Creating a Mad Biologist’s Desktop

Firstly before getting into this post, I’d like to introduce it by welcoming new people to the site. I realise I’m getting a huge amount of traffic from UsingMac after winning their competition. My name is Myles O’Neill and I am a mad scientist in training (ie. biology university student) from Australia. I hope you enjoy this article on the desktop and take the time to look around the rest of the website, if you are interested in biology, computers, the future or philosophy I think you’ll find a lot of interesting pages here and I hope you’ll subscribe!

So to get down to it, I am writing this blog post because I was the winner of the UsingMac Desktop Competition. A lot of people there have requested information on what actually makes up the desktop and I am more than happy to oblige. I am a huge fan of computer modification. Hacks, tweaks, mods – its all great. Recently I went to great lengths to design a new desktop which would be ideal for myself. I wanted to combine a simplistic and artistically stylish desktop with something which is functional and works well. After some serious planning, the use of many third party applications and some hard work I think I finally got to what I wanted. The desktop is themed on a unification between biology and computers – essentially the fields I am most interested in. So lets get into the details!

Screen Shots:

Before I go off explaining things, here are some screenshots of what I’m talking about. Click the images to see the fullsizes.

We’ll start simple, here is a picture of the desktop as it is right now, I’ll go through the individual aspects in a bit but part of this screenshot is that it hasn’t obscured the pictures in the top right and bottom left, which are a little harder to see in other pics.

This picture is an older one which showcases the use of growl notifications and lyrics being displayed.

Most of the time with this desktop the middle section between the two columns and under the top time bar is where applications are run, however for larger images one column can be gone over whilst still maintaining some nice aesthetics, as show with itunes here:

How The Desktop Is Created

This is the bit you’re reading for. You want to know how its created and how you can use parts of it yourself. I am entirely fine with you copying any design I have under the conditions you do not use such copies for profit and that you mention that I am the original author of the design.

So to start, the desktop is really a combination between a variety of thirdparty apps which are running, combined with some clever use of settings and a desktop designed and created in photoshop. The first thing you’ll want to know are the pictures I used. The tree in the middle comes from here. Next up we have the red telephone poles from here and the blue DNA molecule from here. Other than that the DNA helix at the top comes from the extensive editing of a stock DNA helix (the great thing about DNA helices is that you just need one complete rotation and you can extend it as far as you like). The only other important thing to note on the whole is that I used the font Bank Gothic. For the record I’m running this on the latest version of Snow Leopard (10.6.1) and on my 17″ MBP (early 2009 release). I can’t guarantee all apps will work on older (or futuristic newer) computers.

For the rest of this explanation refer to the pictures above as I go through each section one by one going down the columns from left to right.

Left Column

Lets start in the top left corner. Anaitis is the name of my computer and I have tried to emphasise it here, with the explanation of her name meaning the “Greek Goddess of the creative powers of nature.” This is all done through the background image itself.

Below this we see five tabs, each one has space for a hard drive in it. The tabs themselves are just basic backgrounds from photoshop. Notice that in the first screenshot most of them are unplugged and thus grey, while the second screenshot has them coloured. This is achieved by having a semi-transparent (and greyscale) version of each of the hard drives added to the desktop by taking a screenshot of the screen. It comes out as a nice effect.

Below this we have a lyrics box. The box and picture is in the background, but the program used to display the lyrics is called DesktopLyrics, its a little app but it does the job well and I love it.

Middle Column

At the very top we have a nice bar which displays the date and time in numerous ways. This is achieved through the use of simple scripts in GeekTools and the program Dateline. The little green number in the top right is the time in seconds. The DNA helix is just for awesomeness .

In the middle a lot of space is left to avoid clutter and allow the tree to shine through. You will however notice my contact lists on the left side of the middle. These are done through Adium (using MSN, AIM and Facebook chat) using custom themes loosely based off of ProBlack for colours and Decay 2.0 for structure. This window floats below all other apps and is on every space (from adium preferences) but its also set to exist in one of my spaces from the mac preferences, meaning all chat windows automatically open there.

Right Column

On the right we have a space for “notifications”, this specifically refers to Growl notifcations. If you own a mac and don’t use Growl you are really missing out. The theme I’m using in growl is called SmokeStack. The box has space for roughly  three notifcations at any one time which is usually more than enough, but in the case it is more its really not a big deal as they just continue down the page.

Finally there is a nice custom themed app called DestroyTwitter, it is particularly good because of it uses very little cpu in the background unlike most twitter apps. This window is set to display on all spaces in the mac preferences.

Menubar

My menubar is inverted in colour thanks to the program Nocturne (latest update) [I must warn however that I've found the functionality to be a bit buggy, causing weird graphics to display esspecially in combination with VCL and Isolator]. From left to right from the second screenshot the programs on my menu bar are: pollux, adium, isolator, Alarm Clock 2, InstantShot, Notify, Nocturn … and included with the core mac menubar items I have Menumeters.

Dock

I’m using a black dock image instead of the default. Coupled with this are some black arrow pointers which I am quite fond of. I’m using spacers to make navigating the dock easier. On the far right of the left side of the dock are two stacks which display ‘Recent Applications’ and ‘Recent Documents’ respectively. The moleskin note books correspond to some of my most commonly accessed folders, which are using the secret list view. I use generally use Quicksilver or my applications stack to open apps not on the dock. The new list view is shown off in one of the screenshots above and I am currently using it for my stacks. I also have it so that when apps are hidden they appear translucent in the menubar.

ScreenSaver

Finally I wanted to showcase the screensaver I use because it is crazily awesome. I guarantee that if you use this screensaver you will turn eyes every time. The screensaver is called fractal clock and you can get it here. This screenshot can hardly do it justice:

Can you help me make this even better?

Well that concludes this explanation of roughly how the desktop I won with works. I’m loving it so far. If you have any questions or comments about the desktop please leave them. I’d also love to see alterations, variations, extensions or anything else like that of the theme I’ve made. I’m always on the lookout for ways to improve my desktop.

Postgenderism

Postgenderism is a topic I’ve only come across recently but its something which I have put some thought towards. I’m guessing most people have no idea what I’m talking about right now, so I had best explain what postgenderism is.

The concept is fairly simple, organisms on earth reproduce. Some do so asexually (one parent) others do so sexually (two parents). Sexual systems are further divided into two types. The first are the hermaphrodites where all members of the species are the same ‘gender’, they all have both female and male reproductive organs. The second is the type we are used to, where there are two separate genders and you need one of each to reproduce.

However we really should ask ourselves why this is the case. Why have two genders in the first place? Why not stick with asexuality? The answer is an evolutionary one, having two genders means you get genetic mix in a population ergo more diversity ergo a more resilient species on the whole. You may then ask, why is it that we do not see species with more than two sexes? Surely it makes sense that if you had more than two sexes you would see greater diversity. The answer to this question is a harder one and one I can only make a guess at. The most likely reason is practicality, its just too much work to deal with three sexes, it just makes reproduction more difficult. Furthermore the evolution which developed into sexuality occurred very early in evolutionary history (in an early Eukaryote) thus there may be the problem of finding an appropriate evolutionary pathway to a third (or more) gender. In other words, because of that early evolutionary pathway we’re stuck with it.

So now I have explained what genderism is. Having two genders seems natural to us, but is it for the best? The postgenderism movement says it is not. One of the main reasons for this is equality. Genders are not equal – they are in no biological way equal. Up until recently women have been way behind men in human rights, even now in many countries around the world they suffer horrible injustice. The feminist movement says that females should have equal rights to males, the humanist movement says both genders should be equal and the postgenderism movement says we should not have genders at all. So what would a world without gender be like? Is such a world even possible? And is such a world desirable?

A World Without Gender

I’ll start with whether a world without gender is possible. The short of it is that currently it isn’t possible, but it might very well be possible soon. I’ve mentioned transhumanism before, the genetic modification of our species for beneficial reasons, and if this movement continues we will see the possibility to remove gender appear. In Japan scientists have already succeeded in turning rat eggs into sperm (which produce viable offspring), furthermore work on artificial wombs is ever increasing. Scientists are now growing whole organs in vitro and our understanding of genetics and the human brain is ever increasing. The power will be in our hands – the question is how shall we use it?

Before I go further I should mention the malleability of what people like and are attracted to, these traits are purely genetic and changeable. Just because something doesn’t sound appealing to you in your current body doesn’t mean you couldn’t be changed to feel that way – its just replacing one imperative with another.

A world without gender could take a few different forms. The first and most obvious choice is to make all humans hermaphrodites – that is with both sets of sexual organs. Another slightly more complex and cunning way of achieving this may be to design the organs such that they can be grown (by choice) into one type or the other through specific hormones. Another possible world is where humans pass on the ability to reproduce themselves and instead entrust this process to professionals and machines – who can take and work with genetic code in complex manors (in effect they could gain the advantages of having a race with as many genders as it has individuals) using advanced technology to make reproduction something different.

Benefits of Postgenderism

But what is the point? Why should we change from our current system? There are a few key benefits of such new systems:

1. Social

Postgenderism argues that our current system is deeply flawed and will never be able to reach an equilibrium. We live in an awkward world which values equality of all people on earth, yet which cannot achieve even simple equality thanks to the vast differences between genders. Thus the removal of gender, or the combination of it, would lead to a world which is more equal for all humans.

2. Biological

Postgenderism could yield vital biological advancement to the human race. In the early days of the human race our ability to use technology outpaced our evolution. Culture became our new form of advancement and while we have advanced past our wildest dreams culturally and technologically we have been by and large stuck in the same bodies we started with. Postgenderism is not only a change we can make to our species – it enables other changes to be made more easily.

Imagine a world where each person in the world contributes their DNA into a database for reproduction. This database can work with our DNA (and other dna for that matter) to create the next generation of children. We will get amazing diversity and combination of genomes. In a single generation we will lose the concept of race (another one of those huge issues facing social equality), we will all be the same “race” and we will all be equally related. No longer will your parents be more related to you than others, every human will be just as closely related to one another. We will be able to engineer a tremendous diversity in our species and through that diversity, strength.

Problems of Postgenderism

There are also problems with postgenderism however. One of the main concerns would be our increased reliance on technology – although one could argue that we are already beyond the point of no return in that regard. A second problem of course is that we can’t just enforce postgenderism on people, it needs to be chosen by the public as a whole. Even if the majority favor the concept there will be a minority which will resist it – this may be good or bad, perhaps this resistance will just die out eventually.

There are some other concerns with the concept but most are unfounded. I believe a lot of people will have a natural distaste of the concept because they will fear it. Humans LIKE having two genders, we are attracted to one, the other or both. These attractions are natural and its hard to imagine a world where that is not the case. This is not to say that this is the death of sexuality. Postgenderists go to lengths to mention that that is NOT the emphasis of their movement, sexuality can be preserved and even enhanced – but it will no longer be tied to undesirable social inequality. Depending on the way things go sexuality may become a construct outside of reproduction in which case it will likely move to either a more recreational place or something more deeply rooted in relationships. Love would  not be a casualty of postgenderism, but it would become different to the way it has been.

Time will tell what direction this movement goes in and there is still a long time before it becomes something which is a public topic. However the movement is growing and if equality is the ideal we hold it to be – it may be the path humanity takes.

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Humans vs Zombies @ ANU – Part 2

Five months ago I posted a blog post about HvZ@ANU. At the time it was a concept in my head, something I had just began to formulate. Like many of my schemes and plans I didn’t have significant hopes of its success. However with the help of many dedicated and hard working friends it became a reality. Over the last months we became an official non-profit organization, joined the student association, ran a large scale advertising campaign, had an awesome market day stall and managed to create a website and sign people up for the game.

Over the last week however the actual game ran. I can honestly say I have never worked harder on anything in my life. But it was so worth it. We had roughly 200-250 people playing the game, which was very awesome. About a quarter of the players in the game were organised into official “squads”, of which we had 14. These squads did amazingly and their leadership, coordination and sheer dedication to the game was astounding.

Throughout the week you could not go anywhere in the university without seeing groups of humans cautiously moving from building to building, or swarms of zombies running after prey. The game has been the talk of the campus and you’d be hard pressed to find someone who hasn’t seen the players.

As a moderator I didn’t not play the game as such but rather acted like a referee/organizer. As much as playing would be good being a moderator was fun too. I got to follow groups of both humans and zombies around and see what everyone was doing in the game. It was very cool being able to go up to any group of humans or zombies and being able to ask them to recount their tales of daring and pure awesomeness.

During the week we also ran some missions. These on the whole went very well. Some were better than others, but they were all very epic. The humans and zombies had excellent tactics and everything was very hard fought. In the end however the humans died in a last siege, falling at last behind zombies hands. To end the game we had a huge pizza / awards / zombie movie night. It was very fun and I think everyone enjoyed it.

In conclusion, the game was awesome on the whole. We had a few issues, largely stemming from our inexperience in running this sort of things, but we’ve learnt lessons and next time is going to be bigger, better and more organized. This time around we will have a huge group of people helping run the game, rather than the small bunch we had for this first one. For the moment though, I’m going to get back to that university study thing I am supposedly meant to be doing.

Oh and I made a short summary video of the game – its certainly not comprehensive and we hope to make something better later on, but it does the job:

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GBW1: Chris Capon – Entropy and the Shape of The Universe

This is the first ‘Guest Blog Week’ to be run on Dreams in Vitro – click the banner above to find out more about it. Finally this week is Chris Capon an engineering student from the University of Queensland. This is the last guest blog for the first guest blog week – I hope you enjoyed it. Normal blogs by me will resume soon (maybe).

Entropy and the Shape of The Universe

By: Chris Capon

Ok, after a reasonable bit of pressure from Myles, I have finally written this guest blog entry and it’s a little different from Myles’s own entries due to a deffernce in interests. I’m currently studying first year engineering, majoring in mechanical and aerospace at the University of Queensland and am tossing up between doubling with physics. As such, things that I write will most likely be based on new technologies, ideas for technologies or physics (though physics will most likely feature in them all XD). Hope you enjoy.

In science there are laws and theories. The difference between them is that laws have been deemed unbreakable, while a theory can be disproven with a single contradictory event. Taking this into account, it got me thinking about the about the three laws of thermodynamics, more specifically though the second law, which is:

A process in a system will always tend to increase the entropy of the universe.

The entropy of the universe tends towards a maximum.

There are many ways the law may be phrased or for a thermodynamically reversible system you can take the time derivative of entropy, where it is greater than 0. This law is thought to be one of the only unbreakable laws in physics, indeed a certain physicist named Albert Einstein famously stated:

A theory is the more impressive the greater the simplicity of its premises, the more different kinds of things it relates, and the more extended its area of applicability. Therefore the deep impression that classical thermodynamics made upon me. It is the only physical theory of universal content which I am convinced will never be overthrown, within the framework of applicability of its basic concepts.

Another, perhaps less well known person named Seth Lloyd, a Professor of Mechanical Engineering at MIT stated:

Nothing in life is certain except death, taxes and the second law of thermodynamics. All three are processes in which useful or accessible forms of some quantity, such as energy or money, are transformed into useless, inaccessible forms of the same quantity. That is not to say that these three processes don’t have fringe benefits: taxes pay for roads and schools; the second law of thermodynamics drives cars, computers and metabolism; and death, at the very least, opens up tenured faculty positions.

Now, I didn’t started questioning this law to put myself against these minds, I was just thinking about the law itself and it came to me that it makes some assumptions about the universe that as of yet haven’t been conclusively proven and as such the validity of this law cannot be ascertained as of yet but I’ll get to that later. Firstly though, what is entropy?

Entropy is quantitative measure of disorder in a system. A nice little analogy I came up with is sitting a class down in a lecture and making them listen to increasingly discordant violin music. As time goes on the not only does the music become more discordant but so does the class, which becomes increasingly restless. Their energy is no longer as useful as it was at the start of the class and requires an addition on energy from the lecturer to silence the room and reduce disorder; the usefulness of energy with time decreased. So perhaps a good way to think of entropy is the measure of the usefulness of energy in the system. I would like to note that the increasingly discordant violin music was not a good example of entropy…but that’s just my opinion.

Now you may be thinking, “hey but he just said you can put energy into a system to decrease entropy! Gasp, entropy decreased, second law = broken :O” This is not true because the entropy of a non-adiabatic (an adiabatic system is isothermal…no heat flows) system may decrease through heat flows out of the system. I’m not entirely sure about the validity of inputting energy into a system to decrease entropy but I would assume that it is acceptable because an ordered system has a higher internal energy than a disordered system. Though that does lead to the question why a decrease in energy would result in an increase order as well (decrease in entropy)? It is really a balance of energy flows, if you imagine a ground state atom; it’s in its most ordered and stable state. If energy is input, its electrons jump up energy levels, so in order to return to its preferred state ordered state it must release energy and thus a heat flow out of this system increases microscopic order. Hmm now that I think about it, input energy that increases order must simply allow a heat flow out of the system because I can’t think of an example that would allow entropy to decrease via an energy input in the form of heat. Entropy could decrease with electrical or chemical energy though through the formation of crystal structures in a liquid resulting in a solid.

Ok so now that you have a general understanding of entropy, whereby it can decrease in a system but must always increase according to the second law, can we find any way to break it? As I mentioned before, I believe the second law makes some interesting assumptions that, if incorrect, would break it. The first is that it assumes the universe is infinite. As I stated early, a way of expressing entropy is to take it’s time derivative because the only factor that entropy seems to be dependent on is time. If you were to increase time into infinity, the only way for the value of the entropy gradient (think of a graph) to remain greater than zero is for space also be infinite. If space is not infinite then after an infinite amount of time, the entropy gradient across the universe would be equal zero and therefore the second law is broken because it cannot equal zero. This is to say that there would be no more useful energy in the universe because it would be distributed everywhere equally. Despite this though, even this assumption also contains its own assumption that the universe is flat.

Einstein himself provide conclusively that the universe could just as easily be curved as flat and indeed, I’m sure all readers have seen graphically representations of classic space-time under the influence of gravity, which definitely does not look flat (this isn’t exactly the same as what I’m talking about because that’s local warping of space-time and not the entire sheet of space-time as it were). Now we have already said that the only factor that entropy is dependent on is time, which at first thought is constant/straight. Yet at the same time, using the laws or general or even special relativity it can be shown that time is dependent on an observers frame of reference and whether they are accelerating or not. Therefore isn’t it also fair to assume that there will be natural fluctuations in the fabric of the universe due to a combination of both gravity and accelerating frames of reference?  If these two assumptions (finite universe & warped space time) hold, what does it do to the second law though?

If parts of the universe are aging at different rates and we set time to infinite in our entropy derivative, you get an interesting occurrence whereby the second law holds. This is because you would essentially get a Swiss cheese sort of distribution of entropy, where the holes are points where entropy has decreased to zero (perfect order, massive amounts of energy) and increased to infinite because, unlike with a flat universe, the higher ordered system can still undergo processes, which would result in a transfer of excess entropy that (what I shall call our entropy hill) cannot contain.

Thus in order for the second law to hold in both a infinite and finite universe, the finite universe must at the very least be curved.

Hope you enjoyed and would love to hear any opinions, everything I have written, aside from the quotes of course, is stuff that I came up with is not necessarily correct and it’d be interesting to hear any opposing views or flaws in my logic (or if not flaws, perhaps things that I need to explain better).

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GBW1: Teifion Jordan – How to Start Your Own Turn Based Strategy Game

This is the first ‘Guest Blog Week’ to be run on Dreams in Vitro – click the banner above to find out more about it. Third up this week is computer programming genius Teifion Jordan from the fabled isle of Albion. Teifion is the creator of a very successful online game known as World of Arl which I cannot recommend enough.

How to start your own turn based strategy game

By: Teifion Jordan

Introductions

My name is Teifion and this post will hopefully explain how to setup and run a turn based strategy game through a web board. I have my own turn based strategy game which has been running for several years. This guide will be light on specifics as each game is different and I’m not here to tell you what your game needs to be. I am here to tell you what you need to know about starting it.

What sort of a game is it

My game WoA will be the example that I use to explain each point, each player is a member of a team, each team is a nation within the game and they then do stuff. “Do stuff” is pretty vague and in this case justifiably so, the joy of making a game like this is that you can allow it to be exceedingly open, so open that there is no single objective for a player. The game is as the title implies, turn based, each turn is a year of game time and in that time each nation performs actions of their choice, most often the invasion of somebody they don’t like.

Step 1: The big picture

Before you create a site or even tell anybody about the game you need to do something. You need to know what the game will be, what will it be focused on? In WoA’s case this was the idea that you could create whatever nation you wanted to, for it to be your nation and it’s nature be shaped by your choices. Other examples include very detailed military simulations, extensive and deep magical systems. Once you know what you want your game to be in a rough manner you can proceed to step 2.

Step 2: Your house

Your next port of call is to setup a forum or board somewhere. When WoA started I signed up for an invisionfree board and it worked well. I later upgraded to having my own site and installed phpBB on it. Hosting for phpBB is not as easy as Invision but there are places that do it for free. When I moved to phpBB I paid for hosting with siteground and have used them for several years now and been very happy.

Step 3: Bare bones

Once you have your forum and possibly a site next to it you need to start putting up the game rules. Start small and don’t go into detail just yet. Separate your rules into sections for ease of browsing and then get some friends to proof-read them for you. Setup some forums on your board and work out how the admin CP works for each of them. If you can I suggest applying a design to your site to help it stand out. As you can see if you visit my board, I’m well behind on skinning my board.

Step 4: Beta testers

It’s time to party. You need beta testers, get some friends and ask them if they’d like to play, if you visit blogs such as this one then email the blog owner and ask them if they want to play or if they’d like to give you a shoutout. Of course you are missing out on the big goldmine of possible players that are games like yours. Of course, if you came to WoA and posted “I have a totally cool game at xyz.com, come and play it”, your post will be marked as spam so fast your screen will spin (there maybe some exaggeration there). The best plan is to sign up and message the GM of that game, tell them about your game and how you’d love if they could look at it and if possible tell their players about it. A good GM will not expect you to play their game before they look at or link to yours, if they are snotty and uptight then simply move on and forget them.

Step 5: First round

Stuff will go wrong, it’s a fact. With WoA I didn’t give the players enough solid information about what they actually had. As would be expected this caused some confusion. The key is not preventing mistakes but reacting to them, you need to be responsive, polite and admit that you are at fault. If you can do all those three then you are off to a great start and your game will probably go far.

Step 6: Launch

It’s up to you to work out how many players you can cope with in your game at once, you still need to flesh out the rules and probably change some based on how they worked for the beta testers. I’ve helped you get started but it’s up to you as to how you continue. Feel free to drop by Arl and join in, everybody is welcome.

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