This paper says this “Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed.”, who selected it?If it was a scientist then it is an Intelligent agent.
That’s not valid @jorronet.
I’m new in this blog so I’m learning how to use it, please excuse me if I’m breaking any rule. Please also clarify.
No rule broken. The issue is that the scientists are simulating what happens in nature. So that isn’t a valid reason to call what they did ID.
4 Likes
Oh!! Thanks!! I was worried!! My point is if natural selection would do it or the scientist chose the optimal result.
1 Like
If the scientist chooses in a way that simulates nature, as was done here, the experiment is still valid.
2 Likes
I don’t doubt about the validity of the result but my question is , would natural selection do it? How can we test it?
1 Like
The rounds of mutation and selection within the experiment are important. What they did was randomly mutate a portion of the phage genome, and they blindly chose a handful of those random mutants without knowing how effective they would be. The randomly chosen mutants were then tested for infectivity, and the one with the highest infectivity was selected for the next round. The process then repeats. Mutate the selected high infectivity mutant, randomly select a handful, and then see which of those randomly selected mutants has the highest infectivity. They were letting the results of the experiments choose which mutants to pass onto the next generation.
This is a good approximation of how natural selection works. The phage that infect the most cells will usually be the phage with the highest fitness. Mutations that increase infectivity will be selected for.
5 Likes
Then the way in which the paper was written was not the most appropriate? It indicates that someone made the choice.
1 Like
The scientists did choose to make infectivity the criteria for fitness. However, they didn’t choose specific mutations, but instead used phenotypes to determine which phage made it into the next generation. This is a valid way of modeling natural selection since natural selection also selects based on phenotype.
6 Likes
That explains it better. I still think the language wasn’t clear, that is why my question. Thanks.
1 Like
The language in the abstract wasn’t clear at all, I completely agree. I had to read through their methodology in the full paper to understand what they were doing.
3 Likes
I will be asking more questions , I’m new in this blog , so bear with me please.Thanks!!
4 Likes
Look at the other paper I cited. Why are you ignoring it?
1 Like
I asked a specific question for a specific paper, I read the abstracts only because I’m not going to pay for a paper that I don’t need, and as you saw the abstract was misleading , that is why it is better to read the whole paper. But you didn’t explain it to me, another person had to do it, but if you find that paper without paywall I will gladly read it.
2 Likes
Yes, and to be clear, someone did make that choice, but it’s a bit complicated to understand why.
The ultimate goal of the experiment was to determine if an arbitrary protein sequence could in principle evolve into acquiring a useful biological function. In order to minimize complications arising from mutations in other portions of the phage genome, they chose to design the experiment in a way that would allow scientists to constrain mutations to only occur in the piece of the page genome that encodes the protein domain of interest. This would then allow scientists to better answer the question without having to worry about other factors influencing the result.
In principle the scientists could have allowed the phages to evolve all on their own, by just letting them grow along the bacteria, but this would entail allowing mutations elsewhere in the phage genome, and also allowing bacteria to evolve along with the phages, which could then potentially mask the effects of mutations in the protein they were interested in. In such a situation the scientists would have had a much harder time determining whether any observed phenotypic effects, such as any potentially higher evolved infectivity, would only be due to mutations in the specific protein of interest, or whether they were also due to mutations elsewhere in the phage (or bacterial) genome.
In a way, the scientists are basically only allowing a small portion of the phage genome to evolve, and for various practical and technological reasons, that means they had to set up the experiment in a way where they had to “play the role” of natural selection by comparing the infectivity of multiple different phage-mutants and picking the most infectious one.
4 Likes
How so?
2 Likes
If they are controlling the outcome, how similar would it be to what we observe in real life?
3 Likes
They didn’t control the outcome. They emulated the effects of natural selection as to remove one of the variable factors from the experiment. That’s a standard practice in science when investigating a specific phenomenon.
3 Likes
I assume you are really asking whether, if they had not constrained the evolution to only occur in the protein in question, would it still have evolved towards acquiring a biological function?
In the real world the whole phage genome would be evolving, not just the piece of the genome encoding the protein. We can’t really predict how the rest of the phage genome would respond(it is possible mutations elsewhere in the phage genome could also compensate for the reduction in infectivity the experiment started at), but there isn’t a good reason to think that the gene encoding the protein would not evolve too. Overall the result would be slower in the real world. What they have done is basically to speed up the process a lot(the number of mutations that accumulated in the gene would take decades in the wild), but they’re not forcing the result. Mutations would still occur, and they’d still affect infectivity, and those that increased infectivity would outcompete those that did not(that basically follows by logical necessity).
2 Likes