Dan's blog

[DanEnsign]

Howdy folks,

I'm making an effort to get back into posting science-stuff-for-the-layman, though not specifically FAH users. So, I've started a blog: http://freerangescience.blogspot.com/.

I hope you enjoy it. I've been very busy for the past couple of years, and obviously have not posted fun stuff on the FAH forum in that time. I'm getting closer and closer to graduation, and I want to get back into the habit. I hope a blog will serve as a place to fan my science-communication flames -- and allow folks like you to get a (hopefully) entertaining science fix.

I should emphasize: Free Range Science is not a Folding@home blog. Help, as always, is best gotten here. On the other hand, my blog is a great place to ask questions, about nearly any science-related issue.

Have fun,
Dan

[^w^ing]

Ahh, very nice, I have always enjoyed reading your posts on this forum and I like the way you write, I will certainly keep an eye on your blog

[DanEnsign]

Ahh, very nice, I have always enjoyed reading your posts on this forum and I like the way you write, I will certainly keep an eye on your blog

Excellent! I've recruited Del and Imran, who will certainly come up with lots of interesting stuff, too.

Dan

[Flathead74]

Cool stuff, Dan, thanks!

[susato]

Very cool Dan! I've already forwarded the Bayesian statistics post to my dad, who 1) appreciates good science writing and 2) would not have had to be reminded (as I had to) that the first moment of the exponential distribution is the characteristic length.

When you get to the thermo pasture, I'll be waiting.

[uncle_fungus]

I approve of this especially if it means we get more recipes and amusing anecdotes like we did back on the old fcf. In fact I may have to dig around and see if I can find that rather special post including a recipe for chinese beef and dumplings (at least I think that's what it was)

Edit: No, it was wontons and here's the complete quote from March '06 for all of you who weren't around back then (or had forgotten):

Everything, I think, must be done with style in consideration. I'm at home this Saturday, browsing through the FAH forum, doing a thing here and there to get dinner ready, and listening to the Easy Star All-Stars' Dub Side of the Moon, a reggae rendition of one of the best albums of all time.

Talk about style. I mean, two of the greatest achievements of humanity, reggae and Pink Floyd, all in one. This is incredible music.

But allow me to be frank for a moment. I've been thinking a lot about benchmarking, and points, and why people contribute their processor power to Folding@home. I'm going to tell you some of what I think about these things, and I hope that I don't get in trouble or offend anyone, so to help prevent that I'm going to tell you what I'm having for dinner.

This is not a hollow offer. Before I was in biochemistry, I was in kitchens. I know what I'm doing when it comes to fire, food, and salt. I offer you my dinner not as a gift, however, but as a bribe. Maybe you won't think so badly of my words here if you're busy thinking about beef noodle soup and fried wontons.

Not that what I'm going to say is that controversial, or new, at least to seasoned FAH veterans. This is all still very new to me. I am not used to thousands of people taking an active interest in my research, or at dealing with the feelings that come with all the work of designing a project to answer fundamental scientific questions, and then having people dread downloading your WUs. Not that I can see too many complaints, mind you, but even one is a new kind of hurt that is difficult (and interesting) to deal with. I suppose this is a little what it feels like to be in American politics -- you always have to be sensitive to what people think of your projects. I don't have a thick skin yet, but soon enough, I suppose. This, also, is why I intend to wrap this message up in style.

The other day the Pande Group went down together to the cafeteria for lunch. It was the last lunch with Edgar around. I had lasagne, and it was really good. Sanghyun had soup -- beef and noodles.

In my opinion, good soup is a gift from the gods. Clear, mild liquid just more bodied than water, brown with flavor, noodles swimming around pieces of beef more tender than tofu, and ten times more flavorful. Spring onions for color and texture. Sanghyun let me have a bite. I said to myself, I'm going to make that for my wife.

My wife took me out for Chinese last night, so I didn't cook, but it gave me some time to ferment ideas. And to have a little bit of fun with her. (See, style! Dinner tastes so much better with anticipation!) I said, "I'm was going to make that soup that Sanghyun had, but I'll make it tomorrow."

She said, "Sounds good."

Then the fun. "I also have a plan for those wontons. It's going to be waay better than any krabmeat and cream cheese thing." We do like the imitation krab and cream cheese deep fried wontons, but I can do better than that.

She perked up. (She likes my cooking.) "Oh, really, what do you have planned?" I just smiled. Yeah, like I'm going to tell her.

But I'm going to tell you now. My wife doesn't read this forum, but even if she did, she wouldn't see this until after eating. By then I will have ALL the bonus points. (A little like QMD WUs, perhaps? ) Then I'll send her out for beers and we'll watch a movie.

I regret, a little, that bonus points were ever awarded for some WUs, but that is a decision that Professor Pande and other FAH scientists made when setting up those projects, because of the details of crunching those WUs. In some ways, it is regrettable that there are points at all.

Wait! Dont' leave yet! Here's some enticement: this morning after coffee I took a 14 or 16 oz. piece of sirloin and trimmed as much of the fat off as possible. (I'm making soup, and I want as little grease floating on the top as I can manage.) I cubed it up and put it in with 1/2 C. soy sauce, 1/3 C. "lite" rice vinegar, 1/4 C. white sugar, and two drops of sesame oil (this stuff is strong-flavored -- it doesn't take a lot ot get the flavor. This has been sitting in the 'fridge for about eight hours now.

I cooked up the trimmings, and chopped them up for the dog. Now, here's some style I'm quite proud of. I've been using them to train my dog to open the beer fridge on the command, "Pete! Get the beer!" Oh, yes, one day, my dog will bring me beer. All for a few beef scraps. I guess I do worry that he'll open up the fridge without being asked. What if I came home one day and he'd opened the refrigerator and made himself a sandwich? I suppose then I'd have to train him to close the door when he's done.

Like I said, it's sometwhat regrettable to award points for donating to FAH clients. I mean, they aren't redeemable at Denny's, or anything. They're worth something only as a measurement of relative FAH work done. For example, an individual donator can look at a point total and reminisce about when she had, say, only 1,000 points, or 5,000, or 25,000. Look at how much work has been done! And it's for a good cause, isn't it? It's a measure of accomplishment.

Points also ferment competition. Which means, actually, that points are very good, from my point of view. The situation has evolved to where people build or buy machines just to rack up points for their teams, to try to beat out the other guys. From our point of view, the more people want to fold, the more data we get returned, and the more investigation we scientists get to do!

But people COMPLAIN. Endlessly. This gets frustrating.

By the way, I saved a tablespoon of the fat from cooking up those beef trimmings. (Update: the dog knows there are beef trimmings in a bowl in the beer fridge, and will respond to the command, but he can't open the door without help. Soon enough!) I heated it up and threw in about 2 T. chopped fresh ginger and a minced garlic clove. After frying that a while, I threw in 1/3 C. of basmati rice. When the rice started to brown a little I added some water and covered the pan until the rice was cooked. This constitutes the base of the filling for the wontons. Of course, I'm utterly nuts to use beef grease as saute oil, so if you're more sensible, use just some vegetable oil or something.

Anyway, I feel pretty sensitive about this points issue, like I said, and I really feel that since we have points they ought to be as fair as possible. Actually I would like that people were always pleased with my WUs, but this can't be the case: it won't ever be. There's always someone whose rig is slower on a WU than the benchmark machine, but only for some WUs. Hopefully the benchmark machine, on an average WU (if such a thing exists), represents a typical machine running the FAH client.

Back to the wontons: there's this hot sauce, called "Sriracha," I think, with a rooster on the bottle (some people call it "Rooster sauce"), which is some tangy, sweet, beautiful, red stuff. I mixed a good bit (like maybe as much as 1/4 C.) with a couple of tablespoons of soy sauce, and some white sugar -- enough to enhance the natural sweetness of the chile peppers. I cooked up a piece of chicken and tossed it in the food processor with the chile sauce and half of the rice, and gave it a quick chop, to break down the chicken. I then mixed this up with the other half of the rice.

If a person can't stand spicy food, then do this. Roast a red bell pepper or two by lightly oiling the skin and baking. The skin should peel off after a little while. Peel the pepper and take out the core and the seeds. Then just throw these into the food processor with the chicken, and some soy sauce and maybe some sugar.

Taste the chicken, rice mixture. Guard it from friends or family members -- they will try to take it from you before you can build the wontons. If they get it, they will not give it back.

All in all, I think the points and the benchmarking is fair. Some WUs will be undervalued, some will be overvalued, and some will come with a bonus. Hopefully this variability will be matched with assignment sever variability. Hopefully, everyone gets good WUs sometimes, and gets "bad" WUs sometimes. (We at FAH think they're all good. We love data more than we love pie -- and well, we like pie a lot.)

But this of course doesn't alleviate the complaining. It wouldn't. Nothing would. But that's okay. People *should* complain. Only getting 150 ppd on your best machine? Well, that's better than the benchmark, but it's not a QMD. Don't like how long 2107 WUs take? They *are* worth more than 400 points, but maybe they don't run as hot as GB projects, or something else, on your folding farm.

Maybe this is where I really offend you. If you're the type that's touchy about these things, skip this part. We're going to be frying wontons, and making soup, in the last couple of paragraphs.

Maybe if your ppd production goes down, you can remind yourself why you're contributing. After all, there is some really fundamental and medically important research you are contributing to -- namely the Alzheimer's a-beta projects, but there are others as well. And think about this. I've read someone was crunching 2108's in about two days. My eyes boggled at this (I didn't know my eyes could boggle). Two days? 2108's take about 5 days on my desktop machine. They're running 50 nanoseconds of molecular dynamics simulation. That's 25 ns/day if you're crunching these in two days.

In 1997, when Duan and Kollman published their 1-microsecond villin headpiece trajectory, one of the fastest supercomputers in the world took a little more than a month to complete the computation. If you're crunching 2108's in two days, that means your little, desktop computer is about 80 % as fast as that supercomputer.

Now THAT is COOL. (1) It's a triumph of human achievement, not quite, of course, as cool as Pink Floyd, but definitely as cool as The Allman Brothers. (2) It's on YOUR computer, and to me, that means braggin' rights. Way to go! and (3) You are helping us to crack fundamental problems in biophysics: how alpha helical proteins fold, why villin can fold so fast, and how small proteins behave in their "folded" states. These, I think, are good reasons to think well of project 2108, even if it's taking 8 days on your machine, rather than 2. Is it perhaps your teammate that's crunching these in 2 days? Then soon you will defeat the evil Overclocking Power Cow Fried Wonton Team, and leave them behind, smoking in the rankings!

I understand that points are one of the only objective measures of accomplishment in the job of runnign FAH clients. I wish there was a way we could reward you which is more substantial. But you're doing good work. We don't use your processors lightly: every project is designed to teach us something fundamentally important about molecular dynamics algorithms, biophysics, and human disease. These are VERY good reasons to fold.

And remember this: if your team's points production is down, then most likely the Overclocking Power Cow Fried Wonton Team's points production is down, too. This is like the curvy parts of a car race: no one can really get ahead. Soon enough, the vagaries of FAH benchmarking and the demands of science will conspire to give you a straight stretch, when you will rake in the points and finally defeat those treacherous lying sons of bi ... erm, mean folks that when we mention them we spit, "Overclocking Power Cow Fried Wonton Team! Hah! Bunch of losers, soon enough!" or whoever else it is that needs to be put in their place. Oh, yes, then victory will be yours, oh ... yes. And my dog will bring you a beer. (He's getting very good at this.)

Speaking of wontons, if you have the rice and chicken mixture all ready, and you've battled your grandma for control of the bowl and won, you should take some wonton wrappers (we found them in the grocery store, oddly enough, near the prepackaged salad), wet one corner of each wrapper and the adjacent sides with cold water, put a small bit of filling on the center, fold the dry sides over onto the wetted side, and fold it into a triangle. Press the edge to make sure it's sealed. Then fold the corners of the triangle around the wonton and press them together.

Get some oil hot. (I have a fryer, which is the best way. If you heat up some oil, be VERY CAREFUL because it's always when the oil is super hot that some moron wanders in and burns himself and threatens to sue. Luckily, if this happens to you, you have the wonton chicken-and-rice filling. This helps in two ways: as a poultice for hot oil burns, and as a bribe.) Wontons don't take too long to cook -- maybe a minute on each side. If you're looking for lean, you can bake them, but then I will call you sissy.

I love watching wontons in hot oil -- at first it's as if they don't realize they are in hot oil, so they hang in the oil like the coyote hanging for a moment in midair in the roadrunner cartoons, then, suddenly, they start to sputter and fry, curling around in delicious agony, crisping a bubbling. When the wontons are light brown, carefully remove them from the oil with a slotted spoon and put them on a stack of paper towels to drain. Don't cook took many wontons at once, else they won't fry up right.

You can save extra, uncooked wontons, and the leftover wrappers, in the freezer for a couple of days. The first time we had fried wontons at my house, we made like 30 and that was way too many for the two of us.

Now let me tell you about the soup. At this point I only have the beef marinating, but here's my plan (and I guarantee this will taste good -- exactly as I guarantee that your points production will go up). I'll make up some light beef stock (if you can use real stock that's best, but if you have real stock lying around you don't need my instructions to do this). I'll make it just hot, like about 150 degrees fahrenheit, not bubbling at all but steaming like a maniac. Then I'll put the cubed beef in and let them cook for maybe an hour or so. It's important that the stock doesn't boil, because your nice, tender sirloin will get tough. After this I'll toss in some cubed tofu (almost as much as there is beef), a touch of the marindate (for a bit of flavor), and one package of ramen noodles. When the noodles are just cooked, the soup is done. I'll just sprinkle the top generously with sliced up green onions.

I'm in California, but I can't stand Chardonnay. Gerwurztraminer is the way to go with beef noodle soup and fried rooster sauce wontons. My wife will be a very happy woman, as usual. The dog will have, hmm, let's see ... dog food for dinner. If he can get me a beer, he can have some beef noodle soup (but no wontons, those are for creatures that can do the dishes).

By the way, I expect people to keep complaining about points. I'm cool with it. I know for a fact I'll soon be releasing a project which is worth way too many points for some rigs, since it will use the double precision core, which runs something like five times faster than the benchmark machine in rigs with especially clever hamsters and well-oiled excercise wheels. (AMD something or another, I think, but maybe not.)

I know points seem low, lately, to some people. Just bear with us. We'll be back in the straight bits, soon. And always remember: the overarching goal is the science. Sometimes the science is skimpy with the points, because of differences with the benchmark. Sometimes, the benchmark machine is the slow one, and the rest benefit.

There will be points, oh, yes, sure as I'm having dinner tonight.

Dan "If this science thing doesn't pan out I'll be a race car driver" Ensign

[Leoslocks]

This should be 'Required Reading' for all folders. Call it Folding 101

Thanks for sharing that with us newbies. How about making this thread a stickie?

[MtM]

Bookmarked, and thanks I know I will enjoy every piece

[DanEnsign]

Sorry, I've been amazingly busy and haven't done very much with this blog in the last few months. HOWEVER, we just started brewing beer at home, and you might not believe how sciency that kind of thing can be ... maybe we'll get some beer posts ...

[MtM]

Lol I didn't even notice I was so late to the party, that's what you get when you're absent for a few months

[DanEnsign]

Yeah, I've gone done and graduated, so I'm not even a Pande Group Member any more.

[MtM]

Congratulation Dan, I'm happy for you

Beer might be sciency but I liked the laymans f@h info the most of all. The first in my opinion who treid to explain to me what others would deem 'above my paygrade' and in honesty it offcourse all was above my paygrade but alas, it was fun trying to wrap my head around the details of what you were/are trying to accomplisch and how.

I'll never forget that.

If you're ever in The Netherlands, I will buy you a beer if you want

[rhavern]

Dan, where have you gone? Did you become a race car driver after all?