Readers may recall that in a previous series on how new biological information arises during evolution we discussed an ongoing experiment on the bacterium E. coli taking place in the laboratory of Richard Lenski. Named the Long Term Evolution Experiment, or LTEE, this research is very simple in its approach. As we described previously, the experiment merely allows twelve separate populations of E.coli to replicate in a controlled environment, and notes what changes appear over time:

“The LTEE started in 1988 with twelve populations of the bacterium E. Coli all derived from one ancestral cell. The design of the experiment is straightforward: each day, each of the twelve cultures grow in 10ml of liquid medium with glucose as the limiting resource. In this medium, the bacteria compete to replicate for about seven generations and then stop dividing once the food runs out. After 24 hours, 1/10th of a ml of each culture is transferred to 9.9 ml of fresh food, and the cycle repeats itself. Every so often, the remaining 9.9 ml of leftover bacterial culture is frozen down to preserve a sample of the population at that point in time – with the proper treatment, bacteria can survive for decades in suspended animation. Early in the experiment this was done every 100 generations, and later this was shifted to every 500 generations. A significant feature of the LTEE is that these frozen ancestors can be brought to life again for comparison with their evolved descendants: in essence, the freezers in the Lenski lab are a nearly perfect “living fossil record” of the experiment.”

To date, the most dramatic change that has been noted is that some bacteria in one of the twelve cultures have acquired the ability to use citrate under aerobic conditions (i.e. when oxygen is present). While E. coli have the ability to import citrate and use it as a carbon source when oxygen is absent, they cannot do so when it is present. Since the LTEE takes place under aerobic conditions, this new ability, labeled “Cit+”, was very advantageous, since it allowed Cit+ bacteria to use a new food source in the culture medium that the rest of the culture could not. In very short order, the Cit+ bacteria nearly took over one of the twelve cultures. We have discussed this result as an evolutionary gain of information before, though the precise nature of the mutations that led to the Cit+ phenotype was not known at that time.

Behe and the LTEE

Lenski’s work on the LTEE has also been of significant interest to promoters of Intelligent Design, such as biochemist Michael Behe. Behe discusses the Lenski LTEE in his 2007 book, The Edge of Evolution at some length, and uses it as an example of, in his view, “what Darwinism can do” – i.e. slightly modify or destroy existing biological systems:

“Even in a controlled lab culture where bacteria are warm and well fed, the bug that reproduces fastest or outcompetes the others will dominate the population. Like gravity, Darwinian evolution never stops.

But what does it yield? … By now over thirty thousand generations of E. coli, roughly the equivalent of a million years in the history of humans, have been born and died in Lenski’s lab. Over the whole course of the experiment, perhaps ten trillion, 10¹³, E coli have been produced. Although ten trillion seems like a lot (it’s probably more than the number of primates on the line from chimp to human), it’s virtually nothing compared to the number of malarial cells that have infested the earth. In the past fifty years there have been about a billion times as many of those as E. coli in the Michigan lab, which makes the study less valuable than our data on malaria.

Nonetheless, the data has pointed in the same general direction. The lab bacteria performed much like the wild pathogens: A (sic) host of incoherent changes have slightly altered pre-existing systems. Nothing fundamentally new has been produced. No new protein-protein interactions, no new molecular machines. As with thalassemia in humans, some large evolutionary advantages have been conferred by breaking things… The fact that malaria, with a billion fold more chances, gave a pattern very similar to the more modest studies on E. coli strongly suggests that that’s all Darwinism can do.” (pp 141-142)

Behe, then, appears to see “Darwinism” as capable of “breaking things” to gain an evolutionary advantage, but unable to produce “fundamentally new” things. While The Edge of Evolution predates the report from the Lenski group (in 2008) describing the evolution of Cit+ E. coli in the LTEE, a paper published by Behe in 2010 does address this new development. However, as we have noted above, the precise nature of the mutations leading to Cit+ remained a mystery at the time.

In his 2010 paper, Behe reviews a large swath of experimental evolution studies, including the LTEE, with a view to placing the observed changes into one of three categories. These categories center around what Behe defines as a Functional Coded elemenT, or “FCT”:

An FCT is a discrete but not necessarily contiguous region of a gene that, by means of its nucleotide sequence, influences the production, processing, or biological activity of a particular nucleic acid or protein, or its specific binding to another molecule. Examples of FCTs are: promoters; enhancers; insulators; Shine-Dalgarno sequences; tRNA genes; miRNA genes; protein coding sequences; organellar targeting- or localization- signals; intron/exon splice sites; codons specifying the binding site of a protein for another molecule (such as its substrate, another protein, or a small allosteric regulator); codons specifying a processing site of a protein (such as a cleavage, myristoylation, or phosphorylation site); polyadenylation signals; and transcription and translation termination signals.

With this definition in hand, Behe then undertakes a large review of work in experimental evolution with bacteria and viruses. Understandably, loss-of-FCT mutations predominate, since mutations can easily break genes, and gene losses in some environments can be an advantage for the organism. Similarly, adaptive modification-of-FCT mutations are relatively common. Gain-of-FCT mutations, however, are rare. Once again Behe returns to the LTEE experiment as a prime example to consider:

With a cumulative population size of about 10¹⁴ cells, Lenski’s investigation is large enough and long enough to give solid, reliable answers to many questions about evolution.

After a thorough review of the results of the LTEE, however, it becomes clear that one of the “solid, reliable answers” that Behe has in mind is that Lenski’s work demonstrates the paucity of gain-of-FCT mutations, much like his critique of the LTEE in Edge of Evolution. Since the nature of the mutation that led to the ability to use citrate under aerobic conditions (Cit+) was at that time unknown, Behe speculates as to which category it will fall into, and discusses some possible underlying molecular mechanisms for the Cit+ mutation:

“If the phenotype of the Lenski Cit+ strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT, it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation.

The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.”

This point is a major one in Behe’s paper: the LTEE is the best experiment of its kind to date, and all there is to show for it are loss-of-FCT and modification-of-FCT mutations. Though Behe is blunt in The Edge of Evolution, and more subtle in the review, the same point is clear in both sources. According to Behe, we’ve been watching what evolution can do for quite a while, and what it can do amounts to “not much.”

Fortunately for us, the Lenski lab kept watching, and working diligently to understand the changes that led to the Cit+ development. As we will examine tomorrow in Part 2 of this series, what they have discovered does not square easily with Behe’s ideas. Indeed, a careful analysis of their findings and Behe’s key arguments in The Edge of Evolution is in order, and that’s what we’ll do in tomorrow’s post.

References cited:

Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism (New York: Free Press, 2007).

Michael J. Behe (2010). Experimental evolution, loss-of-function mutations, and “The first rule of adaptive evolution”. The Quarterly Review of Biology 85(4); 419-445.

Populations and genetic diversity

One consequence of speciation being a population event is that populations have genetic diversity – not all members of the population are genetically identical. For any particular gene, then, a population may have several slightly different forms present within it. These different forms are called alleles. An example in humans that is fairly well-known is the different alleles that control blood types: one allele gives rise to the A type, another to the B type, and a third allele the O type. Individuals may be either blood type A (either two A alleles or A + O); blood type B (either two B alleles or B + O); type AB (one A allele + one B allele) or type O (two O alleles). Any one individual can have only two alleles of this gene (one from mom, the other from dad), but as a population we collectively maintain all three. Other human genes have many more alleles than three (for example, some genes of the immune system have hundreds of alleles) despite the fact that any given individual can have at most two. The larger a population is, the more alleles of a given gene it can maintain. Smaller populations are more at risk of losing alleles due to chance (something called genetic drift).

Genetic diversity and speciation

The fact that populations maintain genetic diversity is important to remember when considering speciation. Speciation events are commonly represented with branching tree diagrams (“phylogenies”, or “species trees”) such as this one:

Here we see that Species 1 and Species 2 are more closely related to each other than they are to Species 3. What this says is that Species 1 and Species 2 shared a common ancestral population more recently with each other than either did with Species 3. So far, so good – but what this doesn’t mean, however, is that comparing gene sequences between these species will always group 1 & 2 together as more similar to each other than to 3. While this will be true most of the time, it is expected that some of the time this pattern will not hold. The reason is due to something called incomplete lineage sorting, and it has to do with the fact that populations going their separate ways carry genetic diversity with them. Let’s try to explain what is going on here.

Imagine that the ancestral population of all three species (the 1,2,3 common ancestor) has four alleles of a certain gene (represented by different colors in the diagram). These alleles originally arose due to a single mutational difference during DNA copying. Once there is a difference in place, two alleles can go on to acquire other differences over time, again, through copying errors. As a result, alleles can be compared to each other, just like species. Alleles that are recently separated will have more similarities in common, and alleles that have been separate for longer will have acquired more differences. In this example, the blue and green alleles are more similar to each other than either is to red or orange, and vice versa. The blue and green alleles arose from a common ancestral allele, and the red and orange alleles arose from a common ancestral allele. Further back in time, these two ancestral alleles themselves arose from one common starting allele. All four alleles will have a great deal in common (nucleotide sequences inherited from the single ancestral allele), as well as differences (for example, the red and orange alleles will share all changes that occurred between the time they split off from the blue/green lineage and when they themselves separated into two distinct alleles).

Now consider the time when the (1,2,3 common ancestor) population divides to become the (1,2 common ancestor) species and the Species 3 ancestor (the first branch in the diagram). As this population divides into two species, it is not guaranteed that all four alleles will be present in the founding population of each new species, simply by chance. Each founding population is a sample of the original population, but any given sample may omit certain alleles:

In the example above, we see that the red allele has been lost from the (1,2 common ancestor) species, and that the Species 3 ancestor has lost the blue and orange alleles. What this means is that the founding population of the (1,2 common ancestor) species didn’t have any individuals that carried the red allele, and that the Species 3 ancestor founding population didn’t have any individuals that had the blue or orange alleles. Both events happened simply by chance, because the founding populations are not representative samples of the original population.

Later, as the (1,2 common ancestor) species separates again into Species 1 and Species 2, the same issues arise. The two founding populations may not transmit all of the genetic diversity of the (1,2 common ancestor) population:

In this case, the founding population leading to Species 1 did not include a member with the green allele, and the founding population leading to Species 2 did not include any members with either blue or orange alleles. Also, the green allele has been lost in the lineage leading to Species 3 (it became rare and was eventually not passed on due to chance).

In the present day, examining the alleles of the three modern species will reveal different levels of similarity. The blue allele is now only found in Species 1, and it is most similar to the green allele in Species 2, and less similar to the red allele in Species 3. This pattern matches the overall “species tree” pattern for these three species:

The orange allele in Species 1, however, tells a different story: it is most similar to the red allele in Species 3, and less similar to the green and blue alleles. If we knew only about the orange allele in Species 1, we might conclude that Species 1 and Species 3 are the closest relatives. This is because the “gene tree” for these alleles places orange closest with red, even though the true “species tree” reveals an overall pattern of speciation that is different:

The orange allele thus has a gene phylogeny that is said to be “discordant” with the overall species phylogeny.

How do biologists assemble species trees if gene trees can be discordant?

It might seem from the above discussion that assembling a species phylogeny from gene phylogenies is a hopeless task: after all, if any individual gene tree might be misleading, how can we be certain we have the correct species tree?

The solution is to realize that while any individual gene tree might be discordant, gene trees that match the species tree will be the most common category. In our example above, Species 1 and Species 2 share a common ancestral population for some time after the (1,2 common ancestor) and the Species 3 common ancestor populations diverge. This means that any event that happens to this population (loss of an allele, for example) will be reflected in all descendant species (in our example, Species 1 and Species 2). This common history favors gene trees that match the species tree. For a discordant tree, the ancestral (1,2) population needs to maintain two alleles, and these alleles cannot sort equally into Species 1 and 2. This can happen, but it is less likely.

What this means in practice is that biologists expect a certain pattern of gene trees when comparing related organisms. Using our three species as an example, most gene trees should match the species tree. The less likely outcome is a gene tree where an allele from Species 1 is more similar to the allele in Species 3. We can be confident we have the correct species tree because the majority of the gene trees favor one species tree over the alternatives.

A problem for common descent?

The fact that gene phylogenies/trees and species phylogenies/trees don’t always match is not something that surprises scientists, since it is a well-known phenomenon and the mechanisms underlying it are understood: species arise from genetically diverse populations and that diversity does not always sort completely down to every descendant species. Discordant phylogenies, however, are commonly used among Christians as a means to cast doubt on to common ancestry and/or evolutionary biology as a whole. One example from the Intelligent Design movement will serve as an illustration. In a blog post discussing discordant trees found when comparing the human genome to that of other primates, Casey Luskin argues

Since humans are typically said to be most closely related to chimps, this data conflicts with the standard supposed tree … the basic problem is that one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree. This leads to discrepancies between molecule-based trees, wherein DNA data fails to provide a consistent picture of common ancestry.

In the end, molecular trees are based upon the sheer assumption that the degree of genetic similarity reflects the degree of evolutionary relatedness … Clearly this assumption fails when different genes paint contradictory pictures of evolutionary relationships.

As we have seen, these differences are the natural, expected consequence of genetic diversity from an ancestral population sorting itself incompletely into different descendant species. The data set Casey is concerned about is primate evolution, where the species tree for humans, chimpanzees, gorillas and orangutans is as follows:

In the article linked above, Casey is discussing a recent comparison of the newly-completed orangutan genome with the human genome. The availability of the orangutan genome allowed researchers to scan the human genome for locations where humans are more similar to orangutans than to chimps. These regions are rare in the human genome, and very short in length. Indeed, the researchers found a pattern: chromosome segments in humans most often match chimpanzees, and do so for thousands of nucleotide base pairs at a time, on average. Those regions that match orangutans are tiny (on average less than 100 base pairs) and rare. This is exactly what one expects from the species tree: humans and chimps are much more likely to have gene trees in common, since they more recently shared a common ancestral population (around 4-5 million years ago). Humans and orangutans, on the other hand, haven’t shared a common ancestral population in about 10 million years or more, meaning that it is much less likely for any given human allele to more closely match an orangutan allele. It is certainly possible, however, and in scanning over the entire genome rare sites that have this pattern can be found. Indeed, the authors of the paper above used previously-determined speciation times and population size estimates to predict what fraction of the human genome would be expected to match more closely with orangutans. Based on these parameters obtained in other studies, they predicted 0.9% of the human genome would have a human : orangutan gene tree. Their observed value was 0.8% - a result that provides additional support for the population size estimates and speciation times from other studies.

Why is this data interesting?

Aside from its misinterpretation by the ID movement, this sort of data actually provides us with information about the population size of the species that went on to give rise to orangutans, gorillas, chimpanzees and humans, as well as times for the various speciation events. I have discussed similar data for the (gorilla/chimpanzee/human) and (chimpanzee/human) common ancestor populations elsewhere; this new data merely confirms previous estimates of the population sizes of the various ancestral groups, and extends back to the (orangutan/gorilla/chimpanzee/human) common ancestor population with greater precision. As before, these results continue to strongly support the hypothesis that the human lineage has never been as low as two individuals at any point in our evolutionary history. Indeed, these new results confirm that the human : chimp common ancestor population was large (about 50,000 members). As Darrel Falk and I have discussed here on BioLogos in the past, all methods used to date (numerous approaches, all using independent assumptions) would have to be wildly wrong (by several orders of magnitude) if indeed our species arose from just two individuals.

Transitional Fossils

Some time ago, the Discovery Institute’s Casey Luskin commented on the human origins exhibit at the Smithsonian Institution, suggesting that palaeoanthropologists use evolutionary theory to describe the progression of the human lineage even when they don’t have transitional fossils with which to work. He writes:

What's ironic, however, is that if you ask the question How Do We Know Humans Evolved? the answer you’re given is, “Fossils like the ones shown in our Human Fossils Gallery provide evidence that modern humans evolved from earlier humans.” So whether you find fossils or you don’t, that’s evidence for evolution.

Indeed, it has become an article of faith for those espousing both the young earth creation (hereafter YEC) model and many who hold to the intelligent design model that transitional fossils do not exist and therefore evolution has not taken place. Support for this position usually entails attacking the weak areas of the fossil record, where burial processes have left us little with which to work, or the creation of straw men arguments in which transitional fossils are defined in such a way that none could ever be found. Often this centers on the concept of “missing link,” a term that is habitually used in the popular press and young earth creation and intelligent design literature when referring to fossil remains but which has little to no meaning for biologists or palaeontologists. As Ahlberg and Clack (Ahlberg and Clack 2006) write:

But the concept has become freighted with unfounded notions of evolutionary ‘progress’ and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transitions. Much of the importance of transitional fossils actually lies in how they resemble and differ from their nearest neighbours in the phylogenetic tree, and in the picture of change that emerges from this pattern.

Contrary to common misconceptions, the fossil record does not record one single lineage for any family of organisms but rather a series of branches, with many related species coexisting synchronously. Darwin hypothesized that the evolutionary record reflected this bushiness and drew such a diagram in his journal. At the time, though, he had little in the way of fossil evidence to back up this position. Much has changed since his day.

An analogy for understanding this “bushiness” was best described by Prothero and Buell (Prothero and Buell 2007). They suggest that the reader consider his or her own genealogy. You and your siblings are the direct descendents of your parents and, while you are similar to them, each of you has different characteristics not shared with them as well as characteristics that you do share. Your parents have siblings as well (your aunts and uncles), and your grandparents are their last common ancestors. These siblings have their own children (your cousins), who have different and similar traits relative to their parents. They are broadly recognizable as being related to you (“oh, I see you have Aunt Edna’s nose”) but three or four generations out, they will become less and less so. These are the “nearest neighbours” that Ahlberg and Clack describe. In this analogy, each of these cousins represents a transitional form from what was (your grandparents) to what will be down the road.

For example, no one would confuse a frog with a salamander but if you trace the fossil record of each back in time, eventually you encounter a fossil, Gerobatrachus hottoni which was recently discovered (Anderson et al. 2008) that is best described as a “frogamander,” having the basal characteristics of both frogs and salamanders. Had we seen such an animal at the time, it is likely we would not have found it remarkable because it would have resembled the species around it. One lineage eventually diverged into frogs, salamanders and other amphibians. Most (just like Darwin proposed in his tree diagram with the little hatch marks at the tip of many branches) went extinct.

Taxonomy and the Beginnings of Human Origins

All life is classified based on a system devised by Carolus Linneaus in 1735 in his remarkable work Systema Naturae. This system gives all recognized species an individual place based on a system of hierarchy. The study of classification is known as taxonomy. A taxonomic ranking for humans would be this:

When a fossil is excavated, the first thing that the palaeontologist does is make a taxonomic assessment of where it fits in a sequence of known fossils. Traits that are shared with other like species or genera are referred to as primitive traits. Examples of this in humans are five fingers and the presence of three arm bones. We share this with all mammals. Traits that are new or are not shared with other like species are referred to as derived traits. Examples of this in humans are the skeletal changes in the pelvis and the foot to allow for walking upright. We do not share these with any other primates.

Transitional fossils in the human fossil record are distinguished at both the genus and species level. This group includes the extinct genera Ardipithecus and Australopithecus and the current genus Homo. All species except Homo sapiens are extinct. Much of the recent study of early humans focuses on the transition from Ardipithecus (‘Ardi’) to Australopithecus (‘Lucy’ and similar fossils) and from Australopithecus to Homo, the genus that led eventually to us. While each of the australopithecine species identified in the fossil record has derived characteristics that separate them from their ancestors and from each other, only one led to the genus Homo.

In future posts, I will describe the evidence for human evolution and why this evidence is compelling. It suggests that we have had a long, varied history filled with great leaps of change, crushing defeat, and eventual expansion into all areas of the globe.

Notes

Ahlberg, P. & J. Clack (2006) A firm step from water to land. Nature, 440.

Anderson, J. S., R. R. Reisz, D. Scott, N. B. Frobisch & S. S. Sumida (2008) A stem batrachian from the Early Permian of Texas and the origin of frogs and salamanders. Nature, 453, 515-518.

Prothero, D. & C. Buell. 2007. Evolution: What the fossils say and why it matters. Columbia Univ Pr.

The procedure of classifying organisms is called taxonomy, and the general name for individual groups is “taxa.” Significantly, the first question that needs to be addressed is -- What is a phylum? A phylum is often identified as a group of organisms sharing a basic "body plan," a group united by a common organization of the body. However, phyla can be understood fundamentally, like all other taxonomic categories, as groupings of taxa that are more closely related to each other than to any other group.

The most widely accepted method for grouping organisms today is called cladistics. In cladistics all taxonomic groups are monophyletic, that is all of the members of the group are descended from a common ancestor that is the founding member of that taxon. A branch of the tree of life whose members all share the same ancestor is called a “clade” - thus the term cladistics. Closely-related taxa that do not share the same common ancestor are called “sister” taxa. These sister taxa commonly resemble each other more than the descendant relatives resemble the ancestors of their clade. As a result, placing these organisms into their correct monophyletic groups can be very difficult. Thus, organisms within a given phylum may bear close similarities to those from another closely-related sister phylum. In fact, the assignment of a given organism or fossil specimen to a phylum can be just as problematic as assignments to lower-ranked taxa such as classes, orders, families, etc.¹

Further complicating the assignment of fossil organisms to phyla is that the anatomical characteristics that are used to define living phyla did not appear simultaneously, but were added over time. This has resulted in the distinction between "crown groups" and "stem groups" in the scientific literature (see figure above). A crown group is composed of all the living organisms assigned to that phylum, plus all the extinct organisms that were descended from the common ancestor of those living organisms. The stem group is composed of organisms more closely related to one living phylum than to another, but that do not possess all of the distinguishing characters of the crown group. It turns out that the organisms appearing in the early Cambrian are, with few exceptions, not crown groups but stem groups. That is, the complete suite of characters defining the living phyla had not yet appeared. Many crown groups actually do not appear in the fossil record until well after the Cambrian.²

The existence of stem groups provides a way to understand how the basic body plan of a living invertebrate could have been built up in steps. The major invertebrate groups are often portrayed by evolution critics as possessing anatomies that are both irreducible in organization and separated from other groups by unbridgeable gaps. No transitions could exist even in principle. This view is illustrated by the following comment by John Morris.

“Let's suppose you want to find the forefathers of the clams, a prominent resident of the Cambrian Explosion, for instance. As you follow the fossil clues into ever "older" strata, what do you find? You find clams. The first or lowest occurrence of clams is abrupt or sudden. There are no ancestors that are not clams. An evolutionary lineage is impossible to discern, for clams have always been clams. Fossil clams are quite abundant, found all over the world in rocks of every age, and clams live today. Great variety among them abounds, but they are still clams. Variety does not speak to ancestry. The same is true of all animals found in the Cambrian Explosion. How can evolutionary scientists use the fossils as evidence of a common descent of all life?”³

The phylum Mollusca, to which clams belong, actually illustrates well how modern body plans could evolve from earlier stem groups. There is a well-documented series of transitional forms that extends from pre-mollusks (stem mollusks) through primitive early mollusks to the first unambiguous clams. The animals in this group gradually acquired the whole set of characteristics we now use to define “clam”. The earliest known mollusk-like organism is Kimberella (fig.1) from the late Neoproterozoic Ediacaran. It is a primitive organism that appears to lack several features characteristic of modern mollusks and is thus a considered a stem mollusk. The first likely “crown group” mollusks appear in the earliest Cambrian as part of the “small shelly fauna.” While recognizable as mollusks, many of these fossils belong either to sister groups or to stem groups of living classes. The earliest fossil bivalves (“clams”) are linked through a series of transitional forms to two of these extinct groups - the rostroconchs (fig. 2) and the cap-shaped helcionelloids (fig. 3). The hinged valves of clams appear to have evolved by the lateral compression of cap-shaped shells and then the thinning and loss of shell material along the hinge line.³ The characters that we use to identify “clams” did not appear as a complete package, but were acquired over time.

Some critics of evolution make much of the "top-down" versus the "bottom-up" pattern of appearance of higher taxa. That is, phylum-level diversity reaches its peak in the fossil record before class-level diversity, and the class-level diversity before that of orders, etc. These critics interpret this apparent "top-down" pattern as contrary to expectations from evolutionary theory. For example, Stephen Meyer and others have argued:

“Instead of showing a gradual bottom-up origin of the basic body plans, where smaller-scale diversification or speciation precedes the advent of large-scale morphological disparity, disparity precedes diversity. Indeed, the fossil record shows a “top-down” pattern in which morphological disparity between many separate body plans emerges suddenly and prior to the occurrence of species-level (or higher) diversification on those basic themes.”⁴

However, this pattern is an artifact, being generated by the way in which species are assigned to higher taxa. The classification system is hierarchical with species being grouped into ever larger and more inclusive categories. When this classification hierarchy is applied to a diversifying evolutionary tree, a "top-down" pattern will automatically result. Consider species belonging to a single evolving line of descent given genus-level status. This genus is then grouped with other closely related lines of descent into a family. The common ancestors of these genera are by definition included within that family. Those ancestors must logically be older than any of the other species within the family. Thus the family level taxon would appear in the fossil record before most of the genera included within it. Another way of looking at this is the fact that the first appearance of any higher taxon will be the same as the first appearance of the oldest lower taxon within the group. For example, a phylum must be as old as the oldest class it contains. Most phyla contain multiple classes, which in turn include multiple orders, and so forth. Thus, each higher taxon will appear as early as the first of the included lower taxa.

Additionally, higher taxonomic levels typically reflect more general aspects of the body plan. Thus, a poorly preserved specimen may be confidently assigned to a particular phylum, but not to any one class. Similarly, a primitive fossil might have the distinctive features of a particular phylum, but not be clearly assignable to any particular class because it is a transitional form -- that is, a stem group or a sister group to a living class of organisms. Both of these factors would promote the earlier recognition of higher taxonomic categories than lower ones. The "top- down" pattern of taxa appearance is therefore entirely consistent with a branching tree of life.

There is one last bias in our reconstruction of the past that is generated by the process of assigning organisms to particular phyla. Because phyla are defined by particular anatomical character traits, they cannot be recognized in the fossil record until after those specific characters evolve. However, the splitting of the branch of the tree of life to which a phylum belongs may have occurred many millions of years previous to the evolution of those characters. The actual first appearance of a phylum thus occurs after significant anatomical evolution has occurred along that particular branch of the tree. Branching points in the tree of life will always be older than the named taxa.⁵

Notes

1. See the discussion in the chapter “The Nature of Phyla” in Valentine J.W., 2004, On the Origin of Phyla, Univ. of Chicago Press. Also see Miller, K.B., 2003, “Common descent, transitional forms, and the fossil record,” IN, K.B. Miller (ed.), Perspectives on an Evolving Crreation, Wm. B. Eerdmans, Grand Rapids.
2. Budd, G.E. and S. Jensen, 2000, “A critical reappraisal of the fossil record of the bilaterian phyla,” Biological Reviews 75: 253-295. Conway Morris, S., 2000, “The Cambrian ‘explosion’: Slow-fuse or megatonnage?”, Proceedings of the National Academy of Science 97(9): 4426-4429.
3. Morris, J. 2008. The Burgess Shale and Complex Life. Acts & Facts. 37 (10): 13.
4. Gubanov, A.P., , A. V. Kouchinsky, and J. S. Peel,1999, "The first evolutionary-adaptive lineage within fossil molluscs," Lethaia 32: 155-157. Kouchinsky, A.V., 1999, “Shell microstructures of the Early Cambrian Anabarella and Watsonella as new evidence on the origin of the Rostroconchia,” Lethaia 32: 173-180.
5. Meyer, S.C., M. Ross, P. Nelson, & P. Chien. 2003. The Cambrian explosion: biology's big bang. Pp. 323-402 in J. A. Campbell & S. C. Meyer, eds., Darwinism, Design and Public Education: Michigan State University Press, Lansing, p. 346.
]]> Sat, 11 Dec 10 08:00:10 -0800 Keith Miller http://biologos.org/questions/complexity-of-life?utm_source=RSS_Feed&utm_medium=RSS&utm_campaign=RSS_Syndication http://biologos.org/questions/complexity-of-life?utm_source=RSS_Feed&utm_medium=RSS&utm_campaign=RSS_Syndication A complex biological structure with many interacting parts might appear, at first glance, as if it were originally created in its present form with all its interlocking components fully formed and intact. It doesn’t seem possible that they developed step by step via biological evolution. In Darwin’s Black Box, Michael Behe introduces a term that he and other proponents of Intelligent Design use for this concept: irreducible complexity. A complex biological structure with many interacting parts might appear, at first glance, as if it were originally created in its present form with all its interlocking components fully formed and intact. It doesn’t seem possible that they developed step by step via biological evolution. In Darwin’s Black Box, Michael Behe introduces a term that he and other proponents of Intelligent Design use for this concept: irreducible complexity. No part of an irreducibly complex system has any apparent function except in its relation to the other parts.

Behe suggests that the parts of irreducibly complex biological structures would be useless unless they appear all together, and evolution has no mechanism to build complex structures like this. Natural selection, after all, works just one step at a time. Furthermore, natural selection has no foresight. Put simply, if a change is going to be preserved, that change will generally need to confer some extra benefit—no matter how small—to the next generation. Behe has oversimplified things a little. Evolutionary theory predicts that in small populations, neutral changes—and even changes that are slightly deleterious—will survive sometimes. Still, in general, he is correct. So let’s examine what evolutionary biologists believe about how complex structures are built.

A Seemingly “Irreducibly Complex” System

As Scott Gilbert shows in his textbook Developmental Biology, Eighth Edition, the evolution of the interconnecting bones of the middle ear illustrates how supposedly irreducibly complex structures can in fact be generated by the stepwise process of gradual change and natural selection. Fish, for example, have a special system called the lateral line system that extends along the length of their bodies and enables them to detect vibrations in the water. They also have an inner ear, which is useful for balance and supplements the lateral line system in detecting vibrations. With the movement of certain water-dwelling species to land, the lateral line system became obsolete because what was needed was a way of amplifying the vibrations in air, not water. A bone that had previously been used as a support for the skull became the stapes. Along with supporting the skull, the stapes also transmitted sound vibrations—which come in part through the skull and jaw—to the inner ear. How do we know it’s the same bone? By examining its embryological origin in fish and reptiles. In reptiles, there is just one bone that transmits air vibrations to the inner ear: the stapes.

We can also trace the origin of the two other middle ear bones, the incus and malleus, by looking at fossils from the time of the origin of mammals about 230 million years ago. Until that point, two bones—the articular and quadrate bones—served as the hinge of the jaw. Investigators, however, believe they carried out a second function. Because they were located adjacent to the stapes, it is likely they also aided in transmitting sound vibrations to the stapes.

Here is where the story gets especially interesting. Right at the time of the origin of mammals it turns out there were several species—perhaps many, paleontologists are sure they don’t have all of the transitional species preserved in the fossil record—that had a double hinge at the jaw. Not only did the articular/quadrate bones serve as a hinge, but another pair of bones, the dental/squamosal bones, served that purpose as well. So the articular/quadrate bones, which transmitted sound, no longer had to also serve as a jaw-hinge. This second function became redundant because there was another set of bones doing the same thing.

With that redundancy, the articular/quadrate bones of the jaw were free to become the incus/malleus of the middle ear. We have a record of the transition, and we have a record of the building of a so-called irreducibly complex structure. Parts that were initially used for one function became, for a period of time, useful for two functions. Then, one function was refined while the other function became redundant or unnecessary. In other words, parts that were initially used for one purpose become co-opted for another purpose; and looking back through the fossil record, we can see the intermediates.

The Bacterial Flagellum

In Darwin’s Black Box, Behe focuses on three things he considers to be irreducibly complex: the bacterial flagellum, the blood clotting cascade and the immune system. The elements of these systems are molecular in nature and therefore the evolutionary intermediates are somewhat harder to document. Interacting molecules are not preserved for historical analysis like fossil bones of the skull and middle ear. In his book, Behe suggests that biochemistry gives no clue as to how complex interacting parts like these might have come about, and he confidently states that investigations have run up against a blank wall.

It has now been 13 years since Darwin’s Black Box was written. The structures and processes Behe chose to focus on have been studied quite extensively. Although it is impossible to go back and analyze step by step what actually did happen, much evidence for straightforward evolutionary explanations has accumulated over the years. The diversity in a given structure that we see when we compare different species tells us a great deal about how that structure might have come about.

Consider the bacterial flagellum, the example most commonly used to illustrate the principle of irreducible complexity. First, it is important to point out that the bacterial flagellum comes in many different varieties, sometimes with profound differences between one species and another. This alone illustrates that the flagellum is probably not irreducibly complex. It can be altered, and when it is altered, it does not necessarily lose its function.

There are many species of bacteria, for example, that use the basal parts of the flagellum to deliver toxins into their host. A different set of bacterial species uses a portion of the flagellar machinery for another purpose. Species of the genus Buchnera live inside the sheltered environment of aphid cells in a symbiotic relationship. These bacteria no longer need flagella. However, each tiny Buchnera cell is studded with hundreds of copies of the flagellar base. As a recent paper in the journal Trends in Microbiology shows, the purpose now is to serve as a passageway for the export of proteins and other material into the surrounding environment—the aphid cell in which the bacterium resides. So while we cannot follow the sequence of events step by step to illustrate how the various types of flagella have arisen, we can see how they have changed and, in some cases, even taken on whole new functions. The term for adapting a structure for a different purpose than that for which it originally arose is “exaptation.” This is one important way in which complexity arises.

That is not the whole story, however, because individual parts have to be added into the structure as it becomes more complex or takes on new function. Where do those parts come from? Recently, investigators have shown that the key protein in the molecular motor that causes the flagellum to rotate has a very similar structure to another protein that is used to transport magnesium into and out of cells. Both protein molecules have sections that fold in almost exactly the same manner, and when we analyze the order of their building blocks (amino acids), we see profound similarities. This illustrates a second principle in building complexity: It is done by co-option. Parts that are used for one purpose are co-opted to take on a second function as well. Sometimes, the instructions to build a part are encoded by identical duplicate genes. When that happens, co-option is especially straightforward. One set of instructions for making the original part is preserved while the duplicate set of instructions can gradually be modified through mutation and natural selection, allowing the part to become better and better at carrying out its new function. This illustrates a third principle of assembling complexity: adaptation through natural selection.

Even more revealingly, the supposedly irreducibly complex bacterial flagellum turns out not to be irreducible after all. For example, there is a protein at the base of the flagellum, an ATPase, that drives the key structural subunit (flagellin) of the long hollow tube through its inner core, causing the flagellum to grow in length. Yet, it has been shown that flagellin can be transported to the end of a flagellum without this ATPase. The protein that was thought to be one of the flagellum’s most important parts can be done away with. This illustrates a fourth principle of building a complex structure: redundancy. Inside of cells, there is often more than one way to accomplish a particular purpose; as evolution “tinkers” with a complex structure, there is likely to be redundancy with certain parts at certain stages. One of these redundant mechanisms may become more specialized, and even perfected, as time goes by.

The Eye

Another system that is often held up as an example of irreducible complexity is the eye. People often ask: What good is a partly assembled eye? Is there any logical series of steps that could result in the creation—through the process of natural selection—of a structure so elegant as the eye of an eagle? What would be the starting point, anyway?

Watch "The Evolution of the Eye" from PBS' Evolution: "Darwin's Dangerous Idea".

All light-sensing devices in the animal world make use of a single light-sensitive molecule, retinal, which is derived from Vitamin A. Retinal can change its shape when it absorbs a photon of light. This molecule is always complexed with a protein known as an opsin. The two work together to sense light.

By analyzing the arrangement of the building blocks, or amino acids, in opsin, it is possible to show that all opsins are derived from a single ancestral gene. What purpose could the retinal/opsin combination have had in the earliest days of animal history? It likely functioned to detect light in order to set the internal body clock that regulates the 24-hour cycle of biological processes, known as the Circadian rhythm. In recent years, it has become apparent that living processes inside of cells are tuned to function in a manner that is synchronized with the cycle of sunlight.

Circadian rhythms function throughout the living world, including single-cell organisms. It seems likely, then, that the simplest light-detecting device arose through exaptation of a molecular device that was used to detect light—not so that an organism might move toward or away from the light, but so it could reset its molecular clock. Even the origin of opsin illustrates a basic principle of building complexity, co-option. Opsin is one of many G-protein receptors, which have come to take on many different functions through the history of life. When coupled with the light-sensitive molecule retinal, a G-protein receptor allows the cell to be sensitized to the presence and absence of light. Although we have no fossilized transitions that allow us to trace the various eye intermediates that have occurred in animal history, as we do with the middle ear, we do have a myriad of light-sensing devices in the animal kingdom that allow us to piece together how sophisticated eyes could have been created through a gradual process driven by natural selection. (You can read more about the prospective intermediates that exist in the animal world in a wonderful paper by Ryan Gregory.)

If you choose to explore eye development in detail, be watching for examples of exaptation, co-option, step-by-step adaptation and redundancy. For example, you will note that the evolution of the lens illustrates co-option and redundancy. There are two ways to focus the image on the light-receiving cells at the back of an eye. One way is through an independent lens. The other way is through the transparent cornea in front of the lens. The lens is simply transparent crystallized protein molecules that are assembled in such a manner that they bring the image into sharp focus. There are a variety of proteins that can be crystallized to serve as an effective lens. It turns out that, depending on the evolutionary lineage, various proteins—including enzymes such as alcohol dehydrogenase (an enzyme for breaking down ethanol), glutathione S transferase and protein chaperones—are used for this purpose. This is a simple example of co-option and redundancy functioning together as part of the tinkering mechanism used for building a complex structure like the eye.

Two-thirds of animal phyla have some sort of light-sensing device. Although all of these light-sensing devices make use of retinal and opsins, there are differences in structure that we can trace to differences in evolutionary origin. In his 2003 book, Life’s Solution, Simon Conway-Morris documents at least seven independent origins of the eye resulting in very similar outcomes. For example, the eye of a squid and the eye of a mammal work in a remarkably similar manner. However, the ways the two eyes are constructed during development are quite different. Differences in structure are constrained by how particular bodies are constructed as the embryo develops. Eyes also bear telltale signs of the fact that there has been a certain amount of jury-rigging in their construction. They are not perfect. They have blind spots, are subject to retinal detachment, glaucoma and macular degeneration, all of which are a function of the history of how the eye has been assembled through time.

Read how a recent study has shot down the idea that protein transport is irreducibly complex.

Although we don’t have the eye intermediates preserved in stone the way we can see the simpler assembly of the parts of the mammalian middle ear, we do have a vast array of eye structures in the animal kingdom, any one of which might appear to be irreducibly complex but which, in fact, has been put together through a set of processes that has included exaptation, co-option, step-by-step adaptation and some redundancy at various stages along the way. Indeed, these eye structures themselves are likely intermediates. Everything changes as it passes through the eons of time. This is the legacy of creation through the process of natural selection.