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)

Figure 6
Putative interactions between the MAnkyphage, two bacterial endosymbionts (M. polyxenophila and G. numerosa), and the cryptomonad host.
Cryptomonas gyropyrenoidosa harbors 4 genomes (in green): nuclear, mitochondrial (MT), nucleomorph (NM), and plastid. Mobile elements are found in the endosymbionts’ chromosomes and plasmids, particularly in M. polyxenophila. Only G. numerosa encodes a flagellum, but both endosymbionts have type IV secretion systems (T4SS) and ATP/ADP translocases. The endosymbionts and phage also encode eukaryotic-like protein domains like ankyrin repeats (ANKs) and leucine-rich repeats (LRRs). Other putative eukaryotic interactions include the MAnkyphage-encoded protein (DUF3685) with homology to response regulators in plastids and cyanobacteria. MAnkyphage harbors a type II toxin-antitoxin system present in M. polyxenophila. The tally of genomes in this single-celled cryptomonad comes to 7 plus 3 bacterial plasmids. See also Figures S3 and S5–S7 and Data S1.

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

The organism is a type of free-swimming single-celled algae called a cryptomonad, that normally predates on other single-celled organisms. The origin of the laboratory strain was collected in about 1970. The predatory naturel of the organism gives a clue to the origin of the symbionts within the cell, in the same endosymbiotic way other organisms were incorporated by prokaryote cells to form the eukaryote cells that all multicellular organisms have evolved from.

But what is unique about this strain of cryptomonad, which the researchers have identified as Cryptomonas gyropyrenoidosa is that so many of what are assumed to be symbionts have retained so much of their own DNA. Cryptomonads are not true algae, which incorporated a cyanobacterium inside their cells to become the chloroplasts which perform photosynthesis. Instead, cryptomonads incorporated a complex red alga, complete with its own chloroplasts. This red alga has retained a shrunken form of its own genome.

To complicate things further, of the two bacteria, Grellia numerosa and Megaira polyxenophila, that have also been incorporated, one of them, M. polyxenophila has a phage virus living within it. The fact that the phage virus hasn't killed off its host suggests it conveys a benefit of some sort to the bacterium, and so has become an endosymbiont in its own right. This view is supported by the fact that M. polyxenophila is more abundant in the host cryptomonads than Grellia numerosa, so seems to be the more successful of the two.

The relationship between the different organisms in the complex is shown in the following table:

Summary of sequenced genomes from Cryptomonas gyropyrenoidosa SAG 25.80

Genome

Taxonomy

Host

MAnkyphage

Caudoviricetes

Megaira polyxenophila

Megaira polyxenophila

Rickettsiales; Rickettsiaceae

Cryptomonas gyropyrenoidosa

Grellia numerosa

Rickettsiales;
Midichloriaceae

Cryptomonas gyropyrenoidosa

Plastid

Cryptomonad

Cryptomonas gyropyrenoidosa

Mitochondrion

Cryptomonad

Cryptomonas gyropyrenoidosa

Nucleomorph Chromosome 1

Cryptomonad

Cryptomonas gyropyrenoidosa

Nucleomorph Chromosome 2

Cryptomonad

Cryptomonas gyropyrenoidosa

Nucleomorph Chromosome 3

Cryptomonad

Cryptomonas gyropyrenoidosa

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

What is not clear is whether this situation arises in the wild and was in the original sample from which the laboratory strain is descended, or whether this has arisen in the special conditions i the laboratory.

To make matters worse for creationists struggling to fit this organism into their hopelessly muddled and inadequate definition of 'kind' in the Bible, this is not the only example of a single-celled species containing multiple genomes derived from multiple organisms which have become incorporated in its evolutionary history. Dinoflagellates, for example, host single-celled algae called diatoms and can have up to six distinct genomes within them. One example was found by Norico Yamada at the University of Konstanz in Germany to have incorporated diatoms on four separate occasions and so may have had nine genomes, however, Yamada thinks the same species may have been incorporated several times, so, although the genomes of earlier incorporations may have degenerated over time, they are not really distinct genomes, depending on how you define 'distinct'.

The team's findings are published in the online journal, Current Biology:

Highlights

• A cryptomonad hosts two distinct bacterial endosymbionts and a bacteriophage
• The bacteriophage infects the endosymbiont, Megaira polyxenophila
• Both bacterial endosymbionts and bacteriophage encode eukaryotic-like proteins
• Seven distinct genomes are present in the single-celled cryptomonad

Summary

Symbiosis between prokaryotes and microbial eukaryotes (protists) has broadly impacted both evolution and ecology. Endosymbiosis led to mitochondria and plastids, the latter spreading across the tree of eukaryotes by subsequent rounds of endosymbiosis. Present-day endosymbionts in protists remain both common and diverse, although what function they serve is often unknown. Here, we describe a highly complex community of endosymbionts and a bacteriophage (phage) within a single cryptomonad cell. Cryptomonads are a model for organelle evolution because their secondary plastid retains a relict endosymbiont nucleus, but only one previously unidentified Cryptomonas strain (SAG 25.80) is known to harbor bacterial endosymbionts. We carried out electron microscopy and FISH imaging as well as genomic sequencing on Cryptomonas SAG 25.80, which revealed a stable, complex community even after over 50 years in continuous cultivation. We identified the host strain as Cryptomonas gyropyrenoidosa, and sequenced genomes from its mitochondria, plastid, and nucleomorph (and partially its nucleus), as well as two symbionts, Megaira polyxenophila and Grellia numerosa, and one phage (MAnkyphage) infecting M. polyxenophila. Comparing closely related endosymbionts from other hosts revealed similar metabolic and genomic features, with the exception of abundant transposons and genome plasticity in M. polyxenophila from Cryptomonas. We found an abundance of eukaryote-interacting genes as well as many toxin-antitoxin systems, including in the MAnkyphage genome that also encodes several eukaryotic-like proteins. Overall, the Cryptomonas cell is an endosymbiotic conglomeration with seven distinct evolving genomes that all show evidence of inter-lineage conflict but nevertheless remain stable, even after more than 4,000 generations in culture.

George, Emma E.; Barcytė, Dovilė; Lax, Gordon; Livingston, Sam; Tashyreva, Daria; Husnik, Filip; Lukeš, Julius; Eliáš, Marek; Keeling, Patrick J.
A single cryptomonad cell harbors a complex community of organelles, bacteria, a phage, and selfish elements
Current Biology. DOI: 10.1016/j.cub.2023.04.010

© 2023 Elsevier Inc.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

So, then, which creationist, confident in the belief that all the answers are to be found in "God's Holy Word", is going to be brave enough to look for the correct classification of this complex, multi-genomed organism in the Bible, or be honest enough to admit that they can't find it?

---

Thank you for sharing!

Tweet Link