Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Newly Discovered Example of Convergence Challenges Biological Evolution

A few weeks ago, while on a hike, I had to climb uphill through a boulder field. It was tough treading. Several times I wound up stuck amid the rocks with seemingly no way to maneuver. You might say I was literally, and metaphorically, stuck between a rock and a hard place.

Similarly, a recent study on the origin of a group of flightless birds called ratites puts the evolutionary paradigm in a difficult position.

To complete this study, scientists used 20 different regions of nuclear DNA taken from 18 different bird taxa to build an evolutionary tree for ratites. It turns out that they identified three distinct lineages for this group of birds. The lineages include: one for ostriches; one for rheas; and one for kiwis, emus, and cassowaries. In other words, flight appears to have been lost not once but on three separate occasions in ratites.

Previously, I’ve discussed this example of biological convergence and its troubling implications for biological evolution. This week I would like to raise an additional problem posed by this study.

Traditionally, biologists have used anatomical comparisons (morphology) to characterize evolutionary relationships and build evolutionary trees. Recent advances in DNA sequencing techniques and data analysis have now made genetic comparisons fodder for evolutionary analysis.

One key expectation is that the evolutionary trees built from anatomical comparisons (morphological phylogenies) will agree with trees built from DNA sequence data (molecular phylogenies). This expectation stems from the fundamental notion that molecular evolution should mirror organic evolution. In many instances, however, evolutionary biologists are discovering that molecular phylogenies contradict those built using morphological features. This latest study on the origin of ratites represents one more example of this disparity. Based on morphological features, evolutionary biologists concluded that the ratites must have had a single evolutionary origin. The foundation for this view stems from the fact that all ratites share common anatomical features, like the absence of keels in breast bones, smaller, simpler, and fewer wing bones, bigger leg bones, and non-aerodynamic feathers, as well as similar behavioral traits.

Yet the evolutionary tree for ratites based on molecular data generated from nuclear DNA sequences indicates something quite different. An earlier study of ratite origins using [mitochondrial DNA] sequences proves equally troubling. It suggests a single origin for the ratites, agreeing with the morphological data but contradicting the most recent study using nuclear DNA data.

This is not the first time that the question of bird origins has caused problems for evolutionary biologists. A few weeks ago I wrote about another large-scale study that yielded similar consternation.

A pivotal idea of the evolutionary paradigm, namely that evolutionary trees built from molecules should agree with those constructed from morphology, is not supported by the evidence. As I pointed out earlier, this disagreement is more problematic than it seems on the surface. According to Morris Goodman in an article he wrote for The Cambridge Encyclopedia of Human Evolution,

If the biblical account of creation were true, then independent features of morphology, proteins and DNA sequences would not be expected to be congruent with each other. Chaotic patterns, with different proteins and different DNA sequences failing to indicate any consistent set of species relationships, would contradict the theory of evolution.

These words were published in 1994, before the widespread use of DNA sequences to build evolutionary trees.

Between Goodman’s observations and the latest work on bird evolutionary relationships alone, it looks as if the evolutionary paradigm is running out of room to maneuver.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Newly Discovered Example of Convergence Challenges Biological Evolution

Lately, my wife has had trouble hanging onto cell phones. Within the span of two weeks she lost not one cell phone, but two.

But my wife is not the only one who has lost the same thing over and over again. Recently, evolutionary biologists have discovered that birds lost the ability to fly on several separate occasions.

According to new research each time birds lost the ability to fly, the outcome was virtually identical. This remarkable result makes little sense within an evolutionary framework, raising significant questions about the validity of the naturalistic explanation for life’s history and diversity.

Evolutionary biologists have long had interest in understanding the origin of a group of flightless birds known as ratites. This group consists of birds like ostriches, emus, kiwis, rheas, cassowaries, and the extinct moas and elephant birds.

According to the standard evolutionary fare the ratites had a single origin, with all of them descending from a common flightless ancestor. The basis for this view stems from the fact that they all share common behavioral traits and anatomical features like the absence of keels in breast bones, smaller, simpler, and fewer wing bones, bigger leg bones, and non-aerodynamic feathers.

One nagging problem with this evolutionary model is the biogeographical distribution of the flightless birds. They are found all over the world, with ostriches in Africa, rheas in South America, emus and cassowaries in Australia and New Guinea, kiwis and moas in New Zealand, and elephant birds in Madagascar. One way that evolutionary biologists account for this pattern is by appealing to continental drift. Accordingly, the common ancestor of the flightless birds supposedly emerged before continental breakup. Then as the different lineages formed they became separated and distributed around the world as landmasses drifted apart.

As appealing as this explanation appears to be, it doesn’t quite mesh with other evolutionary studies that estimate the emergence of the various lineages of flightless birds to have occurred at times that don’t correspond to the breakup of the continental landmasses.

A new study helps resolve this problem, but in turn creates other more significant issues for the evolutionary explanation of flightless birds and the evolutionary paradigm in general.

As part of this study, scientists used 20 different regions of nuclear DNA taken from 18 different bird taxa to build an evolutionary tree for ratites. It turns out that they identified not one but three distinct lineages for the ratites. The lineages include: one for ostriches; one for rheas; and one for kiwis, emus, and cassowaries. In other words, flight was lost on three separate occasions in ratites, not once.

This result nicely accounts for the biogeographical distribution of ratites. Loss of flight occurring at separate times is not that hard to envision. What is difficult to fathom is how independent instances of loss of flight would yield practically the same behavior and anatomical adaptations. This makes little sense within the evolutionary framework because evolution shouldn’t repeat.

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 let the tape run again, the results would be completely different each time.

The very essence of the evolutionary process renders evolutionary outcomes non-repeatable. According to the concept of historical contingency, 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 also 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. This term refers to the widespread pattern in nature in which unrelated organisms possess nearly identical anatomical, physiological, behavioral, and biochemical characteristics. (Go here, here, and here for some recent articles I wrote on biological convergence.) The loss of flight in the ratites, on three separate occasions, adds one more example of biological convergence to an already lengthy list.

Fazale ‘Fuz’ Rana, Ph.D.

Rational Design of Novel Enzyme Highlights Biochemical Design

In 1978, three scientists (Hamilton Smith, Werner Arber, and Daniel Nathans) were awarded the Nobel Prize in Physiology or Medicine for the discovery of restriction enzymes and their applications. These proteins make genetic engineering possible. They have also contributed to the wave of advances that led to the sequencing of the human genome and to the emergence of other biotechnologies.

Restriction enzymes (or endonucleases) are important for another reason. They represent an interesting example of a chicken-and-egg biochemical system and comprise part of the collection of evidence that indicates life must stem from a Creator. Recent work on these proteins highlights this point.

Endonucleases are a family of proteins. This class of biomolecules cleaves DNA. Restriction endonucleases cut both strands of DNA at specific nucleotide sequences, called restriction sites. Specifically, restriction endonucleases protect the cell from foreign DNA, like viruses, by cutting the invading DNA into fragments.

These vital biomolecules occur in conjunction with proteins (called DNA methylases) that attach methyl groups to the same DNA sequences that would normally be cleaved by restriction endonucleases. When these sequences are methylated, restriction endonucleases cannot cut them. Restriction sites of the bacterial DNA are methylated to completely protect the bacterial DNA from being chopped up by its own restriction endonulceases. Foreign DNA, however, is not afforded this same protection.

DNA methylases and restriction endonucleases form a chicken-and-egg pair. Restriction endonucleases would destroy bacterial DNA without DNA methylases. On the other hand, if bacteria did not utilize restriction endonucleases there would be no need for DNA methylases. These two proteins are interdependent and must come into existence simultaneously.

New research by scientists from the Indian Institute of Science (Bangalore, India) helps demonstrate why biochemical systems like restriction endonucleases require the work of an intelligent Agent. These researchers performed experiments to understand the origin of restriction endonucleases from an evolutionary perspective. They also wanted to develop a strategy for engineering novel, nonnatural restriction endonucleases.

Evolutionary biologists think restriction endonucleases evolved from non-specific endonucleases through point mutations in the gene region that codes the DNA binding site on the protein surface. According to this model, once specificity was established recombination and genetic shuffling of the DNA sequences that encode the DNA recognition sites would have generated new restriction endonucleases with different specificities.

To explore this possibility the research team attempted to engineer a highly specific restriction endonuclease from one (R. KpnI) that promiscuously binds to DNA. To accomplish this goal, the scientists employed a rational design strategy to determine which amino acids in the R. KpnI structure to change. These workers had to make use of the detailed understanding of this protein’s structure and functional properties in order to develop the redesign strategy.

They successfully achieved their intended goal by replacing an aspartic acid residue with an isoleucine moiety at amino acid position 163 in the R. KpnI protein chain.

This research illustrates how carefully-thought-through single amino acid substitutions can alter the specificity of restriction endonucleases. This is important work that paves the way to engineer novel, nonnatural restriction enzymes that can expand the arsenal of tools available to molecular biologists and biochemists.

The researchers involved in this study also interpreted their success as support for the evolutionary origin of restriction enzymes with point mutations ushering in the first stage in the molecular evolution of these proteins. At first glance, this interpretation seems warranted.

Still, it’s important to keep in mind that the production of the highly specific restriction endonuclease from the original promiscuous protein required intelligent input from a team of highly trained biochemists who relied on the past work of other highly accomplished scientists. In a sense, this study empirically demonstrates that protein “evolution” requires the work of an intelligent Agent.

It’s also important to note that the researchers didn’t design the companion methylase protein. This protein isn’t necessary for most biotechnology applications. But without the methylase cohort, the reengineered restriction endonuclease would wreck havoc in vivo, destroying DNA that comprises the bacterial genome.

It’s very unlikely that a restriction endonulcease and its partner methylase would simultaneously appear in an evolutionary scenario. These coordinated events would require that changes in the restriction endonuclease would take place at exactly the same time as corresponding changes in the methylase. The only way for coordinated changes like this to happen is under the auspices of an intelligent Agent.

As I point out in my new book The Cell’s Design, human engineers frequently encounter chicken-and-egg problems when designing systems and processes. Everyday experience teaches that chicken-and-egg systems can come to fruition only through intentional planning and implementation. Chicken-and-egg systems, therefore, serve as a potent indicator of intelligent design.

I describe several other examples of chicken-and-egg systems in The Cell’s Design.