow up into first little savages, then big savages. Hobbes had a better idea of the undisciplined state of mankind than Rousseau did.
If there are any natural (uncreated) Platonic forms, they are most compatible with chaos, disorder, death and destruction. Virtually every thing good is synthetic (i.e. a creation), not natural in the metaphysical sense. Now we might overload the word, and speak of a second nature, a divine nature, but metaphysically speaking there is no such thing - nature simply doesn’t care one way or the other - only people care, and without cooperation and common consent, they mostly war one against another rather than accomplish anything worthwhile, whether they have an inclination for the worthwhile or not.
True righteousness and salvation are the most radically contigent concepts ever developed - so contingent that it has taken God a veritable eternity merely to establish them in their present form, and by all indications (cf. D&C 130:10) he doesn’t plan to stop his creative development of newer, higher, and more sophisticated modes and manners of righteousness and salvation.
Now as far as speculation goes, if you cannot see the connection, I would simply say that is because you have not treated the scriptures seriously or intensely enough. There can be a diversity of opinion of course, but I certainly would not strongly hold to a belief unless I had identified personally compelling reasons to do so. I am not a fan of the doctrine of doubt - come up with a hypothesis and test it against the principles of the scriptures and work and refine it. Revelation does not come to the people who rely on others as crutches.
Where did Brigham Young or Orson Pratt get their opinions? Some sort of magical brain download? I think not. They thought about things and pondered the scriptures for years. Still made some mistakes, but that doesn’t mean they should have just shut their minds to “speculation”. We would all be the poorer for it if they did.
So why don’t you want me to follow their example? Because you think that being ordained to an apostle magically endows you with the gift of coming up viable theology and that everyone else’s thoughts are dirt? Or do you just think that I haven’t been careful enough? Tell me where one finds the scriptural basis for Orson Pratt’s ideas. I can give you the scriptural or logical basis for *all* of mine.
Also, please tell me the authorized revelatory or empirical basis for doctrinaire neo-Darwinism. Isn’t that just speculation that we should stay away from if we want to stay spiritually healthy? A doctrine based on an unwarranted belief in divine impotence?
I did not say in #15, nor anywhere else, that I was a partisan of “doctrinaire neo-Darwinism”—just evolution more broadly speaking. (I am sympathetic to Gould’s critiques of Dawkins’ brand of neo-Darwinism, for instance.) Nor did I claim in #15 that there is any motivation towards evolutionary viewpoints from authorized Mormon revelation; quite the opposite, actually.
By “doctrinaire Neo-Darwinism” I mean the idea that all evolution is by natural selection according to random chance, no teleology or quasi-Platonic forms involved, just abiogenesis followed by stochastic evolution, according to tycho-deterministic natural laws, no free will whatsoever.
Will you or Jared take a stand on what is wrong with that? And tell us why?
If you won’t, would you please tell us what distinguishes your position from Deism - the idea that God authored the natural laws, wound up the clock, and then vacated the premises?
And if not pure Deism then when did he re-enter the picture? After he evolved from a microbe?
Or was his stochastic evolution from a microbe how God came to be in the first place?
This web log is supposed to be about Mormonism and Evolution, right?, but so far it seems no one is willing to discuss the reconcilation between the two, not even in the most hypothetical terms.
Well, for one thing, I bristle at talk of “natural selection according to random chance” and “stochastic evolution.” There is more to nature—including the unfolding of life’s pageant—than statistical mechanics. One would not describe the growth and development of a tree with statistical mechanics, for instance. There are in fact dynamical systems that do their thing in a way that is not random, but that generates interesting and nontrivial outcomes from simple rules acting on simple initial conditions—simple enough in both cases, arguably, to not require intelligence to generate. This is the phenomenon of ‘complexity’ in the technical sense.
Because of this I do not think complexity in nature (in the colloquial sense) proves the existence of God. Rather I think human experience with God is the only thing that could prove his existence, and that his role can only be known by what he may choose to reveal, and not by scientific or philosophic means.
How purported revelations fit with purported empirical evidence of what we are and how we got here is part of what this blog is about. Our collected thoughts to date can be reached under the heading Reconciliation Notebooks on the sidebar. I have not gotten very far at all. I think Jeff G. considers his work here largely complete from his perspective. If you think it’s too slow here, go start a blog!
Like Nephi, “I know that he loveth his children; nevertheless, I do not know the meaning of all things.”
Off the top of my head, what separates me from a Deist is that I believe God communicates with man, works miracles, and that Jesus was God’s son. I believe such things based on my own experience and that of others. And although this is not testimony meeting, I will add that I am holding out for a historical Book of Mormon and a historical Adam (though not necessarily the first Homo sapien–if such a thing exists.)
Nevertheless, King Benjamin notwithstanding, I do not believe that God literally lends us breath from moment to moment–ordinary biological principles are sufficient. Nor do I believe he pushes planets around, etc.
Abiogenesis and subsequent evolution may have suited his purposes just fine, and they should be studied to see what truth is in them. With the millions and billions of years involved, certainly he may have intervened, but if he did not need to, that is alright with me also. At his point I refer back to my comment #14.
Christian (#21),
A couple of minor objections. First statistical mechanics does not have anything to do with stochastic evolution per se. Statistical mechanics is a broad field for making proper calculations in the presence of missing information - i.e. given the proper equations of motion, it provides mathematically precise projections of the state of the system and what can be known about it at any future time. It is the basis of modern thermodynamics in particular. I use the term statistical mechanics instead of statistical thermodynamics because the former is a broader and more general field - i.e. it can deal with systems that are not classical thermo-mechanical hybrids just as well.
Second, there are a lot of technical definitions of complexity, it appears the one you have adopted is one from chaos theory. My criticism here is that chaos theory is based on widely diverging deterministic systems.
Now there are two key properties of all known deterministic systems: First, they are information preserving - i.e. they have time symmetry and can be run backward and forward. Second they have a constant Kolmogorov complexity, because the state at any future time is reducable the the original state, plus the equations of motion plus the time interval. Essentially, in a deterministic system, nothing happens. All the increased “complexity” is an illusion. In fact if you wait long enough, history will repeat itself in every detail (cf. Poincaire recurrence theorem). The actual Kolmogorov complexity of the system is a constant.
[Now it is true that there are information losing deterministic systems, at least in terms of mathematical abstractions, but generally speaking they violate conservation of energy or locality or both. No known natural equations of motion are information losing. Some scholars think that the second law of thermodynamics is based on some unknown proto-principle that is naturally information losing instead of an artifact of missing information, but no one has any evidence for that.]
If the growth and development of a tree is a deterministic system in a thermal environment, which there is reasonable evidence to suggest that is actually the case (trees do not appear to have free will), statistical mechanics, which is a generalization of normal mechanics, would be able to handle the problem just fine.
Jared (#22),
A few points of agreement: I also believe in a historical Adam, but have no idea how he showed up here ca 4000 BC. I definitely believe (more like have a spiritual witness of the fact) that the Book of Mormon is a historical and inspired record.
I have mentioned before that Genesis 2-3 makes no sense to me theologically or historically, so I am open to a broad variety of alternatives including common descent, as long a long list of scriptural principles are satisified, notably the ability to live as spirits with two eyes and ten fingers after death, be resurrected into a glorified body, the existence of pre-mortal spirits of some type, and extensive divine participation in the creative process.
I do not believe in the violation of true natural laws (e.g. conservation of energy, momentum, charge, eternality of intelligences, etc.) That means to me that the exercise of free will is the only way God can get anything done or influence the natural world, usually through the agency of his body, which is the greatest technology ever developed - the working whereby he is able to subdue all things in the process of time, and exercise a subtle spiritual influence over the whole universe (cf. Col 3:20-21)
If further believe that spirit is not that different from ordinary matter, in fact the most useful analogy is simply that the spirit is like the wave component of a Quantum wave-particle hybrid, interestingly enough with non-local phase correlation. My working theory is that the spirit acts at a distance according to the equations described in Bohmian quantum mechanics, a theory which is statistically indistinguishable from ordinary quantum mechanics.
As such I also do not think that God needs to push planets around, or strain to operate any of the natural laws. That would be an enormous bother, even if it were necessary, and is untenable in LDS theology for a wide variety of other reasons, notably divine personal multiplicity and the doctrine of exaltation. I do believe in the Light of Christ by the mechanism of the spirit that I just described however, though I believe that it is normally very subtle, according to the wisdom and economy of God.
I believe that when God wants to make a “miracle” happen, he must expend actual effort and energy to do so. There is scriptural evidence for that. That may mean dispatching angels, it may mean the more intense and temporary exercise of spiritual influence. I have nothing against the use of divine technology to accomplish miracles, provided it is tenable in context - I regard the body as the ultimate piece of divine technology.
Now this is pretty standard stuff from the perspective of earlier LDS scientists from Talmage through Widstoe. I see the universe as a perfectly deterministic system with one major exception - intelligences, which have free will, the most notable natural property of which is to inject non-stochastic information into the system. A perfectly deterministic universe makes no sense to me, and a tycho deterministic universe is even worse.
Jared, what do you believe about the physics of miracles? Violation of natural law, or exercise thereof?
Jared: “It strikes me somewhat as parasitism that when further evidence supporting evolution is discovered, naysayers come in and act like such evidence was consistent with their interpretation of creation all along–as though they were expecting such a discovery.” (#5)
First, I accept evolution in some form, so please don’t mistake me for one of the people you described in #14 as thinking science is evil etc.
That said, it strikes me as extreme hubris when scientists act like they are the only ones allowed to adjust their theories based on new evidence, or try to show that such evidence is not incompatible with a pre-existing world view. Everyone must try to account for the facts as they are currently understood. Failure to do so leads to religious traditions (which I have no sympathy for) where facts are considered evil and faith involves willful ignorance. In fact, that is the kind of tradition you seem to be specifically opposed to here. Arguments like the one above are an attempt to discredit the kind of religious view you actually prefer.
The implication of your comment seems to be that the religious people who try to account for the facts are “parasites” in that they feed on the evidence produced by scientists without contributing to the body of evidence. Thus, the “host” is the scientific community and the “parasite” is the naysayer who tries to show that the evidence produced does not conclusively prove the scientific world-view. This seems like a great zing until you realize that some scientists are religious, so the host/parasite dichotomy is misconstrued.
The idea that evolution can claim evidence, but religious arguments made to account for the same evidence are somehow parasitic bothers me in the extreme. The facts are not the exclusive property of one world view.
Mark,
I have no idea what tycho determinism means. In fact, I just googled it and one of the top hits was one of your comments at The Spinozist Mormon.
As for miracles, I haven’t thought about them extensively but I would go for exercise of natural law. I think I am in line with early leaders who viewed miracles simply as the exercise of laws that we don’t understand.
Jacob,
Thanks for stopping by. I am not against religious people (of which I am one, see #22 above) trying to incoporate new facts into their beliefs. I think you were reading my comment more broadly than I intended, and I think we may be mostly in agreement. There is a difference between accepting a scientific principle based in the evidence and adopting a totally new worldview.
But just as there were people in the scriptures who would not allow fulfilled prophecies to teach them anything, there are people who will not allow fulfilled predictions of science to teach them anything. Rather, they twist the new information to make it fit comfortably with their beliefs. The twisting usually produces something that sounds nice on the surface, but fails to account for many details.
I’m not saying scientists are perfect or are always right, but perhaps you see my point.
Jared,
Yes, I see the point you are making in #27 and I wholeheartedly agree. I think we do largely agree and I apologize if my comment came off as a general attack on you. As a first time commenter here I probably should have been more careful.
If your point in #27 was what you were getting at in the snippet I took issue with from #5, then we are on the same page. I took it as a response to Mark’s comment in #4 and the argument Mark made didn’t seem to me to be of the sort you descibe in #27. Anyway, nice post, I enjoyed reading through.
Jared (#27),
Tycho-determinism is a compound word I made up from “tychist” a word Charles S. Peirce adopted to describe chance based causation, from Tyche, the Greek goddess of luck. Many QM people believe that quantum mechanics is inevitably tychist, however this has not been established. Nonetheless, the ordinary quantum mechanical world view tends to be tycho-deterministic, deterministic evolution of the wave function with some sort of random “collapses” in between.
When I first learned about the theory of random wave function “collapse” (upon measurement) in my first quantum mechanics class, I couldn’t believe me ears, and regarded the theory (despite its most accurate statistical results) with some derision until I learned about quantum determinism some years later.
In short, I don’t believe there is such a thing as tychism, or metaphysical randomness. Coincidence, thermal noise, initial randomness, sure, but nothing that occurs randomly per se. I of course do believe in agent causation, which makes me a libertarian determinist, where liberty is an aspect of intelligences alone, everything else being purely deterministic.
(Peirce’s third mode of causation was agapistic, or love based causation, but I do not understand the details of what he meant by that. I tend to thing he realized that a tycho determinist world was barren, actually running down hill, and made something up to fill in the gap, pending further study)
I could make lots of other arguments that are not so unusual as #4. I made that argument to make a point, that even design from a drawing board has the same phylo-”genetic” structure, when designing a large number of generally related things. Simple economy, that is all.
Jared (#27 continued),
I agree that what you describe is a failing. However scientists are just as guilty of it as anyone else, if not more, refusing to consider any possibility that does not fit within their atheistic, tycho-determinist world view, no matter what the evidence. The amazing thing is that such scientists have any ethics at all, because they clearly do not believe there is any rational basis for them, beyond selfishness and survival, both instincts completely unexplainable from their metaphysical pre-suppositions.
Anybody can be close minded. But let’s not paint scientists with too broad a brush. Many scientific disciplines involve very little thinking about how the universe ticks at the most fundamental of levels, and of course there are a range of views on religion among scientists.
As for atheism and ethics, I read a few blogs written by atheists. From what they write, it seems that atheism is often portrayed in a strawman way, but on the other hand I don’t make it my business to try to fully understand or argue with them.
There are lots of nice atheist or agnostic moral philosophers, but they tend to have a metaphysics that is much more imaginative than Laplacian determinism, or determinism plus dice throwing.
My point is not that scientists, by and large are immoral, just that many of them get enormous amounts of press arguing from propositions that are strictly contrary to morality, indeed strictly contrary to immorality. How can a gene, for example, be selfish?
And worse, they treat anyone who disagrees with them on religious or philosophical grounds as the ultimate in simpletons. That is why scientists are often so universally despised in other professions. The most prominent among them are either amoral or are moral hypocrites.
The scientists who helped Hitler carry out the Final Solution are a typical example. Now modern scientists say that is wrong, but the most prominent among them cannot say why, because their world view is contrary to any basis for morality, other than a purely arbitrary, subjective, coincidental, random one, and hardly that.
So calling such scientists atheists is an understatement. Many of the most prominent ones are monsters.
Mark,
Where do you come off broadly painting prominent scientists as monsters? Bacon, Newton, Huygens, Darwin, Crick, Hawkings? Also, that they are “often so universally despised in other professions”? What are your data for such inflammatory statements? I know your goal is not to win friends, but making enemies with such statements will never accomplish understanding and a dialog that will lead to discovery of truth.
Many of the most atheistic (at least self-proclaimed) people I know are more honest and kind and giving and caring than the self-proclaimed Christians I know. Why is that? So what if they are conflicted in their morals and philosophies; if I were laying off the side of the road beat and broken, I would rather take my chances with the atheistic monsters than the free will believers.
Mike “So what if they are conflicted in their morals and philosophies[?]”
If we are talking about people then I agree it does not make much of a difference. A good person is a good person, and it is obvious to me that many atheists are good people. I have known some quite well personally.
However, if we are talking about philosophies then a conflict between morality and specific philosophies is quite relevant. If we deride various religious traditions for totally ignoring the fossil record and scientific discoveries like that mentioned in this post, why should we not similarly deride scientists whose atheistic world-view has no way to account for an objective morality? Is the fossil record more important than morality? Why is it okay to ignore one but not the other?
The answer to your “so what” question above is that if they are conflicted in their morals and philosophies it may be an indication of a problem with their philosophies. Just as religious people have been known to look for gaps in which God may be found, atheists have been known to look for loopholes through which they can appear to account for the existence of morality.
Jacob,
It’s all fine a good to make it the conflict relevant based on philosophies. However, I doubt there is anyone who doesn’t have some inconsistencies between his morality and philosophy, most of us experience a large gap between what we hold to be true and how we behave. I guess I have more patience with those who doubt or adamantly deny God and yet still do good than the hypocrisy of those who claim to believe in God and then grind the faces of the poor and take advantage of their neighbor at any chance.
Mike,
If you want to make it about _people_ (as you clearly do) then you are right (again) that the good atheist is to be preferred over the bad theist. I agree with you on that and tried to say as much in my previous comment.
Mike W.,
You broadly over read my statements. Nowhere did I say that all prominent scientist were monsters. Nor did I refer to any of the scientists you who name. I was referring, quite explicitly, to modern scientists of the twentieth century who get a lot of press for either explicitly ridiculing the idea that their is any basis to traditional morality, or the world of the spirit while simultaneously advocating some of the most vile behaviors imaginable. I used the German eugenicists who had no qualms assisting Hitler do his thing as a practical example.
That sort of amorality has not dissapeared. It is most prominent in the field broadly described as “bioethics” - the reasoning of the advocates of abortion, euthanasia, infanticide is typical. It is also extremely prominent in sociology and psychology. There have been dozens of books written on the effect that the doctrines of many prominent psychologists have had on religious communities intensely exposed to them - in many cases, completely devastating them.
Now tell me, how are we to distinguish the activities of such “scientists” from a man like Korihor? And how can we distinguish the activities of scientists who preach the doctrine than man does not have a soul, that there is no ground of morality, just eat drink and be merry for tommorrow we die, from a monster?
According to those scientists, all of us are monsters - as in creatures without a soul. So it is hardly surprising that the worst of them behave that way, and teach others to do the same. In fact “monster” is a kind term, some of them have been so endowed with the spirit of immorality that a “devil” would be more accurate description.
What is a devil anyway, except someone who actively seeks to destroy the work of God, an enemy of all righteousness. Most agnostics are not devils. Most atheists are not. But some of them, it is very hard to tell the difference, because they preach the gospel of Korihor. And many scientists are the most prominent defenders of Korihor’s particular brand of “faith”, or rather anti-faith.
I am not speaking of skepticism or agnosticism here, I am speaking of those who are dead set on preaching the doctrine that there is no God and no ground for morality. Unwitting missionaries of the evil one.
Mark,
While I agree with your sentiment to a degree, I don’t think I over read your opinion when you use words like “often so universally despised” and “many of the most prominent scientists are monsters.”
That said, I agree that placing complete trust in self-proclaimed or institutionalized and credentialed experts, be they scientific or religious, is full of danger. There have been as many mosters/devils from the religious side of the spectrum as from the scientific; and the religious ones have a much longer history of using their philosophy and theology to manipulate and oppress their followers. Although Korihor’s accusations of Alma teaching the people abolut God in order to opress them doesn’t apply to a lay priesthood that follows Christ in their principles and behaviors, there are widespread historic examples. Jim Jones and other cultists can fall into this category. Currently Pat Robertson makes statements that are so inconsistent with Christianity that luckliy most recognize him as a crackpot.
I guess my point is that what’s good for criticism of the scientist is also appropriate for criticism of religionists, when applicable. Generally anyone who has unchecked influence (the Church in the Middle Ages and science to a degree now) will use that influence to retain power and control.
Oh, c’mon Mark. You’ve got to be kidding in this last comment of yours. While there certainly are some scientists who aren’t exactly a pillar of excellence, you can say the exact same thing about any group of people. What exactly is your point with this?
Is it the scientists fault that every single bit of evidence from cognitive science suggests that there is no extra-body soul-stuff? What do you want them to do, lie? I fail to see how that would make them any more respectable in any way.
A rightfully non-theistic science does not necessarily imply an atheistic-science, although it certainly will if anybody’s God is one of the gaps. To set the record a little bit more in line with reality: The scientist (using your negative example) does think that we have a soul … of sorts. It’s just not the same kind of soul that mankind has always assumed that we had. The soul which we actually have is made up of lots and lots of biological machines and is not immortal. But this doesn’t make us into “monsters” at all.
Furthermore, the boogey-scientist doesn’t say that morality has no ground at all, only that it doesn’t have the grounding which traditional religion has always taught that it had. They claim that there is no transcendent justification for a moral system, and that any appeal to religious doctrine or God is simply begging the question. In fact, they go even further than this today, in claiming that morality has a universal, though still not transcendent basis in our evolved psychology. Again, they claim a ground for morality, but simply reject your ground.
Additionally, the idea that scientist are preachers of a full-blown hedonism is simply a joke. If anybody lives a life in contrast to the hedonist it is the well-known and credentialed scientist. Just because you see these things as being the only alternative to your religious beliefs, does not mean that everybody you disagrees with you must feel that way as well.
(By the way, the Korihor story is the biggest joke in the entire scriptures. Who can’t help but roll their eyes when the cliche atheist who presents some serious questions turns out to have been lying the entire time? C’mon, couldn’t they at least try to address the issues he brings up rather than simply calling him a servant of the devil, an accusation which conveniently happens to turn out to be literally true?)
Jeff, wouldn’t the proper formulation be “. . . not one single bit of evidence from cognitive science suggests that there is extra-body soul-stuff”?
Thank you, Tom. ;-p
Mike W.(#38),
I understand and appreciate your perspective. If I were born in the Middle Ages I would probably be dissenting against the evils of the Church of the time as well. However, in our day and age, the evils as I see them gain critical and often mockingly explicit intellectual support from a certain small number of outspoken scientists.
Jeff G.,
I do not have much of a problem with agnostic or secular science. I have a problem with scientists who use their public persona to preach against religion. In other words, the problem is not the science, it is the philosophy, and its unwarranted anti-religious and anti-spiritual conclusions.
Now you have made a summary of the arguments against an absolute or transcendent morality. Now what I would like to hear from you is any explanation of how our sense of morality has any grounding in natural law, e.g. the laws of physics. And if it has no grounding in the necessary, and you deny agent causation or free will, then how is morality anything other than an accident of nature, i.e. a strictly arbitrary consequence of an arbitrary physiology.
And if you think physiology is not arbitrary, could you explain where its normative content comes from, beyond the most basic laws of physics?
In other words please explain to me why we should have any nomological component of morality at all, instead of a strictly utilitarian one, in the common sense of the term. Say for example two people are starving in the wilderness. Is it okay for one to eat the other, without his consent? Please explain from the laws of physics.
[…] See also my previous posts, Mobile Genetic Elements and Animal Relationships and Understanding Trichotomy. […]