Earth was born 4.6 billion years ago.  Life on earth was born about a billion years later – sometime between 3.85 and 3.5 billion years ago.  For the next three billion years, life on earth was comprised of simple microscopic critters.  Complex life emerged toward the end of the story – after 88.5% of earth's history had already passed.  But once it got here, complex life wasted no time diversifying into an impressive array of different forms.  During a comparatively short period of time called the Cambrian Explosion, which occurred about 530 million years ago, complex life underwent a dramatic increase in evolutionary diversification that has never been equaled before or since.  As Wicander and Monroe put it,

 

The basic body plans for all animals were apparently established by the end of the Cambrian Explosion, and only minor modifications have occurred since then.[1]

 

Carroll states that all the major body plans (phyla) came into existence within 5 million years, from 530 to 525 million years ago, and that,

 

There is no evidence for the gradual evolution of the major features by which the individual phyla or classes are characterized.[2]

 

Gould expounds,

 

Even our strongest opponents admit that in less than twenty million years, from the inception of the Cambrian Explosion to the deposition of the Burgess Shale, marine invertebrate life reached a fully modern range – and that more than 500 million years of subsequent evolution has not at all enlarged the scope of basic anatomical variety.[3] 

 

Schulze-Makuch and Irwin add,

 

Most of the extant higher order taxa of plants and animals were fixed at that (Cambrian) time and have remained essentially unchanged to the present.[4]

 

     The Cambrian Explosion records the first truly diverse ecological system in the history of the planet.  Among the life forms present were the first mollusks, including gastropods and bivalves; and also the brachiopods with their shells; the arthropods with their segmented bodies and hard exoskeletons, including the trilobites; the trilobites' cousins, the chelicerates, which had the basic framework of their descendents the scorpions and spiders, complete with antennae, long stinger tails, and  legs near their mouth; and their cousins, the crustaceans, some of which looked similar to crabs and lobsters even back then; the echinoderms, which were the ancestors of the starfish; the cnidarians, which were primitive precursors to jelly fish and corals; sponges; comb jellies; sea anemones; sea cucumbers; velvet worms; carnivorous worms; and segmented worms.  All of these extremely diverse body plans were present during the Cambrian Explosion. 

     The Cambrian Explosion also saw the first species of the phylum chordata, which gave rise to that most illustrious critter known as Homo sapiens.  One such distant relative of ours, Haikouella, had a rather large brain, which has caused some to suppose that intelligent life is common in the universe and may arise more quickly in the natural course of evolution than previously thought.[5]  These animals had most of the guts modern chordates now have, including a heart, arteries, gills, a spinal chord, large muscles, and teeth.[6]

     The ancestors to these chordates were the annelid worms.  Yet annelid worms first appear in the Cambrian too, thus compounding the amount of evolution which must have occurred in the Cambrian.  Moreover, the genealogy breaks off at the annelids, with no ancestor in the fossil record known before it.  Dzik writes,

 

There is no evidence for the presence of annelids in the Precambrian and recent findings of extraordinarily preserved segmented Ediacaran (Precambrian) metazoans show that their anatomy is different from annelids.[7]

 

This means there were two quick jumps; one from some unknown ancestor to annelids, and another from annelids to chordates – back to back quantum leaps in a short period of time.

     There were even more body plans which quickly went extinct.  Often called evolutionary "experiments," these strange creatures don't even have any known relatives – no parent species, no descendant species, and nothing similar in the fossil record.  At least 20 such "dead end" phyla emerged in the Cambrian only to quickly suffer extinction.[8]

     The Cambrian Explosion was the most remarkable event in the history of life, because so many completely different creatures evolved so quickly, without evidence for gradual change over long periods of time. 

     The Cambrian Explosion flies in the face of Natura non facit saltum.  The sudden emergence of so many entirely different body plans defies the expectation that evolution should happen gradually.  Some believe that the Cambrian was too short a time to account for the amount of evolution in the fossil record, and so they look for a way to rationalize how complex life could have been evolving before the Cambrian.  However, the fossil evidence for ancestors of Cambrian forms is weak, so they imagine that small soft bodied forms were evolving before the Cambrian, before hard exoskeletons and shells were prevalent.  Because the fossil record preserves hard parts better than soft body tissue, they say that the fossil record before the Cambrian is simply incomplete.  However, even though soft body tissue is rare, it is occasionally preserved, and the fossil record for soft body tissue indicates that there was an increase in the diversity of soft body tissue as well as in hard body tissue during the Cambrian.  Many more burrows of soft bodied animals are found in the Cambrian than in previous time frames.[9]

 

The Molecular Clock and the Cambrian Explosion

     The molecular clock is a way to estimate how many millions of years ago two or more lineages diverged.  It does this by measuring differences between two or more species' DNA.  It is often calibrated to data points in the fossil record, and assumes that mutation rates are predictable and/or relatively constant.  If mutation rates were higher during certain times in earth's history, then the molecular clock will record a greater degree of difference between the DNA of the two lineages, and will therefore overstate the age of their most recent common ancestor.  This is exactly what happens. 

     Across a very large number of lineages, the molecular clock tells us that lineages diverged much earlier than the fossil record allows.  That is, the estimated time of divergence as predicted by DNA comparative differences is significantly earlier than the age of the first fossils that confirm the divergence. 

     According to the fossils, the Cambrian Explosion was completed, start to finish, in about 10 million years or less.  But the molecular data indicates that the divergences between Cambrian lineages must have taken place at least 100 million years beforehand, if not more; otherwise, there would not have been enough time for genetic mutation to accomplish such a great amount of diversity.[10]  There are only two possibilities to explain this:  Either the mutation rate increased about ten-fold during the Cambrian Explosion, or there was no Cambrian Explosion.  Levinton et al indicated this as follows:

 

The divergence in animal phyla was neither Cambrian nor explosive… The only obvious way to escape these conclusions is to argue that the rate of molecular evolution was greater during the Cambrian Explosion than in subsequent times.[11]

 

What could cause such a sudden increase in molecular evolution? 

     Levinton et al suggested that the ancestors of the Cambrian biota were so small that we don't see them in the fossil record.  Yet they also acknowledged that this is problematic in light of the fact that the most recent common ancestor of protostomes and deuterostomes must have had a circulatory system, which is the prerequisite for large size.[12]  Thus, the lack of large-sized Cambrian-like animals before the Cambrian confirms the reality of the Cambrian Explosion.

     Apparent increases in the rate of mutation are not confined only to the Cambrian Explosion.  The phenomenon remains a fixture across many ages and many lineages.  Molecular evidence suggests that modern birds first diversified 90 million years ago; however, the fossil evidence cannot support their diversification until about 30 million years later.  Moreover, even genetic studies of the molecular data itself indicate that the divergences were not staggered or gradual, but rather were explosive, as Poe and Chubb concluded, "Neoaves (i.e. – modern birds) differentiated so rapidly that the radiation might be considered essentially simultaneous."[13] 

     Likewise, molecular data places the most recent common ancestor of rodents and primates at 110 million years ago, but neither order emerged with their distinct features until 55 million years ago, just half the time predicted.[14] 

     In a third example, molecular evidence suggests snakes arose 125 million years ago,[15] but the fossil record does not produce indisputable snakes until 20 million years later.[16]

     The same kind of phenomena has been observed when the molecular clock for flowering plants in calculated.  Numerous specimens of flowering plants appear as a well-represented lineage in the fossil record starting 132 million years ago, and become diversified by 125 million years ago.  However, molecular evidence based on strict constancy in the mutation rate indicates that they should have appeared much earlier – perhaps back as much as 450 million years ago.  From the perspective of the fossil record, this is absurd, because plants did not even exist 450 million years ago.  Yet that is what the DNA evidence tells us.  Even when the fossil record is used to calibrate molecular clocks, the results still indicate a date for the first flowering plants which is much older than the fossil record can substantiate.  More than a few molecular studies have been done, all but one yielding a range of dates for the first flowering plants which predate their earliest fossils.  Often, the date suggested by molecular data predates the earliest fossils by dozens and in some cases even hundreds of millions of years.[17] [18] 

     Such large gaps between the molecular data and the fossil evidence suggest that accelerations in the mutation rate occur near the base of lineages. 

     What could cause an acceleration in the mutation rate of plants?  There was no great ecological calamity 132 million years ago that could explain a change in the mutation rate.  The climate during this time was stable and hospitably warm.  We lack a natural explanation.

     Brochu et al summarized the various deficiencies in the molecular clock, saying,

 

The more we look at fossils, molecules, or algorithms, the stronger the disparity seems to grow… (Either) we assume… imperfections in the fossil record… Or, we assume that the fossil record closely approximates the origination times of these orders and that the molecular clocks are being misled by mysterious simultaneous speedups of evolutionary rate (emphasis added).[19]

 

The only rational basis on which to deny that these magical mystery "speedups of evolutionary rate" have happened is to deny the accuracy of the fossil record.

 

Hox Genes and the Cambrian Explosion

     Shortly before the Cambrian, the first arguably genuine members of the phylum cnidaria appeared.  These were the likely ancestors of corals and jellyfish.  Genetically, the cnidarians have only two hox genes, and at that time, the cnidarians were the most complex life form on the planet.  By the end of the Cambrian, the number of hox genes in the most complex life forms had apparently increased somewhere in the vicinity of about twenty-fold.[20]  Hox genes code for variable proteins, and are responsible for the diversity we observe across the various life forms.  The magnitude of this rapid and exponential multiplication of hox genes during the Cambrian has no parallel in evolutionary history.

     The genetic history of the Cambrian can be reconstructed as follows:  A lineage diverged from the cnidarians, called the bilaterians, which became the common ancestor of all clams, worms, insects, reptiles, humans, and virtually every other animal that comes to mind except sponges.  This primordial common ancestor of most every animal had 7 hox genes.[21]  Thereafter, the bilaterians diverged into protostomes and deuterostomes – the former including all insects, crustaceans, brachiopods, worms, mollusks, etc; and the latter including starfish, humans, birds, reptiles, fish, etc.  These quickly diversified, adding as many as 7 more hox genes, depending on the lineage.[22]  The common ancestor of the vertebrates then underwent a four-fold duplication, forming four hox complexes, each complex having multiple genes.  This must have happened extremely early in vertebrate history, for even the jawless lampreys participated in this event – indicating it happened even before jaws evolved.  Today, all tetrapods, including all amphibians, reptiles, birds, and mammals, have 39 hox genes spread across these four hox complexes[23] – which indicates that this must have occurred prior to their divergence about 360 million years ago.  Since then, the only large scale duplication of hox complexes to occur has been that of the teleost fish.[24]

     The implications are stunning.  Prior to the Cambrian, we have no clear fossil record confirming the divergence of the bilaterians from the cnidarians.  This means that the greatest number of hox genes any life form had achieved was still just two, since the cnidarians have just two.  Moreover, the emergence of the vertebrates occurred in the Cambrian, and the vertebrates had an exponentially larger number of hox genes.  Hence, it appears likely that the number of hox genes in the most advanced life forms jumped from 2 to approximately 39 or so during the Cambrian or shortly thereafter – a remarkable increase in the number of hox genes for such a short period of time.  What is more, in over 360 million years since the first fish climbed out on land and grew legs, the number of hox genes in the tetrapods has remained constant at 39 – for all frogs, lizards, birds, and humans.  To be sure, within each gene, a tremendous amount of evolution has occurred since then.  Yet the number of hox genes has not changed for tetrapods since the mid Paleozoic. 

     Why did the number of hox genes increase so dramatically in the early Paleozoic?  And why, with the exception of the teleost fish, have they remained stable since then?  What prompted such a sudden blossom of life in the Cambrian?  Why did so much evolutionary change, diversification, and progress take place in such a short time?  The Cambrian Explosion, both in terms of fossil evidence and in terms of genetic evidence, remains the most confounding enigma in all evolutionary science.