I did this in the beginning and realized I never went back to it. I think we have to learn to embrace the chaos. We can try to place a couple of anchors in the search space by having Claude summarize the code base every once in a while, but I am not sure if even that is necessary. The code it writes is git versioned and is probably enough to go on.
It's a different skillset and way of thinking. Engineers tend to think vertically deep on technical problems. With AI, you have to think horizontally broad and vertically up on the architectural problem. The trick is to be comfortable relegating the details to AI.
One concrete example of this realization was when I was researching how to optimize my claude code environment with agents, skills, etc. I read a lot of technical documents on how these supplemental plugins work and how to create them. After an hour of reading through all this, I realized I could just ask Claude to optimize the environment for me given the project context. So I did, and it was able to point out plugins, skills, agents that I can install or create. I gave it permission to create them and it all worked out.
This was a case of where I should not think more technically deeper, but at a more "meta" level to define the project enough for Claude to figure out how to optimize the environment. Whether that gave real gains is another question of course. But I have anecdotally observed faster results and less token usage due context caching and slightly more tools-directed prompts.
Pretty cool technique using complementary overhangs and toehold sequences to generate a 3-way heteroduplex, ligate knick, and then remove barcode duplex.
They don't give much details on how the barcode duplex is removed though. I guess ultimately the barcode duplex strands can just be melted off and the ligated strand can be used to template off of.
If this can be made into an easy to use kit, can really make vector generation much easier and hopefully not locked into proprietary systems.
I can imagine a company that bioinformatically generates libraries of common long oligos with corresponding barcode and allow end-users to select oligos to modularly ligate together in a one pot reaction. Cool stuff.
We’ve been able to do this type of nucleotide 3D engineering for a while. I used to use large DNA branched complexed fluorophores to label cDNA back when I was in grad school. They were more or less mixed of DNA that self assembled into larger hairballs.
But branched DNA is really interesting. It’s a bit hard to get my head around. We spend so much time thinking about DNA in the 2D sequence sense, it’s easy to forget that it exists in 3D space.
I’m honestly not sure how different this really is to the traditional ways of doing this (with custom oligos). The common set of large self-hybridizing oligos is definitely easier, but you still have to have compatible tag overhangs between your two fragments. Meaning, it isn’t quite as universal and you’ll still need work to pair the fragments together. But where I think it might be useful is if you have a set of common hybridizing pairs that can be easily located onto the custom flanking oligos. You’ll still need some sequence analysis to get your custom oligos, but it would make the process more “standardized”.
I think the main bonus here is the self correcting selection… that you only end up with matching pairs linking together, so you could really have a mix in a one tube reaction that links many kilobase fragments together. That’s quite nice. And useful. And still cool.
One thing that is interesting is that this is another step towards getting the “writing” step of DNA analysis better. For the past 50+ years, we’ve developed all sorts of tools for reading DNA. It’s only really been the past 20-ish or so that we’ve had tools for writing. And now we can write longer chunks. That’s all a good thing.
Not sure I think it’s revolutionary (yet), but that’s a university PR release for you! I’m still thinking about the paper.
I am unsure of the impact of this to the regular consumer as this seems like a pretty niche area. But it's kinda shitty that interpersonal relationships of two companies are impacting their customers negatively.
The onus is not up to public opinion or customer politics to resolve your schoolyard differences. We just want to buy your products and not get loaded with baggage. We don't owe you loyalty on top of the price we paid you for the product.
It reeks a bit of tech self importance. From an overall business context, you balance time/effort vs short/long term reward and design or fix things when you need to.
There are many dials to manipulate in a business to make it more efficient. And not all businesses are tech startups. Software, fortunately or unfortunately, has a lot of room to be inefficient due to cheap hardware as long as it gets the job done in a lot of industries.
I have a technical background as a data scientist and developer. If I look back 5-10 years ago, I can definitely recognize my bias towards over-engineering and premature perfectionism. Identifying that sweet spot between over-designing and unplanned failure is key.
So the queen can lay 3 types: hybrid female, Ibiricus male, structor male. Did they do karyotyping? Is it actually that the queen somehow removed its own genetic material from the nuclei or does it somehow get silenced when the M. structor genetic material is present in the nuclei (which is interesting by itself). Perhaps some kind of complex imprinting is happening.
I think this sentiment has probably been echoed through the ages.
It feels like there's an assumption that we've reached some kind of a complexity ceiling and compressing complexity below us will just make us dumb? What if we've black-boxed complexity below us so we can explore more complexity above us?
Maybe the argument is that the rate of compressing complexity below us is faster than expanding the complexity space above us? And the result is that it makes us run out of knowledge of digest and explore? Perhaps the answer to that is to make people more curious to go out and explore the complexity above us so we can generate that knowledge.
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