5 ms·

Horizontal gene transfer is well established. Existence of a small number of common genes between two species does not necessarily indicate a common ancestor.

niels_olson 10y ago
It would seem to me that bacteriophages alone sort of ruin the idea of a phylogeny with a single root.
- civilian 10y ago
  How so? I will happily agree that bacteriophages & HGT ruin the idea that phylogenetic tree can be a perfect tree-- our phylogenetic tree has many undirected cycles in it.
  - niels_olson 10y ago
    How would you reconstruct the phylogeny to see through that mess? We're not even talking about computational complexity yet. Simply, how do you see through a random number of random DNA fragments being inserted in random places of random genomes at random intervals over a billion years?
    - civilian 10y ago
      Hmmm I see what you're saying. It's a mess but I optimistically think it's still something we will be able to tease out, by looking at many genes in a genome. FWIW, It was recently estimated that 2% of core genes per genome are from HGT. https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution#Resolution_of_uncertainty_with_phylogenomics https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_ev... It makes HGT fairly identifiable and gives us a lot of non-transfered genes to work with when reconstructing a tree.
lumpypua 10y ago
They're not looking at things like antibiotic resistance, they're looking at genes core to biological function like cell membrane proteins and ribosomes—and those look like they came from a common ancestor. So, your options: 1. Common ancestor. 2. Not common ancestors, but with enough random chance common biochemistry that this core function gene could be usefully used by the new microbe, and is functional enough in the new host that it isn't ejected immediately, and managed to stay functional and evolve past the original core function gene in terms of fitness so that original core function gene could be ejected, and the original core function gene did get ejected and the microbes with the new core function gene managed to outcompete all the microbes with dual core-function genes. The latter is highly, highly unlikely.
- niels_olson 10y ago
  There's a whole body of literature on how quickly a pile of nucleic acids can self-assemble and self-select to end up with a functioning ribosome. I'm pretty sure we're talking time scales of less than months. More like 10s or hundreds of hours. There's a lot of molecules in the ocean. For example, the water content of the ocean is about 4 x 10^46 water molecules. How frequently are valence electrons available for reaction, per second? A billion? The number of possible configurations over a billion years reels the mind.
  - civilian 10y ago
    From Nick Lane's article "How did LUCA make a living? Chemiosmosis in the origin of life" http://www.nick-lane.net/LAM%20BioEssays.pdf http://www.nick-lane.net/LAM%20BioEssays.pdf > The concept of organic soup is nowadays closely allied to the idea that the origin of life and the origin of replication are the same thing. Natural selection remains the only mechanism known in which more complex forms can evolve, and natural selection requires a replicator. Regarding the nature of that replicator, there is currently no viable alternative to the idea that some kind of ‘RNA world’ existed, that is, there was a time before proteins and DNA, when RNA was the molecular basis of both catalysis and replication. Some elements of the RNA world concept are almost certainly correct. However, there is a strong version of this theory which states that RNA was once the only catalyst as well as the only replicator and so all the basic chemistry of life was invented by RNA.(4) This ‘RNA first’ theory is difficult to accept from the standpoint of the biochemistry of modern cells. For example, many essential enzymes are metalloproteins that contain mineral centres, such as iron-sulphur clusters, at their heart.(5) There is every reason to believe that such clusters, with the structures of inorganic minerals like greigite,(6,7) have more ancient roots even than those of RNA. > The recent abiotic synthesis of nucleotides using UV radiation and phosphate to purify intermediates(8) seems to lend support to the idea that the primordial oceans became a warm broth filled with nucleotides, which spontaneously polymerised into RNA, able to catalyse its own replication as well as organic transformations that ultimately yielded cells with lipid membranes, proteins and DNA – a purely Haldanian distillation, eight decades after Haldane’s essay. But the fact that nucleotides can be synthesised in ‘warm pond’ conditions hardly makes an oceanic RNA world more likely; by the same measure, the circumstance that amino acids can be present in some meteorites does not mean that life must have arisen in outer space. Setting aside the absence of geochemical evidence that a primordial soup ever existed, there are grave difficulties with the soup theory. To give a single example, polymerisation into RNA requires both energy and high concentrations of ribonucleotides. There is no obvious source of energy in a primordial soup. Ionizing UV radiation inherently destroys as much as it creates. If UV was the primordial source of energy, why does no life today synthesise ATP from UV radiation? Worse, every time an RNA molecule replicates itself, the nucleotide concentration falls, unless nucleotides are replenished at an equal rate. UV radiation is an unlikely energy source for rapid polymerisation and replication, and an unpromising initiator of natural selection The ocean's not as warm or as concentrated as the experiments you're referencing.
civilian 10y ago
Of course horizontal gene transfer exists, but that's also a discrete event that we can track. And a horizontal gene transfer event is one directional-- We wouldn't have a world where all archaea and all bacteria share fundamental genes, we'd have a world where some archaea have some freak bacteria genes. We're not talking about two species, we're talking about two domains.
- niels_olson 10y ago
  In a resource constrained world, where a lot of energy is being spent on other things (like fighting), certain fundamentals may well get highly optimized, and indeed outright stolen.
- frenchy 10y ago
  I have no particular side on this debate, nor am I an expert, but wouldn't the current state still be possible if the recipients of the gene transfer out-competed all the other variants in its lineage?
  - civilian 10y ago
    I'm really kicking myself for saying "a few" genes are shared between archaea & bacteria. > The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. https://en.wikipedia.org/wiki/Archaea#Genetics https://en.wikipedia.org/wiki/Archaea#Genetics It's really more like hundreds or thousands of genes. And they're around the foundations of translating DNA to RNA and RNA to amino-acid chains. And we share the genes that are related to DNA maintenance and translating DNA to proteins. The idea is that, without these shared genes, horizontal gene transfer doesn't even make sense. There would be no shared genetic code. The nucleotides used might not even be the same. Amino-acids have right-handed chirality (which is probably related to our DNA having left-handed chirality). If life independently evolved it would probably use amino acids and nucleotides, but there's no guarantee that the handedness would be the same, or that the genetic code would be the same.
Balgair 10y ago
I mean, at this point you have to define what an 'ancestor' is then. HGT kinda breaks the rules of what an ancestor is. With us, it's a little easier, we have tons of genes and a few viral infections don't break the concept of ancestor. When you have 100 genes total, 75 of which are from HGT, 10 from viruses, and 15 from the mother cell, who can be called the ancestor then? Remember, this was WAY back when too. Modern prokaryotes have some complex stuff to deal with all this, the first million generations did not (maybe). In that early soup, the basic concepts of what life is today don't have relevance. What is a mother cell anyways? Was it really gene transfer, or was that just what they all naturally did all the time? ETC.

niels_olson 10y ago

It would seem to me that bacteriophages alone sort of ruin the idea of a phylogeny with a single root.

civilian 10y ago
How so? I will happily agree that bacteriophages & HGT ruin the idea that phylogenetic tree can be a perfect tree-- our phylogenetic tree has many undirected cycles in it.
- niels_olson 10y ago
  How would you reconstruct the phylogeny to see through that mess? We're not even talking about computational complexity yet. Simply, how do you see through a random number of random DNA fragments being inserted in random places of random genomes at random intervals over a billion years?
  - civilian 10y ago
    Hmmm I see what you're saying. It's a mess but I optimistically think it's still something we will be able to tease out, by looking at many genes in a genome. FWIW, It was recently estimated that 2% of core genes per genome are from HGT. https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution#Resolution_of_uncertainty_with_phylogenomics https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_ev... It makes HGT fairly identifiable and gives us a lot of non-transfered genes to work with when reconstructing a tree.

lumpypua 10y ago

They're not looking at things like antibiotic resistance, they're looking at genes core to biological function like cell membrane proteins and ribosomes—and those look like they came from a common ancestor. So, your options: 1. Common ancestor. 2. Not common ancestors, but with enough random chance common biochemistry that this core function gene could be usefully used by the new microbe, and is functional enough in the new host that it isn't ejected immediately, and managed to stay functional and evolve past the original core function gene in terms of fitness so that original core function gene could be ejected, and the original core function gene did get ejected and the microbes with the new core function gene managed to outcompete all the microbes with dual core-function genes. The latter is highly, highly unlikely.

niels_olson 10y ago
There's a whole body of literature on how quickly a pile of nucleic acids can self-assemble and self-select to end up with a functioning ribosome. I'm pretty sure we're talking time scales of less than months. More like 10s or hundreds of hours. There's a lot of molecules in the ocean. For example, the water content of the ocean is about 4 x 10^46 water molecules. How frequently are valence electrons available for reaction, per second? A billion? The number of possible configurations over a billion years reels the mind.
- civilian 10y ago
  From Nick Lane's article "How did LUCA make a living? Chemiosmosis in the origin of life" http://www.nick-lane.net/LAM%20BioEssays.pdf http://www.nick-lane.net/LAM%20BioEssays.pdf > The concept of organic soup is nowadays closely allied to the idea that the origin of life and the origin of replication are the same thing. Natural selection remains the only mechanism known in which more complex forms can evolve, and natural selection requires a replicator. Regarding the nature of that replicator, there is currently no viable alternative to the idea that some kind of ‘RNA world’ existed, that is, there was a time before proteins and DNA, when RNA was the molecular basis of both catalysis and replication. Some elements of the RNA world concept are almost certainly correct. However, there is a strong version of this theory which states that RNA was once the only catalyst as well as the only replicator and so all the basic chemistry of life was invented by RNA.(4) This ‘RNA first’ theory is difficult to accept from the standpoint of the biochemistry of modern cells. For example, many essential enzymes are metalloproteins that contain mineral centres, such as iron-sulphur clusters, at their heart.(5) There is every reason to believe that such clusters, with the structures of inorganic minerals like greigite,(6,7) have more ancient roots even than those of RNA. > The recent abiotic synthesis of nucleotides using UV radiation and phosphate to purify intermediates(8) seems to lend support to the idea that the primordial oceans became a warm broth filled with nucleotides, which spontaneously polymerised into RNA, able to catalyse its own replication as well as organic transformations that ultimately yielded cells with lipid membranes, proteins and DNA – a purely Haldanian distillation, eight decades after Haldane’s essay. But the fact that nucleotides can be synthesised in ‘warm pond’ conditions hardly makes an oceanic RNA world more likely; by the same measure, the circumstance that amino acids can be present in some meteorites does not mean that life must have arisen in outer space. Setting aside the absence of geochemical evidence that a primordial soup ever existed, there are grave difficulties with the soup theory. To give a single example, polymerisation into RNA requires both energy and high concentrations of ribonucleotides. There is no obvious source of energy in a primordial soup. Ionizing UV radiation inherently destroys as much as it creates. If UV was the primordial source of energy, why does no life today synthesise ATP from UV radiation? Worse, every time an RNA molecule replicates itself, the nucleotide concentration falls, unless nucleotides are replenished at an equal rate. UV radiation is an unlikely energy source for rapid polymerisation and replication, and an unpromising initiator of natural selection The ocean's not as warm or as concentrated as the experiments you're referencing.

civilian 10y ago

Of course horizontal gene transfer exists, but that's also a discrete event that we can track. And a horizontal gene transfer event is one directional-- We wouldn't have a world where all archaea and all bacteria share fundamental genes, we'd have a world where some archaea have some freak bacteria genes. We're not talking about two species, we're talking about two domains.

niels_olson 10y ago
In a resource constrained world, where a lot of energy is being spent on other things (like fighting), certain fundamentals may well get highly optimized, and indeed outright stolen.
frenchy 10y ago
I have no particular side on this debate, nor am I an expert, but wouldn't the current state still be possible if the recipients of the gene transfer out-competed all the other variants in its lineage?
- civilian 10y ago
  I'm really kicking myself for saying "a few" genes are shared between archaea & bacteria. > The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. https://en.wikipedia.org/wiki/Archaea#Genetics https://en.wikipedia.org/wiki/Archaea#Genetics It's really more like hundreds or thousands of genes. And they're around the foundations of translating DNA to RNA and RNA to amino-acid chains. And we share the genes that are related to DNA maintenance and translating DNA to proteins. The idea is that, without these shared genes, horizontal gene transfer doesn't even make sense. There would be no shared genetic code. The nucleotides used might not even be the same. Amino-acids have right-handed chirality (which is probably related to our DNA having left-handed chirality). If life independently evolved it would probably use amino acids and nucleotides, but there's no guarantee that the handedness would be the same, or that the genetic code would be the same.

Balgair 10y ago

I mean, at this point you have to define what an 'ancestor' is then. HGT kinda breaks the rules of what an ancestor is. With us, it's a little easier, we have tons of genes and a few viral infections don't break the concept of ancestor. When you have 100 genes total, 75 of which are from HGT, 10 from viruses, and 15 from the mother cell, who can be called the ancestor then? Remember, this was WAY back when too. Modern prokaryotes have some complex stuff to deal with all this, the first million generations did not (maybe). In that early soup, the basic concepts of what life is today don't have relevance. What is a mother cell anyways? Was it really gene transfer, or was that just what they all naturally did all the time? ETC.