Cathal Garvey
Where I share and muse and stuff
What #hackerspace dads do when they get home from hospital and should be sleeping
#!/usr/bin/python3
# This is how nerdy I'm feeling right now. Run this through the python 3.x interpreter if you're as nerdy as me.
Family = 2
class NewBaby:
'''This class defines a newly minted baby with a full set of
convincingly babylike functions.
Requires the following arguments: Name, Weight, HairColour, EyeColour, Temperament.
All are strings, Temperament is best declared as "Calm" or "Colicky" (case sensitive)'''
def __init__(self,Name,Weight,HairColour,EyeColour,Temperament):
global Family
self.name = Name
self.weight = Weight
self.hairC = HairColour
self.eyeC = EyeColour
self.temperament = Temperament
print("Waaaaa")
Family += 1
def feed(self):
print("Nom nom nom")
print("buurp")
print("paaarp")
def sleep(self):
print("zzzzzzz")
print("squeak")
def bother(self):
if self.temperament == "Calm":
print("gurgle, squeak")
elif self.temperament == "Colicky":
print("waaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
print("aaaaaaaaaaaaaaa")
else:
print("hurr?")
print("waaaaa")
def cuddle(self):
print("sqeak, gurgle")
Clara = NewBaby("Clara","4 kgs","black","dark blue","Calm")
#Clara.feed() #Call function every three hours.
#Clara.sleep() #Call function as often as possible.
#Clara.bother() #Call function when the grandparents visit
#Clara.cuddle() #Uncomment permanently
"Nexus Presents: Happy World: Burma, The Dictatorship of the Absurd", this Wednesday. Admission Free!
Dear all,
This Wednesday, Nexus Cork (Cork's quite awesome local Makerspace) will be hosting a film screening in the Camden Palace Hotel on Camden Quay.
Entry is free, and you can avail of a copy of the film if you bring a USB-capable Android or Laptop. A lower resolution form of the film is also loaded on the Dead Drop just inside the door to the building.
"Happy World: Burma, the Dictatorship of the Absurd" is a highly acclaimed and engaging documentary of the state of Burma, known to some as Myanmar. A state that has suffered crippling and often bizarre proscriptions and revisions under the rule of a Military Junta, Burma shares the dubious distinction of being the only other holdout state to use the Imperial Measurement system in 2011 with the United States. That's probably not relevant to the film, but I thought I'd share a factoid while the opportunity arose. For more amusing or incensing factoids about Burma, join us this Wednesday, and bring your friends.
Did I mention admission is free, and you can get a copy of this excellent, Creative Commons-licensed film to enjoy forever?
Namecrime Exodus: I Suggest Leaving G+ by September 10th if Namecrime Remains
Dear all:
I'd like to start something called a "Namecrime Exodus"; if by September 10th Google are still forcing people to use real names, I'm leaving Google+ and deleting my account.I strongly encourage you to post likewise and commit to leaving a defective service that doesn't understand or want to understand the freedoms and cultures of the internet. Google is a company born of and dependent upon the internet and the people who use it. In a dawning era of P2P culture and infrastructure, Google should know that they cannot afford to alienate their customers.You can find me on Twitter @onetruecathal, so I don't see why I'd bother tolerating another social network if it means violating my principals.Share the good news: I suggest #NameCrimeExodus as a hashtag. Poke this at people whose opinions count. I suggest +Sergey Brin and +Larry Page for starters.
I'd like to start something called a "Namecrime Exodus"; if by September 10th Google are still forcing people to use real names, I'm leaving Google+ and deleting my account.I strongly encourage you to post likewise and commit to leaving a defective service that doesn't understand or want to understand the freedoms and cultures of the internet. Google is a company born of and dependent upon the internet and the people who use it. In a dawning era of P2P culture and infrastructure, Google should know that they cannot afford to alienate their customers.You can find me on Twitter @onetruecathal, so I don't see why I'd bother tolerating another social network if it means violating my principals.Share the good news: I suggest #NameCrimeExodus as a hashtag. Poke this at people whose opinions count. I suggest +Sergey Brin and +Larry Page for starters.
DNA Logic for Chronic HIV Infection
I was just reading through this really encouraging sum-up of progress on preventing and treating HIV:
http://old.news.yahoo.com/s/afp/20110720/hl_afp/healthaids
On the whole, it's great news. I mean, as much as I dislike making circumcision mainstream, if it saves lives in a continent where AIDS is at full epidemic strength, it's a no-brainer. I just hope we can move past it with more advanced methods at some point in the future. However, the bit that caught my attention was the ongoing (though low-level) debate as to whether a practical cure for HIV will ever be possible. That's because HIV, like many common viruses, integrates itself into the genome of the host cell when it infects, and often goes dormant for weeks, months or years in an individual cell. This means that, functionally speaking, there is no viral activity in the cell anymore. Only a string of DNA instructions that could, at some point, emerge as a virus. There's no currently available method of treating a string of unwanted DNA, and some people will argue that there never will be. Not so! There is quite a great deal you can do about DNA, and hopefully we'll see progress on it soon. It falls under the heading of DNA logic; methods of reading and responding to DNA in an intelligent manner. This sort of technology isn't as well-developed as you might expect from the movies, but it's entering a phase of rapid advancement at the moment with falling prices in prototyping costs for DNA. When you can test your idea for only 200 euro, whereas before it would cost either a year of work or 2000 euro, you can make a lot more progress in less time. What's DNA Logic?
DNA logic can either work by protein-mediated reading of DNA, or by RNA-mediated reading of the RNA copies of DNA that are used to make new viruses. The second one could be used to make treatments that prevent viruses from emerging, silencing the nascent virus before it can awaken. The first one, though, is more interesting; when a protein "reads" target DNA, it can be designed to do anything from activating it to cutting it out entirely. This is where the cures will be found. Here's how it would work: A researcher uses web-tools such as those provided by the Zinc Finger Consortium (Open source biotech baby!) to design a pair of small proteins that each bind at either end of a crucial part of the HIV genome that doesn't change much. When used together, these proteins will naturally meet one another and interact only (statistically speaking) when they have bound to the DNA of a secret virus genome embedded within the genome of an infected cell. Great! Payloads for DNA-targeting Proteins
Now, to do something with them. Traditionally, the researcher might add bits of other natural proteins called "nuclease domains" to the little DNA-binding proteins, which only work when they are brought close together by successful DNA binding. These domains cut DNA, creating a lethal break that will probably be repaired to the severe detriment of the virus. Creative selection of nuclease domains might even cut the virus out entirely, rather than just poking holes in its genome. However, you can be more creative if the nucleases don't work well: you can activate the virus. Sounds bad, right? Not exactly. The problem with HIV is precisely that it doesn't activate! When you treat with antiretrovirals, you're preventing the virus from successfully producing baby viruses, while the immune system tracks down cells that are trying to produce new viruses and kills them. However, the immune system fails to find cells that carry the virus but aren't actively producing it. If you combine anti-retroviral drugs with a treatment that activates virus genomes fully, you can slash the number of cells carrying a dormant genome, and approach a cure. Delivering the Treatment
How to get the proteins into the cells you need? That's actually more challenging than designing and testing the proteins, and poses more of an ethical problem. You might try to use a virus to carry them into the cells, but you'll have to fight the immune system to cure it. You could try using synthetic carriers that bring the DNA coding for the proteins, or the proteins themselves, into the cell..but sometimes they're toxic, and the efficiency is pretty low. Probably the best method is to coat the proteins in something that'll hide them from the immune system but which will shed inside the cell, and to include what's called a "Nuclear Localisation Sequence" in the proteins so that the cell will carry them into the Genome immediately on entry. Then you blanket-bomb the body with them, particularly the lymph system, and cross your fingers. Get Back To Work Cathal
For all my talk, you'd think I'd be doing this.. The take home message is that HIV will see a cure, and it'll be from Open-Source Biotech if we're lucky. My job at the moment is making OSB a reality, so perhaps stuff like the above can happen quickly rather than relying on companies that don't wantto cure a multi-billion-dollar-treatment pandemic. Hold that thought, I'm going back to work.
http://old.news.yahoo.com/s/afp/20110720/hl_afp/healthaids
On the whole, it's great news. I mean, as much as I dislike making circumcision mainstream, if it saves lives in a continent where AIDS is at full epidemic strength, it's a no-brainer. I just hope we can move past it with more advanced methods at some point in the future. However, the bit that caught my attention was the ongoing (though low-level) debate as to whether a practical cure for HIV will ever be possible. That's because HIV, like many common viruses, integrates itself into the genome of the host cell when it infects, and often goes dormant for weeks, months or years in an individual cell. This means that, functionally speaking, there is no viral activity in the cell anymore. Only a string of DNA instructions that could, at some point, emerge as a virus. There's no currently available method of treating a string of unwanted DNA, and some people will argue that there never will be. Not so! There is quite a great deal you can do about DNA, and hopefully we'll see progress on it soon. It falls under the heading of DNA logic; methods of reading and responding to DNA in an intelligent manner. This sort of technology isn't as well-developed as you might expect from the movies, but it's entering a phase of rapid advancement at the moment with falling prices in prototyping costs for DNA. When you can test your idea for only 200 euro, whereas before it would cost either a year of work or 2000 euro, you can make a lot more progress in less time. What's DNA Logic?
DNA logic can either work by protein-mediated reading of DNA, or by RNA-mediated reading of the RNA copies of DNA that are used to make new viruses. The second one could be used to make treatments that prevent viruses from emerging, silencing the nascent virus before it can awaken. The first one, though, is more interesting; when a protein "reads" target DNA, it can be designed to do anything from activating it to cutting it out entirely. This is where the cures will be found. Here's how it would work: A researcher uses web-tools such as those provided by the Zinc Finger Consortium (Open source biotech baby!) to design a pair of small proteins that each bind at either end of a crucial part of the HIV genome that doesn't change much. When used together, these proteins will naturally meet one another and interact only (statistically speaking) when they have bound to the DNA of a secret virus genome embedded within the genome of an infected cell. Great! Payloads for DNA-targeting Proteins
Now, to do something with them. Traditionally, the researcher might add bits of other natural proteins called "nuclease domains" to the little DNA-binding proteins, which only work when they are brought close together by successful DNA binding. These domains cut DNA, creating a lethal break that will probably be repaired to the severe detriment of the virus. Creative selection of nuclease domains might even cut the virus out entirely, rather than just poking holes in its genome. However, you can be more creative if the nucleases don't work well: you can activate the virus. Sounds bad, right? Not exactly. The problem with HIV is precisely that it doesn't activate! When you treat with antiretrovirals, you're preventing the virus from successfully producing baby viruses, while the immune system tracks down cells that are trying to produce new viruses and kills them. However, the immune system fails to find cells that carry the virus but aren't actively producing it. If you combine anti-retroviral drugs with a treatment that activates virus genomes fully, you can slash the number of cells carrying a dormant genome, and approach a cure. Delivering the Treatment
How to get the proteins into the cells you need? That's actually more challenging than designing and testing the proteins, and poses more of an ethical problem. You might try to use a virus to carry them into the cells, but you'll have to fight the immune system to cure it. You could try using synthetic carriers that bring the DNA coding for the proteins, or the proteins themselves, into the cell..but sometimes they're toxic, and the efficiency is pretty low. Probably the best method is to coat the proteins in something that'll hide them from the immune system but which will shed inside the cell, and to include what's called a "Nuclear Localisation Sequence" in the proteins so that the cell will carry them into the Genome immediately on entry. Then you blanket-bomb the body with them, particularly the lymph system, and cross your fingers. Get Back To Work Cathal
For all my talk, you'd think I'd be doing this.. The take home message is that HIV will see a cure, and it'll be from Open-Source Biotech if we're lucky. My job at the moment is making OSB a reality, so perhaps stuff like the above can happen quickly rather than relying on companies that don't wantto cure a multi-billion-dollar-treatment pandemic. Hold that thought, I'm going back to work.
On Rule-Of-Law in Ireland, and Preservation of Free Speech: Please Reject Three-Strikes
Dear Mr. Bruton,
I am writing to you (and simultaneously to my blog, where further correspondence will be forwarded) to ask that you reconsider your support of a Three-Strikes policy on internet use in Ireland.
There are many reasons for you to do so. Chiefly among them, I feel, is the threat to our judicial system if this system becomes part of Irish law. By legitimising the surveillance of corporate bodies on Irish citizens, and by permitting these foreign corporate bodies to realise a powerful ability normally reserved for state agencies (the power to effectively silence a citizen of Ireland), the Three-Strikes policy will set a precedent whereby privatisation of legal power becomes acceptable. As things stand, there is already a body of law that protects copyright, through which individuals who infringe upon copyrighted works can be prosecuted; there is no need to "streamline" the law by passing Garda powers to IRMA, especially considering that their internal judgement will be opaque and beyond judicial reproach without a costly legal battle.
However, an erosion of our legal system is only the most obvious reason; there are others which, by reducto ad absurdum, can readily be invoked to show why the Three-Strikes system is not only a threat to Irish law, but to innocent citizens of Ireland and to Ireland's role in the development of the ever-advancing information economy. Not to mention, the Three-Strikes rule will not adequately protect against music infringement even if perfectly implemented.
Firstly and perhaps most tellingly is the assumption that an IP address equates to an individual or even to a family, a pernicious assumption that supports the entire reasoning behind Three Strikes. However, it is a false, misleading and legally dangerous assumption that will certainly lead to a sizeable percentage of illegitimate cut-offs.
The "IP Address" that is supposed to be unique and identifying is anything but; an IP address relates, rather, to an internet router, to which many computers may be connected and which may be at any point in the internet distribution chain. Indeed, users of mobile broadband dongles or phones may often share only a handful of IP addresses between hundreds or thousands of customers. Users of a complementary or even pay-as-you-go Wifi hotspot will share the IP address of the hotspot. Neighbours who share a wifi router, or householders whose router is hacked to gain access by an outsider (a trivial task with the right software, even for a non-professional), will be identified as infringers on account of misuse of their connections. Finally, social routing systems that protect free speech may be misused, with the "exit node" and its owner being associated under a Three-Strikes regime with the offending IP address.
Consider the above; in order to meaningfully implement a law that uses IP addresses in an identifying manner, Ireland would have to force ISPs to set up static IP addresses assigned to each customer, and would have to illegalise the sharing of computers, connections, wifi or bluetooth. Cellular internet would become essentially impossible to implement legally. Free-speech enabling software which currently allows Chinese, Libyan, North Korean and certain American civil rights advocates to communicate without government censure or arrest would become illegal in Ireland; a tacit approval of anti-democratic states globally in favour of private profits.
Even if implemented perfectly with all of those draconian measures (which would succeed in driving Ireland into a stone-age of technology as the internet becomes ever more important to global society), sharing of music, movies and software would continue to be trivial. If bittorrent becomes impractical, individuals will simply choose another method of sharing which is more secure. Examples I might name include highly encrypted onion routing systems such as Tor (which is supposed to be used for Free Speech, I might add), encrypted web-of-trust methods such as Freenet, or simply sharing music in person by Hard Disk or USB drive, a virtually invisible and effortless means of sharing without oversight.
I hope the above demonstrates clearly that Three Strikes will cause more harm than good. If that's not enough however, please consider the state of Irish internet and what this will mean commercially for our development as a state, and what that will mean for business. Exports are already a difficult prospect for Ireland at present, and an information based economy is one of Ireland's most promising opportunities for growth, because of low capital overheads for internet startups and software companies. If Three Strikes forces a burden of internal restructuring and vastly expanded internal surveillance on Irish ISPs, they will be less able to afford competitive plans or further rollouts of broadband. Please look at a comparison of existing broadband in Ireland to our European counterparts; certain countries have a minimally acceptable broadband as a "Human Right" that equals or exceeds some of the best commonly available broadband in Ireland. Bandwidth needs will trend upwards over time without doubt; Ireland is already falling behind and an additional burden on our ISPs will only make matters worse.
Censorship in Ireland is becoming a serious threat to our freedoms of speech and expression, and granting legal power to the chief architects of this trend will only make matters worse. Three Strikes will not protect the Copyright Industry or their local arm, IRMA. It will certainly not protect or benefit Irish artists in need of further protection. It will not prevent, ameliorate or diminish filesharing, which is driven by technology far more advanced than the legislative branch in Ireland has power to counteract, and by ill-will towards the companies that are driving this law.
Three Strikes will damage our freedoms, lead to false accusations and cut-offs of a critical educational, social and commercial pillar of modern life, and prevent Ireland from adapting and taking advantage of an increasingly important area of growth.
Again, please take some time and reconsider Three Strikes. If you still feel that it is best for Ireland, then do the right thing; ask Ireland by a referendum, because the impact of this law will be devastating to our country's future online.
Yours,
Cathal Garvey, BSc
Irish law, ethics and Biohacking - Tomorrow, 1-4pm at Science Gallery
Hey all,
Tomorrow is the last session of the first biohacking workshops in Ireland. It's been awesome fun (even though much of the hastily prepared stuff didn't work as intended!) and really informative to me and hopefully my excellent participants.
Sadly a lot of people couldn't make the weekdays due to pernicious blights such as employment, but tomorrow might be a chance to get a more diverse group together before it's all over.
Tomorrow will be an introductory talk followed by a forum: I'd like to introduce the Irish regulatory framework surrounding biotech, some ways that we could organise and mitigate the costs and difficulties, and some factors to consider when weighing the safety and ethics of a project. Then I'd like to open it up to a forum discussion on the whole thing.
It's on between 1 and 4 tomorrow, and admission is €10 at the main desk. You'll have a chance to take part in some early formative discussions on the hobby. You'll also be helping to show the nice people at Science Gallery that there *is* interest in Diybio despite the low initial uptake. This means future workshops may be more likely to happen, and at more convenient times to facilitate the employed!
If you know anyone who would like to join, please let them know and forward this on. Looking forward to seeing you!
Current Stuff: "Biotech for Homesteaders", CyclerCan, Biohacking Workshops
Hey all,
Over at IndieBiotech.com I've shared some of what I'm up to, and I may as well mirror it here!
In a nutshell, I'm preparing for a five-day course of Biohacking workshops in the Science Gallery in Dublin, starting Tuesday and ending Saturday afternoon. I've had to prepare some mad inventions to make it happen due to equipment restrictions, which you might find amusing or exciting.
The aim of the workshops is to deliver a crashcourse in literacy and skills in biohacking; you should come out of the workshops with a basic understanding of how DNA, RNA and Protein work, how bacteria work, and how to design and build your own GMOs. I don't promise that it'll be easy, but rather that you'll be prepared to work on something exciting with some connecting and collaborating with other biohackers! :)
Here's my outline of the plan for the crashcourse. It was initially going to involve actually making your-first-GMO using my custom-tailored plasmid, but an application timing mixup means the EPA have not licensed Science Gallery for GMO activities yet, so that'll have to be filed for "next time". Instead, I'll be covering how you could go and isolate DNA from wild bacteria, potentially hack that at home, and replicate some of the work done in the late eighties in biotech with minimal equipment.
I'll also be covering the ethics, safety and legal aspects of biotech; don't shy from it, in many ways it's the most interesting part. What good can come of biotech; how transformative could it be? What bad could come of it, and how can we prepare for it? And how can you do all this in Ireland legally? I'll be covering all of that.
Working from that, I'm hoping to inspire some excitement about the possibilities of biotech if you do have decent equipment, and if you do have social connections to other skilled biohackers. Finally before walking out the door, I want to drum up some excitement about the possibility of establishing a bio-makerspace in Ireland where driven people can innovate and develop biotech into a unique Irish cultural strength in Europe.
1 current project: A coffee-can #diybio thermal cycler based on @RussellDurrett's light-bulb PCR machine
A sneak peek at something I'm getting ready for the workshops at Science Gallery on the 14th-18th.
I was hoping to have an OpenPCR by then, but it's looking unlikely. In any case, this will showcase one of the super-cheap approaches you can use to get a thermal cycler going at home.
The easiest but highest-maintainance approach is to use three pots with good upper-range thermometers to get three water baths, but that's not automated and it's annoying to use. I'll probably show how to do that, anyway.
I could have copied the original light-bulb design entirely, but I had a heat-gun to hand.Control is going to be via a solid-state-relay plug socket I hacked up last week, and a car battery/motor controller for the 12V fan. An arduino will handle the thinking, obviously. The tubes will be installed into the lid with the airflow from either the cooling fan or the heat gun flowing over them as it exits the can.
The missing ingredient is LM35 temperature sensors (one of which will go in a tube with mineral oil), and I'm hoping I'll have them in time to prototype this.
Here's my knocked together DIYbio shaker:
Lovingly crafted with a scissors and cardboard, it features advanced Arduino microcontroller operation and a roughly 6hz cycle. Features include flammability and spontaneous failure.
Shown here agitating a glass tube with 3mls of B.subtilis for overnight growth.
