schrodingersCat

This article is an ouroboros of self-citation and speculation. The lead author, McCullough, is a known proponent of Hydroychloroquine, denier of asymptomatic spread of covid, and a paid, invited speaker at right wing and anti-vaxx conferences (see his Wikipedia for citations: https://en.wikipedia.org/wiki/Peter_A._McCullough). This "research" paper offers lots of speculation, and very little data. The number of times these authors made unfounded and spurious confusion spurious is too high to mention all of them. I'll call out one example -"There were 3,657 cases of anosmia (loss of smell), clearly demonstrating that the SARS-CoV-2 spike glycoprotein from the injec- tion in the arm was reaching the olfactory nerve." None of the authors are qualified to make this claim, the authors made no attempt to rule out confounding factors like prior Covid-19 infection, and no direct evidence for thistle claim was presented. Tl;Dr - the article is bad science and should be ignored

I'm a little confused why the NHMFL home page ended up in my hacker news RSS feed, but I received my PhD here and thus feel obligated to comment and upvote...

PhD in molecular biophysics here (did virology rotation in grad school also). There's not enough time to go into how bad the "science" is in this paper. Evidence is cherry-picked, and circumstantial at best. Lots of non-sequitors presented that are unconnected to the actual science. I've read earlier claims that are similar to this and basically they see low alignment similarity to commercially available vectors and claim "AHA it must be engineered". But anyone who has studied molecular biology knows that vectors are almost always derived from natural viruses. Also, while viral linkages are normally linear, crossover between viri in hosts is well documented and does occur "rarely". That's say it's rare compared to normal genetic drift, but common enough that it's not particularly surprising to see genetic material from another "vector" in the wild. It does not have to be lab derived to see the mutations observed. Once you call into question this fundamental premise, everything else looks like the scientific trash that it is.

The major (and really only) criticism of Finder is a lack of an "address" bar. I would really like a bar where I can change directories quickly instead of doing ALL navigation using mouse clicks. Yes, I know you can invoke a Command-Shift-G to do this in a secondary menu, but Explorer has this built in. Having an address bar with tab completion and unix file-system shortcut support (i.e. "~", ".", "..") would be great!

In the terminal (iterm2 of course), I find vim with the solarized theme (http://ethanschoonover.com/solarized) combined with he right plugins to be a beautiful and useful text editor. In the gui, I really love sublime text (http://www.sublimetext.com/). Atom is also quite nice, so you really can't go wrong with that

I assume you want a desktop computer? Dell has great hardware support for debian/ubuntu and RH/Cent OS. I (think) you can purchase a desktop without an OS from their SMB store. Definitely get something with a spinning platter and pop in your own SSD. It will save you a lot of money.Why not build your own desktop? If you want to get the best deal and guaranteed hardware support, read some component reviews on http://www.phoronix.com/ and put it together yourself. Good luck!

The subreddits r/netsec and r/crypto can be helpful

I posted an edit to my original comment. I meant that the equivalent defining of a function (in zsh) does work, but zsh -c won't run the function unless you permanently add the function to your env.

Good call. I posted an edit to my original comment. zsh -c won't run the function outside of the current session. The "extra step" needed to add functions to the environment variables seems to make zsh much more secure than bash in the context of this discussion (perhaps?). This SE thread was really helpful to me in clarifying: https://unix.stackexchange.com/questions/33255/how-to-define...

I just tried this in zsh 5.0.6 (x86_64-apple-darwin13.3.0). It reports vulnerable as well.

edit: Yes, this feature works when formatted correctly for zsh as "function ls () { echo vulnerable }". However, I was wrong in that zsh -c will not run the function (of course running "ls" in the same session will). I'm going to call this not a problem.

edit: When trying this one-liner in zsh: "env x='() { :;}; echo vulnerable' zsh -c 'echo hello'" (as suggested by https://superuser.com/questions/816622/does-the-shellshock-b...), the output indicates my shell is vulnerable. Could someone please try and replicate?

I went ahead and recompiled a patched version of system bash as described in this SE thread: https://apple.stackexchange.com/questions/146849/how-do-i-re.... Thanks!

New rfid applications would be great and by means pursue them! The reason I think this is a great problem for CV is that right now, only a nurse would be able to tell if there is a puddle on the floor from a leaking IV, patient's puke, overflown catheter bag, etc. Also is there air in a line, does the label on the drug match the prescription in EMR? These are common sense, cheap to fix / prevent problems that I'm not sure rfid could solve. RFID would be great for matching drug labeled with rfid with chip in patient's armband. One could think of lots of implementations for that sort of thing!

I guess it really comes down to what sort of focus you want your project to take, and what idea you think your PI will be interested in considering. Good luck!

Sexual selection is a huge area of research in evolutionary biology. You don't have to like the wikipedia article, but a quick search on google scholar on the term reveals over 2M+ results. Check it out. Peter's description of sexual selection was much better than mine, so thanks! I brought up the Giraffe's neck because its one of the best examples of bad scientific method leading to incorrect evolutionary conclusions. Giraffe males joust as a dominance ritual prior to mating, and generally the giraffe that can exert more force will win and hence mate. There are no advantages to the neck outside of this ritual as far as anyone has been able to determine, hence it is understood to be a purely sexually selected trait.

A little off topic, but am I still vulnerable?

I'm running OSX mavericks 10.9.5, use zsh as my default shell, and have a patched version of bash build from homebrew repo set as secondary in /etc/shells (on the occasion I need bash, I like to have completions). System bash is still vulnerable. With my current configuration, how worried should I be?

Any insight is appreciated!

This really depends on how practical you want to get. One of the biggest problems in hospitals is (lack of) staffing. Having a robot that could go around the rooms and check on low-level, treatment related problems would be a huge improvement in patient care. Imagine using CV to check on IV pumps for flow rate, how much of the drug is left, is it leaking, does the patient need more IV fluids, does the name on the drug label match the patient's, etc. These are low level problems that can lead to injury and death of patients in hospitals, and usually handled by overworked nurses. Seems like a perfect application of CV to me.

While the fact that cross-over during meiosis does in fact contribute to increased genetic diversity leading to resistance to disease, parasites, and other adaptational advantages, one still needs to answer why did sexual reproduction evolve at all? Bacteria and protists are quite good at promoting genetic diversity through horizontal gene transfer, and viral infection with natural DNA replication error rates provide enough sources of "random" genetic variation to keep a diverse gene pool. One can think of competition to share genetic material as a primordial form of sexual selection. Getting from this kind of competition to orchestrated sharing and cross over of large genomes is a huge jump. The real question may be, did increasing organismal complexity necessitate a different type of reproduction to maintain genetic diversity? The answer to this may be yes, but alternative, less sexy hypotheses have to be tested as well. Another question to answer would be – What evolved first: multicellularity or sexual reproduction?

Its generally understood that traits that encourage reproduction regardless of whether or not they encourage fitness will outperform other traits (https://en.wikipedia.org/wiki/Sexual_selection). This is why you will see the appearance of coloration and seemingly useless adaptations faster than actually beneficial traits within a population (i.e. a giraffe's neck; its not for reaching those high leaves). Natural selection is generally concerning traits that promote survivability over time, a much slower process. A major hypothesis is that sexual selection may be a driving force behind differentiation of the sexes, probably originating from genetic information sharing among single-celled organisms. A competing hypothesis is that there is an intrinsic advantage to sexual reproduction versus asexual reproduction. I generally favor the former hypothesis because it generally fits the "short-sightedness" principle of evolution.

This paper makes a 0th order assumption that there is an inherent advantage to sexual vs asexual reproduction. There are certainly advantages to both, but the author is correct that the answer may come out of addressing complexity. Algorithmically, there are many approaches to modelling sexual selection (rather than natural selection). Sexual selection occurs much faster than natural selection and may be one of the reasons why we have such apparent gender differences within species. Describing the effect of complexity in terms of "fitness" is one of the largest challenges faced by computer scientists and biologists this century. If you are interested in exploring some different algorithmic models, "Computational Molecular Evolution" is an excellent book (http://www.amazon.com/Computational-Molecular-Evolution-Oxfo...).

There may be a story behind this post as it feels quite personal, but this is a pretty good composite of bad management behaviors. I see this more of a collage than a specific rant. I could be wrong, but I've seen one or more of these traits expressed by almost any supervisor I've encountered (not all the time or all at once).

Or things behind a paywall

Of course this is not universally true, but there is definitely a culture problem within the field. Furthermore there's a repeatability problem in a ton of biological research. More time has to be spent repeating findings even at the expense of slower progress (retraction watch is mostly full of biological/medical research). I don't meant to dismiss charisma outright, but it needs to be backed up with originality and good science to be worth a damn.

I haven't read all the responses, so I hope I am not repeating anyone's insight. I'm finishing my PhD in biophysics, and I wanted to share my perspective from conversations I've had with my boss/PI and other investigators. In life science research, there are huge incentives to not repeat others research and furthermore to not publish negative results.

The first disincentive comes from funding bodies: NIH et. al (NIGMS, NIEHS, ...) don't like to pay for you to do "someone else's science". If you manage to get a grant, and it comes out in a progress report that you did repeat too much of other people work, be prepared to get that funding reduced and or cut.

Academic departments strongly discourage new hires from publishing negative results and /or repeating other peoples work (mostly because this will likely decrease chances of getting published and funded).

Academic journals hate to publish negative results, but seemingly have no problem publishing bad science (yes Nature, I'm looking at you: http://retractionwatch.com/2014/09/11/potentially-groundbrea...). Early in my PI's career, she tried to publish a very important negative fining in a high impact journal. The article's acceptance was accompanied by a personal letter from the editor urging her to consider other journals for negative results.

Another barrier quite honestly is ego. While it may sound as if my boss is "one of the good ones", alas, she is not. On occasions that I have asked to repeat other group's seemingly unbelievable results myself, I've been flatly denied on grounds that this kind of work does not express the sort of originality of research produced by her lab. In other words, nobody wants to be known as "that lab", the nay-sayers of the field, those that would dare to question a colleague's ideas.

Finally, this lead me to the last barrier I have observed: scientific communities / societies. If you are of the lucky few that end up publishing negative results of major significance, prepare to not be invited to dinner at next years Society for X annual meeting. Yes, in many ways life-science is stratified just like high school. You have the cool kids on track for the nobel, the weirdoes in their corner pushing the boundaries of what is possible, the "jocks"/ career scientists who manage to turn a couple of tricks and some charisma into a living, and finally the tattle-tales who seem to piss everyone off with their negative results. These are HUGE oversimplifications / generalizations, but I really think that all of these barriers need to be addressed in some way to fix life science.

Feedly + Reeder on OSX

I hate to be the cynical one here, but the countries with the power to stop this outbreak aren't going to start taking it seriously until more people from western nations start dying. It is true, it will be really bad if it is not stopped soon. Containing an outbreak of >5000 is out of the reach of most of the states affected by the disease and quite honestly very expensive for any nation. Once this spreads closer to Europe, watch people start to take more action. I hope it won't be too late

Any word on what site(s) were hacked leading to this leak? I don't reuse any passwords so I'm not very concerned, but I'm the kind of person who just likes to be sure

Just from a users perspective, this approach sucks. Ever tried to install a package on an older Ubuntu box only to find that the binary for this version has not been updated in over a year? Then you find out why: installing the (old versions) of shared libraries inevitably breaks installation of normal packages, and is usually followed by headaches and backtracking. I'm sweating just thinking about this!

Honestly, a feature for distraction free note-taking / writing would be nice with better formatting support than the standard app. I always think evernote would be a great idea for writing rough drafts of memos or articles but I very quickly realize that its text formatting is crap. Seriously, it is aggravating to write anything more complicated than a grocery list. Don't get me wrong, its great for importing and searching PDFs and especially scanned documents, but its really bad for writing. I'm not sure what the focus of your client is, but if you fixed this, I would very quickly become an adopter.

Thank you for posting this. I do not personally work with animals, but I knew there must be a way to convert doses between mice and humans given how often my colleagues test drugs on rats and mice.

There may be pharmacokinetic reasons for using these higher doses in mice. The rate at which drugs absorb through the blood brain barrier, are metabolized by the liver, and are eliminated by the kidneys are all factors one must consider. Not to mention the does response for MPD in mice may in fact be different. The goal of this study was not to simulate therapeutic dosing of MPD, but of chronic (short term, high dose) application of the drug. You are correct in noting that this study does not directly translate to humans taking the typical therapeutic dose, but it certainly does raise questions.

Thank you for bringing this to my attention. As an avid Evernote user, I will shoot them a feature request email. MITM attacks are a real problem (how do you think Gamma's Fin–Fisher was deployed?), and there is no excuse for this not to be implemented on such a popular app.