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Human Genome Contaminated With Mycoplasma DNA
KentuckyFC writes "The published human genome is contaminated with DNA sequences from mycoplasma bacteria, according to bioinformatics researchers who blame an epidemic of mycoplasma contamination in molecular biology labs around the world. The researchers say they've also found mycoplasma DNA in two commercially available human DNA chips made by biotech companies for measuring levels of human gene expression. So anybody using these chips to measure human gene expression is also unknowingly measuring mycoplasma gene expression too. The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards."
No, they're not saying that the mold itself is appearing in the chips, just that the mold's DNA is. Therefore, the presence (or absence) of the mold in a sample would skew the results when using these chips. And yes, saying that the DNA appears "in silico" is perfectly valid here - whether you care for the term or not.
The topic is not about "vestigial" DNA.
TFA talks about bacteria being mixed in with human samples accidentally, then sequenced. The bacterial DNA shows up with the human DNA, and the bacterial DNA is being documented as human.
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Experiments done in a cell are in vivo (life); experiments done in a test tube are in vitro (glass); experiments done in a computer are in silico (silicon computer chips). In silico is used to describe computational modeling experiments (think FoldIt or Rosetta@Home), or manipulation and searching of large DNA/RNA/protein sequence databases. You'd expect it to apply to stuff like weather modeling or nuclear physics, but there the analogy to vivo/vitro is lost so I believe those fields don't use the term.
This article was horribly written. They go between using terms with their literal meaning and using terms in metaphorical creative language but do not differentiate between the two using context at all. It's an incredibly confusing read. Actual ancestral human DNA is not contaminated with actual mycoplasma DNA sequences.
Here's what I gather is going on:
Researchers took a sample of human DNA and sequenced it, while doing so the sample was contaminated with DNA from mycoplasma (possibly from bacteria in the lab or on the researchers themselves). While sequencing it, the data is assumed to be a representation of pure human DNA (which would be incorrect). Other researchers then use this data set as a reference to compare other human DNA samples they sequenced themselves. They use this to test gene expression and so forth. So if their DNA samples show gene expression for mycoplasma they would incorrectly think it was normal human gene expression. What they did is use software to strip the mycoplasma DNA data from the original data set (that had both human and mycoplasma DNA sequences) to only use the actual human DNA data as a reference. The biological contamination was first in the original sample that was tested, and then the contamination referred to elsewhere is computational data "contamination." This is the software they are referring to as antivirus software and virtual immune system (which isn't antivirus software or similar to a biological immune system, it's DNA data filtering software).
These people really need to think about what they're trying to say before puking up jargon salad on the readers' brains.