The Language of God: Deeper DNA Comparisons

The Language of God, Chapter 5

By B.J. Marshall

In the last post, we saw Collins give a foothold to Creationists who want to deny macroevolution. Even granted that he should have never allowed this foothold in the first place, he makes a valiant effort to tear the false micro-v-macro wall down by comparing our genome to those of other animals. It is here that Collins asserts that "[t]he study of genomes leads inexorably to the conclusion that we humans share a common ancestor with other living things" (p.134). Aside from the genetic similarities discussed in the previous post, Collins presents three additional lines of evidence that help lead us to his inexorable conclusion: the order of DNA sequences, ancient repetitive elements (AREs), and pseudogenes.

I think Collins doesn't spend much time on the first line of evidence, the order of DNA sequences, because it's pretty easy to follow. The argument is something like this: If you find human genes A, B, and C in that order, you are also likely to find A, B, and C (same order) in other animals. The spacing might differ, but it's there. (AREs fill in most of the gaps between these protein-coding genes, so that'll come into play shortly.) His example to demonstrate this is a comparison between a human and a mouse genome. Particularly, virtually all the genes on human chromosome 17 are found on mouse chromosome 11. Collins here takes a stab at a potential objection. While one might argue that the order of genes is critical in order to function properly - therefore hinting at a Designer - there is no evidence supporting the claim that this would have to occur over such large chromosomal differences.

Now we get to these AREs, called "jumping genes" or transposons, that fill most of the "junk DNA" portion of genomes. They comprise about 45% of our genome and, when one aligns these AREs in human and mouse genomes, they occur in the same order. So, not only do the protein-coding portions line up, but so do these AREs. Collins points out that the process of transposition often damages the jumping gene, and that's what makes them "junk." And these don't bode well for the Creationist; "[u]nless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable" (p.136-7).

Bringing AREs closer to humans, Collins moves to comparing us with chimpanzees. Humans have 23 pairs of chromosomes; chimps have 24. The difference appears to be where two proto-chimp chromosomes fused together to create human chromosome 2. (I say proto-chimp as means of refering to the common ancestor that led to chimps and humans. It's my attempt to avoid that horrendous claim "we evolved from monkeys.") What's more, Collins argues, is that scientists found this fusion exactly where they predicted it would be! The fusion would be "very difficult to understand ... without postulating a common ancestor" (p.138).

Finally, Collins comes to pseudogenes, which are genes that have almost the same properties of a functional DNA instruction packet but have some glitches that muddle things up. Three examples include capsase-12; MYH16, the gene for a jaw muscle protein; and FOXP2, involved in the development of language. Capsase-12 is inactive in humans but active in chimps. This gene works just fine in nearly all mammals except us. So, Collins asks, why would God have gone to the trouble of inserting such a nonfunctional gene in this precise location?" (p.139). MYH16 plays a significant role in the development and strength of jaw muscles in other primates. Collins states that inactivating this gene freed our skulls from having to anchor larger jaws and enabled us to expand our skulls outward to accommodate larger brains. Finally, FOXP2 enables language. Collins talks about uncovering this gene on chromosome 7 via a single family in England where members for three generations had severe difficulty in speaking. They found that a simple one-letter misspelling was occuring. This gene has been remarkably stable in nearly all mammals, and two significant changes have occurred in the coding region of this gene to finally (as in, as recently as 100,000 years ago) imbue humans with the capacity for language.

At this point, Collins mentions, "godless materialists might be cheering. If humans evolved strictly by mutation and natural selection, who needs God to explain us? To this, I reply: I do" (p.140). Stay tuned for Collins' explanation of why he thinks that; the next post will get to the heart of Theistic Evolution.

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January 23, 2011, 1:33 pm • Posted in: The ObservatoryPermalink4 comments
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The Language of God: Micro vs. Macro

The Language of God, Chapter 5

By B.J. Marshall

Before tackling the gritty details using DNA evidence to support human evolution, Collins addresses Darwin, mutations, and the "rather arbitrary" distinction between microevolution ("incremental changes within a species") and macroevolution ("major changes in species") (p.131-2). In my discussions with Creationists, the micro- v. macro-evolution thing always comes up. So I was pretty excited to see how Collins would cover this topic.

He does a fairly decent job mentioning how we've seen lots of changes within species, such as finch beaks changing shape over time. He also discusses saltwater v. freshwater sticklebacks and rapid variation in viruses. He even brings stickleback evolution into a DNA setting by stating that the specific gene - EDA - has repeatedly and independently appeared in freshwater, resulting in sticklebacks losing their plates. Oh, but it gets better, because humans also have an EDA gene, and "spontaneous mutations in that gene result in defects in hair, teeth, sweat glands, and bone" (p.132). So, Collins adds as he tries to connect sticklebacks to humans, it's not tough to see how the differences between sticklebacks could be extended; "larger changes that result in new species are a result of a succession of smaller incremental steps" (p.132). And that's fine for highlighting "microevolution," which is something Creationists can believe anyway. And it's even good for alluding to macroevolution given his "succession of smaller incremental steps." But he only ever leaves it at the hypothetical.

He does his readers a disservice when he claims "we haven't seen new species arise" without expanding on what speciation is (p. 132). Additionally, he leaves the door open to Creationists by saying macroevolution only consists of "major changes" in species. Speciation is kind of a vague line but is usually delimited by two species' ability to interbreed; they usually can't or, if they do, their male offspring are sterile. And the fact is that we have observed speciation in a number of instances. One example is in polyploidy organisms that contain a multiple or combination of complete genomes; these usually result in new organisms that, due to the number of chromosomes, can't reproduce with their originating species. It's called allopolyploidy if genome duplication happens through crossing two different species. Another way speciation can occur is through sexual isolation, such as in ring species such as the Ensatina eschscholtzi salamander.

But, regardless of whether we've observed speciation, Collins gives Creationists a foothold by leaving it up to interpretting what constitutes "major changes" in species. For example, perhaps the inability to breed isn't too bad, because all those salamanders still look very salamandery. It's not like you get a crocodile and a duck together!

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January 16, 2011, 4:30 pm • Posted in: The ObservatoryPermalink8 comments
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The Language of God: Size Doesn't Matter

The Language of God, Chapter 5

By B.J. Marshall

In this section, Collins describes how "the study of genomes leads inexorably to the conclusion that we humans share a common ancestor with other living things" (p.133-4). There are a lot of ideas in this chapter to unpack, so I'd like to start by reviewing Collins' material on DNA at a high level: size and broad similarity. It would be my hope that, even if Creationists only heard some of the material in this chapter, they would quickly see the flaws in Intelligent Design.

First, to lay some groundwork: There is a common misconception made particularly among Creationists that atheism necessarily follows from believing in evolution. This argument is as logically flawed as saying that atheism necessarily follows from believing in gravity, eschewing the entirely-poorly publicized view of Intelligent Falling. Granted, I think evolution poses difficult challenges to theism, but evolution is not theism's death knell. Atheism is a lack of a belief in god(s); the strongest form of atheism takes it one step further to declare "there are no gods." That's basically it. One could hypothetically be an atheist and still believe in the Tooth Fairy, The Loch Ness Monster, or the efficacious treatment of homeopathy. Or, more to the point of evolution, an atheist could believe in Intelligent Design so long as the designing was done intelligently by some space-faring aliens. So long as you don't believe in a god, you're an atheist; this is despite all the other nonsense you might believe. Of course, Collins wants you to see that, too. He's trying to harmonize science and religion, so it would do him no good whatsoever to make all these compelling assertions about the validity of evolution if he thought you were going to jump ship and become an atheist.

Now, that being said, Collins called the genome "the book written in the DNA language by which God spoke life into being" (p.123). Although we still don't know how abiogenesis occurred, Collins appears to be incorrect in waxing poetic about DNA's crucial role. It appears that RNA, acting as simple enzymes, might have paved the way for life to begin. But even beyond waxing poetic, Collins treats DNA as something sacred, as "uncovering this most remarkable of all texts was both a stunning scientific achievement and an occasion of worship" (p.3). And, although Collins has admonished his readers to steer clear of god-of-the-gaps arguments, he states that "DNA... seems an utterly improbable molecule to have 'just happened'" (p.91). Indeed, Collins confesses that he is "in awe of this molecule" (p.102) and regards the "digital [sic] elegance of DNA" as "deeply satisfying" (p.107). (Since DNA is based on four letters, it's really a Quaternary system.) It's probably that deep sense of awe that one can only get through belief in god.

Regarding the size of the genome, Collins makes the observation that a surprisingly small portion of it actually codes for proteins. There are only about 20,000-25,000 protein-coding genes in the human genome. Collins states that the total amount of DNA used by those genes to code for protein is about 1.5-2.0% of the total genome. Collins notes that some observers have been insulted at this. Surely as monarchs of the animal kingdom, we should be special! Well, these observers contend, perhaps "our complexity arises not from the number of separate instruction packets, but from the way they are utilized. Perhaps our component parts have learned how to multitask" (p.125). He disappointingly never expounds on whether genes can multitask, so we're left wondering. Answer: at least some can.

To quell the righteous indignation of some, Collins offers an analogy by way of the language used to write books. He goes on to say the average educated English speaker has a vocabulary of about 20,000 words. (Actually, that is a very low estimate, as Stephen Pinker in "The Language Instinct" points out that the average high school graduate knows about 45,000 words; it might even be 60,000 if you count proper names.) Collins says these words can be used in simple ways (owner's manual) or really complex ways (James Joyce's Ulysses). Unfortunately, I think the analogy fails in a way that subverts Collins' intent. If you want to bring the faithful around to seeing how evolution (unplanned, no ultimate goal, no creator) works, then it doesn't do well to relate it to a construct (language) whose entire function hinges on the intent of, and usage by, intelligent actors. I think I would have offered the reader an analogy of chemistry: you got some protons, neutrons, and electrons to form a few basic building blocks. From different combinations of these, you get the periodic table. For the theoretical physicists in you all, you could even punt to the different vibrations of strings a la Superstring Theories.

Regarding the similarities, Collins mentions that humans are all about 99.9% the same DNA-wise. This certainly makes me feel better, since my hometown was jokingly known for its residents meeting their future spouses at family reunions. He points out that this fits well with the fossil record, which places us in East Africa about 100,000-150,000 years ago to a common set of founders about 10,000 in number. Now, before you get all antsy, making your way to AnswersInGenesis (I can't bring myself to link to it) to refute the fossil record, I want to tell you we will disregard for now this line of evidence; we're really interested in seeing how Collins can back up his claim that DNA alone is sufficient to demonstrate evolution.

Back to just DNA. Here's a nifty table!

Animal Protein Coding Genes Random Segments between Genes
Chimpanzee 100% 98%
Dog 99% 52%
Mouse 99% 40%
Chicken 75% 4%
Fruit Fly 60% ~0%
Roundworm 35% ~0%

The significance of that table is this: If you asked a computer to construct a tree of life based solely on similarities of DNA sequences of multiple organisms, you'd get (courtesy of this site):

Tree of Life, made only through DNA evidence

The DNA similarities also show that genetic mutations that do not have deleterious effects on survival will accumulate over time - the stuff quite arrogantly dubbed "junk DNA." Indeed, mutations in coding regions of genes are observed far less frequently, since the deleterious effects of these are more pronounced.

If these genomes, Collins asks, were created by some intelligent designer, why would these particular features appear? Collins poses more challenges to Creationists, and we'll address them in the next posts.

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December 31, 2010, 5:13 pm • Posted in: The ObservatoryPermalink23 comments
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Spread the Good News

By Richard Hollis (aka Ritchie)

Two rather interesting and welcome stories have hit the headlines in as many days that I thought I'd bring up here.

The first bit of news is that from next week, for the first time, an abortion advisory service is to screen an advert on TV in Britain. Centred around the slogan 'Are you late?' the commercial will advertise the services of the organisation Marie Stopes, which offers advice on sexual health matters, including abortion services.

Abortion has been legal in Britain since the Abortion Act of 1967, but Marie Stopes is adamant that there is a need to promote sexual health issues. "Clearly there are hundreds of thousands of women who want and need sexual health information and advice, and access to services." (source)

Unsurprisingly this has been met by a backlash from pro-life organisations who insist that the advert will be promoting abortion. The campaign Pro-Life had this to say: "The purpose of an abortion commercial is clearly to 'sell' abortion and it will not provide full information about foetal development, the abortion procedure itself, the health risks which abortion poses for women, let alone the alternatives to abortion." (source) While religious organisations are more hysterical. "These adverts will just mean more women will end up on the abortion industry conveyor belt," said the Christian Medical Fellowship. "Getting an abortion is not like buying soap powder, and it shouldn’t be advertised on TV," said the Christian Institute. (source)

I for one, however, am delighted at the news. This is more than about advertising a particular helpline - it is about introducing the topic of sexual health into the public domain and breaking through this taboo topic. It is about power and control. It is about shame and repression.

While the media is absolutely awash with images of a superhuman ideal of female perfection, marketing everything from cosmetics to operations to endow youth and beauty, actual frank discussion about sexual health is still woefully sparse. If organisations which promote impartial advice on such matters are not to be advertised, then how are women to know about them? How are they to know the options if faced with an unplanned pregnancy?

Presumably pro-life groups would prefer it if women never knew about such organisations - and never needed to. Women should never have sex unless they intend to get pregnant and then should turn into good little breeding machines.

Granted I haven't actually SEEN the advert. For all I know it might be the tasteless promotion of cheerful abortion Pro-Life and the Christian Institute envisage. But I doubt it. I am confident this is nothing more than an impartial advisory service offering their services. And its presence encourages open debate on a sensitive subject. I applaud this and certainly intend to tune in to watch its first screening (Monday 24th May, Channel 4, 22.10, to those who want to do the same).

The second news item is that US scientists, led by Dr Craig Venter has developed a cell controlled entirely by synthetic DNA. He and his team had already succeeded in transplanting a genome from one bacterium into another, and in creating a synthetic bacterial genome, but this is the first time they have combined the two already remarkable achievements. (source)

The potential of this breakthrough is massive. This could be the start of gigantic leaps in the fields of medicine, biology, and even climate change. It is also another milestone reached by dedicated scientists doing empirical research into unlocking the mysteries of life itself.

As the religious right never tire of reminding us, we don't know exactly how life started or works. We do not have all the answers. Yet we are making progress. Scientific investigation based on methodological naturalism and materialism is yielding results. Answers are being uncovered. And those who care about human progress should rejoice that we are one step nearer to an answer which will never be found just by sitting around in slack-jawed bewilderment at how complex everything is and concluding magic fills in the gaps in our knowledge.

The rather tepid reaction to scientific progress was demonstrated well by the Vatican's response to the news. While, to their credit, Catholic church officials praised the pioneering scientists, they tempered this with words of caution. "Pretending to be God and parroting his power of creation is an enormous risk that can plunge men into a barbarity," warned one. "In the wrong hands, today's development can lead tomorrow to a devastating leap in the dark," cautioned another. (source)

So it's, 'Well done on getting us this far, but think twice before you take us any further', is it? How encouraging.

While outraged accusations of 'playing God' and visions of the imminent zombie apocalypse inevitably accompany the experiment, I am left wondering if there has ever been a significant scientific achievement that was NOT met with such cries? Were we 'playing God' when we performed the first organ transplant? When we discovered antibiotics? When we drew up the periodic table? When we discovered how to make fire?

Yes, new technology always needs to be handled with caution. But that is no reason to be afraid of it. Science puts the 'ability' in 'responsability' (if you spell it wrong).

May 21, 2010, 4:00 pm • Posted in: The RotundaPermalink23 comments
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The Case for a Creator: Soup's On!

The Case for a Creator, Chapter 9

Chapter 9 is ostensibly about the origin of biological information, but what it's really about is the origin of life. We've discussed this in part in an earlier chapter, but Meyer has some other objections to raise.

First up, Strobel raises the question of the "prebiotic soup" - the dilute broth of organic molecules that's believed to have existed in the Earth's oceans before the origin of life, a fitting stage for many kinds of complex chemical reactions. This is a plausible environment for abiogenesis to take place, so Meyer tries to sow some doubt:

"I hear scientists talk a lot about this prebiotic soup," I said. "How much evidence is there that it actually existed?"

"That's a very interesting issue," he replied. "The answer is there isn't any evidence... If this prebiotic soup had really existed... it would have been rich in amino acids. Therefore, there would have been a lot of nitrogen, because amino acids are nitrogenous. So when we examine the earliest sediments of the Earth, we should find large deposits of nitrogen-rich minerals... Those deposits have never been located." [p.227]

There's no footnote for this, and I find it a puzzling and implausible argument. Earth today contains billions of tons of organic molecules locked up in life. But the Earth is a closed system. Aside from negligible contributions by comets and meteorites, the atoms on this planet today are the same ones that were here when it was first formed. As I mentioned in an earlier post, we know from Miller-Urey-type experiments that organic molecules like amino acids readily form in the presence of a source of energy. How could there not have been a prebiotic soup? What does Meyer imagine all those molecules were doing prior to the origin of life? (Then again, as I pointed out in chapter 4, Meyer appears to be a believer in the young-earth mythology - so maybe the alternative he's really trying to push is the Garden of Eden.)

Meyer also fails to qualify his mention of "earliest sediments". The earliest sediments, if by that he means sedimentary rocks of the same age as the origin of life, do not exist: erosion and plate tectonics tend to destroy and recycle the very oldest rocks. Most of the oldest surviving rocks that we possess are zircons, tiny mineral grains that form in igneous and metamorphic rocks. Zircons can be radiometrically dated, and some are known that are over 4 billion years old, but they don't offer any clues as to when life got started.

The oldest geologic evidence of life is significantly later. There are fossil stromatolites about 3.45 billion years old in rocks from the Warrawoona Group of Western Australia, which is the oldest clear evidence of living things. More controversially, there are rocks from Greenland about 3.85 billion years old that may contain "chemofossils". Living things concentrate the C-12 carbon isotope, rather than the slightly heavier C-13. These rocks show that same altered ratio, which could be a chemical marker left by early life. Evidence this subtle is still being debated by the scientific community, and given the extensive recycling of the Earth's oldest rocks, it's not reasonable to expect "large deposits" of nitrogen-rich minerals dating back to the origin of life to have survived.

Meyer has only one source to back up all of this, and it's a real laugh riot:

"In fact, Jim Brooks wrote in 1985 that 'the nitrogen content of early organic matter is relatively low - just .015 percent.' He said in Origins of Life: 'From this we can be reasonably certain that there never was any substantial amount of 'primitive soup' on Earth when pre-Cambrian sediments were formed; if such a soup ever existed it was only for a brief period of time.'" [p.227]

Strobel labels this an "astounding conclusion", but what he should be more astounded by is how far Meyer had to stretch to find a source for this claim. Wanting to verify this, I did a search for Jim Brooks' Origins of Life, only to find that it's long out of print according to several online booksellers. But more comical is that Strobel cites the publisher of this book as "Lion" - which I found out is Lion Hudson, which is, in fact, a Christian publishing house. A twenty-year-old, out-of-print book by a Christian publisher - that's the most reliable source that could be found to back up these assertions! Couldn't Meyer find even one actual scientific source to quote-mine?

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March 8, 2010, 1:21 pm • Posted in: The ObservatoryPermalink11 comments
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The Case for a Creator: Complexity Is Scary!

The Case for a Creator, Chapter 8

In the previous installment, I discussed how creationists steer well clear of doing any real science. We can see another example of this in, ironically, the way Strobel falls all over himself lauding Michael Behe as a Real Scientist:

He has authored forty articles for such scientific journals as DNA Sequence, The Journal of Molecular Biology, Nucleic Acids Research, Biopolymers, Proceedings of the National Academy of Sciences USA, Biophysics, and Biochemistry... He is a member of the American Society for Biochemistry and Molecular Biology, the Society for Molecular Biology and Evolution, and other professional organizations. [p.196]

(Side note: Why is Behe a member of the Society for Molecular Biology and Evolution?)

But never mind that parentheses. Just take a look at Michael Behe's impressive scientific track record! See how many prestigious peer-reviewed journals he's published in! Just try to refute the ID-supporting scientific arguments of... but wait a minute. Strobel has swiftly stepped around a very obvious question. How much of that vaunted publication record actually supports the arguments of ID?

The answer, if you don't stop at Strobel's glossy superlatives and actually go on to look at the papers, is: not much. If you look at Behe's CV, you can see that most of his work is about technical aspects of DNA and protein structure (with scintillating titles such as, "Quantitative assessment of the noncovalent inhibition of sickle hemoglobin gelation by phenyl derivatives and other known agents"). And if you look a little more deeply, you'll notice an even more interesting fact: Behe's already modest scientific output nosedives in the early 1990s. Not by coincidence, I'm sure, his much-hyped Darwin's Black Box was first published in 1996. Perhaps that was when he found out that working the creationist lecture circuit was a much easier, and far more profitable, line of business. (There was one new paper by Behe in 2004 - the only exception to what's otherwise a decade-plus publication drought. We'll come to that in a later post.)

There may be another reason for this, and we'll see it in the first section of this chapter. Guided by Strobel, Behe begins the conversation by talking about how simple Charles Darwin and his contemporaries thought that cells were.

"In Darwin's day, scientists could see the cell under a microscope, but it looked like a little glob of Jello, with a dark spot as the nucleus... Electricity was a big deal back then, and some believed that all you had to do was to zap some gelatinous material and it would come alive. Most scientists speculated that the deeper they delved into the cell, the more simplicity they would find." [p.196-7]

This claim, which apparently originated with Behe, has become a touchstone of creationist literature. Many prominent ID advocates, all using each other as their only sources, have spread the claim far and wide that early Darwinists thought cells were extremely simple. The trouble for them is that this claim is utterly false. Darwin himself (who was a skilled microscopist), wrote about the "astounding complexity" implied by what he could see of cells' organization and behavior. For details, see this post by Wesley Elsberry, which also catalogues the sloppy anti-evolutionists repeating this falsehood.

I'm sure you've guessed Behe's motivation for making this false claim: so he can dramatically whisk the curtain back and proclaim (much to Darwinists' imagined horror) that no, those tiny little cells are really complicated!

"We've learned the cell is horrendously complicated, and that it's actually run by micromachines of the right shape, the right strength, and the right interactions." [p.197]

This is Behe's cue to launch into a description of some of the molecular processes that operate within the cell. I'll spare you pages of verbiage about mousetraps and highways and motors - ID advocates still love these cartoonishly simple, Paleyesque analogies - except to note that Strobel chimes in on cue, gasping theatrically at the "stupefying complexity" [p.209] of this processes that stand revealed.

All this buildup is just so Behe can get to his overall point, which can be summed up thusly: "Look how complicated this is! Look how many different parts it has and how well they have to work together! I just can't imagine any way this could have developed gradually through evolution, can you? Let's just give up, say it must have been intelligent design, and then go home."

Lest you think that I'm being unfair to Michael Behe, he actually says something like this in this book, and in very nearly these words. Here's how he puts it:

"Now, does this microscopic transportation system [Behe is speaking about the endoplasmic reticulum —Ebonmuse] sound like something that self-assembled by gradual modifications over the years? I don't see how it could have been. To me, it has all the earmarks of being designed." [p.209]

"I don't see how it could have been": this is the argument of intelligent-design advocates in a nutshell.

I do wonder if this way of thinking is partly responsible for creationists' near-total lack of scientific output, even those who were actual scientists before joining the ID movement. Their argument is based on treating the complexity of the living world as utterly intractable and inexplicable. Is it not likely that this attitude discourages them from trying to study it? When your theology teaches you that science is a futile pursuit, why even attempt to do science?

The error at the root of this complexity phobia is the belief that evolution is incapable of creating complex things. This is implied in Behe's arguments throughout this chapter, though it's never explicitly spelled out. But why should we believe this? Evolution has been running on this planet for billions of years. It's not at all surprising that, with so much time to accumulate beneficial mutations and acquire new genes, the end products that we see today would be very complex indeed. And those molecular systems that Behe is so awed by? Many of them are found in bacteria, which number in the trillions and have generation times measured in hours. If evolution were a contest, bacteria would be the undisputed champions. Is it any wonder that there's so much complexity down at the bottom?

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January 29, 2010, 6:45 am • Posted in: The ObservatoryPermalink19 comments
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Weekly Link Roundup

A couple of noteworthy articles from this week that I didn't have time to write more about:

• To begin with, there's this excellent and in-depth profile of the FFRF's Dan Barker and Annie Laurie Gaylor, from a local alternative paper in Madison.

• Archaeologists have discovered a genuine burial shroud from the first century CE. Unlike the Shroud of Turin, its radiocarbon date fixes it to the correct time period; it also has a very different weave than the more famous Turin hoax.

Churches in Malaysia are being attacked by Muslims, who are angry over a court ruling that struck down a government ban on the use of the word "Allah" by Christians. Perhaps we should get Nancy Graham Holm over there to explain to the Christians that it's their own fault they're getting firebombed, because they rudely persist in using a word of which Muslims are the rightful owners.

• A muckraking blogger named Failed Messiah exposes the scandals of the Orthodox Jewish world. (HT: New York Times).

• The Telegraph tells us that heroic behavior among animals is more common than previously thought. Who was it that said only human beings have a sense of morality?

• And finally, a story I may return to later: New York City mayor Michael Bloomberg has invited atheists to the city's annual interfaith breakfast for the first time ever. Bravo, sir! It feels good to be taken seriously by politicians for once.

January 9, 2010, 9:29 pm • Posted in: The FoyerPermalink1 comment
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A Sense of Kinship

This past summer, I was visiting the New York Botanical Gardens when serendipity struck: this beautiful little creature alighted on a stone railing around the edge of a pool, staying just long enough for me to snap this shot:

I think, though I'm not an expert, that this is a blue dasher, Pachydiplax longipennis.

I don't usually like close-up photos of insects - they have an eerie, alien feel that I find disturbing. (I admit it, I'm a mammal chauvinist.) But this one is one of the rare exceptions. Looking at it again, it's hard for me not to feel admiration for this sleek, graceful creature.

With its iridescent blue scales, its impossibly frail and transparent wings, its delicate jointed legs, it scarcely seems to belong to nature at all. It looks almost like a device, a tiny whirring clockwork machine made by some detail-obsessed jeweler - except, of course, that we humans haven't yet learned to make machines of such fine and precise workmanship, nor any that pack so many marvelous capabilities into such a small package.

So much of its head is taken up by those huge, gorgeous compound eyes, it seems it has scarcely any room for a brain to process the information they take in. Yet dragonflies have keen eyesight, and are blurringly fast and acrobatic fliers - and imagine how well-tuned their organs of balance must be, to control their pitch, roll and yaw in three-dimensional space at such speeds, a task that would overwhelm a human vestibular system. And though they seem so clumsy, so fragile - adult dragonflies can only fly, not walk, and their wings can't be folded in like a beetle's but must be held out at all times - on their own small scale, they are fearsome and effective predators. And of course, like all living things, dragonflies have one more astounding ability that human-designed devices can't match: they can make copies of themselves from the raw materials of their environment!

All in all, despite all our brains, we humans can't create anything nearly as clever, as intricate, as adaptable, or as beautiful as a dragonfly. But we shouldn't feel too bad: when it comes to forging machines, we've had barely a few hundred years of practice. Evolution has had hundreds of millions of years to refine its designs, to hone and sharpen them against the ruthless grindstone of natural selection. With that much of a head start, and with all the resources of a planet to use for trial and error, it's no wonder that even this blind algorithm produces results of a beauty and craftsmanship we can't match.

And yet, the stunning truth is that we ourselves are products of the same evolutionary process. Look at your hands, your arms, and imagine tens of millions of years of natural selection pushing and tugging on them like a sculptor kneading clay, slowly molding flesh and bone into new shapes. Imagine the skeins of DNA coiled in your cells, woven out of evolution like a tapestry from a loom. Imagine the unbroken chain of your ancestors stretching back into the misty recesses of time, each one only subtly different from the last - but even subtle changes add up, until you reach a point, untold millions of generations ago, where the ancestral lines of human and dragonfly merge into the same track.

This knowledge should fill us with awe. The fact of universal common descent via evolution means that I and this glittering blue dragonfly, no matter how distant the links, are related. When I snapped that picture, it was a family reunion, of sorts - and the admiration I felt for its intricacy and beauty is the same kind of admiration I'd feel for any talented relative whose glory reflects, even if only a little, on his siblings and cousins.

The human species is like a hiker who, having scaled a long and arduous path, can finally stop at a vantage point and look back on the journey he's taken. Looking out across the landscape, we can see our fellow travelers, each one taking a different course from all the rest, all of them spreading out from a single point of origin in the far distance. Why should we not feel a sense of kinship for all the other beings who are traversing life's winding, contingent paths along with us? And why should we not marvel all the more that our astonishing existence is not the result of deliberate planning, but of a glorious, messy, freewheeling cauldron of chance?

November 23, 2009, 6:51 am • Posted in: The ObservatoryPermalink16 comments
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Another Branch on the Human Family Tree

I haven't written about any new transitional fossils in a while, so it's a great pleasure for me to mention this one: a hominid skeleton nicknamed "Ardi", a specimen of Ardipithecus ramidus. This species was known from other fossil fragments, but Ardi is one of the oldest and most complete hominids found so far, and may give us the most insight yet into what the common ancestor of humans and chimpanzees looked like.

Image copyright 2009, Jay Matternes.

Ardi lived about 4.4 million years ago (by comparison, Lucy and her fellow australopithecines are about 3.4 million years old), in the Middle Awash region of modern-day Ethiopia. Today it's an arid badlands, but in that era, it was a lushly forested woodland, cool and wet but geologically active, with frequent volcanic episodes (a great boon to biologists, since volcanic rock and ash strata are easily dated with radiometric methods and give us good estimates of when a certain fossil lived). Primitive elephants, giraffes, horses, antelope, rhinos and monkeys are well-known from this area, as are other hominid specimens.

The fossil itself is believed to be a female. The bones were so poorly fossilized, according to the Science paper by Tim White and colleagues, that they would crumble if touched. The researchers painstakingly chipped them free of the rock they were encased in with dental picks, bamboo, and porcupine quills (!). From the fossil's discovery to its publication took nearly 15 years of preparation and study - but from all accounts, it was worth the wait.

In life, Ardi would have stood just under four feet tall and weighed about 110 pounds. The skull was small, about 325 cc, about the same size as a chimp's. Ardi's teeth suggest she was an omnivore, and from comparing other A. ramidus teeth and bones found in the region, White and his colleagues found little difference in tooth size or body size between male and female individuals. This suggests that their mating style was relatively peaceful, with little competition for mates (as compared to chimpanzees, who have massive canine teeth which are used to intimidate potential rivals) and possibly more stable pair-bonding and group cohesion.

Ardi's hands, feet and pelvis tell us a lot about how she got around. Hominids like Lucy show a mosaic of bipedal and arboreal adaptations - as Laelaps puts it, they "had their hands in the trees and their feet on the ground" - and Ardi shows a more primitive version of the same pattern, much as we'd expect from an ancestor of that age.

She stood and walked upright, though not as well as Lucy or as us, and her feet were becoming more rigid like ours, except that she also had an opposable big toe useful for grasping. Her arms were long enough to reach to her knees when standing upright, but her hands were not adapted for knuckle-walking. Nor did they have the specializations for climbing and hanging from trees that we see in modern apes. She still lived in the trees, but would have moved through them more slowly and carefully than chimps or orangutans, and was capable of descending to the ground and walking. This refutes the once-popular belief that bipedalism first developed when human ancestors left the forest for the savanna and adapted to stand upright so as to see over the grass - as shown by species like Ardi, bipedalism evolved before we left the trees.

Another popular but erroneous idea that Ardi refutes is that the common ancestor of humans and chimps looked basically like a chimp, and that humans have changed significantly while modern chimps are little different from our common ancestor. This is probably tied to the misconception of the "great chain of being" that sees humans as the highest or most advanced form of life on Earth. Ardi, who probably lived relatively near the time when our two lineages split, instead shows that both humans and chimpanzees have evolved and specialized since the time of our common ancestor, becoming adapted to two very different ways of life.

Other articles:

Ardipithecus: We Meet At Last. The Loom, 1 October 2009.

Tim D. White, Berhane Asfaw, Yonas Beyene, Yohannes Haile-Selassie, C. Owen Lovejoy, Gen Suwa, and Giday WoldeGabriel. "Ardipithecus ramidus and the Paleobiology of Early Hominids." Science, 2 October 2009: 64, 75-86. (full text online, requires free registration).

October 3, 2009, 3:18 pm • Posted in: The ObservatoryPermalink6 comments
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The Case for a Creator: Dysteleology

The Case for a Creator, Chapter 4

In the last section of his interview with Stephen Meyer, Lee Strobel brings up the dysteleological argument, asking how intelligent design can account for the faults and imperfections in the natural world that would seem to cast doubt on the wisdom or benevolence of the designer. He begins with a classic argument, the inverted retina. Quoting Ken Miller:

"We would have to wonder why an intelligent designer placed the neural wiring of the retina on the side facing the incoming light... This arrangement... produces a blind spot at the point where the wiring is pulled through the light-sensitive retina to produce the optic nerve that carries visual images to the brain." [p.86]

Meyer waves this off, claiming (without further explanation) that this arrangement is "a tradeoff that allows the eye to process the vast amount of oxygen it needs in vertebrates" [p.87], which Strobel accepts without qualm. He admits that this arrangement produces a blind spot, but "that's not a problem because people have two eyes and the two blind spots don't overlap". I'm sure the families of people killed in car accidents because they didn't see the other car in their blind spot will be relieved to hear that.

Although Meyer doesn't go into any more detail about what he means, I'm assuming it's the same argument as given here by Michael Denton. But even if one accepts the creationist argument that the retina needs extra blood supply, that still doesn't explain why there has to be a hole in it for those vessels to pass through. (It also doesn't explain why octopuses do just fine with a non-inverted retina and no blind spot - unless the designer liked them better than us.)

Moving on from this point, Meyer tries to ward off the dysteleology argument by claiming that all design has "inevitable tradeoffs and compromises". This is true, but misses the point. We're not faulting adaptations for being less than theoretically perfect, but for being demonstrably suboptimal, such that they could have been unequivocally improved by an intelligent designer without making any tradeoffs. The inverted retina is one. Another, possibly even better example is the human appendix, which in the absence of modern surgery results in about 1 in 15 people dying slowly in great pain from peritonitis. If this is the result of design, one shudders to consider the intelligence of the designer.

We move on to another classic evolutionary exaptation:

"For instance, Gould claimed the panda's thumb looks jerry-rigged and not designed. Well, experts on the panda say it's a pretty efficient way of scraping the bark off bamboo." [p.88]

Again, Meyer has obscured the argument here. It doesn't matter how efficient the panda's thumb is: the point that matters is what the panda's thumb is.

Like most vertebrates, human beings have five digits - in our case, four non-opposable fingers and one opposable finger, the thumb. Pandas have the same five digits, but they are all non-opposable. The panda's "thumb" is a sixth digit, a pseudo-finger created by enlarging and extending a wrist bone called the radial sesamoid.


The panda's thumb. On the left is the hand of a modern giant panda, Ailuropoda melanoleuca. Note the five digits and the enlarged radial sesamoid. On the right is the hand of an extinct carnivorous mammal, Simocyon batalleri, a possible panda ancestor (source).

The panda's thumb is not an example of dysteleology in the sense that the inverted retina is. It's an example of evolutionary tinkering - the haphazard, jury-rigged kind of adaptation that we see again and again in the natural world, what led Richard Dawkins to call evolution a "blind watchmaker". Because of the random nature of mutation, it's to be expected that evolution would sometimes solve the same problem in different ways. On the other hand, if there is an intelligent designer, why didn't he just give the panda four fingers and an opposable thumb, the way primates have?

The jury-rigged, ad hoc nature of adaptation is just what we would expect from evolution. ID, on the other hand has no explanation for this, other than postulating a capricious, whimsical designer who repeatedly reinvents the wheel rather than reusing his own solutions from other lineages. In other words, ID advocates have to assume a designer whose work looks like the product of evolution.

To close out the chapter, Meyer resorts to another all-purpose excuse to explain any examples of dysteleology he might have missed:

"The Bible says there has been decay or deterioration because evil entered the world and disrupted the original design... Based on the biblical account, we would expect to see both evidence of design in nature as well as evidence of deterioration or decay - which we do." [p.88]

In other words: everything good can be credited to God, everything bad can be blamed on sin (although it's not explained why human sin resulted in "deterioration or decay" among other species - this is something that Christian apologists since Milton have had difficulty with). One wonders if the appendix represents "deterioration or decay", and if so, from what. Did pre-Fall humans have an herbivore's cecum filled with cellulose-digesting bacteria? Did Adam and Eve browse on grass in Eden?

On that note, it's worth pointing out that this statement seemingly places Meyer in the camp of the young-earth creationists, those who believe in a literal Garden of Eden, a literal serpent tempter and a human race descended from just two people. If that's the kind of outright nonsense that Strobel is endorsing, his claim to be presenting the latest cutting-edge science goes up in smoke. We'll get more into this topic in the next chapter.

Other posts in this series:

August 24, 2009, 7:02 am • Posted in: The ObservatoryPermalink24 comments
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