Refuting Creationism - Co-Evolution Of Humans And Their Gut Microbiome

Development of the infant gut microbiome

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(complete with spelling idiosyncrasies)

Natural probiotic discovered in UK newborns’ microbiomes

In a very nice example of how humans and their gut microbiome have co-evolved, researchers from the Wellcome Sanger Institute, University College London (UCL), and the University of Birmingham, have identified a bacterium that helps digest breast milk and protects the baby from harmful pathogens.

As an example of intelligent [sic] design, this comes as close to a Heath-Robinson solution to a problem of the designer's own making as it's possible to imagine.

No designer who designed a baby's digestive system so it is susceptible to the harmful pathogens that it also designed, and created the baby to feed on breast milk that is difficult to digest, then solved those problems by creating another bacterium to fight the pathogens and help digest the milk, and infecting the baby with it, doesn't deserve the adjective 'intelligent'. 'Bloody stupid' would be a more appropriate term.

It's almost exactly as though the designer of these systems is a mindless automaton, simply obeying the natural laws of chemistry and physics and working without a plan!

The researchers have completed the largest study of UK baby microbiomes to date, carrying out whole genome sequencing to analyse stool samples from 1,288 healthy infants, all under one month old from the UK Baby Biome Study^1.1.

Refuting Creationism - Selfish Genes Evolved Cooperative Alliances

Complex human gut microbiome

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Fish swimming past coral and marine sponge. The researchers are currently using the proposed framework to investigate microbes inside marine sponges.

Researchers create new framework to help understand how microbial communities emerge - Swansea University

One of the lines of attack against the science of evolutionary biology is the lie that Richard Dawkins was advocating selfishness with his seminal book, The Selfish Gene, so 'proving' that rejection of the Christian god as the explanation for biodiversity is because 'Evolutionists' just want to sin.

It is, of course, like other creationist attacks on science, utterly devoid of any factual basis and reflects badly both on those who seek to fool their target dupes with it and on their dupes who eagerly believe them in order to justify a pretense of moral superiority.

In fact, natural selection and differential success of different alleles within a selective environment is devoid of any moral contents because it is devoid of intelligent input and genes are passive in the process. In Dawkin’s analogy, the result is as though genes behave selfishly, not that they make moral decisions or have the ability to choose which environmental selectors act on them.

One of the predictable outcomes of this gene-centred approach is that in a competition, the result which suits all competitors is cooperation since in a cooperative alliance, all the genes are winners, just as with a human group, a cooperative group is invariably more successful than a group of competing individuals in perpetual conflict.

Refuting Creationism - How New Zealand's Fungi Evolved

Scarlet Pouch Fungus

Leratiomyces erythrocephalus

Waipoua Forest, New Zealand

By Prof.Chen Hualin - Own work, CC BY-SA 4.0, Link

Colourful fruit-like fungi and forests ‘haunted by species loss’ – how we resolved a 30-year evolutionary mystery

Fungi, like some primitive plants such as ferns and mosses reproduce with spores - tiny packages that contain the entire genome of the parent which have the capacity to grow and develop into a new adult able to produce spores of its own. The key to success is getting those spores dispersed and how a fungus manages that will depend on the environment in which it lives and reproduces.

Most fungi use wind dispersal, their spores being light enough to be carried considerable distances but where they land is a matter of chance, so must wind-dispersed fungi produce millions of spores to give them a good chance of just one or two landing in a suitable place.

A few others have evolved a different, more targeted strategy such as being eaten by animals and excreted in their faeces. This increases the chance of being deposited in the same environment in which the parent fungi lived as the dispersing animal also lives in that environment. This is the method adopted by truffles which produce their fruiting body (where the spores are produced) underground and emit a scent which is attractive to the target animal (pigs, dogs, etc.) which dig up the fruiting body and eventually disperse the spores. This is probably the reason that humans like the taste of truffles, although we lack the ability to sniff them out for ourselves, but possibly an early ancestral species could.

But what happens to these fungi if there are no mammals, other than bats, as was the case with New Zealand before humans brought their commensal species with them? This is the subject of an article in The Conversation by three experts: Jamie Wood, Senior Lecturer in Ecology and Evolution, University of Adelaide, Australia, and Amy Martin, Post-Doctoral Researcher in Evolutionary Ecology and Anne Gaskett, Associate Professor of Biology, both of the University of Auckland, Waipapa Taumata Rau, New Zealand.

Their article is reproduced here under a Creative Commons license, reformatted for stylistic consistency:

Refuting Creationism - The Choanoflagellates Of Mono Lake Show How Multicellular Organisms Evolved

A 3D reconstruction of a spherical colony of 70 choanoflagellates from the newly-named species Barroeca monosierra discovered in Mono Lake.

Davis Laundon and Pawel Burkhardt,
Sars Centre, Norway;
Kent McDonald and Nicole King, UC Berkeley

Creature the size of a dust grain found hiding in California's Mono Lake - Berkeley News

Mono Lake, located east of the Sierra Nevada, just outside Yosemite National Park. Dotted with tufa formations, the lake’s salty water is laced with arsenic and cyanide, but is home to unique flies and brine shrimp as well as choanoflagellates.

Nicole King.

To be fair to them, the simple pastoralists from the ignorant and fearful infancy of out species who invented the creation myths that got included in the Bible, later decreed to be the inerrant word of a creator god and therefore deemed to be real science and history, could have known nothing of Mono Lake in Present day California and even less about the microscopic organisms about the size of a dust grain known now as choanoflagellates because, quite simply they lacked the technology to be able to see them - which is also why neither cells nor micro-organisms are mentioned nor even hinted at, anywhere in the Bible.

What are choanoflagellates and how do they relate to other organisms? Choanoflagellates are a group of free-living, single-celled organisms that are considered to be the closest living relatives of animals (metazoans). They are part of the clade Opisthokonta, which also includes fungi, animals, and some protists. Here’s a closer look at what choanoflagellates are and their relationship to other organisms:

Characteristics of Choanoflagellates

• Structure: Choanoflagellates are characterized by a distinctive cell structure. Each cell has a single flagellum, which is a whip-like structure used for movement, surrounded by a collar of microvilli (tiny, finger-like projections). The flagellum beats, drawing water through the collar, which traps bacteria and other small particles for the choanoflagellate to feed on.
• Habitat: These organisms are commonly found in aquatic environments, including both freshwater and marine ecosystems.
• Lifestyle: Choanoflagellates can exist as single cells, but some species form colonies. Their colonial forms are of particular interest because they offer insights into the possible evolutionary steps that led to multicellularity in animals.

Relationship to Other Organisms

• Closest Relatives to Animals: Genetic and molecular studies have shown that choanoflagellates are the closest living relatives to animals. This means that they share a common ancestor with animals, which is believed to have lived over 600 million years ago.
• Evolutionary Significance: The relationship between choanoflagellates and animals is crucial for understanding the origin of multicellularity. It is thought that the transition from single-celled to multicellular organisms may have occurred through mechanisms similar to those seen in choanoflagellate colonies. The study of choanoflagellates helps scientists understand the early evolution of animals and the development of complex tissues and organs.
• Shared Genes: Choanoflagellates possess many genes that are also found in animals, including those involved in cell adhesion, signaling, and extracellular matrix formation. These genes are essential for the development and maintenance of multicellular structures in animals, suggesting that the genetic toolkit required for multicellularity was already present in the last common ancestor of choanoflagellates and animals.

In summary, choanoflagellates are not only fascinating in their own right as unique protists, but they also play a key role in understanding the evolutionary steps that led to the rise of the animal kingdom.

And, being unaware of the history of life on a planet that they thought was only a few thousand years old and had been created out of nothing by magic with all the animals and plants fully formed, they could never in a million years, have guessed how multicellular animals evolved several hundred million years ago out of colonies of single-celled organisms.

And, of course, it's the yawning chasm between what the Bible's authors believed and what we now know, that tells us the Bible can't be the work of an omniscient creator god.

But of course, there are still a few (shrinking) gaps in what we know too. For example, although we have the genetic and structural evidence that multicellular organisms evolved out of single-celled organisms, we don't yet know the precise details, which is why a team of researchers from University of California, Berkeley have been studying a little-known choanoflagellates found in Mono Lake, near the Sierra Nevada, California. choanoflagellates are known to form colonies of organisms so can help shed some light on how related organisms originally got together to form simple multicellular organisms.

An additional discovery of this research was how these colonies incorporate a bacterial biome in a process analogous to the way most multicellular animals have associated biomes like out gut biome, for example.

The Berkely team's work is the subject of an open access paper in the American Society for Microbiology (ASM) journal mBio. It is also explained in a University of California Berkely news release:

Creature the size of a dust grain found hiding in California’s Mono Lake

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Colonies of these choanoflagellates — members of a group considered to be the closest living relatives of all animals — have their own unique microbiomes.

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Mono Lake in the Eastern Sierra Nevada is known for its towering tufa formations, abundant brine shrimp and black clouds of alkali flies uniquely adapted to the salty, arsenic- and cyanide-laced water.

University of California, Berkeley, researchers have now found another unusual creature lurking in the lake’s briny shallows — one that could tell scientists about the origin of animals more than 650 million years ago.

The organism is a choanoflagellate, a microscopic, single-celled form of life that can divide and develop into multicellular colonies in a way that’s similar to how animal embryos form. It’s not a type of animal, however, but a member of a sister group to all animals. And as animals’ closest living relative, the choanoflagellate is a crucial model for the leap from one-celled to multicellular life.

Surprisingly, it harbors its own microbiome, making it the first choanoflagellate known to establish a stable physical relationship with bacteria, instead of solely eating them. As such, it’s one of the simplest organisms known to have a microbiome.

Very little is known about choanoflagellates, and there are interesting biological phenomena that we can only gain insight into if we understand their ecology.

Professor Nicole King, senior author
Professor of molecular and cell biology
Howard Hughes Medical Institute and Department of Molecular and Cell Biology
University of California, Berkeley, California, USA.

Globular colonies of the choanoflagellate B. monosierra seen under a microscope. As indicated by the 50-micron scale bar, these colonies are at the limit of what’s visible to the naked eye.

Alain Garcia De Las Bayonas, Nicole King lab.

Typically visible only through a microscope, choanoflagellates are often ignored by aquatic biologists, who instead focus on macroscopic animals, photosynthetic algae or bacteria. But their biology and lifestyle can give insight into creatures that existed in the oceans before animals evolved and that eventually gave rise to animals. This species in particular could shed light on the origin of interactions between animals and bacteria that led to the human microbiome.

Animals evolved in oceans that were filled with bacteria. If you think about the tree of life, all organisms that are alive now are related to each other through evolutionary time. So if we study organisms that are alive today, then we can reconstruct what happened in the past.

Professor Nicole King.

King and her UC Berkeley colleagues described the organism — which they named Barroeca monosierra, after the lake — in a paper published online Aug. 14 in the journal mBio.

A beautiful colony

Nearly 10 years ago, then-UC Berkeley graduate student Daniel Richter came back from a climbing trip in the Eastern Sierra Nevada with a vial of Mono Lake water he’d casually collected along the way. Under the microscope, it was alive with choanoflagellates. Aside from brine shrimp, alkali flies and various species of nematode, few other forms of life have been reported to live in the inhospitable waters of the lake.

The newly named species Barroeca monosierra discovered in Mono Lake. Colonies of these organisms consist of numerous identical cells (cyan), each with flagella (green) that allow them to propel themselves through the water. This choanoflagellate colony hosts its own microbiome (red), something never before seen in these organisms. The extracellular matrix with which the bacteria interact is shown in white.

Video credit: Davis Laundon and Pawel Burkhardt, Sars Centre, Norway; Kent McDonald and Nicole King, UC Berkeley.

It was just packed full of these big, beautiful colonies of choanoflagellates. I mean, they were the biggest ones we’d ever seen.

Professor Nicole King.

The colonies of what seemed to be close to 100 identical choanoflagellate cells formed a hollow sphere that twirled and spun as each individual cell kicked its flagella.

One of the things that’s interesting about them is that these colonies have a shape similar to the blastula — a hollow ball of cells that forms early in animal development. We wanted to learn more about it.

Professor Nicole King.

At the time, however, King was occupied with other species of choanos, as she calls them, so the Mono Lake choanos languished in the freezer until some students revived and stained them to look at their unusual, doughnut-shaped chromosomes. Surprisingly, there was also DNA inside the hollow colony where there should have been no cells. After further investigation, graduate student Kayley Hake determined that they were bacteria.

A colony of choanoflagellates stained to show its features. Cyan indicates DNA — the doughnut-shaped DNA of the choanoflagellate cells and a cloud of bacterial DNA inside the colony — while flagella are white and microscopic hairs (villi) on each cell are red.

Kayley Hake, Nicole King lab

The bacteria were a huge surprise. That just was fascinating.

Professor Nicole King.

Hake also detected connective structures, called extracellular matrix, inside the spherical colony that were secreted by the choanos.

Only then did it occur to Hake and King that these might not be the remains of bacteria the choanos ate, but bacteria living and grazing on stuff secreted by the colony.

No one had ever described a choanoflagellate with a stable physical interaction with bacteria. In our prior studies, we found that choanos responded to small bacterial molecules that were floating through the water, or [that] the choanos were eating the bacteria, but there was no case where they were doing anything that could potentially be a symbiosis. Or in this case, a microbiome.

Professor Nicole King.

King teamed up with Jill Banfield, a pioneer in metagenomics and a UC Berkeley professor of environmental science, policy and management and of earth and planetary science, to determine which bacterial species were in the water and inside the choanos. Metagenomics involves sequencing all the DNA in an environmental sample to reconstruct the genomes of the organisms living there.

After Banfield’s lab identified the microbes in Mono Lake water, Hake created DNA probes to determine which ones were also inside the choanos. The bacterial populations were not identical, King said, so evidently some bacteria survive better than others inside the oxygen-starved lumen of the choanoflagellate colony. Hake determined that they were not there accidentally; they were growing and dividing. Perhaps they were escaping the toxic environment of the lake, King mused, or maybe the choanos were farming the bacteria to eat them.

Much of this is speculation, she admits. Future experiments should uncover how the bacteria interact with the choanoflagellates. Past work in her lab has already shown that bacteria act like an aphrodisiac to stimulate mating in choanoflagellates, and that bacteria can stimulate single-celled choanos to aggregate into colonies.

For her, the Mono Lake choanoflagellate will become another model system in which to study evolution, just like the choanos that live in splash pools on the island of Curaçao in the Caribbean — her main focus at the moment — and the choanos in pools at the North and South Poles. It might be a challenge to get more samples from Mono Lake, however. On a recent visit, only six of 100 samples contained these energetic microorganisms.

I think there’s a great deal more that needs to be done on the microbial life of Mono Lake, because it really underpins everything else about the ecosystem,. I’m excited about B. monosierra as a new model for studying interactions between eukaryotes and bacteria. And I hope it tells us something about evolution. But even if it doesn’t, I think it’s a fascinating phenomenon.

Professor Nicole King.

In addition to King, Banfield, Hake and Richter, UC Berkeley co-authors of the paper include former doctoral student Patrick West, electron microscopist Kent McDonald and postdoctoral fellows Josean Reyes-Rivera and Alain Garcia De Las Bayonas. The work is supported by HHMI and the National Science Foundation.

• A large colonial choanoflagellate from Mono Lake harbors live bacteria (mBio)
• Newly Discovered Microorganisms Band Together, ‘Flip Out’ (2019)
• Bacteria act as aphrodisiac for the closest relatives of animals (2017)
• Did bacteria spark evolution of multicellular life? (2012)
• Nicole King’s lab website

ABSTRACT
As the closest living relatives of animals, choanoflagellates offer insights into the ancestry of animal cell physiology. Here, we report the isolation and characterization of a colonial choanoflagellate from Mono Lake, California. The choanoflagellate forms large spherical colonies that are an order of magnitude larger than those formed by the closely related choanoflagellate Salpingoeca rosetta. In cultures maintained in the laboratory, the lumen of the spherical colony is filled with a branched network of extracellular matrix and colonized by bacteria, including diverse Gammaproteobacteria and Alphaproteobacteria. We propose to erect Barroeca monosierra gen. nov., sp. nov. Hake, Burkhardt, Richter, and King to accommodate this extremophile choanoflagellate. The physical association between bacteria and B. monosierra in culture presents a new experimental model for investigating interactions among bacteria and eukaryotes. Future work will investigate the nature of these interactions in wild populations and the mechanisms underpinning the colonization of B. monosierra spheres by bacteria.

IMPORTANCE
The diversity of organisms that live in the extreme environment of Mono Lake (California, USA) is limited. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist in Mono Lake, a hypersaline, alkaline, arsenic-rich environment. We repeatedly isolated members of a new species of choanoflagellate, which we have named Barroeca monosierra. Characterization of B. monosierra revealed that it forms large spherical colonies containing diverse co-isolated bacteria, providing an opportunity to investigate mechanisms underlying physical associations between eukaryotes and bacteria.

OBSERVATION

A newly identified choanoflagellate species forms large spherical colonies

Choanoflagellates are the closest living relatives of animals and, as such, provide insights into the origin of key features of animal biology (1, 2). Over five sampling trips to Mono Lake, California (Fig. 1A; Table S1), we collected single-celled choanoflagellates and large spherical choanoflagellate colonies, many of which were seemingly hollow (Fig. 1B). In colonies and single cells, each cell bore the diagnostic collar complex observed in other choanoflagellates: an apical flagellum surrounded by a collar of microvilli (1, 2). In the spherical colonies, each cell was oriented with the basal pole of the cell body facing inwards and the apical flagellum facing out (Fig. 1B). We know of no prior reports of choanoflagellates having been isolated and cultured from any hypersaline alkaline lake, including Mono Lake.

Fig 1

Fig 1 A colonial choanoflagellate isolated from Mono Lake. (A) Choanoflagellates were collected from three sampling sites (asterisks) near the shore of Mono Lake, California (modified from a map in the public domain, formatted as USGS Imagery Only; https://www.usgs.gov/volcanoes/long-valley-caldera) (B) B. monosierra forms large colonies (differential interference contrast image). Scale bar = 50 µm. (C) B. monosierra (shown in bold) is a craspedid choanoflagellate closely related to S. rosetta and Microstomoeca roanoka. Phylogeny based on sequences of three genes: 18S rRNA, EFL, and HSP90. Metazoa (seven species) were collapsed to save space. Bayesian posterior probabilities are indicated above each internal branch, and maximum likelihood bootstrap values are below. (A “—” value indicates a bifurcation lacking support or not present in one of the two reconstructions.) Also see Fig. S1C for further phylogenetic analyses. (D and E) Two colonies from the ML2.1G culture (Fig. S1, Box2) reveal the extremes of the B. monosierra colony size range (D, 58 µm diameter; E, 19 µm diameter; scale bar = 20 µm). In B. monosierra colonies, each cell is oriented with its apical flagellum (white; labeled with anti-tubulin antibody) and the apical collar of microvilli (red; stained with phalloidin) pointing out. Nuclei (cyan) were visualized with the DNA-stain Hoechst 33342. (F) Colonies of B. monosierra span from 10 µm in diameter, a size comparable to that of small S. rosetta colonies, to 120 µm, over an order of magnitude larger. The diameters of B. monosierra and S. rosetta colonies were plotted as a violin plot; the median is indicated as a thick black line. Diameters of the colonies in panels D and E are indicated as colored bars behind the violin plot (D, red bar; E, blue bar).

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Fig 2

Fig 2 Bacteria reside in the lumina of B. monosierra colonies. (A and A′) The center of a B. monosierra colony from culture ML2.1G (Fig. S1, Box 2), shown as a maximum intensity projection (A) and optical z-section (A′), contains DNA (revealed by Hoechst 33342 staining; cyan). Apical flagella were labeled with anti-tubulin antibody (white); microvilli were stained with phalloidin (red). Hoechst 33342 staining (cyan) revealed the spherical choanoflagellate nuclei along the colony perimeter and an amorphous cloud of DNA sitting within the central cavity formed by the monolayer of choanoflagellate cells. (B, B’’ and B′) A thin section through a B. monosierra colony, imaged by transmission electron microscopy (TEM), revealed the presence of small cells in the central cavity. (B′) Inset (box from panel B) reveals that the interior cells are each surrounded by a cell wall. (C, C’’, C’’’, and C″′′) The small cells inside B. monosierra colonies (grown from cultures ML2.1E/ML2.1EC) are bacteria, as revealed by hybridization with a broad-spectrum 16S rRNA probe (C, green) and a probe targeting Gammaproteobacteria (C′, red). Choanoflagellate nuclei and bacterial nucleoids were revealed by staining with Hoechst (C″, cyan). (C″′) Merge of panels C, C′, and C″. Scale bar for all = 5 µm. (D, D’ and D″) 3D reconstruction of a 70-cell B. monosierra colony from transmission electron micrographs of serial ultrathin sections revealed that the bacteria are closely associated with and wrapped around the extracellular matrix (ECM) inside the colony. (D) Whole colony view. (D′) Cut-away view of colony center. False colors indicate cell bodies (cyan), microvilli (orange), flagella (green), bacteria (red), ECM (white), intercellular bridges (yellow; see also Fig. S5), and filopodia (purple). (D″) Reducing the opacity of the choanoflagellate cell renderings revealed the presence of bacteria positioned between the lateral surfaces of choanoflagellate cells (brackets; see also Fig. S7). (E) Representative B. monosierra colony from an environmental sample shown as an average intensity projection (planes 17–27 from 1-µm optical sections). Choanoflagellate nuclei and bacterial nucleoids (examples indicated by arrowheads) were revealed by staining with Hoechst (cyan). To allow visualization of the much smaller bacterial nucleoids, the imaging of the choanoflagellate nuclei was saturated. Concanavalin A staining (magenta) revealed the branched extracellular matrix. (F and G) Optical sections 19 and 24, respectively, of the B. monosierra colony shown in panel E. (F′ and G′) Higher magnification Hoechst-stained DNA from the boxed regions in F and G, highlighting the resident bacteria (examples indicated by arrowheads). Scale bars in panels E–G = 10 μm.

This discovery shows a plausible route to multicellularity from a related single-celled eukaryote organism and offers an explanation for the early stages of embryo development where a single-cell zygote gives rise early on to a hollow gastrula. This could have formed in an ancestral multicellular metazoan as somewhere for a symbiotic colony of bacteria to reside and provide nutrients in return for protection. It also offers a plausible explanation for our commensal, symbiotic microbiome in our gut which has its embryonic origins in the hollow gastrula.

Creationists might also like to ignore the fact that the research team believe they are explaining a fundamental step in the evolution of multicellularity 650 million years ago, and have found no need to abandon science and the scientific method and turn to creationism with its magic and unproven entities for a more rational explanation of the facts.

And of course, as with 99.9975% of all history, this stage in the evolution of multicellular life happened in that long, pre-'Creation Week', period of Earth's history.

Unintelligent Design - Why Do Males Have Useless Nipples? - It's Evolution, Naturally!

New mathematical model sheds light on the absence of breastfeeding in male mammals - News and events, University of York

Ask an intelligent [sic] design creationists why males have nipples, and you'll get lots of evasion and avoidance but no answer beyond mutterings about an 'ineffable god', and 'not knowing the minds of the creator', betraying the religious underpinning of creationism.

So, why exactly do males have nipples?

The answer is, of course, evolution.

Refuting Creationism - More Evidence of Endosybiosis in Progress

A group of diatoms with their fluorescently-labeled symbionts.

© Max Planck Institute for Marine Microbiology Bremen/Mertcan Esti

The rhizobial nitrogen fixing symbionts (fluorescently-labeled in orange and green using genetic probes) residing inside diatoms collected from the tropical North Atlantic. The nucleus of the diatom is shown in bright blue.

© Max Planck Institute for Marine Microbiology Bremen/Mertcan Esti

Long-standing marine mystery solved: How algae get nitrogen to grow

Readers my remeber my article about how a team of scientists have discovered a new cell organelle in the process of transforming from a free-living nitrogen-fixing bacterium to becoming an endosymbiont of a marine alga, in much the same way that cyanobacteria became the chloroplasts of plant cells and rickettsia bacteria became the mitochondria of all eukaryote cells.

Now a different team, from the Max Planck Institute for Marine Microbiology, the Alfred Wegener Institute and the University of Vienna, have reported on a similar phenomenon in the form of a bacterium closely related to the Rhizobia that form a symbiotic association with leguminous plants such as peas and bean, which has teamed up with a marine diatom. This symbiotic relationship involves the bacterium living within the single cell of the diatom, unlike the relationship between Rhizobia and legumes in which the bacteria live in special nodes on the roots of the plants, but not inside the plant cells as such.

What is the chemical pathway by which nitrogen-fixing bacteria convert atmospheric nitrogen into ammonia and nitrates? Nitrogen-fixing bacteria play a crucial role in the nitrogen cycle by converting atmospheric nitrogen (N₂) into ammonia (NH₃), which can be further converted into nitrates (NO₃⁻) by other microorganisms. The chemical pathway for nitrogen fixation primarily involves the enzyme nitrogenase, which catalyzes the reduction of atmospheric nitrogen to ammonia. Here is an overview of the pathway:

1. Nitrogen Fixation
   Nitrogenase Enzyme Complex:
   • Components: The nitrogenase complex consists of two main proteins: the iron (Fe) protein and the molybdenum-iron (MoFe) protein.
   • Reaction:
     \[ \begin{equation*} \begin{aligned} \text{N}_2 + 8H^+ + 8e^- + 16ATP & \\ \rightarrow 2NH_3 + H_2 + 16ADP + 16Pi & \end{aligned} \end{equation*} \]
   • Steps:
     1. Electron Donation: Electrons are donated from ferredoxin or flavodoxin to the Fe protein.
     2. ATP Hydrolysis: ATP binds to the Fe protein and is hydrolyzed, providing energy for the transfer of electrons.
     3. Electron Transfer: Electrons are transferred from the Fe protein to the MoFe protein.
     4. Nitrogen Reduction: The MoFe protein reduces atmospheric nitrogen (N₂) to ammonia (NH₃) in a series of steps involving the binding and reduction of N₂.
2. Ammonia Assimilation
   Once ammonia is produced, it can be assimilated into organic compounds or further processed into other nitrogenous compounds.
   
   Conversion to Nitrates
   The conversion of ammonia to nitrates occurs in two steps involving nitrifying bacteria:
   
   
   Step 1: Ammonia to Nitrite
   Bacteria Involved: Ammonia-oxidizing bacteria (AOB), such as Nitrosomonas. \[ \text{NH}_3 + \text{O}_2 \rightarrow \text{NO}_2^- + 3H^+ + 2e^- \] Step 2: Nitrite to Nitrate
   Bacteria Involved: Nitrite-oxidizing bacteria (NOB), such as Nitrobacter. \[ \text{NO}_2^- + \frac{1}{2}\text{O}_2 \rightarrow \text{NO}_3^- \]

Summary of Pathway

1. Nitrogen Fixation: Atmospheric nitrogen (N₂) is converted to ammonia (NH₃) by nitrogenase enzyme complex in nitrogen-fixing bacteria.
2. Ammonia Assimilation: Ammonia can be incorporated into organic molecules or further processed.
3. Nitrification: Ammonia is first oxidized to nitrite (NO₂⁻) by AOB and then nitrite is oxidized to nitrate (NO₃⁻) by NOB.

This pathway is essential for making atmospheric nitrogen available to plants and other organisms in a usable form, thereby sustaining the nitrogen cycle in ecosystems.

This association in the oceans accounts for the supply of fixed nitrogen in the seas which is then available for plant and ultimately animal life.

Of course, any intelligent designer would have given the diatoms the necessary genes to fix nitrogen themselves, just as it would have given legumes the same ability, but evolution, in its haphazard, unplanned and unintelligent way often produces sub-optimal, overly complex solutions to problems simply because that solution was better than what went before; there is no intelligence to think about using processes designed earlier or of the elegance of the solution.

The discovery is the subject of an open access paper in Nature and a press release from Vienna University (Universität Wien):

Long-standing marine mystery solved: How algae get nitrogen to grow

Newly discovered symbiosis between Rhizobia and diatoms could also open new avenues for agriculture

In a new study, scientists from the Max Planck Institute for Marine Microbiology, the Alfred Wegener Institute and the University of Vienna shed light on an unexpected partnership: A marine diatom and a bacterium that can account for a large share of nitrogen fixation in vast regions of the ocean. This symbiosis likely plays a key role for global marine nitrogen fixation and productivity, and thus uptake of carbon dioxide. The newly-discovered bacterial symbiont is closely related to the nitrogen-fixing Rhizobia which live in partnership with many crop plants and may also open up new avenues for engineering nitrogen-fixing plants. The results were published in the current print edition of the renowned journal Nature.

Nitrogen is an essential component of all living organisms. It is also the key element controlling the growth of crops on land, as well as the microscopic oceanic plants that produce half the oxygen on our planet. Atmospheric nitrogen gas is by far the largest pool of nitrogen, but plants cannot transform it into a usable form. Instead, some crop plants like soybeans, peas and alfalfa (collectively known as legumes) have acquired Rhizobial bacterial partners that "fix" atmospheric nitrogen into ammonium, which can be used by plants. This partnership makes legumes one of the most important sources of proteins in food production.

Yet, how marine plants obtain the nitrogen they need to grow has not yet been fully clarified. Scientists from the Max Planck Institute for Marine Microbiology, the Alfred Wegener Institute and the University of Vienna now report that Rhizobia can also form similar partnerships with tiny marine plants called diatoms – a discovery that solves a long-standing marine mystery and which has potentially far-reaching agricultural applications.

An enigmatic marine nitrogen fixer hiding within a diatom

For many years it was assumed that most nitrogen fixation in the oceans was carried out by photosynthetic organisms called cyanobacteria. However, in vast regions of the ocean there are not enough cyanobacteria to account for measured nitrogen fixation. Thus, many scientists hypothesized that non-cyanobacterial microorganisms must be responsible for the "missing" nitrogen fixation.

For years, we have been finding gene fragments encoding the nitrogen-fixing nitrogenase enzyme, which appeared to belong to one particular non-cyanobacterial nitrogen fixer but, we couldn’t work out precisely who the enigmatic organism was and therefore had no idea whether it was important for nitrogen fixation.

Marcel M. M. Kuypers, lead author
Max Planck Institute for Marine Microbiology, Bremen, Germany

In 2020, the scientists travelled from Bremen to the tropical North Atlantic to join an expedition involving two German research vessels. They collected hundreds of liters of seawater from the region, in which a large part of global marine nitrogen fixation takes place, hoping to both identify and quantify the importance of the mysterious nitrogen fixer. It took them the next three years to finally puzzle together its genome.

It was a long and painstaking piece of detective work but ultimately, the genome solved many mysteries.

Bernhard Tschitschko, first author
Max Planck Institute for Marine Microbiology, Bremen, Germany Now: Department of Microbiology
University of Innsbruck, Innsbruck, Austria.

Based on the nitrogenase gene fragment we had seen in many marine samples before, one would have expected to find this gene in a Vibrio-related organism, but by carefully piecing together the genetic information it turned out that instead, it belonged to a genome closely related to known Rhizobia, which typically live in symbiosis with legume plants.

Daan R. Speth, co-author
Max Planck Institute for Marine Microbiology, Bremen, Germany Now: Centre for Microbiology and Environmental Systems Science
Division of Microbial Ecology
University of Vienna, Vienna, Austria,

Together with its surprisingly small genome, this raised the possibility that the marine Rhizobia might be a symbiont.

The first known symbiosis of this kind

Spurred on by these discoveries, the authors developed a genetic probe which could be used to fluorescently label the Rhizobia.

This allowed us to visualize the Rhizobia directly in their native habitat - the complex environmental samples collected in the Atlantic.

Katharina Kitzinger, co-author
Max Planck Institute for Marine Microbiology, Bremen, Germany
Now: Centre for Microbiology and Environmental Systems Science
Division of Microbial Ecology
University of Vienna, Vienna, Austria.

Indeed, their suspicions about it being a symbiont were quickly confirmed.

We were finding sets of four Rhizobia, always sitting in the same spot inside the diatoms. It was very exciting as this is the first known symbiosis between a diatom and a non-cyanobacterial nitrogen fixer.

Marcel M. M. Kuypers.

The scientists named the newly discovered symbiont Candidatus Tectiglobus diatomicola. Having finally worked out the identity of the missing nitrogen fixer, they focused their attention on working out how the bacteria and diatom live in partnership. Using a technology called nanoSIMS, they could show that the Rhizobia exchanges fixed nitrogen with the diatom in return for carbon. And it puts a lot of effort into it:

In order to support the diatom’s growth, the bacterium fixes 100-fold more nitrogen than it needs for itself.

Wiebke Mohr, co-author
Max Planck Institute for Marine Microbiology, Bremen, Germany

A crucial role in sustaining marine productivity

Next the team turned back to the oceans to discover how widespread the new symbiosis might be in the environment. It quickly turned out that the newly discovered partnership is found throughout the world’s oceans, especially in regions where cyanobacterial nitrogen fixers are rare. Thus, these tiny organisms are likely major players in total oceanic nitrogen fixation, and therefore play a crucial role in sustaining marine productivity and the global oceanic uptake of carbon dioxide.

A key candidate for agricultural engineering?

Aside from its importance to nitrogen fixation in the oceans, the discovery of the symbiosis hints at other exciting opportunities in the future. Kuypers is particularly excited about what the discovery means from an evolutionary perspective.

The evolutionary adaptations of Ca. T. diatomicola are very similar to the endosymbiotic cyanobacterium UCYN-A, which functions as an early-stage nitrogen-fixing organelle. Therefore, it’s really tempting to speculate that Ca. T. diatomicola and its diatom host might also be in the early stages of becoming a single organism.

Marcel M. M. Kuypers.

Tschitschko agrees that the identity and organelle like nature of the symbiont is particularly intriguing.

So far, such organelles have only been shown to originate from the cyanobacteria, but the implications of finding them amongst the Rhizobiales are very exciting, considering that these bacteria are incredibly important for agriculture. The small size and organelle-like nature of the marine Rhizobiales means that it might be a key candidate to engineer nitrogen-fixing plants someday.

Bernhard Tschitschko

The scientists will now continue to study the newly discovered symbiosis and see if more like it also exist in the oceans.

Original publication:
Bernhard Tschitschko, Mertcan Esti, Miriam Philippi, Abiel T. Kidane, Sten Littmann, Katharina Kitzinger, Daan R. Speth, Shengjie Li, Alexandra Kraberg, Daniela Tienken, Hannah K. Marchant, Boran Kartal, Jana Milucka, Wiebke Mohr, Marcel M. M. Kuypers (2024): Rhizobia-diatom symbiosis fixes missing nitrogen in the ocean. Nature (2024) DOI: 10.1038/s41586-024-07495-w

Participating institutions:

• Max Planck Institute for Marine Microbiology, Bremen, Germany
• Alfred Wegener Institute - Helmholtz-Centre for Polar and Marine Research, Bremerhaven, Germany
• University of Vienna, Vienna, Austria

Abstract
Nitrogen (N₂) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean¹ and has a key role in fuelling the biological carbon pump². Oceanic N₂ fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N₂ into ammonia, are widespread among marine bacteria and archaea^3,4,5. Little is known about these non-cyanobacterial N₂ fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N₂-fixing symbiont, ‘Candidatus Tectiglobus diatomicola’, which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N₂-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N₂-fixing rhizobia–legume symbioses on land⁶. Our results show that the rhizobia–diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N₂ fixers in the tropical North Atlantic, and that they might be responsible for N₂ fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.

Main
Nitrogen is an essential component of all living organisms and limits life in the ocean. Atmospheric N₂ gas is the largest reservoir of freely accessible nitrogen, but it is biologically available only to microorganisms that carry the nitrogenase metalloenzyme and thus can fix N₂ into ammonia⁷. Even though a wide diversity of marine bacteria and archaea encode nitrogenase, the bulk of nitrogen fixation in the ocean has been attributed to cyanobacteria (ref. ⁴ and references therein). These phototrophs are capable of both free-living and symbiotic lifestyles, and can directly or indirectly contribute to carbon fixation and export production in the regions where they are abundant, such as oligotrophic coastal waters and margins of subtropical gyres⁸. Notably, in vast regions of the ocean, such as the centres of subtropical gyres, cyanobacterial N₂ fixers are too rare to account for the measured rates of N₂ fixation. Instead, a role of non-cyanobacterial N₂ fixers has been invoked, on the basis of the abundance of nitrogenase-encoding gene sequences (nifH), most of which belong to uncultured proteobacteria (for example, refs. ^3,5,9,10,11). So far, the most frequently detected non-cyanobacterial N₂ fixer is the so-called gamma-A, named after its nifH gene phylogeny that clusters within the Gammaproteobacteria¹². This enigmatic microorganism has been shown to be distributed in most world oceans, and its potential activity has been inferred from in situ nifH transcription^13,14. To date, however, there is no proof that gamma-A fixes N₂ in situ, and essentially all aspects of its physiology remain unknown.

An N₂-fixing rhizobial diatom endophyte We investigated the role of non-cyanobacterial N₂ fixation in the tropical North Atlantic during an expedition in January–February 2020. This region is responsible for around 20% of oceanic N₂ fixation⁸, and cyanobacteria can only explain approximately half of the rates measured in the region¹⁰. We detected high N₂ fixation rates of up to 40 nmol N l⁻¹ d⁻¹ in the surface waters (Extended Data Table 1), and the presence of both cyanobacterial and heterotrophic N₂ fixers—specifically, gamma-A—was confirmed by metagenomic sequencing (Extended Data Fig. 1a). Gamma-A nifH sequences were retrieved only from the large size fraction (greater than 3 µm) suggesting particle attachment or an association with a host organism (Extended Data Fig. 1a). We recovered a near-complete metagenome-assembled genome (MAG; 1.7 Mb, 37.8% GC, 98% completion with 0% redundancy) containing the gamma-A nifH gene, as well as a complete cluster of rRNA genes (Supplementary Table 1). Although the retrieved nifH sequence clustered within the Gammaproteobacteria as previously reported^3,14,15 (Extended Data Fig. 2), both 16S-rRNA-gene-based and whole-genome-based taxonomy¹⁶ firmly placed this MAG within the alphaproteobacterial family Hyphomicrobiaceae (Fig. 1a). This family belongs to the order Rhizobiales, which comprises the prominent rhizobial symbionts of nodule-forming terrestrial legumes^6,17,18. In addition to nifH, most other genes of the nif regulon are of gammaproteobacterial origin, including nifD and nifK, which encode the catalytic component of the nitrogenase; nifE, nifN and nifB, which encode the iron-molybdenum cofactor assembly proteins; and nifS, which is involved in metallocluster biosynthesis (Extended Data Fig. 2a). Almost all other genes in the gamma-A MAG are of alphaproteobacterial origin (Supplementary Table 1). On the basis of these results, we conclude that the gamma-A N₂ fixer is, in fact, an alphaproteobacterium that has acquired its nitrogenase genes through horizontal gene transfer from a gammaproteobacterial donor. Besides gamma-A, several other bacteria, including members of the order Rhizobiales, obtained their nitrogenase genes through horizontal gene transfer from a gammaproteobacterial donor (Extended Data Fig. 2b). Such horizontal gene transfer across classes, resulting in the acquisition of nitrogenase genes, has been reported previously for other N₂ fixers^19,20.

Fig. 1: Phylogeny and visualization of Candidatus Tectiglobus diatomicola and its diatom host.

a, Maximum likelihood phylogenetic tree of concatenated bacterial marker genes from the order Rhizobiales, showing the placement of Ca. T. diatomicola within the Hyphomicrobiaceae family (see Methods). The novel genus Ca. Tectiglobus, comprising Ca. T. diatomicola and its closest relative Ca. T. profundi, is highlighted in pink. Families within the Rhizobiales that contain known N₂-fixing legume symbionts and their exemplary host plants are shown. The order Parvibaculales was used as an outgroup. Black dots indicate more than 95% bootstrap support. Scale bar indicates amino acid substitutions per site. Plant icons were designed by Freepik (Neptunia oleracea) or created with BioRender.com. b,c, False coloured scanning electron microscopy (SEM) image (b) and confocal laser scanning microscopy image (c) of a Haslea diatom. Four Ca. T. diatomicola cells (pink, overlay of Hypho1147 and Hypho734 fluorescence in situ hybridization (FISH) probes; Extended Data Table 2) were detected next to the host nucleus (white; stained with DAPI). Scale bars, 5 µm.

We name the newly discovered species ‘Candidatus Tectiglobus diatomicola’ within a novel genus ‘Candidatus Tectiglobus’ (see Methods for etymology). One other marine MAG from the North Pacific, which we now name ‘Candidatus Tectiglobus profundi’, is affiliated with this novel genus, with 72% average amino acid identity with Ca. T. diatomicola (Supplementary Methods). Compared with their closest relative, a MAG from the Mediterranean Sea, both Ca. Tectiglobus species have a substantially reduced genome size (around 1.7 Mb versus around 5 Mb) and a strongly decreased GC content (around 38% versus around 54%) (Extended Data Fig. 3), which are features typical of endosymbionts²¹. Notably, a similar reduction in genome size and GC content is observed for the N₂-fixing cyanobacterial endosymbiont Candidatus Atelocyanobacterium thalassa, or UCYN-A, which lives in symbiosis with a haptophyte alga^22,23. Thus, the genome properties of Ca. T. diatomicola, together with its presence in the large size fraction, strongly indicate a host-associated lifestyle.

A couple of points here for creationists to ignore or lie about:

• The authors show no doubts that this is an evolutionary process and show no evidence of adopting creationist superstition as a better explanation.
• The endosymbionts have a much reduced genome compared to their free-living relatives, showing that their evolution has involved a loss of genetic information typical of both endosymbionts and endo-parasites, despite the creationist assertion that a loss of genetic information is either fatal or 'devolutionary' [sic]
• This process illustrates the processes involved in the earlier evolution of biodiversity which produced eukaryote cells from associations of prokaryotes, which itself illustrates how 'selfish' genes form co-operative alliances with other 'selfish' genes, despite creationists assertions that selfish genes can only produce selfish individuals.

Unintelligent Design - An Over-Complex, Heath-Robinson Solution To A Simple Problem

Antarctic landscape (Ross Sea)

Small Antarctic worms (zoom) rely on microbes to resist the chill of the frigid waters where they live.

Michael Tangherlini, Marco Lo Martire

Bacteria found to produce proteins that act like antifreeze, helping marine worms survive in polar waters

Imagine you're a designer with all the power you need and all the solutions you've designed earlier at your fingertips and your task is to redesign some marine worms that you designer earlier and put into an arctic environment, perhaps not realising they wouldn't survive if they got frozen.

So, what you have to do is give these marine worms some way to prevent this happening and so mitigating your earlier blunder.

At your disposal is the method you gave to some marine bacteria, and even some fish known as icefish, when you made similar blunders years earlier - you gave them some genes for making antifreeze to stop the contents of their cells freezing and the ensuing ice crystals from destroying them.

Do you give these marine worms the same genes you gave the bacteria?

Not if you're creationism's putative intelligent [sic] designer, you don't. That would be far too simple.

Unintelligent Design - A Heath-Robinson Solution To A Simple Problem

Convolutriloba longifissura.
Fluorescence imaging shows the algal cells in red, and the acoel cells in blue and green.

Dania Nanes Sarfati

Convolutriloba longifissura. The green body color of the adult comes from algal symbionts integrated in its skin. The red stripes in the middle of the body of this 3 millimeter long worm indicate mature oocytes.

Credit: Eric Rottinger/www.Kahikai.org
National Science Foundation - Media Gallery

The surprising relationship between marine worms and the algae that live inside them | Stanford Report

Creationists who like to cite complexity as evidence of intelligent design, either don't understand design or believe the designer is a bumbling idiot who never settles for a simple solution when a more complicated one is available, and never misses an opportunity to make a mountain out a molehill, as my old mother used to say if we turned a small problem into a big one.

That's of course, if you believe that creationist superstition of magic creation and not the scientifically proven, evolution, as an explanation for the form of living things.

Imagine you're a creator who is designing a simple marine flatworm and you decide that just what it needs is to be able to make food the way plants do, using the energy in sunlight to turn carbon dioxide into sugars. You previously designed some bacteria to perform this process, then, in an earlier invention, you put some of these bacteria in a single-celled plant and made algae. You could have given the single-celled plant the same enzymes and metabolic pathway you gave the bacteria but that was too simple, so you put the bacteria inside the plant cell as cell organelles called chloroplasts.

Tell me all about the marine flat worm Convolutriloba longifissura, please. Convolutriloba longifissura is a species of acoelomorph worm that inhabits marine environments. Here are some key details about this fascinating organism:

Taxonomy and Classification

• Kingdom: Animalia
• Phylum: Acoelomorpha
• Class: Acoela
• Order: Acoelida
• Family: Convolutidae
• Genus: Convolutriloba
• Species: Convolutriloba longifissura

Morphology and Anatomy

• Size and Shape: Convolutriloba longifissura are small, flattened worms. They are typically only a few millimeters in length.
• Body Structure: They lack a true gut and body cavity, characteristic of acoelomorphs. Instead, their digestive system consists of a simple gastrovascular cavity.
• Symbiotic Algae: These worms often contain symbiotic algae within their tissues, which provide them with nutrients through photosynthesis. This relationship is beneficial for both the worm and the algae.

Reproduction

• Asexual Reproduction: Convolutriloba longifissura is well known for its remarkable method of asexual reproduction, specifically through transverse fission. The worm can split itself into two or more parts, each of which regenerates into a complete organism. The name "longifissura" hints at this long splitting process.
• Regeneration: Post-fission, each segment is capable of regenerating the missing parts, making this species a subject of interest in the study of regenerative biology.

Habitat

• Marine Environment: These worms are found in marine environments, often associated with coral reefs and shallow coastal waters. They prefer habitats where they can benefit from their symbiotic algae.

Behavior

• Locomotion: Convolutriloba longifissura moves using cilia on its ventral surface, gliding smoothly over substrates in its habitat.
• Feeding: The diet consists mainly of small particles and microorganisms. Their symbiotic relationship with algae also plays a crucial role in their nutrition.

Ecological Role

• Symbiosis and Ecosystem Interaction: As part of the marine ecosystem, they play a role in nutrient cycling and serve as a food source for other marine animals. Their relationship with symbiotic algae also contributes to primary production in their habitats.

Research Significance

• Regeneration Studies: The ability of Convolutriloba longifissura to regenerate its body parts makes it an important model organism in scientific research, particularly in studies related to developmental biology and regenerative medicine.
• Evolutionary Insights: Studying this worm provides insights into the early evolution of bilaterian animals, given its position in the phylogenetic tree.

Conservation Status

• Population and Threats: There is limited information on the conservation status of Convolutriloba longifissura specifically. However, like many marine organisms, they could be affected by habitat degradation, pollution, and climate change.

Fun Fact

• Bioluminescence: Some species within the Convolutriloba genus are known for their bioluminescence, although it is not well-documented if Convolutriloba longifissura exhibits this trait.

In summary, Convolutriloba longifissura is a small but remarkable marine worm notable for its asexual reproduction through fission, its symbiotic relationship with algae, and its significance in scientific research on regeneration and evolutionary biology.

But what about these flatworms?

You now have three choices: you can give them the same enzymes and processes you gave the bacteria, but that was too simple for the algae, so why make it that easy for the flatworm? You could put the bacteria in the flat-worm cells like you did with the algae; but why do that when there is an even More complicated method? The third choice is to put the algae inside the flatworms and, as that's the most complicated way of doing it, why not go for that solution?

Creationism in Crisis - How Ancient Symbiotic Relationships Drive Evolution - Naturally

Selection of lichens
symbiosis between cyanobacteria and fungi

Symbiotic relationship between clown fish and anemone.

Species living closely together in symbiosis is far older and way more common than you might think

Biologically, symbiotic relationships are alliances of genes that give the lie to creationist claims that 'selfish' genes are genes for selfishness. In fact, if it's in the interests of genes, and it usually is, genes form alliances that put the two species in the partnership on an evolutionary trajectory in which both species benefit from the evolution of one or the other in a process known as co-evolution.

When you understand this, you can find examples almost everywhere you look - think how many wild jungle fowl there would be today if they hadn't formed an alliance with humans to become the commonest bird on Earth - the domestic hen. The same goes for sheep, pigs, cattle, horses, cats and dogs. The 'selfish' genes are of course, unconcerned about the ultimate fate of their carriers, hence the term 'selfish'; the only thing that matters is how many of them there are in the world, and there are unarguably now more human and more of our domestic animals’ genes in the world than when they were wild animals and we were hunter-gatherers.

And, when you look inside a complex cell, you see more examples of symbiosis - several cell organelles such as mitochondria and (in plants) chloroplasts, are really bacteria in symbiotic association with the cell.

Our gut microbes, and the often-unique gut microbes of other species such as cockroaches, are locked in a symbiotic co-evolution from which neither can escape because to do so would lose the benefit of mutuality.

In the following article, reprinted from The Conversation under a Creative Commons licence, Gregory Moore, Senior Research Associate, School of Ecosystem and Forest Sciences, The University of Melbourne, explains how symbiotic relationships are commonplace in nature and have shaped evolution. His article has been reformatted for stylistic consistency:

Evolution in Action - New Study Finds Evidence for Evolution Of A New, Nitrogen-Fixing Cell Organelle

Composite of catalized reporter deposition fluorescence in situ hybridization (CARD-FISH) images showing the range of sizes of the different UCYN-A sublineages.

Cornejo-Castillo, F.M., et al (2024)

Transmission electron micrograph images of the C. parkeae stage of B. bigelowii. Light microscopy images (A,C) and corresponding TEM images are shown (B,D) for strain MK90-06. Usually, one endosymbiont is found per cell in the posterior of the cell (A,B); however, some of the cells had two endosymbionts per cell during cell division (C,D). Scale bars represent 5 μm in (A and C), and 2 μm in (B and D). E, endosymbiont; G, Golgi apparatus; M, mitochondrion; N, nucleus; P, plastid; and Py, pyrenoid.

Suzuki, Shigekatsu, et. al, (2021)

Evolution in action? New study finds possibility of nitrogen-fixing organelles – Rhody Today

Most biologists now accept the Endosymbiosis Theory which explains how simple prokaryote cells became complex eukaryote cells by a single-celled prokaryote such as an archaea incorporating other single-celled prokaryotes inside its cell membrane. This may have been by engulfing them as prey or by being parasitised by them. Whatever the mechanism, a symbiotic relationship ensued which progressed to the extent that the incorporated cell's DNA was transferred to the host genome and the incorporated cell became a cell organelle.

This explains the origin of cell organelles such as the mitochondria which metabolise glucose to turn adenosine diphosphate (ADP) into adenosine triphosphate (ATP) which can then be used to power metabolic processes within the cell. Mitochondria have some similarities with rickettsia bacteria which strongly suggests they have evolved from free-living rickettsia.

Likewise, chloroplasts in plant cells were once free-living, photosynthesising cyanobacteria which became incorporated in what was to become algae, so giving rise eventually to almost all plant life.

And now we have evidence that another incorporation is evolving, in the form of nitrogen-fixing bacteria being incorporated as organelles into a marine alga, which gives the algae the ability to create ammonia and so nitrates directly from atmospheric nitrogen. This was discovered by researchers from the University of Rhode Island, the Institut de Ciències del Mar in Barcelona, the University of California at Santa Cruz and the Massachusetts Institute of Technology. They have published their findings, open access, in the journal Cell.

Although nitrogen is abundant, comprising about 79% of Earth's atmosphere, it exists as the diatomic gas dinitrogen (N₂) which is notoriously stable making molecular nitrogen almost an inert substance and requiring a lot of energy to break the N-N bond. However, some bacteria, the nitrogen-fixing bacteria, have evolved the ability to do this using the enzyme nitrogenase:

Unintelligent Design - How A Virus Saved The Unintelligent Designer's Blushes Early In Multicellular History

A virus that infected animals hundreds of millions of years ago has become essential for the development of the embryo

I've remarked before how similar biological systems are to the machines the late William Heath Robinson designed for solving simple, everyday problems. Simple solutions were eschewed for more complicated ones and unlikely items were used in ways they weren't intended for, such as a grandfather clock standing on a piano to support a platform balanced on top. Everything was held together by pieces of knotted string and labour-saving devices took far more people than would have been needed to do the job more simply.

And yet, the whole contraption worked, or at least looked as though it would if were ever made, but take any part away and the whole thing would fail, in an example of what creationists call 'irreducible complexity'.

So, let's pretend that creationism's, 'intelligent'[sic] designer really is behind the design of living organisms and see how closely Heath Robinson unwittingly parodied it:
Just such an example of a Heath Robinson machine in biology was revealed a few days ago in an open access paper published in Science Advances, explaining how a virus which became incorporated in the genome of an early multicellular organism provided a solution to a problem of the designer's own making. The problem it solves was how to overcome the problem created by choosing the same method of cell replication in multicellular organisms that single-celled organisms use, where the entire genome needs to be replicated at each division.

The entire 'point' of multicellularity, and what gave it its success over single-celled organisms is division of labour, in other words, specialisation, so the organisms can be divided into tissues and organs that perform a specialised task. This means that every cell has to have the potential to carry out every function, in the genes it inherits from its parent cell, yet only a few genes are need for its particular specialty.

The process by which this is achieved is the complicated epigenetic system which turns off unneeded genes as the cells differentiate into different cell lines in the developing embryo, and these settings can't normally be reversed.

However, the sperm and egg which then fused to form the zygote from which a new embryo develops, are themselves specialised cells with all the epigenetic settings of their parent cells with an additional few of their own, and these are inherited by the zygote, so to make cell differentiation possible again, the zygote is quickly (within minutes of fertilisation) reset to a state of totipotency.

So, to overcome the epigenetic settings problem that is a problem of the designer's own making, the zygote needs to be epigenetically reprogrammed and this happens in two stages: first to produce a 'totipotent' cell with the potential to produce all the different cells in the embryo as well as the placenta, umbilical cord, and amniotic sack in which the embryo will develop, and then, soon after cell division begins, 'pluripotent' cells from which the different stem cells for the required specialised cell lines will develop.

How this was helped by a virus is the subject of the paper by researchers from the Spanish National Cancer Research Centre (CNIO), Madrid, Spain. First, a little AI background:

Creationism in Crisis - How Evolution Produced Full Cooperation Between Mitochondrial Endosymbionts and Host Cells

Mitochondria communicate intensively with their host, the higher (eukaryotic) cell.

Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy

Louisa Howard via Wikipedia
Public Domain

Cell biology: How cellular powerhouses call for help when under stress | Aktuelles aus der Goethe-Universität Frankfurt

Four Scientists from Goethe University, Frankfurt, Germany have shown just how fully mitochondria have integrated into their endosymbiotic host cells over the course of their evolutionary history.

First a little background from ChatGPT3:

Mitochondria and how they evolved>

Mitochondria are double-membraned organelles found in the cells of most eukaryotic organisms, including plants, animals, fungi, and protists. They play a crucial role in cellular respiration, where they generate adenosine triphosphate (ATP), the primary energy currency of cells. Mitochondria are believed to have evolved from endosymbiosis, a process where one organism lives within another and both organisms benefit from the relationship.

The endosymbiotic theory suggests that mitochondria originated from a free-living bacterium that was engulfed by an ancient eukaryotic cell. Over time, the bacterium and the host cell developed a symbiotic relationship, where the bacterium provided energy through respiration, and the host cell provided protection and nutrients. Eventually, the bacterium lost some of its independence and became a specialized organelle within the host cell – the mitochondrion.