Structural model at atomic resolution of bacteriophage T4
Creationism's latest hobbyhorse, designed by Michael J Behe to revive the flagging fortunes of his Discovery Institute’s Wedge Strategy and the abysmal failure of his Intelligent [sic] Design ploy to get creationism inserted into the US public school science curricula at US taxpayers' expense, is the silly notion of 'genetic entropy' and 'devolution'.
This unintelligently designed strategy contains the seeds of its own failure at being regarded as a science because it starts off with the assumption that all species were created perfectly by a perfect creator, in compliance with Christian superstition, and so any mutation must be devolutionary away from that perfection. Mutations are called 'genetic entropy', so incorporating the idiotic notion that genetic 'information' is subject to the same law of physics as energy, so the Second Law of Thermodynamic make evolution impossible.
This is supposed to make creationists think Darwin must have been wrong because mutations can't improve fitness, being devolutionary, not evolutionary because of 'genetic entropy'. It ignores the fact that only an improvement in fitness in a given environment can produce more descendants than a deleterious mutation because fitness is defined as the ability to survive and reproduce. How increased fitness can be defined as a reduction in perfection is never explained because Behe 'forgot' to define 'perfection' leaving his marks to assume it means something made by their god.
And this daft notion is now cited by creationists to explain why an intelligent, omniscient and supposedly omnibenevolent god would design parasites. These are now explained as devolved from some initial perfection because of 'genetic entropy' made possible by Adam & Eve's 'sin' - Which is not religious superstition, because it was a historical fact! Got it!
So, we now have an explanation for bacteria, viruses and other parasites, that absolved creationism's god of any responsibility for them while blaming humans for their 'devolution'. However, the problem for this childish nonsense arises when we have parasites on those parasites, such as viruses that infect bacteria - how are bacteria responsible for Adam & Eve's sin and if they aren't why are they being punished for it?
Then it gets even more bizarre when we discover that many bacteria have mechanisms for protecting themselves from these viruses. How can 'devolution' produce an improvement in the organism's ability to survive and reproduce, and in what sense is an improvement a reduction in perfection?
And of course, creationists still have the embarrassment of Behe using the bacteria flagellum as 'proof' that their god indeed designs bacteria and makes them better at doing what it designed them to do, just as it designed the malarial parasite, Plasmodium falciparum, to become resistant to anti-malarial drugs!
The prospect of Michael J Behe trying to defend his 'genetic entropy' and 'devolution' arguments in court the way he abysmally failed to defend his 'intelligent design' creationism as real science in the Kitzmiller trial, is something to look forward to.
That was by way of setting the background for this paper by a team of researcher led by Tian-Min Fu, from Ohio University, published in the journal, Nature Structural & Molecular Biology, sadly behind an expensive paywall, which described how bacteria protect themselves from phage viruses. Their research is explained in an Ohio University news release:
One of the many secrets to bacteria’s success is their ability to defend themselves from viruses, called phages, which infect bacteria and use their cellular machinery to make copies of themselves.
Technological advances have enabled recent identification of the proteins involved in these systems, but scientists are still digging deeper into what those proteins do.
One of the many secrets to bacteria’s success is their ability to defend themselves from viruses, called phages, which infect bacteria and use their cellular machinery to make copies of themselves.
Technological advances have enabled recent identification of the proteins involved in these systems, but scientists are still digging deeper into what those proteins do.
We think the two proteins need to form the complex to play a role in phage prevention, but we also believe one protein alone does have some anti-phage function. The full role of the second protein needs to be further studied.
Zhangfei Shen, co-lead author
Department of Biological Chemistry and Pharmacology
Center for RNA Biology
The Ohio State University, Columbus, OH, USA.
The findings add to scientific understanding of microorganisms’ evolutionary strategies and could one day be translated into biomedical applications, researchers say.
Shen and co-lead author Xiaoyuan Yang, a PhD student, work in the lab of senior author Tianmin Fu, assistant professor of biological chemistry and pharmacology at Ohio State.
The study was published April 16 in Nature Structural & Molecular Biology.
The two proteins that make up this defense system are called Gabija A and Gabija B, or GajA and GajB for short.
Researchers used cryo-electron microscopy to determine the biochemical structures of GajA and GajB individually and of what is called a supramolecular complex, GajAB, created when the two bind to form a cluster consisting of four molecules from each protein.
In experiments using Bacillus cereus bacteria as a model, researchers observed the activity of the complex in the presence of phages to gain insight into how the defense system works.
Though GajA alone showed signs of activity that could disable a phage’s DNA, the complex it formed with GajB was much more effective at ensuring phages would not be able take over the bacterial cell.
That’s the mysterious part. GajA alone is sufficient to cleave the phage nucleus, but it also does form the complex with GajB when we incubate them together. Our hypothesis is that GajA recognizes the phage’s genomic sequence, but GajB enhances that recognition and helps to cut the phage DNA.
Xiao-Yuan Yang, co-lead author
Department of Biological Chemistry and Pharmacology
Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
The large size and elongated configuration of the complex made it difficult to get the full picture of GajB’s functional contributions when bound to GajA, Shen said, leaving the team to make some assumptions about protein roles that have yet to be confirmed.
We only know GajB helps enhance GajA activity, but we don’t yet know how it works because we only see about 50% of it on the complex.
Zhangfei Shen.
One of their hypotheses is that GajB may influence the concentration level of an energy source, the nucleotide ATP (adenosine triphosphate), in the cellular environment – specifically, by driving ATP down upon detection of the phage’s presence. That would have the dual effect of expanding GajA’s phage DNA-disabling activity and stealing energy that a phage would need to start replicating, Yang said.
There is more to learn about bacterial anti-phage defense systems, but this team has already shown that blocking virus replication isn’t the only weapon in the bacterial arsenal. In a previous study, Fu, Shen, Yang and colleagues described a different defense strategy: bacteria programming their own death rather than letting phages take over a community.
This work was supported by the National Institute of General Medical Sciences.
Additional co-authors are Jiale Xie, Jacelyn Greenwald, Ila Marathe, Qingpeng Lin and Vicki Wysocki of Ohio State, and Wenjun Xie of the University of Florida.
Abstract
As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.
Yang, XY., Shen, Z., Xie, J. et al.
Molecular basis of Gabija anti-phage supramolecular assemblies. Nat Struct Mol Biol (2024). https://doi.org/10.1038/s41594-024-01283-w
© 2024] Springer Nature.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.
I wonder if any creationist can explain how parasites evolving resistance to other parasites can be explained by one of the various Behe/Discovery Institute political anti-science strategies, like 'intelligent [sic] design', 'genetic entropy' or 'devolution'.
The Unintelligent Designer: Refuting The Intelligent Design Hoax
ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.
Available in Hardcover, Paperback or ebook for Kindle
The Malevolent Designer: Why Nature's God is Not Good
This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.
Illustrated by Catherine Webber-Hounslow.
Available in Hardcover, Paperback or ebook for Kindle
Illustrated by Catherine Webber-Hounslow.
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