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polyfractal

2,877 karma · joined May 17, 2011

Molecular and cellular neurobiologist turned software developer.

https://polyfractal.com

[ my public key: https://keybase.io/polyfractal; my proof: https://keybase.io/polyfractal/sigs/AvkaCfWRV93NjdW1RyX0-nQHgsP30ZvmbNkUdIbxidU ]

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polyfractal··on Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]
It is probably more accurate to say that cDNA represents a snapshot in time of a particular mRNA "species". Any particular mRNA could lead different lives, depending on what kind of post-translational modifications are made to it (e.g. different proteins editing the mRNA differently before it is eventually transcribed).

So any particular mRNA might actually have several different products, or may just get chopped up into shRNA or microRNA.

polyfractal··on NSA leaker Edward Snowden: U.S. targets China with hackers
OR he's just a whistleblower trying to do the right thing for the States.
polyfractal··on GM Wheat found in Oregon 10 years after abandoned by Monsanto
Cross-breeding is fine, inbreeding is not. When you identify A+B makes a taller plant, you start breeding the children C with each other to isolate the "tall" gene. Soon you are inbreeding the descendent's of A+B.

Most "breeds" of dogs are horribly inbred so that they maintain their traits. Same goes for "heritage" vegetables, "fancy" rats, or any other organism that humans have selectively cultivated.

polyfractal··on GM Wheat found in Oregon 10 years after abandoned by Monsanto
These are reasonable arguments. My biggest problem is that all GMO gets lumped together. Legit GM that helps increase drought-hardiness in water-starved Africa gets lumped with Roundup-GMO.

I agree my post was way over the top, but damn, you never hear anyone advocating for GM. It is all going to kill you, spread to every other plant and sterilize the whole world.

As with most things, the truth is somewhere in the middle. :)

polyfractal··on GM Wheat found in Oregon 10 years after abandoned by Monsanto
As a biologist, the furor over GM plants drives me crazy. Crazy! Why?

We've been genetically modifying plants for hundreds of years. Mendel himself fucked around with plant genetics - crossing plants is nothing more than fiddling with genetics. People were messing with genetics hundreds - thousands - of years before Mendel and they just didn't realize it.

Hell, people have been messing with the genetics of animals for thousands of years, selectively breeding dogs, horses, goats, cows.

Just because we are able to modify genetics precisely doesn't mean it is any different. If anything, we should have fewer problems (e.g. how many german shepherds have hip dysplasia because of inbreeding?)

Edit: Don't have time to respond to all the replies, but there are some good arguments there. I acknowledge that this post was over the top - but simply because all the press one sees about GM = evil. Things are never black and white.

polyfractal··on Why Java is still relevant
Touché. I should read more clearly, and be less angsty. Sorry about that :)
polyfractal··on Why Java is still relevant
Rails is not a language. Rails is not ruby. I wish people would stop conflating the two.
polyfractal··on Why Java is still relevant
Lucene (and projects built on Lucene like Elasticsearch and Solr) make Java relevant, even ignoring everything else built in Java.
polyfractal··on The Myth of America's Tech Talent Shortage
> btw why is he looking through the lens if the microscope is plugged into a monitor? Seems redundant...

Actually, this is pretty common, especially if you are doing fluorescence microscopy (complete derail from your main point, sorry):

- The optics leading to the eye-piece is usually superior to the quality of the camera. You'll have a cleaner, crisper picture looking through the eyepiece

- Most cameras tend to have a refresh rate which is laggy.

- Eyepiece optics tend to have a wider field of view, making it a lot easier to find interesting areas to focus on

- Especially for fluorescence, using the eyepiece helps block out background light, letting you focus on faint details. Some details are just really hard to make out on the computer screen, without fiddling with contrast/brightness settings

- You may have the computer settings at a particular level where "browsing" the field is impossible. E.g. your "picture taking mode" is set to long exposures, or very quick exposures with high contrast. These settings make it difficult to actually use the computer for anything except taking the picture.

- You are taking pictures in fluorescence, but selecting/focusing with bright-field.

polyfractal··on This Page Is Why The Internet Sucks
Search for "convert PDF to HTML linux" and you have a whole page of relevant, useful links. I don't understand your complaint.

Google isn't making anything seem "difficult". They offer advertising space, and companies happen to sell pdf conversion software. Therefore, those ads show up on searches. It isn't Google's fault if the companies advertising pitch is "PDF Conversion is hard!". That's the company, not Google.

Google hasn't forced the internet to do anything. The reason we have terrible pages like the one in the OP is because of the economics of giving away free content and relying on advertising.

I'm not a huge fan of Google, but your complaint is pretty :tinfoil:

polyfractal··on A Personal Statement from Iain Banks
I don't doubt that cryonics is a valid science, but it is not a valid business model right now. The things I did in my lab were valid science, but I would be thrown in jail for ever giving those reagents to actual patients.

Like I said, the current state of "businses cryonics" is basically astrology and wishful thinking. I also don't doubt that in ten, twenty, fifty years, scientists will have figured out how to do it (much better).

But right now? I'm saying nope.

(Addendum: most of those publications listed at 21cm are about thin slices, which isn't exactly relevant. The even better ones are oocytes, which are practically tanks of the cellular world. Drosophila oocytes are so large you can see them with your naked eye and can withstand enormous punishment before dieing. Using them as case studies of vitrification is not really being honest.

This brings me back to my original point: the science is solid...at an academic level. Once you move past 50 micron tissue slices, it all goes to hell.)

polyfractal··on A Personal Statement from Iain Banks
That's fair enough, although it should be noted that proteins/molecules are still active at -80C, just very slow. Things still break down, some enzymes are still active, etc.
polyfractal··on A Personal Statement from Iain Banks
>No, that's not very rational. Cryopreservation may have low chances of success, but it's like a billion billion billion times better than just dying (which has zero chance of success). Nobody is claiming that cryopreservation is very probable, but it's a lot better than nothing.

Ok, I'll give you that there is a non-zero chance. Other's have touched upon that in this thread, and I would contend that giving 200k to some family/friend is more useful than throwing it away, but it's your money. If you are happy with a negligible-but-non-zero chance, go for it.

>I don't think your critique is very relevant, when almost all cryopreservation is only done to the brain, not the whole body.

There is exactly zero evidence that a brain/mind is functional without it's body. And there is currently no computer simulation or interface capable of simulating a human body and its various sensory input, so this is a moot point.

>Thawing is not relevant to be discussed at this point, because the bodies will not be thawed using current technology. If the cryopreserved brain has enough information to be reconstructed, it will be done at some point using advanced nanotechnology. Nobody will be thawing brains using 21st century technology.

Bit of a cop-out, no? Is the flying spaghetti monster going to thaw you? At this point your theories are no better than saying a big bearded guy in the sky is going to resurrect you. Except he'll do it for free.

>By the way, scientists don't refer to the cryopreversation as freezing, they call it vitrification.

I guess I wasn't a classically trained biologist working in neuroscience labs for 6 years then, sorry. Also, it was before my cup of coffee in the morning.

Appropriate terminology or no, my points were and are still valid.

polyfractal··on A Personal Statement from Iain Banks
That is not peer-reviewed research, and therefore I treat it about as seriously as I treat any other comment on the internet: at best incompetent, at worst maliciously deceiving. Considering its published by a company that makes money from freezing people...probably the latter.
polyfractal··on A Personal Statement from Iain Banks
Hmm...except that cryopreservation is still, as of this point, a complete crock of shit. Trying to find a necromancer would be more productive.

As an ex-biologist, I can assure you that horrible cellular damage is being committed to these "preserved" people. I used to flash-freeze all sorts of cells, ranging from bacteria (e. coli) to animal (IMCD3 and MDCK kidney) to human (Human Embryonic Kidney, Primary cortical and hippocampal neurons).

These protocols are pretty simple. Pellet and re-suspend a small vial of cells to dilute out the media, replace with a special preservation media then dunk the entire 5mL vial in a big pot of liquid nitrogen for a few minutes. Then it goes into the deep freezer (-80C).

Sadly, even though this is a tiny aliquot that is frozen almost instantly, cell death on thawing and resuspension is immense. Like, it's a good day if 50% of the cells live. It usually doesn't matter, since these cell lines are immortalized and they just start growing again, but it illustrates the point. Despite the most ideal circumstances, cells hate to be frozen.

Now, imagine you are trying to flash freeze an entire body. They do this by perfusing preservation media through your blood, relying on your body's circulatory system to get the media in all the right places. This takes time. Perfusing a small mouse with formaldehyde takes at least 5-10 minutes. A human body? Practically ages I would guess.

All the while, cells are dieing left and right because they are no longer getting a steady supply of oxygen (and instead a bath of relatively cytotoxic preservation media). When the body is finally perfused fully and dunked into liquid nitrogen...flash freezing isn't immediate. The outer layers freeze much faster than the inner layers.

Ok, so just freeze the brain? Same problem as before, just on a slightly smaller scale.

Ignoring all the cell death that has been happening for the last hour, how about thawing? Well, let's pretend its a "good day" and 50% of your cells live. That might be ok for your skin, liver, or spleen - they are going to be unhappy but still alive. But 50% of your neurons dieing? Hmm. Also take into account that neurons don't regenerate. You just killed half your brain. Even super optimistic numbers, 70%-80% survival rate, still leave a lot of your brain as goo.

This is all just biology. I'm not even touching the morals and ethics of companies that are under no obligation to actually do what you paid them to do (since you are dead).

polyfractal··on Growing Tomatoes
Agreeing with everything you've said. In addition, there are some really excellent gardening tutorials on Youtube. Last year I learned how to sucker tomatoes from youtube, as well as constructing those vertical string things that allow your tomatoes to grow up instead of out.

Tomato tip: make sure you understand the difference between determinate and indeterminate plants before you buy. Determinate plants fruit all over the bush at one time, and then pretty much die. Indeterminate are more like vines and keep fruiting sporadically over the entire season.

You'll be sad if you are expecting a long tomato season from one or two plants but accidentally buy a determinate plant.

Semi-related, if your climate is warm enough for Jalapeños...those plants just never die. I abused and neglected mine all winter (South Carolina, so never freezing temps) and the poor little plant kept producing fruit. I hardly watered it, never fertilized and it lived in a pot outside. Despite that, it's still happily trucking along ready for the summer :)

polyfractal··on Blog Or Get Off The Pot (2006)
To be fair, even your original observation is complete speculation that may or may not apply, as admitted by yourself. You could easily reformulate your statement as:

> I noticed an uptick in hellbanned after the baked-goods incident. It seems several otherwise rational individuals turned into violently cupcake and confectionery haters during that whole debacle.

I'm not saying that's the case here (I haven't looked), [...]

And it would carry about the same meaning. "Here is an event that happened, which I admit I have no idea if it applies to this other event, but here is some speculation linking the two events together.

Note: I didn't downvote you, but I can see why people are. Plus if you only have one word to say about a subject, a downvote is a better choice.

polyfractal··on How Google Sliced Away Our Knife Ads
> A large minority of the civilian population would have a much easier time deposing the government and instituting a new one than a foreign state (or group of US states attempting to secede) would. [...] A large minority of the population rising up against the government would likely gain the support of some of the military and could blend in with the rest of the population when not fighting.

I think this is pretty rosy-colored view of what would happen. A "large minority" would have to be several hundred thousand people, perhaps a few million. Anything less is just a radical cult that will promptly be put down...and everyone will say "thank goodness" as they watch on the evening news. If something big enough happens that a few million people take up arms, you have a full blown civil war and things are totally different.

Stockpiling guns and weapons is the opiate of libertarians - "it's fine, I have the weaponry I need to overthrow the government if things get bad enough". In reality, you have a better chance fighting zombies than successfully overthrowing the government through violent means.

To be clear, I have nothing against guns. I'll probably purchase one once I've moved into a more rural area. But I'm under no illusion that the weapon will ever be useful in deposing any government.

polyfractal··on Why Use Nginx?
FWIW, I routinely run WP + W3TotalCache on nginx. Sure, their config files were a little interesting to get setup the first time, but now it's smooth sailing. It's only easier for Apache because the .htaccess files are readily available and ship with the product/plugin. Nginx takes a little googling to get started.
polyfractal··on Google backslides on federated instant messaging, on purpose?
Fun fact, Google doesn't play nicely with ESPs either. Most mail providers (Yahoo, Hotmail, etc) use a feedback loop when you report spam. After you mash the spam button, the ESP that sent the mail is notified that a particular email was flagged as spam.

This allows the ESP to curtail spam problems on their end (for example, Mailchimp heavily throttles your emails or outright bans you if your spam rate creeps past a very low percentage). It's an all-around good thing for the ecosystem, with the exception perhaps of publishers that get the unlucky "spam instead of unsubscribe" user action.

But Gmail does not participate in this loop. They don't tell any ESP that a user has marked an email as spam...that data all stays in house. Why? Hell if I know - perhaps they don't want to tip off spammers to being detected. On the flipside, reputable ESPs get less leverage on spammers in their network.

polyfractal··on What It Feels Like to Launch a Startup With Two Weeks of Runway
Hehe, sorry, I always get into a fit when these threads pop up. :)

Totally understand your point about needing a certain minimum threshold to start saving. If you are living paycheck to paycheck, you don't really stand a chance.

I just looked up my paystubs and it appears my monthly take home was just about $2000, after taxes. Perk of being poor in Massachusetts is that I was in the lowest tax bracket at least :)

polyfractal··on What It Feels Like to Launch a Startup With Two Weeks of Runway
Hm, I understand your comment but I'm going to push back on it.

Two years ago I was a Research Technician working for a neuroscience lab in Boston. I was paid 32k a year (USD), paid 700/month in rent (with three roommates), 150/month heating during the winter (each roomate!), various utilities etc etc.

In Boston, the "Living Wage" is considered around $12/hour [1]. I made $15/hr, technically less because I worked longer than 40 hour weeks.

Despite that, I still managed to hit my employer's 401k yearly match ($1600), a good chunk of my personal IRA (around $3000) and saved $7000 to an emergency account. I had calculated that 7k gave me around 5-8 month runway should things go pear-shaped, or if I wanted to start something on my own. If you add that up, I saved or invested nearly 36% of my yearly salary.

To be fair, I was single and young. Kids, mortgages, etc add a lot to your burden. But still, you'd be surprised how much money you can save when you just sit down and eliminate silly things sucking down your money.

[1] http://livingwage.mit.edu/places/2502507000

polyfractal··on Former TSA screener says the job does little to keep fliers safe
TSA != FAA
polyfractal··on PHP is the right tool for the job (for all the wrong reasons)
Ah fair point, I misinterpreted the grandparent's statement in terms of persistence, not necessarily pooled persistence.
polyfractal··on PHP is the right tool for the job (for all the wrong reasons)
> No it's not. You'll have to re-open connections to databases all the time. You can't use keep-alive to external HTTP APIs. You'll have to re-parse the PHP for every request.

What? This is all factually incorrect.

1) PHP has supported persistent database connections for ages. The fact is, persistent DB connections aren't really that great for websites, where you need a few resources quickly and then nothing for a long time. Having 10,000 idle DB connections is a great way to eat up resources. But you can do it.

2) PHP can use cURL's multi-handles, providing a per-application keep-alive connection pool (e.g. see Guzzle: http://guzzlephp.org/tour/http.html#managed-persistent-http-...).

3) While not part of PHP itself, most serious PHP applications use something like APC, which caches PHP opcodes to prevent constant reparsing.

polyfractal··on You aren't getting any better
I think that was the parent's point...the term "hacker" has been diluted to where it can mean anything and everything. Just like the "pivot", "traction", etc.
polyfractal··on The Serenity of a 5pm Bedtime
Agreed, although it should be stated that Ceasar Milan ("Dog Whisperer") is basically a fraud that has no dog training experience and just makes shit up. There are tons of documented examples where he makes things up on the fly, entirely contradicting what he's said in previous shows.

Sure, you can control any dog by beating them (literally) into submission...but you won't have a dog that enjoys your presence. His tactics are effectively "Be the boss, choke that dog, ALPHA ROLL....see how well it's behaving now? Shaking and with it's tail between it's legs?"

If you get a dog, invest some time in learning about positive reinforcement training and buy yourself a $1 clicker. Your dog will love it, love you and retain it's natural curiosity...instead of crushing all sense of self-importance and initiative.

polyfractal··on StackExchange Founder Vows to Reinvent Online Discourse
I think that depends on the audience of a forum. I'm a pretty regular poster at the SomethingAwful forums, which still utilizes a flat, quoted forum style.

Say what you want about SA, but the average poster is pretty good. We routinely carry on huge megathread discussions about a single topic with no difficulty. Just pop into any of the subforums and check it out. The Recipes subforum, for example, may have a huge megathread dedicated to Cookies. Another about Stews. Another about Chicken.

Within those, there will be all sorts of discussions, quoting, etc...but it never becomes unmanageable. You just learn to skim posts that don't interest you, read those that catch your eye, quote those that you want to respond to.

The SA forum automatically limits quoting depth, so you only see the last quote or two.

Frankly, I prefer a flat forum over threaded any day. Threaded forums are where discussions die. Once you leave the real-time, "in the moment" posting of a threaded discussion...it's impossible to spark the conversation again. Threads get too deep, there is no sense of what is new vs. old. New readers have an impossible time getting "into" the conversation, often piling into the top of a thread instead of the more active inner-parts.

With a flat forum, you just skip to the end and see what's going on, maybe browse back a few pages to catch up.

polyfractal··on Dear brilliant students: Please consider not doing a PhD.
I think it is highly dependent on field. My field, biology, is basically like flipping a coin. Do you graduate in five years or nine? Will you come out with a golden road to tenure or a life destined to work sad, lonely, post-docs? Flip that coin!

No matter how smart you are, the Gods of Biology are fickle. You may end up with a shitty protein, an assay that only works when the moon is aligned with Venus or cells that only grow when you swirl counter-clockwise.

As much as people like to pretend Biology is science...the sad truth is that a lot is practically voodoo incantations to the protocol devised 15 years ago by a post-doc.

It's one of the main reasons I left. You have to be Smart, Persistent AND Lucky. I'm fine with the first two, but when my career is hinged on luck...well, I started exploring fields that didn't quite as much require blind faith in the universe.

:(

polyfractal··on What is up with the insane long Google results URL now?
I don't have a problem with the _escaped_fragment_ stuff, since no human is supposed to ever see those. I utilize those on my single-page JS website and it is fantastic. Google can index my site while I can serve blazingly fast pages to my users.

If a human ever sees an _escaped_fragment_ page...something terribly wrong has happened.

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