Creationism in Crisis - Now its A Living Nematode From 46,000 years Ago in Siberian Permafrost

Permafrost melts into the Kolyma River outside of Zyryanka, Russia, in 2019. The worms in the new study seem to have survived buried deep in the permafrost for tens of thousands of years.

Michael Robinson Chavez / The Washington Post via Getty Images

Duvannyi Yar thaw site on the banks of the Kolyma River, Siberia, Russia.

Credit: Robert G. M. Spencer

Genome analysis of 46,000-year-old roundworm from Siberian permafrost reveals novel species: MPI-CBG

The problem with clinging to counter-factual beliefs like Bible-literalist creationism, for fear of having to contemplate being wrong, is that you have to keep deciding whether to believe the Bible or the evidence.

Here, for example, is a (to a creationist) key passage from the Bible:

Fifteen cubits upward did the waters prevail; and the mountains were covered.

And all flesh died that moved upon the earth, both of fowl, and of cattle, and of beast, and of every creeping thing that creepeth upon the earth, and every man:

All in whose nostrils was the breath of life, of all that was in the dry land, died.

And every living substance was destroyed which was upon the face of the ground, both man, and cattle, and the creeping things, and the fowl of the heaven; and they were destroyed from the earth: and Noah only remained alive, and they that were with him in the ark.

Genesis 7:21-23

Leaving aside the absurdity of believing there was a time just 4000 years ago when the highest mountain would have been covered by a fifteen-cubit (i.e., about 22.5 feet) flood, it is necessary to believe that everything outside the Ark was destroyed. The Bible is quite specific on that point - every living substance was destroyed, including the 'creeping things'!

And that claim has to be set against the evidence provided a couple of days ago by an international team of scientists led by Anastasia Shatilovich, of the Institute of Physicochemical and Biological Problems in Soil Science Russian Academy of Science, Pushchino, Russia, and Vamshidhar R. Gade of the Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany, that they have revived, analysed the genome of and C14-dated a nematode worm recovered from Siberian permafrost, shown to be 46,000 years old.

So, not only was this not destroyed as the Bible claims, it was around some 36,000 years before the Earth was created, according to creationist fundamental dogma.

And of course, a corollary to that is that the permafrost containing the nematode in suspended animation, also survived a catastrophic flood a few thousand years ago.

But then, to be fair on the Bronze-Age Canaanite hill farmers who plagiarized that Mesopotamian local flood myth, what did they know of real mountains, as opposed to low hills, permafrost, or nematodes? They thought Earth was small, flat and ran on magic, and the sky was a dome to keep the water above it out.

The account of the discovery, and its significance, is explained in a news release by the Max Planck Institute of Molecular Cell Biology and Genetics:

Genome analysis of 46,000-year-old roundworm from Siberian permafrost reveals novel species

International research team shows that a newly discovered nematode species from the Pleistocene share a molecular toolkit for survival with the nematode Caenorhabditis elegans.

Scanning electron pictures of Panagrolaimus kolymaensis, female. (Scale bar - 20 µm)

© Alexei V. Tchesunov and Anastasia Shatilovich
Institute of Physicochemical and Biological Problems in Soil Science RAS

Some organisms, such as tardigrades, rotifers, and nematodes, can survive harsh conditions by entering a dormant state known as “cryptobiosis.” In 2018, researchers from the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia found two roundworms (nematode) species in the Siberian Permafrost. Radiocarbon dating indicated that the nematode individuals have remained in cryptobiosis since the late Pleistocene, about 46,000 years ago. Researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, the Center for Systems Biology Dresden (CSBD), and the Institute of Zoology at the University of Cologne, all located in Germany, used genome sequencing, assembly, and phylogenetic analysis and found that the permafrost nematode belongs to a previously undescribed species, Panagrolaimus kolymaensis. They showed that the biochemical mechanisms employed by Panagrolaimus kolymaensis to survive desiccation and freezing under laboratory conditions are similar to those of a life-cycle stage in the important biological model Caenorhabditis elegans.

When Anastasia Shatilovich at the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia revived two frozen individual nematodes from a fossilized burrow in silt deposits in the Siberian permafrost, she and her colleagues were beyond excited. After thawing the worms in the lab, a radiocarbon analysis of plant material from the burrow revealed that these frozen deposits, 40 meters below the surface, had not thawed since the late Pleistocene, between 45,839 and 47,769 years ago. At the same time, the research group of Teymuras Kurzchalia at the MPI-CBG (Teymuras Kurzchalia is now retired) was already addressing the question of how larval stages of the nematode Caenorhabditis elegans survive extreme conditions. When the team heard about the permafrost nematodes, they immediately reached out for a collaboration with Anastasia Shatilovich.

Vamshidhar Gade, a doctoral student at that time in the research group of Teymuras Kurzchalia, started to work with the permafrost nematodes. “What molecular and metabolic pathways these cryptobiotic organisms use and how long they would be able to suspend life are not fully understood,” he says. Vamshidhar is now working at the ETH in Zurich, Switzerland.

The researchers in Dresden conducted a high-quality genome assembly of one of the permafrost nematodes in collaboration with Eugene Myers, Director Emeritus and research group leader at the MPI-CBG, the DRESDEN-concept Genome Center, and the research group of Michael Hiller, research group leader at that time at the MPI-CBG and now Professor of Comparative Genomics at the LOEWE-TBG and the Senckenberg Society for Nature Research. Despite having DNA barcoding sequences and microscopic pictures, it was difficult to determine whether the permafrost worm was a new species or not. Philipp Schiffer, research group leader at the Institute of Zoology, co-lead of the incipient Biodiversity Genomics Center Cologne (BioC2) at the University of Cologne, and expert in biodiversity genomics research, joined forces with the Dresden researchers to determine the species and analyze its genome with his team. Using phylogenomic analysis, he and his team were able to define the roundworm as a novel species, and the team decided to call it “Panagrolaimus kolymaensis”. In recognition of the Kolyma River region from which it originated, the nematode was given the Latin name Kolymaensis.

By comparing the genome of Panagrolaimus kolymaensis with that of the model nematode Caenorhabditis elegans, the researchers in Cologne identified genes that both species have in common and that are involved in cryptobiosis. To their surprise, most of the genes necessary for entering cryptobiosis in Caenorhabditis elegans so-called Dauer larvae were also present in Panagrolaimus kolymaensis. The research team next evaluated Panagrolaimus kolymaensis's ability to survive and discovered that mild dehydration exposure before freezing helped the worms prepare for cryptobiosis and increased survival at -80 degrees Celsius. At a biochemical level, both species produced a sugar called trehalose when mildly dehydrated in the lab, possibly enabling them to endure freezing and intense dehydration. Caenorhabditis elegans larvae also benefited from this treatment, surviving for 480 days at -80 degrees Celsius without suffering any declines in viability or reproduction following thawing.

According to Vamshidhar Gade and Temo Kurzhchalia, “Our experimental findings also show that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously documented. Overall, our research demonstrates that nematodes have developed mechanisms that allow them to preserve life for geological time periods.”

“Our findings are essential for understanding evolutionary processes because generation times can range from days to millennia and because the long-term survival of a species' individuals can result in the re-emergence of lineages that would otherwise have gone extinct,” concludes Philipp Schiffer, one of the authors who oversaw the study. Eugene Myers adds: “P. kolymaensis's highly contiguous genome will make it possible to compare this feature to those of other Panagrolaimus species whose genomes are presently being sequenced by Schiffer’s team and colleagues.” Philipp Schiffer is convinced that “studying the adaptation of species to such extreme environments by analyzing their genomes will allow us to develop better conservation strategies in the face of global warming.” Teymuras Kurzchalia says: “This study extends the longest reported cryptobiosis in nematodes by tens of thousands of years.”

The team presents their findings in an open access paper in PLOS Genetics:

Abstract
Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus kolymaensis. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in P. kolymaensis and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

Author summary
Survival in extreme environments for prolonged periods is a challenge that only a few organisms, are capable of. It is not well understood, which molecular and biochemical pathways are utilized by such cryptobiotic organisms, and how long they might suspend life. Here, we show that a soil nematode Panagrolaimus kolymaensis, suspended life for 46,000 years in the Siberian permafrost. Through comparative analysis, we find that P. kolymaensis and model organism C. elegans utilize similar adaptive mechanisms to survive harsh environmental conditions for prolonged periods. Our findings here are important for the understanding of evolutionary processes because generation times could be stretched from days to millennia, and long-term survival of individuals of species can lead to the refoundation of otherwise extinct lineages.|

Shatilovich A, Gade VR, Pippel M, Hoffmeyer TT, Tchesunov AV, Stevens L, et al. (2023)
A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva. PLoS Genet 19(7): e1010798. https://doi.org/10.1371/journal.pgen.1010798

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

(A) Location of the Duvanny Yar outcrop on the Kolyma River, northeastern Siberia, Russia. https://climate.copernicus.eu/sites/default/files/inline-images/C3S_indicator_sea_ice_sidebar_figS2_branded.png) (https://climate.copernicus.eu/data-protection-and-privacy-statement) (B) View of the upper part of outcrop composed of ice wedges and permafrost silty deposits. (C) Lithostratigraphic scheme of deposits, showing location of studied rodent borrow (red circle). (D) fossil rodent burrow with herbaceous litter and seeds buried in permafrost deposits; m a.r.l. = meters above river level.

https://doi.org/10.1371/journal.pgen.1010798.g001

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Scanning electron pictures (A, C), light microscopy photographs (E, F) and graphic presentations (B, D, G) of holotype: A, B) entire body, C, D) anterior ends, E) anterior body, F) perivulvar body region, G) tail. Abbreviations: l.f.–lateral field, ov–ovary, pro–procorpus of the pharynx, t.b.–terminal bulb of the pharynx, u–uterus with eggs, v–vulva, v.p.–ventral pore. Scale bars: A, D, E, F, G– 20 μm, B– 100 μm, C– 2 μm.

https://doi.org/10.1371/journal.pgen.1010798.g002

It's fascinating to realise that when this nematode entered into a state of suspended animation, 46,000 years ago, the human inhabitants of Siberia were Neanderthals and Denisovans and possibly other descendants of Homo erectus, but almost certainly not anatomically modern humans, Homo sapiens, who were just beginning to venture out of Africa into the Middle East, ironically to the same area occupied thousands of years later by their descendant, who wrote the imaginative Hebrew origins myths that became incorporated into the Bible.

The whole of Eurasia human evolution, dispersion across the globe, and cultural evolution has happened during the extended lifetime of that nematode, which had been asleep, if suspended animation can be called sleep, for about 40,000 when the pyramids were being built.

To summarize then, what creationists now need to cope with is the evidence of:

1. Frozen silt that shouldn't be there is there was a genocidal flood 4000 years ago
2. A nematode that shouldn't be there if the Bible is correct in its claim that all living substance outside the Ark was destroyed in that genocidal flood.
3. And all of it over 40,000 years older than they believe the Universe is.

And all to try to exist in what they see as a hierarchical society where being privy to deep secrets and superior knowledge to scientists enhances your social status in a sub-culture which values such things above education and intellectual achievement. And this enhanced status is of course much easier to achieve that the hard graft of study and the intellectual chore of understanding science.

And in pursuit of that enhanced status and ego-preening from fellow cultists, they see nothing wrong with presenting what they claim to be the creation of a god they claim to worship, as a simple conjuring trick, and minimising the spectacular grandeur and magnificence of the Universe, because learning about that takes too much effort.

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Thank you for sharing!

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