Evolution Intelligent Design

Do viruses play a hidden role in evolution?

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Stories like this raise that question:

Viruses are justly feared as ingenious pathogens, causing diseases in everything they invade, including virtually all bacteria, fungi, plants and animals. Recent advances in the field of virology, however, suggest that viruses play a more significant and complex role than previously appreciated, and may be essential to the functioning of diverse ecosystems…

Intriguingly, a number of insect-transmitted plant viruses may have evolved mechanisms to influence vector behavior, making infected plants more attractive to sap-feeding insects or ensuring that infected plants produce chemicals that promote insect behaviors that help facilitate transmission.

In addition to their complex and varied chains of infection, some plant viruses have another unique property. Such viruses transmit their genomes in multiple packets, each containing only part of the virus’ complete genetic code, encapsulated in a separate virus particle. This peculiar strategy, which requires the co-transmission of several viral particles to a new host in order to ensure the integrity of the viral genome, is a feature believed to be unique to plant viruses. The nature and evolution of these so-called multipartite viruses remains a biological puzzle.

Plant viruses display considerable ingenuity in their strategies, which are highly dependent on their given environment. Some are generalists, invading multiple species, while other viruses are specialists that favour a narrow range of plant hosts. This selectivity may develop with time, through a process known as adaptive radiation. This typically occurs when a virus faces a heterogeneous habitat and becomes adaptively specialized to exploit particular ecological resources while becoming maladapted to exploit others. Such specialization acts to limit competition between different viral lineages or species. Alternatively, generalist viruses infect multiple plant hosts but must compete for these resources with other viruses. This situation tends to result in a viral population of low diversity dominated by the most acutely adapted viral genotypes.

Biodesign Institute, “Plant viruses may be reshaping our world” at Arizona State University

Viruses seem to be everywhere, doing a lot of things, with apparent “ingenuity.” Maybe a discovery down the road will be that they cause many changes currently interpreted according to some Darwinian theory (kin selection, costly fitness, what have you … )

Here’s the article (paywall). \

See also: Virus expert highlights the conflict over whether viruses are alive In short, it is an open question. The question relates to the role viruses can play in evolution, among other things. Are they precursors of life, detritus of life, or something in between? Or all three? Keep the file open. 

Viruses invent their own genes? Then what is left of Darwinism?

Why viruses are not considered to be alive

Another stab at whether viruses are alive

Phil Sci journal: Special section on understanding viruses

Should NASA look for viruses in space? Actually, it’s not clear that RNA came first. Nor is it clear that viruses precede life. A good case can doubtless be made for viruses being part of the scrap heap of existing life. But no matter. If you think you can find viruses in space, boldly go.

Why “evolution” is changing? Consider viruses

The Scientist asks, Should giant viruses be the fourth domain of life? Eukaryotes, prokaryotes, archaea… and viruses?

Viruses are alive.

and

Are viruses nature’s perfect machine? Or alive?

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8 Replies to “Do viruses play a hidden role in evolution?

  1. 1
    Brother Brian says:

    What hidden role? We have known that retro viruses can insert their genes in host cells for many decades. And we know that they can, if inserted in the right cells, be transferred to the next generation. As such, they obviously play a role in evolution. Nothing hidden about it.

  2. 2
    Belfast says:

    Brian, get a grip.
    The question is do viruses play another role (hidden) in addition to the ones we already know.

  3. 3
    Brother Brian says:

    Belfast

    Brian, get a grip.
    The question is do viruses play another role (hidden) in addition to the ones we already know.

    Again, this is not new. It has long been known that some viruses can change the behaviour of their hosts in such a way to enhance their transmission. This is also found in many parasites. There is a parasite that requires two hosts (ants and sheep) to complete its life cycle. An ant infected by the parasite changes its behaviour resulting in the ant climbing to the top of blades of grass. This then makes them more susceptible to being eaten by sheep. Another one (toxoplasmosis) requires two hosts (cats and mice). An infected mouse is attracted to cat urine. I think you know what happens next.

    I’m not arguing against the complexity of these behavioural changes. I am just arguing against the idea that these are new or hidden effects.

  4. 4
    ET says:

    Perhaps Brian should at least read the article, if not the paper the article is based on, BEFORE running its mouth. He doesn’t seem to have a clue what it is about.

  5. 5
    martin_r says:

    Viruses – my favorite topic.

    Viruses are the most abundant organism on Earth, 10 x more than bacteria, but the theory of evolution can’t explain the existence of viruses. You can not use the concept of common descent when talking about viruses – the theory of evolution fails …

    Most abundant organism on Earth and the theory of evolution can not describe its existence 🙂

    I can’t understand why evolutionists are so self-confident ?

    Most laymen don’t realize it, but viruses are completely different system compared to cellular life.

    From Virology.ws:

    “Viruses don’t have a structure derived from a common ancestor
    Cells obtain membranes from other cells during cell division. According to this concept of ‘membrane heredity’, today’s cells have inherited membranes from the first cells that evolved, and provides evidence that cells are derived from a common ancestor. Viruses have no such inherited structure.”

    And, it gets worse:

    “Viruses are polyphyletic
    In a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors. Viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins.”

    Many evolutionary origins !!!

    Many evolutionary origins of viruses – it is like to explain the origin of life 1000x times over and over 🙂

  6. 6
    martin_r says:

    Brother Brian mentioned endogenous retroviruses (ERVs) – and how ERVs can insert into genomes in order to change it …

    Brother Brian,
    are you aware of this ?

    The evolution of placenta, the same retroviral gene was ‘co-opted’ 7 times independently for the same purpose (evolution of placenta) in various mammals :)))
    What is wrong with you guys?

    “Domestication of the syncytin genes represents a dramatic example of convergent evolution via the cooption of
    a retroviral gene for a key biological function in reproductive biology. In fact, syncytin domestication from
    a retroviral envelope gene has been previously shown to have independently occurred at least seven times during
    mammalian evolution ”

    https://www.pnas.org/content/109/7/2184

  7. 7
    OLV says:

    Martin_r,

    that’s an interesting paper you linked to. Thanks.

    Here’s a related one:

    The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification
    Mona Abed,Erik Verschueren,Hanna Budayeva,Peter Liu,Donald S. Kirkpatrick,Rohit Reja,Sarah K. Kummerfeld,Joshua D. Webster,Sarah Gierke,Mike Reichelt,Keith R. Anderson,Robert J. Newman,Merone Roose-Girma,Zora Modrusan,Hazal Pektas,Emin Maltepe,Kim Newton,Vishva M. Dixit

    PLOS   DOI: 10.1371/journal.pone.0214110

    Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotransposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiating TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.

    Transposable elements (TEs) are one of the biggest threats to the integrity of prokaryotic and eukaryotic genomes because their insertion into coding or regulatory regions could disrupt essential genes [13]. Therefore, TEs are often inactivated through mutagenesis [4] or silenced through methylation [5]. Some TEs, however, have been repurposed during evolution for the benefit of the host in a process termed domestication [6], and have important roles in development and immunity [710].

    In summary, despite its domestication, Peg10 maintains several hallmarks of retroviral and retrotransposon Gag proteins. The Gag domain of PEG10 supports the budding of virus-like particles, which are released from the cell and can be recovered from exosome preparations. ARC (activity regulated cytoskeletal-associated protein) is another retroviral-like Gag protein that drives the budding of extracellular vesicles [5152]. ARC, like PEG10, binds to its own mRNA. The release and uptake of Arc-containing VLPs by neurons is considered a mechanism of intercellular communication [5152]. Additional work is needed to determine if PEG10 fulfils a similar function.

  8. 8
    OLV says:

    Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development
    Int. J. Mol. Sci. 201920(3), 790; DOI: 10.3390/ijms20030790

    Pre-implantation embryo development encompasses several key developmental events, especially the activation of zygotic genome activation (ZGA)-related genes. Endogenous retroviruses (ERVs), which are regarded as “deleterious genomic parasites”, were previously considered to be “junk DNA”. However, it is now known that ERVs, with limited conservatism across species, mediate conserved developmental processes (e.g., ZGA). Transcriptional activation of ERVs occurs during the transition from maternal control to zygotic genome control, signifying ZGA. ERVs are versatile participants in rewiring gene expression networks during epigenetic reprogramming. Particularly, a subtle balance exists between ERV activation and ERV repression in host–virus interplay, which leads to stage-specific ERV expression during pre-implantation embryo development. A large portion of somatic cell nuclear transfer (SCNT) embryos display developmental arrest and ZGA failure during pre-implantation embryo development. Furthermore, because of the close relationship between ERV activation and ZGA, exploring the regulatory mechanism underlying ERV activation may also shed more light on the enigma of SCNT embryo development in model animals.

    Misinterpreting the observations?
    Viroids-First—A Model for Life on Earth, Mars and Exoplanets
    PDF

    The search for extraterrestrial life, recently fueled by the discovery of exoplanets, requires defined biosignatures. Current biomarkers include those of extremophilic organisms, typically archaea. Yet these cellular organisms are highly complex, which makes it unlikely that similar life forms evolved on other planets. Earlier forms of life on Earth may serve as better models for extraterrestrial life. On modern Earth, the simplest and most abundant biological entities are viroids and viruses that exert many properties of life, such as the abilities to replicate and undergo Darwinian evolution. Viroids have virus-like features, and are related to ribozymes, consisting solely of non-coding RNA, and may serve as more universal models for early life than do cellular life forms. Among the various proposed concepts, such as “proteins-first” or “metabolism-first”, we think that “viruses-first” can be specified to “viroids-first” as the most likely scenario for the emergence of life on Earth, and possibly elsewhere. With this article we intend to inspire the integration of virus research and the biosignatures of viroids and viruses into the search for extraterrestrial life.

     

     
    That is life: communicating RNA networks from viruses and cells in continuous interaction
    PDF

    All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.

     

     
     

     

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