Artificial molecules

Origins research is beginning to really heat up (hilarious pun intended). One team of researchers is working with RNA (but then again, who isn’t?)

A new molecule that performs the essential function of life – self-replication – could shed light on the origin of all living things.

If that wasn’t enough, the laboratory-born ribonucleic acid (RNA) strand evolves in a test tube to double itself ever more swiftly.

“Obviously what we’re trying to do is make a biology,” says Gerald Joyce, a biochemist at the Scripps Research Institute in La Jolla, California. He hopes to imbue his team’s molecule with all the fundamental properties of life: self-replication, evolution, and function.

By building a molecule that can self-replicate, Joyce’s team has shown a pretty solid principle of how scientists believe life began: begin with something simple which makes copies of itself, then…

Not content with achieving one hallmark of life in the lab, Joyce and Lincoln sought to evolve their molecule by natural selection. They did this by mutating sequences of the RNA building blocks, so that 288 possible ribozymes could be built by mixing and matching different pairs of shorter RNAs.

What came out bore an eerie resemblance to Darwin’s theory of survival of the fittest: a few sequences proved winners, most losers. The victors emerged because they could replicate fastest while surrounded by competition, Joyce says.

As Joyce notes, this isn’t truly life. It’s a very promising experiment, however, and that’s where the excitement lay. By inducing mutations, evolution began to take place. It’s so simple a child can understand it.

The confusion over Steve Jones

Steve Jones has, according to media reports, made the claim that human evolution has stopped, or is at least slowing down in the West. At times we see conflicting statements from Jones himself over this.

I really just know about snails, and the beauty of evolution is that it gives biology a structure, so the rules that apply to snails or to fruit flies to some extent apply to ourselves. Obviously there’s much more that applies to us. But if you ask the simple Darwinian question about natural selection, inherited differences in the ability to pass on genes (which is only part of the evolutionary argument) it’s pretty clear to me that at least for the time being and at least in the developed world, natural selection has stopped or at least slowed down.

First, snail evolution is quite beautiful. Second, we see here that Jones is referring to natural selection, not evolution. Some sort of argument can be made that there is much less selection pressure on humans in Western nations than there was in the past. Of course, that wouldn’t be a very satisfying argument since natural selection is still ‘weeding out’ people with certain diseases and predispositions. It’s just that some of them, depending upon their economic situation as well as their particular affliction, happen to have reduced overall selection pressure on their alleles. But even then, there are people with diseases which will kill them before they get a chance to reproduce.

At any rate, this whole argument becomes rather moot because Jones also goes on to specifically speak of evolution rather than just one of its mechanisms. In fact, his talk is titled “Human Evolution is over”. He is wrong. Even if we were to ignore all the problems involved with making an argument that natural selection is over in humans (in the West), the evolution-is-over argument still does not fly because evolution is not simply selection. Genetic drift and mutation are two other major mechanisms. While he seems to ignore drift, Jones does, however, argue that there are fewer mutations in the population. His argument goes like this.

Men are fathering children at far younger ages than they did in the past. Given the fact that mutations accumulate in a person over time, these young men have fewer mutations than older men. Thus, subsequent generations are inheriting fewer and fewer mutations.

Okay, the first question which comes to mind is “So what?” The mutation rate of younger fathers is still, by far, substantial enough to maintain the continuing of human evolution. There is no shortage of mutations in each and every person at birth. Jones probably was born with around 100 mutations. You, too.

The second thing which comes to mind is to wonder why Jones would first make this age-mutation argument, but then go on to argue this.

Similarly, child survival rates, abysmal in antiquity, have dramatically improved in much of the world, cutting natural selection pressures.

In other words, more people live to reproductive age. This means there are more people reproducing, which means more mutations. His argument is dreadfully weak.

One wonders why such a quality scientist would make such a poor proposition.

John Lott is wrong again

It has been well-documented that John Lott is a big, fat liar. He writes slanted pieces to pursue his own agenda, not truth. So it comes as no surprise that he would post an article on his blog which claims that an Obama advisor is “wacky” for being concerned about global warming. Okay, so no big deal. Just another ignorant mook that cites non-scientific sources in order to pursue lies. Sure, it’d be nice if he would just go and post at Conservapedia, FOX News, or WorldNetDaily, but the whole concept of free speech does allow for anyone to speak his mind, even if the thoughts within said mind are utterly ignorant. Ignorant how? As is so common (especially among conservatives – extra-especially among FOX News conservatives), John Lott is ignorant in science. In this case, it’s sun spots.

First let’s note how Lott cites an article from Investor’s Business Daily (that highly regarded scientific organizati…business newspaper). He excludes eight grafs on his blog. Three of the grafs are either introductory or conclusion grafs. The other five are as follows.

The Little Ice Age has been a problem for global warmers because it serves as a reminder of how the earth warms and cools naturally over time. It had to be ignored in the calculations that produced the infamous and since-discredited hockey stick graph that showed a sharp rise in warming alleged to be caused by man.

The answer to this dilemma has supposedly been found by two Stanford researchers, Richard Nevle and Dennis Bird, who announced their “findings” at the annual meeting of the American Geophysical Union in San Francisco. According to them, man not only is causing contemporary warming. He also caused the cooling that preceded it.

According to Bird and Nevle, before Columbus ruined paradise, native Americans had deforested a significant portion of the continent and converted the land to agricultural purposes. Less CO2 was then absorbed from the atmosphere, and the earth was toasty.

Then a bunch of nasty old white guys arrived and depopulated the native populations through war and the diseases they brought with them. This led to the large-scale abandonment of agricultural lands. The subsequent reforestation of the continent caused temperatures to drop enough to bring on the Little Ice Age.

Implicit in this research is that the world would be fine if man wasn’t in the way. We either make the world too cold or too hot, a view held by many in high places.

Given the derisive nature of these grafs, it may actually may have made sense for Lott to publish them, but two of them contain some contradictory science to his silly dogma. That just doesn’t fly for these global warming denialists. I’m beginning to think Lott maybe does visit Conservapedia.

So now that we have Lott’s continued dishonesty out of the way, let’s tackle the main issue: sun spots. The unscientific, babbling article the unscientific, babbling Lott cites tries to stake a claim that all this hoo-hah about global warming is really just scientists misinterpreting data because they never considered sun spots.

When the sun is active, it’s not uncommon to see sunspot numbers of 100 or more in a single month. Every 11 years, activity slows, and numbers briefly drop near zero. Normally sunspots return very quickly, as a new cycle begins. But this year, the start of a new cycle, the sun has been eerily quiet.

The first seven months averaged a sunspot count of only three and in August there were no sunspots at all — zero — something that has not occurred since 1913.

According to the publication Daily Tech, in the past 1,000 years, three previous such events — what are called the Dalton, Maunder and Sporer Minimums — have all led to rapid cooling. One was large enough to be called the Little Ice Age (1500-1750).

(Don’t worry, Lott posted that part).

Okay, so because there are few sun spots to be seen toward the end of this current solar cycle and global temperatures have dropped in 2008, global warming is due to that. There are so many things wrong with this it makes me mad.

First of all, this horrific article cites the first seven months of this year. Guess what? Those months correspond to the end of the last solar cycle. It wasn’t until the past three months that the new 11-year cycle was detected (Hey, John, that’s a scientific citation; use it sometime).

Of course, it’s possible to go so far as to use the misleading information provided by this business newspaper and still show it to be wrong. Let’s assume this solar cycle does correspond with the change in global temperature. It would necessarily follow because there was a rise in temperature in the first seven years of this century that there was also a rise in solar activity. In truth, this past 11-year solar cycle peaked in 2000 and has been decaying ever since. Wow! The wonder of slight research and knowledge! Oh, how it destroys ignorance so quickly. It’s too bad John Lott isn’t interested in doing that.

What’s more, this article cites the Little Ice Age, as if it was entirely and decidely caused by solar activity. The issue is far more nuanced than that – and certainly too nuanced for such an unqualified business newspaper.

Global thermometers stopped rising after 1998, and have plummeted in the last two years by more than 0.5 degrees Celsius. The 2007-2008 temperature drop was not predicted by global climate models. But it was predictable by a decline in sunspot activity since 2000.

Wow. This is just so fucking wrong that it just made me go and fucking swear at its wrongness. Global temperatures have been rising since 1998. From 1995-2006, 11 of the 12 warmest years on record were recorded. As far as this past year goes, it was a decline over the first years of this century – of course, that doesn’t really matter when it was still the 10th warmest year on record. In fact, part of the reason it was cooler than other years was the moderation experienced from La Niña. As is well known (except by John Lott, in all likelihood), water is tremendously useful for retaining temperature. Since La Niña shrinks the warm pool of water in parts of the Pacific, it can make a noticable difference in global temperatures. Still, because of man-made pollution and deforestation, La Niña was not strong enough to prevent 2008 from being the 10th warmest year on record.

It’s unsurprising that John Lott would make a post like this. He has a history of making posts concerning things on which he has no knowledge. Take a look at his posts on evolution. They’re disparate, sometimes contradictory, often with no commentary to give some context. Granted, he shouldn’t be giving commentary on anything, but he also shouldn’t be making posts first concerned with human evolution accelerating and then subsequent posts concerned with human evolution slowing down. Bah. I don’t know why I continue to expect more out of these far-right, a-science mooks.

Texas gets it right

Texas actually managed to get something right.

The final proposal for the state’s science curriculum pleases scientists and watch groups, who say it will help protect Texas public school classrooms over the next decade from what they call “watered-down science” — specifically during the instruction of evolution.

Much of the concern over earlier versions of the proposed curriculum centered on a requirement that students be able to analyze the “strengths and weaknesses” of scientific theories, a phrase which some say is being used by creationists — including some members of the State Board of Education — to subvert the teaching of evolution.

It’s high time this was settled. Creationists compose the most dishonest bunch of crazies we have running around in the world. They’ve never added anything of worth to the world that comes directly from creationism. Everything they believe is worthless garbage that deserves nothing but ridicule and derision. They explain nothing while taking the beauty out of the world. They want us to be satisfied with not understanding the Universe because doing so allows them to continue in their delusion. The fact that this group had a voice at all in a worthy process such as the creation of science standards for children shows a pathetic lack of education among those involved in the process.

The third and final draft says students should be able to analyze and evaluate scientific explanations. There is also a new requirement that students should be able “to evaluate models according to their limitations in representing biological objects or events,” but it would take a mind-boggling leap for anyone to interpret that as applying to evolution, Quinn said, particularly when viewed through the plan’s new definition of science.

The old definition — which included phrases like “a way of learning about nature” and “may not answer all questions” — has been replaced with a definition from the National Academy of Sciences. It states that science involves using evidence to form explanations and make predictions that can be measured and tested. It also warns that questions on subjects that cannot be scientifically tested do not belong in science.

Bam. Peace out, creationism. Magic cannot be used to make predictions, cannot be tested, and is unfalsifiable. Fail, fail, fail. There is no point where supernatural beliefs have any relation with science. Well, to be fair, that isn’t entirely true. I can imagine an SAT question that says “False is to true as creationism is to ____” with the correct answer being “science”. That relation works quite well, actually.

Don McLeroy, the state board’s chairman, has said that science should admit the possibly of the supernatural when natural explanations fail. But he has also said that he is not trying to put creationism in public schools.

There’s a pretty good explanation of some more creationist dishonesty. McLeroy (who is a dentist) wants nothing more than to sneak magic into public schools. It is his raison d’être. All he wants to do is find a point where science has yet to explain something and then institute something which can absolutely never explain anything. That is creationism. He may as well have said “I want creationism in our public schools, but I don’t want creationism in our public schools.” Jackass.

Emotional Appeals

Ben Stein tells us that evolution leads to genocide. It leads to atheism (which is implicitly bad, apparently). Chaos, murder, cancer, and sad puppies will infest the world if evolution is embraced. It only makes sense then that we should necessarily reject evolution if we want to live in a world of peace and goodness.

Of course, that all sounds utterly silly. But it’s the argument being put forth by Christians all the time (if not in form, then principle): because X leads to something bad, it should be rejected. It is an appeal to emotion. No one wants something bad to be true, so claiming a falsehood on that thing can bring some sort of sense of mind. These people are not ones with which to be reasoned easily.

Emotional appeals are useless in determining what is true. It is the simple truth of something which is important to me. I do not accept or reject evolution based upon an philosophical underpinings or relations. To do so is to make my acceptance or rejection irrelevant and meaningless. If evolution somehow automatically leads to the philosophy of Hitler, that’s unfortunate. That, however, has zero bearing on the truth of evolutionary theory. Either life evolved through small, gradual steps over billions of years of common descent or it didn’t. Nothing Hitler ever thought can change that.

It should not be acceptable for a person to make an emotional appeal on an issue of truth. Save that for the subjectivity of a relationship. We should believe not based upon what we want to believe, but based instead upon evidence. It is evidence which holds so much importance to our lives and to our ability to discern what is true and what is not. Our emotions have no influence over truth.

Aversion to education (rant)

I find myself wondering why the aversion to education from so many. It has become a popular thing to say “Well, such-and-such told me this about Subject X, so I’m not really interested in learning about it.” Well, that isn’t a good reason, is it? It’s no more than an Appeal to Authority. Basically, a person who is held in some modicum of respect declares this or that to be true and so others take it to be true and worthwhile.

I specifically want to take this down the road of science (of course). There is a massive aversion to this subject, almost to the point where it’s popular to play up one’s ignorance of this powerful, powerful tool. It’s a shame. A big, fucking shame. What’s tragically ironic is that many of these same people fully embrace their Internet, cars, toilet paper, inexpensive food, iPods, mass-produced (and inexpensive) clothing, and so many other things which are the result of science and technology. Science is within nearly every moment of our lives, yet few realize this because it is applied science, not research or theoretical science. Instead, we embrace the pseudosciences of acupuncture, intelligent design, and astrology.

To bring this to my favorite subject, it is of course important to wonder aloud why so many people have been taught that it is okay to be told by a pastor, priest, minister or other authority figure that evolution is untrue and that that person’s opinion on such a topic is worth its weight in salt. It isn’t. In fact, most Appeals to Authority are useless. It seems to me that if one is actually, genuinely interested in a topic that there would be a certain level of necessary inquiry that would be taken. That is, so many people reject evolution on the flimsy basis that because it contradicts their pre-held beliefs, it must be wrong. In other words, they recognize that if evolution is true, at best they can become theistic evolutionists, but even then they must recognize that such a god is superfluous. That means whether evolution is true or not is wholly central to the belief system of anyone that realizes the importance of the issue. If we can agree that this is the case, then shouldn’t we also agree that an aversion to education about evolution comes across as rather silly?

Nothing makes sense except in the 'light' of creationism

At least not in Louisiana.

Not far back, I warned that we need to watch out for Bobby Jindal. He’s the anti-science mook of a governor from Louisiana that recently signed into a law a bill which targets the facts of evolution and global warming.

Remembering Jindal as a good student in his genetics class, Landy hoped that the governor would recall the scientific importance of evolution to biology and medicine. Joining Landy in his opposition to the bill were the American Institute of Biological Sciences, which warned that “Louisiana will undoubtedly be thrust into the national spotlight as a state that pursues politics over science and education,” and the American Association for the Advancement of Science, which told Jindal that the law would “unleash an assault against scientific integrity.” Earlier, the National Association of Biology Teachers had urged the legislature to defeat the bill, pleading “that the state of Louisiana not allow its science curriculum to be weakened by encouraging the utilization of supplemental materials produced for the sole purpose of confusing students about the nature of science.”

But all these protests were of no avail. On June 26, 2008, the governor’s office announced that Jindal had signed the Louisiana Science Education Act into law. Why all the fuss? On its face, the law looks innocuous: it directs the state board of education to “allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied,” which includes providing “support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied.” What’s not to like? Aren’t critical thinking, logical analysis, and open and objective discussion exactly what science education aims to promote.

s always in the contentious history of evolution education in the U.S., the devil is in the details. The law explicitly targets evolution, which is unsurprising—for lurking in the background of the law is creationism, the rejection of a scientific explanation of the history of life in favor of a supernatural account involving a personal creator. Indeed, to mutate Dobzhansky’s dictum, nothing about the Louisiana law makes sense except in the light of creationism.

It’s fascinating that the group of people who claim to be the most moral of all mankind are the ones who are constantly seen lying about their intentions. Rather than to continue saying “We are creationists. We believe absurd things which have no basis in science. We want these things taught in the secular school system. Oh, and by the way, we need to talk about the whole “secular” thing”, they instead say “Academic freedom is being quashed because our ideas are not being accepted.” Of course, academic freedom has nothing to do with accepting every bad idea that comes around. If it did, not only would the Bible be an acceptable alternative discussion to the fact of evolution, but so would the Koran, Greek myths, and whatever the hell it is Tom Cruise believes. We would see Christian Science being regarded as an acceptable alternative to actual medicine and medical practices. We would see astronomy professors attempting to inform students of stellar evolution while in the next class an astrologer would tell the students why it’s a lucky week for capricorns.

Creationism and its twin in a cheap tuxedo, Paley’s Watchma…I mean, intelligent design…are not rejected on the basis that evolution cannot stand up to criticism. They are rejected because evolution already has stood up to criticism. That is why it’s a scientific theory. It stands with equal validity to cell theory, atomic theory, and the theory of gravity. It is established beyond all doubt. Proposing a necessarily complex (not to mention invisible) creator only raises more questions – namely, if the question is “How do we explain complexity?” then we are raising that very question with such a proposition. That is, saying life is so complex it needs a creator raises the question of the existence of the complexity of that creator.

Nothing makes sense except in the ‘light’ of creationism

At least not in Louisiana.

Not far back, I warned that we need to watch out for Bobby Jindal. He’s the anti-science mook of a governor from Louisiana that recently signed into a law a bill which targets the facts of evolution and global warming.

Remembering Jindal as a good student in his genetics class, Landy hoped that the governor would recall the scientific importance of evolution to biology and medicine. Joining Landy in his opposition to the bill were the American Institute of Biological Sciences, which warned that “Louisiana will undoubtedly be thrust into the national spotlight as a state that pursues politics over science and education,” and the American Association for the Advancement of Science, which told Jindal that the law would “unleash an assault against scientific integrity.” Earlier, the National Association of Biology Teachers had urged the legislature to defeat the bill, pleading “that the state of Louisiana not allow its science curriculum to be weakened by encouraging the utilization of supplemental materials produced for the sole purpose of confusing students about the nature of science.”

But all these protests were of no avail. On June 26, 2008, the governor’s office announced that Jindal had signed the Louisiana Science Education Act into law. Why all the fuss? On its face, the law looks innocuous: it directs the state board of education to “allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied,” which includes providing “support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied.” What’s not to like? Aren’t critical thinking, logical analysis, and open and objective discussion exactly what science education aims to promote.

s always in the contentious history of evolution education in the U.S., the devil is in the details. The law explicitly targets evolution, which is unsurprising—for lurking in the background of the law is creationism, the rejection of a scientific explanation of the history of life in favor of a supernatural account involving a personal creator. Indeed, to mutate Dobzhansky’s dictum, nothing about the Louisiana law makes sense except in the light of creationism.

It’s fascinating that the group of people who claim to be the most moral of all mankind are the ones who are constantly seen lying about their intentions. Rather than to continue saying “We are creationists. We believe absurd things which have no basis in science. We want these things taught in the secular school system. Oh, and by the way, we need to talk about the whole “secular” thing”, they instead say “Academic freedom is being quashed because our ideas are not being accepted.” Of course, academic freedom has nothing to do with accepting every bad idea that comes around. If it did, not only would the Bible be an acceptable alternative discussion to the fact of evolution, but so would the Koran, Greek myths, and whatever the hell it is Tom Cruise believes. We would see Christian Science being regarded as an acceptable alternative to actual medicine and medical practices. We would see astronomy professors attempting to inform students of stellar evolution while in the next class an astrologer would tell the students why it’s a lucky week for capricorns.

Creationism and its twin in a cheap tuxedo, Paley’s Watchma…I mean, intelligent design…are not rejected on the basis that evolution cannot stand up to criticism. They are rejected because evolution already has stood up to criticism. That is why it’s a scientific theory. It stands with equal validity to cell theory, atomic theory, and the theory of gravity. It is established beyond all doubt. Proposing a necessarily complex (not to mention invisible) creator only raises more questions – namely, if the question is “How do we explain complexity?” then we are raising that very question with such a proposition. That is, saying life is so complex it needs a creator raises the question of the existence of the complexity of that creator.

Shared errors

Over at Pharyngula, PZ Myers has a post which first destroys some creationist misconception, but then, far more interestingly, goes on to interpret a recent peer-reviewed paper on copy number variants, or CNVs. The whole piece is worth reading, but what I think is worth of a little extra attention is the brief point our shared errors.

An architecture does not imply intent or purpose, but they often imply a history. The pattern described — that chimps and humans share some common structural elements in their genomes — is better described as evidence of common ancestry than of well-designed function. An intron, for instance, is a piece of random, usually useless DNA inserted into the middle of the sequence of a gene that must be excised from RNA before it can be used to make a functional protein. It’s a little piece of garbage that must be cleaned up before the gene product can do its job. That a human and chimpanzee gene has identical introns is an example of an architecture, true enough, but it is of a shared error. Some all-knowing god—he seems to be consistently making the same mistake.

Okay, let’s take the recent hoo-hah with Coldplay and Joe Satriani. Basically, Satriani is claiming Coldplay ripped off one of his songs. There is some fairly compelling evidence to this claim, but it is far from airtight. What we have are four of the same chords repeating through parts of the songs, but only three consecutive notes are truly in common. We can potentially call this one a coincidence (especially since this song has been around forever and Satriani is only suing now that after Coldplay has won a slew of awards. Essentially, we see two instances of people creating similar things.

Now let’s consider someone learning the Satriani song. I don’t feel like finding the actual chord progressions, so let’s just say it goes A, B, C, D. The person begins to learn things, but is apparently a horrible musician and substitutes an F# for the C. Okay, fine. So we have a version of the song out there which is now A, B, F#, D. Now let’s say this person has a friend who wants to rip the song off. But instead of listening to the original Satriani version, he listens to the mutated version with the F#. Now we have some evidence of a copycat. It isn’t very strong evidence because there is just one error. In both instances, we have just four chords. But let’s say another error is made further along in the song. A chord in the bridge is misinterpreted by the original person learning the song. And, naturally, the copycat makes the same error. As we go deeper and deeper into errors, we begin to get better and better evidence of a common origin – the friend was learning from the interpreted version of the song, not the Satriani version, because it is unlikely he would make, say, 5 of the same errors as his friend. The chance for coincidence shrinks while the odds of identifying the correct source rise.

The way this is like CNVs is that we are seeing common errors being made again and again – and these errors are present in both human and chimp genomes. Of course, it should be noted that it isn’t entirely clear if these errors were directly inherited from a common ancestor or if it was the hotspot for ‘making’ errors is what was inherited, but at any rate, it is evidence for our common ancestory with the other apes. There are far too many common errors being made to simply file this under ‘God did it’. The evidence says that is – still and again – superfluous.

Discussing science

I find I often subject myself to a surprising amount of anti-science misery, otherwise known as the Crosswalk forums (with alternative names such as ibelieve.com). If you dare to read that rubbish, you’ll actually find a thread linking to one of my posts. I was banned long ago (it’s lifelong; I’m so flattered!), so it was actually a friend who made the thread. Anyway, it has generated a good deal of traffic for me, as well as quite a few responses, even if a large number of them are wholly devoid of any education. One reason it has generated traffic is because this blog (and science) tends to be a tad abrasive toward creationism and I guess there’s a whole slew of other people who like subjecting themselves to material which disagrees with what they believe, too.

Here’s a sample of the rubbish which is put on these forums.

NS [natural selection] is just a filter. It doesn’t create anything, it just weeds out stuff. Contrary to Darwinism, it doesn’t necessarily keep stuff either. There is nothing that stops deleterious mutations from undoing neutral and/or good ones.

Natural selection is a filter, but it does not exist, apparently.

Well, just speculating here, but if the tooth of a little dinosaur was made into a necklace, would anyone necessarily think of it being a dinosaur? A lot of what we see in the museums are people’s ideas of what they may have looked like, so I’m not entirely sure that what we see in the pictures are what they really even looked like.

Those silly misleading fossils. Scientists just guess how they go together.

So the pattern, rather than gradual changes through incremental and incidental modification of ongoing mutation, appears to be a rapid appearance of various groups [of horseshoe crabs] followed by extreme stasis, presumably comprising in some cases hundreds of millions.

This would seem to directly contradict the fundamental notion of Neo-Darwinian evolution.

Please see Gould.

Ok so here are some of the major reasons why I believe Darwinism will collapse.
Darwinism will ultimately collapse as a valid theory of life origins because :

It fails to explain the origin of complex coded information contained in all living organisms
It fails to explain the origin of nano bio-machinery contained in all living organisms
It fails to account for irreducibly complex systems contained in all living organisms
It fails to account for the human moral sense and altruism
It fails to explain the general lack of transitional forms in the fossil record which should number in the multiple millions but don’t
Natural selection (originally a creationist concept) has failed as a sufficient explanatory mechanism for the level of complexity and diversity in nature
Random mutations can never account for the sophisticated, factory-like organization within the cell
It fails to account for how, in the midst of greater numbers nefarious mutations, any of the rare beneficial mutations could dominate bio history = see 1st quote below
… IDists and creationists are invited to add to this list if you have more reasons

My head hurts.

Okay, I’m sorry for posting this, but I wouldn’t do it if I didn’t have a redeeming link, I promise. For actual discussion on evolution where people have [i]actual[/i] educations, the Richard Dawkins forums are excellent. I don’t personally post very much, but simply reading good discussions about science is refreshing and wonderful. And it isn’t necessary that you be an atheist to post or enjoy the read.