Fossil Record


The Fossil Record - Life's Epic

Also see:
Punctuated Equilibrium

The fossil record is life’s evolutionary epic that unfolded over four billion years as environmental conditions and genetic potential interacted in accordance with natural selection. It could be likened to a movie recording the history of life across nearly four billion years of geological time. The problem is that only a small fraction of the frames are preserved, and those that have been preserved have often been chronologically scrambled. Viewed in this way, reconstituting the movie seems intractable, and yet science has done so. Frames are still missing, but the intricate, interwoven plots are largely revealed. The movie shows a cycling planet, with life originating in the sea, and the appearance and disappearance of, as Darwin described in Origin of Species in 1859, “endless forms most beautiful and most wonderful”. The process of descent with modification through natural selection, or evolution, that Darwin published in the mid 19th century became the framework for many scientific disciplines to use fossils to recover the missing frames and their ordering in time. Some one hundred years after Darwin the mechanisms of genetic memory and common descent have been elucidated at the molecular level. In this new era of sequencing the genomes and proteomes of multiple species, where science can infer protein lineage dating back into the Proterozoic, the tangible evidence in the imperfect fossil record remains paramount to the delineation of still missing frames of the movie.

Darwin envisioned an incremental graduation in descent with modification to new forms for which most frames of movie are non existent in the fossil record. The movie frames that survive reveal great leaps from apparent ancestor to descendent with no intermediaries, much a continuityThe highly conserved estrogen receptor protein of incremental forms. Species or entire taxa suddenly appear in the sparse fossil with no certitude of ancestry. Others disappear with similar suddenness. Still other fossils are enigmatic regarding ancestors and descendents, and to which twig or branch of the great tree of life they belong. The sometimes huge discontinuities in the fossil record and absence of transitional forms worried Darwin, and still provides the most demonstrable evidence that creationists and proponents of intelligent design proponents present to promulgate superstition over science. Even without fossils, however, comparison of sequences (of DNA, RNA and proteins) alone and molecular phylogenetics analysis confirm evolution and deny creationist concepts. The process of evolution by natural selection saves (i.e., conserves) important DNA coding sequences over vast expanses of geological time. Molecular analyses show that the proteins responsible for basic cell organization and function have truly ancient Precambrian origins. A highly conserved sequence is a strand of DNA in a gene that contains a sequence of nucleotides that is highly similar (i.e., homologous) across a wide range of organisms. Such highly conserved sequences code for proteins essential for survival, and have their origins in a common ancestor. Natural selection retains the sequence since adverse mutations would likely impair survival or reproductive function in the species. Among the most commonly conserved genome sequences are those that code for the sites where small molecules bind to protein receptors, often initiating gene transcription of RNA, and subsequent protein production. For example, the figure to the right depicts the primary estrogen estradial (the small green molecule) attached to the binding domain of the estrogen protein nuclear receptor (the red ribbon). The estrogen receptor is found to be highly conserved in all extant vertebrate organisms and is essentially to endocrine system functioning in reproduction, development, and throughout life. A significant body of research supports origin of the nuclear receptor protein into the precambrian. Research has demonstrated that vertebrate estrogen receptors (even the ancient lamprey are estradiol (female sex hormone) receptors, though non-vertebrate estrogen receptors (e.g., amphioxus or lancelet, marine organisms that may be the most basal subphylum of chordates) are not; Ockham's razor then suggests that most primitive estrogen receptors were not able to bind estradiol but had a different function, and that hormone regulation by estradiol evolved in the vertebrate lineage, possibly following gene duplication.

So why have we digressed so far from the physical, macroscopic world of fossils to the molecular world. There are two reasons:
  1. First, to emphasize the astonishing accomplishments of Charles Darwin (and many of his contemporaries) in using empirical, phenotypical evidence (i.e, physical appearances) from living and fossil organisms to correctly deduce many aspects of how evolution works.
  2. Second, to affirm that the fossil record, or more particularly its shortcomings and gaps about which Dawin worried, is of much diminished concern due to modern molecular phylogenetics across genotypes, that even without fossils can infer decent with modification, and validate theories of evolution.
The fossil record, nonetheless, remains crucial to unfolding major and minor branching points of the great tree of life. Without fossils, inferring when genotype change occurred requires the use of the molecular clock hypothesis, which states that nucleotide or amino acid substitutions (mutations) occur at a constant rate. In other words, the amount of difference between two sequences can be used to infer when in geological time that ancestral sequence diverged occurred, thereby forming a phylogenetic branching point. Actually, the rate of mutation differs among groups of organisms, among genes, and even among different portions of the same gene. Because of this, molecular clocks used in molecular phylogenetics must be calibrated with fossils to ascertain when groups and clades of organisms appeared. To repeat, the fossil record is absolutely critical for calibration in phylogenetics.

Creation of the Fossil Record

First, a working definition of the fossil record is needed. We will use an overarching definition: all fossils known to science. The question constantly arises: is the fossil record complete? The short answer is, like the film metaphor above, way far from it. The other question is: Is the fossil record adequate? Here the answer is, it depends on who you ask. A survey of the opinions leads to the conclusion that the fossil record is pretty much adequate, and constantly improving particularly in recent decades. We will revisit these questions later, but first a large amount of background is required.

It is important to address the rarity of fossils in the context that for any particular organism that once existed, the probability that it today is part of the fossil record is infinitesimally small. Such profound rarity is a consequence of three factors: 1) fossil formation is a rare event; 2) fossil survival is a rare event; and 3) an exceedingly tiny fraction of surviving fossils will ever be accessible to be found, though the crust of the earth is filled with them. We’ll examine these factors in sequence.

Fossil Formation

The likelihood of an organism becoming fossilized is poor, and even less likely is that more than a small portion of tissues will become fossilized. If death is the primary prerequisite for fossil formation, then the second prerequisite is the forestalling of the gory ravages of decay, where the deceased becomes an ecosystem and feast unto its own for an astonishing diversity of life forms from microscopic bacteria to large predators. The transformation of an individual deceased organism into a fossil is a probabilistic rarity, and the vast majority of remains that are not eaten are either turned to dust or dispersed as dissolved molecules.

The science of fossil formation is complex in terms of biological, chemical, and physical processes, and is multidisciplinary, but many aspects are part of a relatively new field termed Taphonomy, which studies the decay and destruction of an organism’s remains through time.

We can envision that, as the ancient earth’s crust cooled, a time was eventually reached when rain from a dense atmosphere containing all the water was not immediately evaporated. Once begun, hard rains fell and fell for countless millennia finally filling the awaiting ocean basins. With the first rainfall, the inexorable processes of erosion and dissolution began, wearing away the then barren earth’s crust and ultimately filling the awaiting ocean basins with not only water, but also the dissolved elements needed for life in its most primitive manifestation to appear in the primeval seas.

The rain begat the seas, where life appeared, and began wearing the land away, forming the sediments needed to cover and preserve the traces of living organisms known as fossils. The formation and transport of sediments might be likened to a never ending snow storm. Relentlessly the sediments have been carried by the rainwater, down, down, down by the inexorable force of gravity. Perhaps the flakes were sometimes light and sparse, and other times a veritable blizzard, but without cessation. The sediments were also an implacable force grinding away everything in its path. We now know that geological time is replete with orogeny (Greek for "mountain generating") events that are the result of plate tectonics. These events have pushed up huge mountain ranges, on the land, or in the seas, many of which have been mostly or completely worn away (see example – the Appalachian Orogeny). Mountains that were miles high have been ground down to remnants of former greatness, testimony to the scale and power of the rain and the sediments.

A) Oceanic-continental convergence resulting in subduction and volcanic arcs illustrates one effect of plate techtonics.

Although they are present, transitional forms are rare in the fossil record. In fact, the fossil record demonstrates that some species have remained essentially unchanged for millions of years. This makes sense, because if a species is well adapted to its environment, its current traits will continue to be selected for. A species will only undergo major change, if its environment changes in a way which leaves it significantly less well adapted to survive. Such transitions tend to occur rapidly. A mammal species for example, might evolve into another distinct mammal species in less than a hundred thousand years. In the history of life, that is a short period of time. Speciation of plants and simpler animals, can occur much more rapidly. This evolutionary pattern of long periods of geologic time with little change, punctuated by short periods of rapid change, is referred to as punctuated equilibrium.

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