4 ms·

So this was not a gain-of-function experiment So what's the definition of gain of function? Does it have to add a function that isn't found in the wild? I'm st

by causi 4y ago

So this was not a gain-of-function experiment So what's the definition of gain of function? Does it have to add a function that isn't found in the wild? I'm struggling to come up with a definition that excludes this experiment but includes everything that is considered gain of function.

Vecr 4y ago
It's gain of function if the virus gains any sort of function. Splicing two viruses that have different properties into one that shares at least some the properties from both, even if both of the original viruses are natural, is gain of function.
- DiogenesKynikos 4y ago
  That's not what what virologists mean when they say "gain of function." By that definition, almost all lab virology would be considered "gain-of-function." If you strictly regulated that, virtually all virology research would grind to a halt. The gain-of-function debate began in the 2010s over a specific set of experiments that were done on influenza. The term is used to describe changes that render a virus that has the potential to become a pandemic more virulent or more transmissive.
  - peteradio 4y ago
    Sars-cov-2 is already a pandemic causing agent.
  - COGlory 4y ago
    This is the correct answer. GoF has, and has had for years, a very narrow and specific meaning when applied to virology. This is not some arbitrary meaning, but rather is used by funding and regulatory agencies to evaluate risk. Gain of function as described, has to increase the virulence of a potential human pandemic-causing pathogen. To those who might counter that this definition needs to be changed: I don't disagree, but until it is, scientists are going to grade themselves on the scales they are given by the funding and regulatory agencies.
- beebmam 4y ago
  I'd recommend deleting or editing your comment. The actual definition of "gain-of-function" is quite easy to find if you want to take this matter seriously: https://en.wikipedia.org/wiki/Gain-of-function_research https://en.wikipedia.org/wiki/Gain-of-function_research
  - Kranar 4y ago
    I'm no expert but it seems from the comments and the Wikipedia article you link to that OPs position isn't that far from the truth, certainly not so blatantly false that it warrants editing or deleting. The article you linked to says gain of function research is "medical research that genetically alters an organism in a way that may enhance the biological functions of gene products", which seems like a more technical way of saying what OP said. The example Wikipedia gives explicitly states specifies, and I quote, a "situation would be considered a gain-of-function experiment, as the virus did not previously have that function." The journal Nature states that gain of function is "GOF is a classic genetics term to describe mutations that give a gene, RNA or protein new abilities". Not much different from what OP stated, unless there is a nuance you wish to point out: https://www.nature.com/articles/d41586-021-02903-x https://www.nature.com/articles/d41586-021-02903-x NIH's website states gain of function (as well as loss of function) research is any selection process involving the alteration of a genotype in order to produce a corresponding change in phenotype: https://www.ncbi.nlm.nih.gov/books/NBK285579 https://www.ncbi.nlm.nih.gov/books/NBK285579 That is a much more technical way of saying gain of function research is what happens when you modify genes to produce a change in phenotype, which is the technical term for the observable behavior and characteristics of an organism, ie. function. So anyhow, it's possible OP is wrong, Wikipedia is wrong, and a host of comments/sources are wrong, in fact it may very well be likely, but without a better source available it does seem like gain of function research is fairly open-ended research that attempts to modify an organism's genetics so as to add additional functions that it did not otherwise have.
  - Vecr 4y ago
    I stand by my statement.
factsarelolz 4y ago
docandrew 4y ago
Yeah to me the definition seems dependent on the experimental results. If the experiment succeeds in creating Captain Trips, it was GoF. If not, it wasn’t?
rolph 4y ago
modifying the potency of a function is not gain or loss of function. GoF is aquisition of a new tool or capability.
- qeternity 4y ago
  But this isn’t how GoF works, it’s not like you can just turn a dial up to 11. GoF almost always works by acquiring some new function which in combination with other functions results in drastically increased aggregate function (ie infection). So I’m not really sure how that excludes this research. The Ba1 spike is new function.
  - rolph 4y ago
    is it something the virus didnt do before? if yes, thats Gain of function. if its something that the virus already did, but now does it to greater extent that is attenuation of function
    - spfzero 4y ago
      "Attenuation" is a decrease. Gain is an increase. I may not understand the nuances of virology-speak, but: When we talk about GoF research as a dangerous activity, it is dangerous because a virus got better able to infect and hurt humans or other animals. Therefore if it escaped the lab, we'd be faced with a new, more dangerous pathogen, then if the research had not gone ahead. This research seemed to accomplish that, unless I'm missing something, which I might well be. But if we're nuancing the definition of GoF to say this research was not GoF, then I think we've lost track of what the concern was in the first place.
      - rolph 4y ago
        gain also means aquisition if you are not talking about signals the function of "lethality" was reduced in association with the recombination, thus attenuated in summary, if you look hard enough you may be able to find gains, but overall it is attenuation. this isnt the research you seem to be concerned about. you should be more concerned with codon scale editing of the nonstructural features of the virus as there is a direct influence upon interferon dynamics that is understood, and can be easily influenced by editing additional codons into the code at the "region" associated with interferon cascade mediated lethality. i will not give details here, but i you choose to look around and do some hard reading, you will discover, that the recipe for extremely lethal corona virus is not complex, but requires a lab capable of keeping and using the accesory biochemicals that allow primary sequence editing- that is to say any molecular genetics lab

by causi 4y ago

Vecr 4y ago

It's gain of function if the virus gains any sort of function. Splicing two viruses that have different properties into one that shares at least some the properties from both, even if both of the original viruses are natural, is gain of function.

DiogenesKynikos 4y ago
That's not what what virologists mean when they say "gain of function." By that definition, almost all lab virology would be considered "gain-of-function." If you strictly regulated that, virtually all virology research would grind to a halt. The gain-of-function debate began in the 2010s over a specific set of experiments that were done on influenza. The term is used to describe changes that render a virus that has the potential to become a pandemic more virulent or more transmissive.
- peteradio 4y ago
  Sars-cov-2 is already a pandemic causing agent.
- COGlory 4y ago
  This is the correct answer. GoF has, and has had for years, a very narrow and specific meaning when applied to virology. This is not some arbitrary meaning, but rather is used by funding and regulatory agencies to evaluate risk. Gain of function as described, has to increase the virulence of a potential human pandemic-causing pathogen. To those who might counter that this definition needs to be changed: I don't disagree, but until it is, scientists are going to grade themselves on the scales they are given by the funding and regulatory agencies.
beebmam 4y ago
I'd recommend deleting or editing your comment. The actual definition of "gain-of-function" is quite easy to find if you want to take this matter seriously: https://en.wikipedia.org/wiki/Gain-of-function_research https://en.wikipedia.org/wiki/Gain-of-function_research
- Kranar 4y ago
  I'm no expert but it seems from the comments and the Wikipedia article you link to that OPs position isn't that far from the truth, certainly not so blatantly false that it warrants editing or deleting. The article you linked to says gain of function research is "medical research that genetically alters an organism in a way that may enhance the biological functions of gene products", which seems like a more technical way of saying what OP said. The example Wikipedia gives explicitly states specifies, and I quote, a "situation would be considered a gain-of-function experiment, as the virus did not previously have that function." The journal Nature states that gain of function is "GOF is a classic genetics term to describe mutations that give a gene, RNA or protein new abilities". Not much different from what OP stated, unless there is a nuance you wish to point out: https://www.nature.com/articles/d41586-021-02903-x https://www.nature.com/articles/d41586-021-02903-x NIH's website states gain of function (as well as loss of function) research is any selection process involving the alteration of a genotype in order to produce a corresponding change in phenotype: https://www.ncbi.nlm.nih.gov/books/NBK285579 https://www.ncbi.nlm.nih.gov/books/NBK285579 That is a much more technical way of saying gain of function research is what happens when you modify genes to produce a change in phenotype, which is the technical term for the observable behavior and characteristics of an organism, ie. function. So anyhow, it's possible OP is wrong, Wikipedia is wrong, and a host of comments/sources are wrong, in fact it may very well be likely, but without a better source available it does seem like gain of function research is fairly open-ended research that attempts to modify an organism's genetics so as to add additional functions that it did not otherwise have.
- Vecr 4y ago
  I stand by my statement.

factsarelolz 4y ago

docandrew 4y ago

Yeah to me the definition seems dependent on the experimental results. If the experiment succeeds in creating Captain Trips, it was GoF. If not, it wasn’t?

rolph 4y ago

modifying the potency of a function is not gain or loss of function. GoF is aquisition of a new tool or capability.

qeternity 4y ago
But this isn’t how GoF works, it’s not like you can just turn a dial up to 11. GoF almost always works by acquiring some new function which in combination with other functions results in drastically increased aggregate function (ie infection). So I’m not really sure how that excludes this research. The Ba1 spike is new function.
- rolph 4y ago
  is it something the virus didnt do before? if yes, thats Gain of function. if its something that the virus already did, but now does it to greater extent that is attenuation of function
  - spfzero 4y ago
    "Attenuation" is a decrease. Gain is an increase. I may not understand the nuances of virology-speak, but: When we talk about GoF research as a dangerous activity, it is dangerous because a virus got better able to infect and hurt humans or other animals. Therefore if it escaped the lab, we'd be faced with a new, more dangerous pathogen, then if the research had not gone ahead. This research seemed to accomplish that, unless I'm missing something, which I might well be. But if we're nuancing the definition of GoF to say this research was not GoF, then I think we've lost track of what the concern was in the first place.
    - rolph 4y ago
      gain also means aquisition if you are not talking about signals the function of "lethality" was reduced in association with the recombination, thus attenuated in summary, if you look hard enough you may be able to find gains, but overall it is attenuation. this isnt the research you seem to be concerned about. you should be more concerned with codon scale editing of the nonstructural features of the virus as there is a direct influence upon interferon dynamics that is understood, and can be easily influenced by editing additional codons into the code at the "region" associated with interferon cascade mediated lethality. i will not give details here, but i you choose to look around and do some hard reading, you will discover, that the recipe for extremely lethal corona virus is not complex, but requires a lab capable of keeping and using the accesory biochemicals that allow primary sequence editing- that is to say any molecular genetics lab