Life blog

Swimming the sea of knowledge (the Concept Web?)

I've been spending a lot of time thinking about how to find, navigate, recombine, and contribute to ... what's out there, though mostly focused on science and the next generation of science 'publishing' (in quotes, since it'll be quite different from traditional publishing, more back in the hands of the scientists like in the old days).

A friend pointed me to this cool site called WikiProfessional, where they have these cool info navigators. A quick perusal suggests that they focus on the 'find' and 'navigate', though I think they also have a wee bit of 'contribute' through the addition of semantics as you navigate and annotate.

There are a ton of collaborators working on this and I dug a bit deeper into the main one, Knewco, It was on their pages that I stumbled upon the image to the right, about the Knowlet, trademarked, but spot on representing what knowledge really is: a concept with a cloud of facts, co-occurring items, with a few predicted concepts thrown in.

I like.

UPDATE: And here's a paper that goes into the details.

I like. A lot.

Not only are they doing a good job, but it's scaringly real

A while back I found out via the Twitter site that the Mars Phoenix Lander had a Twitter channel. I don't know, but maybe at the time it didn't seem to be an interesting stream, what, but I didn't follow.

Well, seems like Alex is following the Lander and re-tweeted the big news below. So, I went to see the stream and am very pleased with how well they are using the stream. Not only is the person doing the tweeting very funny, but she has been responding to questions and such.

This is an excellent way of using Twitter in a corporate setting.

Did I say corporate? Indeed, this is NASA using Twitter to send out updates for one of their programs. Someone who represents the Lander is the one Tweeting, so that's marketing communications to me. And companies can learn a lot by just following this stream.

Way to go NASA!

Link: Twitter / MarsPhoenix:

Are you ready to celebrate? Well, get ready: We have ICE!!!!! Yes, ICE, *WATER ICE* on Mars! w00t!!! Best day ever!! about 7 hours ago from web

Billion-dollar life sciences bill passes Massachusetts Senate

Does Massachusetts need a stimulus in biotech? I don't think so. It's doing pretty well.

This bill sounds like a bone thrown to biotech biz leaders around the state. One person in the article below even uttered the p-word "pork".

Oink oink, indeed.

On the plus side, maybe I should be thinking of heading back. That's a lot of moolah to go around.

Link: Billion-dollar life sciences bill passes Senate; governor to sign Monday - Local News Updates - The Boston Globe

"I just remind you that it's the taxpayers that are paying. ... It's taxpayers' money, it doesn't grow on trees," he said.

Image from extrudedaluminiu

Kevin Kelly and the New Rules of the New Biology

Kevin Kelly whipped up 9 rules for the Century of Neo-Biology (that label thrills me).

I reproduce them here, but you might want to head over to his post (link below) to leave other rules there too.

1) All rules in biology have exceptions.
2) Anything that can be done with organisms (including our own), will be done.
3) Every biological action invokes a biological reaction.
4) All inovations follow a one-way migration from enhancements to normalcy.
5) One person's biological ideal is another's horror.
6) Understanding is not necessary for use.
7) The tolerence for uncertainty goes up as death becomes certain.
8) The difference between 99% reliable and 100% reliable is God (or a million years of evolution).
9) Health care is finite resources applied to an infinite appetite.
from: Kevin Kelly -- The Technium

I left the following comment

0) Biology is messy

Some folks think biology behaves properly and regularly like electronics (which we all know is a passing fad). Go into any laboratory and you will see the modern-day alchemist repeating experiments that work one day and not the other, joking about the phases of the moon or position of the chairs.

Do I feel this way because it is so early in the neo-biology game? Am I just an old fuddy-duddy who learned biology in the previous century?

I think that's irrelevant. Digital electronics have distracted us from the analogue world, such that when we turn our attentions to biology, we've forgotten how to think in gradients, thresholds, probability, or chaotic flows in regulatory networks. Indeed, the biochemistry I learned and did was all about this and it's a thrilling way of doing things. I think those with strong digital sensibilities will have a hard time embracing the uncertainty and variability so common in biological systems.

More Earth presence on Mars

Call me an optimist, but I think it's inevitable that Earth-folk will eventually be wandering over Mars. Eh, not sure if it will happen in my lifetime or in my children's. I'm taking a long term view on this.

But last night, one more entry has been made in the time line: NASA set down a lander in the Mars arctic region.

I had comletely forgotten about it until I noticed an article in the Boston Globe. When I went to the mission site I found out that landing was immanent (but on the middle of my night). Of course, being the geek that I am, when I woke up the next morning I flipped open the computer to see what images were to be seen.

The one below seemed most interesting. Note the scalloped pattern to the dirt. Alas, what I hate about this pics is the lack of scale. When the first rover pics came in, things looked big and daunting, only to find out that they were tiny rocks and such. Sigh.

Nonetheless, I find this all exciting.

From my sideline seat, Thompson Reuters seems awfully archaic

Can someone please explain to me how and why Thompson Reuters Scientific has such a grip on scientific journal Impact Factors?

If you look at the list of various indexing services, you can see that they are all brushed aside for Thompson Reuters. It seems to me that unless a journal is indexed by Thompson Retuers, then it really is not considered to have any relevant impact on the scientific literature.

OK, so maybe these guys were anointed by the community to stand in as the über-authority index. I can deal with that. But, I think also there is an opportunity for an independent authority index, à la Technorati.

I think it just might be my natural inclination to suspect a single source of authority ranking. But I think it's more likely because I see so many tools available to measure impact that could be more responsive and maybe more granular than what the current system seems like to me.

I've started looking into this. People are coming up with alternatives. It also seems like Thompson Reuters realizes that they might lose a hold on their position.

Yeah, my brain has been munging on this lately.

Link to article that set off this brainwave: BioMed Central Blog : Orphanet Journal of Rare Diseases tracked by Thomson Reuters and set to receive first impact factor in June 2008

Orphanet Journal of Rare Diseases was recently accepted for tracking by Thomson Reuters. It is included in the ISI Web of Knowledge database and will receive its first impact factor this summer. We are delighted with this achievement, which confirms the prominence and reputation which Orphanet Journal of Rare Diseases  has achieved in its field.

Link to recent journal article: Effectiveness of Journal Ranking Schemes as a Tool for Locating Information

As de Solla Price observed [3], the number of scientific journals and the number of papers published in those journals is increasing at an approximately exponential rate. The size and growth of the research literature places a tremendous burden on researchers—how are they to select what to browse, what to read, and what to cite from a large and quickly growing body of literature?

Biology is messy! Synthetic biology will be synthetically messy, too! (plus BONUS)

I've been reading about iGEM and the Registry of Standard Biological Parts. It's a component view of biology - that there are parts in biology that can be used much like electronic parts.

Eh, I know they don't think it's that simple, but it sure can be misleading what they are trying to do.

These folks are characterizing biological parts and creating a catalogue from which to plug and play and mix and match to create circuits that do something. They are looking to establish standards, construction tools, and some abstraction to make it easier to build synthetic systems. And that's all fine and good. It's like the early days of electronics. And they have done some amazing things, light replicating photography with bacteria, some cool circuits, and more.

But, in my biomedical-scientist eyes, I just wished they would think more than just creating digital circuits on analogue systems. Also, I feel that biology doesn't gate well, I mean, it's very non-linear and hard to do on-off 'mathematics' with biological components. And by trying to build digital stuff, they lose the value of analogue.

In short, I think the questions they are asking are not the right ones for the system.

And thinking back to Craig Venter, moving forward, synthetic biologists are going to have to think of analogue, of biological answers to questions. We are so accustomed to neat and clean binary fixes to things, but seem to forget that in biology, so much is probability, fuzziness, and selection, and failure is so much more nuanced.

I've designed many macromolecules and expression systems, grew all sorts of micro and macro organisms, and dealt with all sorts of biological systems. In so many ways, we were not far from the brewers of Mesopotamia, coaxing and praying for a healthy growth and production of the right enzymes.

Yet, we have had in the past 30 years, and even more so in the past 5, a deeper understanding of the mechanisms. But, we mustn't just translate that all into our digital minds, we need to think of these organisms and molecules on their terms.

When I was a grad student, my advisor was a physical chemist doing biochemistry. To him, DNA wasn't just A T C and G, but a chemical entity. I came out of there seeing proteins and DNA in a way that my molecular biologist colleagues did not, and a deeper understanding of the complex interactions in biological systems.

In the same way, synthetic biology is going to have to go beyond linear circuit building, but take advantage of the strength of these marvelous billion-year evolved systems.

Here's a video of Drew Endy, a leader in this field, putting synthetic biology in perspective:

BONUS: If you really get a kick out of visualizations, the Machinery of Life, by David Goodsell, is a really neat peek into the molecular world at the scale of proteins and bacteria.

Bacteria still rule: Great Long Now seminar by Craig Venter (and Bonus!)

I finally got to listen to the Long Now seminar by Craig Venter. And, wow, was it great.

If you've been a regular reader of mine, you know that I think Venter deserves the Nobel many times over. He's been the big disruptor in genomics for decades, taking technological risks that made the industry jump forward farther than our prejudices would have expected.

The talk followed a thread through his disruptions, providing a foundation for why he's doing what he's doing now, which is to define the genome of an organism for practical purposes, such as creating biofuel.

One thing that he made me think about was bacteriology. When I was a scientist, we studied mammalian genes, proteins, and diseases. A bacteriologist always felt like someone from the distant past, with a lab full of smelly slimy plates, studying a 'boring' organism. A real microbiologist was studying fungi, like brewer's yeast, the laboratory workhorse and a model system for mammalian genetic and cellular processes.

Well, after listening to Venter, and aligning my perspective with his, it's clear that bacteriology is the domain to be in.

His recent Sorcerer II expedition has re-ignited interest in bacteria and bacterial ecology. With the recent rise in metabolomics (the analysis of all the metabolites in the body), we're starting to realize that our mammalian cells are an even smaller part of the body functions we have than we previously suspected. And as, I hope, the antibiotic era starts to wind down and people start redefining our relationship with bacteria, understanding bacteria has become ever more important.

That makes me think that the kinds of professions that will be on the rise in the post-genomic age are bacterial ecology, bacterial genomics, bacterial virology (phage therapy to replace antibiotics, is a new one for me), and bacterial biochemisty.

Questions I now would like to see answered: what are there bacteria who are exclusive inhabitants of humans, what is the total genomic signature of a human (the sum of human and microbiological), how can we live in a sceptic world (the rise of super-bugs is partly a consequence of our cleanliness).

I don't know if it's just me, but it seems like there's been a phase shift in biology on the order of the early days of molecular biology, with the excitement and promise of a very interesting future.

BONUS: One thing that I heard about that was intriguing was the Personal Genomics project, an open source community kind of project to not only get more genomes to sequence and analyze but also to drive the technology to cheaply sequence genomes (see X Prize, too). Indeed, I've been reading about the biological parts registry and wondering weather we are at a stage of garage molecular biology. But that's a later post. :-)

Old calculators and future steampunk

Whipple Museum of the History of Science, Cambridge
Originally uploaded by blackbeltjones

Heh. My Dad also had some of these types of clunker calculators. Uh, I was curious to see how it worked and opened it and, well, destroyed the whole thing. It was expensive, but my Dad was kind.

Funny, also, to see these photos today. Earlier I was wondering what would be the 'steampunk' version of my grandchildren's generations, as they look back at how backwards were were.

What got me thinking was a segment from Science Friday about folks who are reviving a pre-antibiotic anti-bacterial treatment (bacteriophage).

It also dovetalis with a recurring thought of setting up a bio-lab at home and trying to remember all I learned about early genetics labs and such. That's my 'steampunk' - milk bottles with fruit flies (I used to use them), capillary tubes with rubber hoses to measure microliters, funky autoclaves, light microscopes, different stains, and ... ah, it's so cool.

Michael Arrington gets sequenced: His 23andMe DNA Results

I haven't been paying much attention to 23andMe. I heard about them, but have yet to dig deep into what they are up to.

To me, it's bringing genetics to everyone. Michael Arrington did a nice post on what you get for a $1000.

Well, for starters, his DNA didn't get sequenced (that would be much more expensive). It was passed over a chip to detect hundreds of thousands of known DNA segments that as a whole determine some of his genetic make up. But, it seems like the set of DNA segments chosen are enough to create a relevant and interesting genetic profile (Mike goes over his a bit).

What seems interesting is the genealogical aspects. If 23andMe get enough people, might it start dong the 'friending thing' of 'oh, this person shares your haplotype for soft-earwax Bretons', would you like to add him to your watch list?

The turkey and the butcher

Just wanted to get this little ditty out:

I was listening to a very interesting Long Now seminar by Nassim Taleb, about his insight into randomness, predictability, and the like.

If you don't know who he is, Taleb wrote a very popular book called 'The Black Swan', which takes it title from an old English saying that equated something impossible with seeing a black swan. Well, that saying got messed up when black swans were seen in Australia in the 18th century.

A great anecdote, created by his brother, he brought up to illustrate the overall point of the 'black swan' was the story about the turkey and the butcher.

Basically, the turkey views the butcher as this benevolent person, who constantly attends to the well-being of the turkey. And when the butcher comes one day to kill him, the turkey is astounded at the unpredictability of the butcher's behavior. Of course, to the butcher, it was all very predictable. Down to the chop.

Moral of the story: You can't always predict things based on past trends.

Corollary (for me at least): There are views that do make these 'black swans', these amazingly unpredictable events, predictable.

One other thing he mentioned that keeps me thinking and ties to the Long Now perspective is about the wisdom of old folks being a resource in how to deal with black swan moments. Hm...

Great essay by Kevin Kelly on Human Identity

Kevin Kelly has written a great essay on the current challenges to human identity, challenges from tech, society, and new knowledge.

I think this ties a lot into some previous comments I made related to emergence and the like.

Link: Kevin Kelly -- The Technium:

A major theme of this present century will be the pursuit of our collective identity. We are on a search for who we are. What does it mean to be a human? Can there be more than one kind of human? In fact, what exactly is a human?

I posted the following comment:

A while back I had a thought about how things go from simple to complex, hopping to the next layer of complexity and then complexifying once more (the basic emergence thinking). It's similar to SBJohnson's Long Zoom and comments from Alex Wright on information architecture.

One thing that struck me was some sort of subservience to the network above - best exemplified by ants, who seemingly have subsumed their lives to the network at the hive-organism level.

Logically, I concluded that humans (who are clearly a network of individual cells who have subsumed their existence to the human-organism) must at some level subsume their existence to the network above them - society.

Sure we do that, sort of. But I get a feeling that current society is like the volvox to multi-cellular creatures. Or isn't it?

And consequently, what _is_ the network next up that societies must be subsumed under?

But, in all this, I see what gives us humans the anxiety of identity is that we think we _must_ be individuals with free will. But as the network above us gets more complex (indeed mobile phones and the intarwebs are part of this) we refuse to turn ourselves into subsumed parts of a greater network. We try to have a global view or control of that network a layer up.

In summary, our identity was simply a construct as we solidified the strength of the organismal network. Now as we become 'cells' in the next network up, that network will force us to subsume our global views as we become parts in a network.

One more thing: Arthur C Clarke's 'Childhood's End' sort of is a story of humans stepping up into the next level and subsuming their identity.

Thoughts on the Journey of Mankind

A Long Now post pointed to a cool animation showing the migration of humans over the past 160,000 years, since modern humans arose in Africa.

There's a lot the gets me thinking when I read about ancient human history, such as what was life like, or what did the world look, smell, and sound like.

The post references an event that made my head spin when I found out about it long ago - a massive volcano eruption that caused a 6 year extended winter and left an estimated 10,000 humans alive. That's one heck of a bottleneck.

In 'Dragons of Eden, Carl Sagan suggested that our myths and fears of reptiles might be some genetic memory of the age of dinosaurs (there were only teeny mammals back then). But, that has always made me wonder what deep ingrained memory we might have from events 10-, 20-, or 100-thousand years ago. Might we have some sort of recollection of this massive volcano eruption, some memory encoded in our culture, way of living, or language?

And looking at this animation, I was reminded how much of the human population was along the coastlines. Yeah, I read that many time before, but seeing it in an animation made the point stick.

All this beach-combing reminded me of one of the many questions I have been carrying unanswered: 'Why are children so in love with water - pools and beaches?'. Might the extreme psychic draw to play in water that children exhibit be to learn some sort of critical survival skill for a coastal species?

Well, what do you know? Craig Venter going to Harvard as a visiting scholar

My wife pointed out, once more, a link to something on Venter (link below to blurb). I wonder if she wants me to work with him. [Nope, irrelevant inference.] And she has no idea I made another reference to him already today. Do I tell her?

This group he's going to work with is cool.* This whole thing is cool. Could have been cooler is I were still there. It's not at the medical school where I worked at in Boston, but the main university in Cambridge. But, I still would have gone out of my way to see him speak.

Link: J. Craig Venter named visiting scholar | HarvardScience:

J. Craig Venter, the visionary biologist and intellectual entrepreneur who was a leading figure in the decoding of the human genome, will join Harvard University as a visiting scholar at the University’s Origins of Life Initiative.

*As usual, I've met a few of the people where he's going to work.

Entropy is over-rated. Long live Complexity! (Bonus: The Venter)

Does everything tend towards Entropy?

One of the first things we learn in chemistry is that everything tends towards entropy.

How can that be? Whereas Steven Johnson calls it the Long Zoom (in that you can zoom up and down levels of complexity) we constantly are seeing lower-order networks yielding a new level that itself begets new levels.

I lost my notes long ago, but I remember trying to grapple with the way sub-atomic particles glommed on to form atoms to form molecules to form auto-catalytic systems to form cells to form organisms to form societies to form <ad infinitum>. I tried to recapture that thought in an earlier essay, but there are a ton of other folks like Steven Johnson and the folks at the Santa Fé Institute who are also trying to understand the properties of complex systems.

But if all tends towards Entropy, how to we form these complex emergent systems in the first place? Do we have to Zoom all the way down to the fabric of the Universe to understand that single simple little principle that allowed a slight formation of a complex network that caused the domino effect that leads to today, a little principle that has been at War with Entropy since the formation of Everything?

Ufa!

A lot to think of. And I know I am way over simplifying somehow.

Bonus! The Unit of Measurement for Complexity
I don't know if it exists (but I am sure Hugo can find it), but, in the course of writing a script for a graphic novel set in the far future (which I am set to overhaul under the 'show-don't-tell' principle), I started thinking about how reductionist we are and that we have no way for describing complexity in a system (that I know of).

And, as you probably know my fascination (fanboi?) with Craig Venter, I thought he'd be an appropriate label for the measurement of Complexity - he's re-written the books on the Genomic Age so many times and has ushers in the Age of Meta-Genomics.

Venters (Vn), a logarithmic scale of biological complexity. A virus is 3Vn, bacteria 3-10vn, fungi 10-30Vn, single cell 10-20Vn, complex 20-50Vn, planaria+ 50-100Vn, social athropods 100-500Vn, reptiles, birds, fish, mammals, social netoworks...

My original thought was that the Venter would be a logarithmic scale of _biological_ complexity. But I suppose it could be a measure of complexity in general. Complexity can be measured by nested levels of networks, levels of connections between networks, and level of energy to maintain network (the inverse of Entropy, I suppose).

The symbol for Venters would be Vn, as V is widely used and taken for Voltage or Volume.

Any takers?

Heh, really being a geek.

On the balance of top-down and bottom-up

Kevin Kelly is on of the founders of the Long Now Foundation, which you all know I am pretty fond of. He wrote an article (link below) recently on the balance of bottom-up emergence and top-down guidance (not necessarily 'control', more like 'leadership'), that has tipped my hand to finally writing down some thoughts.

Top-down or botton-up?
This topic of balance has been on my mind quite a bit - I have followed emergence (I call it 'complexification') for many years now (heck, I'm a scientist at heart); just finished Steven Johnson's book 'Emergence', heard some great talks by Juan Enriquez and Alex Wright, and had my own personal struggle trying to understand megacorporations (aka 'The Borg').

Kevin revisits (and discusses through the many comments on the article) his 10-year old book 'Out of Control', a book on swarm theory, hive mind, bottom-up emergence. One thing he has learned is that bottom up is not enough.

He uses Wikipedia as an example of something that might seem bottom up - people 'randomly' contributing and editing encyclopedia articles, forming a global encyclopedia of knowledge from the collective actions of a collection of individual. Kevin points out that, actually, there is some level of top-down control in Wikipedia through a set of über-contributors who do have a modicum of editorial control.

The book 'Emergence' relates in many example how 'dumb' local behaviour in a network leads to a 'higher-order' behaviour. The famous example is an ant colony, where the sum total of the colony members' behavior, based on simple rules, leads to a a comlex colony-level (colony as organism) behaviour.

Networks within networks
Alex Wright and Juan Enriquez point out, in their work, that one level network leads to members that then operate at a new level. My example for this is the body. Our cells go about their single-minded business, creating a higher order network that is the body. The body then is the unit item in a network that is our social network.

Yet, Kevin struggles with his interaction with the world of user-generated-content, the swarm of content that leads to something like Wikipedia. Coming from a publishing background, he sees the need for the editor. And I think that's fine. The editor is actually from one level up in the network and not on the level of the swarm. As with the body, the control does come from the next level up, what ever the selected forces on the next level up are.

Global control from above
Drawing a parallel back to ants, Steven Johnson points out that the colony would be in trouble if one of the ants took a global view of the colony and tried to take over. That's because the ants are part of the swarm and should not have global control. The colony has that global control, a control that comes from the selective pressures on the colony, not the ant. The selective pressures of the colony are its survival, interaction with other colonies, its relations with the environment.

I'd claim that what Kevin is struggling with is the publishing process of Wikipedia taps into the swarm perfectly. Contributors are elements following simple rules to just spew content into Wikipedia. But, WIkipedia as an organism needs to compete at another level, which gives Wikipedia a global mandate to force a selective pressure upon the members that constitute its internal network. Yet, this will only work if 1) the network one level down subsumes itself to the collective, and 2) that none of the members of the network one level down try to assume a global view or impact.

Corporations can learn from this
This all leads me to why large corporations are so dysfunctional: too many people taking the global view.

For a network to function, there needs to be rules of action for the members and rules of interaction between the members (think of workers as cells, departments as organs). In corporations, this is done through role definition. Indeed, I think it is wonderful how much individual responsibility my corporation give the workers. And that should be sufficient for emergent behaviours to be visible. And they are, as one can see with how products and services are created.

But, the impact of the corporation (think of it as the body) is at the corporation level (bodies in a social network) and the selection is at the corporation level. Hence, the members of the corporation should not have a global view, or attempt to commandeer the global view. And It think in corporations, the members tend to know the rules, do what the corporation asks, but never return and make sure that what ever potentially global effort they have been asked to do by the corporation does not violate the original rules of being a member of the collective. Likewise, I do not see the corporation exerting its global view in culling activities that violate the network rules and try to act on the level of the corporation (the global level).

I suppose that's my long winded way of saying that employees keep screwing things up by taking on the role of the corporation and the corporation keeps screwing up by not exerting its influence on its employees who try to commandeer the global direction. (I've seen this happen too many times)

Summary
Yeah, global top-down works if it comes from the next layer of network above. It won't work from within the network.

Do folks in the open source world (or others) agree?

Link: Kevin Kelly -- The Technium:

Judged from where we start, harnessing the dumb power of the hive mind will always take us much further than we can dream. Judged from where we hope to end up, the hive mind is not enough; we need an additional top-down push.

Notes on notes of essays someone else never wrote

I've heard a lot about Matt Web through those closest to him, but never really met him.

Matt is half of an interesting and insane design duo, Schulze & Webb (I have met Schulze, BTW). It's safe to say that Schulze & Webb are racing forth, defining what happens when you mix design and Web and bits and atoms (and mobile).*

At the end of last year, Matt wrote down some notes on essays he'd wish he'd have written, but didn't. The notes are a loosely connected series of topics that joggled more than a few conceptual pinballs in my head.

Surface binding
One topic Matt touches on is 'surfaces', basically, recognizable bits of structure (data) on the Web. This is really about micro-formats.

But, and this pleases the bio-geek in me, he compares Web surfaces to protein surfaces and browsers as recognizing these surfaces and making sense of the surface structure.

If I understand it, there are patterns in the categories of structures in Web pages. Matt seek the range of these types of structures to be finite and stable, hence such a classification of types to recognize is possible.

Hm, this may be a solution to extracting meaning (tying to another thread of though of mine). I suppose this begs for some taxonomical survey of Web structures, if there isn't one already.

Refactoring code
It was a blast from the past for me when Matt stated his wish that code not be refactored, but added to. In the late 90s, I was at an amazing talk by Marvin Minsky to us biomedical post-docs. Minsky also said that we should not rewrite code, but patch it - there was value in the old stuff.

Matt likes to use biology or chemistry example, but doesn't here. So I offer: Genomes are not necessarily refactored by evolution, but usually written over. And a lot of variability in the genome is derived from cutting and pasting of new and old code, rearrangements, duplication, and divergence of old code, and repurposing of old code (and don't get me going about 'junk DNA').

Bringing about change

Matt has a few great points on change and ultra-stability. But one thought that is radically funny is devilishly deviant: drive badly to accelerate the adoption of self-driving cars.

He takes it further in relation to mind enhancing drugs.

For example, 'erectile dysfunction' was hyped and marketed as a problem, so that pharma could create and sell the performance enhancing drug, Viagra. Therefore, Matt asks, we could start pointing out a problem with mental abstraction as a risk. Then, after papers and studies and articles come out about 'the problem' a market would arise, demanding solutions to the 'abstraction problem'. Then pharma could be provided with the material to persuade regulatory bodies that pharma should and could come up with the solution to the problem, for the benefit of business and society.

Heh, that's be something cool to try (reminds me of the Frindle). Kinda like a Saffo Mind-bomb for the future.

Path through services
Fred Stutzman who writes on social networks keeps pointing out the need for services to answer the 'What's Next?' after adding all your peeps to the network. On a similar note, Matt mentions the never-ending game quality Flickr has (indeed, Flickr was first called the 'Never-Ending Game'). The game aspect keep leading the users back, 'auto-catalyzing' engaging behavior.

In the end, Matt's insight is to keep the path the user takes through the services to never end (and designed to bring in others, to grow).

I think that this path is not always the utility (feature of service) path, nor the best path, though I have no examples to base this on. Also, with the mobile lifestyle in mind, how can that path have interruptions and long gaps?

Product evolution
his very last topic is about evolving a product locally. Matt devises a vending machine that optimizes the product flavor based on popularity.

For me, it touches a bit on what randomness can bring a product. Since most products are about consistency, could a machine be made to randomly dispense a product to surprise the buyer? Kinda like Bertie Bott's Beans. Indeed, there is a drink that sort of does this.

What's with the biology?

Until I read this big article by Matt, I had not really read any of his ramblings (though I have seen him speak and read some of his more formal writing). The biggest surprise was the number of hard-core biology (and chemistry) examples. It could just be my bias to see these topics stand out, but I think I need to ask some folks what the story is here.

For example, one of his notes completely surprised me with the items places in one sentence, ranging from metabolics, to tectonics, to the Austro-Hungarian Empire (need to follow up in this, too).

I think he's just a well-read curious guy, who revels in mixing disciplines. For sure, this guy is as scattered in his interests as I am. And tis explains all the interesting things he and his gang spout off. I suppose I do need to introduce myself to him, if only for his bio references, but also because we have a lot of overlap in the people we interact with (though his are much tighter in time and place than mine).

As for you, go read him. He's a trip.

*Indeed, the crowd Matt hangs with, which I mostly follow second-hand via @blackbeltjones and @anti-mega, are all brilliant and creative.

BioMed Central article on Semantic Web and biomedicine

What got me thinking all over again about the Semantic Web and how to find, navigate, recombine, and contribute to the flow of knowledge was a brief series of meetings with the folks at BioMedCentral. Of course, it helps that I am also a bio-geek.

BMC Bioinformatics had a special supplement on semantic e-science in biomedicine. The articles were very interesting, especially since seeing a problem solved in another discipline gives many pointers as to how to solve similar problems in your own discipline.

If you read the quote below, about infoglut, complexity, social networks, and information sharing, once sees similar activities in the social and living Web we all use.

But so much of the BMC Bioinformatics supplement is about librarian-like structuring of data. What's more, there is an element of structures that authors need to understand and adhere to to make their publications and data more machine understandable.

Yet, what is the benefit to the author? Currently, scientific publications establish primacy, prestige, and are a tool to get grants. By going through the extra effort of adding semantics to their data, what then does the individual author gain?

The rise of tagging and folksonomies were not only about helping others, but arose out of tools that made things easier for the user. Can we change the mentality of the scientist to understand the other benefits of adding semantic info to their data and publications, benefits that are different from traditional science publishing?

How may we do this?

Link: BioMed Central | Full text | Introduction to semantic e-Science in biomedicine:

Advances in biotechnology and computing technology have made the information growth in biomedicine phenomenal. With the exponential growth in complexity and scope of modern biomedical research, it is becoming more and more urgent to support wide-scale and ad-hoc collaboration and exchanging ideas, information and knowledge across organizational, governance, socio-cultural, and disciplinary boundaries. Researchers working on one aspect of analysis may need to look for and explore results from other institutions, from other subfields within his or her discipline, or even from completely different biomedical disciplines.

We're moving into an oral culture on so many levels

We're rapidly approaching an oral culture. The fluidity of the Web seems to have many aspects of an oral culture in terms of how we can interact with so much of it in a non-literate manner - think videos, audio, images.

This is not necessarily a bad thing. But oral cultures had methods for maintaining what was transmitted orally. For us, everything is going digital. How will we preserve our digital memories?

The Long Now Foundation has been leading a lot of discussions around how to preserve digital records. They have countless stories of how, just in the past few decades, we have been losing data and access to information stored in digital format.

For example, they mention how on the USS Nimitz, opening older files in newer software showed slight differences in annotation and the like. Not a good idea on a nuclear powered war vessel.

In the same article, they bring up a great favorite of mine:

In 1986, for example, the British Broadcasting Corp. compiled a modern, interactive version of William the Conqueror's Domesday Book, a survey of life in medieval England. More than a million people submitted photographs, written descriptions and video clips for this new 'book.' It was stored on laser discs - considered indestructible at the time - so future generations of students and scholars could learn about life in the 20th century.

But 15 years later, British officials found the information on the discs was practically inaccessible - not because the discs were corrupted, but because they were no longer compatible with modern computer systems. By contrast, the original Domesday Book, written on parchment in 1086, is still in readable condition in England'€™s National Archives in Kew. (The multimedia version was ultimately salvaged.)

The thing is, digital data requires software, in addition to hardware. And software is very difficult to recover to to its format, how it is compiled (software to make software), and how fast it changes relative to hardware changes.

In another article, they point out that the Society of American Archivists were going to delete their listserv data. Whoah. If the archivists are not keeping stuff, who will?

The Long Now Foundation asks:

Can anything last forever? The Long Now Foundation is micro-etching its 15,000-page Rosetta Project, an archive of data on human languages, onto a 3-inch metal disk it hopes will last at least 10,000 years. But we still may not have improved on 4,000-year-old technology. Asked what the most permanent medium is, Kahle doesn'€™t miss a beat: '€œThe clay tablets of the Babylonians. Their libraries are readable to us today.'€

Go and read these articles for more examples.

Link: Long Views » Blog Archive » The Digital Ice Age
Link: Long Views » Blog Archive » Publish or Perish

UPDATE 03mar08: I'm not the only one thinking of this (Steven Johnson).

Craig Venter giving a Long Now seminar today (25feb08)

Dang, I was not able to finagle a trip to SFO to see this talk. But, if you live in the Bay Area, don't miss this!

Link: Long Now Seminars

Craig Venter is on a roll these days.  He has revolutionized science twice already---with the human genome project and with metagenomic analysis of whole microbial populations.  He is about to do it again by creating a new life form with a wholly synthesized genome.  His memoir, A LIFE DECODED, is a thrilling read.  He has shocking new perspectives to report every time he speaks in public.

Last month in Germany he said, "In one milliliter of sea water, there's a million bacteria and ten million viruses.  In the air in this room---we've been doing the air genome project---all of you just during the course of this hour will be breathing in at least 10,000 different bacteria, and maybe 100,000 viruses....  This is the world of biology that we live in, that we don't see, where evolution takes place on a minute-to-minute basis.... The air that we breathe comes from these organisms. The future of the planet rests with these organisms.  And the question is: If we take over the design of these organisms, does that really shift the balance in any way?  Or is it such a small portion of what's out there that we'll only affect industrial processes, not the living planet?"

"Joining 3.5 Billion Years of Microbial Invention," Craig Venter, Herbst Theater, San Francisco, 7pm, MONDAY, February 25.  The lecture starts promptly at 7:30pm.  Admission is free (a $10 donation is always welcome, not required).

The Herbst Theater is downtown at the Civic Center on Van Ness at McAllister (inside the War Memorial Veterans Building).

Another great Long Now seminar: Juan Enriquez "Mapping Life"

Saying that the Long Now seminars are great is starting to feel repetitive. So, please go out and listen to ALL of them.

I've caught up with all the seminars that have been made available. One that I want to point out is Juan Enriquez's seminar on biology, politics, evolution, and science (link to post on seminar, below).

Wow.

He's such a low key speaker, but delivers such strong points. (though if you look at some of the comments in the post linked below, some folks were not as pleased)

There were a few items he mentioned that were pretty interesting:

1) He's friends with Craig Venter and traveled for a time on Venter's yacht, Sorcerer II, which was traveling the oceans, sampling micro-organisms every 200 miles by sequencing the whole she-bang. It's one more amazing Nobel-worthy thing Venter has been doing that has absolutely upended biology, genomics, and science. Enriquez called it the age of Metagenomics.

Of note, off all the organisms that they sequenced, about 75% were absolutely new. That's 75%. New. It really made clear the prevalence of microorganisms in the ocean and points to microbes being half the biomass on Earth. And these organisms are critical to the health of the planet and we are risking up-turning the cart through warming and acidification of the oceans.

2) In his lateral thinking way, Enriquez pointed out that the gas in coal mines is due to bacterial digestion of the coal. He said that mining is so dangerous, why don't we just use bacteria and pipe the gas out safely? It sure would be better than strip-mining. Heh.

3) He went off on superbugs, bacteria that are resistant to every antibiotic we can throw at it. He blames it in part to our (inevitable) cleanliness in hospitals. As we wipe everything down, only the hardiest can survive. And then, we provide these bugs a great chance to infect people as we hack them open in the very same areas.

Made me pause and think about how we do medicine.

4) He also had a good comment on the decrease in the number of new drugs pharma has been able to come out with. He ascribes that in part to the mounting difficulty in passing safety standards. He called it the 'Precautionary Principle' - we are forcing pharma to make drugs that kill no one. But, how many thousand will die without the drug? He called on folks to weigh the needs of the very many versus the needs of the very few.

Kevin Kelly, a Long Now founder, suggested Enriquez call his view the 'Pro-actionary Principle'.

Link: Long Views » Blog Archive » Juan Enriquez '€œMapping Life'€:

"All life is imperfectly transmitted code," Enriquez began, "and it is promiscuous."€ Thus discoveries like the one last month of an entire bacterial genome inside the DNA of a fruitfly is exploding the old tree-of-life models of evolution. The emerging map replaces gene lineages with gene webs.

Something about the Clock of the Long Now chimes

The Clock of the Long Now will have chimes that play 10 tones, in unique combination, every day over the course of 10,000 years.

I tend to listen to a bunch of Long Now seminars in a row and noticed something about the chimes played at the start and end of every recording: they are the same.

So that got me thinking. They should be playing different chimes every day. And, I am not sure about the algorithm, but if you can calculate the chimes for each day, then why not play the chime particular to the day of the seminar?

I also started wondering if there was somewhere I could hear the chime for a particular day. And indeed there is. Seam M Burke, on his site Interglacial, has built a generator of MIDI chimes for any date. Brian Eno, in his exploration of the chimes (he was a big part of the idea behind the 10 notes and chimes) came out with a CD, too. The folks at the EMUSIC-L site also have been toying with this, trying to make better tones through their own chimes generator (MIDI is a bit ugh), but I haven't played with it.

from: Clock: Chime Generator (Long Now Foundation site)

Data does not equal knowledge

At LIFT 08 last week, François Grey gave a great talk about the intersection of grid computing, crowdsourcing, and science.

One thing that miffed me was when he was talking about the CERN Large Hadron Collider (LHC) creating huge amounts of data per collision of protons. I don't agree with people who stress the amount of data an experiment produces, comparing it to all the knowledge humanity has produced.

Data is not knowledge.

The LHC indeed will produce oceans and oceans of data, but the amount of knowledge will be much smaller. Indeed, when they make their big discoveries, each will be expressed in a simple hyperlinked publication - a regular scientific paper.

Alex Wright and the history of information systems over the past few billion years

I got through another amazing Long New Seminar (long dog walks are great for that). This one was by Alex Wright, author of 'Glut: Mastering Information Through the Ages'.

What I thought was really well done is how he charts the course of the evolution of social systems from bacteria to humans today and showed how such evolution influenced information systems. Very interesting. He also reveals some lost nuggets of history, re-introducing some information systems visionaries that are not well known (particularly Otlet's Mundaneum).

One other interesting thread of his talk was a discussion of literal and oral culture and information. In one of those Long Now kinda of twists, he points out that literal culture is actually not too old. But also, the way the Web is going, there are plenty of analogies to oral culture in terms of how we share and communicate in social networks.

Very interesting.

Link: Long Views » Blog Archive » Alex Wright, The Deep History of the Information Age:

That’s the pattern for the evolution of information, Alex Wright
said. Networks coalesce into heirarchies, which then form a new
level of networks, which coalesce again, and so on. Thus an unending
series of information explosions is finessed.

Venter's team takes the next step toward custom-built organisms

The biology maverick, Craig Venter, has rapidly taken the next step in creating custom organisms (link below to news article).

Recently, his team managed to test if they could replace a genome in a bacteria with one of their choosing. Now they took the next step and stitched together a whole genome.

He's taking the right first steps. But, just keep in mind that there are many intermediate steps in what he is doing. He's using existing organisms to help him build and grow the sequences he needs, something done in labs all the time.

That's fine. I don't think his goal is some purist ideal of creating a synthetic organism from scratch. I think his goal is to be able to create an organism that does exactly as he wants it. Hence, the first step was being able to prove he could hi-jack the whole machinery of a cell by replacing the genome. Next, he then creates a completely synthetic genome, based on an existing sequence, but with 'watermarks' and some deletions (for control reason). Which is what he's done now.

I think his next step is to create 1) larger and larger genomes; 2) a set of lab organisms based on synthetic genomes to be used as a foundation for creating products (whatever they may be).

Heh, once again, this guy is radically changing the face of biology.

Link: Genome stitched together by hand : Nature News:

The genome for the pathogenic bacterium Mycoplasma genitalium was made in the laboratory by Hamilton Smith and his colleagues at the J. Craig Venter Institute in Rockville, Maryland. The genome has 582,970 of the fundamental building blocks of DNA, called nucleotide bases, making it more than a factor of ten longer than the previous-longest stretch of genetic material created by chemical means.

It's not infoglut on my mind, but infoswim (or something like that)

After a deep conversation with my dad on semantic web stuff, he pointed me to a site (of some guys he works with) that had this quote (below, pulled from another site to give it more - context).

Link: Managing Information: Infoglut:

"Information overload is not a function of the volume of information out there," he says. "It's a gap between the volume of information and the tools we have to assimilate that information into useful knowledge."

But, it is really not infoglut that is on my mind, but how we can revel in the glut, navigate it, annotate it, contribute to it, and extract knowledge from it to generate new knowledge.

A lot of thoughts on this in my backlog of posts. I hope I can get them up during my lifetime...

The future of zoos

Society has come a long way in animal welfare. But we still are caught trying to balance the needs of humanity and the needs of the animal. Zoos are one example.

How do we balance conservation (needed due to the effects of human activities), education, and animal welfare?

Certainly, large carnivores always seem to suffer.

Link: Tiger escapes pen, kills visitor at San Francisco Zoo - The Boston Globe:

A tiger escaped from its pen at the San Francisco Zoo yesterday evening, killing one visitor and injuring two others before police shot it dead, authorities said.

Book by Craig Venter - A Life Decoded: My Genome: My Life

Well, I was wondering when someone would write a book about Venter (who deserves a Nobel, a few times over).

Turns out he wrote one himself. I think I gotta get me a copy.

I found out about this book through an article on him in Salon that my wife sent me. I haven't read the article, but will on my long trip tomorrow.

Link: Amazon.com: A Life Decoded: My Genome: My Life: Books: J. Craig Venter:

A great deal has been written about Venter as the head of Celera, the private research company that won a race with the National Institutes of Health's Human Genome Project to sequence the human genome. His role in this historic accomplishment has been both vilified and praised. Now, in a clumsily written autobiography, Venter offers his side of the story, portraying himself as the eternal underdog, fighting for truth and attempting to make scientific discoveries solely to help others. (Publishers Weekly).

Do community tools mix with scientific papers?

I've been doing some reading on Open Access Publishing, providing free public access to scientific papers. The two publishers I know the best are Public Library of Science and BioMed Central.

These two publishers are trying hard to change the current publishing model in science, where a journal acts as gatekeeper, selecting the best articles, and then charging readers to subscribe to the journals. Indeed, not only are the subscription prices astronomical sometimes, but authors pay the publisher to publish their paper.

PLoS and BMC therefore, have many reasons to turn this model on its head (and chuck it out the door). But, in the end, to me, they seem like the same publishers they are trying to change - they still do peer-review (gate keeping?) and publish article for reading only.

Of course, being a service designer in this day and age, I wonder how one could take these publishers even further, such as how to bring in the readers to participate via the current common community tools (without digressing on the existence of community), or how to bring in some intelligence (folks or robots) to add value to the large mass of info so that, as a total, the publication can drive more discoveries and insights.

PLoS has done something interesting, creating Journal Clubs online. Journal clubs, a staple in universities, are regular meetings to discuss a research paper of interest (like a book club, except more focused and more geeky). PLoS's take on it is interesting (see below) - if the discussion around a paper is captured over time, one could chart the evolution of the thinking over time.

Alas, I would not ask someone to read _all_ the comments. To me, this suggests that in this area, the post-comment model might be insufficient.

Link: Journal Clubs - think of the future! | Public Library of Science:

There it is: all laid out - the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science.

From the Boston Globe comes a great essay on colleges ignoring life's bigger questions

The Boston Globe has this great essay, by Yale Professor Anthony Kronman, about the teaching of the meaning of life in US colleges and universities. It's long, but an excellent read.

Link: Why are we here? Colleges ignore life's biggest questions, and we all pay the price (registration may be required)

The essay was prompted in part by the start of the school season in the US. The author ponders the history of the teaching of the meaning of life, tracing the history of upper education in the US in the process.

"In a shift of historic importance, America's colleges and universities have largely abandoned the idea that life's most important question is an appropriate subject for the classroom."

The author goes on to describe how the focus on research, while bringing great benefits, also seemed to give the humanities short shrift. I was once part of this focused research world. But, as one may be able to guess after being with me for a bit, or reading my stuff, it wasn't enough for me - there was always a part of me that had questions outside my domain. In college, I tried hard to get as much exposure to things like philosophy, art, history, often with more interest than my major subject (of which I took the minimum requirements).

The author makes a great comment:

"In the humanities, however, the legacy of the research ideal has been mixed. We know vastly more today than we did even 50 years ago about the order of Plato's dialogues, the accuracy of Gibbon's citations, and how Benjamin Franklin spent his time in Paris. But the research ideal has excluded the question of life's meaning from serious academic concern as a question too large, too unformed, too personal, to be a subject of specialized research. A tenure-minded junior professor studying Shakespeare or Freud or Spinoza might re-inspect every scrap of his subject's work with the hope of making some small but novel discovery - but would be either very brave or very foolish to write a book about Spinoza's suggestion that a free man thinks only of life, never of death; or about Freud's appealing, if enigmatic, statement that the meaning of life is to be found in work and love."

Heh, that's something I can sink my teeth into.

It was interesting to learn that in the 20s, the president of Amherst College, Alexander Meiklejohn, "defended the idea of spiritual seriousness in a nonreligious age, and thought it could be studied without dogmatic commitments". I agree with the author that we need more programs that do this, and the author lists a few. Indeed, my freshman year (the one year I was at Allegheny College), I was fortunate to take a humanities course that I can say significantly shaped the way I think, learn, and interpret the world.

And the author makes no bones about the complexity of the question. But it is the complexity that enriches the student:

"The first is that there is more than one good answer to the question of what living is for. A second is that the number of such answers is limited, making it possible to study them in an organized way. A third is that the answers are irreconcilably different, necessitating a choice among them. A fourth is that the best way to explore these answers is to study the great works of philosophy, literature, and art in which they are presented with lasting beauty and strength. And a fifth is that their study should introduce students to the great conversation in which these works are engaged - Augustine warily admiring Plato, Hobbes reworking Aristotle, Paine condemning Burke, Eliot recalling Dante, recalling Virgil, recalling Homer - and help students find their own authentic voice as participants in the conversation."

The author points out that in many ways, education has split long dogmatic lines, such as race and gender, and all that comes with political correctness. But my feeling is summed up as in the essay:

"There is an increasing demand among undergraduates for courses that address the big questions of life, in all their sprawling grandeur, without reticence or embarrassment."

Complexity and honesty are critical here. And this is about spiritual direction, a spiritual direction that the simplification of religion and belief have usurped.

"What it needs is an alternative to religion, for colleges and universities to become again the places they once were - spiritually serious but nondogmatic, concerned with the soul but agnostic about God."

And my thoughts echo what the author thinks, that this kind of education could go far in fixing the dogmatic thinking that now pervades the US.

"A richer and more open debate about ultimate values; an electorate less likely to be cowed into thinking that only the faithful have the right to invoke them; a humbler regard for the mystery of life in a world increasingly dominated by technocratic reason."

It's long, but a good read.

Incidentally, the author has also written a book (drink!) on the subject: "Education's End: Why Our Colleges and Universities Have Given Up on the Meaning of Life."