Genomes are sequenced when they're both accessible and are of scientific/economic interest. This results in an overrepresentation of:
- Humans and their pathogens
- Economically important organisms (e.g. crops and farm animals) and their pathogens
- Model organisms
For example, compare the number of Genebank sequences for HIV-1 [1] versus Feline immunodeficiency virus [2]. HIV-1 is additionally problematic because it has an extremely high mutation rate [3], making it more likely for a random sequence to match some sequenced HIV-1 genome.
Using the number of BLAST hits as the basis of an argument is about as reliable as using the number of results when searching for a string on GitHub. Without further analysis of the specific sequence and its biological context it can be highly misleading. See a previous Twitter thread on some other purported HIV inserts: https://twitter.com/trvrb/status/1223666856923291648
There also seems to be some circular reasoning the argument. Apparently we can ignore RaTG13 because it’s obviously synthetic, which makes SARS-CoV-2 look even more synthetic. It would be interesting to compare to the BANAL family of SARS-CoV-2-related viruses that are even more closely related to SARS-CoV-2 than RaTG13 [1].
I’m not sure why only viral genomes were searched for the furin cleavage site sequence. Viruses famously exchange genetic material with their host organisms. The “smoking gun” sequence also appears Mycobacterium smegmatis, for example [2].
The GitHub example actually is pretty spot on. If you wrote a non trivial piece of code in 2016, then in 2020 it was used verbatim in another program, what would your conclusion be?
For a non-trivial piece of code, the conclusion might be that it was copied (horizontal code transfer??). But the 6 amino acids is not a "non-trivial piece of code" -- it is a trivial short string of letters. So the more relevant question is, how often do we see "dogcat" in GitHub (468 repository names). Or perhaps something more nonsensical: "ifdlog" (6 letters from "goldfish" reversed): 1 repository and 25 code results. "hsifdl" - 1 code result.
Sure I will not argue that the code showing up somewhere is statistically interesting. What’s interesting is that it showed up exactly once and in a Moderna patent. What’s the probability of that? That of the random strings in the Moderna patent that it would be an exact match to a string in the COVID genome but nowhere else?
You are correct. I should have stated furin cleavage sites have not been observed in another beta coronavirus. (Cold, MERS, SARS) I corrected my statement. Thank you for pointing that out.
Nuclear weapons do not have situational awareness. They’re intended to be used as part of a larger deployment system with a human in the loop. There’s no threat model for them that includes self-arming when mysterious aircraft approach their storage location.
Existing Intel software (with potentially broken version checks) will work on ARM Macs under emulation. Once they rebuild with the new SDK they'll get the receive the correct version.
The T2 chip is a derivative of the A10. It has similar power requirements to the SOC in modern iPhones.
They could probably use a cut down derivative of the W2 chip used in AirPods with the audio codec etc. removed. I’m guessing phone batteries reach a point where they’re still storing energy but can’t provide enough current to safely boot the whole phone. The BLE chip could sip on the remainder of the battery for a long time.
This would be excellent. I'm hesitant about the prospect of an ARM based macbook, but having both seems mighty compelling. As a lower power application CPU for light usage, or a full x86 with accelerators / co-processors when needed.
The way I’ve approached it in my compiler [1] is that garbage collection can never occur while Lisp/RFI (Rust function interface) code is executing. Once the program returns to the event loop GC can occur with a small number of known roots. This works because there will be no way to block without waiting on a future which can then return to the event loop. I’m considering adding a `conditional-gc` macro for long running computations that’s internally implemented as waiting on a future that’s immediately resolved.
This means that RFI code can treat GCed values as having a `'static` lifetime. One caveat is that RFI code cannot capture values except for a few special runtime functions. This works naturally with the language’s pure functional design, however.
As far as data structures go its impossible to support performant Lisp code by implementing lists as native vectors; the guarantees and idioms are too different. My runtime [2] provides Rust bindings for data types that e.g. allow you to create an `Iterator` from a list or construct a list from one. That should allow transparent interoperability with idiomatic Rust patterns and data structures.
You’re not parsing XML at that point. You’re parsing a text based data format that looks superficially like XML. This can work if you strictly control the encoder but it’s not generally interoperable.
Why does general interoperability matter in the context of two devices that you control both interoperating? I mean, if I had written the software on the other end I would've used a different interchange format altogether. But when you constrain the problem down from your software connecting to any and all systems on the internet to your software connecting to a specific system for the purpose of exchanging well-defined messages, you don't need a general-purpose parser with validation. And you end up spending a lot of time validating and analyzing the same message over and over again even though you can guarantee that it's the same message.
The flip side of time dilation is Lorentz contraction. As you approach the speed of light objects in your direction of motion will become shortened from your frame of reference.
For example, there are particles from cosmic rays that should not be able to make it to the surface without decaying. However, they're detected all the time. Two valid ways to think of this are:
1. From the Earth's frame of reference time moves more slowly for the particle. This slows down the process of decaying.
2. From the particle's frame of reference the Earth's atmosphere is considerably shorter so it doesn't need to travel as far.
Things get a bit hairy to talk about once you actually reach the speed of light. One way to think of it might be from the photon's frame of reference its entire path has become infinitely short so it had no distance to travel at all.
> One way to think of it might be from the photon's frame of reference its entire path has become infinitely short so it had no distance to travel at all.
From the photons frame of reference, then, they do not move at all?
And the environment that photon "experiences", being the path in the universe that it traverses from our point of view; is the past, present, and future (from our point of view) all in instant simultaneity for the photon?
Unfortunately when talking about physics, sloppy human languages and our tendency to anthropomorphize when describing very non-human-like things cause a lot of communication/learning problems. Concepts like "experiencing an environment" and "time" don't make sense for the photon, which is sort of equivalent to "moving at c" because experiencing something like "time" requires interactions (events) at different places in spacetime.
Saying "neutrino has a very small mass" is roughly equivalent to saying "neutrinos very rarely experience an oscillation event (changing into a different flavor)". The distance between the rare events is the "time" it experiences. These are so far apart in spacetime for the neutrino it's experience of time (the way it evolves over spacetime) is extremely slow. More massive particles are "more massive" because they frequently interact with the Higgs field. More interaction events means their experience of time happens faster.
The photon (and anything else with 0 mass) only experiences two events: it's creation and destruction. It moves at c because it's never being slowed down by experiencing interactions.
For a very good explanation of this (with helpful animations) this[1] short playlist (6 ep) of PBS Spacetime episodes.
edit: TL;DR - When speed-of-light particles pause to interact with things (thus moving < c)slowing it down), we say that particle "has mass". Mass is a measure of how frequently those interactions occur (aka how much "time" it experiences).
> The photon (and anything else with 0 mass) only experiences two events: it's creation and destruction.
This is not correct. The worldline of a photon contains events between its creation and its destruction. The spacetime interval between any such pair of events is zero, but that does not mean the events aren't there.
If you flash a laser at a detector on the Moon, there is a whole continuum of events between the source (the laser) and the destination (the detector on the Moon). The spacetime interval between the source and destination events is zero, but there is still a whole continuum of events between them (all the events the photon passes through between the source and the detector).
> From the photons frame of reference, then, they do not move at all?
There is no such thing as "the photons frame of reference". It is not even a well-defined concept.
> And the environment that photon "experiences", being the path in the universe that it traverses from our point of view; is the past, present, and future (from our point of view) all in instant simultaneity for the photon?
No, none of this is correct. The reason I keep insisting that all these concepts are not well-defined for a photon is to make it clear why you cannot draw all these inferences that you are trying to draw--they are all wrong. The only way to stop drawing them is to recognize what "not well-defined" means. It means the questions you are trying to ask about photons are meaningless; they are like asking how long the color red is or how much time passes for it. Photons are simply not in the category of things for which those questions make sense.
Every single comment you've written on this subject closes all discussion on it. So what is there to discuss? Or shall I remain silent in the ignorant darkness of my status as a (physics) layman?
Even Einstein inserted an anthropomorphized frame of reference into the thought experiments of the celestial objects he contemplated, to explain to others. If we can't ask questions about photons in relation to spacetime as we know it, then what questions can we ask? We certainly don't know spacetime as photons "know" it, since its not "well defined."
Interestingly still, you use the term worldline to describe the totality of the temporal-spatial existence of a photon, so clearly there are concessions to be made and all this is more defined than you assert... and you're lightly reproving us for not using the same dictionary as you...
I'm interested in this subject but not interested enough (or rather, have the time and energy) to become a physicist to understand, if that's what you're going to ultimately suggest to get even a dim, but accurate understanding of the nature of light.
> Every single comment you've written on this subject closes all discussion on it
I have done no such thing. I have only closed discussion based on a fallacious premise. If you drop the fallacious premise there is plenty to discuss.
> We certainly don't know spacetime as photons "know" it, since its not "well defined."
I did not say spacetime is not well-defined. Spacetime is not "as photons know it" or as any observer "knows" it. Spacetime is the underlying geometric entity; it requires no "point of view" to exist, or even to be described; you can describe spacetime without ever using inertial frames, which are what your "points of view" actually are.
> you use the term worldline to describe the totality of the temporal-spatial existence of a photon
That's because "worldline" is the standard physics term for it, as used in physics textbooks and peer-reviewed papers.
> you're lightly reproving us for not using the same dictionary as you.
If you want to discuss physics, it helps a lot to use the standard language of physics.
> I'm interested in this subject but not interested enough (or rather, have the time and energy) to become a physicist to understand
You don't have to become a physicist. But you do have to be willing to drop fallacious premises.
Just note that however you try to define "the photon's frame of reference" you end up with a division by zero, so the definition becomes meaningless.
Eg distance traveled is 0 due to length contraction. Time taken is 0 due to time dilation. So what's its velocity? 0/0 = undefined, the question is meaningless. But the velocity is arguably more fundamendal than the distance travelled or time taken, so those aren't truly 0. They're also undefined quantities.
> One way to think of it might be from the photon's frame of reference its entire path has become infinitely short so it had no distance to travel at all.
No, that is not a correct way to think of it. See my other responses to the poster you responded to.
- Humans and their pathogens
- Economically important organisms (e.g. crops and farm animals) and their pathogens
- Model organisms
For example, compare the number of Genebank sequences for HIV-1 [1] versus Feline immunodeficiency virus [2]. HIV-1 is additionally problematic because it has an extremely high mutation rate [3], making it more likely for a random sequence to match some sequenced HIV-1 genome.
[1]: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mod...
[2]: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mod...
[3]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574155/