WAMP Step 2: Install PHP

As detailed in our previous post, we are building towards a WordPress installation on a desktop PC. In step 1, we successfully installed and tested the Apache web server.

As mentioned last time, some documents that are served by the web server to your web browser are static documents - just files sitting on the hard drive. Other documents are actually queries into a database, where the data has been dressed up and presented as a web page. Still other documents are mostly static, but with some customization by a script running on the server.

To support WordPress, we are going to need both a database and a script engine. A very popular scripting language for web pages is PHP, and that is what WordPress requires. The rest of this post will walk through installing PHP.

WAMP step 1: the Apache httpd server

Our goal in this process is to set up WordPress to serve the test content of a website and blog. Therefore the very first thing we are going to need is a web server.

I should say at the beginning that you don't need a web server to test basic web pages, you can write HTML files with any text editor, and then point your web browser at the file. You can teach yourself a lot of HTML and client-side JavaScript programming in this way. I think it is better to learn the fundamentals of how web pages work by typing it out for yourself instead of starting with a web development environment - you really understand what is going on.

Web servers deliver content to browsers. This content (web pages, music, images, etc.) is either a file on your machine's hard drive, or data stored in a database (on the hard drive). If it is data from the database, then a program (a script) must be run first to turn it into a document that is served out by the web server.

So even before we set up our Apache web server, we need to set up some space on our hard drive where this content will live. Importantly, we want this space to be independent of the Apache server file structure, so that we can back it up separately, and update Apache if necessary without moving our content. We could even change web servers entirely and our content would still be in the same place.

Setting Up WordPress on a Desktop

My wife is setting up her business and wants to have a website with blog, etc. Great! She'll be getting her domain name and contracting with a web hosting company - we haven't decided which at the moment.

For the blog support, I'm going to test WordPress, since it is very popular. Being the geek that I am, this means setting up WordPress on our home desktop machine.

WordPress (WP) runs on top of several other popular Web tools. Apache is a free web server, PHP is a free scripting engine, and MySQL is a free database. If these tools were running together on a machine using the Linux operating system the whole stack would go by the acronym LAMP. Since I'm using a Windows PC, it will be a WAMP stack for me.

While there are products that claim to install WP and all of these prerequisite pieces of software, I'm going to do it myself and write series of blog posts about the process.

Wish me luck!

ps - The process I will follow is based on Jessie Forrest's blog. Thank you Jessie for putting so much in one place! My posts will include a little background info and changes to the process Jessie posted a few years ago, based on the problems I encountered and how I solved them.

How can a virus see?

Proteorhodopsin genes in giant viruses

This is teh awesome! Rhodopsin is a key protein used in the eye, the first step in capturing light and turning it into sensory information. It can be found even in single celled creatures that swim towards or away from light as a feeding signal. Here, the virus is modifying the behavior of the infected cell with its own rhodopsin gene.

There are many examples of parasites modifying the behavior of their host. A creepy example (aren't all parasites creepy?) is the fungus that makes zombie ants leave their nest and climb up where they will get eaten, which helps the fungus spread.

So how do these giant viruses see with their rhodopsin gene? By making their host see for them. Giant viruses are very different from very small viruses, like the famous Ebola virus. Ebola is less than 20,000 nucleotides long (single stranded RNA) and makes only eight proteins, according to Wikipedia. In contrast, mimivirus has a genome of almost 1.2 million base pairs of DNA. While Ebola just replicates as fast as possible before destroying the host cell, giant viruses are more long lived parasites.

Getting the Most from your Arthur Murray Dance Package

My wife, Blanka, and I have been dancing at the Arthur Murray studio in Montclair, NJ for a little less than a year. It all began as a birthday present from her of a few private lessons, but it has grown into an important part of our life and growth within the Montclair community.

Put simply, the people and staff of the dance studio are wonderful. We have met so many people from different backgrounds that we otherwise would never have met. Our instructors, Gregory and Emma, are simply the best. They are fantastic at communicating quickly and clearly, and giving us maximum value in each 40 minute lesson.

If you are also interested in learning to dance through the Arthur Murray system, or you are in the process of comparing studios, here are a few of the things we have learned that will help you maximize your enjoyment, progress, and value of your purchase.

• Buy a package of lessons if you can afford it. It helps lower the total cost and increases your commitment to continuing.
• Stay an informed consumer, and manage your package to make sure you are learning the dances you want. Ask questions and give feedback. You're paying a lot of money to the studio, make sure you feel that you are getting your money's worth.
• At the same time, I can't emphasize enough how helpful it has been for me to spend entire private lessons just on the basics of framing and leading that are fundamental to every dance. Creating a connection with another person on the dance floor is probably the best part of dancing! Don't cheat yourself out of it by making the mistake of focusing on memorizing steps. That will come at its own pace. The body awareness of your dance frame and the 'other' awareness of your lead (or follow) skills are the most important benefits of dancing - they will extend far into other parts of your life.
• Take advantage of all the free training that Arthur Murray studios give you. Attend at least one group lesson and practice party a week.
• Come early to your lesson and warm up. Practice time is also free! This is an important benefit that I don't see a lot of students taking advantage of. You'll get more out of your lesson time if you've warmed up and practiced a bit on your own beforehand.
• Keep a dance journal. We were told that more serious students did this, and now that we do it also, we can see the benefits. It really helps to review what you've learned, and writing out the ideas by hand helps you remember them better. We haven't got to the point of videoing our steps, but it could happen!
• Make friends and have fun. You are there to have fun, right? Moving to music is a pure, visceral joy. Everyone else is also there to have fun. Smile at all your dance partners in group lessons. Our studio is blessed with a diverse student body, and I think mutual encouragement is important to keeping everyone coming.

I hope your studio does not pressure you to participate in additional activities. These balls, festivals, showcases, or competitions are completely extra - do them if they make sense to you, at your comfort level. Don't respond to any high-pressure sales tactics, and if you experience such tactics from your instructor or the studio owner tell them directly that it is inappropriate when you've already committed to spending thousands of dollars with them. (I'm saying that I've experienced anything like this at our studio, but I have read some horror stories on the web...)

Tomorrow, Blanka and I dance in our first "Freestyles" and we are thrilled to do it, having passed up several earlier opportunities that were available to us. Now we are ready, and now we will have fun. We've geared up, bought some extra 'bling' for each of us and we're looking forward to showing off our skills and getting some constructive feedback on our progress. It is going to be a great, fun day! I hope you have a lot of fun days during your dance experience, and I hope these tips will help you.

It's a HYBRID!!!

How time flies. Just yesterday, it seems, I was seeing my son Nathan for the first time, a pudgy five month old straight off the plane from South Korea. Now he's starting college in September.

Since he has to drive to school, I'm giving him my old car, an Altima with over 100,000 miles on it. Still works fine, but definitely old. So I got a new car for myself.

Normally, I would never buy a new car, I'd buy a newer used car. I hate the car buying/selling experience. My father taught me to buy from a fleet owner - the price is fixed, the car is well maintained. No hassle. That's how I got my old car.

But I wanted to reduce my carbon footprint, and after reading The Weathermakers I was convinced that the best way to do that was to make my next car a hybrid. So I bought one.

Softening the blow is that the Altima hybrid still qualifies for a tax credit. It is not sold everywhere, only six states in the US. Since I wasn't trading in, I couldn't get the cash for clunkers incentive also, but that was ok. (I know, a big part of the carbon reduction is supposed to be taking the old car off the road. Ooops.)

Anyway, after 3 weeks of new car ownership, I have to say that I love this car. The hybrid engine is very powerful on acceleration, the regenerative system contributes to powerful braking also. My average MPG is now up to 32. The instantaneous MPG feedback is helping me to learn to drive "greener".

The nice folks at Hackensack Nissan sold me a great car. Thank you!

Star Trek movie review

Yes, I was going to go eventually, but my son Daniel deserves the credit for pestering me to go this weekend to an IMAX showing of Star Trek. It was an 11 PM show, so it was almost the full geek experience possible.

I agree with a lot of other people, this is definitely worth your popcorn money, and IMAX is the way to go.

Likes-

• mix of old and new
• plenty of homage to TOS (the original series, for the non-Trekker), to the level of some audio cues
• humor
• Zoe Saldana's way retro outfit
• Zoe in general
• Zoe in specific
• Zoe Zoe in a bar
• Zoe Zoe in a car
• Zoe and Green Eggs and Ham (or whatever that girl's name was)

Dislikes

• way too much lens flare
• naval tactics of the WWI era
• Romulan mining vessels that look like goose roadkill
• destroy two planets (Vulcan and Romulus) and stick us in an alternate universe
• Scotty's mascot - should get an award for Establishing Annoying Alien Sidekick Persona In the Fewest Scenes
• all the Star Wars homage, i.e. Ice Planet, there's always a bigger fish, Kirk as Han Solo punching bag, planet destroying ship, older Spock as Obi Wan

I don't think the big open sets made sense as the machinery spaces of the Enterprise. No one would build a military spaceship that way.

By far, the best line in the film is "Your father was captain of a starship for twelve minutes, and saved 800 lives."

I like the set up of the Kirk/Spock/Uhura triangle. As a reboot, I would have been happier if the creative team had just established that much in this film. The film crowds in all of the basic characters, and is a bit too hyperactive in doing so. In comparison, the Bond reboot is two films old and we still haven't met Moneypenny and Q.

Bottom line: Go!

Wolverine movie review

I saw the new X-Men Origins: Wolverine movie last night, an early Friday night show. My showing was half full, later shows looked much more full.



I enjoyed the movie, and felt I got my money's worth of entertainment. The opening credits reminded me of the opening of Watchmen.



I am not a Marvel fanboy by any means. The anti-military tropes of the Cold War and the Viet Nam war are really really dated. Last year's Iron Man was a good attempt to move on from these.



Deadpool as a wiseass was better than the finale's Deadpool-I-Have-No-Mouth-And-I-Must-Scream.



Why oh why does Wolverine have to stop and monologue in New Orleans before offing Creed? Oh, I forgot, its a superhero movie.



Professor X showing up at the end was a bit creepy. 'Nuff said.



What do I want next from Marvel? A Magneto/Iron Man team up. The two best acted roles in the Marvel film universe. Its such a natural! But it has to include Mystique, because, well, do I have to explain?

IEEE Computational Intelligence Symposium

I spent Monday and Tuesday of this week in Nashville, Tennessee. Well, not really. In a hotel just off the runway is more like it, the Sheraton Music City was the venue for the IEEE symposium of the title. It was OK, but the food was terrible. Since we weren't downtown there was not a good chance to get out and experience more of Nashville.

But the science was great! I was there to speak on two panel discussions in the financial engineering track. I actually spent most of my free time in the A-Life track. By pure coincidence, I met up with Wes Elsberry of MSU. Wes is a key figure in the fight against intelligent design and anti-evolutionary creationism.

I thought Wes' talk on his research using Avida to explore the evolution of motion strategies was very interesting.

I made two points I think are worth repeating here. The research opportunities I think will be most helpful to the financial world are ontologies for law, accounting, and financial regulation, and agent based modeling as a way to escape the failed Rational Man hypothesis. One point raised by an audience member was that US federal level financial regulators should be supporting more academic research. I completely agree. Given the billions that are being thrown at problems, it wouldn't hurt to support some hard thinking.

Watchmen review

I watched the film without having ever read the graphic novel, so I've tried to think about it simply as a film. As such, I prefer V for Vendetta, which covers most of the same points.

Nixon's makeup was awful. The initial shot of Nixon from a distance had the best voice impression, from there it went downhill. Even in 1985 we knew Nixon was much more obscene out of the public eye, so his dialogue was as rubbery as his makeup. This Nixon is still the anti-communist cold warrior of the 1960 election, not the President who went to China and toasted Chou En Lai.

I thought the movie was effective at trying to give the feeling of simultaneity of experience that Dr Manhattan felt, by cutting back and forth in time. It also did acheive the effect of convincing me that anyone with God like powers is going to be aloof and apathetic to the human condition, that vigilantism becomes thrill seeking too easily. The other supers were more then Batman-esque characters. I think the movie is pretty clear that Ozymandias is both super-smart and super-fast, for example. They all can take a lot more punishment than the normal folks they beat up.

I enjoyed Rorshach's voice overs and dialogue, but as I said earlier, preferred V doing the same schtick. So V for Vendetta will remain my favorite Alan Moore adaption for a while. until they make a trilogy out of Lost Girls!

Folding Progress

I'm quite enthusiastic about Folding@Home. My own folding just passed a milestone that means something, at least to me.

F@H awards points for finishing work units (WUs) on time. You can sign on with a user name, even join a team, and watch your individual contribution to science grow. Are points really pointless? Yes, but they appeal to our competitive urge, so they help keep people participating.

So my personal milestone - my number of points is now more than my standing on the leader board! Yes, comparing to different quantities, I know. It happened somewhere between 65,000 and 70,000. Since there are more than 1.2 million folders (not all active right now), I'm in the top 5% of contributors to F@H. Yeah, me! Also, Team Deloitte is in the top 5% of all folding teams. Pretty good for only three guys.

Actually, there are two other lessons you can draw from this progress. 1 - most people who do fold, fold anonymously. 2 - a lot of people tried folding, then forgot about it.

The Origami of Life

I just wanted to share my experience with this participatory science project.
Folding@Home is a protein folding research project that is part of Stanford University. While understanding how proteins fold up into their three dimensional shapes is very important, it is also very difficult. The process in the cell takes place in microseconds as the proteins are synthesized from the instructions in messenger RNA (copied from the DNA in the nucleus). Therefore the method of choice today is to simulate the motions of the atoms using computers.
Obviously, this takes a lot of computer power. More than even the largest supercomputer, in fact. So the only alternative is to reach out to thousands of PCs and borrow their spare CPU time. Modern computers are idle most of the time. Even when browsing the web and listening to music through your computer, its processor is just idling away. Distributed computing, also called grid computing, is a way to use those spare cycles to do some good.
Folding@Home is the largest distributed computing project in the world today. Anyone with a PC, laptop, or Sony PS3 and an internet connection can join. The joint efforts of hundreds of thousands of volunteers create a computing engine that is currently five times faster than the biggest supercomputer!
I recently joined, and it is very satisfying to know that for the cost of the electricity to leave my PC on, I am contributing in a significant way to curing Alzheimer's Disease, Mad Cow Disease, Huntington's Disease, studying cancer, and advancing basic science.
To join, I went to the F@H web page http://folding.stanford.edu/English/Download to download and install the right F@H client for my machine and operating system. Now F@H just sits in the background while I use the PC normally. Because F@H only uses the spare cycles on the machine, it never interferes with other uses. I can also pause F@H whenever I want.
As you might expect of a grid computing project, the security of the software is a top priority. The software has been downloaded over 800,000 times, and no one has ever gotten a computer virus from joining F@H.
Anyone reading this message probably has all that it takes to participate in F@H. Please try it. It's fun and rewarding to see the molecules your PC is working on, and to earn points for completing work. But the real reward is knowing that you are helping to make life better, one spare cycle at a time.


ps - SETI@Home is a similar project aimed at detecting signals in radio waves collected from the Arecibo radio telescope.
pps - This is not meant to be an internet chain letter, but obviously a volunteer grid computing project grows mostly by word of mouth. If you try F@H and like it, you have my permission to forward this message to your friends, or use parts of it to convince the powers that be at local school districts and college campuses that F@H is safe, fun, and something that can make kids excited about science. PCs in classrooms are exactly the kind of underutilized resource that would greatly benefit Folding@Home.

Sketch of comics hero team

Oh yeah, I like comics and manga, too. Sorry I forgot to tell you earlier.

I visited an Oscar site yesterday, and was happy to see that Cate Blanchett was nominated for Elizabeth: The Golden Age. I feel really stupid for not realizing that this movie is a sequel.

Anyway, it got me thinking about a hero team set in the Elizabethean Age.

In the backstory, Elizabeth really is the Faerie Queen. The last test of a new Queen of Faerie is to seduce a mortal lover, but Elizabeth instead falls for the mortal and renounces her throne in Faerie. This choice angers a large number of powerful spirits, who were planning on using Elizabeth's control of two thrones (Faerie and England) to transform England into the New Atlantis. (Not the New Atlantis of Bacon, sorry.)

Our heroes:
Gloriana - Queen Elizabeth in disguise. Or is Elizabeth the disguise, and Gloriana her real identity?
Sir Francis Walsingham - the spymaster of Elizabeth in real life. Here, a bit more "hands on".
Dr. John Dee - a link between the scientific and the supernatural. Capable of a bit of wizardry with the help of the right artifacts.
The Golem of Prague - on loan to Dee from the Maharal of Prague, who made him. Think Ben Grimm with a Yiddish accent.
Thomas Phelippes - asistant of Walsingham. Inventor, cryptographer, etc. The Q to Walsingham's M. Deciphered the Book of Soyga for Dr Dee.

Our villains:
Phillip II of Spain - wants to conquer England and create his own version of the New Atlantis.
Duetia - beautiful faery, would be Queen of Faery if she could eliminate Gloriana.
John Kelley/Talbot - worked with Dr Dee but has fallen under dark influences.
Quetztlcoatl - the Aztec god, making a deal to stay alive in the New World's New World Order.
Talus - a mechanical man/animated suit of armor. Sometimes comic relief for being too literal.

I know you're asking already, who would win a Golem vs. Talus smackdown. Is the occult science of Dr Dee any match for the pure pagan fury of a God? Can Walsingham outwit Phillip? Can Gloriana save England from drowning beneath the waves if Duetia has her way? And what about Naomi?

Find out in our next issue!