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Tuesday, September 17, 2013

The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes

Darwin's Doubt is a book about the problems surrounding the Cambrian Explosion. It's written by a prominent Intelligent Design Creationist and, like most books by IDiots, the main theme is how scientists get everything wrong.

The "problem" is how to account for the very rapid appearance of complex animals about 530 million years ago. Intelligent Design Creationists think that they can ignore all of the evidence for evolution for the following 530 million years and focus on this one problem to discredit naturalistic explanations for the history of life.

You might expect that they would offer an alternative explanation. Like, perhaps, an intelligent being who visited Earth 530 million years ago, created a bunch of different animals with similar body plans, then allowed evolution to proceed for the next half a billion years?

Don't hold your breath waiting for a scientific explanation. They aren't that clever.

I'm interested in the arguments that Stephen C. Meyer proposes to deal with the science that doesn't conform to his worldview. In this case, it's the molecular evidence that he dismisses in the Chapter called "The Genes Tell the Story." I summarized the chapter in: Darwin's Doubt: The Genes Tell the Story?. I also discussed the issue in a post from a few years ago: The Cambrian Conundrum: Fossils vs Genes.

Scientists wondered whether molecular data could shed some light on the Cambrian Explosion. If the various species radiated quickly then the sequences of the genes of their descendants might show this. On the other hand, if the animals of the various phyla arose more gradually over a long period of time then the molecular evidence might show much deeper roots supporting the idea of a long fuse. In that case, the absence of a long chain of transitional fossils might be an artifact of some sort.

The experiment was done and the data strongly suggests deep divergence as shown in the figure (left). This is how science is supposed to work.

The result of this experiment is embarrassing to Stephen C. Meyer so he has to discredit the work in order to support his (nonexistent) alternative explanation. As I explained before, he has five objections. The first one is that the fossil record doesn't support the molecular data!

Here's what he says on page 105,
... there is now good reason to doubt this allegedly overwhelming genetic evidence. In the idiom of our forensic metaphor, other material witnesses (fossils) have already come forward to testify ....
He then goes on to explain that the molecular data suggests deep divergence. But the problem with deep divergence is that there are no fossils to support it.
Any plausible ancestor to such organisms would have likely left some hard body parts, yet none have been found in the Precambrian. Yet the deep-divergence hypothesis, whatever its other merits, requires a viable artifact hypothesis to explain the absence of fossilized Precambrian ancestors.
Here's a short summary of Stephen Meyer's first argument.
  1. There are no obvious precursors to the Cambrian animals in the fossil record.
  2. Scientists looked to molecular data to test various hypotheses; namely, whether there was rapid radiation or whether the explosion might be an artifact of the fossil record.
  3. The molecular evidence shows deep divergence, indicating that there are probably missing precursors to the existing Cambrian fossils.
  4. The molecular evidence must be rejected because there are missing fossils.1
If you don't find that convincing, hang on. Meyer has four more arguments showing that the molecular data is wrong.

1. That's because absence of evidence is strong evidence of absence. So strong, in fact, that it trumps some real evidence of presence.


Unknown said...

I wonder if Meyer has read this one?

Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion

Anonymous said...

I thought you had said you were no expert in the field, so you were not going to review the book. Now, every time I try to focus on some real work, I see you "diverging" from your earlier
promises... Please Larry!!! Let me go way...FES!

BTW: Your cyanobacteria comment, really stinks bad... I don't know if you don't understand the word "to harvest" or you don't understand the process of how cyanobacteria harvest

Larry; I had to delete a lot of sh..t in this comment just to keep it calm.. .

Mikkel Rumraket Rasmussen said...

Any plausible ancestor to such organisms would have likely left some hard body parts, yet none have been found in the Precambrian.
That is simply a plain, flat lie. Matzke already annihilated this lie over on Panda's Thumb so. There are plenty of precambrian(ediacaran) fossils.
It is also a strange thing to see that Meyer wants there to be hard body parts in the fossil record before they evolved. How the fuck does that even make sense?

Anonymous said...

@Mikkel Rumraket Rasmussen,

How can you live on in your igloo, if you can't answer the life's profound questions? How? Don't pretend you don't know what I'm talking about... World's greats's brains like R. Danwkishitkins can't explain this shit so, you only have two choices...

Faizal Ali said...

Maybe Meyer thinks that, if there were ancestors of starfish in the Precambrian, that means there must have been starfish in the Precambrian.

Sorry, that's the best I can do.

John Harshman said...

I thought you said you were going away.

I had to delete a lot of sh..t in this comment

Not enough.

John Harshman said...

He uses the old argument that some body plans make no sense without hard parts. This encapsulates a misunderstanding of the difference between "hard" and "mineralized". Chitin is hard but not very preservable. Calcite is both. Most of the Burgess fossils have chitin (or some sort of cuticle) but no mineralization, and thus would be preserved only in exceptional circumstances. But Meyer does't know that, or anything else about taphonomy, apparently.

DGA said...

I wonder why Quest is still allowed to post here. I think he must have worn out his welcome by now ...

christine janis said...

Meyer makes the claim that a body plan that evinces a hard exoskeleton would be impossible without such a supporting skeleton.

I've not seen anybody note that the basic vertebrate body plan (above the level of hagfish and lamprey) is for a hard exoskeleton of dermal bone (retained in our skull bones). That's what we start to pick up in the Ordovician. But the Cambrian vertebrates (Haikouichthyes and Myllokumingia) lack this exoskeleton.

John Harshman said...

I wonder if that is indeed the vertebrate body plan, or if the fossil record of "agnathans" and perhaps early gnathostomes is highly biased in favor of armored forms. I suspect a fair diversity of non-armored "agnathans", with "thelodonts" being a sort of half-way case. What we know of cnidarians, after all, is almost entirely "corals".

Robert Byers said...

Meyer is a scientist. He just has a correction in the usual way that sciences works. He examined the evidenced and found there was need for a better interpretation.
One doesn't need a other explanation before one demonstrates the failure of the existing hypothesis/theory.

It all does depend on the fossil record and all conclusions in biological processes based on the fossil record are worthless as biological evidence. Everyone makes that logical flaw I notice.
Evolutionists sin in demanding the fossil record proves evolution instead are being shown it proves its unlikely.
Its odd.

Unknown said...

So Matzke dealt with this on Panda's Thumb? That is great, so I guess the mystery is solved...or maybe not..."Evidence" of pre-cambrian complex body plans is mostly restricted to interpretation of burrows and trackways. Very wide conclusions are drawn on very little evidence. The result is that scientists differ in opinion, see e.g. what Matz et al wrote in Current Biology, Dec 9 2008 as explanation for your pre-cambrian trackways.
"One of the strongest paleontological arguments in favor of the origin of bilaterally symmetrical animals (Bilateria) prior to their obvious and explosive appearance in the fossil record in the early Cambrian, 542 million years ago, is the occurrence of trace fossils shaped like elongated sinuous grooves or furrows in the Precambrian [1–5]. Being restricted to the seafloor surface, these traces are relatively rare and of limited diversity, and they do not show any evidence of the use of hard appendages [2, 6]. They are com- monly attributed to the activity of the early nonskeletonized bilaterians or, alternatively, large cnidarians such as sea anemones or sea pens. Here we describe macroscopic groove-like traces produced by a living giant protist and show that these traces bear a remarkable resemblance to the Precambrian trace fossils, including those as old as 1.8 billion years. This is the first evidence that organisms other than multicellular animals can produce such traces, and it prompts re-evaluation of the significance of Precam- brian trace fossils as evidence of the early diversification of Bilateria. Our observations also render indirect support to the highly controversial interpretation of the enigmatic Ed- iacaran biota of the late Precambrian as giant protists [7, 8"

Larry Moran said...

I'm wondering the same thing.

Anonymous said...

Ediacaran worm-like trace fossils represent burrowing activity just beneath bacterial mats. This implies a coelom/pseudocoel and excludes cnidarians and protozoans. Further, an unambiguous complex bilaterian, Kimberella, was present by at least 555 Ma.

Anonymous said...

One of those choices would be to ignore Quest the ignorant troll who is too stupid to be educated.

Anonymous said...


Sometimes you manage full sentences and I keep wondering if you are just a very elegant example of a Poe. I find it hard to believe that somebody can be stupid enough to deny evidence because they don't think that the evidence belongs in the field of biology. Confess already, it's all pretence, right? You're not truly like that, right?

Faizal Ali said...

@Andy Wilberforce:

"Evidence" of pre-cambrian complex body plans is mostly restricted to interpretation of burrows and trackways.

So did you not read Larry's post? Or did you just not understand it?

steve oberski said...

The top and bottom of his posts are too far apart.

With apologies to Ambrose Bierce in what I consider to be the most succinct negative book review ever:

“The covers of this book are too far apart.”

Peter Perry said...

Fortunately for all of us, Quest can indeed answer those profound questions. The true answer, which should be obvious to everyone, is a booming voice from the top of the mountain followed by a puff of smoke.

Piotr Gąsiorowski said...

@Andy W.

Did you read the whole paper, or just the abstract for quote-mining pourposes? Enthusiastic as the autors are, they admit that there is more tangible evidence of Ediacaran bilaterians:

However, the fossil evidence of bilaterian animals in the Precambrian is scarce. There is only one common Precambrian body fossil — that of Kimberella quadrata — whose interpretation as a primitive mollusk has stood up to scrutiny thus far.

Limited or not, it's better than the direct body-fossil evidence of giant Precambrian amoeboid protists, which is simply nonexistent.

Piotr Gąsiorowski said...

Self correction (I pressed "Publish" too early). The first paragraph should have read:

Did you read the whole paper, or just the abstract for quote-mining purposes? Enthusiastic as the autors are about the giant protist hypothesis, they admit that there is more tangible evidence of Ediacaran bilaterians:

John Harshman said...

Andy: You are confusing matters in exactly the same way Meyer did, ignoring the first 20+ million years of the Cambrian. The "obvious and explosive appearance in the Early Cambrian, 542 million years ago" is something Meyer never, ever mentions, because he goes straight from the Ediacaran to the Atdabanian, around 520 million years ago (though he thinks it's 530). They're referring here to the increase in variety and complexity of trails and burrows and the appearance of the small, shelly fauna. Again, this isn't the Precambrian, just a part of the Cambrian that Meyer pretends doesn't exist.

Unknown said...

I am afraid that Booby Byers is really like that. The folks over at Panda's Thumb where he also entertains us with his breathtaking inanities are convinced that he is not a Poe.

Unknown said...

Who is doing quote mining? I quoted the entire summary, you quoted half a passage in the discussion section...which do you think captures the essence of the paper better?Further more Kimberella is not less controversial or evidently bilaterian than it was generally seen as a jellyfish until relatively recently.

I think that you need to read the text or at least the summary again. The main subject of the paper is: Giant Protists as explanation for trackways in the pre-cambrian (i.e. before 542 m.y. ago, some as old as 1.800 m.y.) that has previously been attributed to bilaterians.

John Harshman said...


I'm pointing out that the trackways the article attributes to giant protists are not the trackways that people usually point to when talking about the long fuse of the Cambrian explosion. Those are instead the increasing diversity of tracks clearly made by bilaterians, beginning in the very latest Ediacaran and expanding throughout the first two stages of the Camrbrian. Meyer completely ignores these and the accompanying small, shelly fauna, and goes directly from the Ediacaran to the Atdabanian. This increase, around 542ma, is that Matz et al. are calling the "explosion", but that isn't Meyer's explosion. Meyer begins his with the first appearances of trilobites and the Chengjiang fauna, some 20+ million years later.

Note that Matz et al. accept Kimberella as not only bilaterian but a mollusk. That is, they aren't claiming that *all* Ediacaran fossils were giant protists.

Piotr Gąsiorowski said...

@Andy. Let me repeat: the evidence of Precambrian bilaterians is not restricted to tracks and burrows (which, by the way, as pointed out by Anaxyrus above, do not actually look amoeba-made, pace Matz). The position of Kimberella was indeed controversial "until recently", but now, with 1000+ known specimens, it's no longer an enigmatic jelly blob but an abundant, cosmopolitan taxon. The original interpretations have been abandoned in the light of new evidence (which, in addition to body fossils, includes feeding and crawling tracks, and impressions of non-mineralised shells disassociated from the body). Whether Kimberella is or isn't a stem mollusc is disputable, but its bilaterian status is not really in doubt any longer.

Piotr Gąsiorowski said...

which do you think captures the essence of the paper better?

PS My point (illustrated with the quote) is that while Matz et al. question the mainstream interpretation of the Precambrian crawling marks and burrows, they accept at least one other important piece of evidence and by no means claim that bilaterians sprang up out of nowhere in the Cambrian.

steve oberski said...

Andy seems surprised that in science one is willing to revise one's hypotheses in the light of new evidence.

Why does Andy find this concept so strange and foreign ?

Could it be that Andy has already been instructed on what the conclusions are and his purported spirit of scientific inquiry is really an exercise in post hoc rationalization of a position arrived at by non rational means ?

Robert Byers said...

Its NOT (negative) denying evidence. Its a greater equation of a point.
That biological evidence(if science is the methodology here) is demanded if biological conclusions are drawn that are being claimed to BE on biological evidence.
I'm insisting that fossils(bio data points on a rock) are not biological evidence for descent and so not evidence for evolution.
They are just snapshots of some creature in a moment of time.
The connections to other fossils, above/below depositions, is not from biological evidence or investigation but a mere line of reasoning after presumptions of the origin of the depositions of the segregated fossils.
Even if they were telling the tale of evolution it STILL would not be biological evidence.
Just a secondary piece of evidence.
Without the geology there is NO biology conclusions of descent.
Therefore it is no conclusions from biological investigation.
Its all been a grand flaw of methodology. Its not obeying scientific principals of investigation.
Evolution is still only a hypothesis and not a theory.
Otherwise show us why its a theory !!

Everybody just convinces themselves the fossil sequences are telling a tale in history.
True or not they are not telling a tale of science methodology.
I'm right or I'm wrong with my equation.

Diogenes said...

Andy writes: "Kimberella is not less controversial or evidently bilaterian than it was generally seen as a jellyfish until relatively recently."

I have 6 questions I want answered.

1. Why on Earth do you accept Matz et al. as authorities when they say some tracks are caused by giant protists, but you reject their authority when they say Kimberella is a bilaterian and stem mollusk?

2. Did Matz et al. say that all Precambrian tracks are caused by giant protists or just some tracks? What caused all the others?

3. Why are tracks and burrows getting more complicated in the early Cambrian pre-Atdabanian, pre-explosion? Were giant protists getting superpowers? How did they get those powers?

4. Is it just a big coincidence that the "Explosion" happens thereafter to totally "unrelated" (according to Meyer) organisms? Isn't Meyer demanding us to believe BOTH that God suddenly felt an inexplicable urge to create trilobites by magic, AND that, by an amazing coincidence, at about the same time, some totally unrelated organisms just happened to be evolving superpowers without God's help, no relation 'tall?

5. If Kimberella is a stem mollusk, it's not fully formed. Creationism predicts all basic kinds appear fully formed. Is creationism falsifiable?

6. If hypothetically there really were giant protists around making tracks but leaving no body fossils, doesn't that prove preservation was extremely imperfect in the Precambrian, thus demolishing the whole thesis of Meyer's book?

Diogenes said...

And a seventh question.

Meyer says the Cambrian explosion lasted 5 million years (a number he gets by cherry picking a 20 year old, out of date paper.) He says 5 million is a small number. As Harshman keeps saying ad infinitem, Meyer ignores the 20+ million years of fossils from latest Ediacaran through early Cambrian up to the "explosion."

7. Is 20+ million smaller than 5 million?

Piotr Gąsiorowski said...

By the way, has anyone seen this?

Cambrian Explosion,

featuring a musical instrument (called the dobro) I've never heard of before.

Arek Wittbrodt said...


I've seen ;)

Have you seen "Symphony of Science"?

John Harshman said...

Just another word for "steel guitar", which I'm sure you've heard of before. A brand name, really.

Their dating is off, by the way. 545ma? A few million years into the Ediacaran, and long before any of the animals they talk about, in the Atdabanian, around 520ma. Nice cello solo.

Piotr Gąsiorowski said...

Their dating is off, by the way.

People apparently tend to have a blind spot for the "dark ages" of the Cambrian. I suppose trilobites are so emblematic of the lower Palaeozoic that it's hard to visualise any part of the Cambrian without them.

Diogenes said...

The idea of the Cambrian Explosion is an old pagan mythology-- from primordial Chaos, Order arises. This idea is so powerful, even Stephen Jay Gould promoted it in "Wonderful Life", which hangs about our neck like an albatross, or an Opabinia.

It's even in the Bible-- Yahweh moves on the surface of the deep, Tehom, cognate to Tiamat, the Babylonian chaos deity/dragon. In Psalm 74, Yahweh breaks the many heads of Leviathan, the chaos deity.

Nowadays Ken Ham says Leviathan was a plesiosaur. Anything to cover up the pagan, polytheistic origins of Christianity.

Piotr Gąsiorowski said...

There's a brief but interesting review of Meyer's book by Charles R. Marshall in today's issue of Science (p. 1344): "When Prior Belief
Trumps Scholarship" (under Books et al.: Religion and Science).

John Harshman said...

If the Science review is paywalled (I haven't looked), you can find it here.

Amy Blackwelder said...

I am a theists evolution, I have a unique position of being bombarded by two opposing groups...haha.

My take.

My first red flag would be Stephen Meyer has a PH.D in the history/philosophy of science and an undergrad degree in geophysics and earth science. He is smart, and in those areas I would regard is information as more reliable -though not an expert as he has a undergrad degree not PHD in those fields- (earthquakes, volcanoes, thunderstorms, earth's crust)...but this gives him no real credibility to astute himself as an expert about molecular biology and cells, or biological evolution. He can have opinions, but he is not an expert in the least. When you obtain a degree in a field and do work in the field then you are more credible in that field.

My second red flag is the first half talks about debunking Darwin. There are two points of criticism I have with that.

One is that Darwin is not the be-all-end-all on evolution. Many who debate on the side of 'spontaneous appearance of all life' seem to think he is and if they could just somehow ruin his credibility then all will be good; however, since Darwin there has been hundreds of years of scientific work in the fields of evolutionary biology, plate tectonics, paleontology, archeology, cosmology, meteorology, astrophysics, molecular biology, genetics, anthropology, general biology, fossil succession and possibly others that support evolution. Further, predating Darwin this concepts were prevalent among various cultures/philosophers/and religions. Yet, the 'spontaneous appearance of all life' side hardly ever incorporates all the other sciences and all the other scientists work- why...because that would require thousands upon thousands of scientists and papers to debunk.

Second is that any scientist is going double think their work, any good scientist proposes something and then often tries to disprove it. Simply listing out of context 'questions' that a scientist like Darwin has, does not debunk their work or what they really thought about it.

Amy Blackwelder said...

I just can't resist @Robert Byers...

You are heavily misinformed if you actually believe that the fossil record does not support evolution. Have you heard of the laws of Fossil Succession? Have you read any recent papers on fossils? There are countless examples of this.

On other evidence:

Genetics Antique Roadshow
Believe it or not, 8% of human DNA is actually old virus DNA. Some viruses, called retroviruses, put their DNA into the DNA of the cells they infect. HIV is a virus like this.
Some of the strongest evidence for common ancestors can be found by looking at where these viruses insert themselves into a cell's DNA. See, these viruses tend to land in random places.
So when the virus inserts itself into a human cell, it has 6 billion places to choose from. The odds that two people will have the virus insert in the same place are very small. The odds are even worse that lots of different kinds of retroviruses will all land in the exact same place in two different people.
...In fact, chimps and humans share way too many of these old viruses that inserted themselves in the same place for it to be by chance. Common ancestry is the only reasonable explanation.

Unknown said...

I wonder if you know the difference between evidence in the fossil record and a phylogenetic hypothesis using current world species strains and based on morphological data...