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.

Creationism in Crisis - A Newly-Discovered Non-Genetic Mode for Inheritance, But It's No Comfort For Creationists

Because babies acquire their first gut microbes passing through their mother’s birth canal, mothers’ microbiomes form the basis of their offspring’s.

Photo: Sarah Chai/Pexels

Hardship affects the gut microbiome across generations | UCLA

Human gut microbiome

Source

The old scientific debate from the early 19th century between Darwinian evolution and Lamarckian evolution all hinged on whether characteristics acquired after birth could be inherited by offspring, as Lamarck thought, or whether what we inherit from our parents is a variation (within limits) of what they inherited from their parents:

Darwinian and Lamarckian evolution are two contrasting theories of evolution that were proposed in the past. Though both sought to explain the process of biological change over time, they differ in their fundamental mechanisms and assumptions.

1. Darwinian Evolution (Theory of Natural Selection):
   • Proposed by Charles Darwin and Alfred Russel Wallace in the mid-19th century.
   • Central concept: Natural selection is the main driving force behind evolution.
   • Mechanism: Variation exists within populations, and individuals with traits better suited to the environment are more likely to survive and reproduce. Over time, these advantageous traits become more common in the population, while less favorable traits are selected against.
   • Inheritance of acquired characteristics: Darwinian evolution does not rely on the inheritance of traits acquired during an organism's lifetime. Instead, it is based on the passing down of genetic information from parents to offspring.
   • Example: Consider a population of giraffes with varying neck lengths. If the environment favors individuals with longer necks (e.g., taller trees for feeding), those with longer necks have a survival advantage and are more likely to pass on their long-necked genes to the next generation.
2. Lamarckian Evolution (Theory of Inheritance of Acquired Characteristics):
   • Proposed by Jean-Baptiste Lamarck in the early 19th century.
   • Central concept: Evolution is driven by an organism's effort to adapt to its environment and the inheritance of acquired traits.
   • Mechanism: Lamarck proposed that if an organism acquires new characteristics or traits during its lifetime due to its environment's demands, these acquired traits can be passed on to its offspring.
   • Example: Lamarck suggested that if a giraffe stretches its neck throughout its lifetime to reach higher leaves, the elongated neck acquired during its life will be passed on to its offspring, leading to the gradual evolution of longer-necked giraffes over generations.

The key difference between the two theories lies in their view on the inheritance of acquired characteristics. Darwinian evolution relies on natural selection acting on existing genetic variation, while Lamarckian evolution suggests that acquired traits during an individual's lifetime can be inherited by their offspring, driving evolutionary change. Lamarckian evolution, however, has been largely discredited by modern genetics and molecular biology, as it does not align with the principles of inheritance through genes and DNA. Instead, the modern understanding of evolution is based on the principles proposed by Darwin, which include the processes of mutation, genetic variation, and natural selection acting on heritable traits.

ChatGPT3 "What is the difference between Darwinian and Lamarckian evolution?" [Response to user request]
Retrieved from https://chat.openai.com/

That debate has now been opened up again in an unexpected way with the news that an international team of scientists led by UCLA psychologists has shown that information produced during hardship suffered by a woman during pregnancy can be passed on to her baby via its microbiome.

Creationism in Crisis - So What 'Kind' is This Strange Thing?

Creationism in Crisis

So What 'Kind' is This Strange Thing?

George, Emma E., et al.(2023)

Evolutionary oddball has seven genomes inside a single cell | New Scientist

The Bible that creationists turn to for a source of scientific information, is of course, as hopelessly muddled and simplistic about biology as it is about cosmology, morality and medicine. For example, this is how it tries to classify the birds that it is forbidden to eat under the irrational food taboos it mandates for believers:

And these are they which ye shall have in abomination among the fowls; they shall not be eaten, they are an abomination: the eagle, and the ossifrage, and the ospray, and the vulture, and the kite after his kind; every raven after his kind; and the owl, and the night hawk, and the cuckow, and the hawk after his kind; the little owl, and the great owl, and the swan, and the pelican, and the gier eagle, and the cormorant; and the stork, the heron after her kind, and the lapwing, and the bat.

Leviticus 11:13-19

Not surprisingly, and not just because of the hilarious gaff of including 'the bat' in a list of birds, and the muddle over the different 'kinds' of owl, biologists soon realised how hopelessly inadequate the Biblical notion of 'kinds' is as a means of classifying biological taxons, so had the devise the modern classification system.

And, presumably because the authors didn't realise that plants are alive because they don't breath like vertebrates do, there is no attempt to classify plants. In fact, the author's show their muddle over plants by this strange piece from Genesis:

Then God said, 'Let the earth put forth vegetation: plants yielding seed, and fruit trees of every kind on earth that bear fruit with the seed in it. ' And it was so. The earth brought forth vegetation: plants yielding seed of every kind, and trees of every kind bearing fruit with the seed in it.

Genesis 1:11-12

Clearly the Bible's authors thought there were only angiosperms (the most advances plants) since they are the only ones mentioned. Incidentally, more of their muddle is illustrated by the fact that this creation of green plants occurs before the sun is created, showing the authors knew nothing of photosynthesis.

And of course, there is no hint that the authors were even aware of single-celled micro-organisms, otherwise they might have mentioned germ theory, of which there is not a single word. Imaging how many lives could have been saved and how much suffering would have been avoided if God had thought to mention bacteria and viruses and how to avoid being infected by them, assuming it didn't know what it had created them for in the first place...

But that's an aside. The real muddle comes with the authors attempt to come up with a classification system, as Bible-literalist creationists assume that's what they were trying to do.

So, here is a curveball inadvertently thrown to creationists by researchers led by Emma E. George, now of the Scripps Institution of Oceanography, Integrative Oceanography Division, University of California, San Diego, La Jolla, CA, USA, when working at the University of British Columbia in Canada.

Her team have discovered single-celled algae that are not single organisms at all, but a complex community of seven different organisms, each with its own genome, and each playing a part in a complex relationship within the algal cell body.

Figure 3
Microscopy of Cryptomonas gyropyrenoidosa SAG 25.80 with bacterial endosymbionts.

(A) DIC; (B) DAPI; (C) FISH-M. polyxenophila probe; (D) FISH-G. numerosa probe; (E) overlay of (C) and (D); (F) endosymbionts clustered in the host cytoplasm, including endosymbionts with virus-like particles (Sv); (G) endosymbiont with virus-like particles within the bacterial cytoplasm and attached to the bacterial cell’s surface (arrowhead); and (H) bacterial endosymbionts and a membrane-like structure (i.e., putative autolysosome vacuole) that potentially contains virus-like particles (arrowhead). See also Figures S4A and S4C and Table S2.

George, Emma E., et al.(2023)