April 1, 2021

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This article was originally published as a chapter in the book “Design and Catastrophe: 51 Scientists Explore Evidence in Nature"

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Evolution means change. Textbooks in all biological disciplines state that organisms change throughout time, acquiring new characteristics that fit them best to adapt to the environment. However, if the basic engine of evolution is change, why are so many important molecular features so similar in different species that have supposedly been subjected to hundreds of millions of years of evolution? Ever since I started graduate school, I have been amazed by numerous instances where the phrase “highly conserved throughout evolution” is used to “explain” the striking similarities that distinctly different types of organism share at the molecular level. This essay presents a few examples of systems described as “conserved throughout evolution,” arguing that they rather illustrate the wisdom and greatness of an Intelligent Designer.

Histones

The histones are a group of four (H2A, H2B, H3, and H4) basic, positively charged proteins. Two units of each one of them form the nucleosome, a very important structure that plays a key role in chromatin condensation and regulation of genetic expression. To have an idea of what condensation means, think about storing a 2-m-long DNA string inside a 6-µm capsule (nucleus) that has to be enclosed in a 25-µm diameter cell.[1] At this condensation level, a soccer ball would contain enough DNA to cover the distance between the earth and the sun more than 650 times. The interaction between the histone tails and the DNA is important also for the efficient utilization of genetic information by means of replication and transcription present in all eukaryotic cells.

When the amino acid sequences of histones of different organisms were analyzed, scientists concluded that they had been “highly conserved throughout evolution,” because of their high level of similarity in a whole range of organisms from plants to mammals.[2] This conservation includes both the part of the sequence that participates in the DNA folding as well as the part that participates in the regulation of gene expression. These similarities can be explained as the result of Creation by the same Designer. When God designed the nucleus of the eukaryotic cell, He addressed the issue of how to pack its DNA and created the histones. He fine-tuned (2%–20% change) the sequences for the same purpose in different organisms.

Nonsense-Mediated Decay (NMD)

Nonsense-Mediated Decay (NMD) is one of several quality control surveillance systems in cells guaranteeing that the mRNAs translated into proteins are of the appropriate length and that their translation product will be fully functional. The NMD system was first discovered in yeast and nematodes, but has since been documented in all eukaryotes. Several diseases have been associated with aberrant mRNAs that escape this surveillance system.[3] NMD also serves as a fundamental post-transcriptional regulatory mechanism for eukaryotic gene expression. NMD depends on three proteins known as UPF1, UPF2, and UPF3 in yeast. UPF1 participates in the surveillance of the defective mRNA as part of the SURF complex. UPF2 and UPF3 participate more specifically along with UPF1 as part of a complex known as DECID in the degradation of aberrant mRNAs. In organisms as different as yeast, nematodes, fruit flies, and humans, the same mechanism is performed by a set of three similar proteins with the same specific function: surveillance and degradation of aberrant mRNAs. The amino acid sequences and domains of the proteins, as expected, are highly conserved. Again, these similarities can be interpreted as evidence of common design.

Homeobox Genes (Hox)

The Hox genes are so named because mutations in them cause homeotic transformations.[4] In fruit flies these genes determine the identity of insect body segments following the anterior/posterior axis. Researchers have shown that mutations of these Hox genes can put a leg where the antenna should be and make eyes appears on flies’ legs. Experiments comparing Hox genes in chickens and mice showed that the genes controlling where thoracic vertebrae are converted to lumbar vertebrae (not articulating with ribs) are the same.

Even more interesting is that both insects and humans, organisms that are anatomically very different, have several genes in common. In humans, as in fruit flies, these genes control the development of our head to tail anatomy in embryos. Similar genes controlling the development of eyes of insects and humans have been discovered. Development of the eye in mammalian embryos is regulated by the Pax 6 Hox gene. In Drosophila (fruit flies) the Pax 6-like gene is eyeless. Loss-of-function mutations of Pax 6 result in syndromes affecting eye development, and in eyeless, result in loss of eyes in adult flies. Pax-like proteins are found in all higher metazoans and are transcriptional regulators involved in eye formation in all bilaterian animals.[5]

The evolutionary scenario requires that after supposedly 600 million years of evolution of the eye, the genes regulating eye development did not change much, yet produced eyes with radically different structures.

Conclusion

The three examples discussed here are just a few of the hundreds that are routinely presented as “conserved throughout evolution,” and the list continues to grow. Every time I run into a scientific article or textbook addressing an important mechanism as “conserved throughout evolution,” I see it as evidence of an Intelligent Designer who creates what is appropriate for life and uses that basic model for different types of creatures. It can be concluded that all these processes, genes, and proteins are rather “conserved throughout creation,” because they are intelligently designed to be applicable in a variety of living organisms.

NOTES

[1] A Annunziato. DNA packaging: nucleosomes and chromatin. Nature Education 2008; 1(1):26.

[2] AD Baxevanis, D Landsman. Histone sequence database: a compilation of highly-conserved nucleoprotein sequences. Nucleic Acids Research 1996; 24(1):245.

[3] H Xin, W Yanling, W Hua, W Feilong, J Zhenyu, L Tangliang. Nonsensemediated mRNA decay: a “nonsense” pathway makes sense in stem cell biology. Nucleic Acids Research 2018; 46(3):1038–1051.

[4] A Veraksa, M Del Campo, W McGinnis. Developmental patterning genes and their conserved functions: from model organisms to humans. Molecular Genetics and Metabolism 2000; 69(2):85–100.

[5] T Czerny, G Halder, U Kloter, A Souabni, WJ Gehring, M Busslinger. Twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development. Molecular Cell 1999; 3:297–307.

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José A. Cardé-Serrano is an associate professor of biology at the Natural Sciences Department of the University of Puerto Rico, Aguadilla’s Campus. He holds a PhD in Biology from the University of Puerto Rico, Rio Piedras Campus. He teaches several undergraduate and graduate biology labs and classes, and his research interests include the effects of endocrine disrupting chemicals in reptiles, fruit flies, and sea urchins, as well as bioremediation with bacteria.