More on Sex

Well it appears that sex is the topic of the week here--this time in yeast. Given the prevalence of sexual reproduction among organisms on this earth, there must be some purpose or advantage for it. The trouble is that evolutionary biologists have had a hard time figuring out what it is. They've generated hypotheses, but testing them is difficult to do. This is where the yeast come in.

Yeast have the ability to divide asexually, or they can undergo a process of meiosis that results in 4 spores equivalent to gametes (ie. sperm/eggs). Two spores can later fuse to form a dipliod yeast again. In the latest Nature a group has published the results of their experiments comparing yeast that reproduce sexually to those asexually. The sum-up is that the sexually reproducing yeast were better able to adapt to a harsh environment.

For a better and more thorough explanation, see Pharyngula.

Continue reading...

The Birds and the Snails

Carl Zimmer has a post discussing the evolution of love darts in snails. You may not be particularly interested in the sexual practices of snails--I can understand that. But you should read the post anyway because it is an interesting example of an evolutionary sexual arms race.

Continue reading...

With the Discovery Institute, Who Needs Cable?

I don't have cable, so I miss out on such entertainment as the Discovery Channel. I do have internet access so I get a different kind of entertainment--the Discovery Institute. Their Center for Science and Culture operates a blog, which appears to mainly be used for complaining about media coverage of intelligent design "theory." One of their consistent complaints of late is that they are being unfairly and inaccurately lumped together with creationists. They know that it will be difficult for them to make any scientific or legal headway as long as they are associated with creationism.

Continue Reading

Now I can appreciate the challenge of trying to have others define your beliefs as you define them. I recognize that it must be frustrating to always be catagorized with a movement you are trying to distance yourself from. Recently one exasperated ID advocate challenged anybody to find a leading ID intellectual that did not accept the Big Bang or the age of the earth. The Panda's Thumb accepted the challenge, with humorous results. (Read the whole thing--including comments.)

The latest from the CSC is a complaint about how they were portrayed in a segment of PBS's The Newshour with Jim Lehrer. The post tries to draw a clear distinction between creationism and intelligent design.

The theory of intelligent design and creationism are different. Let me make this point very clear:

Creation Science is defined by the following six tenets, taken together:

-The universe, energy and life were created from nothing
-Mutations and [natural] selection cannot bring about the development of all living things from a single organism.
-The earth is young, in the range of 10,000 years or so.
-Humans and apes have different ancestries.
-Created kinds of plants and organisms can vary only within fixed limits.
-Earth's geology can be explained by catastrophic events, primarily a worldwide flood.

Intelligent design on the other hand, involves only two basic sceintific assumptions:

-Intelligent causes exist for origins of life.
-These cause[s] can be empirically detected.

First let's take the assumptions of ID. The first one is not very specific. Are we only talking about ID vs abiogenesis, or does the origin of any species fall under ID? The second assumption is really a hypothesis--one that is yet to be demonstrated convincingly. Now, I thought that the main way of detecting design was to find irreducibly complex systems. But earlier in the post there is talk of molecular machines. So is any and every enzyme without a clear precursor designed? After all, enzymes do some pretty specific chemical reactions.

Now what is interesting to me is that the tenets of creationism were not denied here. In fact, ID proponents hold to several of them. You don't have to search hard to find ID support for the second, fourth, and fifth creationist tenets. Not only are some of these tenets necessary assumptions for many of their arguments, but ID advocates often argue them explicitly.

They try hard to distance themselves from religious conservatives:

The story moves quickly to the typical stereotype of religion vs. science saying that is an issue mostly focused on religion and faith. To bolster that they have lots of high school students who express their doubts about Darwinism in overtly religious terms. The story leaves no doubt that evolution is under an attack led "mostly by religious conservatives." Interesting. David Berlinski would be surprised to hear that. So would Stanley Salthe. Or, Giuseppe Sermonti. Or any number of other non-religious scientists skeptical of the claims of Darwinism. Contrary to the Newshour's premise at the outset, doubting Darwinism is not solely a consequence of religious belief.

The interesting thing here is that the Scientific Dissent From Darwinism document is subject of the link. It is portrayed here as though the scientists on the list are non-religious. While some may be, many (probably most) certainly are religious. I once picked an actual biologist on the list, at random, and looked to see at what institution they were a professor. Answer: A Christian college.

Finally, the reason such superficial treatment of ID is given in the piece is: "because the issue for the media isn't about the science involved, it's about making this a culture war issue." Ooohhh, I see. So it's all about the science for the Discovery Institute. In that case, they may want to quit putting out books like Defeating Darwinism where the call to culture war is blatant and the attack on evolutionary theory is unabashedly about its conflict with Christianity.

With entertainment like this, why should I want cable?

Note: be sure to see update in comments.

Continue reading...

Publishing Pecking Order

My last post on dinosaur flesh reminded me that many of you are not familiar with scientific literature so I thought I would give a quick tutorial. First there is a distinction between popular science publications and primary journals. They are not necessarily easy to differentiate by name. For example, Scientific American is a popular science magazine--it is geared toward the educated lay person. It does not publish actual research, though it may report on research published elsewhere in the primary literature.

Primary research articles are contained in innumerable journals. This is where the nuts and bolts of research are reported. Each discipline has its own hierarchy of journals. Some journals are bread-and-butter journals. However there are several publications that form a sort of hub. Nature Magazine, Science Magazine, Proceedings of the National Academy of Sciences (PNAS)--are all prestigious journals (probably in that order) that cover a wide range of scientific disciplines. Nature has several more specialized journals that are also prestigious. Some people go their whole career without publishing in one of these journals. Really good researchers publish there repeatedly. Now this doesn't mean that every article in these publications is flawless--you can find bad papers in any journal. But when you see the names Nature, Science, or PNAS, a little flag should go up and remind you that these are journals that are pretty selective in what they publish.

Continue reading...

T. rex Flesh Recovered

I'm late to blog on this but if you are not aware of it already, the recent issue of Science Magazine has a paper discussing the recovery of soft tissue from a Tyrannosauraus rex fossil. The tissue was taken from a femur and demineralized which resulted in tissue that is stretchy and appears to have pretty good preservation of microscopic structures. My understanding is that there is a slim to none chance of obtaining any genetic material. Nevertheless it is interesting and amazing. You can read a little more about it at Scientific American.com.

Continue reading...

Polygamy is Pretty Mild By Comparison

They're talking about polygamy over at BCC and T&S. It's certainly a topic that raises many questions with few real answers. Compared to what's going on elsewhere, however, it's pretty mild.

Purely by coincidence I've been reading about the evolution of sex in Evolution: The Triumph of an Idea, by Carl Zimmer. It's a really good book and I plan to review it here when I finish it. Anyway, when it comes to sex and reproduction, it's a strange and twisted world out there. If you view nature as fundamentally fallen and antithetical to God's plan and purposes, then this will not suprise you. If, on the other hand, you view nature as more or less an expression of God's glory and purposes--well the puritan in you may be shocked.

I'll get into more details later. But for now you can read a little about Bonobos, a type of chimpanzee. (I'm just giving you the article link. What internal links you follow are your own business.)

To get ahead of myself, I'll pose a question: To whatever extent polygamy operates in time or eternity, is God trying to effect (yes, I mean effect, not affect) a biological purpose?

Continue reading...

Approach to the Masculine

[This topic has explosive potential, but I wan to raise it anyway. My purpose is to ask questions rather than give answers. Nothing in my post should be interpreted as pertaining to specific situations and circumstances, nor should it be interpreted as excusing sin or casting judgment.]

Recently my bishop decided that we would devote one of our priesthood lessons to Pres. Hinckely's talk from last conference dealing with p0rn0graphy. The Relief Society, instead, were to use the 13th Article of Faith as the basis for their lesson. I couldn't help but wonder if women should be excused from discussions of this issue. (None of this should be construed as criticism of my bishop--I think he does a great job.)

Continue Reading

This approach seems to carry a subtle message: sexual interest is a male problem and it's wrong. ("We're sorry, dear sisters, that your husbands are so carnal and devilish. Their interest in sexuality clearly runs counter to the gospel message. We're whacking them on the knuckles for it again--hopefully they'll get the message. You sisters are as pure as spring flowers and we hope you'll continue in your virtuous ways.")

Now I don't dispute that we men need some whacks to the knuckles from time to time. Some need them often. But I want to dig a little deeper. What is it about the male brain that makes it so susceptible to this problem? Is the circuitry in the brain responsible for this a product of pathology and only detrimental, or is it possible that it can be used in good ways? What things can wives do to help bind their husbands to them?

Pres. Hinckley's talk last conference included part of a letter from a woman whose husband had this addiction. She said, "All I ever wanted was to feel cherished and treated with the smallest of pleasantries . . . instead of being treated like some kind of chattel." Getting men to understand and remember what women want is a huge challenge. Maybe we should talk about it in our lessons more. But is there something that men want that is going unfulfilled and contributes their development of this problem?

In The Miracle of Forgiveness, Pres. Kimball makes the point that Jesus recognized that sin was often a symptom of deeper unmet needs. Of course sex is part of the issue, but it is more than that. Emotional and intimacy issues are involved. Can these be addressed in a way that minimizes, as much as possible, the risk for men? Is it possible that in trying to get men to behave, masculinity has been denigrated in the process and as a result neither men nor women understand what the legitimate needs of men are? Yes, men need to exercise self-control, but are there things that women need to do? If there are, should they hear about it in Relief Society?

I don't know what light science (both the hard and social) can shed on the problem, but to the extent that there is any I think we ought to discuss it. Let's understand what makes us tick. LDS Social Services has professional counseling for this addiction, but the only real advice that most of us hear is "don't touch it." It seems to me that the more men and women understand what's going on in the psychological roots, the better they can address this issue.

Continue reading...

IMAX: Culture Wars in 3-D

I'm late getting to this but this news article reminded me of the issue. Apparently there are IMAX theaters in the south that have decided not to show the film "Volcanoes of the Deep Sea." The reason is that they are afraid that references to evolution in the film will result in poor ticket sales.

I haven't seen the film so I don't know how extensive the discussion of evolution is. However the reason for the reference is that there are microbes that live in some of the most inhospitable places on earth, including deep sea vents. Some scientists think that given the inhospitable place the earth used to be, maybe these microbes hold clues to the development of life on earth. I guess this drew complaints from test-screening audiences.

Well, what can I say? It's the free-market system at work. I can't blame the theater owners for worrying about their bottom line. At least the public schools still teach science...

Continue reading...

Adam and Eve: How?

[The following is a cross-post from Mormons and Evolution.]

The year following the First Presidency's statement, "Origin of Man," the following was published in the Improvement Era, April 1910:

Origin of Man.-"In just what manner did the mortal bodies of Adam and Eve come into existence on this earth?" This question comes from several High Priests' quorums.

Continue Reading

Of course, all are familiar with the statements in Genesis 1:26, 27; 2: 7; also in the Book of Moses, Pearl of Great Price, 2: 27; and in the Book of-Abraham 5:7. The latter statement reads: "And the Gods formed man from the dust of the ground, and took his spirit (that is, the man's spirit) and put it into him; and breathed into his nostrils the breath of life, and man became a living soul." These are the authentic statements of the scriptures, ancient and modern, and it is best to rest with these, until the Lord shall see fit to give more light on the subject. Whether the mortal bodies of man evolved in natural processes to present perfection, through the direction and power of God; whether the first parents of our generations, Adam and Eve, were transplanted from another sphere, with immortal tabernacles, which became corrupted through sin and the partaking of natural foods, in the process of time; whether they were born here in mortality, as other mortals have been, are questions not fully answered in the revealed word of God. For helpful discussion of the subject, see IMPROVEMENT ERA, Vol. XI, August 1908, No. 10, page 778, article, "Creation and Growth of Adam;" also article by the First Presidency, "Origin of Man," Vol. XIII, No. 1, page 75, 1909. [emphasis added]

For more discussion about this passage see Duane Jeffery's article here.

Since Joseph F. Smith was one of two editors at the time, this passage has been attributed to him and although it probably did not reflect his own opinion it shows that no specific creation process was officially endorsed. Although the creation of Adam and Eve has been the topic of continued discussion in the years since this statement, the lack of official clarification has been maintained.

Some cite certain scriputures was well as statements by Joseph Smith, Brigham Young, and others, to argue that Adam (and presumably Eve) was physically born of Heavenly Parents and later became mortal in the manner described in Genesis. This would seem to contradict the scriptural teaching that Jesus was the only physical son of God. Elder Bruce R. McConkie resolves the contradiction this way:

Father Adam, the first man, is also a son of God (Luke 3:38; Moses 6:22), a fact that does not change the great truth that Christ is the Only Begotten in the flesh, for Adam's entrance into this world was in immortality. He came here before death had its beginning, with its consequent mortal or flesh-status of existence. ("Son of God" in Mormon Doctrine)

However Stephens, Meldrum, and Peterson in their book, Evolution and Mormonism, rightly point out that the phrase "Only Begotten in the flesh" is not contained in the scriptures.

For some, the idea of a divine origin of our physical bodies presents a significant impediment to accepting the concept of common descent as being applied to mankind. And yet investigation of the anatomy, genome, and development of humans does not reveal any marks of special creation. Rather they strongly support that we and other primates have common ancestors. Stephens et al. write:

The unsupported notion that our physical bodies must be in some way special, i.e., apart from nature, and directly descended from God's immortal body is a major source of conflict with evolution theory. There are no scientific data to support any of these supernatural hypotheses; in fact, the body of accumulated scientific evidence stands against them. If our physical bodies are in some way "special," in that our ancestors' physical bodies came from some other planet or directly from God, then we could predict that the physical nature of our bodies should be in some way different from those of life forms originating on this earth.

Regardless of whether Adam was a literal son of God or was "transplated from another sphere," the basic conflict with science remains the same. Whatever the truth is regarding the origin of our physical bodies, it must explain the evidence that we see for common descent. The following are two hypothetical scenarios that might resolve this discrepancy:

1. Stephens, Meldrum, and Peterson propose a theistic evolution scenario where Adam and Eve's physical bodies were the result of hominid evolution. However, at some point after their spirits were placed into their physical bodies, they became immortal by partaking of the fruit of the tree of life in the Garden of Eden. (Perhaps they experienced something similar to translation.) This is the immortality that they later fell from. Variations on this scenario are possible, including the geographical and organismal range involved.

2. Another scenario might be a compromise between theistic evolution and the idea of a divine origin of our physical bodies. Perhaps Adam and Eve were born (physically) of Heavenly Parents. Their Fall entailed taking on the physiology of the most similar hominids by some sort of tissue transplantaion. Although I am not sure whether it can be reliably traced to Joseph Smith (I cannot trace it past Joseph Fielding Smith), a common doctrinal concept is that Adam and Eve did not have blood while in the Garden of Eden. Since blood is derived from bone marrow, perhaps something like a bone marrow transplant occured where the donors were the most similar mortal (non-children of God) hominids. Certainly this scenario is highly speculative, but something like it allows for our close genetic relationship to other animals while retaining our spiritual and physical relationship with God. Adam and Eve thus fell by taking mortal physiology and genetics into their bodies, and our relationship to other animals is therefore a partial illusion.

Comment at Mormons and Evolution

Continue reading...

Terri Schiavo: It's Either Cruel or Not--Pick One

I wasn't going to post again about Terri Schiavo again--it's such a circus. But there has been some discussion in the bloggernacle here, here, and here, so I just want to say my piece. (I also posted once before here.)

Continue Reading

I have no reason to disbelieve doctors who say that she is not conscious and that her movements, such as smiles, are actually involuntary reflexes. I am therefore alright with letting her pass on. On the other hand since her family is so against it, it seems like the honorable thing for her husband to do is to give them full custody and move on. I agree with Kaimi at T&S that much of the current argument is over evidentiary nuances and politics. I think both sides of the debate raise legitimate issues. However some things that people are saying drive me crazy.

First, on talk-radio people talk with disgust and horror about how Terri is going to be starved to death--it's so barbaric. Yet they turn around and emphasize the importance of a living will. They seem to be saying that the withdrawl of the feeding tube is only cruel and wrong unless the person left a living will stating that they don't want to be kept alive artificially. It seems to me that the issue of whether it is cruel or not is independent of Terri's pre-injury wishes. If it is cruel, are we prepared to euthanize when someone doesn't want to be kept alive artificially? I doubt conservatives would go for that--slippery slope, you know. If it isn't cruel then talking about how horrible the manner of death is, is really an appeal to emotion, not reason.

Second is the hyperbole. I have repeatedly heard people say that we don't even treat our animals this way. One person even said that if we did, we'd be "taken out and shot." Good grief--is this supposed to convince anybody? We put animals down all the time--healthy or not. And that's just the domesticated ones. Others we shoot, poison, trap, etc.

I think that the complexities of this case make it very easy to "look beyond the mark."

Continue reading...

Rubella Banished From U.S.

According to this article, Rubella (the "R" in MMR vaccine) has been elminated from the U.S. The only reported cases in the last year have been imported.

Continue Reading

Rubella, also commonly known as German measles, soft measles or three-day measles, is a usually mild viral infection that causes a fever and a rash.

But early in pregnancy it can cause birth defects ranging from deafness to severe brain damage and death.

"During 1964 and 1965 a rubella epidemic in the United States caused an estimated 12.5 million cases of rubella and 20,000 cases of congenital rubella syndrome which led to more than 11,600 babies born deaf, 11,250 fetal deaths, 2,100 neonatal (newborn) deaths, 3,580 babies born blind and 1,800 babies born mentally retarded," the CDC said in a statement.

A vaccine was licensed in 1969 and since then the rubella virus has been included in the measles, mumps and rubella or MMR combined vaccine routinely given to babies and young children.

Now the CDC estimates that 93 percent of the nation's children younger than 2 get the vaccine.

Of course, this doesn't mean we stop vaccinating. Importation of the virus is always a threat, but this is good progress.

Continue reading...

Petrified Wood at Meridian Magazine

Meridian Magazine recently posted an article about petrified wood. You can find the article here. The authors comment on a news story that reports that scientists have been able to petrify wood in the laboratory in a short amount of time. They raise the question of how long it actually takes petrifaction to occur in nature. Rather than millions of years, they suggest a much shorter amount of time. They wonder whether decay processes require a short timescale for petrifaction.

Continue Reading

Now the issue of petrifaction is interesting enough, but their purpose in writing the article appears to be to neutralize arguments against a young earth or worldwide flood. They seem to think that some petrified wood could be a result of Noah's flood--that the timescale is plausible. However, they state that they are not trying to be dogmatic about age of the earth or flood issues. They also propose that the reason that science does not convincingly point to God is because it would degrade the testing ground of mortality. Finally as proof-of-principle that petrifaction can occur quickly, they discuss a wall in England where objects placed in the flow of highly mineralized water petrify in months.

In discussing the petrifaction process they offer only a couple of references--one of them World Book Encyclopedia. Now I don't mean to be snobbish or anything, but World Book Encyclopedia? Is that really the most authoritative source they could dig up? Wouldn't a geology textbook or an interview with a geologist be a little more authoritative? I'm not saying that the encyclopedia information is incorrect, just that if they really want answers to their questions a more authoritative and specialized source would be prudent.

Well, I don't have time to go to the library and research the issue--although next time I'm there I may see what I can find--but I did some internet searching as well. I found this page on the North Dakota Geologic Survey website. It seems to answer some of the questions about petrifaction. The specimen is buried in a manner that excludes oxygen--thus slowing, if not halting, the decay process. It also points out that various amounts of detail are retained. Perhaps this reflects varying amounts of decay. Oh, and there is an "ask a geologist" feature. As for the time required, my limited reading suggests that it depends on the circumstances. It seems obvious to me that the concentration of the relevant minerals would be an important factor, as illustrated by the wall discussed in their article.

One other thing about the article struck me as strange. They refer to Christian Sunday school manuals and then quote from Gospel Principles. Now the book is a Sunday school manual for us, and we do consider ourselves Christian. It's just that their use of a generic designation suggested to me that the quote would come from another denomination.

As to the issue of testing in mortality--I don't disagree with their basic suggestion. However, I wonder if they would go the next step to arguing that the many evidences that contradict the young-earth view of the earth are deliberately made to test us. I don't want to put words in their mouth. However I find this extension of the argument distasteful because not only does it mean that God is deliberately tricking us (or perhaps allowing us to be tricked by Satan), but the whole charade was orchestrated for the very tail end of mortality (assuming the Second Coming is within a couple hundred years.) It has only been within the last couple of hundred years that we have begun to understand physics, geology, and biology in unprecedented depth and accuracy. Why, in all of human history, are we the ones who need to be tricked? Isn't that a lot of work to go through just to "test" of few of us?

Ultimately I don't think that the time required for petrifaction is that important of an issue in our understanding of the history of the earth and life on it.

Continue reading...

Review of Defeating Darwinism

I recently checked out Defeating Darwinism by Opening Minds, by Phillip Johnson, from the library and thought I would share my thoughts on it. Hopefully in the process I can clarify why I do not support the Intelligent Design movement, which is primarily lead by the Discovery Institute. Please note the following abbreviations I will be using: DD = Defeating Darwinism; ID = Intelligent Design; IC = Irreducible Complexity.

Continue Reading

DD was published in 1997 and follows Darwin on Trial and Reason in the Balance, written by Johnson, as well as Darwin's Black Box, written by Michael Behe. (See here for my review of Behe's book, as well as my first post about intelligent design. Because some of the arguments apply here, also see my post on the randomness of evolution.) I have not read Johnson's other books.

The purpose of DD was to provide a simple, straightforward explanation of ID and criticism of evolutionary theory that could be understood by someone in high school. It is less than 150 pages and is a easy read. If you want to quickly determine where Johnson is coming from, I recommend this book. One of the broad purposes of this book, and Johnson's work in general, is to help enable students to maintain religious faith in the face of the mountain of evolutionary theory. He seems genuinely concerned that people are needlessly jettisoning their faith (especially Christian faith) and wants to help. In this respect I am sympathetic. It is his approach and conclusions that I disagree with.

Johnson begins the book by relating how some students try to reconcile their faith with science. The reconciliation is usually some form of theistic evolution--that God used evolution in his creative processes. Johnson argues that no reconciliation can be made because evolution is based on naturalism/materialism and therefore, by definition, excludes God. Therefore science, and education in general, must be stripped of naturalistic assumptions. His argument is essentially an ultimatum--choose God or naturalism. He writes:

The evolutionary story is a story of humanity's climb from animal beginnings to rationality, not a story of a fall from perfection. It is a story about learning to rely entirely on human intelligence, not a story of the helplessness of that intelligence in the face of the inescapable fact of sin.

There is no satisfactory way to bring two such fundamentally different stories together, although various bogus intellectual systems offer a superficial compromise to those who are willing to overlook a logical contradiction or two. A clear thinker simply has to go one way or another.

Unfortunately, I do not believe either story is free of logical contradictions. It is for this reason that I believe that when the whole truth is known, there will be a perfect compromise. False dichotomies are easy to make.

He goes on to discuss issues of critical thinking, ID and IC, and then quite frankly and openly discusses the overall cultural strategy he is charting. He also lays out his general critiques of the evidence supporting evolutionary theory. Prominent among them is the fossil record, and he includes the usual quotes from Eldridge and Gould admitting to its weaknesses. (Scientists, including Eldridge and Gould, insist that their arguments have not been properly understood. Neither Johnson nor I are paleontologists so I will not engage this argument. However, note that evidence for common descent does not rest on fossils alone.) He also tries to draw a distinction between the medium of DNA and the message it contains, arguing that the message could not have come about by chance. My following comments will be a mixture of reaction to the book and ID in general.

The critical problem with ID, in terms of science, is testability. If God has intervened in the development of life on earth, how would we know it? Proponents of ID argue that design can be detected by positive evidence. What is this positive evidence? The answer is IC. But the very notion and implications of IC are disputed--or ignored--by mainstream science. And at root, IC is an argument from ignorance--we don't know how something could have evolved by natural means and therefore it must have been designed. It is a subtle trick to turn an argument from ignorance into "positive evidence"--create a category that is derived from an argument from ignorance, find a biological system that fits the criteria of your category, then call that positive evidence for design.

What I don't think many people realize is that ID really cannot get them what they want. For the sake of argument, let's say that IC is a legitimate concept and really does indicate ID. The reason it can detect design is because it is the only marker that can distinguish natural processes from intelligent ones. In other words, it distinguishes organisms created with ID from those related just by common descent. The IC systems that have been proposed thus far might distinguish some higher taxa, but most species and genera would probably be unaffected. For example, what kind of IC system would distinguish chimpanzees from humans? The only IC systems proposed so far are things like vision, the immune system, blood clotting, and cilia. Both humans and chimpanzees--most vertebrates for that matter--have all of those. Given the very high degree of DNA identity between these two species, I think it is highly unlikely that any IC biochemical systems will be identified to differentiate them. With the main tool of ID being useless in distinguishing between humans and chimpanzees, we are left with naturalism. So we can infer ID throughout the tree of life except where it really counts--us. The concepts of IC and ID are therefore useless to anybody hoping to establish that humans are uniquely created apart from the rest of the animal kingdom and we are essentially left with a concept that Johnson finds unacceptable--naturalism/materialism responsible for the ultimate creation of humans!

My point here is not to argue that mankind are merely animals or that God has nothing to do with our creation. It is to show that ID is utterly useless to show otherwise where the theological stakes are highest. If the tools of ID cannot establish a unique creation for humans, does the rest really matter?

As I stated above, Johnson spends some time drawing a distinction between the information contained in DNA and the medium of the information (ie. the DNA itself.) He argues that it is ID that is responsible for the information contained in DNA. This is because matter cannot organize itself to contain information--just as ink and paper have no ability to produce words and sentences. I'm not quite sure I fully understand his argument here, and I'm not prepared to persue it. I'll just say that his analogies are fundamentally different than biological processes and they smell funny to me--but I can't quite put my finger on it yet.

If you have any question about whether cultural issues are really at the bottom of the ID movement, just read the last few chapters. Johnson believes that, like Freud and Marx, Darwin must be overthrown. He blames naturalism/materialism for social and moral decay, and he issues a Christian call to arms to help overthrow materialism.

Although I disagree him on a number of issues, I think Johnson and I can agree on this: all people should know more about science and the assumptions and philosophies that govern it. Whereas Johnson thinks that the rules governing science are arbitrary and in need of overhaul, I think that they are necessary and should be maintained. However I also support clear explanations of what they are and why they are needed. With a proper understanding of the issues involved, I believe students can make good (not just reactionary) judgments as to how much of their worldview should be shaped by science, and how much by religion.

Continue reading...

Let's Start Light

Well I'm back, and I see the blogesphere has been quite active in my absence. So I'm going to start light by linking to this post at The Panda's Thumb that explains why "teaching the controversy" over evolution is a bad idea. It makes some great points.

As I see it, if you wanted to teach the non-existent controversy in public schools, there’s only one way you could do it and give it justice. First, you’d have to give the students a very thorough background in biology and evolutionary theory. You could then introduce the ID claims and the mainstream scientific responses, and the responses to those responses, etc. You could then take things a step further and have students “critically examine” the scientific evidence, including reading important contributions to the literature. The problem is, once you manage to successfully do all this, the kids are ready to graduate college.

Now technically the Discovery Institute does not advocate teaching ID in classrooms. They only advocate teaching "evidence" against evolution. (They seem to use this strategy a lot, like how they decline to identify the IDer, thus allowing them to officially deny criticisms against them while allowing popular perception to do their work for them.)The points in this post apply nonetheless.

Continue reading...

Administrative Notice

I'll be unavailable for blogging for a few days, so you can either ponder some of my past posts or go have a look at the other quality blogs in the bloggernacle. But don't get too attached, because I'll want you back later next week.

-The Management

Continue reading...

Random Until Further Notice

I believe that much of the anxiety that people express about evolution is rooted in a single concept--its randomness. After all, if evolution accounts for the existence and diversity of life and is truly random, we have a number of theological difficulties on our hands. The scriptures clearly teach concepts of planning and foreordination, and so would seem to be at odds with evolutionary theory. As we shall see, if we really probe this problem to its depth we will get into unanswerable questions concerning the foreknowledge of God. These kinds of questions have been kicked around for a long time by people much smarter than I am. I doubt that definitive answers are available in this life. Rather than get into philosophical speculation I want to discuss the nature of science and its limitations.

Continue Reading

Like many other fields of study, evolution is usually a study of history. Based on present experiments and observation, and on evidence from the past, scientists are able to reconstruct processes and events that have lead to conditions we see today. However just like other studies of history, reconstruction of the past is of limited use in predicting the future with precision.

Let's take climatology and meteorology as an example. If we wanted to learn about past weather conditions we would pursue several avenues of research. We would gather records that contained measurements of past weather data. We would look at things affected by weather such as agriculture. We might also look at remaining physical evidence, such as tree rings, for indications of flood, rain, or drought. All of this together would give us a good picture of what happened in past weather systems. But as we all know, it is of limited use in making specific predictions about future weather. This is because the number of variables involved are enormous. But we can ask a rhetorical question here: does God know whether it will rain on my house a year from today?

Let's look at a biological example: cancer. In many types of cancer the root genetic problem can be identified. While some people may have a predisposition to certain cancers, others apparently do not. Yet exact predictions about whether a person will get cancer cannot be made because of the enormous number of variables in play. On the predictive side, all we can do is talk in terms of probabilities.

Now let's ask some questions: Does God know who will get cancer? Does he know which particular cell will start the cancer? Does he know what the specific cause will be? Does God cause all cancers? Are all cancers a result of pure chance? If God did, from time to time, cause a person to get cancer (as a trial, for example), could we identify those instances by scientific means?

These same types of problems and questions apply not only to evolution, but other areas of biology, medicine, public health, multiple areas of physics, cosmology, astronomy, linguistics, anthropology, ecology, geography--all areas of life, really. We do not have a way to distinguish any direct role God has played in these things from natural processes, except through revelation. But since revelation is largely non-transferable, we prefer natural explanations until God specifically identifies his role. (These issues also touch on why I am not hot on the intelligent design movement.)

So let's not fret over whether life's origin and diversity is a result of chance or not. Scientists talk in terms of chance and randomness because, whether they believe it's the whole story or not, they cannot do otherwise.

[This is a cross-post from Mormons and Evolution. Clicking comments will re-direct you there.]

Comments

Continue reading...

ID in Arkansas

According to the NCSE, a bill has been introduced in the Arkansas house of representatives which,

"if enacted, the bill would require the state Department of Education to include "intelligent design" in its educational frameworks and encourage teachers in the state to include it in their lesson plans."

Since the Discovery Institute claims that they oppose teaching ID in schools (just criticisms of "Darwinsim," which leaves--what?) it will be interesting to see if they oppose this bill.

More on ID later.

Continue reading...

Additional Support for Out of Africa

As I understand it, there are two main competing models for the origin of modern humans. As Science News puts it:

The origin of modern humans is a debated topic. One leading theory postulates that the ancestors of all modern humans originated in East Africa and then left the continent around 100,000 years ago. From there, they colonized the world, displacing previously established hominids such as Neanderthals in Europe. The best evidence so far for this theory is the higher genetic diversity (and thus inferred older age) of the African population compared to populations from other continents.

A minority theory proposes that modern humans evolved simultaneously in different regions of the world from populations of archaic humans and that both contributed to the current human genetic pool. The modern Homo sapiens species is, therefore, seen as the result of the sharing of genes and behaviors between archaic and modern humans.

For more information see this.

Continue Reading

A new paper has been published that supports the leading model. Here is the abstract:

A leading theory for the origin of modern humans, the ‘recent African origin’ (RAO) model, postulates that the ancestors of all modern humans originated in East Africa and that, around 100,000 years ago, some modern humans left the African continent and subsequently colonised the entire world, displacing previously established human species such as Neanderthals in Europe. This scenario is supported by the observation that human populations from Africa are genetically the most diverse and that the genetic diversity of non-African populations is negatively correlated with their genetic differentiation towards populations from Africa.

Using a dataset of 377 autosomal microsatellite loci from 51 populations, the authors looked at the correlation between genetic diversity and geographical distance from Ethiopia, where the oldest human remains have been found. They found a pretty smooth negative correlation between the two. That is, the farther away the population sampled was from Ethiopia, the less genetic diversity was found.

Now this certainly is not my field and I am not qualified to critique the paper, but it does seem to support the leading model. Also in the news summary one of the authors says, "The lack of stark differences suggests that humans cannot be classified in discrete ethnic groups or races on a genetic basis."

Continue reading...

A Different Kind of Blog

Jeffery of Issues in Mormon Doctrine and I have launched a new blog called Mormons and Evolution. Before you get all bent out of shape about another blog in the bloggernacle, let me explain. The scope of the new blog is intended to be very narrow. I anticipate that it will not move as quickly as most other blogs because we are trying to be more methodical and thoughtful.

I anticipate that many of my posts there will be cross-posted here, but I plan on maintaining a broader scope here.

Continue reading...

A Chromosomal Argument with Strings Attached

Over at Times and Seasons they're talking about the conception of Jesus and whether it was sexually-based as some of the early brethren seemed to think it was. I have not had a strong opinion one way or another--I'm not creeped out either way.

In order to support the doctrine that Jesus is literally the Son of God, however, some (Stephen Robinson comes to mind) have argued that Jesus had 46 chromosomes--23 from each parent. I used to think this was a pretty persuasive argument, but now I'm not so sure.


Continue Reading

Enter Evolution: (Always with the evolution!) Our genomes seem to have been shaped by somewhat random forces. In terms of organization and sequence they appear to be quite similar to other primates, especially chimpanzees. Not only are they similar, but there are clues that allow us to infer common ancestry. One change that has occurred in humans since the split from chimpanzees is that two chromosomes in the common ancestor fused to form our chromosome #2. (For a little more on this subject see here.) I don't know if a successful human-chimpanzee hybrid could be produced, but I doubt it. The difference in chromosome number would cause problems. There is a certain point where chromosomal abnormalities lead to cell death.

What I'm saying is that there may be no reason to assume that if God has DNA, that he has 46 chromosomes. Now if you assume that Adam was literally the offspring of God then the chromosomal structure would match up, I suppose, but then we have to explain why other primates have DNA so similar to ours. Not only similar, but as I said, with evidence that suggests a directionality of change opposite of what we would expect under this assumption.

This leaves several possible senerios:

1. On the divine side, no DNA was involved.
2. God shaped our genomes to be like his.
3. God modified his DNA (in specific cells) to be like ours.
4. The problems from apparent chromosomal mismatches were overcome in some other fashion.

I doubt that Jesus's abiltiy to lay down his life and take it up again was due to any coding in his genome, so I don't think it really matters. Helaman 5:11 says "And he hath power given unto him from the Father to redeem them from their sins because of repentance." Furthermore we do not receive priesthood power by any biological means, so I don't see why Jesus's unique abilities were necessarily genetically based. Similarity in appearance could probably be achieved without much trouble. (Just a couple of weeks ago somebody told me that I look exactly like their younger brother. And for that matter, I've run into somebody that looked a whole lot like my younger brother.)

My point is that perhaps we should be more careful in using the 46 chromosome argument because it raises more questions than we are prepared to answer.

Continue reading...

Lewis, Freud, and The Question of God

Last fall I picked up and read (mostly) the book, The Question of God, by Dr. Armand M. Nicholi, Jr. A program by the same name, based on the book, aired on PBS as well. The purpose of the book is to compare and contrast the lives and worldviews of C.S. Lewis and Sigmund Freud. Dr. Nicholi is an associate professor of clinical psychiatry at Harvard Medical School where he has taught a course on Lewis and Freud for more than 25 years.

Continue Reading

The Book

The intention of the book is to engage Lewis and Freud in a virtual conversation and to examine how their philosophies influenced their lives. There is no evidence that they ever met and Freud died long before Lewis did, so in a sense Lewis has the last word. Lewis, of course, was an atheist for much of his life but eventually converted to Christianity and wrote prolifically. On the other hand, Freud was the foremost atheist and materialist of his time.

I do not claim to be a student of C.S. Lewis, although I have read Mere Christianity and Miracles, as well as several of the Narnia series--I am even less familiar with Freud. For those who have a casual interest, but do not have a thirst to read the many writings of these two men, this book is the one to read--even if you are only interested in one of them. The book deals with a number of topics including belief in God, conscience and moral law, and the nature of happiness, sex, love, pain, and death. Each chapter contains selected writings of both Freud and Lewis, as well as biographical components that relate to the topic under discussion.

Although the chronology may be partly to blame, it seems clear that the author favors Lewis's worldview. If you are an admirer of Lewis this book will not challenge--and will most likely enhance--your opinion of him. One of my favorite parts is the discussion of Lewis's conversion, which was facilitated in part by J.R.R. Tolkien. Although Lewis's conversion may not match my experience, I find it insightful and faith-promoting nonetheless. (Quick digression: When the first Lord of the Rings movie came out, a member of my ward said that his father-in-law, who probably had not seen the movie, called the movie "anti-Christian." I'll give you "violent", or "not appropriate for young viewers", but "anti-Christian?" I explained that this could not be as Tolkien helped convert Lewis to Christianity!)

I was not impressed by the picture painted of Freud. He seems to me to have been a prideful, miserable man who disliked most people. Although he was a poster-boy for atheism, one senses that deep down he was insecure about his rejection of God. In one way, Freud was somewhat redeemed in my eyes. If I understood Dr. Nicholi correctly, Freud used the term "sexual" in a very broad way. Thus the strange sexuality popular culture attaches to Freud's name appears to be a misunderstanding of his thinking. Also, in my view, Freud's confrontation and discussion of the dark side of human nature has merit in that it is a study of the natural man. I thought this connection was insightful:

One of Freud's theories that has proved helpful clinically relates to the unconscious process of transference, the tendency to displace feelings from authority figures in our childhood onto those in the present, thus distorting and causing conflict with the present authority...We must be careful that our concept of God--whether the God we reject as unbelievers or that we worship as believers--is firmly based on the Creator revealed in history and not on our neurotic distortion of Him.

The "discussion" between Freud and Lewis is a little disappointing in that Freud seems largely irrelevant to today's atheists--not that I'm any expert on atheism. However, if I'm not mistaken Freud has been largely discredited on other grounds, thus it seems to me that Lewis is largely shadow-boxing. I would be more interested in how Lewis's arguments fit into today's discussion.

Nevertheless, I recommend the book and think it worth reading, if only to understand Lewis better.

The PBS Program

The program was in two parts of two hours each. I only saw the first part but I was not all that impressed. The production had value in that it was somewhat of a documentary of the life of Lewis and Freud. Interspersed throughout the program were discussion sessions led by Dr. Nicholi. The guests were a range of believers (not necessarily Christian) and non-believers. One notable non-believer was Michael Shermer of Skeptic Magazine and Scientific American. For the most part I thought the discussions were worthless. I quickly tire of people rambling on about what they believe--especially when it consists of a bunch of platitudes and abstract ideas. Whereas a couple of the non-believers were pretty articulate, for the most part the believers did not seem persuasive to me. It reminds me of Elder Packer's story about "fighting out of context."

My advice is to read the book and pass on the PBS program.

Continue reading...

Homo floresiensis

If you are interested in hominid evolution at all, you should check out this article by Carl Zimmer discussing the recent Homo floresiensis find.

Here is a graphic to help orient you on relationships.

Continue reading...

Simon Southerton Responds

Simon Southerton, the author of Losing a Lost Tribe, has responded to several apologetic arguments. He'll have to excuse us (the believing LDS intellectual community) for not rolling over easy, but he is giving us an intellectual workout.

This criticism and response deserves highlighting:

Continue Reading

7. The bottleneck effect, genetic drift, and other technical problems would prevent us from detecting Israelite genes.

In 600 BC there were probably several million American Indians living in the Americas. If a small group of Israelites, say less than thirty, entered such a massive native population, it would be very hard to detect their genes today. However, such a scenario does not square with what the Book of Mormon plainly states and with what the prophets have taught for 175 years.

His answer confirms that this is a legitimate issue. At the same time, however, he tries to make us carry the weight of past commentary by church leaders and superficial interpretation of scripture. This is a critical point. It is like anti-Mormons who try to make us defend controversial statements by past prophets and apostles. I do not feel obligated to do so. I have no problem with most Native Americans being "adopted" Lamanites, if not literal descendants (see Stephens and Meldrum's article at FARMS).

I have not read Southerton's book and at this point am not inclined to, simply because I think I have a pretty good idea of the issues involved. His recent response seems like a pretty good summary to me. If anybody can give me good reasons to read it I might change my mind.

Continue reading...

Evolution of Snake Venom

The principle of natural selection has two components to it. First is the generation of diversity, which as far as we can tell is a random process. The second part is non-random--the survival and reproduction or death of an organism. The generation of diversity is often driven by mutation of genes. The definition of "mutation" that immediately comes to mind is usually the simplest kind--single base-pair changes. Critics of evolution often express incredulity that such a process could be responsible for the diversity of life. One out-dated argument calculates the probablility of a particular amino acid sequence coming into existence at random and comes up with some astronimical number, thus showing that mutation could not be responsible for the existence of the protein.

Continue Reading

However, if we broaden the definition of mutation to be any changes in the genome, the picture becomes more plausible. New genes can be created in several ways, one of which is gene duplication. There are at least a couple of ways a gene can be duplicated--the specifics are not important here. Once a gene has been duplicated, the forces of mutation (in the stricter sense) and natural selection can play on one copy while the other copy retains its original function. Often mutation will render the new copy junk, resulting in a pseudogene. However, sometimes a new function can be gained.

This is apparently how snakes evolved venom. New research indicates that most venomous proteins made by snakes are very similar to proteins contained elsewhere in the snake's body.

From Science News:

By comparing the venom gene sequences with other known sequences, Fry was able, in three-quarters of the cases, to infer which gene had duplicated. He found that the various toxins traced their way back to proteins that play diverse roles in an assortment of organs, from the brain to the testes. For example, proteins in the acetylcholinesterase group are common neurotransmitters for muscle control, but the snake's venomous form induces paralysis and difficulty breathing; similarly, kallikrein proteins regulate blood pressure, but the toxic versions induce a fatal drop in blood pressure.

From Nature News:

"Despite the incredible changes in bioactivity that occur, the basic molecular scaffold and three-dimensional shape doesn't change notably," Fry says. The results of his analysis appear this week in Genome Research.

So here we have an example of a novel biological function arising from existing genetic information.

Continue reading...

BYU: A House of Faith

A few of weeks ago I blogged about Michael Ash's article, "The Mormon Myth of Evil Evolution." I raised the question of documentation for a rumored rift between David O. McKay and Joseph Fielding Smith. Since nobody knew the source for sure, I emailed Michael Ash to find out. His computer files were not available at the time, but he was pretty sure his source was Brigham Young University: A House of Faith, by Gary Bergera and Ron Priddis. The book is out of print now, so I bought a used copy on-line for a few dollars--a good investment in my view. It does appear to be the source for the rift rumors. However, the supposed rift is only mentioned in passing and is contradicted by others, as pointed out by Justin.


Continue Reading

I find the book quite interesting since it details various developments and controversies at BYU over the years, with many behind-the-scenes views. There is a 40-page chapter on organic evolution at BYU which is certainly worth reading. I've been particularly impressed with Dallin Oaks's administration on a number of issues. Among them, he seems to have been instrumental in getting the sciences at BYU a little breathing room.

When Dallin Oaks replaced Ernest Wilkinson as BYU president in August 1971, he soon learned of serious problems on campus regarding the role of evolution at the university. In his first address to the faculty in September he asked that guilty parties, particularly among members of the religion faculty, "stop casting aspersions on [the] testimony and devotion of their colleagues" in the sciences.

(It strikes me that it isn't only science professors who can live in ivory towers.)

He also initiated a series of seminars to facilitate dialogue between the science and religion faculty, although some religion faculty apparently refused to attend. (Elsewhere, Duane Jeffery says that one of the religion faculty wrote a 4(?) page letter on why he would not participate in anything that Satanic.)

Shortly after Duane Jeffery published "Seers, Savants, and Evolution: The Uncomfortable Interface," the then Elder Benson spoke at a BYU fireside and said

"one of our church educators [has] published what he purports to be a history of the church's stand on the question of organic evolution...To hold to a private opinion on such matters is one thing,...but when one undertakes to publish his views to discredit the work of a prophet [ie. Joseph Fielding Smith], it is a very serious matter."

Jeffery promptly wrote to Oaks, emphatically denying that he was on a "campaign to disparage the reputation of anyone." While he had decided not to respond publicly, he explained, his "silence should not be construed as a concession" to Benson's criticisms. Sympathetic, Oaks replied, "I am hopeful and confident that with a little love and understanding and patience and patience and patience that these things will work out."

(Elsewhere, Jeffery says that the then Elder Benson had not actually read his article, but got his information from an aspiring underling who had distorted the article.)

At a later point, Oaks wrote the following to the then Elder Hinckley:

There is a clear issue here: Should the board continue or should it revise its policy that permits Brigham Young University faculty to teach the theory of organic evolution--teaching it as a theory and not as a proven fact?

...If we stopped teaching this theory, within a few years students from BYU would not be admitted to...graduate schools. At that point we would cease to function as a recognized university and would, in the eyes of the world (especially the world of higher education), be little more than a seminary with added courses in the humanities.

...There are thousands of our faith who feel threatened by that openness, and while I have sympathy with that as a personal point of view, in my judgment that kind of narrowness should never be allowed to impose the darkening hand of censorship on this university."

In fairness we should keep in mind, as Stephens and Meldrum point out in their book, that much of the best supporting evidence for evolution has come forth since 1970. Man, His Origin and Destiny was published only a year after the structure of DNA was solved. But the Jeffery episode does raise some interesting questions. Setting aside doctrinal disagreements, if Joseph Fielding Smith's book contained inferior scientific arguments, should the LDS scientists have remained silent--thus appearing to have no answer for JFS's claims? It seems like a tight rope to walk and I'm glad such tension is largely set aside these days.

It came much later, but the BYU packet (available on the side bar), I think, was a great idea and protects both points of view. It also diplomatically frees us from having to account for every statement made by every General Authority (including JSF) because it emphasizes the role of First Presidency Statements.

Continue reading...