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New paper claims that evolution has stopped in a bacterial species. Is it true?

24 points by tokenadult 12y ago

Udo 12y ago
> if there’s no selection pressure on the organism, it will not evolve This is (and the article agrees) a statement not compatible with modern evolutionary understanding. Primary school-level knowledge about biology should be enough to debunk this claim: a set of genes survives if there are organisms that pass those genes on, it's as simple as that. If there is a mutation in a homogenous group of individuals, and that mutation is not lethal or otherwise causes the individual to die before procreation, that mutation survives - selection pressure or not. There are also genomes that remain highly preserved over long stretches of time, which should likewise not be surprising. This occurs even at the gene level: there are genes in all of us pretty much unchanged compared to early eukaryotes, mostly because the proteins they produce work well, but also because mutations to those sequences are generally lethal. While most mutations are lethal, it's not true that the remaining ones are beneficial either. This means there are lots of individuals with sometimes distinctive properties which are still causally disconnected from selection pressure. Anyone who spent some time experimenting with evolutionary models on a computer should know this, because those are intrinsic properties of genetic systems. We expect them to behave that way. We expect ancient versions of organisms to stick around if there was no reason for them to die out. That doesn't mean the reverse is true in the sense that no change in selection pressure leads to genetic stagnation.
- deleted 12y ago
  [deleted]
tsomctl 12y ago
There are so many different species of bacteria that it is hard to estimate how many there even are, but according to Wikipedia, it might be between 10^7 and 10^9. I'd be willing to bet that there is a healthy species of bacteria that has stopped evolving, that perfectly copies its dna when it divides, and never transfers dna horizontally. There's no technical reason not to, and the numbers are so huge that they almost guarantee it.
- Udo 12y ago
  It's an interesting thought, although that would mean the species opted out of having a working problem-solving mechanism. This is probably not associated with long-term survival. There are several reasons why genomes remain more stable than others, including - as you stated - replication accuracy (which can nevertheless not be 100%), but also survival chances of random mutations, and environmental factors that make deviations from the plan unfit for survival. Yet, bacteria in general show tremendous genetic mobility. They're easily the most promiscuous lifeform on the planet, considering the fact they have evolved a P2P genetic data transfer mechanism that doesn't require procreation. So, all things being equal, the rate of genetic change is expected to vary a lot. It's also worth considering that just because ancient versions are still around, that might still mean there are diverse offspring which are also doing fine. It's not automatically the case that earlier versions get replaced. > I'd be willing to bet that there is a healthy species of bacteria that has stopped evolving It sounds weird, but that's mostly a matter of definitions. If a species has stopped evolving, let's say because it developed a 100% accurate replication mechanism, that species will have trouble surviving changing environments. Sooner or later there will be a virus or something else that just wipes it out.
- api 12y ago
  "Species" gets muddy with asexually reproducing organisms like bacteria that can also transfer genes via various mechanisms like plasmids. Bacteria are kind of like a distributed massively parallel learning algorithm in goo form. There are major types, but within these things get hard to distinguish and highly variable.
- chrisamiller 12y ago
  > I'd be willing to bet that there is a healthy species of bacteria that has stopped evolving, that perfectly copies its dna when it divides, and never transfers dna horizontally There are several flaws in your argument: 1) There is no known polymerase that has a fidelity of 100%. There will always be some number of replication errors when DNA is synthesized. 2) There are lots of mutagens in the environment. UV light, mutagenic chemicals, hell, even radioactive decay of mostly-stable elements will occasionally hit a base and cause a mutation. So, no, there is certainly no species that meets your criteria for non-evolving.
Houshalter 12y ago
Well organisms do get stuck in local optima all the time. If you only climb up, eventually you will get to the top of the hill and stay there. Second, sexually reproducing organisms, theoretically, will decrease their mutation rate over time until eventually they no longer mutate at all. And so no longer evolve. Most (non-neutral) mutations are harmful. So any gene that decreases mutations (e.g. better DNA copying or repair) will have fewer unfit, mutant children. These children will than propagate the gene more. Even if a gene that causes higher mutations eventually creates beneficial mutations, they will just mix into the general population after a few generations, and not provide a fitness advantage.
- GuiA 12y ago
  1. The notion of "local optima" for biological species is ill conceived. The world is complex and extremely dynamic; "local optima" isn't a very meaningful concept in the context of evolution. 2. "Most mutations are harmful" -> this is patently false. A lot of mutations are inconsequential, some are harmful, some are beneficial. 3. "sexually reproducing organisms, theoretically, will decrease their mutation rate over time" -> this isn't true. Mutation rate is variable over species and over time. 4. DNA duplication is a complex biological process with many moving parts. There isn't such a straightforward thing as a "gene that decreases mutation".
  - Houshalter 12y ago
    >The notion of "local optima" for biological species is ill conceived. The world is complex and extremely dynamic; "local optima" isn't a very meaningful concept in the context of evolution. Changing environments can help organisms break out of local optima, but that doesn't imply they don't exist. There are countless examples of organisms getting stuck in local optima. E.g. horseshoe crabs haven't changed in hundreds of millions of years. Most traits in general are stuck in local optima. Theoretically large changes could improve them, but it's unlikely to happen by random chance. >"Most mutations are harmful" -> this is patently false. A lot of mutations are inconsequential, some are harmful, some are beneficial. Who are you quoting? I never said that. I said most non-neutral mutations are harmful. Neutral mutations don't do anything and so don't matter. >Mutation rate is variable over species and over time. >DNA duplication is a complex biological process with many moving parts. There isn't such a straightforward thing as a "gene that decreases mutation" There are many mechanisms that control mutations, like DNA repair and copying mechanisms, or shielding from radiation and mutagens, etc. Of course it's probably very difficult to reach perfection, which is why organisms still evolve. I just said theoretically, evolution is always pushing towards less evolution.
lotsofmangos 12y ago
Even if it had stopped in this bacteria, and it sounds as though there is nowhere near enough evidence to make that claim, it doesn't mean it cannot start again. Evolution is an event driven process and given there is time between events, there can be a long time between events. And if there were no possibility of time between those events, everything would look like the end of Akira.

24 points by tokenadult 12y ago

Udo 12y ago

> if there’s no selection pressure on the organism, it will not evolve This is (and the article agrees) a statement not compatible with modern evolutionary understanding. Primary school-level knowledge about biology should be enough to debunk this claim: a set of genes survives if there are organisms that pass those genes on, it's as simple as that. If there is a mutation in a homogenous group of individuals, and that mutation is not lethal or otherwise causes the individual to die before procreation, that mutation survives - selection pressure or not. There are also genomes that remain highly preserved over long stretches of time, which should likewise not be surprising. This occurs even at the gene level: there are genes in all of us pretty much unchanged compared to early eukaryotes, mostly because the proteins they produce work well, but also because mutations to those sequences are generally lethal. While most mutations are lethal, it's not true that the remaining ones are beneficial either. This means there are lots of individuals with sometimes distinctive properties which are still causally disconnected from selection pressure. Anyone who spent some time experimenting with evolutionary models on a computer should know this, because those are intrinsic properties of genetic systems. We expect them to behave that way. We expect ancient versions of organisms to stick around if there was no reason for them to die out. That doesn't mean the reverse is true in the sense that no change in selection pressure leads to genetic stagnation.

deleted 12y ago
[deleted]

tsomctl 12y ago

There are so many different species of bacteria that it is hard to estimate how many there even are, but according to Wikipedia, it might be between 10^7 and 10^9. I'd be willing to bet that there is a healthy species of bacteria that has stopped evolving, that perfectly copies its dna when it divides, and never transfers dna horizontally. There's no technical reason not to, and the numbers are so huge that they almost guarantee it.

Udo 12y ago
It's an interesting thought, although that would mean the species opted out of having a working problem-solving mechanism. This is probably not associated with long-term survival. There are several reasons why genomes remain more stable than others, including - as you stated - replication accuracy (which can nevertheless not be 100%), but also survival chances of random mutations, and environmental factors that make deviations from the plan unfit for survival. Yet, bacteria in general show tremendous genetic mobility. They're easily the most promiscuous lifeform on the planet, considering the fact they have evolved a P2P genetic data transfer mechanism that doesn't require procreation. So, all things being equal, the rate of genetic change is expected to vary a lot. It's also worth considering that just because ancient versions are still around, that might still mean there are diverse offspring which are also doing fine. It's not automatically the case that earlier versions get replaced. > I'd be willing to bet that there is a healthy species of bacteria that has stopped evolving It sounds weird, but that's mostly a matter of definitions. If a species has stopped evolving, let's say because it developed a 100% accurate replication mechanism, that species will have trouble surviving changing environments. Sooner or later there will be a virus or something else that just wipes it out.
api 12y ago
"Species" gets muddy with asexually reproducing organisms like bacteria that can also transfer genes via various mechanisms like plasmids. Bacteria are kind of like a distributed massively parallel learning algorithm in goo form. There are major types, but within these things get hard to distinguish and highly variable.
chrisamiller 12y ago
> I'd be willing to bet that there is a healthy species of bacteria that has stopped evolving, that perfectly copies its dna when it divides, and never transfers dna horizontally There are several flaws in your argument: 1) There is no known polymerase that has a fidelity of 100%. There will always be some number of replication errors when DNA is synthesized. 2) There are lots of mutagens in the environment. UV light, mutagenic chemicals, hell, even radioactive decay of mostly-stable elements will occasionally hit a base and cause a mutation. So, no, there is certainly no species that meets your criteria for non-evolving.

Houshalter 12y ago

Well organisms do get stuck in local optima all the time. If you only climb up, eventually you will get to the top of the hill and stay there. Second, sexually reproducing organisms, theoretically, will decrease their mutation rate over time until eventually they no longer mutate at all. And so no longer evolve. Most (non-neutral) mutations are harmful. So any gene that decreases mutations (e.g. better DNA copying or repair) will have fewer unfit, mutant children. These children will than propagate the gene more. Even if a gene that causes higher mutations eventually creates beneficial mutations, they will just mix into the general population after a few generations, and not provide a fitness advantage.

GuiA 12y ago
1. The notion of "local optima" for biological species is ill conceived. The world is complex and extremely dynamic; "local optima" isn't a very meaningful concept in the context of evolution. 2. "Most mutations are harmful" -> this is patently false. A lot of mutations are inconsequential, some are harmful, some are beneficial. 3. "sexually reproducing organisms, theoretically, will decrease their mutation rate over time" -> this isn't true. Mutation rate is variable over species and over time. 4. DNA duplication is a complex biological process with many moving parts. There isn't such a straightforward thing as a "gene that decreases mutation".
- Houshalter 12y ago
  >The notion of "local optima" for biological species is ill conceived. The world is complex and extremely dynamic; "local optima" isn't a very meaningful concept in the context of evolution. Changing environments can help organisms break out of local optima, but that doesn't imply they don't exist. There are countless examples of organisms getting stuck in local optima. E.g. horseshoe crabs haven't changed in hundreds of millions of years. Most traits in general are stuck in local optima. Theoretically large changes could improve them, but it's unlikely to happen by random chance. >"Most mutations are harmful" -> this is patently false. A lot of mutations are inconsequential, some are harmful, some are beneficial. Who are you quoting? I never said that. I said most non-neutral mutations are harmful. Neutral mutations don't do anything and so don't matter. >Mutation rate is variable over species and over time. >DNA duplication is a complex biological process with many moving parts. There isn't such a straightforward thing as a "gene that decreases mutation" There are many mechanisms that control mutations, like DNA repair and copying mechanisms, or shielding from radiation and mutagens, etc. Of course it's probably very difficult to reach perfection, which is why organisms still evolve. I just said theoretically, evolution is always pushing towards less evolution.

lotsofmangos 12y ago

Even if it had stopped in this bacteria, and it sounds as though there is nowhere near enough evidence to make that claim, it doesn't mean it cannot start again. Evolution is an event driven process and given there is time between events, there can be a long time between events. And if there were no possibility of time between those events, everything would look like the end of Akira.