11 Matching Annotations
  1. Feb 2024
    1. Additionally, SARS-CoV-2 takes over autophagy pathway components in unconventional methods (Brüggemann et al., 2023; Zhao et al., 2021). SARS-CoV-2 E, M, ORF3a, and ORF7a cause autophagosome accumulation, but Nsp15 suppresses autophagosome formation (Hayn et al., 2021). Moreover, ORF3a of SARS-CoV-2 blocks autophagosomes by preventing the HOPS complex from assembling the SNARE complex, which is necessary for autolysosome formation (Miao et al., 2021). Another coronavirus, SARS-CoV, can induce incomplete autophagy by interacting between Nsp3 and Beclin1, which in turn modulates coronavirus replication and antiviral innate immunity (Chen et al., 2014).

      All of these papers need checking - just in case. could it be related to the fact that the DMVs and autophagosomes have much in common?

  2. Sep 2022
    1. The scalability issue is somewhat related to the versionability issue. In the small, checked exceptions are very enticing. With a little example, you can show that you've actually checked that you caught the FileNotFoundException, and isn't that great? Well, that's fine when you're just calling one API. The trouble begins when you start building big systems where you're talking to four or five different subsystems. Each subsystem throws four to ten exceptions. Now, each time you walk up the ladder of aggregation, you have this exponential hierarchy below you of exceptions you have to deal with. You end up having to declare 40 exceptions that you might throw. And once you aggregate that with another subsystem you've got 80 exceptions in your throws clause. It just balloons out of control. In the large, checked exceptions become such an irritation that people completely circumvent the feature. They either say, "throws Exception," everywhere; or—and I can't tell you how many times I've seen this—they say, "try, da da da da da, catch curly curly." They think, "Oh I'll come back and deal with these empty catch clauses later," and then of course they never do. In those situations, checked exceptions have actually degraded the quality of the system in the large.

      This is another case where I think inference would solve most of the issue.

    2. Anders Hejlsberg: Let's start with versioning, because the issues are pretty easy to see there. Let's say I create a method foo that declares it throws exceptions A, B, and C. In version two of foo, I want to add a bunch of features, and now foo might throw exception D. It is a breaking change for me to add D to the throws clause of that method, because existing caller of that method will almost certainly not handle that exception. Adding a new exception to a throws clause in a new version breaks client code. It's like adding a method to an interface. After you publish an interface, it is for all practical purposes immutable, because any implementation of it might have the methods that you want to add in the next version. So you've got to create a new interface instead. Similarly with exceptions, you would either have to create a whole new method called foo2 that throws more exceptions, or you would have to catch exception D in the new foo, and transform the D into an A, B, or C. Bill Venners: But aren't you breaking their code in that case anyway, even in a language without checked exceptions? If the new version of foo is going to throw a new exception that clients should think about handling, isn't their code broken just by the fact that they didn't expect that exception when they wrote the code? Anders Hejlsberg: No, because in a lot of cases, people don't care. They're not going to handle any of these exceptions. There's a bottom level exception handler around their message loop. That handler is just going to bring up a dialog that says what went wrong and continue. The programmers protect their code by writing try finally's everywhere, so they'll back out correctly if an exception occurs, but they're not actually interested in handling the exceptions. The throws clause, at least the way it's implemented in Java, doesn't necessarily force you to handle the exceptions, but if you don't handle them, it forces you to acknowledge precisely which exceptions might pass through. It requires you to either catch declared exceptions or put them in your own throws clause. To work around this requirement, people do ridiculous things. For example, they decorate every method with, "throws Exception." That just completely defeats the feature, and you just made the programmer write more gobbledy gunk. That doesn't help anybody.

      The issue here seems to be the transitivity issue. If method A calls B which in turn calls C, then if C adds a new checked exception B needs to add it even if it is just proxying it and A is already handling it via "finally". This seems like an issue of inference to me. If method B could dynamically infer its checked exceptions this wouldn't be as big of an issue.

      You also probably want effect polymorphism for the exceptions so you can handle it for higher order functions.

  3. Jul 2021
  4. May 2021
  5. Feb 2021
  6. Nov 2019