Monday, August 10, 2020

The Virome: Viruses are an essential part of the human holobiont


Eradicating viruses and bacteria may not be so easy as some people think. We are surrounded by viruses, we eat viruses, we drink viruses, we breathe viruses. And the "virome" is an essential part of the human holobiont.

From "Half-Earth" by E. O. Wilson (p. 125).
"Although recognized only in 1988, Prochlorococcus are far from rare. They are in fact the most abundant organism in tropical and subtropical seas around the world. They live in waters as deep as two hundred meters and reach local densities of more than a hundred thousand per millimeter. Because the tiny cells account for 20 to 40 percent of the biomass of all photosynthetic organisms present between 40 N and 40 S in the open ocean, they are responsible for up to half the local net primary production.
Yet, if Prochlorococcus along with a second superabundant bacterium, Pelagibacter, are the most important organisms, might they be the prey of viruses that are even smaller? Experts used to think that such micro-predators are at best relatively rare. In 2013, however, new methods in the fast-moving field of ultramicroscopic research revealed the presence of viruses on an averaged of billions per liter of seawater, all are bacteriophages (literally, eaters of bacteria), of which one HTVC010P is the most abundant... it must be classified as the most abundant known species on Earth.

Thursday, August 6, 2020

But what is a "superorganism," in the end?

What is a superorganism, exactly?

I was mulling over this question and I came up with the classic example: the ant colony is supposed to be a superorganism in the sense that all the organisms in it share the same genome, just like in a human beings all cells have the same DNA (except mitochondria, of course).

But no, wait! That cannot be: ants are sisters, not clones. They may even have different fathers. For a quirk of the genetic setup of male ants, ant sisters share 75% of their genes, not 50% as human siblings do. But they are not clones. So an ant colony is not a superorganism, but a kind of tightly knit holobiont.

But then, a discovery: that's not true, either! As reported in this paper, there are ant colonies where all the ants are clones of each other! Unbelievably, some ants have discover tricks to completely eliminate the need of males: yes, no males and no queens. They reproduce by parthenogenesis. These colonies are true superorganisms, not holobionts. And I keep discovering new things: one that starts to be very common is that males seem to be obnoxious and useless in all species!

Saturday, August 1, 2020

The Earth Goddess According to Jenny Jinya

Jenny Jinya is a phenomenal German artist who knows something about empathy, the fundamental element that keeps together the multiform creatures we call "holobionts."

For a taste of her awesome work, you may start from this one. (be careful, this is powerful stuff -- it may make you cry like a child).

In the most recent comic strip by Jenny Jinya, we even see appearing the Goddess of life herself, mistress of all the holobionts of Earth. You can find it here. Enjoy the good ending!

Wednesday, July 29, 2020

A happy holobiont is a holobiont that takes care of its microbiome

An obviously unhappy holobiont engaged in exterminating its own microbiome. Bad idea.

The epidemic of biophobia is still raging worldwide, with people still washing their hands with poisonous substances, convinced to do something good, or forced by law to do so.

Not a good idea. You skin microbiome is precious to you, among other things it is the first true barrier against infections. Some people are recognizing the problem, as it is described in a recent article on "The Guardian"

Just an excerpt:
Hand-washing aside, James Hamblin has not used soap for five years. He warns that our obsession with being clean is harming the microbiome that keeps us healthy
Take care of your microbiome, and be a happy holobiont!

(h/t Miguel Martinez)

Tuesday, July 21, 2020

Sex and Death among Holobionts and Organisms

My mother in law, Liliana, turns 100 today. Happy Birthday, Liliana!

Both holobionts and organisms have to fight entropic decay. Holobionts do that by continuously changing their hologenome in a horizontal exchange of information. Organisms do the same by the vertical mixing of their genome in the process called sexual reproduction. Both methods are driven by natural selection.
The second strategy, sexual reproduction, brings the need of eliminating the old genomes by the process of aging. True holobionts never die (think of a forest), but organisms do. Too bad for organisms, but it is a choice (and a lot of fun, too!). 
Liliana turned out to be a successful and resilient organism. So far, she has three daughters, a son, three grandsons, one grand-daughter and, recently, two great-grand daughters. Not bad!

Saturday, July 18, 2020

The March of the Holobots

I am just back from a scientific meeting held in a small city in the mountains, you know, like things were.... when? Was it the Pleistocene, when people met in person to discuss things? Or was it before the PETM, during the Paleocene? Anyway, you learn things while having discussions at dinner with the other attendees. And I had a very interesting dinner with a group of roboticists. Many, many ideas. One I came up with is that of the "Holobot" -- the solid state equivalent of the holobiont! 

Bots are not based on cells, and they have no genetic code, either. So they are born holobionts.We are witnessing the birth of a new ecosystem that we might describe with the words of a recent article on Quanta Magazine (h/t Chuck Pezeshky): 

"Within this theory, individuals can be cells, tissues, organisms, colonies, companies, political institutions, online groups, artificial intelligence or cities — even ideas or theories, according to Krakauer. “What we’re trying to do is discover a whole zoo of life forms that extend far beyond what we have conventionally called living,”
So, the bots we are building can be seen as individuals and they do fulfill this extended definition of "life" -- a dynamic phenomenon that extends in time, not being just limited in space. It is just that they are not the same kind of life as ours. And so, onward, fellow holobots!

This subject is also being discussed on the Facebook group "The Proud Holobionts"

Thursday, July 16, 2020

Why human society is not a good holobiont.

Colin Campbell, the founder of the association for the study of peak oil and gas (ASPO) explaining the essence of oil depletion.
The problem is that human society is not a good holobiont. It either overreacts or does not react to external perturbations. The result is a destabilization that may lead to a catastrophe. Read the whole story on "Cassandra's Legacy"



Ugo Bardi is a member of the Club of Rome, faculty member of the University of Florence, and the author of "Extracted" (Chelsea Green 2014), "The Seneca Effect" (Springer 2017), and Before the Collapse (Springer 2019)