News Roundup: Surprise, We’re Still Learning New Things

| 93 Comments

Have you ever noticed how boring Creationism and/or Intelligent Design are? How many times must we endure hackneyed claims like “The Flagellum proves Intelligent Design,” or “The Cambrian Explosion Defies Darwinism” ?

Science, however, is continuously being refined and improved, and new discoveries are the order of the day. Here are a few current stories that have relevance to the creationism-versus-evolution “debate.”

  • Darwin’s Dilemma Resolved: Evolution’s ‘Big Bang’ Explained by Five Times Faster Rates of Evolution
  • Functioning ‘Mechanical Gears’ Seen in Nature for First Time
  • DNA Double Take

More below the fold.

Darwin’s Dilemma Resolved: Evolution’s ‘Big Bang’ Explained by Five Times Faster Rates of Evolution

Sep. 12, 2013 – A new study led by Adelaide researchers has estimated, for the first time, the rates of evolution during the “Cambrian explosion” when most modern animal groups appeared between 540 and 520 million years ago.

The findings, published online today in the journal Current Biology, resolve “Darwin’s dilemma”: the sudden appearance of a plethora of modern animal groups in the fossil record during the early Cambrian period.

“The abrupt appearance of dozens of animal groups during this time is arguably the most important evolutionary event after the origin of life,” says lead author Associate Professor Michael Lee of the University of Adelaide’s School of Earth and Environmental Sciences and the South Australian Museum.

“These seemingly impossibly fast rates of evolution implied by this Cambrian explosion have long been exploited by opponents of evolution. Darwin himself famously considered that this was at odds with the normal evolutionary processes.

“However, because of the notorious imperfection of the ancient fossil record, no-one has been able to accurately measure rates of evolution during this critical interval, often called evolution’s Big Bang.

“In this study we’ve estimated that rates of both morphological and genetic evolution during the Cambrian explosion were five times faster than today – quite rapid, but perfectly consistent with Darwin’s theory of evolution.”

Functioning ‘Mechanical Gears’ Seen in Nature for First Time

Sep. 12, 2013 – Previously believed to be only human-made, a natural example of a functioning gear mechanism has been discovered in a common insect – showing that evolution developed interlocking cogs long before we did.

The juvenile Issus - a plant-hopping insect found in gardens across Europe – has hind-leg joints with curved cog-like strips of opposing ‘teeth’ that intermesh, rotating like mechanical gears to synchronise the animal’s legs when it launches into a jump.

The finding demonstrates that gear mechanisms previously thought to be solely human-made have an evolutionary precedent. Scientists say this is the “first observation of mechanical gearing in a biological structure.”

Finally, Carl Zimmer in the New York Times, on Cells in the Same Organism having Different Genomes! DNA Double Take

From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information – or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that – to a surprising degree – we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

“There have been whispers in the matrix about this for years, even decades, but only in a very hypothetical sense,” said Alexander Urban, a geneticist at Stanford University. Even three years ago, suggesting that there was widespread genetic variation in a single body would have been met with skepticism, he said. “You would have just run against the wall.”

But a series of recent papers by Dr. Urban and others has demonstrated that those whispers were not just hypothetical. The variation in the genomes found in a single person is too large to be ignored. “We now know it’s there,” Dr. Urban said

“Now we’re mapping this new continent.”

Discuss.

93 Comments

Aha! This clearly proves that there is a divine Watchmaker with an inordinate fondness for issusseses. Just as the Scientific Theory of Intelligent Design predicted we’d find them! [/snarkasm]

I apologize for my ignorance, after reading the first brief article cited, I remain confused. Evolutionary rates were 5x as fast. Ok. Why were they faster? And specifically 5x faster than what? 5x faster than recent arthropod evolution? 5x faster than all recent rates for all life? How do you measure that?

My own ignorance-based assumption would be rates were much faster then because there were probably huge gaps in the environment which were available for exploitation whereas today (and for a long long time) the whole biosphere is saturated with life.

But yes, science is very cool because the amount of stuff to discover and learn is endless.

daoudmbo said: My own ignorance-based assumption would be rates were much faster then because there were probably huge gaps in the environment which were available for exploitation whereas today (and for a long long time) the whole biosphere is saturated with life.

I think that’s a reasonable guess. Another one would be that having bony bits (when nothing else does) is such an enormous advantage that many many daughter variations of new bony species succeeded dramatically, even in environments that were full of other (soft) competitors.

And there’s probably a whole slew of other possible explanations we’re missing. None of which involve “poof! There it is.”

Maybe there was less specialization back then, so changes were less likely to break something.

As daoudmbo mentioned, maybe there were way more empty niches than there are today or have been recently.

Or maybe it’s what eric said; a new trait arose, with different lineages developing it in different ways, which lead to a major arms race. (Or leg race for species that didn’t have arms.)

Or maybe generation spans were shorter, so more generations per year.

Or maybe there was more oxygen in the air, so things were more energetic back then.

Or some combination thereof. Actually, I’d guess it to be a combination of a huge number of different factors.

Well see those gears? They look just like designed gears. Except for all of the differences, they’re completely the same.

Like life in general. It looks exactly like things that are designed, excepting all of the differences, most notably the dependencies upon inheritance that would be expected from unguided evolutionary processes. Ignore those, plus the fact that intellectual commonalities don’t underlie adaptations, such as those for flight, after genetic exchanges cease to occur (or become extremely rare, at least), and it looks like design.

So see, excepting the evidence for evolution, there’s no evidence for evolution.

Glen Davidson

daoudmbo said:

I apologize for my ignorance, after reading the first brief article cited, I remain confused. Evolutionary rates were 5x as fast. Ok. Why were they faster? And specifically 5x faster than what? 5x faster than recent arthropod evolution? 5x faster than all recent rates for all life? How do you measure that?

They were 5x faster than recent arthropod evolution. What they did was get a phylogenetic tree for extant arthropods using both molecular and morphological data. Then they calibrated it to absolute time using fossils (and a very fancy calibration program). Finally, they looked at the rate of change per unit time along every branch, dividing the branches into two groups: those with a midpoint more than 500 million years ago (which they consider to be the Cambrian explosion, liberally speaking) and those with a midpoint less than 500 million years ago. The average, estimated rate of evolution along the first group of branches is 5x the rate on the second group.

I do think there’s a potential problem with that approach, in that if you look at the tree, the old branches are almost all much shorter in absolute time than the young branches, just because of the way they sampled species. This means that the younger rates are averaged over a much longer time than the older rates are, so that if there were a high rate of evolution for a little while during some Jurassic radiation or other, it probably wouldn’t show up in their plots. So we can say that the evolutionary rate during the explosion was much higher than the average through time, but we can’t say from this study that this was a unique event.

As to why rates were so fast, there are various hypotheses. You need to explain why a speedup happened in both morphological and molecular evolution. Ecological explanations can deal only with the former. The authors suggest that Cambrian arthropods were smaller and shorter-lived than later arthropods (since there is evidence that molecular evolutionary rate varies with generation time), which seems unlikely to me. I don’t have an explanation.

Gears? I want gears! Why does god give all the cool stuff to insects?

John Harshman said:

daoudmbo said:

I apologize for my ignorance, after reading the first brief article cited, I remain confused. Evolutionary rates were 5x as fast. Ok. Why were they faster? And specifically 5x faster than what? 5x faster than recent arthropod evolution? 5x faster than all recent rates for all life? How do you measure that?

They were 5x faster than recent arthropod evolution. What they did was get a phylogenetic tree for extant arthropods using both molecular and morphological data. Then they calibrated it to absolute time using fossils (and a very fancy calibration program). Finally, they looked at the rate of change per unit time along every branch, dividing the branches into two groups: those with a midpoint more than 500 million years ago (which they consider to be the Cambrian explosion, liberally speaking) and those with a midpoint less than 500 million years ago. The average, estimated rate of evolution along the first group of branches is 5x the rate on the second group.

I do think there’s a potential problem with that approach, in that if you look at the tree, the old branches are almost all much shorter in absolute time than the young branches, just because of the way they sampled species. This means that the younger rates are averaged over a much longer time than the older rates are, so that if there were a high rate of evolution for a little while during some Jurassic radiation or other, it probably wouldn’t show up in their plots. So we can say that the evolutionary rate during the explosion was much higher than the average through time, but we can’t say from this study that this was a unique event.

As to why rates were so fast, there are various hypotheses. You need to explain why a speedup happened in both morphological and molecular evolution. Ecological explanations can deal only with the former. The authors suggest that Cambrian arthropods were smaller and shorter-lived than later arthropods (since there is evidence that molecular evolutionary rate varies with generation time), which seems unlikely to me. I don’t have an explanation.

I detect an absence of the term “mutation rate”.

It seems as if they might be saying that mutation rates were comparable to those in the present, but accumulation of genomic change within lineages, over time, was faster during the period that they designate as the Cambrian explosion.

Wouldn’t that fit with a model of less restrictive selection?

(For the sake of completeness let me add that, because there are DNA repair mechanisms, there is both the absolute mutation rate per meaningful unit of DNA per unit of time or generation, and the net mutation rate, after repair. DNA repair mechanisms themselves have been selected for. Conceivably, in a world of wide open niches, ancestral lineages with low repair rates could transiently be selected for. Higher repair rates might be selected for later when lineages are more adapted to narrower niches. However, that would not reflect any major variation in the underlying biochemical absolute mutation rate.)

[nonscientist] Would a higher flux of radiation be a possibility? Would the natural background radiation from soil and minerals have been significantly higher that long ago, a half billion years closer to the formation of radioactive elements?

The item claiming a rapid Cambrian explosion seems to be getting the most attention here. I am having doubts about the paper itself, but I admit that most of its evidence is beyond my pay scale. The authors say in the first sentence of their abstract: “The near-simultaneous appearance of most modern animal body plans (phyla) ∼530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic innovation…”. They are asserting the old idea that the CE was very rapid (without this claim, they cannot make their main arguments), but I thought the consensus these days is that the CE was not rapid. Were there not recent posts at the Pandas’ Thumb that clearly argued the other way, based on piles and piles of evidence? At this time I am not buying the claim of this paper, but I would like to know what others think.

harold said: I detect an absence of the term “mutation rate”.

It seems as if they might be saying that mutation rates were comparable to those in the present, but accumulation of genomic change within lineages, over time, was faster during the period that they designate as the Cambrian explosion.

Wouldn’t that fit with a model of less restrictive selection?

It would fit, assuming that this less restrictive selection applied across the genome, which I find odd. That isn’t what the authors are saying, though. Talking about small/shortlived organisms is all about neutral evolution, i.e. mutation rate. But certainly altered selection is one way to get faster evolution. Their molecular data, by the way, were second and conserved first codon positions of protein-coding exons.

Mark Sturtevant said: They are asserting the old idea that the CE was very rapid (without this claim, they cannot make their main arguments), but I thought the consensus these days is that the CE was not rapid. Were there not recent posts at the Pandas’ Thumb that clearly argued the other way, based on piles and piles of evidence? At this time I am not buying the claim of this paper, but I would like to know what others think.

“Rapid” is of course a relative matter. But they do deal with your objection by allowing the basal node of Metazoa to vary in age from (if I recall) 542ma to 650ma, which makes only small differences in the rates of evolution. In order to get rates with the post-Cambrian average they have to put the node at upwards of 950ma, which nobody is willing to believe.

Boring?? We are the toast of contention in the science world today. We are in a story and a revolution!! The times are very exciting for modern creationism. We are flying high surely. This latest best seller has focused a good point about the sudden complexity arrival relative to the fossil record. Its not a YEC point as we disagree with the presumptions behind the fossil record claim. Its further not a biological scientific point anyways upon closer analysis. Boring??

Robert,

Name one new scientific discovery made by a creationist that supports creationism.

That’s what I thought. Nada, zip, zero, zilch. Boring!

Robert Byers said:

Boring?? We are the toast of contention in the science world today. We are in a story and a revolution!! The times are very exciting for modern creationism. We are flying high surely. This latest best seller has focused a good point about the sudden complexity arrival relative to the fossil record. Its not a YEC point as we disagree with the presumptions behind the fossil record claim. Its further not a biological scientific point anyways upon closer analysis. Boring??

Do you know who Baghdad Bob was?

There’s now a video on the gearlike legs that is jaw-dropping amazing.

Click here right now!

Dave

Gears? Gears? Where’s the automatic transmission?!?!?!?!?!?!!!!!!!!! :p

daoudmbo said:

I apologize for my ignorance, after reading the first brief article cited, I remain confused. Evolutionary rates were 5x as fast. Ok. Why were they faster?

If it helps any, there are some general features of simple systems.

The dispersion in a system made up of N molecules is proportional to N -1/2

Thus we expect to see much larger variability in smaller systems; and if such systems are undergoing natural selection, the selection process is going to produce systems that have larger differences among themselves.

We are flying high surely.

You shouldn’t be using illegal drugs

Although I am still agnostic about whether the CE was extraordinarily rapid, there are ideas for why this period was able to produce so many new animal forms. The molecular clock data says that most of the phyla were present before the CE. The relative lack of fossils from these phyla could be b/c they were small and soft bodied (as the larval forms of these groups tend to be today). The earth was thawing out after a long cold period, and oxygen levels were increasing. This could mean greater availability of new ecological niches, and different animal lineages could adaptively radiate into those niches. Hard parts are easier to develop in warmer seas with high oxygen, and predation pressures would mean selection for hard parts. Finally, gene duplication would expand the genetic toolkit for evolution into the new forms.

Robert Byers said:

Boring? We are the toast of contention in the science world today…

Boring in that C/ID does not come up with new ideas. Boring in that C/ID is soundly defeated, but its pushers will not admit it. The attention paid is more due to annoyance. Attention does not mean respect.

Mark Sturtevant said:

Robert Byers said:

Boring? We are the toast of contention in the science world today…

Boring in that C/ID does not come up with new ideas. Boring in that C/ID is soundly defeated, but its pushers will not admit it. The attention paid is more due to annoyance. Attention does not mean respect.

Boring in the sense of no new data. Boring in the sense that they aren’t even pretending to do any research so they will never have any new data. Boring in that they are reduced to claiming that every new discovery by real scientists somehow magically supports their nonsense. Boring in that they can only repeat the same lies over and over. Boring in that they never learn from their mistakes and keep making the same errors over and over, even after being repeatedly corrected. Now that’s boring.

Robert is like the little kid so desperate for attention that he craves scorn and ridicule and thinks of it as a victory. How sad.

Boring in that C/ID does not come up with new ideas.

What they do is come up with new labels for old ideas. Scientific creation, ID, Teach the controversy, etc.

Robert Byers said:

Boring?? We are the toast of contention in the science world today.

You’re toast all right.

There isn’t any scientific controversy. A mentally unbalanced homeless person can scream at random passers-by, “You stole my aardvark!” Most people ignore him and hurry past, going about their business. A few unlucky or unwise souls will argue with him, and deny stealing the aardvark, because it never existed. That is a “contention” as Byers says; perhaps the crazy homeless person imagines he is “the toast if the contention”– that is self-aggrandizing and flattering for the crazy people. The fact that you manufactured a controversy by lying should make you ashamed instead of proud.

Despite your egocentric fantasy, most scientists cannot name a single creationist and have never heard of Stephen Meyer. They have real work to do, and arguing with crazy people is not a scientific controversy.

“The lack of interest for pseudoscience in some philosophical quarters derives from the tacit assumption that some ideas and theories are so obviously wrong that they are not even worth arguing about. Pseudoscience is still too often considered a harmless pastime indulged in by a relatively small number of people with an unusual penchant for mystery worship. This is far from the truth. In the form of creationism and its challenges to the study of evolution, pseudoscience has done great damage to public education in the United States and elsewhere; …”

Taken from Massimo Pigliucci’s blog, “Rationally Speaking” for August 29, 2013:

Philosophy of Pseudoscience: reconsidering the demarcation problem

which in turn is taken from the introduction to the recently published book

Massimo Pigliucci and Maaten Boudry, eds. Philosophy of Pseudoscience; Reconsidering the Demarcation Problem Chicago: University of Chicago Press, 2013 ISBN 978-0226051963

The Zimmer article on chimeras and mosaics is fascinating, and y’all should mosey over to read it. Zimmer has a great knack for finding illuminating stuff in science, and directing it to the public. The material on chimeras was especially new to me, such as the finding that women often have cells in their brain that appear to be from the children they bore!

Might it just be that at this early point in the evolution of life forms, it was basically a blank slate? As others have noted, likely the competition was not fierce, the environmental niches were wide open, the field of play was subject to genetic change at any time, and the complexity of life forms was only at an initial stage.

Mark Sturtevant said:

The Zimmer article on chimeras and mosaics is fascinating, and y’all should mosey over to read it. Zimmer has a great knack for finding illuminating stuff in science, and directing it to the public. The material on chimeras was especially new to me, such as the finding that women often have cells in their brain that appear to be from the children they bore!

Just to clarify it a bit for lay people, a lot of what is described is mosaicism due to early somatic mutation. That is to say, at some early stage in development when you body has, say, only a few hundred cells, many of which will give rise to millions of cells by the end of development, a cell picks up a mutation which is compatible with life and development. All the subsequent cells it gives rise to share the mutation, but other cells in the body won’t. However, the cells all have essentially the same genome.

There are people who are outright chimeras, often as a result of a multiple gestation situation, with two (or possibly more) truly individual genomes, depending on what body part you sample.

There is also a phenomenon known as microchimerism, the finding of DNA of children in women during and in some cases long after pregnancy. This has mainly been studied by limited methodology, for example simply purifying DNA from a blood sample and seeing what percentage of DNA is male. All studies of microchimerism that I am aware of exploit the situation of pregnancy with a male child, making the Y chromosome an easy target. I’m not aware of significant studies using say, in situ hybridization to see which exact cells in a tissue sample might be of fetal origin. (If you are, please post a reference.)

However, we routinely do cytogenetics on bone marrow samples and other types of samples from patients. I’m not a cytogeneticist but have looked at many, many cytogenetic reports. Of course by many, many I probably mean at most thousands. Many of these are highly abnormal karyotypes of neoplastic cells; that’s the clinical point of cytogenetics in my field. NONE that I have ever seen or even heard of have come back XY, or with a Y at all, from a woman (obviously, not counting transsexual patients). Microchimerism does appear to be quite micro. It’s fascinating, but the proportion of cells in a woman’s body that are of fetal origin appears to be very low, even in multiparous women.

John Harshman said:

harold said: I detect an absence of the term “mutation rate”.

It seems as if they might be saying that mutation rates were comparable to those in the present, but accumulation of genomic change within lineages, over time, was faster during the period that they designate as the Cambrian explosion.

Wouldn’t that fit with a model of less restrictive selection?

It would fit, assuming that this less restrictive selection applied across the genome, which I find odd. That isn’t what the authors are saying, though. Talking about small/shortlived organisms is all about neutral evolution, i.e. mutation rate. But certainly altered selection is one way to get faster evolution. Their molecular data, by the way, were second and conserved first codon positions of protein-coding exons.

My bet is on comparable absolute mutation rate, but less selection, and probably weaker DNA repair mechanisms.

There is a limited range of absolute mutation rates compatible with life at all. An imaginary “zero” mutation rate could be compatible in an imaginary stable environment, I suppose. However, the upper limit of the mutation rate has to be within certain bounds, or the concept of reproduction loses its meaning. Major genes that are required for life at all have to replicate at least well enough much of the time. The basic characteristic of life is genetic replication in a way that produces an imperfect, but similar, copy of the parent genome. I’m not sure what the percent similarity has to be for there to be any reasonable chance of producing viable offspring, but I’m sure it has be pretty high.

Also, of course, the mutation rate is due to chemical reactions. If temperature, pressure, ionic concentrations, level of background radiation, and the chemical formula of DNA and RNA were the at least reasonably similar during the Cambrian to what they are now, and I see no reason to conjecture that any of those were radically different, then the mutation rate must have been somewhat similar. Maybe polymerase enzymes could have been more promiscuous, but at the end of the day, between a basically similar environment, and the constraint that mutation rates be compatible with viable offspring, radically different absolute mutation rates sounds less reasonable to me than less selection, possibly in the context of somewhat higher net mutation rates.

Well, Casey Luskin has now opined on the gearlike legs.

His predictable conclusion:

The paper in Science tried to head off the same kind of dangerous ID-friendly thoughts, stating: “The gears in Issus, like the screw in the femora of beetles, demonstrate that mechanisms previously thought only to be used in manmade machines have evolved in nature.”

Wait a minute. How do we know these gears evolved, as opposed to having been designed? Because we know that everything in biology evolved. And how do we know that everything evolved? Because we know that nothing was designed. Right. But how do we know that nothing was designed? Because we know everything evolved.

Ah, got it now. Everyone clear?

harold said:

Thanks to the goofy “plausible deniability” strategy of ID, which was generated one second after the Edwards v. Aguillard decision, creationists themselves have to deny that ID/creationism is religious.

Historically, I have to dispute that. It’s true that Of Pandas and People was rewritten immediately after Edwards in 1987; however, many of the “Wedge Movement” creationists under Phillip Johnson continued for several years thereafter to describe ID as a subset of creationism and as explicitly religious. Certainly Johnson himself couldn’t keep his mouth shut about Jesus and the Bible, but Stephen Meyer, Bill Dembski, and even Casey Luskin also defined ID in terms of creationism and Jesus.

It tapered off around 2003-2004, and by 2004 was totally replaced by the “ID is totally not religious and not supernatural” line that Casey Lukin indignantly parrots.

2004 was the year Phillip Johnson retired; I have to wonder whether he was thrown under the bus. From what I’ve read of the IDiots, Casey Luskin in 2000, William Dembski in 2002 and the TMLC in 2005 at Dover have all made statements which appear to be throwing Phillip Johnson under the bus. This makes me wonder if Johnson’s senile blathering about the Bible made the other IDiots see their aging leader as a liability who needed to disappear. There are hints of that but I can’t prove it.

I’ve done a lot of analysis of what the IDiots were writing back pre-2004. I myself didn’t pay much attention to them until 2006, so it’s all digging into the past for me. I’d like to reconstruct the history and figure out who was behind redefining ID. It seems to me like the work of Stephen Meyer– it’s his style: intellectual hair-splitting. Luskin is not smart enough to come up with hair-splitting like “ID cannot identify the designer, therefore it’s not religious.” However, Casey Luskin, I suspect, was “the enforcer” who took on himself the role of Definer of ID, who gave approval to what was and wasn’t True ID.

I know the style of most of the ID writers. Most of the IDiots are not subtle. It’s not the style of any of them, except Meyer, who has a Ph.D. in philosophy of science. It might have been Bruce Chapman… I haven’t read much of his stuff.

harold said:

Shorter version - you don’t have to tell people that their idiots, you can just show people that they’re idiots.

Well, on the topic of showing that they’re idiots– I’ve recently been pounding Casey Luskin in the comments at American Spectator.

Topics: Behe’s testimony at Dover on Irreducible Complexity of the blood clotting cascade; and the accusation that “Darwinists” employ personal attacks. It’s a long thread, I showed up late, but gave him a pounding. I suspect he’ll return, but I don’t see how he can save his bacon.

diogeneslamp0 said: How do you make it clear this is not a scientific debate, but a political one?

IMHO that question should always be kept in mind when responding to anti-evolution arguments.

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This page contains a single entry by Dave Thomas published on September 17, 2013 9:01 AM.

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