Creationism in Crisis
What on Earth was the 'Designer' Thinking?
What on Earth was the 'Designer' Thinking?
Credit: Lenora Martinez-Nunez
The ‘Rapunzel’ virus: an evolutionary oddity
Figure 2
Intra- and inter-ring interactions. A The primary intra-ring interface between two subunits (green and cyan) within a ring. B Schematic quantifying interactions from a single subunit (α) to illustrate the extensive, cooperative network. Numbers and line widths (not lengths) correspond to quantification of the interactions between α and neighboring subunits as calculated by the PDBePISA server (Supplementary Tables 3 and 4). C Surface representation of two subunits reveals a ball and socket geometry between rings. A single subunit (orange) has two loops (Loop1 and Loop2) that fit into sockets (Socket1 - gray, and Socket2 - white) of a subunit in the ring below it (green). D Surface electrostatics of ring interfaces demonstrate an important role for electrostatics in inter-ring interactions.
Intra- and inter-ring interactions. A The primary intra-ring interface between two subunits (green and cyan) within a ring. B Schematic quantifying interactions from a single subunit (α) to illustrate the extensive, cooperative network. Numbers and line widths (not lengths) correspond to quantification of the interactions between α and neighboring subunits as calculated by the PDBePISA server (Supplementary Tables 3 and 4). C Surface representation of two subunits reveals a ball and socket geometry between rings. A single subunit (orange) has two loops (Loop1 and Loop2) that fit into sockets (Socket1 - gray, and Socket2 - white) of a subunit in the ring below it (green). D Surface electrostatics of ring interfaces demonstrate an important role for electrostatics in inter-ring interactions.
Agnello, et. al., (2023), Journal of Biological Chemistry
In addition, Creationists believe one of two things:
- Their god didn't know when he created the mythical founder couple, Adam & Eve, that this would result in this 'sin' thing being created.
- It did know, but created them anyway, presumably not understanding the consequences.
I form the light, and create darkness: I make peace, and create evil: I the Lord do all these things.And they also believe that their god created everything on Earth for his special creation, them of course, or more generally, all humans
Isiah 47:7
Not for the first time, Creationism requires its dupes to believe two or more mutually exclusive things simultaneously.
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So, with that in mind, imagine being a Creationist and trying to understand what on Earth your magic god was trying to achieve when it created bacteria, then created the phage viruses to parasitise them, described in the research by a team from the Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA, USA.
Their research is published open access in the Journal of Biological Chemistry and described in the magazine for the American Society for Biochemistry and Molecular Biology (ASBMB). It describes a phage virus, P74-26, nicknamed the “Rapunzel bacteriophage”, with an extraordinarily long 'tail' which is capable of parasitising even extremophile bacteria that live in hot springs where temperatures can reach 170oC. Neither these bacteria nor the phage virus appear to have any benefit to mankind.
The study was to determine the construction and function of the very long 'tail'.
The discovery was of something that the Creationist idol, Michael J Behe would undoubtedly proclaim as 'irreducibly complex', therefore proof that the locally popular god did it.
To make matters worse for Creationists, the study casually and unintentionally refutes one of the lies that their cult leaders fool them with - that the Theory of Evolution (TOE) is being increasingly rejected by mainstream biologists in favour of their childish, magical and supernatural explanation. The scientists who did the study are in no doubt that the 'tail' is a product of an evolutionary process and that the TOE is a perfect model for explaining and understanding the observed facts.
From the ASBMB magazine:
A recent study in the Journal of Biological Chemistry has revealed the secret behind an evolutionary marvel: a bacteriophage with an extremely long tail. This extraordinary tail is part of a bacteriophage that lives in inhospitable hot springs and preys on some of the toughest bacteria on the planet.
Bacteriophages are a group of viruses that infect and replicate in bacteria and are the most common and diverse things on Earth.
The bacteriophage P74-26 has a tail 10 times longer than most other phage tails and is nearly 1 micrometer long, about the width of some spider’s silk.Angnello, et al.(2023) Journal of Biological ChemistryUnlike many of the viruses that infect humans and animals that contain only one compartment, phages consist of a tail attached to a spiky, prismlike protein shell that contains their DNA.Bacteriophages, or phages for short, are everywhere that bacteria are, including the dirt and water around you and in your own body’s microbial ecosystem as well.
Each phage tail is made up of many small building blocks that come together to form a long tube. Our research finds that these building blocks can change shape, or conformation, as they come together. This shape-changing behavior is important in allowing the building blocks to fit together and form the correct structure of the tail tube.
We used a technique called cryo-electron microscopy, which is a huge microscope that allows us to take thousands of images and short movies at a very high magnification. By taking lots of pictures of the phage’s tail tubes and stacking them together, we were able to figure out exactly how the building blocks fit together.
Bacteriophages are gaining ever-growing interest as an alternative to antibiotics for treating bacterial infections. By studying phage assembly, we can better understand how these viruses interact with bacteria, which could lead to the development of more effective phage-based therapies. … I believe that studying unique, interesting things can lead to findings and applications that we can’t even yet imagine.
Emily Agnello, first author
Department of Biochemistry and Molecular Biotechnology
University of Massachusetts Chan Medical School
Worcester, MA, USA.
Phage tails, like hairstyles, vary in length and style; some are long and bouncy while others are short and stiff. While most phages have short, microscopic tails, the “Rapunzel bacteriophage” P74-26 has a tail 10 times longer than most and is nearly 1 micrometer long, about the width of some spider’s silk. The “Rapunzel” moniker is derived from the fairy tale in which a girl with extremely long hair was locked in a tower by an evil witch.
Brian Kelch, an associate professor of biochemistry and molecular biotechnology at UMass Chan who supervised the work, described P74-26 as having a “monster of a tail.”
Compared with most phages, P74-26 uses half the number of building blocks to form stacking rings that make up the tail.transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall; the magnification is approximately 200,000.Professor Graham Beards, (Wikimedia Commons)
Phage tails are important for puncturing bacteria, which are coated in a dense, viscous substance. P74-26’s long tail allows it to invade and infect the toughest bacteria. Not only does P74-26 have an extremely long tail, but it is also the most stable phage, allowing it to exist in and infect bacteria that live in hot springs that can reach over 170° F. Researchers have been studying P74-26 to find out why and how it can exist in such extreme environments.
To work with a phage that thrives in such high temperatures, Agnello had to adjust the conditions of her experiments to coax the phage tail to assemble itself in a test tube. Kelch said Agnello created a system with which she could induce rapid tail self-assembly.
The researchers used high-power imaging techniques as well as computer simulations and found that the building blocks of the tail lean on each other to stabilize themselves.I like to think about these phage building blocks as kind of like Legos. The Lego has studs on one side and the holes or sockets on the other. Imagine a Lego where the sockets start off closed. But as you start to build with the Legos, the sockets begin to open up to allow the studs on other Legos to build a larger assembly. This movement is an important way that these phage building blocks self-regulate their assembly.
We think what has happened is that some ancient virus fused its building blocks into one protein. Imagine two small Lego bricks are fused into one large brick with no seams. This long tail is built with larger, sturdier building blocks. We think that could be stabilizing the tail at high temperatures.
Brian A. Kelch, corresponding author
Department of Biochemistry and Molecular Biotechnology
University of Massachusetts Chan Medical School
Worcester, MA, USA
They found P74-26 uses a “ball and socket” mechanism to sturdy itself. In addition, the tail is formed from vertically stacking rings of molecules that make a hollow canal.
Kelch pointed out that, compared with most phages, P74-26 uses half the number of building blocks to form stacking rings that make up the tail.
The researchers now plan to use genetic manipulation to alter the length of the phage tail and see how that changes its behavior.
Phages occupy almost every corner of the globe and are important to a variety of industries like healthcare, environmental conservation and food safety. In fact, long-tailed phages like P74-26 have been used in preliminary clinical trials to treat certain bacterial infections.
More technical detail is given in the teams open access paper in the Journal of Biological Chemistry:
Creationists also argue that bacteria and viruses were created by 'sin' in some unexplained magical process, so this 'sin' thing is designing parasites to attack the parasites it creates!
It takes some special mental gymnastics to believe these organisms and the relationships between them are the result of an intelligent design process and not the result of a mindless, utilitarian natural process in which neither magic nor magicians was involved.
AbstractSo, from a Creationist point of view, a massively complex solution to the problem of how to get through the defences of a bacterium that was designed to protect it from viruses in order to kill bacteria that, because they inhabit such extreme conditions, are or complete indifference to humans, being neither harmful nor harmless.
Tail tube assembly is an essential step in the lifecycle of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their long, flexible tail tubes. The hyperthermophilic phage P74-26 is particularly intriguing as it has the longest tail of any known virus (nearly 1 μm) and is the most thermostable known phage. Here, we use structures of the P74-26 tail tube along with an in vitro system for studying tube assembly kinetics to propose the first molecular model for the tail tube assembly of long-tailed phages. Our high resolution cryo-EM structure provides insight into how the P74-26 phage assembles through flexible loops that fit into neighboring rings through tight “ball-and-socket”-like interactions. Guided by this structure, and in combination with mutational, light scattering, and molecular dynamics simulations data, we propose a model for the assembly of conserved tube-like structures across phage and other entities possessing Tail Tube-like proteins. We propose that formation of a full ring promotes the adoption of a tube elongation-competent conformation among the flexible loops and their corresponding sockets, which is further stabilized by an adjacent ring. Tail assembly is controlled by the cooperative interaction of dynamic intra- and inter-ring contacts. Given the structural conservation among tail tube proteins and tail-like structures, our model can explain the mechanism of high-fidelity assembly of long, stable tubes.
Agnello, Emily; Pajak, Joshua; Liu, Xingchen; Kelch, Brian A.
Conformational dynamics control assembly of an extremely long bacteriophage tail tube
Journal of Biological Chemistry; (2023). DOI: 10.1016/j.jbc.2023.103021
Copyright: © 2023 The authors.
Published by Elsevier Inc. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Creationists also argue that bacteria and viruses were created by 'sin' in some unexplained magical process, so this 'sin' thing is designing parasites to attack the parasites it creates!
It takes some special mental gymnastics to believe these organisms and the relationships between them are the result of an intelligent design process and not the result of a mindless, utilitarian natural process in which neither magic nor magicians was involved.
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