The Entire Universe Explained Part 2: The Most Fundamental Observation

“The Universe is Powered by Laziness”

(I obviously need more practice – I’m still not sure how coherent this explanation is to anyone but me. Comments welcome here – or if you prefer, you can contact me via XMPP (“Jabber”, “Google Talk”) at )

There you have it, the big secret that is at the heart of every single thing that happens in the natural world. Everything is the result of the Universe’s laziness. This is more or less what the Second Law of Thermodynamics says. In more proper language, it’s the observation that the total “disorder” in the universe is continually and unstoppably increasing.

I like to think of the universe as a big, fat, obnoxious sports fan. Picture him slouching in his couch. In one hand he’s holding a gigantic can of the most awful “lite beer” you can think of – you know, the one that only losers like – and in the other he’s got a giant foam hand with the logo of that team that only complete weenies like. He doesn’t even bother cheering – he just sits there, slouching as much as possible, maybe drooling a little, and wishing he could relax until he was nothing but an ever-spreading lump of flab…

So, what does this mean? Firstly, that there are always some “losses” whenever something happens. Basically, the universe can never manage to open a fresh can of that awful Lite Beer that it drinks without spilling at least a little bit of it on the floor. Secondly, that any bit of the universe you might happen to look at always wants to slouch a little further if it can.

That first part is what accounts for the “losses” in light of the “nothing magically disappears” observation previously mentioned. In the real world, no matter how carefully you build something, you can never quite get as much energy out of something as you put into it. You might get nearly all of it back out if you’re really careful, but no matter how carefully you hand 12 ounces of beer to the Universe, it always seems to end up with only 11.999999999 ounces of beer to drink. Or a lot less. It didn’t “disappear”, it just ended up soaked into the Universe’s filthy carpet where it is no longer available for anyone to drink. That beer-spillage is what physicists call “Entropy”. Or, “Heat no longer available to do Work“, if you want the proper physics definition.

The second part relates to the fact that there is a certain amount of “energy” inherent in the way any kind of matter is arranged. Matter, being part of the universe, is lazy, and doesn’t like having to hold onto all that energy. If you give it an opportunity, a piece of matter will tend to want to rearrange itself so that it’s not holding onto as much.

As an example, if you mix together some chemicals that will burn together if you light them, then seal them completely in a solid container, and set them off (by adding just a little bit of energy), you’ll find that the weight of the sealed container stays the same before and after…but it got really hot. That means there was energy released, and apparently a lot more than the little bit that started the whole thing – where did it come from?

The answer is that it was “built in” to the structure of the chemicals. Setting them off with a little bit of energy shoved the chemicals together just hard enough to let them recombine in a way that they didn’t have to hold on to all the energy they had up until then. All the energy the lazy chemicals let go showed up as heat. The little bit of energy you had to put in to get things started is what chemists call “activation energy”. It’s just there because those molecular slackers sure weren’t going to put out any extra effort to start rearranging – but once a couple of them are shoved together hard enough to make them get started, the energy they release is enough to shove a few more molecules together and get them to release more energy…and so on.

Because cool science types seem to avoid using whole words whenever possible, this energy that comes out is referred to as ?G. The total amount of energy that is “built in” to a particular molecule is referred to as “Gibbs’ Free Energy” (named after William Gibbs.)

So, for the last horrible analogy for now, let’s return to our big fat slob of a Universe slouching on his sofa. He’s been drinking that disgusting beer of his all night, and his bladder’s full. He’d really like to go to the bathroom but, eh, it’s too much effort to stand up. However, if you get behind him and shove hard enough to push him off of the sofa, then he figures while he’s up he might as well hit the bathroom before he sits back down. And, yes, I suppose that means it is my fault if next time you go camping, you end up waxing poetic and describing the nice, comfy campfire as “urinating heat and light on everybody”.

Microbiologically, that means that for a microbe to be able to live on some kind of “food”, it’s got to be possible to convert the food into substances with less energy built in, in such a way that it can capture and store some of the released energy in the process for its own use. It also means that if the microbe needs to make more of, say, some kind of enzyme (a more “ordered” combination of smaller molecules) it’ll have to shove in some energy to make up for the increased “order” while it assembles the parts.

Finally, what enzymes (or any other kinds of catalysts) do is reduce “activation energy” for a particular reaction, so bacteria don’t have to burst into flame in order to “burn” sugars for energy (for example).

And now I think I ought to go back to Microbiology posts before I get myself lynched by angry chemists and physicists for making a mess of this explanation…

Just a little over an hour…

“Just Science” blogging week starts tomorrow, which is to say, in a little over an hour where I am. Starting sometime in the next 24 hours or so, all of the participants are supposed to post at least once each day, and only about scientific topics, for the whole week. Of course, I intend to do my part.

I haven’t decided what to start with yet, though. Depending on how much time I can afford to devote to it, I may either make my ambitious attempt to, in one post, explain the workings of the entire natural world (in Grossly Oversimplified form, of course – e.g. “The Universe is Powered by Laziness“), or I may just start out with a simple post or two on staining methods or how to cheat and quickly identify the “Pseudomonas” cultures when you have to do the “Unknown” identifications in basic microbiology labs, or something like that.

If I can get through the Three Basic Observations that (I boldly claim) describe pretty much everything in the natural world, plus a Grossly Oversimplified explanation of how chemistry works (hint: it’s nothing more than the aforementioned Three Basic Observations plus electricity) then maybe I can get into things like the Electron Transport Chain, the Sulfur, Nitrogen, and Phosphorus cycles, why microbial fuel cells work, and things like that.

Any requests?

About this blog

(I’ve only got a couple more days before the start of “Just Science” week, so if I’m going to get this post up, I’d better get to it…)

Now that I’ve briefly explained who I am, here’s the bit about this blog itself.

My intended audience:
Anyone who’s interested. Okay, that’s kind of a cop-out. Essentially, I’m aiming at anyone who’s sufficiently scientifically-minded to be interested. I’m kind of assuming that if and when I’ve got enough readers to consider a “core audience”, it’ll be made up largely of interested science students, people who are inclined to read magazines like “Scientific American” or “Discover”, and just generally reasonably intelligent people with an interest in scientific matters, particularly but not only microbiology. I’m hoping that I’ll reach the point of being able to write so as to be interesting to some scientific professionals but still comprehensible to people without much of a scientific or technical background. This blog is, in part, an exercise in “public access to scientific information”, so if I write anything badly or fail to explain something, please comment and let me know.

How it works:
It’s easy: I think of something that I find interesting and that I think someone else might also find interesting, and I post something about it here. I expect to focus primarily on microbiology-related science, but a wide variety of topics might come up. I have a particular fondness for subjects that I think are underappreciated or ignored in other venues. Comments on whether or not things I bring up are interesting or boring will help guide the topics. I’ll tend to focus more on informal and hopefully pleasant to read style rather than a dry but detailed technical discussion – though wherever possible I’ll include links to that kind of information for anyone who’s interested (or perhaps thinks I’ve gotten it wrong.).
I also try to make the postings somewhat interactive – at the very least, I try to add extra information, explanations, and comments wherever I think they might be helpful or just entertaining. If you see words or phrases with thick dotted underlining, you should be able to “hover” your mouse cursor over it and get a little bit more information. I generally try to do the same with links and pictures. Maybe once in a while I’ll get bored and plant an Easter Egg or two.
Comments are welcome and encouraged, other than “spam”. What little information you’re required to give in order to comment is entirely to discourage spammers.

Really, this is mainly for personal gratification – I like to write. I like science. I’d like to share this interest, and I think scientific information would be interesting to many more people if more of it was presented in an interesting and accessible manner without making it seem otherworldly or dumbing it down to the point of uselessness. This blog is a cheap and easy way to get practice.
It’s also a cheap and easy way to get free learning for myself – I find trying to explain something helps me recognize when I don’t know something as well as I thought, helps me understand things better, and occasionally is a handy way to find out when something that I think I know is wrong.

Addendum: Yes, my Mom reads my blog. No, she does not wear combat boots. No, she does not dress me funny.

About this blog, Part 1: Me.

I thought it’d be useful to do a couple of posts explaining who I am (this post) and what I’m hoping to accomplish with this blog.

Don’t worry, I’ll try to be concise.

In a metaphorical nutshell: I’m a general-purpose nerd with a 15-year history of being a reasonably hardcore computer geek. I’m now escaping that field, and am a continuing undergraduate (at least as of right now.) who’s been painfully puttering part-time through college for many years off and on until recently – they don’t seem to make much provision for ““Non-traditional” students in US colleges. I’m now hoping to actually finish and graduate this summer – and then find an appropriate graduate program in whatever part of the country I end up in afterwards.

My area of academic interest is Environmental and Industrial (“Applied”) Microbiology. Medical microbiology, which seems to get all of the attention and funding, is somewhat interesting, but I’d rather people be able to benefit from anything I learn without having to get sick first.

In particular, at the moment I’m interested in exotic modes of respiration in prokaryotes. Or, more colloquially, fun (and preferably useful) ways of playing with live bacteria and electricity at the same time.

I’ve also got some interest in science history, public policy, writing and other forms of mass communication, public access to science, travel, food and food science, and at least casual interest in a wide variety of other areas. As such, you can generally expect that most of this blog will focus on microbiology and microbial biotechnology related topics, but will occasionally veer off in odd directions.

I also hope very much that someone besides me will get some pleasant usefulness out of this blog, so I strongly encourage comments, suggestions, corrections, and so forth.

Wow, I guess everything IS bigger in Texas…

…including, at least for today, my audience.

After being linked to from The Tangled Bank I’ve gotten hits from all over. Mostly using Firefox, I notice, and a large number of Mac users (plus at least one and possibly two fellow Penguinistas.)

Hits coming from all over – A few from Canadian colleges, Michigan, California, New York, the U.K., the Sydney, Australia area [update: Oh, and now India – Hello, India!]…and a surprisingly large number from Texas.

Interesting selection of institutions, too. Colleges, research institutions, government agencies…I just want to assure the readers from the disease and mental-health organizations (there was at least one from each) that I’m perfectly healthy and sane. For certain values of “perfectly”, anyway. At least, I’m not 5150 nor afflicted with any sort of terminal condition.

Since at least a few people seemed to come back and look at the rest of the site, I’ll endeavor to put up a post tomorrow on what exactly I’m trying to do in this blog and such (in case anyone’s thinking “that’s nice, but does this get better?…”).

But for now it’s bedtime – early morning Pathogenic Microbiology Lab tomorrow. Goodnight, all.

“Where Was I?” Femto-episode: “Im in ur kitchen, eatin ur c00kiez”

No, You Can't Have a Cookie - Not Yours

Or: “All Your Bake Are Belong To Us”

Yes, tonight “Where I Was” was in my kitchen.

Introducing “Righteous Fire of Purification Ginger Cookies”, version 1.1! Now with more Culinary Grace! And before anyone asks – no, I don’t have any idea what possessed me to combine internet memes with cooking in this post.

New Features:

  • Reduced pH
  • New Flavor:Lemon Juice!

Source Code: Dry Ingredients

  • 3 Cups of “All-Purpose” bleached flour
  • 1 tsp baking powder
  • 3 Tablespoons (Yes, Tablespoons) Ground Ginger
  • 1.5 Tablespoons (Yes, Tablespoons) Ground Cloves
  • Around 3 teaspoons Cassia Powder
  • A teaspoon or two of Mace (or Nutmeg)

Wet Ingredients:

  • A couple of teaspoons of vanilla extract
  • 2 Large “Grade A” Eggs
  • 0.75 Cups of Molasses
  • A tablespoon or two of lemon juice
  • Not really “Wet” but treated as such:

  • About 1.25 Cups of Unsalted Butter
  • 2 Cups of Granulated White Sugar (Sucrose)
  • About 0.3 Cups of Brown Sugar (Sucrose with a little bit of Molasses added back to it)

How to Compile:

  • Cream the sugars into the butter
  • Add the rest of the “wet” ingredients
  • Add all of the dry ingredients and mix them in thoroughly – add the baking powder LAST (the order of the other ingredients doesn’t matter).
  • Stick the dough somewhere cold to chill
  • Put some baking parchment on a cookie sheet – sprinkle it with sugar.
  • Once chilled, scoop out balls of dough onto the cookie sheet.
  • Sprinkle some more sugar on top of the proto-cookies.
  • Bake 12 minutes at about 350°F
  • Sprinkle more sugar on top of the cookies immediately before they cool.


  • Pick up a cookie
  • Insert as much of the cookie into your mouth as will comfortably fit in a manner that would not be considered obscene or freakish
  • Bite off portion of cookie. Chew.
  • Savor the sensations. Be sure to notice and appreciate how the flavors explode on the tongue, like an orgy of purification, preparing your palate for paradise (or at least gratuitous alliteration)
  • Swallow. Repeat the previous two steps until cookie is completely devoured and has become a part of your very being.
  • Visible shudders and audible moans of pleasure and “MMMM!” noises are optional, but recommended.

The only mortal flaw imposed upon these otherwise unmarred cookies is that they keep coming out “crispy-chewy” instead of “soft-chewy” as I want. I was hoping the added acid would help keep the cookies firmer and prevent flattening as they baked – as Tako, the Octopus mentioned in the “Chocolate Chip Cookies” episode – but no luck. Or at least not much. However, as I’d hoped, the lemon juice flavor goes PERFECTLY with the ginger. The texture is a minor flaw (and is actually preferred by some people. Not that there’s anything wrong with that.)

Oh, I know, SOMEBODY is bound to recommend that “shortening” or “margarine” crap instead of butter, since they don’t melt as suddenly as real butter. Feh! Those are An Abomination Unto The Cook! There has to be another way – I refuse to defile these cookies. (Hmmm, how does the melting temperature of lard compare?)

Incidentally, I was completely wrong when I was guessing that the ginger pungency meant it had a mustard-like flavor chemical. It’s nothing of the sort – in fact it turns out that several of my favorite spice flavors have very similar structures – Eugenol (clove), Vanillin (vanilla), Zingerone… All of them have the same sort of “ortho-methoxy phenol” type shape in them. If you look up Zingerone, Vanillin, and Eugenol on Wikipedia, you can compare the chemical structure and see the similarities around the “ring” that I’m talking about.

Oh, and for the internet meme references:

  • See “im in ur base, killin ur d00dz” (Numerous parodies exist – such as This One, though for some reason most of them have cats in them – like this one. (Ran into this one on BoingBoing
  • The picture parodies a picture that appears to be turning into a cliche’ on You can see the original here. Incidentally, the photo I used to make this parody comes from “strph” on (Original here) released under Creative Commons “Attribution/Share-alike” terms – so if for some reason you can’t resist remixing my masterpiece here…go for it. Just give me credit and allow others to remix yours as well.
  • I’m pretty sure “All Your Base Are Belong To Us” is well covered by the “Internet History” class you have to take to be allowed on the intertubes nowadays, right? No? Well, Wikipedia has the details.

And there you have it – Where I Was™, some food science, and some Internet Nerd History lesson, all in one post. You’re welcome.

Preparing to go “live”…

For a limited time only – yes, I left “registration” open on purpose. Any requests, suggestions, or comments, feel free to post ’em. In fact, I strongly encourage it.

I’ve gotten to play a bit with the theme/style and I think I see now where stuff gets added. The browser detection plugin is now active and appears to be working.

“Where Was I?” Episodes will eventually be backported from “LiveJournal” to here, probably with somewhat better formatting and additional features.

Stay tuned…