Unintelligent Design - The Complex Lengths to Which Creationism's Idiot Designer Goes To Solve the Problems Its Incompetence Causes

Unintelligent Design

The Complex Lengths to Which Creationism's Idiot Designer Goes To Solve the Problems Its Incompetence Causes

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Your baby’s gut is crawling with unknown viruses – University of Copenhagen

Human gut microbiome

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If you've bought into the Creation Cult's intelligent [sic] design notion, it's probably best to ignore articles like this that might cause you to doubt the competence of your putative designer, but you're probably used to ignoring evidence that refutes creationism or you wouldn't have fallen for the intelligent [sic] design hoax in the first place.

Nevertheless, it discoveries such as this by Danish Scientists led by Shiraz A. Shah, of Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark, together with colleagues from France and Canada, that highlight the way arms races can lead to ludicrous levels of complexity of which any even half-competent designer would be rightly ashamed.

It comes about because the human gut, especially that of babies, is an ideal, warm, moist, and nutrient-rich environment for micro-organisms, so is teeming with bacteria, protozoa, and viruses, some of which are harmless but some of which parasitize both the microbes and the human cells of the gut.

One incidental benefit that creationists will point to is that the presence of these organisms probably helps train the developing babies’ immune system so it is more effective in later life, so the presence of these organisms can be beneficial.

But hold on! What are they 'training the immune system' for? They are training it to protect us from the very bacteria that the supposedly intelligent designer designed to harm us. At least, since it is supposedly omniscient, it knew what its bacteria and viruses would do when it designed them, so we must assume it designed them for that purpose.

And, if we accept that it designed bacteria to train our immune system, why did it then design the viruses that kill these beneficial bacteria?

But whatever it was thinking of, if 'thinking' is the appropriate term, the result is a baby’s gut teeming with more than 200 different families of virus, many of which were unknown prior to this study. The team's findings are published, open access, in the journal Nature Microbiology.

The research and its significance is explained in a University of Copenhagen news release:

Your baby’s gut is crawling with unknown viruses

GUT MICROBIOME Babies tumble about with more than 200 previously unknown viral families within their intestines. This large number comes as a surprise to researchers from the University of Copenhagen and COPSAC, who closely studied the diapers of 647 Danish babies and made the first mapping of its kind. These viruses most likely play an important role in protecting children from chronic diseases.

Viruses are usually associated with illness. But our bodies are full of both bacteria and viruses that constantly proliferate and interact with each other in our gastrointestinal tract. While we have known for decades that gut bacteria in young children are vital to protect them from chronic diseases later in life, our knowledge about the many viruses found there is minimal.

A few years back, this gave University of Copenhagen professor Dennis Sandris Nielsen the idea to delve more deeply into this question. As a result, a team of researchers from COPSAC (Copenhagen Prospective Studies on Asthma in Childhood) and the Department of Food Science at UCPH, among others, spent five years studying and mapping the diaper contents of 647 healthy Danish one-year-olds.

We found an exceptional number of unknown viruses in the faeces of these babies. Not just thousands of new virus species – but to our surprise, the viruses represented more than 200 families of yet to be described viruses. This means that, from early on in life, healthy children are tumbling about with an extreme diversity of gut viruses, which probably have a major impact on whether they develop various diseases later in life.

We work from the assumption that bacteriophages are largely responsible for shaping bacterial communities and their function in our intestinal system. Some bacteriophages can provide their host bacterium with properties that make it more competitive by integrating its own genome into the genome of the bacterium. When this occurs, a bacteriophage can then increase a bacterium's ability to absorb e.g. various carbohydrates, thereby allowing the bacterium to metabolise more things.

It also seems like bacteriophages help keep the gut microbiome balanced by keeping individual bacterial populations in check, which ensures that there are not too many of a single bacterial species in the ecosystem. It's a bit like lion and gazelle populations on the savannah.

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It is thought-provoking that all children run around with 10-20 of these virus types that infect human cells. So, there is a constant viral infection taking place, which apparently doesn’t make them sick. We just know very little about what’s really at play. My guess is that they’re important for training our immune system to recognise infections later. But it may also be that they are a risk factor for diseases that we have yet to discover.

Our gut is sterile until we are born. During birth, we are exposed to bacteria from the mother and environment. It is likely that some of the first viruses come along with these initial bacteria, while many others are introduced later via dirty fingers, pets, dirt that kids put in their mouths and other things in the environment.

Professor Dennis Sandris Nielsen, senior author
Department of Food Science
University of Copenhagen, Copenhagen, Denmark

ABOUT VIRUSES

• A virus is a microorganism consisting of a genome – either DNA or RNA – encapsulated in a protein membrane. Viruses cannot multiply. Instead, a virus attacks a host cell, which it uses to make copies of itself.
• Viruses are classified into viral families, which are then divided into a larger number of viral genera and viral species. A more well-known example of a viral family is coronavirus, to which the viruses Covid-19, MERS, SARS and several common cold viruses belong.

The researchers found and mapped a total of 10,000 viral species in the children's faeces – a number ten times larger than the number of bacterial species in the same children. These viral species are distributed across 248 different viral families, of which only 16 were previously known. The researchers named the remaining 232 unknown viral families after the children whose diapers made the study possible. As a result, new viral families include names like Sylvesterviridae, Rigmorviridae and Tristanviridae.

This is the first time that such a systematic an overview of gut viral diversity has been compiled. It provides an entirely new basis for discovering the importance of viruses for our microbiome and immune system development. Our hypothesis is that, because the immune system has not yet learned to separate the wheat from the chaff at the age of one, an extraordinarily high species richness of gut viruses emerges, and is likely needed to protect against chronic diseases like asthma and diabetes later on in life.

Previously, the research community mostly focused on the role of bacteria in relation to health and disease. But viruses are the third leg of the stool and we need to learn more about them. Viruses, bacteria and the immune system most likely interact and affect each other in some type of balance. Any imbalance in this relationship most likely increases the risk of chronic disease.

A lot of research suggests that the majority of chronic diseases that we’re familiar with – from arthritis to depression – have an inflammatory component. That is, the immune system is not working as it ought to – which might be because it wasn’t trained properly. So, if we learn more about the role that bacteria and viruses play in a well-trained immune system, it can hopefully lead us to being able to avoid many of the chronic diseases that afflict so many people today.

Shiraz Shah, first author
Senior researcher
Copenhagen Prospective Studies on Asthma in Childhood (COPSAC)
Copenhagen University Hospital, Herlev-Gentofte, Denmark

Bacterial viruses are our allies

Ninety percent of the viruses found by the researchers are bacterial viruses – known as bacteriophages. These viruses have bacteria as their hosts and do not attack the children's own cells, meaning that they do not cause disease. The hypothesis is that bacteriophages primarily serve as allies.

ABOUT BACTERIOPHAGES

• There are generally two types of bacteriophages. Virulent bacteriophages take over the bacterium and produce 30-100 new virus particles inside it. After this, the bacterial cell explodes from the inside and the new virus particles escape into the environment. Virulent bacteriophages help to keep the intestinal ecosystem in balance.
• So-called temperate bacteriophages can reproduce by integrating their genetic material into the genome of the host bacterial cell. When the cell divides, so does the bacteriophage. Temperate bacteriophages help transfer new genes to the bacteria so it becomes more competitive. However, there are also studies suggesting that an imbalance in the temperate bacteriophage population is associated with various diseases, e.g., inflammatory bowel disease.

The remaining ten percent of viruses found in the children are eukaryotic – that is, they use human cells as hosts. These can be both friends and foes for us.

Could play an important role in inflammatory diseases

The researchers have yet to discover where the many viruses in the one-year-olds come from. Their best answer thus far is the environment.

As Shiraz Shah points out, the entire field of research speaks to a huge global health problem.

The research groups have begun investigating the role of gut viruses in relation to a number of different diseases that occur in childhood, such as asthma and ADHD.

Bacteriophages seen through a microscope

Credit: Horst Neve

ABOUT THE STUDY

• The research team mapped the gut "viromes" from the guts of 647 healthy Danish one-year-old children. "Virome" is an umbrella term for all viruses found in a given environment. This includes both viruses that attack bacteria (bacteriophages), as well as those that go after human cells (eukaryotic virus).
• The 647 infants are all part of the mother-child cohort Copenhagen Prospective Studies on Asthma in Childhood (COPSAC2010), that has been followed very closely clinically throughout childhood at COPSAC. The children are now 13 years old.
• This interactive atlas allows you to see the diversity of viruses in the children and download information about the individual viral families.
• The results have been published in the renowned scientific journal Nature Microbiology.
• The researchers behind the study come from COPSAC, University of Copenhagen; Department of Food Science, University of Copenhagen; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen; Department of Health Technology, DTU; Université Laval, Canada; Université Paris-Saclay, France; Université Clermont, France and the University of Copenhagen’s Department of Biology.

For those interested in the details of the viruses the team found, they have provided an interactive version of the following map that allows you to expand each family.

Fig. 1: An atlas of infant gut DNA virus diversity.
Faecal viromes from 647 infants at age 1 year were deeply sequenced, assembled and curated, resulting in the identification of 10,021 viral species falling within 248 VFCs. Predicted host ranges for each VFC are given, and the VFCs have been grouped into 17 VOCs. Trees show how VFCs are interrelated within each VOC, and heat maps and histograms encode their genome size, lifestyle, host range, abundance and prevalence across the cohort as well as in published gut virus databases. For the 16 previously known viral families, names are written in red.

An interactive version of the figure with expandable families can be accessed online, for browsing the gene contents and downloading the genome of each virus: http://copsac.com/earlyvir/f1y/fig1.svg.

Shah, S.A, et al. (2023)

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Fig. 4: Phages and their bacterial hosts in the 1-year-old infant gut.
Prediction of bacterial hosts for the 10,021 vOTUs found in the infant gut virome shows that Bacteroides, Faecalibacterium and Bifidobacterium are the three most prominent host genera. a, Distribution of virus host predictions collapsed to bacterial order and genus levels, respectively. Numbers in parentheses denote the number of vOTUs with a given host genus or order, respectively. b, The top 100 gut bacterial genera found in gut metagenomes from the same infant faecal samples, as represented by a taxonomic tree. The MRA of each bacterial genus is shown in the blue heat map, while the fraction of the 647 infants harbouring the host genus (that is its prevalence) is shown with the brown bar plot. The outer ring displays per bacterial genus, the proportion of infant gut vOTUs (yellow) relative to reference phage species with known hosts⁴¹ (dark blue). Numbers behind each genus name denote the total number of vOTUs versus reference phage species per bacterial host genus. The 16 major host genera from a are indicated by a dot in front of their names in b. c, Each dot represents a genus from b, by its MRA in the metagenome against the aggregate MRA of all its vOTUs in the virome. Host abundances correlated strongly with corresponding phage abundances as tested by a Spearman’s rank test (two-sided P value).

Shah, S.A, et al. (2023)

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access. (CC BY 4.0)

Abstract

The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother–child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.

Shah, S.A., Deng, L., Thorsen, J. et al.
Expanding known viral diversity in the healthy infant gut.
Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01345-7

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

To recap then, and remember, creationists believe this is all the work of a single creator who is omniscient, omni-benevolent, and omnipotent, this creator made humans with their digestive tract, then it created bacteria, protista and viruses which live in all our guts, including babies, and do us harm. Knowing they would do us harm when it created them must mean it created them for that specific purpose. It then designed an immune system to protect us from those microorganisms and prevent them doing what they were designed to do.

But, because the immune system it designed isn't very good at doing what it was designed to do, it allowed the microorganisms to be used to 'train' it so it would be better at defending us from the organisms designed to harm us later in life.

But that doesn’t work very well, either, so, as this Copenhagen team suggest, a lot of the inflammatory conditions we suffer from in later life are caused by our immune system and how well or badly the harmful microbes in out gut as babies trained it.

Now, assuming creationism's putative creator blundered in creating bacteria, viruses, etc. to inhabit out guts in the first place, the ridiculously complex way it has tried to overcome that initial blunder makes it look like an incompetent fool, inventing ever-more complex solutions to the problems its incompetence causes, resulting in a massively complex and wasteful solution to the problem it caused, because, although omniscient, it didn't understand what it was creating and how it works.

The only logical conclusion is that creationism's putative creator is indistinguishable from a mindless, blind, natural process that has no plan and no intelligence, driven only by the interactions between different organisms in a complex ecosystem, sch as arises in the digestive tracts of babies as they interact with their biotic environment.

Meanwhile the organisms in our guts are being continually redesigned by an equally mindless natural process in a never-ending arms race that sees a huge proliferation in different taxa, and all adding greater complexity to the system for no discernible benefit to anyone or anything.

Creationists regard this as evidence of an ingenious, super-intelligent creator, which says more about the intellectual abilities of creationists than they might wish us to know.

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