Ward Cunningham – What If Bacteria Designed Computers?

cunninghamcartoonportraitThere is a pattern of successful technological innovations I can summarize the following way: there is a nerd engineer who actually invents something and builds the first functional prototype, and there is a geeky enough yo who recognizes the value of the prototype and makes the bigger money/fame/other beneficiaries out of it by turning it into a commercial product: the archetypal nerd/geek pair in this respect is Wozniak/Jobs. In case of the wiki software the programmer/inventor was Ward Cunningham, while Jimmy Wales became the official Mr. Wiki due to Wikipedia.

Recently I discovered Cunningham on Twitter and I learnt that for coding he takes inspiration from life’s processes ranging from cell signaling to cultural evolution. His coming speech: Continue reading

Friday Gumbo Journal Club: hESC line differences and a killer MSC review

It’s Friday, that is a lunch heaven for a Gumbo loving biogeek at Tulane:

gumbojournalclub

Stem Cell Express: Copy Number Variant Analysis of Human Embryonic Stem Cells from the Teitell Lab (It’s good to see that CIRM funded results and papers are coming out): Continue reading

Low budget, high tech: Microfluidics device out of a $50 plotter!

7550AplotterBuilding and using low budget but high tech devicesplotterink at home is a main motivation behind hacking. A Harvard Chemistry Research Group now created a microchannel producing device using a Hewlett Packard 7550A Graphics Plotter (see some eBay prices) to perform a diagnostic protein assay with it amongst others. /See my SciFoo microfluidics coverage./

According to the current Nature by Tim Lincoln:

“The system works like this. By replica moulding, the pens of the plotter are replaced with PDMS versions that can deliver various types of ‘ink’. The purpose of the ink, when cured, is to create channels in a filter-paper substrate, and after experimenting with the possibilities Bruzewicz et al. found that a syrupy mixture of 3:1 PDMS:hexane did just fine. Having chosen the appropriate paper, the trick then is to use the plotter to draw channel shapes, with the PDMS syrup penetrating the full depth of the paper to create water-tight chambers in various patterns.”

Hardware-Software Specs from the supporting information:

Computer.
• Computer: Dell Dimension 4100, Pentium III Processor (1 GHz)
• Plotter: Hewlett Packard 7550A Graphics Plotter
• Operating System: OpenSuSE Linux 10.1, Novell Corporation. Available for free download
• Additional Software:
1. Inkscape – vector drawing program, for design of channels. Included in OpenSuSE, also
available for free.

The HP Computer Museum highlights this particular plotter: Continue reading

Mitowheel now helps you design PCR primers for mitochondrial DNA!

mitowheelallelebarsGábor Zsurka, scientist and developer made another upgrade on our favorite human mitochondrial DNA visualization tool, MitoWheel: this time allele frequencies at polymorphic positions are included in the sequence bar in the form of a gray bar above or below a nucleotide representing the number of individuals carrying the SNP.

This is really cool as it is a definite step to turn MitoWheel into a tinkering, engineering, mtDNA hacking tool besides its core science mission:

“This can help you to design reliable PCR primers for the human mitochondrial genome. After all, you don’t want your primer’s 3′-end sitting right on a very frequent polymorphism (risking that under certain conditions you will not be able to amplify a PCR fragment from a subset of individuals).” Source: MitoWheel Blog.

Larry Page is 35 years old today: long live to live long enough!

larrypage35

I’ve always loved the following scene from LOTR, but I’ve always imagined that they are the words of a man who is in a healthy physiological condition due to a robust life extension technology and not due to a mystical ring:

Bilbo: “Today is my one hundred and eleventh birthday!”

Hobbits: “Happy birthday!”

Bilbo: “Alas, eleventy-one years is far too short a time to live among such excellent and admirable hobbits.” [cheers abound.] “I don’t know half of you half as well as I should like, and I like less than half of you half as well as you deserve.”

Larry Page is 35 years old today and it’s really easy to consider him as a representative man of his/our generation (I am 33 years old) including his future prospects. A company with an unlimited potential was built on Page’s unfinished PhD. research project.

Blow your Brain Explorer out with the Human Allen Brain Atlas!

At the SciFoo Camp last year at the Googleplex I suggested a little unconference session (ok, there were some slides ready on my MacBook) and one participant was Chinh Dang (another was this inventor) Technology Director of the Allen Institute for Brain Science who made a little intro to the work of the Institute to the 9-10 attendees after this slide of mine:

SciFoo Brain Atlas

Paul Allen is the likable, Steven Wozniak-type co-founder of Microsoft, but I guess a bit richer (once we estimated with a friend of mine that he could buy all the Budapest condos circa 180 times or sg like that).

But instead of doing that he provided $100M – amongst others – in seed money to fund the Allen Brain Atlas.

Continue reading

Kurzweil follow-up in life extension exhausted Wired

Last year I approached a powerful Wired editor with the following story pitch: “A full and deep but cool report on the current (scientific) life extension technologies, persons, battles, camps, grants, problems, perspectives.”
His reply was a diplomatic and definite naysaying:

“Thanks for the idea. Alas, we’ve done *way* too many stories on life-extension over the years, from profiles of the singularity guys and Aubrey De Gray (sic) to shorter takes on various startups and stuff. There may be cool stuff out there, but I’m afraid we’ve exhausted our appetite on the subject.”

kurzweilwiredHowever the life extension appetite is not something that could be exhausted until the problem is solved systematically and the Wired guys’ appetite seems to be restored and healthy again as in the April Wired issue (not online yet) there is a full story (or rather follow up) on the No.1 singularity guy and baby boomer escapist artist Ray Kurzweil called Stayin’ Alive by senior Wired contributing editor Gary Wolf (whose book Wired – A Romance is a good reading).

What is interesting in Kurzweil for experimental scientists/robust life extension supporters is not his meditations on singularity, accelerating change and mind uploading (see the counterarguments by Mark Anderson in the same Wired issue), but his experimental, futuristic, life extensionist lifyestyle:

Kurzweil takes 180 to 210 vitamin and mineral supplements a day, so many that doesn’t have time to organize them all himself. So he’s hired a pill wrangler, who takes them out of their bottles and sorts them into daily doses. K. also spends one day a week at a medical clinic, receiving intravenous longevity treatments. The reason for his focus on optimal health should be obvious: If the singularity is going to render humans immortal by the middle of this century, it would be a shame to die in the interim.

Kurzweil’s physician and coauthor is Terry Grossman (also a SENS3 conference attendee) with an interesting clientele. Continue reading

Thesis live: Introduction, “contents” draft

From now on I start every “thesis live” post with the standard introduction: In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential

I am not aiming any perfection, my focus is clearly on getting things (the PhD) done here. Anyway, I found the idea of “writing” a complete, lengthy and formal thesis outdated and inefficient (after all, scientists should conduct nice experiments and publish their results in short, inforich and accessible research papers in order to share it ASAP with the research community, not in book-length, otherwise unaccessible PDFs) and so I try to keep myself motivated by

- doing this “thesis live” series as an open science experiment and getting useful feedback from my fellow scientists and readers

- trying to include as many systemic, whole body level material into it that could be relevant for systemic regmed approaches

- reminding myself every day that without a PhD it is hard to move further in science officially (that’s the least motivating factor though as it is official)

After the blah-blah let’s start with the planned introduction points:

1. Introduction:

1.1 Stem cells and regenerative medicine

1.2. Tissues, organs with different turnover and regenerative potential

Gut epithelium,
Blood – hematopoietic system
Epidermis,
Mammary epithelium,
Vascular endothelium,
Continue reading

Warming up to write my thesis on the blog

Not much happened since my announcement on Editing my doctoral thesis on stem cells in a blog: Why not?. I went to the U.S. first and started doing research instead of finishing my PhD education. But now I am back in this “getting a PhD” business as in January I passed the prerequisite comprehensive stem cell and mitochondrial biology exam with a plus. Continue reading

Life extension people are happy: keep living, please!

I found this picture of Aubrey de Grey with his book Ending Aging on his head at the BIL conference in Quinn Norton‘s Flickr Stream. Quinn Norton is a bodyhacker technophiliac journalist photographer. Robust, healthy lifespan extension can easily be interpreted as an extreme body-, life- and biohack so no wonder that more and more geeks are turning their attention to this little, unsolved hack. Maybe with time they will learn not just how to write the names properly but how to set up a private lab and isolate DNA and stem cells, at home. (blogging pictures = not enough time to write posts)

aubreyendinghead

What is Genentech CEO Art Levinson doing for biotech as a Google board member?

artlevinsonThe title question is my million (not billion yet) dollar question for this year. Arthur Levinson is a board member of Google (Apple too) and in his leftover time he is the CEO of the most successful biotech company so far, that’s Genentech. I would be curious to hear about his biotech-related activity as a G board member from my readers even in the form of guesses. Maybe he is teaching biotech classes to Googlers after both Genentech’s and Google’s investment into 23andMe or just sitting around sometimes at the nice cafeterias at the Amphitheatre Parkway, Mountain View and explaining knockout technology to coders.

levinsonapplegooglink

Peer blogging the question marks of the Warda-Han paper’s peer review

DunnPeerReviewThe Warda-Han paper was retracted from journal Proteomics exactly one month ago unofficially due to its “mighty creator explanation” (covered here first)/officially due to its heavy plagiarism (flashmobbed so efficiently by the Pharyngula commenters).

Yet we are still very short about the details of what happened during the pseudo peer review of the paper.

So here I’d like to participate in the joint blogging iniciative of Lars Juhl Jensen and like to ask my readers to scan through the detailed questions of the following scientist/bloggers concerning the Warda-Han paper:

Buried Treasure by Lars Juhl Jensen: Update: Warda and Han, one month after the storm: “To prevent similar incidents inthe future, it is important to know whether the editor and the peer reviewers overlooked glaring flaws of the manuscript or if the flawed parts were introduced after peer review.”

Pharyngula by PZ Myers: One month of stonewalling: “We want to know how this paper slipped through the cracks, because we want to know how large the cracks in the peer review process at Proteomics are.”

Genomics, Evolution, and Pseudoscience by Steven Salzberg: Creationism in a science journal, redux: “Finally, I noticed that the Warda and Han article is listed by the journal’s website as the most-accessed article for the past month. Controversy brings attention, obviously, and Proteomics should use the attention to provide a full explanation of the Warda and Han fiasco.”

PS: I shot the picture last week: that is an editorial by Mr. Michael Dunn, editor-in-chief of Proteomics in Proteomics and another book – I’d like to offer it to Mr. Dunn – in the Wiley stand at PITTCON:


Biotech firm funded by Life Extension Foundation to push regmed therapies

Press release:

“We at Life Extension Foundation are pleased to help finance BioTime‘s entry into the field of regenerative medicine. We believe that one of the most important applications of embryonic stem cell technology is the slowing and reversing of aging and age-related disease. Continue reading

Biotech DIY for aging/life extension research: the double future?

“The best way to predict the future is to invent it.” – said Alan Kay, computer legend in 1971.

Recently I had a comment dialogue with Chris on whether state-supported research or industrial business enterprises can (or should) lead to big progress in robust and healthy life extension technologies. Besides the government and corporation coin the research breakthrough could come from an aging focused foundation like the non-profit Methuselah Foundation behind the SENS approach, which supports research projects (like MitoSENS and LysoSENS) and scientists (like Mark and John) through cooperation with university labs. And finally, there is going to be another option to contribute:

agingbioDIYtoast

Imagine the following future scenario: biotech DIY is becoming an accepted home activity so geeks are setting up private labs and conduct basic in vitro (but not in vivo) research. Continue reading

Mitowheel upgrade: phylogenetics in motion

mitowheel creating groupsGábor Zsurka has built some killer functions into Mitowheel, the human mitochondrial DNA visualization tool:

- compare GenBank‘s circa 3000 fully sequenced human mitochondrial genome to the revised Cambridge Reference Sequence mutation by mutation

- by harnessing the power of the colorful group view and using the +, – mutation operators (see detailed introduction) you can dig deeply into phylogenetics and haplogroups

- navigation became more sophisticated

PITTCON, 2008: bioDIY questions, RFVials, and Science’s new web hirings

pittconchildAs a local New Orleans face (my colleagues just call me Mitoman in the lab) I had the chance to just simply walk into the grandiose PITTCON exhibiton at the Ernest N Morial Convention Center and I liked it. In addition to getting answers to some strictly lab related questions concerning filters and fuges (nevermind), I satisfied my 2 major side interests: the older bioDIY and the brand new RFID.

1. I surprised every biotech vendor - some of them laughed, others were meditating a bit - with the question: ok, but what is the cheapest gadget you have for somebody who wants to set up his basic DNA private lab at his backyard?

In my coming series to help launch a grassroots biotech DIY movement I’ll put together concrete suggestions on what to buy, but according to the experts:

- the price of a new benchtop centrifuge (6-8000 x g) is $800-1200, but the manufacturer is simply not interested in individual service and recycle used machines for low-throughput hobbyist end-users

- liquid nitrogen: 24 liter tank around $5000 (you can get it lower), LN itself is not that cheap but it’s worth storing your cells in a local repository bank instead, at least an expert guy told me

- a laminar hood for sterile work with cells is also around $5000, way too much for garage biofreaks, but you can still build your own out of a household air purifier

2. Have you ever thought of tracking, reidentifying your eppendorfs and tiny PCR tubes in the lab instead of the almost impossible hand marking? Well, we are not there yet, but Baytek developed an RFID kit for glass GC or HPLC vials. Continue reading

First DIY RFID experience: Arduino controlled Parallax reader

RFIDParallaxArduinoiBookIn the last couple of weeks I became heavily interested in RFID (Radio Frequency Identification) technology probably because the dangerous idea of all pervasive computing and the opportunities to build sg from the bottom-up. So here is a how-to to my first installed low frequency, read-only RFID system hopefully followed by a more juicy stuff in the ultra high frequency range up to 9 meters.

Hardware:

Parallax RFID reader with 2 tags ($49.99+shipping, Radio Shack)

9-Position Female Crimp D-Sub Connector($1.99, Radio Shack)

4 hook-up wires

Arduino Diecimila microcontroller ($34.99)

Macbook, iBook

Software, code:

Code in C programming language for using the Arduino with the Parallax RFID reader but in order to upload it to the Arduino board and make it actually work I had to put the reader activator line:

 digitalWrite(2, LOW);                  // Activate the RFID reader

into the

 void loop()

function just like in the the sample Wiring tutorial

Arduino software: different packages for Intel based Macbook and PPC iBook

Here is a screenshot on the Serial Monitor reading the tags on iBook: Continue reading

The $20 life extension blogging challenge and change

Scott Wainner – an old timer, professional internet revenue generator and recent maximum healthy life extension advocate (the ideal target group) – wants you (in this case, me) to blog about life extension for $20 (first 100 bloggers only) and thereby also boosts his site’s traffic (I am sure there is a special marketing term for this type of activity): Living Well, Indefinitely + $20 Blogging Challenge. Continue reading

The conditions of a mass biotech DIY movement

jobswozniakPCR

The idea of doing biological experiments with current biotechnological methods and conducting research projects at home is quite new. There are already many names in use referring to the same concept: bioDIY, home biology, biotech DIY, garage biology.

We have a detailed case example which can be considered as the first registered, high profile biotech DIY activity starting the era of useful garage biology: Recently Hugh Rienhoff amplified his daughter’s DNA at home to help doctors figure out her genetic disorder. From the Nature cover article:

“So he bought a used PCR machine, a microcentrifuge, some small-volume pipettes and a brand new gel box. All told, the equipment cost him about $2,000. With these simple tools and some sequence-specific DNA primers of his own design, he could pick the relevant genes out of his daughter’s genome and amplify them enough for sequencing. Freezing the samples and packing the tiny tubes on ice, Rienhoff sent them off for sequencing at about $3.50 a pop. He prepared upwards of 200.”

Another suggested project was the How to isolate amniotic stem cells from the placenta, at home! but so far I haven’t heard of anybody who really did that at home and I only isolated the cells at the lab.

In my coming series I’d like to examine the following conditions of a mass biotech DIY movement: acquiring skills, affordable kits, tools, hardware, motivations, business opportunities and impact.

acquiring the how to skills:

- good education tools, protocols, videos, howto-s on the web

- short intensive academic or industrial lab courses available for every citizen

- self-education in community: forming Homebrew Biotech Clubs

available, affordable tools, hardware:

- cheap kits: based on the Rienhoff example, a very basic home lab can be set up out of 2-3000 dollars, which is the price of a good laptop.

says Mr. Rienhoff in an email: I bought all the equipment used from a local vendor who buys equipment at auction and from universities. All the gear is at least ten years old so it was very used and low throughput. But given that my project was incredibly focused I did not need the more sophisticated equipment.

- used equipment network: Continue reading

Very well informed Stanley Bing on life extension

Huffington Post, Fortune’s Stanley Bing: The Next Big Thing? Please pay extra attention to the language here (especially transmogrification).

stanleybingHuman genome schmutz: Nobody wants to get old or worse, appear old. And forget about dying. That’s the ultimate bummer. Genetic research has been held back recently by a series of disasters too terrible to mention in this venue, or even look up right now, since we’re very busy. But the three-headed midget sheep problem will be solved by 2014 and recombinant DNA, stem-cell and mitochondrial transmogrification technology will begin making inroads into the problem of aging, extending human life to its ultimate limit and even beyond, particularly for really rich people who are on everybody’s nerves already. Another enormous opportunity for confabulators here.

Well, why exactly am I working with human mitochondria and stem cells at the bench? Maybe it’s time again to recall.

Biotechies at O’Reilly ETech, March 3 – 6, San Diego

The O’Reilly Emerging Technology Conference (ETech) is on and this year they had a growing number of biotech related sessions. Fellow SciFoo Campers like Hugh Rienhoff and Timo Hannay, Makers like Phil Torrone and Limor Fried, Brain Hackers like Ed Boyden are visiting and many more.

ETechbiotech

How much data is produced by a life scientist/day?

3TBThe current operational idea behind Google’s Palimpsest Project is to ship 3TB (terrabyte= 1.0995 x 1012 bytes) drive array (Linux RAID-5) for scientists, who upload their data and FedEx the hard drives back to Google. Google then make those data publicly available and manageable. This file transfer method was heavily criticized by Dai Davies in Ars Technica. “This is a bit like using Flintstones technology in the Internet era.” although there are arguments behind this choice, see Jon Trowbridge’s 11th slide. Forget about this uploading/updating problem to the amount of this post. Here I only care about the end-user, the scientist who is provided with whatever tool to upload 3TB of research, measurement data on behalf of her research facility. While for an astronomer hundreds of gigabytes/day can seem as a normal output my angle is on how a life scientist and his data fits to this 3TB equation and eventually to the Palimpsest Project. Accordingly, my question is this:

How much data is produced by an average wet lab scientist, biomedical researcher/day?

I try to come out with a rough guess in the hope of subtle corrections from the commenters: I assume the following (rather busy) daily production of data by our average scientist in an average lab:

running a gel – making a gel photo 300 KB .tiff

preparing 5 samples for sequencing at the core facility, output: 500 KB – 1MB ab1, seq files

FACS sorting of different cell populations: 1 MB of special FACS files and 100 KB pdf out of it

Continue reading