Can you tell a good article from a bad based on the abstract and the title alone?

Many times people only have access to the abstract of peer-review articles, and nothing more. There are different abstract styles (sometimes they’re going too far or on the contrary) in the literature and I’d be curious to hear about your opinion on the following review abstract and title. I became interested and suspicious reading these lines especially the one highlighted in bold.

Mitochondria, the missing link between body and soul: Proteomic prospective evidence.

My iPhone 2.0 wish list: from the RFID reader/writer to the solar panel!

According to the Wikipedia approved rumor by the AT&T boss: “A new version of Apple’s iPhone will be introduced in 2008 that is capable of operating on faster 3G cellular networks.” Besides the 3G support I have some other expectations (at least 6 should be satisfied) too in order to become a next generation iPhone upgrader:

hardware:

- built in RFID reader/writer: because I’d like to buy and order without standing in line. Also a bit experimental RFID hacking with things around me, like opening the hotel room with a cream cheese box must be fun. (I would wire the RFID modul in the place of the Bluetooth modul on the motherboard) see: Will the Apple iPhone be RFID powered?

- video out to use the iPhone with projectors: giving presentations on science conferences and seminars with my SciPhone and watching movies back at home with my wife.

- GPS (although I am quite satisfied with the Google Maps Mobile): in the car and on the bike.

- video recorder: basics

- video telephone: just for fun

- longer battery life: a must

- solar panel: for climate change

software:

- Skype enabled: do I need to explain it why?

MitoWheel 1.0: the human mitochondrial genome just got visual!

Your 16569 basepair long human mitochondrial genome does a lot for you and tells a lot about you. It encodes protein subunits playing crucial role in the production and conversion of ATP, the body’s main chemical energy currency. On the other hand the actual sequence of one’s mitochondrial DNA in a particular tissue or cell population gives a lot of health associated (mitochondrial diseases, aging) and ancestry information.

So far users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA. But now with MitoWheel version 1.0 (yes, it is beta) the situation is about to change. From now on you can spin MitoWheel and play MitoRoulette (details on the game later)! MitoWheel is a graphical representation of the circular human mitochondrial genome, hence the name. The sequence used is the standard Revised Cambridge Reference Sequence. The 3 main components of the app is: a search box, a sequence bar and the wheel.

MitoWheel is the brainchild of Gábor Zsurka, a human mitochondrial geneticist we’ve already met in the post on The power links of the mitochondriologist. Gábor has been doing 100% of the programming too. Disclaimer: With some suggestions and testing I qualified myself to become a member of the developer team! The wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript , a scripting language designed specially for Flash.

What are the basic things you can do with MitoWheel, if you are a scientist in the lab or a student in the seminar or just a tech geek eager to learn biology?

- spin the wheel: browse the genome by clicking the left and right arrows in the sequence bar

- search for a nucleotide position or sequence in the search box with numbers: input: 15450 output: T

Xoogler goes biotech

I found this quote in John Battelle’s blog from a recent CNET article on ex-Googlers by Stephanie Olsen, but I’d like to repeat it just with a different emphasis as I found all the other parts interesting for the biotech community except the one sentence bolded by Battelle. So I bolded those parts:

The Spittoon: the eminent corporate blog of 23andMe and Consumer Enabled Research

The personal genomics service 23andMe just launched publicly a corporate blog called The Spittoon that has been internally up for a few weeks. It is a new chapter in biotech corporate blogging. Just like the web page of 23andMe, The Spittoon’s WordPress blog platform, the concept and design is excellent: amongst others you can find scientific blog posts written by Matt Crenson science writer and posts written by founders Linda Avey and Anne Wojcicki in the name of radical transparency. As Wired fellow Clive Thompson wrote:

Radical forms of transparency are now the norm at startups – and even some Fortune 500 companies. It is a strange and abrupt reversal of corporate values. Not long ago, the only public statements a company ever made were professionally written press releases and the rare, stage-managed speech by the CEO. Now firms spill information in torrents, posting internal memos and strategy goals, letting everyone from the top dog to shop-floor workers blog publicly about what their firm is doing right – and wrong. Jonathan Schwartz, the CEO of Sun Microsystems, dishes company dirt and apologizes to startups he’s accidentally screwed. Venture capitalists now demand that CEOs be fluent in blogspeak.

Radical transparency could be standard in the case of Silicon Valley tech startups but in the Biotech Industry the standards are light years away from that. For instance the 23andMe research team communicates publicly on the biparental inheritance of mitochondrial DNA which is a sensitive issue concerning their genealogy service. The reason why Spittoon is so web-friendly and uptodate and is in fact a paradigm corporate blog for every other biotech company in the future is its web-based business model and Google-like corporate culture thanks to its networking background.

For instance, Anne Wojcicki co-founder introduces the concept of Consumer Enabled Research in her introductory blog post The Power of We:

Our goal at 23andMe is to enable individuals to form communities around shared interests and to empower those communities to be actively involved with research. We call it Consumer Enabled Research. We don’t just want communities to have a voice, we want to provide a platform for them to collectively aggregate their genetic information. One of the significant bottlenecks in research is the lack of data. Researchers and physicians rarely have enough of it to really understand a disease or how to treat it. Our goal is to change that.

After registration readers can make comments and I strongly hope that the comment system will not be shut down (just like in the past at BoingBoing), but for that commenters should be on-topic and moderate. I’ve just commented Wojcicki’s post, but I’d like to share it with you here too:

9 year old stem cell trial pioneer dies in Batten disease

This is exactly the type of clinical trial news that should be taken extremely carefully with all due respect and grief.

A girl enrolled in a stem-cell trial for a fatal disease has died. In January, the nine-year-old received a brain transplant of neural stem cells derived from fetal tissue. She was one of six children in the trial for Batten disease, in which children rarely live into their teens. An independent group monitoring the trial decided that the death was due to the disease not the experimental treatment and said the trial could continue.

The quote is from Monya Baker’s Niche post.

From the press release on StemCells Incorporation’s Phase I clinical trial of its proprietary HuCNS-SC^®product candidate (purified human neural stem cells):

The trial is designed to evaluate the safety and preliminary efficacy of HuCNS-SC cells as a potential treatment for infantile and late infantile neuronal ceroid lipofuscinosis (NCL). NCL, which is often referred to as Batten disease, is a rare and fatal neurodegenerative condition afflicting infants and children.

The patient, a nine-year-old girl, was transplanted with HuCNS-SC cells in January 2007 and was due to return this month to the trial site, Oregon Health & Science University’s (OHSU) Doernbecher Children’s Hospital, for her 12 month follow-up. She was hospitalized nearly two weeks ago, suffering from an apparent viral infection, seizures and respiratory distress before succumbing earlier this week.

induced Pluripotent Stem cells from a 69 year old human: the hidden story?

The successful reprogramming (dedifferentiation) of differentiated human somatic cells into a pluripotent, embryonic stem cell-like state called induced pluripotent stem cells (iPS) using just 4 (and recently 3) introduced transcription factors is the biggest news of current stem cell biology. In the paper published in Cell by the Yamanaka group (Takahashi et al.) the iPS clones derived from the facial dermis of a 36-year-old Caucasian female were highlighted. Out of 50 000 retrovirally transduced fibroblasts 10 hES cell-like colonies were observed. But what I found really thought provoking (and poorly discussed in the blogosphere) is that with the same approach iPS cells were generated from the synovial tissue of a 69-year-old Caucasian male. Interestingly out of 50 000 modified cells 17 hES cell-like colonies were found. This finding could easily be relevant from a stem cell aging point of view.

During ageing there is an overall decline in tissue regenerative potential, but it is not clear whether it is due to the intrinsic exhaustion of the adult tissue stem cells or the diminished functionality of the stem cell niche or a change in the systemic milieu. Answers could be different – tissue by tissue.

But if a terminally differentiated connective tissue cell, like the synoviocyte above could be completely reprogrammed from a 69 year old, otherwise health individual into a pluripotent state….well it could it be interpreted as an argument against the cell-intrinsic genetic aging program in adult and aged connective tissues with some cautions.

Caution 1: What if the source of the iPS cells were not really terminally differentiated, but undifferentiated stem or progenitor cells coexisting in fibroblast culture. This problem has been discussed in the paper and forms the Achilles’ heel of it.

Caution 2: The reprogrammed iPS cells from an aged person are behaving the same way as the iPS cells from a younger person with no additional cellular aging characteristics.

As the critical tail of almost every peer-reviewed paper used to say: Further study is needed.

Here is the paragraph on the synoviocytes and the tables and figures are in the supplemental data.

Craig Venter and the life extension drive: blogterview questions

One strategy (call it Life Extension Gets Personal) to raise awareness for the idea and technology of healthy life extension is to publicly encourage life extension “coming outs” on behalf of mainstream celebrities. In order to get an academic legitimacy for LE (which is one of the most important aim of Pimm) I am interested specially mainstream or at least well established scientific celebrities. To accomplish this project a man needs to identify target persons to interview (finding hints that the person is positive about LE), contacting these persons and publish the final piece somewhere.

As a first target Craig Venter, the genomics pioneer seemed unconventional and free minded enough to approach with the idea of a LE blogterview. On the other hand I found definite signs of his interest in longevity and life extension suggesting that if Craig Venter had been given a technological-medical chance to extend his healthy lifespan significantly he would definitely not like to die due to accumulating functional declines associated with aging within the next, say hundred years. Maybe I am wrong here, maybe I am not but to figure this situation out I translated these signs into the following blogterview questions and tried to contact him in early December, 2007. So far I reached only his nice and diplomatic PR agent, who said that maybe we have a chance to get the blogterview done in the near future. Till we get there below please find my targeted questions to Craig Venter:

1. Once I’ve read somewhere but was unable to recall later that one particular motivation behind the sequencing of your own genome was your serious life extension commitment and the belief that genomics has something to say about life expectancy. Is it true? If yes, what is the story of your life extension commitment? Is it a commitment for moderate or maximum life extension? In A Life Decoded I’ve found only one paragraph in your molecular biography explicitly on Long Life about the I405V of the CETP gene but no more hint to this important topic.

2. What do you think about Aubrey de Grey’s SENS approach? You’ve been one of the judges on the The SENS Challenge Prize organized by the Technology Review in 2005 for those “who could prove that SENS was “so wrong that it is unworthy of learned debate.” ? Who got the point there?

3. What do you think about the mitochondrial theory of aging? I was a little surprised when I’ve found that your circa 16.5kb mitochondrial DNA sequence was not published in the PLOS Biology paper: The Diploid Genome Sequence of an Individual Human Obviously it is not part of the diploid genome but I expected it at least as an appendix as those 37 genes and D-loop region can give important genetic information. Have your mitochondrial genome been sequenced already?

4. In a recent Rolling Stone interview you are saying that “There is probably nothing more important to study about human biology than stem cells.” What do you think about regenerative medicine’s role in a robust and healthy life extension technology?

Out of 8 embryo cells: if 1 turned to an ES cell, 7 could still become a child

At least I know how to start my stem cell comprehensive exam tomorrow (The trick is to use blastocyst medium supplemented with laminin and fibronectin):

Human Embryonic Stem Cell Lines Generated without Embryo Destruction

Young Chung, Irina Klimanskaya, Sandy Becker, Tong Li, Marc Maserati, Shi-Jiang Lu, Tamara Zdravkovic, Dusko Ilic, Olga Genbacev, Susan Fisher, Ana Krtolica, and Robert Lanza

“To date, the derivation of all human embryonic stem cell (hESC) lines has involved destruction of embryos. We previously demonstrated that hESCs can be generated from single blastomeres (Klimanskaya et al., 2006). In that ‘‘proof-of-principle’’ study, multiple cells were removed from each embryo and none of the embryos were allowed to continue development. Here we report the derivation of five hESC lines without embryo destruction, including one without hESC coculture. Single blastomeres were removed from the embryos by using a technique similar to preimplantation genetic diagnosis (PGD). The biopsied embryos were grown to the blastocyst stage and frozen. The blastomeres were cultured by using a modified approach aimed at recreating the ICM niche, which substantially improved the efficiency of the hESC derivation to rates comparable to whole embryo derivations. All five lines maintained normal karyotype and markers of pluripotency for up to more than 50 passages and differentiated into all three germ layers.”

Legend: “(A) Stages of derivation of hES cells from single blastomere. (a) Blastomere biopsy, (b) biopsied blastomere (arrow) and parent embryo are developing next to each other, (c) initial outgrowth of single blastomere on MEFs, 6 days, and (d) colony of single blastomere-derived hES cells.”

Context link: Wired: Embryonic Stem Cells Created Without Harming Embryo, for Real This Time

Startup recipe: collect hair at the barber, isolate keratin, regenerate nerves

Biotech entrepreneurs and wantrepreneurs, here is a tip for Ya to launch a regmed business (and don’t forget to market the product as recycled and green) :

Winston-Salem Journal: Human hair could hold key to regeneration of nerve tissue, Wake Forest research shows

The study, published in the current issue of Biomaterials, found that the protein keratin found in human hair enhances nerve regeneration and improves nerve function – compared with current treatment options – in animal research.

As part of the study, the scientists used hair cut at a local barber shop and chemically processed it to remove the keratin. The keratin protein was purified and used to form gels that filled the nerve guidance conduits.

CIRM and NIH stem cell grants to the biotech industry

Different attitudes, same endeavors.

1. The folks at the California Institute of Regenerative Medicine (CIRM) started to offer grants for biotech companies up to $55,000 out of the 3 billion ‘hope’ dollars.

San Diego Union Tribune: Industry and academia team up:

For the first time in its three-year existence, the state taxpayer-funded stem cell institute is offering grant money to biotechnology companies….The stem cell institute wants to issue up to 20 planning grants to allow prospective disease-team members to hold teleconferences and travel to meetings around the state with potential collaborators to work out the details of how their group would function.

The idea is to form a team whose members have expertise in all areas of developing a drug or diagnostic – from the initial idea to testing it on animal models, producing enough of it for experiments and figuring out how it meets the needs of patients.

2. On the other hand, the NIH people in Bethesda, Maryland like the West and East Coast United Advanced Cell Technology (ACT) but not because the company’s single cell biopsy method for creating ethical ES cells.

Reuters: Advanced Cell Technology Awarded Grant from the NIH

Working without a personal assistant on the top of the big G…is fun!

I’m on my way to a Friday comprehensive exam from stem cell and mitochondrial biology which gives me no time to immerse into blogging this week. I mostly think of big holes in my knowledge like mitochondria and Ca²⁺ signalling. That’s why I can only offer soft things like the following quote from a fresh New Yorker article by Ken Auletta called The Search Party on Google:

Gabe Rivera of Techmeme: A Self-Meme Man

This would better fit to be a Twitter update, but I cannot resist to cite this sentence from Gabe Rivera Techmeme inventor in an older Wired conversation:

Partial immortalisation goes mainstream with an ’s’ – thanks to the Economist!

The Economist print edition (Jan 3rd) has a summary article on the current healthy and scientific life extension scene starting with Aubrey De Grey’s engineering, umbrella SENS approach and talking about anti-oxidants, mitochondria, sirtuin activators and stem cell based regenerative medicine amongst others.

To my positive surprise the unknown writer of the article (do you know who wrote it?) is using the term partial immortalisation when talking about regmed’s chance to extend healthy lifespan with a link to Pimm saying “Pimm is a blog focussing partial immortalistaion” in the web version:

Stemming time’s tide

One way that might let people outlive the limit imposed by disposable somas is to accept the machine analogy literally. When you take your car to be serviced or repaired, you expect the mechanic to replace any worn or damaged parts with new ones. That, roughly, is what those proposing an idea called partial immortalisation are suggesting. And they will make the new parts with stem cells….

Some partial immortalisers seek to abolish the Hayflick limit altogether in the hope that tissue that has become senescent will start to renew itself once more. (The clock that controls it is understood, so this is possible in principle.) Most, though, fear that this would simply open the door to cancer. Instead, they propose what is known as regenerative medicine—using stem cells to grow replacements for tissues and organs that have worn out. The most visionary of them contemplate the routine renewal of the body’s organs in a Lincoln’s axish sort of way.

The term Pimm – Partial immortalization was introduced by me in this blog referring the idea, gradual and continuous replacement process and future technology of systemic regenerative medicine aiming indefinite life extension. There is a compelling logic behind I explained it many times here. The difference is in the letters, the sense is the same: ‘immortalisation’ is a British English ’s’ version while ‘immortalization’ with a ‘z’ is rather American English (see the Google Fight graph on the right). Enough said, it is an ad hoc translation from the Hungarian “részleges immortalizáció” by me.

The source and short history of the term: For my MA thesis in philosophy (in Hungarian) I chose the term “weak immortalization” to address the philosophical problems of a though experiment of an unlimited healthy life extension technology through regenerative medicine which would eliminate problems concerning ageing (ageing related physiological problems), while strong and (technologically impossible) immortalization would eliminate death related problems. Later I replaced the weak – strong opposition to the more proper partial – whole opposition and the credit here goes to János Kis philosopher who suggested the term “partial immortalization” for me instead of the more metaphorical ‘weak’ and the modified version of my thesis was published in a book using ‘partial’. You can download the pdf here.

Since then I totally switched back to science and today I am more inclined to use the term systemic regenerative medicine (I adopted this ‘term’ used first by Maximum Life CEO David Kekich in a life extension blogterview for Pimm) which denotes the future branch of regenerative medicine focusing on otherwise ‘healthy’, aged, ‘normal’, ‘physiologic’ people instead of the characteristically and FDA approved diesased and catches the technology that is needed to reach reversible unlimited healthy lifespan, that is partial immortalization. Systemic regmed is a rather immature from a scientific point of view without an established experimental basis, I admit and more of a theoretical frame of my thoughts on the science I am practicing right now. Nevertheless it gives a fruitful, heuristic and holistic angle on regmed.

Here is the whole text referring to Pimm in the Economist piece:

Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Finally the Google PageRank algorithm, the core analysis tool of the current web is back to where its idea is originated from, scientific citation analysis. The recently launched SCImago Journal & Country Rank database uses an algorithm very similar to PageRank. It has a new metric: the SCImago Journal Rank (SJR). According to Nature:

A new Internet database lets users generate on-the-fly citation statistics of published research papers for free. The tool also calculates papers’ impact factors using a new algorithm similar to PageRank, the algorithm Google uses to rank web pages. The open-access database is collaborating with Elsevier, the giant Amsterdam-based science publisher, and its underlying data come from Scopus, a subscription abstracts database created by Elsevier.

The SJR also analyses the citation links between journals in a series of iterative cycles, in the same way as the Google PageRank algorithm. This means not all citations are considered equal; those coming from journals with higher SJRs are given more weight. The main difference between SJR and Google’s PageRank is that SJR uses a citation window of three years.

From now on every stat geek can compare journals to journals, countries to countries based on different metrics like citable documents, cites, self-cites or the new h-index and get a ticket to recursive heaven. Of course I started with the comparison of Nature and Science to find something very different. I couldn’t. I predict that self-cites will show a lot on how things are going on at different scientific journals and the stats will be used as serious arguments in many blog posts. But here let me share some graphs on the quick comparison of USA, UK and China in the category of Aging.

First graph: citable documents

Nature Editor-in-Chief’s changed mind on enhancement drugs for healthy people

Philip Campbell, the open editor-in-chief of Nature was asked by John Brockman under the cover of the 2008 Edge Annual Question: WHAT HAVE YOU CHANGED YOUR MIND ABOUT? WHY?

Campbell writes in his thoughtful answer:

“I’ve changed my mind about the use of enhancement drugs by healthy people. A year ago, if asked, I’d have been against the idea, whereas now I think there’s much to be said for it.”

Before citing further the argument of Campbell I’d like to remind the analogous problems of biotechnological life extension products targeted for healthy people in a “normal” physiologic state. Good example are the resveratrol-like but more effective sirtuin activators with a probably positive healthy lifespan extension effects developed by David Sinclair and his group at Sirtris. The trick is to market Sirtuin activators as anti-diabetes drugs, or find other registered diseases to target with the drugs. According to Mass High Tech:

“Aging is not a disease to the FDA,” Sirtris co-founder Christoph Westphal said, so Sirtris is focusing on drugs to treat ailments of old age.

With this story in our changed and future focused mind it is very promising to read for healthy life extension supporters what Campbell, a mainstream academic science representative has to say on cognitive enhancement drugs:

New cognitive enhancing drugs are being developed, officially for therapy. And the therapeutic importance — both current and potential — of such drugs is indeed significant. But manufacturers won’t turn away the significant revenues from illegal use by the healthy.

That word ‘illegal’ is the rub. Off-prescription use is illegal in the United States, at least. But that illegality reflects an official drugs culture that is highly questionable. It’s a culture in which the Food and Drugs Administration seems reluctant generally to embrace the regulation of enhancement for the healthy, though it is empowered to do so. It is also a culture that is rightly concerned about risk but wrongly founded in the idea that drugs used by healthy people are by definition a Bad Thing. That in turn reflects instinctive attitudes to do with ‘naturalness’ and ‘cheating on yourself’ that don’t stand up to rational consideration. Perhaps more to the point, they don’t stand up to behavioral consideration, as Viagra has shown.

Research and societal discussions are necessary before cognitive enhancement drugs should be made legally available for the healthy, but I now believe that that is the right direction in which to head.

Science.tv launched a blog

I haven’t done any strict fact checking but as far as I know science.tv’s new blog, called simply Science.tv Blog is the first web log launched by a science video sharing site in order to communicate and explore. (Usually I am accustomed to the other way in the world of online video: blog first, vlog or tv second, think about BoingBoing or Make.)

Matt Thurling, science.tv founder has some valuable considerations on how to catch (video) school kids conducting genuine experiments attempting to answer their very own hypotheses be it on Nintendo or ants.

2008 Edge Annual Question: What data have changed your mind? Why?

The science part is emphasized in the title of this post on the 2008 Edge Annual Question, which is again well formulated and thought provoking. The whole question embraces science, philosophy and religion (left).

Last year I had my own answer to the question: 2007 Edge Optimistic Question: systemic regenerative medicine, this year I am still thinking but my answer will probably be something technical and non globally relevant about PCR artefacts.

Based on the quality and quantity of the recent contributors the 2008 answers offer an exciting intellectual journey to the readers, let me highlight the following, not specially science restricted ones, many of them recurring references on Pimm: Beatrice Golomb, Chris DiBona, PZ Myers, Tim O’Reilly, Philip Campbell, Aubrey de Grey, Kevin Kelly.