Evolution in Action, or Evolutionist Inaction?

When critiques have been forbidden, lazy evolutionary biologists get away with incompetent scientific work and inept thinking.

Here are more examples of a theme concluded by Dr Jerry Bergman in yesterday’s post: claims of “evolution occurring before our eyes” fall apart when examined. Why don’t other evolutionists pour shame on such lazy thinkers within their camp? The evolution they’re seeing right before their eyes is in their dreams, because their eyes are closed when they ought to be working.

Seeing evolution happening before your eyes (EMBL, Heidelberg). “EMBL researchers find DNA enhancers more complex than thought,” begins this story on a note that seems to be questioning evolution. But since evolution is responsible for everything in the world (because Stuff Happens), that cannot be. It’s only that evolutionists have not marveled sufficiently at the creative power of chance mutations.

Animal diversity and evolution are driven by changes in how our genetic code is expressed. Specific DNA sequences called enhancers control where, when and how strongly genes are expressed during development to create the respective organism. Studying enhancers and how they result in different patterns of gene expression therefore helps us to understand more about how evolution takes place. In addition to driving the evolution of species, enhancers are also relevant to disease: mutations in enhancers are associated with over 80% of all human diseases.

When you get sick from a genetic disease, aren’t you glad you evolved? The authors score more points in silliness by finding ways to link their narrative with climate change. They say that their work (to make it more valuable to the press) could help predict “evolution in the time of climate change, where many animals are under the pressure to adapt quickly to fast changing environments.” They need to find the right genetic mistakes in time!

While studying enhancers is a well-established field in molecular biology, this study is unique in the sheer number of mutations having been studied. The group created more than 700 unique, randomly generated mutations within a single enhancer. “Nobody ever has studied so many enhancer variants at this level of depth before. It was as if evolution was happening before our very eyes!” highlights [Timothy] Fuqua.

Zoologists uncover new example of rapid evolution in Southeast Asia – meet the Sulawesi Babblers (Trinity College Dublin). “The zoologists have discovered that male and female Sulawesi Babblers (Pellorneum celebense, a species of bird) have evolved to attain different sizes on small islands, and in quick-fire time.” What evolved? Size on different islands. Are the birds all the same species? Yes. Gong. Next.

Rapid evolution under climate change (University of Tubingen, via Phys.org). “Certain plant species can evolve very quickly under drought conditions,” these Israeli Darwinites allege. In a 12-year experiment, during which a simulated drought and increase in rainfall, something evolved very quickly! What was it? Flowering time. Are all the plants the same species? Yes. Gong. Next.
P.S.: They needed to end with something to give the climate alarmists something to worry about:

“The message of our study is therefore only partly optimistic,” says Tielbörger. “Although we were able to show that rapid evolution is possible for important plant traits, there are also traits for which the adaptation processes may be too slow to keep pace with climate change.“

Evolution in real-time: How bacteria adapt to their hosts (University of Vienna, via Phys.org). “Parachlamydia are widespread in the environment where they live in amoebae,” this article begins. “The bacteria serve as a model system for studying the evolution of infectivity.” Experiments with 500 generations over 14 months corresponded to about 15,000 human years.

Our results reveal that if the bacteria are able to remain within one host cell and ensure that they continue to live in the daughter cells of the host when the host cell divides, their infectivity does not change. However, bacteria become increasingly infectious when they have to move from one host cell to another host cell in order to survive,” explains Paul Herrera, first author of the study.

What changed? Some genes between the groups had 1,161 differences, and differed also in the expression of genes. How long have these bacteria existed? A billion years, perhaps. So they have had a billion years to evolve “in real time” into humans, but they remain the same species of microbes today? Apparently. Gong. Next.

It’s vitally important that we think about evolutionary relationships not just as a tree, but as a complex network, or we may miss critically important information.

Breakthrough research sheds light on rapid emergence of new species (Monash University). Finally, this is what Darwin needs: new species! (Remember On the Origin of Species?). The breathless headline promises some long-sought evidence for speciation. (If this were commonplace, it wouldn’t be a breakthrough, would it?).

Let’s see what kind of light is being shed here. Here come the cichlid fish in Africa again—you remember, those fish that speciate rapidly into all kinds of colors and shapes (but are still cichlid fish). Unfortunately, this story makes Charlie sad. Whatever evolution occurred apparently did not happen Darwin’s way, but through back-door processes of hybridization and horizontal gene transfer, which involve sharing of existing genetic information.

In order to understand the evolutionary history within Lake Victoria, the researchers used networks instead of branching trees, to account for the ability of different species to exchange DNA with each other.

Non-treelike evolution is often neglected for technical reasons, but it is key to understanding emerging infectious diseases like COVID-19 and Zika. “It’s vitally important that we think about evolutionary relationships not just as a tree, but as a complex network, or we may miss critically important information,” Dr McGee said.

See a quote below from a preprint about the potential for misunderstanding “evolutionary history” when hybridization and gene sharing are neglected.*

Remember when New Scientist claimed that “The theory of evolution is a vibrant, living entity still in its prime”? (see Bergman response, 10/04/20). We supply the evidence that the theory of evolution is a dull, dead myth that deserves to be buried. Drunk evolutionists act like Darwin sycophants, spewing sick offensive, Darwine-smelling e-vomit on the floor. Their drunk reporters hold up the best chunks for the public. Time for Big Biology to clean up its act and get back to the hard work of real science.

Wang et al, “Phylogenomic assessment of the role of hybridization and introgression in trait evolution,” bioRxiv, 17 Sept 2020.

Trait evolution in a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) [convergence] or followed the branching patterns of gene trees, rather than the species tree (hemiplasy). Recent work by Guerrero and Hahn (PNAS 115:12787-12792, 2018) provided a significant step towards teasing apart the roles of homoplasy and hemiplasy in trait evolution by analyzing it with respect to the species tree and the gene trees within its branches.

Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is hybridization between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of bi-allelic traits, including polymorphic ones. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a trait’s evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis when hybridization had occurred could provide misleading hypotheses about trait evolution.