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DNA Repair, Fish Shape, Epigenetics: Science Advances, Darwin-Free

Evolution News

Darwin

According to a robotically repeated talking point favored by evolution proponents, loyal adherence to Darwin’s theory is crucial to the future of biological research. Informing the public, including students, about the theory’s weaknesses as well as its strengths would thus threaten not only the pursuit of knowledge for its own sake. It would even put lives in peril, since medical research would be handicapped. This might or might not explain the addled logic of a phone message we got over the past weekend from a critic of intelligent design who threatened that ID proponents are guilty of “treason” and should be handled by the law accordingly.

Yikes! Endangering your country’s health and wellbeing, if that were the case, would certainly not be a laudable act. But is a skeptical view of Darwinian theory really “anti-science,” as other critics like to say? Well, when you find something amazing, and there are countless amazing things in biology, you want to understand it. Does that require a Darwinian just-so story? These news items show otherwise. Students might become more motivated to study science, in fact, if given a sense of awe at nature’s wonders, without the usual appeals to happenstance.

DNA Repair

News from New York University begins without Darwin, and continues to approach the subject of DNA repair free of evolutionary shackles.

A team of scientists has identified how damaged DNA molecules are repaired inside the human genome, a discovery that offers new insights into how the body works to ensure its health and how it responds to diseases that stem from impaired DNA. [Emphasis added.]

Isn’t that better than “how the body evolved to ensure its health”? They continue with awe-inspiring facts, such as the surprising note that the human genome suffers about a thousand DNA breaks per day in each of us — breaks that could cause cancer or death if not repaired.

“Our findings show that a DNA repair process is very robust, engineered through intricate structural and dynamical signatures where breaks occur,” explains Alexandra Zidovska, an assistant professor in New York University’s Department of Physics and the senior author of the study, which appears in Biophysical Journal. “This knowledge can help us understand human genome in both healthy and disease-stricken states — and potentially offer a pathway for enhancing cancer diagnosis and therapy.”

The human genome consists, remarkably, of two meters of DNA molecules packed inside a cell nucleus, which is ten micrometers in diameter. The proper packing of the genome is critical for its healthy biological function such as gene expression, genome duplication, and DNA repair. However, both the genome’s structure and function are highly sensitive to DNA damage, which can range from chemical change to the DNA molecule to full break of DNA’s well-known double helix.

The scientists made DNA glow green, and introduced breaks that glowed red. Watching the reactions, they found that broken areas became denser and moved more quickly as repair processes acted on them. No evolution was required to increase understanding that could potentially better our health.

“The human genome is constantly exposed to events that damage the DNA molecule,” notes Zidovska. “The cell has robust repair processes that work to eliminate such damage before it can give cause to cancer or other diseases. Now we have a better understanding of how a DNA break behaves differently than the undamaged DNA, which allows us not only to gain insight into these repair processes but also inform our efforts in cancer diagnosis and therapy.”

Fish Shape

Those who like to bake salmon have undoubtedly been struck by the chevron shapes in the muscles. All fish have this characteristic pattern, which “is thought to increase swimming efficiency,” according to research from the National University of Singapore (NUS). How does the pattern come about? Is it genetically driven, or is there some other process at work? The scientists didn’t even consider Darwinian evolution as they sought the answer.

A team of scientists led by MBI Postdoctoral Fellow Dr Sham Tlili and Principal Investigator Assistant Professor Timothy Saunders studied chevron formation in the myotome of zebrafish embryos. Initially, each future developing myotome segment is cuboidal in shape. However, over the course of five hours, it deforms into a pointed ‘V’ shape. To find out how this deformation actually takes place, the team adopted a combination of different techniques — imaging of the developing zebrafish myotome at single cell resolution; quantitative analysis of the imaging data; and fitting the quantitative data into biophysical models.

Based on findings from their experimental as well as theoretical studies, the MBI scientists identified certain physical mechanisms that they thought might be guiding chevron formation during fish development.

The chevron patterns in the myotome (the muscle connected to the longitudinal nerve) “do not simply arise from genetic instruction or biochemical pathways but actually require physical forces to correctly develop.” Because they are physically connected to the center and the sides, which grow at different rates, the patterns develop “by different amounts of friction” that are generated as the embryo grows. This is interesting because it is not genetically based. Instead, “temporally and spatially varying biophysical forces play a role in determining the form of an organism.”

Can Darwin-free research stimulate the interest of scientists? 

Asst Prof Saunders, a theoretical physicist who applies physical principles to characterise biological processes that take place during development, said, “This work reveals how a carefully balanced interplay between cell morphology and mechanical interactions can drive the emergence of complex shapes during development. We are excited to see if the principles we have revealed are also acting in the shaping of other organs.”

 Notably, several mentions of evolution in the PNAS paper have nothing to do with Darwinism, but rather with the unfolding (“evolution”) of the patterns during development. One brief exception mentions that “the shape is tightly controlled and may be evolutionarily optimized.” Performing a Darwin-ectomy on that sentence would cause no harm to the science.

Epigenetics

Another paper in PNAS about epigenetics does perfectly fine without appeals to Darwinian evolution. The “Perspective” article by Aristizabel et al., “Biological embedding of experience: A primer on epigenetics,” includes only one reference to “evolutionary time”:

The relationship between the genome and epigenome is complex and bidirectional. For instance, methylated cytosines are prone to mutation, changing the genome with potential consequences for individuals during their lives and species over evolutionary time.

Whether the idea of “potential consequences” over “evolutionary time” adds meat or fat to the paper, readers can decide. Suffice it to say that the bulk of the paper talks about epigenetic mechanisms, such as methylation, that record environmental influences in genomes. The authors seek to identify causal links between experiences that can be recorded in the epigenome.

In this primer, we explore epigenetic systems as candidate mechanisms for the biological embedding of experience. For clarity, we adopt an inclusive definition of epigenetics proposed by the NIH Epigenomics Roadmap Project initiative, which states, “Epigenetics refers to both heritable changes in gene activity and expression (in the progeny of cells or of individuals) and also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable”.

If evolution were essential to this important research in a burgeoning field, the authors most certainly would have said so. Instead, they focus on “selected examples from the literature to illustrate key points of interest,” using the word “mechanism” 18 times and “system” 11 times words indicative of foresight and planning.

As more scientific research proceeds in the absence of references to unguided evolution, science will get stronger, leaner, and more motivated. Let the Darwin stories go, and free up science for a resurgence of awe and wonder that first motivated early scientists.

Photo: The human genome suffers about a thousand DNA breaks per day in each of us, thus requiring ongoing DNA repair, by Tom Ellenberger, Washington University School of Medicine in St. Louis. [Public domain].