The Uncertain Gene - 5

Pseudomonas shares genes with humans

In this series we have been looking into some fascinating dynamics concerning mutations of genetic molecules in carbon based life forms.

Specifically, we have been discussing dynamics described and explained by theories of quantum mechanics (e.g. proton tunneling) which predict genetic mutations in the RNA and/or DNA of biological organisms which originate at the atomic level, rather than originating at the higher molecular level we would usually expect to take place within biological organisms (The Uncertain Gene).

Today, let's consider whether those quantum dynamics could take place in microbial entities such as prions, phages, viruses, and/or other microbes such as bacteria:

“PrP^C and PrP^SC share the same amino acid sequence and are encoded by the same gene,” says Silva who has found evidence that non-coding RNAs (ncRNAs), the kind that used to be thought of as “junk,” play a role in prion conversion from normal to disease inducing. The transformation probably takes place during transcription. There’s a vast amount of ncRNA in the cytosol of normal cells and the prions might interact with it there.

(Oddly Microbial: Prions, emphasis added). We need to consider this because some new scientific papers tell us that some microbes can and do transfer their genes into our human DNA:

A team of scientists from the University of Maryland School of Medicine has found the strongest evidence yet that bacteria occasionally transfer their genes into human genomes, finding bacterial DNA sequences in about a third of healthy human genomes and in a far greater percentage of cancer cells.
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The trillions of bacteria in our bodies regularly exchange DNA with each other, but the idea that their genes could end up in human DNA has been very controversial. In 2001, the team that sequenced the first human genome claimed to have found 113 cases of such lateral gene transfers (LGT), but their conclusion was later refuted.

This high-profile error “had a chilling effect on the field,” according to Julie Dunning Hotopp who led the new study. Although her team has since found several cases of LGT between bacteria and invertebrates, “it’s still difficult to convince people that it may be happening in the human genome,” she said.

(The Scientist, "Bacterial DNA in Human Genomes", emphasis added). Regular readers know that we have previously discussed the evolution of placental mammals and the impact microbes have historically had on their biological evolution:

If not for a virus, none of us [placental human mammals] would ever be born.

In 2000, a team of Boston scientists discovered a peculiar gene in the human genome. It encoded a protein made only by cells in the placenta. They called it syncytin.

The cells that made syncytin were located only where the placenta made contact with the uterus. They fuse together to create a single cellular layer, called the syncytiotrophoblast, which is essential to a fetus for drawing nutrients from its mother. The scientists discovered that in order to fuse together, the cells must first make syncytin.

What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus.

(Weekend Rebel Science Excursion - 21, quoting Discover). The reason why this issue needs to be discussed is that most of the cells and genetic material that make up our human microbiome are microbial:

... some 90 percent of the protein-encoding cells in our body are microbes ... 99 percent of the functional genes in the body are microbial ... exchanging messages with genes inside human cells ... microbes cohabitating our body outnumber human cells by a factor of 10, making us actually “superorganisms” that use our own genetic repertoire as well as those of our microbial symbionts ... We just happen to look human because our human cells are much larger than bacterial cells ... no matter how you look at it, it’s high time we acknowledge that part of being human is being microbial ...
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Microbes may indeed be subtly changing our brain early on — and for what purposes we cannot yet say ... the mere fact that microorganisms can shape our minds brings up many more questions about how humans develop their identity ... these findings call for a complete re-examination of human physiology and immunology. Attributes that were assumed to be human traits have been shown to result from human–microbe interactions.
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Some would say that genomics has been able to distil some humility into humankind. The finalised version of the human genome deprived us of the illusion that we are one of the most complex creatures on Earth — an illusion that was at the basis of some guesses that Homo sapiens was expected to have at least 100,000 genes. When we look at a table of genomes by species, and specifically at the number of genes that have been counted or estimated for each species, we notice that humans are surpassed by several plants and invertebrates.

(The Human Microbiome Congress, emphasis in original). Thus, if microbial genes can become mutant due to quantum mechanical dynamics such as proton tunneling, we should expect some of those mutant genes to become part of us through subsequent biological dynamics.

That is, if microbial RNA/DNA mutates due to proton tunneling and that microbe subsequently transfers that mutant gene material to our human genetic material, then the chances of quantum proton tunneling induced mutations having an impact on the human genome are increased.

When the quantum proton tunneling induced mutation takes place in purely human genes there is a direct mutation, however, when it happens through horizontal gene transfer (HGT) from microbes, it is an indirect mutation, nevertheless, both mutations will have been induced by abiotic evolution rather than having been induced by biotic evolution.

This would mean that unknown quantities of events of evolution happen without any natural selection (a biological term) having taken place.

That is, natural selection cannot be said to be the sole source or origin of evolutionary changes because DNA is not alive, rather, it is an abiotic molecule which is "machine-like", not "life-like" (Did Abiotic Intelligence Precede Biotic Intelligence?).

[Sample related papers on the reality of quantum tunneling: Quantum tunnelling creates the 'wrong' molecule, Tunneling and delocalization effects in hydrogen bonded systems, More can be done faster and easier than less - in the world of quanta, Quantum Tunnelling - Wikipedia, Tunnelling Diode, Quantum tunnelling - Science Daily, Proton Tunneling - DNA, Proton Tunneling in DNA and its Biological Implications, by Per-Olov Löwdin; Journal: Review of Modern Physics, Vol 35, No. 3, July 1963]

The next post in this series is here, the previous post in this series is here.