Tag: biology

Entangled DNA

one line of evidence is that a purely classical analysis of the energy required to hold DNA together does not add up. It is possible that DNA is indeed quantum-efficient.

if Grover-algorithmic processing is some sort of fundamental property of nature, then you might expect the genetic material to be synthesized most efficiently when the machinery has a choice of 4 different nucleotides. And when translating these into proteins, a triplet code (which requires 3 processing steps) would function most efficiently when working with a palette of 20 amino acids. I will admit to being unusually susceptible to ideas like this, but that makes the hair stand up on the back of my neck.

Anoxic metazoa

This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.

these are the first multicellular organisms that live without oxygen.

Reviving 250 ma Microbe

If it is possible for a bacteria to survive being off the planet and to stay alive within a salt chunk for 250m years, then in a sort of “reverse-exogenesis” it may be possible that earth’s own microbes are already out there.

Or you could try 100 ma:

After a mere 68 days—an imperceptible sliver of time in the microbes’ geological timescale of 100 ma—certain types of microbes increased their numbers by 4 orders of magnitude. Over 99% of the microbes could revive. They must be sitting there over geological time—just waiting for some nicer conditions. Finally, they get a chance to revive. It provides some crucial information for understanding the habitability of life on Earth and elsewhere. Either the individual cells are somehow surviving for “ridiculous lengths of time” or they “are reproducing with less energy than we thought possible”. But one way or another “they are starvation artists”.

Prebiotic Chemistry

The RNA hypothesis is very popular but doesn’t explain how fragile RNA can survive in hostile environments.

Dr. Joyce has been studying the possible beginning of history by developing RNA molecules with the capacity for replication. RNA, a close cousin of DNA, almost certainly preceded it as the genetic molecule of living cells. Besides carrying information, RNA can also act as an enzyme to promote chemical reactions. Dr. Joyce has developed 2 RNA molecules that can promote each other’s synthesis from the 4 kinds of RNA nucleotides. “We finally have a molecule that’s immortal”

2016-02-21: Talk of RNA-like

Perhaps before biology arose, there was a preliminary stage of proto-life, in which chemical processes alone created a smorgasbord of RNAs or RNA-like molecules. “I think there were a lot of steps before you get to a self-replicating self-sustaining system”. In this scenario, a variety of RNA-like molecules could form spontaneously, helping the chemical pool to simultaneously invent many of the parts needed for life to emerge. Proto-life forms experimented with primitive molecular machinery, sharing their parts. The entire system worked like a giant community swap meet. Only once this system was established could a self-replicating RNA emerge.

2019-06-30: Viroids, survivors from the RNA World?

Because RNA can be a carrier of genetic information and a biocatalyst, there is a consensus that it emerged before DNA and proteins, which eventually assumed these roles and relegated RNA to intermediate functions. If such a scenario–the so-called RNA world–existed, we might hope to find its relics in our present world. The properties of viroids that make them candidates for being survivors of the RNA world include those expected for primitive RNA replicons: (a) small size imposed by error-prone replication, (b) high G + C content to increase replication fidelity, (c) circular structure for assuring complete replication without genomic tags, (d) structural periodicity for modular assembly into enlarged genomes, (e) lack of protein-coding ability consistent with a ribosome-free habitat, and (f) replication mediated in some by ribozymes, the fingerprint of the RNA world. With the advent of DNA and proteins, those protoviroids lost some abilities and became the plant parasites we now know.

2022-05-06: RNA “species”

Over 100s of hours of replication, 1 type of RNA evolved into 5 different molecular “species” or lineages of hosts and parasites that coexisted in harmony and cooperated to survive, like the beginning of a “molecular version of an ecosystem”. Their experiment, which confirmed previous theoretical findings, showed that molecules with the means to replicate could spontaneously develop complexity through Darwinian evolution. Some of these results confirmed the predictions of earlier experimental studies of how complexity can arise in viruses, bacteria and eukaryotes, as well as some theoretical work.
“Without parasites, this level of diversification is probably not possible”. Evolutionary pressures that parasites and their hosts place on each other lead both sides to split into new lineages.


2024-02-01: Obelisks

A new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. These “obelisks” have genomes seemingly composed of loops of RNA and sequences belonging to them have been found around the world. The Stanford search yielded 30k predicted RNA circles, each consisting of ~1000 bases and likely representing a distinct obelisk. They were unlikely to be bona fide viruses because RNA viruses typically have many more bases. But some of the obelisk sequences encoded proteins involved in RNA replication, making them more complex than standard viroids. Like viroids, however, obelisks don’t seem to encode proteins that make up a shell. Because obelisks contain genes that are unlike any discovered so far in other organisms, they “comprise a class of diverse RNAs that have colonized, and gone unnoticed in, human, and global microbiomes”

Cell communication

Bacteria use quorum sensing via standardized molecules to communicate, both intra and inter species. New medicine could target this communication to shut down pathogenicity.

2012-06-24: The Social Lives of Microbes

It used to be assumed that bacteria lived relatively independent unicellular lives, without the cooperative behaviors that have provoked so much interest in mammals, birds, and insects. However, research has completely overturned this idea, showing that microbes indulge in a variety of social behaviors involving complex systems of cooperation, communication, and synchronization. Work in this area has already provided some elegant experimental tests of social evolutionary theory, demonstrating the importance of factors such as relatedness, kin discrimination, competition between relatives, and enforcement of cooperation.

2021-07-09: Social Mitochondria

Mitochondria divide up tasks, form groups, synchronize activities and respond to both their environment and each other. The sociability of mitochondria facilitates the cooperation of cells, which in turn allows the formation of organs that depend on one another and the creation of complex organisms. The social nature of animals is an extension of the sociality seen at lower rungs of the ladder. Network approaches could yield clues about new treatments, such as improving mitochondrial communication. Part of what makes exercise healthy is that it promotes communication between mitochondria. “It makes them more social”