Yet more on life's antidarwinian biasII

Life Continues to Ignore What Evolution Experts Say

Denyse O'Leary September 9, 2015 3:18 AM

ecently, philosopher James Barham published a series of articles called "Seeing Past Darwin," in which he looks at the recent growth and enormous implications of non-Darwinian biology and its approach to evolution. We've been discussing some of the specific issues in this series.

One motif recurs: Darwinian evolution -- which most lay hearers assume to be "evolution" period -- assumes that evolution is vertical: Organisms take their form from genes inherited with slight modifications from their ancestors through their parents. And these slight changes add up gradually over time to immense and profound changes.

Non-Darwinian biology studies mechanisms for evolution that don't really work that way, including horizontal gene transfer and epigenetic change.

Demonstrating these mechanisms doesn't "disprove" common ancestry. Rather, it shows that common ancestry drives far less evolution than current popular science media lead us to expect. Also we can no longer assume that when a change does occur, a satisfactory account must be Darwinian. It will take some time to unpack the controversial implications of our newfound knowledge of actual causes of evolution.

Some non-Darwinian mechanisms of evolution we haven't yet looked at play at least a small role in the history of life:

-- Genome doubling. Some plants can duplicate their chromosomes (polyploidy) to foster explosive growth without undergoing cell division. Thus, they can recover quickly from damage, such as being half eaten by grazing animals. The process, long considered a major force in plant evolution, immediately gives the cells much more DNA to work with, favoring adaptation to challenging new circumstances.

-- Jumping gene. We've looked at horizontal gene transfer between life forms. But some genes, transposons, can also move around within them. As Nature Education explains:

Some of the most profound genetic discoveries have been made with the help of various model organisms that are favored by scientists for their widespread availability and ease of maintenance and proliferation. One such model is Zea mays (maize), particularly those plants that produce variably colored kernels. Because each kernel is an embryo produced from an individual fertilization, hundreds of offspring can be scored on a single ear, making maize an ideal organism for genetic analysis. Indeed, maize proved to be the perfect organism for the study of transposable elements (TEs), also known as "jumping genes," which were discovered during the middle part of the twentieth century by American scientist Barbara McClintock. McClintock's work was revolutionary in that it suggested that an organism's genome is not a stationary entity, but rather is subject to alteration and rearrangement-a concept that was met with criticism from the scientific community at the time.

Lee Spetner recounts in The Evolution Revolution:

McClintock pursued her research despite it being considered a backwater area, and eventually the importance of her work was recognized by the Nobel Prize committee in awarding her the Prize in Medicine in 1983. The transposable genetic elements she discovered have been subsequently revealed to be members of a class of genetic rearrangements that do not occur spontaneously by chance but are under strict cellular control.

One jumping gene in the model plant Arabadopsis was found to improvedisease resistance. But jumping genes are not always useful or welcome; they can cause harmful mutations. Some are even under investigation for promoting cancer:

Study author Dr Paul Edwards, at the Cancer Research UK Cambridge Institute, said: "These jumping genes play hopscotch across our genetic code in cancer cells more than in normal cells. When one of these mobile genetic sequences plants itself in the middle of a gene that controls the cell's growth it radically alters how the cell behaves, which can sometimes cause cancer.

-- Hybridization We've already seen that cross-breeding blind cavefish from different caves can restore devolved sight in at least some offspring (because the mutations that result in loss of sight differ from group to group, and some hybrids end up with all the necessary equipment). But natural hybridization can produce such changes too. Characteristics that are not evidenced in a given generation may remain as potentials.

Ferns separated 60 million years have interbred. The wolf and dog populations of North America are so heavily hybridized that it is a challenge to make sense of them at all in the face of "all the contradictory claims." Researchers have also identified at least three potential hybridization events (interspecific mating) in Eurasian mice. One scientist noted that other studies "may have missed evidence of hybridization because the researchers weren't specifically looking for it." That means we do not currently know how frequent it is. More strangely, common baker's yeast turns out to have two different versions of its genome, thought due to a hybridization event 100 million years ago.

As a mechanism, hybridization may have developed a taint due to implausible hypotheses such as the supposed pig-chimp hybrid that, according to one theory, produced humans. But, within the bounds of the plausible, it is a means of producing long-term changes in life forms over time.

-- Symbiosis. The theory of cell mergers (sometimes called endosymbiosis or symbiogenesis) was pioneered by University of Massachusetts biologist Lynn Margulis (1938-2011). She proposed that one organism might absorb another and that the second would continue to function as part of the first one, creating greater complexity. AsBritannica puts it, in 1970 " her theory was regarded as far-fetched, but it has since been widely accepted."

Sometimes it can seem like a series of nested dolls. For example, two species of bacteria live together, one inside the other, inside mealybugs. One researcher said, "The effort has revealed a level of molecular-level integration between bacterial species that scientists have never before seen," in that one bacterium has divested many key life functions, now taken care of by another. An animal (the bdelloid rotifer) avoids sex but escapes extinction by eating other life forms' DNA. One lichen turned out to have at least 126 species of fungi living symbiotically: "As the team notes in their paper published in Proceedings of the National Academy of Sciences, until very recently, the lichen was believed to have just one species of fungus." That's probably still in the textbooks.

Symbiosis can be "almost hilariously complicated," according to University of Montana microbiologist John McCutcheon. For example:

Mealybugs only eat plant sap, but sap doesn't contain all the essential amino acids the insects need to survive. Luckily, the bugs have a symbiotic relationship with two species of bacteria -- one living inside the other in a situation unique to known biology -- to manufacture the nutrients sap doesn't provide....

The researchers discovered the already complex three-way symbiosis actually depends on genes from six different organisms -- three more than the number of species that are currently found in the symbiosis.

Again, we don't know how common symbiosis (termed by one writer "slavery, but with benefits") is. While it is certainly a form of evolution, it does not typically originate new features. Rather, like horizontal gene transfer, it enables life forms to borrow each others' features, sometimes discarding some of their own, in return for more efficient operations overall. In that case, this mechanism of evolution can amount to an overall loss in complex machinery. But life goes on.

Readers may well wonder about the term "mechanism" of evolution, as used here. Consistent with Michael Behe's question, "How, exactly?", it means a process observed to account for inherited change. If a bacterium is observed to absorb antibiotic resistance genes from another bacterium and pass them on during cell division, we will term that a mechanism. It is not a theory about what "must have happened" over vast tracts of time; it is an event we have witnessed, produced by causes we can identify.

But what drives the process? That is, why do living cells attempt to protect themselves in ways that rocks and rotting wood do not? As we shall see, a number of non-Darwinian biologists now focus on the way that cells have changed and do change themselves to respond to challenges in their environment -- natural genetic engineering.