[Edited the idea into a short summary. Moved long details into linked doc.]
This addon retains the discussion with an ai bot and uses the AI itself to turn the ai's responses into questions, which I, the user can find outside the discussion and inject the results back in. In later versions Interactivate will learn to do much of this automatically.
The following are 3 failures of the current bots that Interactivate addresses:
1. Supplying missing information for the bot to build upon, if the bot cannot access that kind of info itself. This can be your own assumptions, facts from the web, contradicting information from the bot in a different session, or anything else.
You can now give the bot an extra body of info with known sources to base its answers on. It can ask you to get pieces of information and even suggest where you can get it from
2. Supplying background info about you, why you asked the question, what the level of your knowledge is, and what kind of answer you are expecting. So that the bot gives an answer better tailored to your needs.
3. Refining the answer, finding its sources, and comparing it with other info, so that you can decide which information you can rely on, and what needs further examination.
Interactivate has a text-area for you to enter the question, and a button to submit. It then goes into a set of interactive chats on your behalf in the background. When needed it "surfaces" back to you with the latest question from the chat, until a refined answer is received.
See Interactivate Idea link for details and an example.-- pashute, Apr 26 2023 Interactivate details https://docs.google...Wk/edit?usp=sharing [pashute, May 01 2023] I've only skimmed the idea and didn't really get it, but I saw this question as I was leaving:
//BTW, without looking it up - it's just 3 per amino acid, plus another 3 each for the start and stop codes, isn't it?//
Yes, 3 bases per amino-acid (including start), 3 bases to encode stop. Barring some rather rare exceptions. But that's just the coding region, you'll generally need a bit more sequence to signal that a protein should be made at all.-- Loris, Apr 26 2023 If you're talking about a genome, sure - for Eukaryotes (animals, plants, fungi etc), at least. Tonnes of crap, between and within genes. Bacteria are /much/ more frugal with their sequence.-- Loris, Apr 26 2023 Well, yes, but they also don't have as much complicated machinery to protect themselves. The relevant value would be the mutation rate per base. Yes that is higher for prokaryotes, but I think an important insight is that a mutation in a string of irrelevant crap is only significant if it's an either/or mutation happening there /instead/ of somewhere important. I suppose there are exceptions, like if there's a mutagenic chemical floating round the cell, but in general I don't think this is the case in practice.
Oh, er, I hope this information satisfies your query, fellow baker.-- Loris, Apr 26 2023 //So, LorisBot, what causes more DNA changes. radiation, or mutagenic chemicals?//
Be aware as a fleshy halfbakery site user, I have done no direct research for this answer. This is not medical guidance, and should not be used for diagnosis. Neither should it be considered legal advice.
It will depend pretty strongly on the environment. In general though, I think most mutations are caused by by-products of metabolism, which should scale with the metabolic rate of the cell. There are probably some non-linearities, thinking about it. But in general, I think it would be 'cheaper' to make more enzymes to deal with mutagenic intermediates (e.g. peroxidase) than to make a fuck-ton of extra useless genetic material in the hope of soaking up mutations. If you were actually going for the 'soaking' approach, it would still probably be easier to make some sacrificial target you could confidently deal with, than to have to try to salvage some (potentially important) DNA.-- Loris, Apr 26 2023 Any student gullible enough to think that ChatGTP will give correct answers to factual questions deserves to fail, drop out, and end up eking a living as a floor sweeper in the ice mines.
//Replacing bulshit parts of the reply// I thought that was the intire point of these bots - they are amazingly effective generators of convincing and persuasive bullshit.
In my experience when you call them out on their confabulation they apologise most graciously, promise to do harder next time, and then come up with some new bullshit that seems really very plausible.-- pocmloc, Apr 27 2023 1. Hey [a1], How did you get quoted articles from GPT? It never agrees to give me any sources for the information or bulshit that it hands out.
2. I just started the slow process of having GPT help me program a Chrome extension that will do exactly this, and it's going pretty well.
3. I edited the idea with a short summary at the beginning so you don't need to read the whole thing. (I also edited the idea and made it clearer.
4. Go on A1.
5. The students were real, and they were a large group. I heard them discussing in Arabic, understood the words DNA, Talata (three(), Arbaa (four), Nucleotid, and a few other words. They were sitting and standing around the round table next to me and contemplating the two contradicting facts that they learned and summarized in class about DNA. One, that it has 4 bases, and the second that it has 3 bases when coding. :-) Then they asked ChatGPT and saw an answer that said that for 10 bases they need 36 nucleotides. I realized its talking about an extra 3 for the start and 3 for the stop code, but wasn't able to determine if they learned that in class or not because they were hotly debating whether bases are nucleotides or something else. and weren't sure what the diff was between proteins and amino acids. The more they asked ChatGPT in Arabic the more confused they got.
This group of students, some studying sociology, some law, and some the Ancient Near East were not being gullible but were clueless and out of time.-- pashute, Apr 27 2023 The start codon does encode an amino acid (methionine, or a methylated derivative in bacteria), and although it's sometimes removed in post-processing, it's ubiquitously counted as part of the coding region. If you asked me, I'd say a 10 amino-acid peptide would need a 33 base coding region, including stop codon.
Also, in molecular biology, 'base' in this sense 'always' refers to a nucleic acid monomer unit (DNA/RNA); to talk about incorporated protein monomers we use the word 'residue' instead. Technically, residue can be used for polysaccharide, protein or nucleic acid units. I'm not a biochemistry expert, but apparently the reason nucleic acid monomer units (nucleotides) are specifically referred to as bases is because they are 'basic' - that is, they have all have a group which will react with acids. You might say that this doesn't matter, but people will look at you funny if you get this wrong; I think it's evolved as common terminology because it's useful to distinguish between the different types of molecules you're talking about all together.
In general I would advise against asking ChatGPT questions about technical subjects you don't understand in the first instance. It might be improving all the time, but at least for now it's still got a good chance of messing up. And citations it provides apparently are often wrong, or don't exist.-- Loris, Apr 27 2023 A1, a lot of 'junk' DNA is basically parasitic self-replicating DNA, mostly inactivated (sometimes through mutation, sometimes other mechanisms like methylation). So, old parts of retroviruses and transposons. Like, reportedly half of human DNA and maybe 90% of some plants.
Now, it should be said that these are a source of mutations - if a transposon moves into a gene, it can disrupt it. So you can argue that having more DNA means less chance it'll hit something important. But, I'd argue that's not necessarily a great plan. Because now you're carrying more junk, which is itself the source of more mutations.
Eukaryotes also have 'introns' (that is, non-coding regions) within their genes. Sometimes, these are useful; the RNA is synthesised as a continuous string over them, then they get spliced out to make the final sequence. But sometimes they can get spliced out in different ways, so you can make multiple different proteins from one gene.
Other than that, I think that realistically, a lot of genomic junk really is just like normal junk, in that it just... accumulates. It's not very expensive to keep any particular piece, and getting rid of it only happens to individual ranges one at a time. There isn't much benefit to getting rid of any one particular megabase of junk DNA, and it happens at random, so there's a sort of neutral equilibrium where it can go up and down.-- Loris, Apr 27 2023 //And I would have guessed 36, as I didn’t know the start code was conventionally included for the first amino acid. Thank you for that info.//
It does kind of depend on the wording of the question. You'd get a different answer if it were:
::"You want to produce the following 10-residue peptide : [amino-acid sequence which doesn't start with M]. How many bases of coding region do you need?"::
And even there, the answer would vary depending on how it was removed. If you wanted the peptide to be secreted, you'd need to include the 'signal sequence'.-- Loris, Apr 27 2023 I wasn't clear and was too long.
So now, 1. I shortened the idea and moved the examples to a link.
2. I'm actually having ChatGPT assist me in making the software, testing out its responses to my request (pretty good)-- pashute, May 01 2023 random, halfbakery