Unintelligent Design
How to Make a Ludicrously Complex Genome for No Apparent Reason
How to Make a Ludicrously Complex Genome for No Apparent Reason
The scientists analyzed several gigabyte of microbial DNA sequences.
Stowaways in the Genome – Universität Innsbruck
Distribution of endogenous MCP clusters across 462 genomes from 238 protist species. MCP clusters (25% identity across 30% length, 73 clusters) are shown as inner circles scaled in size according to the number of MCPs in each cluster. Numbers refer to the MCP cluster number assigned, with the larger viral groups labeled. MCP clusters are connected to the eukaryotic species (based on NCBI taxonomy) they are found in. Clusters with a more diverse host range are drawn closer to the center of the plot.
A. Nothing! They both look like no intelligence was involved in their design, because they will both have masses of waste, ludicrous complexity, and no ultimate purpose, other than making more copies of themselves.
Although creationists have been programmed to point to complexity as evidence of design, it is actually evidence of bad (or no) design, because good, intelligent design is minimally complex.
This point was neatly illustrated in a paper published in PNAS a couple of days ago which showed that the genome of single-celled, eukaryote organisms contains ancient 'fossil' endogenous retroviruses (ERVs) that do nothing but need to be replicated every time the organism replicates, wasting resources and risking error. Altogether the team found remnants of over 30,000 such viruses.
The discovery was made by a group of researchers led by Dr. Christopher Bellas and colleagues from the University of Innsbruck, Austria, with colleagues from the University of Groningen, The Netherlands and Max Planck Institute for Medical Research, Heidelberg, Germany.
The team were interested in the new 'Polinton-like viruses' that two of the team had previously found in protista from an Austrian alpine lake. According to my AI software, ChatGPT:
Polinton-like viruses (PLVs) are a group of large DNA viruses that are found in a variety of eukaryotic hosts, including protists, fungi, and animals. They are named after the first identified member of this group, the Polinton virus (also known as Tlr1), which was found in the genome of the unicellular green alga, Ostreococcus tauri.The University of Innsbruck news release explains the research:
> PLVs are characterized by their unique genome structure, which is similar to that of transposable elements called Polintons or Mavericks. Like Polintons and Mavericks, PLVs have large, non-coding regions flanked by terminal inverted repeats (TIRs) and contain multiple open reading frames (ORFs) that encode for various viral proteins, such as DNA polymerase, helicase, and capsid proteins. However, unlike Polintons and Mavericks, PLVs are able to replicate and form virions, making them true viruses.
PLVs are considered to be a distinct group of viruses based on their genome structure and phylogenetic analysis of their conserved proteins. They have been found to infect a diverse range of eukaryotic hosts, including animals, plants, and protists, suggesting that they have a broad host range. The biological significance of PLVs is not well understood, but they are believed to play a role in the evolution of their host organisms by contributing to horizontal gene transfer and genome rearrangement.
Overall, PLVs are an interesting and poorly understood group of viruses that are characterized by their unique genome structure and ability to infect a wide range of eukaryotic hosts.
References:
- Krupovic, M., Koonin, E. V., & Yutin, N. (2019). Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nature Reviews Microbiology, 17(3), 184-198.
- Koonin, E. V., & Dolja, V. V. (2014). Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303.
- Arslan, D., Legendre, M., Seltzer, V., Abergel, C., & Claverie, J. M. (2011). Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proceedings of the National Academy of Sciences, 108(42), 17486-17491.
ChatGPT. (2023, April 12). What are 'Polinton-like viruses'? [Msg 1234]. Message posted to https://openaidialogbot.com/chatgp
At the University of Innsbruck, scientists have discovered over 30,000 viruses by using the high-performance computer cluster “Leo” and sophisticated detective work. The viruses hide in the DNA of unicellular organisms. In some cases, up to 10% of microbial DNA consists of built-in viruses.I can almost hear creationists shouting jubilantly, "but they had a purpose! They protected the organisms from other viruses!"
During a large-scale study of complex single-celled microbes, Dr. Christopher Bellas, Marie-Sophie Plakolb and Prof. Ruben Sommaruga from the Department of Ecology at the University of Innsbruck made an unexpected discovery. Built into the genome of the microbes, they found the DNA of over 30,000 previously unknown viruses. This "hidden" DNA may allow the replication of complete and functional viruses in the host cell.
These viruses do not appear to harm their hosts. On the contrary, some may even protect them. Many appear to be similar to so-called virophages. These viruses infect and destroy other, harmful viruses that infect their host cell.We were very surprised by how many viruses we found through this analysis. In some cases, up to 10% of a microbe's DNA turned out to consist of hidden viruses.
Why so many viruses are found in the genomes of microbes is not yet clear. Our strongest hypothesis is that they protect the cell from infection by dangerous viruses.
Initially, we wanted to find the origin of the new 'Polinton-like viruses' with our study, however, we did not know which organisms are usually infected by these viruses. That's why we conducted a large-scale study to test all microbes whose DNA sequences are known.
Dr. Christopher Bellas, lead author
Department of Ecology
University of Innsbruck, Innsbruck, Austria
The study, financed by the Austrian Science Fund (FWF), was published in the renowned journal "Proceedings of the National Academy of Sciences (PNAS)" and was carried out in collaboration with researchers from the Max Planck Institute for Medical Research and the University of Groningen.
Viruses as protectors
From bacteria to humans, all life forms are continuously infected with viruses. Some are constantly present, but only occasionally trigger symptoms, such as the herpes virus in humans. Others hide even deeper, becoming part of their host’s DNA. This study found that many of the Earth's abundant single-celled eukaryotic (complex) organisms are packed with viruses. These organisms are found everywhere, and include abundant algae in lakes and oceans, amoebae in soil, as well as human parasites.
Many eukaryotic single-celled organisms are infected by "giant viruses", a group of viruses that can be as large as bacteria. These infections kill the host as they create new copies of the giant virus. However, when a virophage resides in the host cell, it ‘reprograms’ the giant virus to build virophages. As a result, the giant virus can sometimes be fended off and the host cell population is saved from destruction.
The DNA of the newly discovered viruses is similar to virophage DNA. Therefore, it is probable that the host microbes protect themselves from giant viruses through these built-in viruses.
DNA from an alpine lake
The research project was originally based on a new group of viruses that Bellas and Sommaruga discovered in the water of the Gossenköllesee in Tyrol, Austria, in 2021.
The huge data set which the researchers examined only contains DNA sequences, i.e. a sequence of the letters ATGC from which all genes are encoded. Nevertheless, the data set consists of several hundred gigabytes.
The sequences of viruses, tiny by comparison, could only be found in this large amount of data thanks to state-of-the-art technology. With the high-performance computer cluster "Leo" of the University of Innsbruck, the data set could be analysed quickly. DNA sequences from microbes were also read using the new Oxford Nanopore technology. With this technology, DNA is passed through tiny pores in a membrane. Each base – A, G, C or T – interrupts an electric current and thus generates a signal from which the DNA sequence can be read.
In the end, the researchers found much more than the viruses they were looking for. This unexpected discovery will inspire more research to study the roles that these viruses play.
That of course begs the question, why would an intelligent designer design viruses to harm the organisms then design other viruses to protect them? And even if you can think of some convoluted, logic-defying answer to that, it still leaves another little problem, and another difference between something intelligently designed and something that evolved naturally: an intelligent designer would then remove the remnants of the virus once they become useless, not leave them hanging around to be reproduced endlessly through the generations for no apparent reason. Evolution, on the other hand, has no reverse gear and can't undo mistakes once they've been inserted in the genome, unless very slowly over deep time at a rate dependent entirely on chance, and which might not happen anyway.
The scientists' paper in PNAS contains more detail:
SignificanceAll explainable as the result of the evolutionary history of these protista, naturally, and not a hint from the scientists that the Theory of Evolution is inadequate as an explanatory model. And all totally inexplicable as the result of intelligent design.
Protists are a diverse collection of predominantly unicellular eukaryotic organisms that are not animals, plants, or fungi. They make up most of the eukaryotic tree of life, are major components of nearly all ecosystems and are critical for carbon and nutrient cycling. In this study, we found that large parts of protist genomes are viral in origin and that these viral integrations are comparable in scale to prophage integrations in bacterial genomes. Protist EVEs were distantly related to virophages, a group of viruses which parasitize on larger “giant viruses” that infect and kill their eukaryotic hosts. Many EVEs appear to be functional viruses, which suggests that diverse arrays of these elements may be part of a host antivirus system.
Abstract
Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be “genomic fossils.” Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.
Fig. 4
Network analysis showing the relationships between the major capsid proteins from Maverick–Polintons, PLVs, and virophages in eukaryotic genomes. All MCP genes were retrieved from publicly available protist genomes, published works, and environmental metagenomes. To reduce complexity, protist-encoded MCP genes were clustered at 90% nucleotide identity for each individual host genome. Selected species important to the narrative are labeled. Colors represent the genome from which the MCP was retrieved, labeled circles represent the wider virus group to which they belong, designated by MCP type. Light blue diamonds show metagenomically detected MCP genes (17) clustered at 70% identity to reduce numbers, a black border highlights those detected in virus only metagenomes. Initially reported Polinton (14) and Adintovirus (13) MCP genes are shown in black, and vertebrate Mavericks (15) are shown in dark blue (all clustered at 90% identity). Lines (edges) represent a BLASTP alignment at an expectation threshold of <1 × 10−4. Blue abbreviations denote isolated viruses: TSV, Tetraselmis striata virus; PgVV, Phaeocystis globosa virus virophage (Gezel-14T). Bold names denote virus groups, with GKS 1-3 and Trimcap referring to groups described by Bellas and Sommaruga (17). MMN, PaM1-2, and Dino are groups of MCP genes defined in this study. Numbers denote major MCP protein clusters as shown in Fig. 1 and in detail in SI Appendix, Table S4.Bellas, C; Hackl, T; Plakolb,M-S; Koslová,A; Fischer, M.G; Sommaruga, R.
Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses.
PNAS, April 10, 2023. https://doi.org/10.1073/pnas.2300465120
Copyright: © 2023 The authors.
Published by PNAS. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
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