Wednesday, July 6, 2022


Scientists last year discovered a whole new kind of DNA bearing entity. Whether it is an organism itself isn't entirely clear, and if it is one, it doesn't fit into any of the existing categories of DNA bearing entities.

It's one thing to find a new species or even a new family or organisms, it's another to find a whole new kind of organism which is on a par with being the first person to discover viruses. It is quite an exciting discovery.
In the TV series Star Trek, the Borg are cybernetic aliens that assimilate humans and other creatures as a means of achieving perfection. So when Jill Banfield, a geomicrobiologist at the University of California, Berkeley, sifted through DNA in the mud of her backyard and discovered a strange linear chromosome that included genes from a variety of microbes, her Trekkie son proposed naming it after the sci-fi aliens. The new type of genetic material was a mystery. Maybe it was part of a viral genome. Maybe it was a strange bacterium. Or maybe it was just an independent piece of DNA existing outside of cells. . . .

Banfield . . . and graduate student Basem Al-Shayeb were searching for viruses that infect archaea, a type of microbe often found in places devoid of oxygen. They would dig 1 meter or more below the surface and collect mud samples that might harbor archaea and their viruses. Next, they would sequence every stretch of DNA in the samples and use sophisticated computer programs to scan for sequences that signified a virus, rather than any other organism.

"We started off with a piece of mud and 10 trillion pieces of DNA," Banfield says. One sample, taken from the mud on her property, contained a gene-filled stretch of DNA almost 1 million bases long—and more than half the genes were novel. This linear stretch of DNA also had a particular pattern of bases at its beginning and end, distinct stretches of repetitive DNA between its genes, and two places along the sequence where DNA duplication could begin—which indicated the Borg could make copies of itself. Together, this suggested it was not just a random concoction of genes.

After they identified the first Borg sequence, the researchers began to scan microbial DNA in public databases to see whether they could find anything similar. They found a few variations in groundwater from Colorado—there, the first purported Borg showed up about 1 meter deep and got more abundant deeper down. Other versions showed up in DNA from the discharge of an abandoned mercury mine in Napa, California, and from a shallow riverbed of the East River in Colorado.

Altogether, the researchers isolated 23 sequences they think may be Borgs—and 19 they have identified as having all the characteristics of the first Borg they discovered, they write . . . on the preprint server bioRxiv. Some are almost 1 million bases long. "I don't think anything else that's been discovered is as big as these guys are," among previously known extrachromosomal DNA elements, Doolittle says.

In every place, copies of the Borg co-occurred with DNA linked to a methane-oxidizing archaeon called Methanoperedens. That suggests the Borgs may exist inside the microbe, the researchers say. But because Methanoperedens can't be grown in a lab, the team hasn't been able to confirm this suspicion. Meanwhile, team members have ruled out the possibility that the Borg came from another microbe, as they lack many necessary genes for life, or a virus, which typically have shorter chromosomes.
From Science.
Anaerobic methane oxidation exerts a key control on greenhouse gas emissions, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as “Borgs”. We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions.


Mitchell said...

The evidence that this is real seems far from decisive. As far as I can see, their existence is deduced solely from genome assembly... The sentence "Off with his head that wears the crown" can be assembled from fragments of Shakespeare, but doesn't actually occur in any of his plays.

neo said...


David Schroeder
July 7, 2022 at 2:47 pm

andrew said...

@neo Looked at the comment. Not super interested in the specific issue.

May blog about GUT efforts someday.

But, I prefer to focus on what is known or solid or at least supported by credible observational evidence, rather than speculative BSM theories for the most part.

neo said...

are Octonions and the Standard Model a GUT efforts

andrew said...

The SM is by definition not a GUT. It breaks up the model into three groups SU(3)xSU(2)xU(1), rather than a single unified group. The whole point of GUT theories is that the SM isn't one.

Octonions are not inherently a GUT but whether or not you use Octonions and whether it is a GUT are orthogonal questions. There is no intrinsic reason that you can't have neither, both, or one or the other.