Weekend Funnies and Surprises

This is an assortment of news items that update previous posts
with some surprising discoveries tossed in for fun

Darwin’s Tree Is Crumbling

How long has Darwin’s tree-of-life concept ruled biology? Well, get ready for some major changes. A few years ago we posted startling ideas that the “tree of life” metaphor seems to be morphing into a “network of life” metaphor (e.g., 21 Sept 2015). That idea was not a sparkler fizzling out; it’s a bombshell still rumbling. Evolution News reported on this recently (2021 June 1 and 13 Aug 2021). Just yesterday, four scientists posted a preprint that reinforces the revolution. In their paper “Phylogenomic assessment of the role of hybridization and introgression in trait evolution,” (bioRxiv 13 Aug 2021), Wang et al. introduce the word “xenoplasy” to overtake old Darwinian terms like convergent evolution and branching evolution. The implications could be monumental:

Trait evolution among 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) or followed the branching patterns of gene trees, incongruent with the species tree (hemiplasy). Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is gene flow between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of polymorphic or monomorphic binary traits. 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 binary 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 in the presence of gene flow could lead to misleading hypotheses about trait evolution.

Let’s be clear: gene flow between different species is not what Darwin had in mind or even thought about. Introgression, hybridization and other forms of non-Mendelian inheritance speak of sharing of pre-existing genetic information. How revolutionary is that to modern biology?

Say It Isn’t So!

A few days ago we reported on climate change (9 Aug 2021), and the IPCC’s warnings (reverberated throughout the media) that it is now “code red” for civilization. This is spurring calls for “green energy ” solutions to supplant fossil fuels. Well, the Cornell Chronicle just reported this week that “Touted as clean, ‘blue’ hydrogen may be worse than gas or coal.” Hydrogen sounds so clean and beautiful. Blue hydrogen sounds even prettier. Wait till you hear how it is made:

“Blue” hydrogen – an energy source that involves a process for making hydrogen by using methane in natural gas – is being lauded by many as a clean, green energy to help reduce global warming. But Cornell and Stanford University researchers believe it may harm the climate more than burning fossil fuel.

The carbon footprint to create blue hydrogen is more than 20% greater than using either natural gas or coal directly for heat, or about 60% greater than using diesel oil for heat, according to new research published Aug. 12 in Energy Science & Engineering.

Incidentally, two Christian media sites this week reported on the climate hysteria going on. They basically agree with our position.

• John Stonestreet, “Climate Change and The Christian Worldview + Finding Understanding in a Confusing World,” Breakpoint, August 13, 2021.
• John Dawson, “A “code red for humanity”? The latest IPCC climate change report raises the alarm but offers little that’s new,” World Magazine, August 12, 2021.
• Dawson links to another post by By Pierre Lemieux, “Climate Agnosticism,” at the Library of Economics and Liberty. Lemieux gives some reasons for being skeptical of the totalitarians who want to restrict liberty to advance their agenda of fear.

Buried History

The seafloor builds up a record of earth history, doesn’t it? A professor at Washington University at St. Louis has a caveat or two. In a press release, “Muddied waters: sinking organics alter seafloor records,” we learn not to trust our simplistic conclusions.

The remains of microscopic plankton blooms in near-shore ocean environments slowly sink to the seafloor, setting off processes that forever alter an important record of Earth’s history, according to research from geoscientists, including David Fike at Washington University in St. Louis.

Fike shows that the process changes the kinds of signals that can be inferred from seafloor sediments. “We need to be aware of this when trying to extract records of past ‘global’ environmental change,” he warned.

More Racist Insanity

Now fish names are racist, too. Does the phrase “rough fish” bother you? “From art to religion to land use, much of what is deemed valuable in the United States was shaped centuries ago by the white male perspective,” barks some low-IQ demagogue trying to suck up to the Marxists. “Fish, it turns out, are no exception.” Read more if you can stomach it. “The study maintains that the term ‘rough fish’ is pejorative and degrading to native fish.” What’s next, calling the white keys on the piano racist? One wonders how far will this craziness go before sensible people cry, “Enough!”

Think Before You Eat

In New Scientist, James Wong gives some good advice about “toxic” food. “Why is it so hard to say whether plants are toxic or safe?” he asks. He then shows how complicated it is to determine safe and dangerous amounts of various parts of edible plants. Vitamin A, for instance, is necessary but can be toxic in large amounts. Water itself can be dangerous if drunk to excess. Many plant substances can be difficult to run experiments on for ethical reasons. Apricots are great, but the seeds can produce cyanide inside the body. He mentions apricot seeds that some consider a cure for cancer. Wong avoids being an extremist on either side.

Food advice is complicated.

This nuanced, often quite fuzzy, picture of toxicity means that it is indeed technically true to say that all sorts of everyday foods contain toxins, leaving the term open to misinterpretation, particularly if you would like to deploy it to fit a cultural narrative.

Likewise, one might argue, depending on your perspective, that it can mean potentially dangerous foods can be widely sold. That is a real headache for those seeking simple solutions in our beautifully complex world.

This is a worthy article to read as an antidote to some of the claims being made about so-called “toxic foods” or “miracle foods” that accompany website articles.

We could go on and on. These unrelated items illustrate some of the dozens or hundreds of news stories that pass by our desk every day. Many are worth reporting on but time, space and manpower require us to select only a few. Our goal is to help readers to become critical thinkers when encountering claims made in the name of science, so that they can judge whether the epistemic credentials behind the claims are sound or not. “Prove all things,” Paul told the Thessalonians. “Hold fast what is good.”