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) for most MCMC methods.

Although there’s been attempts earlier to express an MCMC algorithm in a distributed manner it was a big question whether it can be turned into an embarrassingly parallel algorithm (let me not discuss here the difference between parallel and distributed). An embarrassingly or, more positively, a pleasingly parallel algorithm can be executed on many separate nodes on different chunks of the input data without requiring those tasks communicating with each other and without the need to maintain a global shared state throughout the process.

Exactly these are the problems MapReduce was designed for and provides a nearly ideal fit.

Today I discovered 2 papers from 2013 that have finally came up with efficient looking pleasingly parallel MCMC designs and prototypes and the whole reason of this post is to share my joy felt over this little insight. These 2 papers finally present the opportunity to write a stable and efficient MapReduce Hadoop library allowing data intensive bioinformatics applications and opening up this important subspace of biological methods. While I’m certainly not the type of bioinformatician who is going to implement these designs in Hadoop, I’m certainly the type of applied scientist who is going to use them. So the race is on, dear Hadoop developers to give another important toolkit in the hands of the bioinformatics crowd.

The 2 papers:

Asymptotically Exact, Embarrassingly Parallel MCMC Continue reading

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 these formats (APIs if you like this term, well I don’t).

2 emerging projects in the genomics standards field, one of them is bleeding, the other one is cutting edge:

1. ADAM

“Global Alliance is looking at ADAM as a potential standard” check slide 12 of this slideshow.

what is it: “ADAM is a genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.”

Currently it includes a complete variant calling pipeline amongst others.

main codebase: http://bdgenomics.org/

some folks behind it: @matt_massie @fnothaft and several other people from places like AMPLab at Berkeley, GenomeBridge, The Broad Institute, Mt Sinai.

2. Google Genomics

Continue reading

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 the chunks independently using thermodynamic methods, and reconstructing the entire secondary structure from the predicted chunk structures can yield better accuracy than predicting the secondary structure using the RNA sequence as a whole.

This is quite unexpected but obviously favourable for a pleasingly parallel implementation MapReduce can offer. Lots of benchmarking and comparison, quite methodology focused.

2. Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes

code and documentation available: http://www2.imperial.ac.uk/~gmontana/parfr.htm but only java classes no project management and automated software build tools used

We have developed a parallel version of the RF algorithm for regression and genetic similarity learning tasks in large-scale population genetic association studies involving multivariate traits, called PaRFR (Parallel Random Forest Regression)… Notable speed-ups are obtained by introducing a distance-based criterion for node splitting in the tree estimation process. PaRFR has been applied to a genome-wide association study on Alzheimer’s disease (AD) in which the quantitative trait consists of a high-dimensional neuroimaging phenotype describing longitudinal changes in the human brain structure. PaRFR provides a ranking of SNPs associated to this trait, and produces pair-wise measures of genetic proximity that can be directly compared to pair-wise measures of phenotypic proximity. Several known AD-related variants have been identified, including APOE4 and TOMM40. We also present experimental evidence supporting the hypothesis of a linear relationship between the number of top-ranked mutated states, or frequent mutation patterns, and an indicator of disease severity.

First impression is of a well-thought, serious study with different types of results.

3. Cloudwave: distributed processing of “big data” from electrophysiological recordings for epilepsy clinical research using hadoop.

code available: I don’t think so Continue reading

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.

But DNAnexus is here to stay and they also made me think personally since the same time NCBI discontinued SRA, they discontinued Peptidome as well that was NCBI’s shotgun mass spectrometry proteomics data repository. Much of my work in 2011 and 2012 went into reprocessing the valuable Peptidome datasets and making them available at EBI’s PRIDE database (where I work), a process which was documented in the open access paper From Peptidome to PRIDE: Public proteomics data migration at a large scale. As opposed to SRA and next-gen sequencing DNA data, Peptidome was shut down permanently.

But back to DNAnexus and the fresh news that Google Ventures “has joined a group of investors seeding DNAnexus‘ cloud-computing services for biomedical researchers with a $15 million C round”. What makes this news interesting is that recently, DNAnexus announced large-scale projects with Stanford and Baylor College of Medicine in processing tens of thousands of genomes and making the resulting data sets securely available. From the press release:

Through these two projects alone, DNAnexus processed over 17,000 genomes and generated more than 500 terabytes of genomic data. The resulting data sets can be accessed on DNAnexus and are available for follow-on analysis and data sharing to researchers participating in the 1000 Genomes Project and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium.

Put this news into the context of Google’s investment into Calico to address aging and healthy lifespan extension and into the fact that the first scientist hires of Calico, like Cynthia Kenyon and David Botstein are coming from genetics/genomics background. Medium boom, it’s still opening game on the board!

This all sounds awesome and I hope that the DNAnexus folks are going to deliver & have fun while doing so. But let me offer an angle here that makes this big data bioinformatics news just a little less awesome: DNAnexus already tried MapReduce and Hadoop for their genomics data processing pipelines and at the end they ditched it for proprietary homegrown software. Continue reading

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 – British – US team makes an interesting argument based on the LACK of mass spec evidence (negative proteogenomics mind you) in a pre-print deposited in arxiv entitled The shrinking human protein coding complement: are there fewer than 20,000 genes? The argument and claim in a nutshell: by pulling together and reanalysing 7 large-scale proteomics studies & mapping them to the GENCODE v12 annotation they identified 60% of protein coding genes. Then applying multiple non-coding features (the real meat of the study) they further restricted the non-coding set yielding at the end a set of 2001 genes out of which they think 1500 do not actual code for proteins at all.

Whether the bioinformatics argument is flawless or not the following findings are exciting: Continue reading

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 statistical results (develop a multi-tissue predictor of age) and apply it on a medically relevant field (20 cancer types exhibit significant age acceleration, with an average of 36 years). Continue reading

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, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication.

2. StemBook: good introductory material (broad and at times, deep), they even have a proteomics chapter.

an open access collection of invited, original, peer-reviewed chapters covering a range of topics related to stem cell biology written by top researchers in the field at the Harvard Stem Cell Institute and worldwide. Stem Book is aimed at stem cell and non-specialist researchers.

3. David Botstein, 71, on Joining Google’s Anti-Aging Play, Calico: a good initial seed of people are needed for this venture, looks like Botstein can think out of the box and does not want to hang on forever in academia.

Page, describing the new venture in a posting on Google Plus in September, said ”don’t be surprised if we invest in projects that seem strange or speculative compared with our existing Internet businesses.”

That’s what got Botstein. “I’m a basic scientist. I’m not a translational anything,” Botstein said. “I start with the opposite premise of the usual translational thinking. I start with the premise that we understand very little of the world. Specifically, we understand a tiny fraction of what’s written in our genomes. We understand a tiny fraction of what parts of medicine work well, and what parts are just tradition. We understand virtually nothing about the microbiome. The value of basic science, of course, is once we do understand something we might be able to do something.”

“We’re scientists, and we’re going to sit together and ask people their thoughts and we’re going to try to define areas that fit into this general but well-defined space, and focus on things that wouldn’t get done,” Botstein said.

 

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 talents to solve.

I picked the rather complex topic of aging and healthy lifespan extension at the age of 14-15 and it helped me to deep dive into a couple of different professions so far, consecutively, not concurrently though:

1. got a masters in biology and worked experimentally on the mitochondrial theory of aging as a thesis work, something related to looking for mutations accumulating with age in the hypervariable regions potentially downregulating the electron transport chain components encoded by mitochondria

2. realised that in order to understand what aging is (that is sg related to changes happening over time) I have to understand what time is and how it is structured that lead me to have another masters in analytical philosophy with a lot of modal logic involved, and my thesis work was entitled “Partial immortalization and the philosophical problems of human biotechnology and regenerative medicine”, basically delineating a technologically foreseeable scenario of unlimited life span and its social context

3. philosophy and timing lead me to journalism/blogging on aging and life extension and that is a separate skill set definitely, let alone an, independent, self-nurturing profession, discovered here my peers interested in the same thing

4. with the rise of stem cell research and regenerative medicine went back to the wet lab and started a PhD, did everything there except finishing the damn thesis, was mainly working on mitochondrial transfer between healthy stem cells and cells in oxidative stress, turns out the energetic reboost by healthy mitochondria can be an alternative way of how injected stem cells regenerate the injured/aged host tissue, to sum up experimental science gave me the insight that stem cells/regmed + mitochondria can be crucial in life extension technologies

5. blogging made me geeky and technologically involved and the rise of systems and omics biology made me realise that aging can be best understood by computational biology or by bioinformatics tools, built some stuff on genes related to aging as my first serious coding assignment

6. learned the basics of coding and turned myself into a bioinformatician in 2009, this is the last and so far most promising chapter in my quest, here I currently have at least 2-3 pet projects related to aging

So in order to understand aging and work on life extension I learned and practised wet lab biology, philosophy, journalism/blogging, coding and bioinformatics all motivated by the same, but continuously redefined aim, looking at it from many angles.

Jack of all trades, master of none? Mostly true concerning the fact that I had worked intensively in these particular fields only for 3-4-5 years. But since bioinformatics as a profession has now found me and since I’m in my late thirties I can’t help mastering it finally. :) Concerning personal investment into aging/life extension: that’s ~ 20 years already.

In a way being motivated & triggered by a big, complex, larger-than-life topic like life extension is a burden (might be harder to go into details when overshadowed by a big idea), but on the other hand it gives me a constant motivation and demand. As a bonus focusing on aging is a person-against-nature thing and not a person-against-person thing (like law as a profession) and somehow this always helped me not to take competitive situations too seriously and follow my inner compass.

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 gadgets like heart rate monitors, blood pressure cuffs, scales and blood-sugar measurement meters, allowing the devices to communicate with a PC and feed real-time medical information directly into Google’s online records.

Hooking up those devices to the Web, IBM argues, will offer a new immediacy and granularity of health monitoring. A user can remotely track the blood pressure readings or glucose levels of a diabetic parent living alone, or stream his or her medical information like weight or heart rate directly to a doctor or physical trainer.

“If there’s something abnormal, you can catch it before you have an episodic intervention, like going to the emergency room,” says Dan Pelino, manager of IBM’s health care division. “This is like OnStar for a patient, keeping constant information about you and sending alerts even before you have a problem.”

More on Google Health on Pimm:

Meet Dr. Google Health: Roni Zeiger, right from Stanford!

Google Factory Tour of Health: watch the pivotal moment!

FriendFeed comments: The hidden backyard

Late Google Health: catching up with the past, first!

A bit of history: The official launch of Google Health, 19/05/08

Are life extensionists mainly driven by a desire to actually live a long time?

How do you interpret the following situation: we have a life extension technologist whose all endeavors is about pushing this issue to its very limits and making things possible but on the other hand this very life extensionist himself is not driven by actually living as long as he can.

It seems that SENS theorist Aubrey de Grey, who is chronologically 45, (BioBarCamp photo by Ricardo) is taking roughly the above position in a recent interview. Aubrey is a good and witty interviewee and of course the interpretation of what he is saying is strongly context dependent so here is the full question and answer:

Question: One hundred years of life can wear you down physically, but it can also wear you down emotionally… perhaps even existentially. For you, is a desire to live long accompanied by a desire to live long in a much-improved human civilization, or is this one satisfactory?

Aubrey de Grey: I’m actually not mainly driven by a desire to live a long time. I accept that when I’m even a hundred years old, let alone older, I may have less enthusiasm for life than I have today. Therefore, what drives me is to put myself (with luck) and others (lots and lots of others) in a position to make that choice, rather than having the choice progressively ripped away from me or them by declining health. Whether the choice to live longer is actually made is not the point for me.

Let’s see 2 possible and extreme interpretations of this answer (neither of them is my own interpretation) and I hope my readers can find fine-tuned arguments in between while thinking a bit about this still rather philosophical topic:

1., Saying that we want the process (a robust healthy lifespan technology) but not necessarily the product (a robust healthy lifespan) of our own business is a disaster Continue reading

“blogs.nature.com v1 is live” and beyond

A new, completely rewritten, integrated nature.com website blogs.nature.com has been launched by the Natureplex people – informed his Twitter pals Euan Adie:

Also, blogs.nature.com v1 is live! Tequila and donuts all round. Early n’ often release v2 coming on the 18th so get any bug reports in now.

natureblogs

Suggest good science blogs that are not listed on the Nature Blogroll yet.

Poll: How will the global economic crisis affect the chances of technological life extension within the next 25 years?

assuming we are heading into a global economic crisis…

Mountain View – Budapest: 20 days to get my 23andMe profile!

I ordered my first commercial genetic profile from 23andMe on the 9th of September online, FedExed my 2 ml saliva from Budapest to 23andMe, Mountain View on the 12th of September. I got the results today. That said within 3 weeks since the birth of the idea I purchased more than 500 000 SNPs of mine analyzed, evaluated and ready to be browsed. With this step I finally and quickly entered into the age of personalized genetics no matter how embryonic it is.

After a superficial first scan of my results I can say that it is a really interesting thing that instantly pushes me towards accumulating more knowledge on the personalized genetics field concerning specific traits, stats, risks and studies.

Here is a first look on what my Y chromosome SNPs are saying on my paternal haplogroup:

I learned for instance that based only on my genotype and not any environmental factors involved I have a lower than average risk Continue reading

Science X2 signals: big pharmas, stem cells, mobile MRI

The Institute for the Future‘s X2 project is all about tracing future trends in science and technology As the steward of the Biomedical Sciences and Biotechnology Group I collect signals in these fields on which some forecasts can be based later on. Here are some issues I found future sensitive enough recently:

GlaxoSmithKline collaborates with the Harvard Stem Cell Institute

Pfizer’s growing and various interests in stem cells

Regaining vision with gene therapy using adeno-associated viruses Continue reading

Even ugly handwriting can fit the informal nature of SciFoo

I had problems with my handwriting since elementary schools, or at least my teachers had continuous problems with it. Even during my university years I was asked sometimes to read out loud my essays, papers to them otherwise risking bad grades. Maybe it’s because I am a hidden right-handed using my left hand for writing or maybe I am just too impatient over the slow pace of handwriting (needless to say computers mostly solved this problem).

On this George Dyson photo here you can see the SciFoo schedule in progress and I think you can easily pick the one with the ugliest handwriting on Aging and Life Extension:

Sergey Brin, Gly2019Ser & a real chance against Parkinson disease/aging!

It was already known that amongst the Google top people Sergey Brin is the one who is most interested in pushing biotechnology and the biomedical sciences: in his Stanford years he was interested in biology courses according to The Google Story, he married Anne Wojcicki (who graduted from biology at Yale), Google invested $4.4 million into 23andMe the pioneering personal genomics company co-founded by Anne, then Google invested into 23andMe competitor Navigenics too.

Now Sergey Brin added another, serious and personal reason to think that he is really, personally committed to the quick progress in the biomedical sciences: in his new blog – already a bit of an Internet history – called Too he disclosed that using the 23andMe personal genetics service he figured out something worrying about his and his family’s risk of Parkinson disease (his mother and her aunt are being already diagnosed with PD):

“I learned something very important to me — I carry the G2019S mutation and when my mother checked her account, she saw she carries it too.
The exact implications of this are not entirely clear. Early studies tend to have small samples with various selection biases. Nonetheless it is clear that I have a markedly higher chance of developing Parkinson’s in my lifetime than the average person. In fact, it is somewhere between 20% to 80% depending on the study and how you measure.

The G2019S mutation is actually the rs34637584 SNP and lies in the gene LRRK2 encoding leucine-rich repeat kinase on chromosome 12. The mutation affects the first codon of the gene and is a guanine (G)-to- adenine (A) substitution resulting known as a missense and  leads to a glycine – serine (hence the name) amino acid conversion in the protein product. Here is how the SNP position looks in the 23andMe browser using the sample family, the Mendels.



23andMe’s amazingly good corporate blog The Spittoon cited a recent article about the chances: Continue reading

My personalized genetics: 2 ml saliva FedExed to 23andMe!

As the second operation of building my genetically well informed future yesterday (2 days after completing the order) I collected 2 ml of my saliva with the help of 23andMe’s Oragene DNA self-collection kit manufactured by DNA Genotek. First operation has been the sequencing of the D-loop of my mitochondrial DNA out of 5 ml of saliva in the lab at Tulane as a last control experiment, more on that later.

I’d be curious to know approximately how many people in Hungary or in Central Europe, or in all Europe have already used personalized genetics services like 23andMe or the Iceland based deCODE genetics’ genotyping services. As the whole industry is less than 1 year old (starting November 2007) there are not too many public stats available or at least I haven’t found any. With the recent (8th Sep) announcement of the modest $399 kit price reduced from $999 the pioneering personalized genetics service is now affordable for a lot more people, like me (compare it to the $600 iPhone early adopter fee, which I was unable not to buy). Continue reading

The marketing problem of life extension technologies

If “Science has a really serious marketing problem” as Larry Page observed, then life extension technologies face even bigger marketing problems. I am definitely not a marketing expert but realized the problem early on when thinking about the lag-phase period of a robust life extension technology.  So I made a short email interview with Dave Gobel, the marketing and business mind/strategist behind the Methuselah Foundation (official title: Chief Executive Officer) following our meeting and chat at the SENS3 conference in Cambridge, UK, 2007.

1. What is the biggest marketing problem of any future (or present) healthy life extension technology?

The biggest marketing problem today is the time it takes for a beneficial effect to present itself. For instance, a product such as resveratrol may take months to present beneficial results, or it may never show up clinically. People who are scientifically sophisticated can appreciate the value of reduced circulating fats or glucose, but to the typical individual, there are much sexier things to spend money on that give immediate gratification and clear utility. The proof of this is illustrated by a counter example – how ridiculously easy it would be to sell a product that biologically reversed grey hair. The effect might be seen gradually but incontrovertably by all and in the mirror directly.

It seems to me that the best way to proceed from a business standpoint therefore is from the outside in. Create legitimate products that improve a person’s visual image and therefore social standing and they will flock for the result. Try to engineer those products to have globally beneficial effects, and marketing becomes easy.

So, for the present, the problem is delayed, and difficult to pinpoint results in exchange for expensive pills/treatments and never ending taking of pills. What about the future? The problem of marketing will evaporate as tissue engineering provides an immediate benefit by eliminating hip, knee and similar pains while restoring or even improving base functionality. When biologically matched teeth can be implanted and grown anew in gums, marketing will be easy.

2. How to market life extension for different generations (teenagers, college students, young adults, mature adults, grandpas and grandmas) and what are the main differences here? Continue reading

Life extension people & session at SciFoo 2008, Googleplex!

Last year I was probably the only SciFoo Camper with an explicit life extension commitment. I suggested & held a session which was related a bit to partial immortalization but was rather about the systems biology perspective in general, illustrated with some examples. So throughout the terrific SciFoo Camp 2007 life extension as a conversation topic remained rather implicit (ok, close to zero) and there was not much room to discuss it in the lack of other fellow life extensionists.

In my opinion the whole point of unconferences is to form the good aggregate of people with a common interest & similar/complementer message to join forces in order to draw enough (intellectual) attention for their topic. In this context, an unconference is about topics at the first place, not just about people. Idea networking is as important as social networking.

And if something fits 100% with the idea of SciFoo it is life extension/aging just as handling terrantic scientific datasets, open science or climate change as all these topics are utterly complicated and quite urgent screaming for the attention of the smartest people.

So I emailed Timo Hannay, SciFoo organizer:

“One thing I’ve noticed is that it would be very good to organize a session on scientific life extension technologies and consequences, because the SciFoo people are ideal to see and discuss all angles of this really important topic.”

And…..here is a session suggestion for SciFoo Camp 2008: Continue reading

Hourglass, a blog carnival devoted to the biology of aging

Finally Chris over at Ouroboros came up with the idea and the quick implementation of Hourglass, a blog carnival devoted to the biology of aging/biogerontology.  For some reason I am not an explicit supporter of blog carnivals – many of my posts were chosen by carnival editors but I never hosted one -, but Hourglass will be the big exception in which I participate, submit posts and host it later. The reason: first it presents aging/biogerontology related posts, which fits my profile and second it was instigated by Chris Patil, whose work is a guarantee for keeping all this in the good direction. So if you want to read on the evolution of longevity and aging, calorie restricition, stem cells/tissue engineering/regenerative medicine, or on the association of long life and intelligence at once, Hourglass is for you.

Understanding Aging Conference is over but it is the end of the beginning

I try to cover some interesting, sciencey points on the conference in later posts, right now just a brief, subjective human- and strategy focused summary:

Congrats to Aubrey de Grey and the team, everything went well and if finally a worldwide consensus is around the corner claiming that robust healthy lifespan extension is technologically possible and worth achieving it is largely due to Aubrey’s relentless networking, organizing activity and American like pushy marketing strategy! Well done!

Had a nice chat with a diverse bunch of interesting people amongst others: Barbara Logan, Nason Schooler, Todd Huffman, Betty Liu, the startupper Andregg brothers, Mark Hamalainen, Keith Causey, Ben Zealley, Brian Martin and sure I forget to mention many more here.

In the photo (thanks Barbara Logan): Neal Van De Ree, Florida auctioneer and activist, John Furber, Legendary Pharmaceuticals, Florida, Aubrey, Paul Logan, Alex Zhavoronkov, GTCBio, BioGerontology Research Foundation Damian Crowe, Genescient, BioGerontology Research Foundation and yours truly.

Conference photo via Bruce Klein: Continue reading

Going to LA to end aging for 3 days & maybe more

It is just good to go to a conference where the overwhelming majority of attendees think (and many of them act) that by science & technology we can actually get rid of aging related health problems and develop a robust life extension technology. I sense a lot of freedom here which I sense since the age 15 but now – thanks to Aubrey de Grey – this is all happening in a community (with a diverse chronological age distribution) that is becoming more established and more funded. Whether this is only a freedom to do something or also a freedom from a constraint or from interference… well you are free to decide it dear readers.

The “Understanding Aging: Biomedical and Bioengineering Approaches” conference will be held from June 27-29, 2008 at UCLA organized by Aubrey de Grey, Irina Conboy and Amy Wagers.

The emphasis this time (just check the coorganizers Conboy and Wagers) is on stem cell research and regenerative medicine, which I think is the only coherent engineering concept outside for robust life extension in the form of systemic regenerative medicine while SENS by definition (strategies) is a flexible enough umbrella term to include other coming life extension technologies and concepts under its brand.

In the age of Twitter and FriendFeed the blog genre is just too slow to cover the event, so I use the FriendFeed room for the conference as it seems to be a perfect place of live microblogging the conference, sharing any kind of links, videos, comments, feeds and feedbacks. I hope others will make it too.

Alexis writes on Wired: Continue reading

Petabyte Age Wiredesque lesson on what science can learn from Google

I argued many times here that biology based biotechnology is the next information technology but in order to do so, biotech should harness good IT patterns and mimic its massive computing practices to handle the enormous amount of constantly accumulating data. Often this trend could be summarized in a simple way: keep your eye on Google and conduct thought experiments in advance in which science is done in a Googleplex like environment in terms of the computing & financial resources and algorithm heavy engineering culture. Use Python and learn cluster computing and MapReduce. With the expected launch of the massive scientific dataset hosting Google service – nicknamed Palimpsest – this year finally a direct interface between scientists and Googlers emerges and hopefully opens up possibilities for scientists to cooperate with Google. (Remember my joke on Google BioLabs back in 2006)? I get emails from biologists, bioinformaticians asking me how to be hired by Google ever since then. As I tweeted yesterday: I growingly have the impression that “being ambitious” today = ‘worked, is currently working, is going to work at/for Google’ Taking Google’s inter-industrial power into consideration I see a real chance that some day the “Google of Biotechnology” title goes not to a startup yet to be emerged, not to Genentech or to 23andMe but……to Google itself. No kidding here. Fortunately Google’s model is “to build a killer app then monetize it later” says Andy Rubin, the man behind Google’s Android mobile software in the July issue of Wired so scientists working for the big G probably won’t have to worry about turning their scientific killer app into an instant cash machine.

And now in the very issue of Wired magazine (not online yet ) there is an exciting cover story on the same pattern I talked about concerning the life sciences but in the broader context of every kind of science with the provocative, Fukuyama-like title The End of Science. There is a witty and short essay from editor-in-chief Chris Anderson entitled The End of Theory followed by examples of the ‘new science’ like the The Large Hadron Collider expected to generate 10 petabytes if data/second, The Sloan Digital Sky Survey heaven catalog maker accumulating 25 terrabytes of data so far, the skeleton scanning project of Sharmila Majumdar and the Many Eyes project “where users can share their own dynamic, interactive representations of big data”.

For many people around the globe, Chris Anderson is a freeconomist & the author of a popular airport book but fewer people are aware that he was actually trained as a (quantum) physicist and even worked at Los Alamos Continue reading

Understanding Aging Conference on FriendFeed!

The “Understanding Aging: Biomedical and Bioengineering Approaches” conference will be held from June 27-29, 2008 at UCLA organized by Aubrey de Grey, Irina Conboy and Amy Wagers. I like to call it UndertsEnding Aging in myself and I am excited to go to LA and meet new people also people from SENS3.

Yesterday I created a FriendFeed room for the conference as it seems to be a perfect place of live microblogging the conference, sharing any kind of links, videos, comments, feeds and feedbacks. Working on aging and the postponement of it (you can bravely say life extension) is always a pioneering work so it’s time to use pioneering web apps for that purpose, just like FriendFeed.

Aubrey de Grey, Kevin Perrott and Kevin Dewalt have already joined the room. What about you? See you on FriendFeed, see you on LA!

Short Twitter/FriendFeed chat on life extension

I asked the following question on Twitter recently:

“A question for all of you Twitterers: Are you for, against, or just neutral on healthy life extension? How long would you like to live? Why?”

I have to tell you it’s hard to give good links to the whole chat without noise. Maybe on FriendFeed.

To my big surprise, many people were neutral about life extension using different arguments & beliefs and those are all smart, well informed geeky persons, many of them biologists.

On the other hand it’s hard to formulate an exact question in 140 characters and to give a good specification on exactly what type of healthy lifespan extension is addressed.

But nevertheless the conclusion for me is that life extensionists should pay a bigger attention to all the ‘neutral’ – ‘pseudo neutral’ arguments. A pseudo neutral argument could turned out to be a for- or anti- life extension argument after a thorough analysis.

Embedding the Future: the X2 Project goes public!

With the public launch of the X2 project, Alex Soojung-Kim Pang realized one of his dreams. Alex is the research director of The Institute for the Future (IFTF), an independent nonprofit research group headquartered in Palo Alto, Silicon Valley. He writes:

The project is called X2, and its aim is to forecast the future of science, technology and innovation. The name may sound like science fiction, but it’s actually an historical allusion. In my previous life as an academic historian, I studied the X Club, a group of Victorian scientists who were very interested in the future of British science. The Club formed when its members were still young, ambitious outsiders, fighting to establish their reputations in a world in which social connections and privilege mattered more than scientific achievement; by the time they retired, its nine members were among the leaders of British science.

That said, dear ‘still young, ambitious outsiders’ you can now sign up for the project and join the groups you’re interested in. I suggest you starting with Quick Start. Disclaimer: I am the so called “steward” of the embryonic group Biomedical Sciences and Biotechnology. Continue reading

BioBarCamp in the Valley before the SciFoo Camp!

It seems that my favorite ever unconference, the SciFoo Camp will be aroundunconferenced by a BioBarCamp this year. The whole idea of the BioBarCamp is based upon the SciFoo Camp, so it is by no means a competitive but a complimentary event.

From the BarCamp wiki: “The BioBarCamp is an idea (fed by the tweets of the BioTwitterer community) to organize a life sciences – biotechnology – personalized genomics & medicine – bioinformatics unconference at the Bay Area around the 3rd SciFoo Camp time, which is 8-10th August. The SciFooCamp generates a lot of enthusiasm & activity but not just for those who are invited (only 200). On the other hand, it would be nice to organize a bio-related BarCamp, just like the Cambridge BarCamb, in which the bio-related SciFoo Campers and all the other biogeeks could gather together.”

The main activity is happening right now at the public BioBarCamp Google Group. If interested please join there or just follow the discussions. We are right now in the process of finding a proper venue and sponsors and any help would be most welcome. Right now 6 or 7 August seems to be the consensus day and we have a very generous offer from The Institute for the Future via Alex Soojung-Kim Pang in Palo Alto (no response from 23andMe so far, see below).

It’s against a classic Twitter story, just like this before. You can reconstruct the whole conversation with Twitter Search Engine Tweet Scan by searching for terms SciFoo, BioBarCamp, SciBarCamp but here are my selected tweets:

Scene One, 04/10/08 How the idea was born on that day in reverse chronological order:

Scene Two 04/22/08 How the biospecificity and name was born alongside with a possible venue idea: Continue reading

3rd SciFoo Camp, Googleplex, August 8-10, 2008!

The 3rd Science Foo Camp, organized by Nature, O’Reilly Media, and Google will be held on August 8-10 and hosted at the Googleplex in Mountain View, CA.

From the mail: “Now in its third year, Sci Foo is already achieving cult status among those with a passion for science and technology. The Economist said that it “capture[s] the essence of innovation”; in a photo essay for Edge, George Dyson wrote of the “the impossible choice” when deciding which sessions to attend; another attendee described it simply as “The best gathering ever. Period.”

Also check the strongly related BioBarCamp idea.


Human proteome project: 21000 genes/1 protein, 10 years, $1 billion?

In order to have the slightest change to design a robust, systemic life extension technology, we need to accumulate every systemic macromolecular, cellular, tissue- and organ level data of the normal, physiological human body, connect the trillions of nodes with scalable software algorithms and suck out the draft of the proper sequence of consecutive treatment/regeneration steps later. Fortunately not only life extension technology needs systems biology projects (this is not enough for getting grants), but more importantly the effective design of new drug targets and the discovery of disease biomarkers are clearly crying for the systemic level. The urgent diagnostic and therapeutic demands are sufficient to launch international, many-lab projects.

Finally a complete ‘Human Proteome Project’ is in the pipeline (illustration via BioMed Search). It aims the tissue-level complete knowledge of the human proteome revealing “which proteins are present in each tissue, where in the cell each of those proteins is located and which other proteins each is interacting with”. Keep in mind also that around 21’000 human genes encode 1 million different proteins and that the effort cannot localize exactly which cell types in a given tissue is producing which protein. According to Nature’s Helen Pearson: Biologists initiate plan to map human proteome

“Those involved in the draft plan say that a human proteome project is now feasible partly because estimates of the number of protein-coding genes have shrunk. It was once thought that there might be around 50,000 or 100,000, but now, just 21,000 or so are thought to exist, making the scale of human proteomics more manageable. And the group plans to focus on only a single protein produced from each gene, rather than its many forms.

The plan is to tackle this with three different experimental approaches. One would use mass spectrometry to identify proteins and their quantities in tissue samples; another would generate antibodies to each protein and use these to show its location in tissues and cells; and the third would systematically identify, for each protein, which others it interacts with in protein complexes. The project would also involve a massive bioinformatics effort to ensure that the data could be pooled and accessed, and the production of shared reagents.”

The idea is to analyze and list all the proteins manufactured by chromosome 21 within 3 years as a pilot study and then finish the whole project within 10 years. Chromosome 21 is the smallest child in the family and likely contains between 200 and 400 genes, so the pilot study can yield us a couple hundreds proteins. Another powerful idea (actually I prefer this) is to start with the human mitochondrial proteome which is around 1000-1500 proteins as far as I know, that is at least 3 times as many as encoded by chromosome 21. Continue reading

Thesis live: 1.2 Kidney and stem cells

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.

1.2. Tissues, organs with different turnover and regenerative potential
In the adult kidney the nephrons (approximately 500 000 nephronic units/kidney) develop from the metanephric mesoderm/mesenchyme while the collecting ducts are coming from the ureteric bud. The kidney is a complex structure with at least 26 different cell types. The renal function is particularly age-dependent (loss of functional renal mass up to 25%). The kidney is an active tissue with high energy demand and contains a lot of mitochondria (especially in the proximal tubules). On the other hand, while the turnover rate is low, there is a robust although limited regenerative response to acute kidney injury. The candidate cellular sources of recovery, replacement: adjacent, less damaged tubular cells, resident adult kidney stem/progenitor cells and circulating mesenchymal cells from the bone marrow. Amongst others the following cell surface markers were used for isolating/enriching stem cell/multipotent renal progenitor populations: CD133, stem cell antigen-1 (Sca-1), CD24, CD90, Pax-2, Oct-4, Rex-1 (see table).

One such population was isolated from the cortical interstitium making up 0.8% of all cortical cells and were capable to differentiate into epithelial and endothelial like cells in vitro forming tubular structures in SCID mice [Bussolati et al, 2005]. In the lack of definitive markers of kidney stem cells not much certain could be said on the kidney stem cell niche.

Literature: Gupta S, Rosenberg ME. (2008) Do Stem Cells Exist in the Adult Kidney? Am J Nephrol. 19;28(4):607-613

Percy CJ, Power D, Gobe GC. Renal ageing: changes in the cellular mechanism of energy metabolism and oxidant handling. Nephrology (Carlton). 2008 Apr;13(2):147-52.

Bussolati B, Bruno S, Grange C, Buttiglieri S, Deregibus MC, Cantino D, Camussi G. (2005) Isolation of renal progenitor cells from adult human kidney. Am J Pathol. 2005 Feb;166(2):545-55.

“What is the meaning of life?” for a life extensionist

In No kidding, I am a cum laude philosopher, and so can you! it turned out that finally I got a philosophy diploma. That said, from now on I am officially qualified to think on the big questions of life. For instance, I can find out new arguments and concepts and I can answer (or at least fine-tune) questions like: ‘what is the meaning of life?’. (The best analysis of this question for me was Robert Nozick‘s Philosophy and the Meaning of Life in the last chapter of his book Philosophical Explanations, for an official intro see Stanford Encyclopedia of Philosophy)

So here is a short analysis and an answer of mine to this most important philosophical question from the point of view of a life extension supporter:

1. premise: this question could be answered only if it not about the general meaning of all life, but the particular meaning of individual human lives.

2. analysis: let’s fill the question up to show the variables in it: ‘what is the meaning of an individual human life (x) for somebody individual (y)?’ Continue reading

36 Life extension idea killers: mental practice for the pros!

Today’s meditation is for serious healthy life extension supporters to consider the following 36 – general and sometimes corporate – idea killers concerning our little project:

1. We tried that already
2. We’ve never done anything like that before.
3. Has anyone ever done anything like that before?
4. That never works
5. You’re fired
6. We will actively work against you
7. Laughter
8. Not in our budget
9. Not an interesting problem
10. We don’t have time/We’ll never find the time to do it. (I specially liked this one.)
11. Execs will never go for it
12. Out of scope/Not in our business
13. But its the law
14. Too blue sky / Holy grail
15. Wont make enough $$
16. That isn’t what people want
Continue reading

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.

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

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

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 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

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.

Why was life extension ruled out of the 14 Grand Engineering Challenges?

questionmark1I emailed some of my life extension supporter friends because I think we have a ‘future’ situation:

Healthy life extension is not 1 out of the 14 Grand Engineering Challenges…that can be realistically met, most of them early in this century according to the Committee on Grand Challenges for Engineering with members such as Larry Page, Dean Kamen, Craig Venter, Robert Langer and …lifestyle life extensionist, nanovisionary Ray Kurzweil. There is a challenge though called Engineer better medicines and the essay behind looks as if it had been hacked together by Kurzweil and Venter themselves during a sunny Californian Soy Beer Baby Boomer Beach Party. It is about personalized medicine in large and the only hint – I was able to find – to a recent discipline named regenerative medicine is a paragraph, not on, say the challenge of systemic regmed, but on synthetic biology.

It is a big challenge to learn how could healthy lifespan extension as a big and realistic challenge have been left out? Why did Kurzweil (author of the book Fantastic Voyage: Live Long Enough to Live Forever) not stand up for it? Why nobody out of the luminaries thought that regenerative medicine and stem cells worth discussing more than a tiny side note? And what about Venter, whom I still like to be interview as there are many points in his activity suggesting a life extension connection. Somebody in the committee was clearly against it?

One friend told me that he is not surprised by this, because it was announced at the AAAS meeting, which is very conservative. Out of the committee members Ray Kurzweil, Daniel Hillis, and maybe Dean Kamen would have been supporters of including LE as a challenge.

But. Continue reading