Saturday, November 27, 2010

Article on Titan's Atmosphere

The other day, I received an email from someone asking questions about a scientific discovery about Titan's atmosphere (a news release about this can be found here). In the discovery, scientists from U Ariz simulated conditions on Titan's atmosphere and found molecules that could be the precursors to life found in the reaction vessel!

What do I think about this discovery, from a Christian perspective? Did God create life, or did life arise naturalistically from non-living material on the early earth?

First of all, I think this discovery (which apparently has not been published yet in a peer-reviewed journal) should draw quite a bit of interest from both the origin of life community and, of course, organizations like RTB. To offer a brief critique of it, let me first start out by saying that the news article, as usual, appears to have grossly over-interpreted the conclusions that can be drawn from this study (as far as I can tell from only reading the scientific abstract, which is all that is currently available). That being said, I want to make the disclaimer that this study appears to be very good science, and I think it's really interesting and hope they do more on it. It's exciting research, and uncovering more about the universe and the conditions that may be necessary for life to form will help uncover the truth, which is always a good thing if you're a Christian.

So, a brief critique. First, note that the scientific results they are looking to publish are the result of a simulation of Titan's atmosphere. They took the small molecule gases that were found in Titan's atmosphere (CO, methane, and nitrogen), loaded them into a specialized chamber, and bombarded them with microwave radiation. What they found aggregated at the bottom of the chamber was a mix of lots of really complex molecules, including the five nucleobases used in DNA and RNA (those are, adenine, guanine, cytosine, and uracil and thymine) and the two simplest amino acids. That alone is amazing! But is that enough (or even close to enough) to lend support to the naturalistic origin of life?

I would say no, for two big, big reasons (and several small reasons).

First, there is either too much oxygen or not enough oxygen. What I mean is this. The article makes a point that there is enough oxygen in the atmosphere (in the from of CO) to promote the formation of the prebiotics, but not too much. You see, if there is too much oxygen in the atmosphere, the prebiotics will become over-oxidized and useless. However, because of the presence of UV radiation, the prebiotics are also destroyed: in the same way UV radiation damages your skin, UV radiation destroys the bonds of prebiotics. The only way to block the UV radiation is by an ozone layer. However, an ozone layer will not form in an oxygen deficient environment. In other words, too much oxygen, you get destruction of prebiotics, and too little oxygen and you get too much UV light, which destroys the prebiotics. The big problem is, there is no middle ground! The amount of oxygen necessary to form an adequate ozone layer far exceeds the level of oxygen where you get too much oxidation! (This is called the UV-oxygen paradox.) And notice that the researchers admit there is UV light in Titan's atmosphere, but in their simulations, they use microwave radiation (instead of UV radiation). I wonder what would have happened if they had used UV radiation in the same way that it is present on Titan's atmosphere?

Second, the article focuses on a few of the exciting molecules they formed, but it says nothing about the "toxic" molecules they also formed. What I mean by toxic is "detrimental to prebiotic chemistry". The goo they scraped off the bottom of the chamber undoubtedly also contained a series of other complex molecules, the presence of which would completely halt the formation of more complex biomolecules, such as proteins or RNA chains. Furthermore, they are still faced with the problem of homochirality (I may discuss this problem more at a future date).

You also have a multitude of other problems, such as a prohibitively small concentration of prebiotics falling into the ocean (if it's not concentrated enough, the prebiotics just won't ever "find" each other to make bonds), an alarmingly fast degradation rate of the prebiotics (most likely far outstripping the production rate from the atmosphere), the unknown mechanism to form bonds between prebiotics in the presence of water (because water inhibits these reactions), and the list goes on. For more about these problems, see where I quoted Dr Robert Shapiro here.

Thursday, June 10, 2010

What if genomes of organisms didn't appear related?

In my opinion, one of the more compelling lines of evidence for evolution is that we can sequence the genomes of any living organism nowadays, and what we've found is a striking similarity among organisms. For example, and oft-quoted number is that the genomes of humans and chimpanzees are 99% similar. Pretty good evidence for common descent, is it not?

And by the way, this isn't exactly a new thing; it isn't just with the dawning of the post-genomic era that this line of evidence was put forth. There was a seminal study by I-forget-who back in I-forget-which-year where a graduate student was determining the primary sequence of some proteins in different organisms. She was attempting to show that these proteins were different in different organisms, and was dismayed to find that there was striking similarity. Her advisor being very wise (as advisors usually are), quickly saw the high-impact factor of such a find: this was concrete evidence for common descent!

Anyway, back to my main point. Is this similarity in genes and proteins and whole genomes compelling evidence for common descent? Or is there a way to explain it from a "God-created-it" standpoint? After all, if you're a creationist, you may not have to explain the mechanism by which genomes became related, but you do have to explain why God would do it that way.

One of the counter arguments is that God used a common design template when creating organisms, and only modified this template in small ways to account for the different purposes that He had for the different organisms. After all, there's no need to reinvent the wheel. In essence, this is arguing that God designs life in the same way that engineers design machines they build.

This argument doesn't really sit well with me. It's not that I don't think God would design life in the same way engineers design machines. To the contrary, I am convinced that He would, or perhaps more appropriately, we design machines in the same manner that God designs life. No, I am uncomfortable with this argument mostly because it's too hand waving. It doesn't have any real substance to it.

I prefer to put forth a counter argument from the basis of the question: What if God had done it another way? That is, what if genomes of organisms didn't appear related?

Wednesday, May 26, 2010

What do we care?

A couple of posts ago, I ended with the question "and what do we care?" This was in regard to whether and how much God has (supernaturally) intervened in the history of the universe to get the events to unfold according to His plan. For example, why in the end should we care whether God had to override the laws of physics to get the solar system to form where it is (ie, in the just-right location in the just-right galaxy) with the composition it has (ie, made of the just-right abundances of elements), etc, or whether the unfolding of the universe under the natural laws He set up at the beginning conspired to make this unlikely place form "naturally"?

I think this is certainly a good point to discuss. It isn't likely that we'll ever know how God did it. Although if we could show that the laws of physics were violated over and over, it would be a good apologetic. But philosophically, who can tell the difference between these two types of miraculous events? The formation of the moon was a miracle, in that it was highly unlikely. The advent of man was a miracle, in that it was an even less likely event. Do either violate the laws of physics? Even that's a difficult question to answer, as statistical thermodynamics, and even more so quantum mechanics, imply that anything can happen, even the most unlikely thing. It is within the laws of physics for all the air in the room you're sitting in to suddenly move to the other side of the room, instantly suffocating you. Its likelihood is on the order of 10^{-25} (or probably less), but it's not impossible. (I'll try to discuss this in a later post, because I'm not doing this justice here.)

Instead, I argue that the question we should be asking is therefore not whether the laws of physics are broken, but instead whether the unfolding of the history of the universe, including the history of life on planet earth, seems to bespeak the supernatural superintent of a creator, i.e., a mind. This is not just a question about probabilities. Rather, it is a question regarding whether the universe's history reflects the expressly-stated purposes of a creator. Sure, regarding evolution, we can try to go and test whether God specially intervened at points, but these would again be based on probability arguments. (For example, the likelihood that whales would evolve from a land mammal given their large body size, low fecundity, and long generation time, is extremely small.)

No, what I am arguing here is that the unfolding of history is following a divine plan. We live in a just right location at the just right time. The history of life on earth followed a just-right trajectory such that we could be here today. The evolution of stars and galaxies prior to the formation of our solar system occurred in a just-right way. In essence, these are all fine-tuning arguments, but they're subtly more than that, I think. It appears that the fine-tuning is no coincidence. It appears that it is following a plan.

And I think this argument demands to be developed further. For now, it's only in its infancy.

Tuesday, May 25, 2010

Humans and neanderthals interbreeding

Recently the report of possible interbreeding between humans and neanderthals has been a hot topic. As I understand it, a research team has compared their draft sequence of the neanderthal nuclear genome with the genomes of five modern (contemporary) humans. They found that there was more sequence similarity between neanderthals and three of the humans than with neanderthals and the other two. They concluded that this meant there was interbreeding.

This raised a host of questions, such as, are we all part neanderthal? If so, then is the image of God tarnished? This fits nicely into an old-earth creation model because (1) it shows that even though there may have been a small amount of interbreeding, humans and neanderthals are distinct species, thereby refuting the young-earth creationist model (that neanderthals were descendants of Adam and Eve), and (2) it shows humans did not evolve from neanderthals, further eroding the multi-regional hypothesis of human evolution (that ancient hominid species such as Homo erectus and neanderthals evolved together into the different races of modern humanity).

In fact, I have heard speculation that the humans and neanderthals interbreeding may be one way in which God could have used as a form of imposing racial diversity at the time of the Tower of Babel.

But there's one hypothesis that I haven't heard talked about: What if the interbreeding was only one-way? What if sinful human males had offspring with neanderthal females, but not the other way around? It would seem to fit the data just as well as the alternative, and perhaps even better. This scenario would definitively explain, for example, why there is no mitochondrial DNA evidence of humans and neanderthals interbreeding.

It also makes "social" sense. What I mean is, if we are all part neanderthal, that means at some time in the past, a half-human : half- neanderthal must have been raised by a human woman/family, and must have integrated into society somehow, and then passed on its genes via
a human partner. Then a 3/4-human : 1/4-neanderthal must have done the same thing, etc. Of course, as the neanderthal part gets diluted out, it becomes more imaginable. But even if a neanderthal male has offspring with a human female, and the mother does not want to "give
up" her baby, and raises it like a fully human child, what are the chances that the child would find a willing human partner to pass on the part-neanderthal genes? Just speculating here, of course. (In this day and age of political correctness, I almost feel like I'm being racist, but my arguments are actually speciesist...)

Sunday, May 2, 2010

Why would God violate His own laws of physics (part 2)?

In my previous post, I introduced this topic and gave a very simple example why He would violate the laws of physics. In addition to that, we know that God did intervene in certain circumstances. For example, He intervened at the beginning of time. He intervened at the incarnation. Jesus (and the old testament prophets before Him) performed many miracles. I don't find this to be a good answer to Ken Miller's question, however, as God had specific purposes in history to perform miracles, and these acts of divine intervention were well-documented in the Bible. Thus, it does not answer generally about the history of the universe.

My next comment is that, in a way, I sympathize with Ken Miller and Francis Collins and other theistic evolutionists on on this point. When creationists argue that God must have intervened in specially creating life, including humans on the sixth day of creation, I wonder how that would be different from a special creation of the moon. We think we know in pretty good detail how the moon was formed, from a mechanistic, laws-of-physics standpoint. However, the fact that it happened is essentially a miracle. If the moon didn't exist in a very finely-tuned fashion, neither would we. In other words, if the moon hadn't formed in just the right way from just the right materials at just the right time in just the right place with just the right mass, advanced life would not have been possible on this planet. (I can't go into the details, as I do not know them. However, take my word for it that the formation of the moon is generally accepted to be a finely-tuned event, even among atheistic scientists. Also, I found a cool movie here about this, narrated by Captain Jean Luc Picard.) The chance that the moon would form in just this way is so small as to be essentially zero. But it can be explained in a very simple way: a Mars-sized body revolving around the sun about 4.4 billion years ago at the same revolution radius as the earth was suddenly kicked out of its stable orbit. It slowly got closer and closer to the earth until the two bodies collided at a low relative velocity and at a highly oblique angle. The laws of physics can completely explain it. But they do not explain why such an event, which must have been so finely-tuned, would have happened.

Applying this to life's history, Darwinian evolution is certainly a plausible mechanism to explain life's history, given the concession that life evolving this way (i.e., in just the right way to produce us) is extremely unlikely. However, I don't see anything in direct contradiction of the laws of physics, barring a second law of thermodynamics hand-waving argument. In other words, it isn't absurd to imagine that God supernaturally superintended each of life's events such that evolution according to the natural laws would occur just as He would have it. In the same way that it isn't absurd to imagine that God supernaturally superintended the formation of the moon just as He would have it such that we could later exist. He guided an extremely unlikely set of events to get us in the end. Did He do this by setting it up from the beginning and forgetting it (like a roticerie chicken machine)? Or did He have to perform "midcourse corrections'" such as NASA ground control often must do? And what do we care?

So, this discussion leads us logically to a point that I have discussed many times, about how all theistic evolutionists should also be proponents of intelligent design, and I won't repeat them here.

Wednesday, April 28, 2010

Why would God violate His own laws of physics?

I was listening to a lecture by Francis Collins recently. The specifics of his beliefs on God's direct creative intervention in history, whether it be in respect to the anthropic principle or the origin/evolution of life, were not that clear. (Perhaps this is a good thing; why be too dogmatic about an unimportant issue. Indeed, the answers to these questions may be something we never know until we ask Him ourselves.)

A few of the things he said, however, reminded me of something Ken Miller once said when I had the great opportunity to have a lunchtime discussion with him. He asked, "Why would God need to violate His own laws of physics to make things happen?" Meaning, if God is the author of the laws of physics, and the creator of the universe, certainly He had the ability to fine-tune the initial conditions of the universe (presumably at the moment of creation) in order to get everything to turn out as He wanted. Ken used this as an argument that evolution and theism are not in conflict; indeed, evolution makes even more sense than special creation in his opinion.

I have several comments about that. I'll talk about the first one here.

I can certainly imagine a hypothetical scenario in which God would need to violate the laws of physics and intervene in a very special way to make things happen. Imagine God wishes to fire a cannon and have the cannonball fly through a ring suspended in the air. (No, the ring being suspended is not the violation of the laws of physics; it could be hanging by a string or sitting on a post.) Simple. All He has to do is aim the cannon correctly, pack the right amount of gunpowder, and He can achieve His objective. (This is, of course, assuming the ring is not so high or so far away as to violate the physical constraints of the cannon. Assume, for this example, that it is an "infinitely powerful" cannon that can be aimed in any direction.)

Now imagine He also wishes to have the cannonball fly through another ring. No problem; it just constrains the parameters further. (In the case of only one ring, there are multiple ways to achieve this goal.)

Now, finally, there is a third ring He wants the cannonball to go through. Now we have a problem. What if the third ring doesn't lie along the parabolic path defined by the first two rings? (Actually, you can also think of a case in which He cannot even shoot the cannon through two rings. However, the illustration with three rings is easier to envision, and also helps lead the reader to the result, which is always the better teaching strategy.) For example, if the second ring is lower than the first ring, but the third ring is higher than the second, we are stuck. With God, however, nothing is impossible. He can simply "perform a miracle," i.e., break the laws of physics, to achieve His objectives.

OK, the illustration was silly and simplistic, but it shows that it is plausible, if not necessary, for God to have intervened in history to ensure the unfolding of events up until this point. This includes the formation of the galaxy, solar system, earth, moon, continents, etc., as well as the origin and history of life on this planet. It isn't entirely clear to me that any of this could have happened solely according to the laws of physics operating on the initial conditions of the universe at the singular cosmic creation event. Note that I have not proved that God intervened specially, I have only answered Ken Miller's question of "why." In other words, his asking that question and leaving it at that, as if that philosophically proves the case for the "fully-gifted creation" viewpoint, is not sufficient.

Saturday, March 27, 2010

Francisco Ayala wins the Templeton Prize

A recent article in the LA Times reports on a local (UC Irvine) professor of biology, Francisco Ayala, winning the Templeton Prize. I think it's great that such a big prize in spirituality is being awarded to a scientist.

Although, I must say I don't agree very much with his philosophical views -- at least, with those espoused in this article. And of course who am I to address these things? Ayala is apparently an ordained priest. He's also a professor of biology, which is more than I can say about myself. (And between the two of us, who has won a Templeton Prize?)

So, he carries more clout than I do. But you can judge his points of view against mine regardless of our backgrounds (so that you avoid the ad hominem argument). For example, the article says, at one point:
Evolution "is consistent with a religious belief in God, whereas creationism and intelligent design are not." This, [Ayala] said, is because intelligent design suggests that the deformities of the world are God's design, whereas science shows them to be "a consequence of the clumsy ways of the evolutionary process."
I don't understand this. Even if evolution were clumsy, doesn't that also reflect in God, just as if He were the creator/designer? I guess this goes along "recent" posts of mine describing how even theistic evolutionists should, at some level, be proponents of intelligent design (note the lowercase letters).

The article then goes on to say:
"The Bible is a book about religious truths; it is not how the Earth was made," [Ayala] said. He added that he rejects the idea that one can read the Bible "as if it were an elementary textbook of biology or physics."
This is a common straw man against reading the bible literally and consistently with science. It doesn't have to be "as if it were an elementary textbook of [science]" in order to have some truths about the world and the way it was made. Indeed, if "the bible is a book about religious truths" (emphasis mine), then wouldn't it necessarily be about truths regarding origins? Because the origins of the universe, of the earth, of life, and yes, even of man, all have religious content.

For example, loooong before any of this became a scientific controversy, there was this little doctrine called creation ex nihilo (for an incomplete list of bible verses, see Gen 1:1, Heb 11:3, and 2 Tim 1:9 ). The earliest Christians believed that God created the universe out of nothing. That is, He did not use existing starting materials. That directly addresses the origins question, and is definitively from a religious point of view. So if the bible is about religious truth, and thus what is says about the origin of the universe is true, then at the very least it is consistent with our current understanding of the beginning of the universe (ie, the Big Bang). You can get all of this from the bible without treating it as an elementary science text. It comes directly out of theological commentaries.

A hiatus

Well, I've been gone from the blogosphere (or, as biologists may put it, the "blogome") since around Thanksgiving time, but I'll try to get things back up and running nowadays. Even at my best, I was an inconsistent blog poster, though...