Experiments in Micropropagation, Part 0

A while ago, I read about the concept of micropropagation, a fast way of propagating/cloning plants. Since I learned years ago about how readily the jade plant can sprout from a single dropped leaf, I’ve always found the idea of propagating plants interesting. Micropropagation extends that idea, by growing in a sterile medium and using plant growth hormones to get things just right. While traditional propagation lets you take a cutting from a plant and get it to root, micropropagation allows you to take that cutting and induce the formation of many shoots, then moving each of them along to rooting. It’s a perfectly nerdy hobby for me.

I have an orchid whose blooms are fading, meaning it’s time to cut it back. I also have a hydrangea that I’ve failed thus far to root conventionally, though I think that’s more me lacking a green thumb than anything. So I decided to try this. Everything is in my pressure cooker now, so this is Part 0 of a series.

The Secret Sauce

Key to the process is the “media” the plants are grown in. It is traditionally solidified agar to keep pieces in place, with plant growth hormones and sugar to nourish the plant. You might also use, if you hadn’t forgotten to order it on Amazon, a cytokinenin to promote cell division, encouraging the growth of multiple shoots.

Based on what I’d read, I made a solution of the following:

  • Murashige and Skoog medium (“M&S”), 4.3g/L per the bottle. This is the exact product I ordered. Note that it’s a powder, but is sold by the final volume, so the 10 Liter container, at 4.3g/L, must be approximately 43 grams of powder. However, I goofed up the math, and used close to double the desired amount. We’ll see how big of a mistake that was. Also a mistake, I think, is that I ordered the version without vitamins, this is the with-vitamins version.
  • Sucrose, at 30g/L. I used table sugar. Well, I should have used table sugar, but I only had powdered sugar, which I naively assumed was the same. After mixing everything, I realized that powdered sugar is actually sucrose and tapioca, in an unknown blend, so I probably have too little sucrose, and random tapioca in the blend. I would make a horrible scientist.
  • Agar, at 8g/L. I purchased this product.
  • Water. I probably should have used purified/bottled water, but didn’t.

As you can see, I’m already off to a rocky start. But I’m doing so kind of knowingly, somewhat expecting failure my first try.


Undaunted by my mis-measurement, use of a vitamin-less medium, and my decision to use powdered sugar to fulfill the “sucrose” requirement, I went about preparing the medium with similar regard for proper scientific precision.

M&S blend

This is the solution I mixed. I conducted this in the sterile lab environment of my dirty kitchen stovetop. Lacking a beaker, I used a mixing bowl. I also used a striped drinking straw as an innovative stirrer / pipette combination. The idea was to blend things in the appropriate concentrations, then place them in test tubes, then put them in an autoclave.

As cool as it would be to have an autoclave at home, I do not. I do, however, have a pressure cooker, and those are recommended as a suitable alternative here. As I understand it, the purpose here is twofold: to sterilize the medium, and to heat the agar in the medium to a temperature sufficient to get it to set.

M&S media in test tubes

I did try to do things right, and sterilized each test tube with bleach, then with rubbing alcohol. I then rinsed them, and used a pipette drinking straw to fill them with around an inch of the solution I mixed. To contain them in the pressure cooker, I used a drinking glass, partly filled with water.


I covered about 2/3 of them with tinfoil, realizing that perhaps, when heated past the boiling point, the liquid might boil off. (The stoppers are plastic, and would have melted.) I left a few as a control to see how much evaporates. I had only made 4 ounces of solution, but it ended up being way too much for 9 (I broke one of the ten…) test tubes, so I filled a couple ramekins partway as well. Here’s what ended up going into the pressure cooker:

Everything is “cooking” now. In the meantime…

Explant preparation

The portion of the plant that’s cut off to be used in tissue culture / micropropagation is called an explant. Keeping things sterile is described as being very important, though I was quite lax in some of my preparation—partly out of lack of experience or proper equipment yet, and partly because I’m curious if things will work at all when done this way.

I tried to use roughly half-inch to 1-inch bits of the parent plant. Each was rinsed in water, soaked in a dilute bleach mix, rinsed, and then dipped in rubbing alcohol, before being rinsed again. The goal is to then move them into test tubes with sterilized tweezers, seating them in the gel.

I’ll try to post an update tomorrow about whether this ends in complete disaster or not. Assuming all goes well, it will probably be a while before anything starts to grow. The results will be anything between 3 orchids and 2 hydrangeas starting to grow, to nine test tubes that start to grow mold and fungus. Tune in next time!

Literature Pop Quiz

I just described something as “rather the worse for wear,” and followed it up with, “Who was the person that described?” After receiving blank stares, I explained that I distinctly recalled those words being the last description of some literary figure (an author, not a character), but I couldn’t remember who and no one had any clue what I was talking about.

A quick bit of Googling backed me up. A well-known author was, indeed, described this way just prior to his death:

“[A] gentleman, rather the worse for wear… and who appears in great distress… I assure you, he is in need of immediate assistance.”

So pop quiz: who was the author described this way? No fair looking it up.


Apparently, a company wrote an application for the iPhone called Baby Shaker. It depicts a crying baby, and you vigorously shake the iPhone to make it stop, at which point its eyes are replaced by X’s.

Apple pulled the application from its store and apologized, saying, “This app is deeply offensive and should not have been approved for distribution on the App Store.”

The Sarah Jane Brain Foundation, however, has had enough, with a spokesperson calling it “the most cynical apology I have ever seen.” They plan to picket Apple stores, calling on them to “mitigate the harm they’ve now caused.”

What I find so interesting is how the Sarah Jane Brain Foundation has had “The PETA Effect” here, at least for me: so vehemently overstating your cause that you steer people to the other side. If I’d seen the application distributed, I’d surely have joined the Sarah Jane Brain Foundation in finding it horrifically offensive. It’s in bad taste and makes light of an abusive practice that kills many babies and leaves even more with permanent injuries and brain damage.

And yet, with them coming across as so overzealous, my “That’s really kind of funny” sense is triggered, just a tiny bit. I guess I find their position so outrageous since:

  • I don’t like Apple having sole control of what I can run on my iPhone. Apple pulled the app, which means that, unless I jailbreak my iPhone (voiding my warranty), I can’t have the application. I’m not sure I want this application, but it’s a sore spot with me. The fact that Apple pulled the app just drives home Apple’s exclusive control.
  • Apple promptly pulled the app. The “most cynical apology” actually seemed to be a pretty emphatic, “That application was horribly offensive. We screwed up big time in approving it!” from Apple. I’ve definitely heard much more cynical. (I’m sorry you feel that way…)
  • The application shows that shaking babies kills them. Sure, it demonstrates it in an awful way, but it’s like showing tapes of babies’ skulls being crushed to lobby against abortion. Isn’t this exactly what the Sarah Jane Brain Foundation should enjoy?
  • I think that, and then get the sneaking suspicion that they are loving this, because it’s giving them tremendous publicity. And calling for protests outside Apple stores, weeks after they pulled the application and apologized for it, only furthers that point.

What do you think? Was Apple’s apology (and prompt retraction) of the app good enough? Should Apple have left it up even though it was controversial?

If I Made Computers

I think you could say with relative accuracy that there are three main bottlenecks in a computer: CPU, memory, and disk. There are some outliers that people might try to pile in: video card performance, or network throughput if you’re tweaking interrupts on your 10GigE card. But the basic three are pretty universal.

To cut to the chase: I hit disk bottlenecks sometimes, CPU bottlenecks almost never, and RAM bottlenecks all the time. And sometimes high load that looks to be on the CPU is really just I/O wait cycles. But RAM is special: if you have enough RAM, disk throughput becomes less important. At least, redundant disk I/O, which seems to account for a lot of it.

What interests me, though, is that almost everything is RAM starved in my opinion. My laptop has 2GB and I get near the limit fairly often. I’m thinking of trying to take it to 4GB. The jury’s out on whether or not it’ll see more than 3GB, and others complain that 3GB causes you to lose out a bit on speed.

But here’s the thing. I maintain things like a MySQL server with 32GB RAM. It’s not RAM-bound per se: we could switch to a machine with 1GB RAM and MySQL would still run fine. The memory is overwhelmingly configured for various forms of cache. But it’s not enough: there’s still a steady stream of disk activity, and a non-negligible number of queries that have to write temporary tables to disk.

RAM is cheap. It’d cost me about $50 to buy 4GB of RAM for my laptop. The reason RAM stops being cheap is that most motherboards don’t give you enough room. Both of my laptops can only take two DIMMS, which means I need dual 2GB sticks. They’re both based on older 32-bit chipsets, so I can’t exceed 4GB, but if I wanted to, I’d need dual 4GB sticks, and those are expensive. Even on decent servers, it’s hard to find many that give you more than 8 slots, making 32GB hard to exceed.

So what I’d really like to see someone bring to market is a 1U box with as many memory slots as it’s physically possible to fit in. 1U is still tall enough to have standard DIMMs standing up, and most of them are extremely deep. I bet you could fit 256 slots in. Then throw in a compact power supply, a standard LGA775 slot (allowing a quad-core chip), a good Gigabit NIC or four, and an optional FibreChannel card. No hard drives. Maybe a 4GB CompactFlash card if you really want it to have its own storage. Oh, and make sure the motherboard is pretty versatile in terms of RAM requirements and FSB. Oh, and don’t force me to go with ECC. If this were a single database server, it might be worth buying top-notch ECC RAM. But if this were just for caching things, I don’t care. Cache isn’t meant to be permanent, so an error is no big deal.

256 slots, and you could fill it with ultra-cheap 1GB DDR2 DIMMs. (Heck, at work, we have a bag of “useless” 1GB sticks that we pulled out.) You can get ’em for $10 a pop, meaning 256GB RAM would cost about $2,560. I suspect the system would command a high premium, but really, it’s just $2,560 worth of RAM and a $200 processor. A 2GB DIMM is about twice as much ($20/stick), but $5,000 for half a terabyte of RAM isn’t bad. Though 4GB DIMMs are still considerably more: they’re hard to find for under $100.

I think this would be a slam-dunk product. memcache is pretty popular, and it’s increasingly being used in previously unheard of roles, like a level 2 cache for MySQL. There are also a lot of machines that just need gobs of RAM, whether they’re database servers, virtual machine hosts, or application servers. And tell me a file server (sitting in front of a FibreChannel array) with 256GB RAM for caches and buffers wouldn’t be amazing.

So, someone, hurry up and make the thing. The key is to keep it fairly cheap. Cheaper than buying 4GB DIMMs, at least.


Lately I’ve felt that things were going pretty well. I was reading a bit of international news and looking at the international reaction to our presence at the G20 summit, for example. Of course not everyone in the world loves us, but I couldn’t help but feel that our presence was a little different than last time. Our President helped get disagreeing parties to agree, and in general seems to have the world eager to work with us. (I don’t really mean this as a condemnation of Bush, nor is it my intention to heap praise on Obama.)

And then I read what conservatives are saying, and it almost seems like we’re looking at two vastly divergent realities. I see a statesman, they see a closet Muslim who was all too eager to bow to an Arab leader and who went out of his way to apologize for being American. I see a fiscal plan inspired by John Maynard Keynes, they see someone deliberately wasting money for his own gain. I see the first black President, they see the first illegal immigrant President. I see a President who came in after Bush’s first round of financial bailouts and pretty much continued the policy, they see a President who nationalized the banks because he’s a Socialist. Oh, and he wants to take everyone’s guns away, and destroy Christianity.

I’d gone a while without reading the “wingnut propaganda,” and in that time period, I’d come to think that things were pretty good. Obama’s approval rating is something like 70%, and the two parties have been known to work with each other a bit lately, even if it’s been far less than I’d like. (And even if it’s been largely Democrat-led, which doesn’t really make for impressive bipartisanship…) And then I realized that there’s a lunatic fringe that seriously believes he’s a Muslim or a Socialist, and became truly worried. Fiscal conservatives and social conservatives may dislike Obama, and I respect their different views. Divergent views, discussed and brought to compromise, truly leave us better off. But there are thousands, if not millions, of Americans who have literally lost touch with reality. They’re like the MIHOPs of the Democrats.

I also want to caution that when I use terms like “neocon” and “wingnut,” I mean them more literally, not as terms to refer to all Republicans. Similarly, I respect Republicans and hate the artifically-created divide between the parties. What I’m complaining about is the wingnut Republicans who use utter lies to advance their own causes. There are Democrats who do the same, surely, but with Democrats leading Congress and the White House, those people aren’t noteworthy right now.

Anyway, two things have interested me lately. Besides the thousands of dead Americans, one thing that always bothered me about the Iraq War was the exorbitant cost. If the money were spent domestically, it could have gone an amazing distance. The military takes up something like 50% of our spending. So I’m waiting to see what the wing-nut faction of Republicans says. They’ve spent weeks protesting Obama’s Socialist spending. But the Democrats have long complained that the Iraq War is too expensive, and Republicans have argued that not giving the military a blank check amounts of waving the white flag of surrender. So I’m curious where this will go, because it could leave Republicans in an awkward state either way. Hopefully it will just be passed and nasty politics will be left out of it.

But then I was reading this article about how Obama may be looking to get the ball rolling on immigration reform. And the general description of his plan seems to amount to increasing border patrol and cracking down on illegal immigration. During the campaign trail one of the things he discussed was a path to citizenship, but with a pretty steep burden: you’d have to learn English, pay back taxes for as long as you’ve been in the country, pay a fine, and only then would you “get in line, behind everyone who came here legally” to become a citizen. Of course, that was something discussed during the campaign trail. The “official” Administration hasn’t even released a plan yet, but has merely made mention of strengthening border control, and the article is little more than speculation.

Yet some Republican activists have already denounced Obama’s (currently non-existent) plan as “dangerous” and “amnesty.” Seriously.


This is getting way too confusing. All along, someone said “Georgia” and I thought of the southern state. And then there was a war in Georgia with Russia, and I was just geographically-astute enough to know that they meant the country.

So that raged on for a while, and now, whenever I hear about something happening in Georgia, I think of the country.

So now, people in Georgia claim to have found Bigfoot. And I was thinking, their country is kind of insane-sounding. Like, one day most people have never heard of them. And then one day President Bush visits and someone hurls a grenade at him. But it’s apparently a dud, and no one notices until afterwards anyway… (Talk about failing at terrorism.) And then we all forget about the country again. And then Russia invades them, confusing everyone who both assumed that the news was talking about the US state, and that Russia was a nice country that wouldn’t go starting wars. And then their war ends. And then like the next day they find Bigfoot.

But it seems that it’s actually our Georgia that found Bigfoot.

*proud to be an American*

A New Take on RAM and Swap?

A really random thought just popped into my head…

UNIX systems have their “swap” partition, a disk partition where unused stuff in RAM is “swapped out” to disk to make room for newer stuff in RAM. Of course, no hard drive is as fast as RAM, so you obviously want lots of RAM so you never touch swap. Windows has the same concept but calls it a paging file.

But what if your disk was as fast as RAM? I remain fascinated by OCZ’s new 64GB SSD, which has an almost-zero seek time, and throughput rivaling the best of hard drives. (Though I’m yet to read any actual reviews, as it seems to have still not quite shipped.) I suspect that, given factors like the direct bus between your CPU and RAM, and all the work on boosting RAM “speeds,” a solid-state disk wouldn’t literally be as fast as RAM. But I also think that the difference between having more RAM and “swapping out” to SSD would be somewhat negligible.

I think it’d be interesting to test the extent of this… Plunk an SSD (one with high throughput!) into a system, and run it on as little memory as you can. (Though I think you’d be hard-pressed to find anything less than 256MB DIMMs these days, and even those might be hard to find? I wonder if Linux has a facility for deliberately overlooking a quantity of its RAM?) And with that set up, go crazy with stuff to ensure that you’re using several gigs of “memory.”

We can sit around all day and measure bus speeds and Mbps throughput and latency and seek time, but I think the only meaningful measure would be to try this and see how it feels. I have a hunch that it wouldn’t be that big of a slowdown (compared to RAM), but that the biggest problem would be ensuring your SSD was on a separate controller/ bus/ channel, so you didn’t obliterate your hard drive performance. While it’s easy to get an affordable system with a couple gigs of RAM now, RAM remains expensive if you need a decent amount of it. Buying a system with 64GB of RAM would still be extraordinarily expensive, but with a 64GB SSD for under $300, you could imitate it fairly well.

Strange Call of the Day

As the massive thunderstorm came in, I flipped on the scanner to listen to local public safety, as there are often interesting things going on.

I don’t know the background, but here’s what I heard:

“Engines 2 and 3, you can cancel… The caller stated that he thought he had been struck by lightning, but he has not.”

I think that’s when you need an officer and an ambulance to respond for, as the Boston PD would call it, “a psych eval.”

Edit: These people tie with the people who called in a “past lighting strike” to report that they’d had a lightning strike in their yard earlier… They stated that their bugzapper, on their propane tank, had been struck earlier and exploded. I’m slightly confused about how their bugzapper got struck (maybe it was mounted to a tall tree, and the plug provided a nice ground?), more confused about why they thought it was a good idea to keep their bugzapper next to their propane tank, and most confused about why their home hasn’t been replaced by a large crater.

For the love of God, and all that is holy!

Do you guys recall Obama’s “fist bump” with his wife when he clinched the nomination? It was a big hit with younger Obama fans.

It was not a big fan with E.D. Hill, a Fox News anchor who called it a “terrorist fist jab,” as I was just reading about. That’s not the real concern, though. I just rolled my eyes at that.

What really concerns me is the “news contributor” Liz Trotta who suggested that Obama should be assassinated.

Are you serious?! How the hell is that acceptable? Can you imagine how outaged everyone would be if a CNN anchor joked that someone should shoot McCain? It would be incredibly inappropriate.

Fight the Smears

The last paper I ever wrote in college was for my Power and Propaganda course, and addressed the propaganda being hurled against Obama. One thing I addressed was that many of the criticisms of him were blatant lies. It’d be like if I started posting here that John McCain said, “Thank God for the Nazis!” and President Bush met with McCain and used “the N-word” to refer to Obama. Total fabrications as part of a smear campaign.

The problem is that they work. I’m going from memory, but if memory serves me correctly, 13% of people in a recent poll said that they thought Obama was a Muslim. Soon it was being reported that he was sworn in on the Qu’ran, too. Of course, the Muslim rumors would soon be contradicted by trying to label him racist because his pastor said some crazy things, and the fact that he was sworn in on the Qu’ran would be refuted by photographs showing him with his hand on the Bible when being sworn in.

Obama Singing the National AnthemThere was also the big row over the photograph of him “refusing to say the pledge,” with some versions of the chain letter or website alleging that he refuses to do it for religion reasons; one even said that he didn’t know the words. In actuality, Obama was singing the national anthem, as a video of the event shows.

There’s another one about him hiding his birth certificate because he’s not actually a citizen. (If you want to get technical, John McCain is the one who wasn’t born in the US… Though it’d be asinine to argue that he’s not a US citizen because he was born on a US military base.)

The Obama campaign has finally launched Fight the Smears, a page refuting the utter falsehoods against him. The latest one seems to be alleging a videotape of Michelle Obama using the word “whitey.” Frankly, I could see this being done in a non-racist manner, but it’s a moot point, because none of the <sarcasm>reputable</sarcasm> sources claiming to have seen / possessing the tape have released it, and because one person has some pointed allegations of exactly where the tape was filmed, most of which seem fabricated.

It’s totally cool with me if you’d prefer to vote for McCain. (Well, I’d still disagree, but I’d at least respect that you had a rational difference of opinion.) Obama isn’t a Muslim, terrorist, or unpatriotic. John McCain isn’t a rapist and he doesn’t eat babies for breakfast. In a time when the truth is so sorely missing, can we please try to stick to reality this election?