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PaperclipPerfector  9d ago (text post)   27456 thread views

Culture War Roundup for the week of May 26, 2025

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You could probably dial that back to a bioweapons program run by George Washington, because, shock and amazement, that study failed to replicate.

To confirm LMAT’s ability to analyze large (real) metagenomes and provide new biological insight, we downloaded the Tyrolean Iceman sequence data (Keller et al., 2012) from the SRA, which constituted 150 giga-bases of raw genomic data. While 78% of the sequenced reads were reported to be human, only a small percentage (0.84%) of the reads was reported to originate from bacteria based on a sample of 8 million reads. Our hypothesis was that LMAT could examine all the reads on a single large memory compute node and efficiently provide a more complete analysis of the microbial contents. For this application, the human genome (v19) was added to LMAT’s database to classify human and microbial reads simultaneously. The analysis on the raw 150 giga-base dataset (2.3 billion reads) ran in <20 h on our single node large memory computer (see Supplementary Material for additional details). LMAT output agreed with the published finding that the vast majority of bacteria were from the phylum Firmicutes and under the class of Clostridia. Similarly, only a small fraction of reads were reported to be from the Spirochaetes phylum. LMAT results did not show evidence for the presence for non-phage, non-retroviral viruses, fungi or protists after adjusting for previously unidentified human contamination in draft eukaryote genomes present in the LMAT reference database. The key observed difference was in the Borrelia species previously reported to be the first documented case of Lyme disease in humans. Although LMAT’s findings support the presence of the Borrelia genus with 16 180 reads assigned a read label score greater than 0, a more complex relationship is shown between the new Borrelia sequence and previously sequenced Borrelia genomes. Although Borrelia burgdorferi was previously reported to be the likely species present, LMAT shows that among the reads assigned to the Borrelia genus, the majority of the reads are assigned to non–species-specific genomic regions with species-specific reads assigned to several Borrelia species, including B.burgdorferi, Borrelia garinii and others. The Borellia reads were compared against all sequenced Borrelia genomes to compute an SNP-based genetic distance matrix. The phylogenetic tree given in Supplementary Figure S10 supports LMAT’s finding that the Borrelia variant is divergent from B.burgdorferi.

https://pmc.ncbi.nlm.nih.gov/articles/PMC3753567/

A movie about George Washington’s secret bioweapons lab would be dope, though.

Is this really a failed replication? It seems that:

  1. Borellia samples are present

  2. Most reads are in non-species specific regions

  3. There are B. burgdorferi specific reads, as well as reads for other Borellia species

So they conclude that the Borellia variant (and I think they implicitly assume there's only one?) is not identical to B. burgdorferi. Maybe, but it's not only B. burgdorferi that causes Lyme disease. B. garinii (also found on the ice man) also causes Lyme disease, and there are other species whose relationship to Lyme disease is just not clear. So I don't view this as contradicting the claim that the ice man had Lyme disease.

You know what, I stand corrected.

I was under the impression that B. burgdorferi was the only Lyme disease causing bacteria. If that had been the case, I would stand by this as a failed replication, but with the new information, I think you are right.

Caveat for: All “Science!” seems prone to fakery in general, but I can’t see why anyone would fake these particular results, so it seems reasonable that I was wrong.

George Washington’s secret bioweapon program would still be dope, though.

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