Jonathan McLatchie

An interesting paper published in Nature by Evgenia et al. documents the ability of the DNA double helix to exist in a functional alternative form for 1% of the time, called an “excited state.” What does this mean for neo-Darwinism?

In my previous post, I highlighted a recent peer-reviewed paper which challenged a key tenet of neo-Darwinian evolution — specifically, the causal sufficiency of gene duplication and subsequent divergence to account for the origin of novel biological information. In this follow-up blog, I want to consider some of the case-studies examined in the paper and relay some of the conclusions drawn.

Last night, I watched as Mike Behe presented a talk at Glasgow Caledonian University’s Carnegie Lecture Theatre. The lecture was titled, Darwin or Design – What Does the Science Really Say?. The event was organized by the Centre for Intelligent Design UK (event website here).

The lecture theatre was filled almost to capacity (about 500 people). Behe was on form, presenting a powerful cumulative, yet accessible, case for design in biological systems. He presented the bare bones of his two core theses, articulated and defended in Darwin’s Black Box and The Edge of Evolution. Behe talked his audience through some of the criteria which we use — as part of our everyday experience — to come to the conclusion of design, arguing that design is immediately recognisable when one encounters a complex and functionally-specific assemblage of parts. Arguing that the appearance of design is not really in dispute at all, he pointed to Richard Dawkins’ The Blind Watchmaker, in which Dawkins asserts that biology is the study of complicated things which have the appearance of having been designed for a purpose. If life gives the overpowering appearance of having been designed, argued Behe, then one is rationally justified in adhering to one’s intuitions unless and until a compelling reason is given to suggest that it the appearance of design is only apparent — that is, illusory.

The question of the evolution of eukaryotic cells from prokaryotic ones has long been a topic of heated discussion in the scientific literature. It is generally thought that eukaryotes arose by some prokaryotic cells being engulfed and assimilated by other prokaryotic cells. Called endosymbiotic theory, there is some empirical basis for this. For example, mitochondria contain a single circular genome, carry out transcription and translation within its compartment, use bacteria-like enzymes/components, and replicate independently of host cell division and in a manner akin to bacterial binary fission.

Despite such evidence, however, when assessing the causal sufficiency of unguided processes, they — predictably — come up short. After all, it is all-too-easy to lapse into a long-discredited Lamarckian “inheritance-of-acquired-characteristics” mentality. It is important to bear in mind that, even if a cooperative assemblage of prokaryotes did by some fluke of luck arise, such an arrangement is of no evolutionary significance unless there is a genetic basis to ensure its propagation.

A second problem with this scenario is that mitochondria use a slight variation on the conventional genetic code (for example, the codon UGA is a stop codon in the conventional code, but encodes for Tryptophan in mitochondria). This implicates that the genes of the ingested prokaryotes would need to have been recoded on their way to the nucleus. The situation becomes even worse when one considers that, in eukaryotic cells, a mitochondrial protein is coded with an extra length of polypeptide which acts as a “tag” to ensure that the relevant protein is recognised as being mitochondrial and dispatched accordingly. The significant number of specific co-ordinated modifications which would be required to facilitate such a transition, therefore, arguably make it exhibitive of irreducible complexity.

I was recently directed to a video lecture on the phenomenon of quorum sensing, the mechanism by which bacteria communicate with one another to establish the population density of micro-organisms of their own kind within their proximal environment. Bonnie Bassler, the lecturer in this video, does a masterful job of portraying fairly technical concepts and ideas to a lay-audience.

The purpose of quorum sensing is essentially to ensure that sufficient cell numbers of a given species are present before initiating a response that requires the population density to be above a certain threshold. A single bacterial cell secreting a toxin into a eukaryotic organism is not likely to do the host any harm and would waste resources. If, however, all of the bacterial cells in a large population co-ordinate the expression of the toxin, the toxin is more likely to have the desired effect.

Each species that employs quorum sensing — which includes most gram negative bacteria, and also some gram positive bacteria — synthesises a tiny signalling molecule (technically called an “autoinducer”), which diffuses freely across the cell’s membrane. Autoinducers are species-specific, which means that each cell of the same species makes the same molecule. This means that the autoinducer is only present in high concentrations inside the cell when there are many cells of the same species nearby. Inside the cell, the autoinducer binds to an activator protein which is specific for that particular molecule and thus signals the bacteria to begin transcription of specific genes. As noted in the video, there is also evidence of a common autoinducer which is shared between many species of bacteria as a “conventional language.”

Proponents of intelligent design (ID) have long predicted that many of the features of living systems which are said to exhibit “sub-optimal” design will, in time, turn out to have a rationally engineered purpose. This is one of several areas where ID actively encourages a fruitful research agenda, in a manner in which neo-Darwinian evolution does not. One such area, and a field for which I have long held an inquisitive fascination for, is the subject of so-called “junk DNA,” and the non-coding stetches of RNA which are transcribed from them.

Skepticism of the “junk DNA” paradigm is not a phenomenon which is limited to proponents of ID. This popular view of the genome — while still resonating as the conventional view among neo-Darwinian thinkers — has also been challenged by John Mattick of the University of Queensland and Jim Shapiro of the University of Chicago.

Earlier this month, an article appeared in the journal Cell by a Spanish team. The article announced the discovery of the ability of long non-coding RNA, which are often encoded in DNA near genes known to be important to both stem cells and cancer, to serve as enhancer elements (which promote gene expression).

According to the paper’s Abstract:

A news article published yesterday on haaretz.com reported that the Israeli Education Minister has dismissed their chief scientist, Dr Gavriel Avital, over — wait for it — questioning particular elements of two theories, specifically those pertaining to Darwinian evolution and global warming.
The article reports,

Dr. Gavriel Avital has generated controversy in the past for his statements questioning the validity of Darwin’s theory of evolution. He has also challenged conventional theory on pollution’s effects on global warming. “Someone who holds the opinions of Avital cannot serve as chief scientist of the Education Ministry,” said a ministry official. [emphasis mine]

What was Dr Avital’s crime? Let’s hear it straight from the horse’s mouth:

[Ed. Note: The previously published version of this post referred to Francisco Ayala as “of the BioLogos Foundation.” While Dr. Ayala has been a guest blogger with BioLogos, he is not directly affiliated with the foundation.]

Late last year, the eminent Christian philosopher and proponent of intelligent design, William Lane Craig, crossed swords in debate with the avid apologist for Darwinian evolution, Francisco Ayala. The debate was chaired by philosopher of physics Bradley Monton of the University of Colorado, an ID sympathizer, though a convinced atheist himself. Monton is the author of the book, Seeking God in Science: An Atheist Defends Intelligent Design. A fascinating ID the Future interview with Professor Monton can be downloaded here.

Following Dr. Ayala’s opening statement, Dr. Craig commenced his presentation by carefully setting out the definition of ID as the study of legitimate design inferences. Craig stipulated that, were Ayala to attempt to refute the inference to design with respect to biological systems, he would need to do one of two things. Either Ayala would need to directly challenge the legitimacy of the explanatory filter (presumably by demonstrating that it incorporates false positives) or demonstrate that the systems featured in biology do not meet the criteria of the explanatory filter. Setting aside the discussions pertaining to the tenability of universal common ancestry, Craig set about to argue that Ayala’s attempts to disqualify ID on scientific grounds were doomed because he had failed to demonstrate, in his published work, that the dual forces of random mutation and natural selection, are causally sufficient to account for macroevolution. He also argued that Ayala’s more numerous attempts to disqualify ID on theological grounds are completely irrelevant to the process of drawing a design inference from biological phenomena, because none of the arguments for ID aspire to show that the designer possesses the qualities of omnibenevolence or omnipotence. After all, Craig argued, a design inference is still warranted with respect to a medieval torture rack, regardless of the malevolent purposes of the system’s design. Questions pertaining to the nature of the designer are for natural theology, not for the scientific research program of ID. This is what distinguishes the modern concept of ID from the Watchmaker argument of William Paley’s Natural Theology.

The Darwinian model of evolution holds that one of the key mechanisms of evolutionary innovation is the duplication of genes and the subsequent divergence of one of the duplicate copies to undertake a new functional role. Because a probability of a single gene stumbling upon a significantly different (yet functionally advantageous) sequence is so small, the idea is that, following a duplication of a gene, one copy is able to retain the original function, while the other is free to explore the vast sea of combinatorial possibilities in search of some novel function.

It is widely believed that a duplicate gene has no phenotypic cost or advantage associated with it – that is, it is selectively neutral. In such a state, it is thought that the gene is free to mutate, independent of selection constraints or pressure. When a previously protein-coding gene incurs deleterious mutations such that it no longer codes for a useful polypeptide, the gene is rendered a “pseudogene”.

One recent paper, which recently appeared in the open-access journal, PLoS Genetics, by Kuo and Ochman, entitled “The Extinction Dynamics of Bacterial Pseudogenes”, offers a potent challenge to this view. According to the paper’s abstract: