Open Lifespan book blog: the philosophy of indefinite healthy living

I started this blog using bits and pieces of my philosophy MA thesis dealing with the philosophical consequences of healthy lifespan extension technologies. And then turned this blog into a mainly scientific and technological exploration dealing mainly with the potential tools enabling healthy lifespan extension. I’m now back in the domain of philosophy and finally…

My AgeCurve talk at Undoing Aging 2018

I’ve been invited by Aubrey de Grey to give a talk on AgeCurve at the Undoing Aging Conference, this March, in Berlin. Here’s the bulk of the talk on YouTube:

Fighting aging and fighting ageism: two sides of the same coin?

Let me delineate one answer to the post title question, quick   Sure, but only if we know what types of aging we are talking about. My original, more boring but less sensational post title elaborates on this: Counteracting biological aging and neutralising chronological ageism should go hand in hand.  (For the record, am not a…

Continuous lifespan extension as a coherent life plan enables super-agency

Introduction In ‘Agency, Life Extension, and the Meaning of Life‘, professional philosopher Lisa Bortolotti argues that the so-called agency objection against a loosely defined life extension technology should be rejected. Briefly put, the agency objection argues that one important component of the meaningfulness of human life is being constrained as an agent and since ‘life extension’…

Robust lifespan extension & ecological awareness: can an exponentially extended human life be a hyperobject?

Warning: this post is only ~30% complete, the rest will be added in case of further interest from you. Hope I can incorporate comments from other humans to give a much better formulation. I am making myself intentionally vulnerable here wanting to engage in a conversation. Imagine the following: you are living potentially not up…

Aging, health, disease: more than philosophical arguments

In this new post series I utilise my philosophical training and formulate, collect and re-phrase arguments around what is aging and what is not. Since aging is conceptualised with the help or in the context of other heavyweight, loaded and complex concepts like health, disease, biomarkers, and last (but also first) time, those concepts will…

AgeCurve Limited and Gen P: my business angle on aging and longevity

After 20 something years of living a diverse educational and professional life motivated by healthy lifespan extension and dominated by science and technology I have reached the riskiest and most rewarding phase: launching a business around it and making it real. I have founded a startup, called AgeCurve Limited and we are already offering a product,…

1 day Apache Spark training: randomish insights

Last week I’ve participated in a one day Apache Spark workshop in London developed by Databricks and organised by Big Data Partnership. Databricks Training Resources is the most important link you need to know in order to get started, contains the whole training material. Let me share some short comments: Spark is the next, logical generalised step leveraging the…

Big list of Markov chain Monte Carlo (MCMC) applications

I became quite obsessed with Markov chain Monte Carlo Methods lately. It is said that MCMC methods form the most frequently used class of algorithms in computer science. However when I was searching for a comprehensive list of MCMC applications across different domains to my surprise I have found none. So I’d like to ask…

Human Longevity Inc. and Calico: healthy lifespan extension is a win-win game and a competition against time

A snippet from the following interview: The Regeneration Generation: A Conversation With Bob Hariri, Vice-Chairman and Co-Founder of Human Longevity Inc.

Hadoop 101 for bioinformaticians: 1 hour crash course, code and slides

Earlier this year (February-April) I ran 9 short 1 hour hands-on sessions (5 persons/session) called Hadoop 101 for bioinformaticians at the Genome Campus for European Bioinformatics Institute and Sanger Institute people. The participants were bioinformaticians, developers and sysadmins. My idea was to start with a ~20 minutes long theoretical introduction so it provides some handles on whether…

Crowdsourcing Google’s new mission statement #newgooglemissionstatement

Larry Page acknowledges in a recent interview that the Google’s mission statement is outdated and became irritatingly narrow:

Changing the game: absolute protein quantification by relating histone mass spec signals to DNA amounts and cell numbers

One thing system biologists want is to have by and large absolute protein concentrations or copy numbers per cells available cheaply for their models leveraging all sorts of omics data. Looks like such results can now be easily delivered based on a study published on the 15th of September by the Mann lab in Molecular & Cellular…

Pleasingly Parallel MCMC: cracked wide open for MapReduce and Hadoop

MCMC methods guarantee an accurate enough result (say parameter estimation for a phylogenetic tree). But they give it to you usually in the long-run and many burn-in steps might be necessary before performing ok. And if the data size grows larger, the number of operations to draw a sample grows larger too (N -> O(N)…

2 recent Global Alliance for Genomics and Health standard candidates: ADAM and Google Genomics

Global Alliance for Genomics and Health includes > 150 health and research organizations to progress/accelerate secure and responsible sharing of genomic and clinical data. GA4GH (for short) is something you will here about more and more in the short term future. In the context of genomics standards think of mainly data formats and code to access and process…

3 recent Hadoop/MapReduce applications in the life sciences: RNA structure prediction, neuroimaging genetics, EEG signal analysis

3 open access papers, 3 prototypes, source code available only for 1, healthy diversification of topics. 1. Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce code available: haven’t found it referenced in the paper Our previous research shows that cutting long sequences into shorter chunks, predicting secondary structures of…

Google invests into DNAnexus: aging-driven big data bioinformatics without the Hadoop Ecosystem?

First time DNAnexus made me think a little about what they can achieve was when they came up with an alternative search and browse interface for the complete Sequence Read Archive (SRA) database. They came to the ‘rescue’ as NCBI discontinued SRA in 2011 although later they’ve changed their mind, so SRA is still up and running there.…

Coming of age for proteogenomics: 10% less human protein coding genes based on mass spec proteomics data?

Guessing the number of real protein-coding genes is an ‘ancient’ bioinformatics game and now a new argument & newish research field has been applied to this problem. Proteogenomics can refer to different type of studies but the basic idea is that mass spectrometry peptide/protein evidences are used to improve genome annotations. Now a joint Spanish –…

Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 17 December 2013

1. DNA methylation age of human tissues and cell types by Steve Horvath: This is the type of relevant data mining study most bioinformaticians are dreaming of: you pull together a large body of publicly available datasets (CpG methylation) that are not too heterogeneous (Infinium type II assay on Illumina 27K or Illumina 450K array platform), derive robust…

Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 8 December 2013

1. Is aging linear or does it follow a step function? A good & simple question on Quora that surprised even Aubrey de Grey. If you are a bioinformatician out there – looking for a new pet project – go pull together some data & try to plot it! Let me know if you have something.…

Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 24 November 2013

Introducing a new post format by reutilising Nat Torkington’s Four short links format over at O’Reilly Radar (thanks, Nat!).   1.  The Hallmarks of Aging: good review by European scientists trying to put some pieces next to each other (but not necessarily together). The 9 hallmarks are: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis,…

How to build a colorful life around life extension using different skills: a personal story

Here’s an edited version of my Quora answer to the question: “Life Decisions: How do people who are talented in many areas decide what to do with their lives?“ Let me provide a personal story illuminating one option Ruchira is talking about: “pick a complex challenge that you are passionate about, that will require many different…

LavaAmp: cheapest pocket PCR thermocycler dreamed for DIY biologists

The LavaAmp is a portable PCR thermocycler that has the potential to become the default garage biology (home biology, bioDIY, DIYbio) tool once it hits the market. Think of Apple II for personal computing or MakerBot for 3D printing. The 1st LavaAmp prototype was shipped this week from Biodesic to Gahaga Biosciences and the process…

Aging-centric genetic health database in California: 100k people, ~65yrs, 700k SNPs, telomeres too

Kaiser Permanente alongside with UCSF plans for genetic analyses of an unprecedented 100,000 older Californians, the Technology Review writes in Massive Gene Database Planned in California The effort will make use of existing saliva samples taken from California patients, whose average age is 65. Their DNA will be analyzed for 700,000 genetic variations called single-nucleotide…

Sage Bionetworks Update: building an OA standard for human disease biology

Sage Bionetworks is a not-for-profit organization developing an open-access “pre-competitive” platform for networked and annotated models of human disease. It’s a huge and unparalleled bioinformatics enterprise: starting with an anonymous $5 million donation and soon making high throughput, large-scale human and mouse biological data (largely from Merck) available in the range that’s already in the…

The Nobel Prize in Physiology or Medicine 2009: telomere/telomerase, Blackburn, Greider, Szostak

“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase” press release The award goes to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak. The problem of telomere/telomerases is highlighting the double but strictly related aging/cancer problem space: Blackburn Lab Greider Lab Szostak Lab

Top 10 PLoS Articles based on online usage

Big news at PLoS: today Mark Patterson announced on the PLoS blog that “As part of our ongoing article-level metrics program, we’re delighted to announce that all seven PLoS journals will now provide online usage data for published articles”. I downloaded the entire dataset and as a starter sorted it according to Combined Usage =…

Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

Nature’s Journal Club column is usually a good & always a short read providing exciting angles on scientific topics/papers from good researchers. Recently ‘neuroscientist’ Dave Featherstone argued for a broader approach to brain mapping by not restricting it only to the connectome between neurons. Neurons are making up less than 10% of the human brain…

Visualize 23andMe haplogroup defining SNPs with Mitowheel!

Last Friday 23andMe came up with Haplogroup Tree Mutation Mapper which is the first experimental feature that can be instantly tested by biogeek customers (a large portion of  the company’s customer base) in its freshly launched technology sandbox 23andMe Labs that is much like Google Labs. Haplogroup Tree Mutation Mapper “shows you which particular mutations…

Bright cells, big city: Cellular images hit Broadway

Surprise email from Conor McKechnie, GE Healthcare proving the aesthetics of science and the value of blogging: A while (!) back you posted an inspiring piece linking to Harvard’s BioVisions inner life of the cell – it was 2006…It got me thinking that we could do something similarly inspiring with actual cellular images entered into…

Why the Dyna-Vision G1 Android Telemedicine App can only be used by licensed physicians???

Let us assume that you are a technological early adopter, a maker, a hacker, a geek. Your software/hardware skills and experiences are much better than the bulk of licensed physicians. You also have a G1. Now imagine a mobile application/gadget-in-a-belt-pouch that is the most advanced telemedicine solution in the market. With this application/gadget you were…

Many Eyes Visualizations: FDA Application Approvals 2000-2008

Take a look at the FDA Application Approvals 2000-2008 visualization (created by user mktlgcs) over at IBM’s Many Eyes to get an aerial view on the US. pharmaceutical industry.

Google Health, IBM: real-time, vital medical data stream

Forbes article: Letting Google Take Your Pulse via @mattcutts: On Thursday, Google and IBM will unveil a new initiative that will allow Google Health, a site where users can store and track information about their medical history, to connect to and stream data from medical devices. In demonstrations, IBM and Google fitted Wi-Fi radios to…

ScienceX2 is dead, long live Signtific!

The folks at The Institute for the Future have been busy lately and as a result Signtific has been launched replacing ScienceX2! Check this, the about and FAQ pages if it’s new to you or just simply explore.

Practical DNA: Hugh Rienhoff’s got a story to tell

After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details…

BioBlocks: outsourcing biotech, one block at a time

Friend Dan Erlanson (Co-Editor in Chief of the niche and smart Fragment-based Drug Design blog Practical Fragments) sent me this story on the recession proof business model of a biotech company called BioBlocks and his founder medical chemist Peter Pallai: Approximately one out of 5,000 compounds pass an initial screen, hit the designated biological target,…

1st UK Maker Faire, Newcastle, March 2009, makers wanted!

The first Euro Maker Faire in Brussels was an evening event but now with the first UK Maker Faire makers have a chance to hang around for 2 days and develop or deepen their DIY skills similar to the original US events (we enjoyed Austin Maker Faire in 2007). Let me know if you’re interested.…

The Decision Tree: Thomas Goetz’s upcoming book on predictive/personalized medicine

In the past months Thomas Goetz begun writing a book on the radical changes already ongoing but mostly upcoming in healthcare due to affordable new technologies and quantitative approaches in personalized genomics and medicine. The book is to be called The Decision Tree (explanation below) accompanied by a new website. Thomas is the perfect man…

Nature Insight: The complex trait of quantitative genetics

Nature’s newest issue has a Quantitative genetics supplement with 3 free access pieces included out which I find this review the most interesting: Reverse engineering the genotype–phenotype map with natural genetic variation by Matthew V. Rockman. There’s a lot information to digest and many patterns to understand in this background field in order to approach…

How to predict the future via Twitter: Kids’n’Kits or 23andMe’s Holiday Family Pack!

After the first Twitter prediction here is my second one back from September, realized today: and here we go….Happy Holidays Grandma you’got a 2fold risk for psoriasis but don’t worry too much about the Alcohol Flush Reaction and your caffeine consumption! Actually I tried to convince