Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Experimental Support for Historical Contingency Challenges Biological Evolution

Philosopher George Santayana, an important intellectual at the turn of the last century, produced a number of influential philosophical works. Ironically, few people know about his philosophy. Instead, he is probably better known for his aphorism, “Those who cannot remember the past are condemned to repeat it.” Still, this statement communicates a profound truth about the importance of history.

Late evolutionary biologist Stephen Jay Gould also came up with a few aphorisms. One has to do with the predictability of large-scale evolutionary processes. According to Gould, if one were to push the rewind button, erase life’s history, and let the tape run again the results would be completely different each time. To say it another way, Gould thought that evolution can’t remember the past and is condemned to never repeat it—a profound truth about the nature of biological evolution.

The very essence of the evolutionary process renders evolutionary outcomes unpredictable, and nonrepeatable. Evolutionary processes are blind and undirected. According to the concept of historical contingency, espoused by Gould in his book Wonderful Life, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. As a consequence, if evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs would repeatedly appear throughout nature among unrelated organisms.

Contrary to what’s expected, however, it looks as if evolution has repeated itself, time and time again. Evolutionary biologists note that evolutionary processes frequently seem to independently converge on identical anatomical, physiological, behavioral, and biochemical systems. (Go here and here to see two articles I wrote on this problem a few weeks ago.) Evolutionary biologists refer to repeated evolutionary outcomes as convergence.

In my new book, The Cell’s Design I document over one hundred examples of convergence at the biochemical level. On this basis I argue that the widespread occurrence of repeated origins of a broad range of biochemical systems raises significant questions about the validity of evolutionary explanations for life’s origin and diversity, if historical contingency truly reflects the nature of evolutionary processes.

Yet, some evolutionary biologists express skepticism about historical contingency. Simon Conway Morris is one. In his book, Life’s Solution Conway Morris argues that the pervasiveness of biological and biochemical convergence reveals something fundamental about the evolutionary process. Though the pathways that evolution takes may be historically contingent, the process always finds its way to the same endpoints under the influence of natural selection. In other words, evolution does indeed repeat itself, with contingency left to the minor details.

Given that large-scale evolutionary processes can’t be observed, how do scientists resolve this controversy? New work by Richard Lenski’s group at Michigan State University provides significant headway toward this end. They provided the first real-time scientific test for historical contingency within the framework of their Long-Term Evolution Experiment (LTEE).

Long-Term Evolution Experiment

Designed to monitor evolutionary changes in Escherichia coli, this study was inaugurated in 1988. The LTEE began with a single cell of E. coli that was used to generate twelve genetically identical lines of cells.

The twelve clones of the parent E. coli cell were inoculated into a minimal growth medium that contained low levels of glucose as the only carbon source. After growing overnight, an aliquot (portion) of the cells was transferred into fresh growth media. This process has been repeated every day for about twenty years.

Throughout the experiment, aliquots of cells have been frozen every 500 generations. These frozen cells represent a “fossil record” of sorts that can be thawed out and compared to current and other past generations of cells.

The forces of natural selection have been carefully controlled in this experiment. The temperature, pH, nutrients, and oxygen exposure have been constant for the last twenty years. Starvation is the primary challenge facing these cells.

Lenski and coworkers have noted evolutionary changes in the cells, some which have occurred in parallel. For example, all of the populations evolved to increase cell size, grow more efficiently on glucose, and grow more rapidly when transferred to fresh media. These changes make sense given the near-starvation conditions of the cells.

Evolution of the Cit+ Strain

One evolutionary change which should have occurred but hasn’t (at least until recently) involves the use of citrate as a carbon source. E. coli grown under aerobic (oxygen-based) conditions can’t use this compound as a food stuff. This bacterium has the biochemical machinery to metabolize citrate; it just can’t transport the compound across its cell envelope.

Lenski and his team have taken advantage of E. coli’s deficiency to monitor for contamination in their experiment. They added citrate at relatively high levels to the growth media. Since other microbes can typically make use of citrate, any contaminating microbe accidently introduced during the transfer steps will grow to greater cell densities than E. coli, causing the media to turn cloudy.

Cloudy media means something is using citrate. Whenever the media turned cloudy, Lenski’s collaborators would attempt to confirm the contamination by identifying the unwanted microbial intruder.

Surprisingly, around 32,000 generations into the LTEE, E. coli started utilizing citrate as a carbon source. Lenski and his coworkers reasoned that this newly acquired ability was due either to a rare, single genetic change, or a series of mutations that formed a pathway culminating in the ability to use citrate.

The E. coli genome consists of about 4.6 million base pairs. (Each base pair could be thought of as a genetic letter in E. coli’s book of life.) The cells that are part of the LTEE have collectively experienced billions of mutations over the course of the experiment. Enough to cause changes in each position of the E. coli genome several times over. Additionally, the mutation rate to yield the citrate-using strain of E. coli is extremely low compared to the rate that mutations, in general, and beneficial mutations, specifically, occur in the E. coli genome. Taken together, these two observations argue that the evolution of citrate-eating cells must have involved a sequence of mutations, not a single rare genetic change.

The evolved ability to use citrate presented Lenski’s team with a rare opportunity to test the notion of historical contingency.

A Test of Historical Contingency

To conduct this test, Lenski and his fellow researchers took frozen samples of ancestral E. coli cells, grew them up, and transferred them to fresh media every day—monitoring them for about 4,000 generations to see if any cells acquired the ability to use citrate.

They did not observe the changes they hoped to see for cells sampled prior to about 27,000 generations. Only the cells taken after that point in “history” developed the ability to use citrate, and only rarely did this change occur.

This result indicates that a potentiating (increasingly effective) series of mutational changes made it possible for E. coli to grow on citrate. Cells that did not experience that same pathway of changes could not evolve citrate-utilizing capabilities. In other words, historical contingency characterized the evolution of the citrate-growing strains.

In the case of the several cells taken after about 27,000 generations, where citrate utilization did evolve repeatedly, these cells required only a single change to make use of citrate. This result means that given enough opportunities, evolution can repeat if it involves a single mutational event. But when several mutations have to be sequenced in the right order, evolution can’t repeat. Evolution is historically contingent.

In a sense the LTEE represents the best possible opportunity for repeated evolution, since the growth conditions and the forces of selection (near starvation) have been constant throughout. The high levels of citrate have also been constant. By incorporating such high levels of this carbon source into the experiment, Lenski’s group was “daring” E. coli to evolve citrate-utilizing capabilities.

In the real world—outside of the controlled conditions of the laboratory—the growth conditions, the forces of selection, and the opportunities for evolutionary advance are variable. This variability adds to the contingency of the evolutionary process.

The Implications

The experimental demonstration of historical contingency in E. coli raises significant questions about the validity of evolutionary explanations for life’s origin and history. Even though evolution shouldn’t repeat, it appears as if it has numerous times at a biochemical level and an organismal level.

Biological convergence not only questions the validity of biological evolution, it points to the work of a Creator. As I argue in The Cell’s Design, designers and engineers frequently reapply successful strategies when they face closely related problems. Why reinvent the wheel? It’s much more prudent and efficient for an inventor to reuse the same good designs as much as possible, particularly when confronted with a problem he or she has already solved.

The tendency of engineers and designers to reuse the same designs provides insight into the way that a Creator might work. If human engineers, made in God’s image, reutilize the same techniques and technologies when they invent, it’s reasonable to expect that a Creator would do the same. If life stems from the work of a Creator then it’s reasonable to expect that the same designs would repeatedly appear throughout nature. Use of good, effective designs over and over again would reflect his prudence and efficiency as a divine Engineer.

One Final Point

Does the evolution of E. coli in the LTEE validate the evolutionary paradigm? Not really. The evolutionary changes experienced by this microbe are equivalent to microevolutionary changes observed in complex multicellular organisms.

The evolution of citrate-utilizing capabilities appears to involve changes in a transport protein associated with the cell envelope. To evolve a transport protein with the capability to move citrate across the cell envelope under aerobic conditions appears to require several changes that work in concert to alter the properties of the transporter. Given the large number of cells and the large number of generations (30,000), it’s not surprising that evolutionary changes take place. Still, the modification of a preexisting protein to transport citrate is a far cry from generating a complex structure like the bacterial flagellum from preexisting biochemical systems.

It looks as if a Creator has remembered the biological past, and has chosen to repeat it, time and time again.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Newly Discovered Example of Convergence Challenges Biological Evolution

I love TiVo. It’s a lot of fun to pause live TV (particularly when the big game is on), rewind it, and play it back again.

Biological evolution has nothing in common with TiVo, however. As the late evolutionary biologist Stephen Jay Gould highlighted in his book Wonderful Life, if one were to push the rewind button, erase life’s history, and then let the tape run again the results would be completely different each time.

The very essence of the evolutionary process renders evolutionary outcomes nonrepeatable. According to the concept of historical contingency, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of an historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. As a consequence, if evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature among unrelated organisms.

Contrary to what’s expected, evolutionary biologists note that biological convergence is widespread. As I noted last week, convergence refers to the extensive pattern in nature where unrelated organisms possess nearly identical anatomical, physiological, behavioral, and biochemical characteristics. According to the evolutionary paradigm, undirected natural processes yielded the identical outcome because the forces of selection channeled evolutionary pathways to the same endpoint.

Researchers Brian Beatty and Bruce Rothschild have uncovered another remarkable example of biological convergence. From an evolutionary standpoint, it appears as if toothed and baleen whales developed the ability to dive deep into the ocean independently from each other. (Go here for a popular article on this discovery and here for a technical paper.)

For whales to dive, they must have physiological adaptations that allow them to avoid decompression syndrome. Rapid pressure changes—such as what occur during deep diving—can force air bubbles out of the blood vessels. When this happens, it can cause the blood vessels to rupture, denying cells of blood, oxygen, and nutrients. This loss causes the cells to die, leaving lesions behind.

The scientists used this principle to assess susceptibility of ancient whales to decompression syndrome. They analyzed vertebrae of 331 individual modern and 996 fossil whales. The conclusion was that the two lineages of whales must have evolved the ability to avoid decompression syndrome independently. This scenario contravenes the expectation of most evolutionary biologists, who postulated that the shared ancestor of toothed and baleen whales must have had the ability to dive deep without suffering from decompression problems.

According to Erich Fitzgerald, an Australian paleontologist, “They have come up with a quite surprising story.” The surprise expressed by Fitzgerald stems from the notion that evolutionary outcomes should not repeat. Yet, in this instance and others it appears as though evolution has generated the same outcomes over and over again.

Biological convergence not only raises questions about the validity of biological evolution, it also points to the work of a Creator. As I argue in my new book The Cell’s Design designers and engineers frequently reapply successful strategies when they face closely related problems. Why reinvent the wheel? It’s much more prudent and efficient for an inventor to reuse the same good designs as much as possible, particularly when confronted with a problem he or she has already solved.

The tendency of engineers and designers to reuse the same designs provides insight into the way that a Creator might work. If human engineers, made in God’s image, reutilize the same techniques and technologies when they invent, it’s reasonable to expect that a Creator would do the same. If life stems from the work of a Creator then it’s reasonable to expect that the same designs would repeatedly appear throughout nature. Use of good, effective designs over and over again would reflect His prudence and efficiency as a Divine Engineer.

It looks as if life is God’s TiVo.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Newly Discovered Example of Convergence Challenges Biological Evolution

“It’s like déjá vu all over again.” This expression, attributed to Hall of Fame catcher Yogi Berra, has become synonymous for something that happens over and over again—and probably shouldn’t.

Evolutionary biologists are confronted with their own form of déjá vu, known as convergence. This term refers to the widespread pattern in nature in which unrelated organisms possess nearly identical anatomical, physiological, behavioral, and biochemical characteristics. The wings of birds and bats represent one textbook example. Birds and bats belong to different groups, with birds assigned to the class Aves and bats to the class Mammalia. According to the evolutionary paradigm, undirected natural processes yielded the identical outcome (wings, in this case) because the forces of selection channeled evolutionary pathways to the same endpoint.

This explanation doesn’t square up, however. If biological systems are the product of evolution, then the same biological systems should not recur throughout nature. Chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should repeatedly appear throughout nature.

The concept of historical contingency embodies this idea and is the theme of Stephen Jay Gould’s book Wonderful Life. To help clarify the concept of historical contingency, Gould uses the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time. The very essence of the evolutionary process renders evolutionary outcomes nonrepeatable.

And yet, over the last decade or so, evolutionary biologists have discovered a number of examples of convergence at the organismal and biochemical levels. (For more information, see these articles on convergence and repeated evolution.)

In my most recent book, The Cell’s Design, I document over one hundred examples of convergence at the biochemical level and argue that the widespread occurrence of the multiple repeated origins of a wide range of biochemical systems raises significant questions about the validity of evolutionary explanations for life’s origin and diversity.

Scientists from Purdue University have really uncovered another remarkable example of biochemical convergence in plants. (See here for journal article and here for popular article.) These researchers demonstrated that a specific enzyme (known as a cytochrome P450-dependent monooxygenase) appears—from an evolutionary vantage point— to have independently emerged in two separate instances in lycophytes and angiosperms. This enzyme plays a key role in the synthesis of lignins.

Lycophytes, such as clubmosses, are an ancient lineage of vascular plants that appeared about 420 million years ago. From an evolutionary standpoint, they represent a separate branch from the lineage that produced flowering plants.

All vascular plants make use of a class of large, complex molecules called phenolic lignins in the xylem. The phenolic lignins are polymers. These types of compounds are large molecules comprised of repeating subunit molecules (called monomers.) The different types of vascular plants produce lignins consisting of characteristic subunits. For example, gymnosperms produce lignin made up of guaiacyl monomers. Angiosperms manufacture lignins composed of a mixture of guaiacyl and syringyl monomers. Plant scientists generally regard lignins derived from syringyl monomers as exclusive to angiosperms. This view implies that the enzymes used to make this monomer must have evolved relatively late in evolutionary history when angiosperms appeared on the scene.

Interestingly, there are lycophytes that possess lignins composed of the syringyl monomer. The Purdue researchers determined that the enzyme (ferulic acid/coniferaldehyde/coniferyl alcohol 5-hydroxylase, a cytochrome P450-dependent monooxygenase) that directs metabolites down the pathway that yield syringyl monomers must have evolved independently in lycophytes and angiosperms to yield enzymes that perform identical functions.

Like Yogiisms, this conclusion makes little sense within the evolutionary paradigm, particularly in light of all the other examples of biochemical convergence. It looks as if evolution has repeated itself over and over again—and it shouldn’t have.

Paleontologist J. William Schopf, one of the world’s leading authorities on early life on Earth, has made this very point in the book Life’s Origin.

Because biochemical systems comprise many intricately interlinked pieces, any particular full-blown system can only arise once…Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA cell line had the same traits that characterize all its present-day descendents.

This pattern, expected by Schopf and other evolutionary biologists, is simply not observed at the biochemical level. An inordinate number of examples of molecular convergence have already been discovered. And undoubtedly more will be uncovered in the future.

Next week I’ll visit the topic of convergence all over again by describing another newly discovered example and discuss how “repeated evolutionary outcomes” provide evidence for the work of a Creator.