Lifeblog

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.

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...

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?

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.

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.

Are Kosovars Albanians or Serbians?

I grew up thinking that nations should be the scale at which people are governed. I could not understand why Israel didn't just make all the Palestinians Israeli, why the Irish and British couldn't just let Northern Ireland be part of the Republic of Ireland. And, as the Balkans, well, balkanized, and the Soviet Union collapsed, why was everyone moving towards smaller units of government centered around cultural lines?

Well, I'm past that. I am beginning to see that the end of the last 10 years has been more about the end of nations, much like the end of the 19th century was the end of empires.

Taking this logic to a further level, I really think current national governments will lose their power as cities and regions (city-states, anyone?) rise in political and economic strength.

For example, many states in the US are clashing with the federal government, making stricter environmental laws. Cities like London and New York are no longer really part of their nation, becoming true city-states, their mayors meeting heads of state for political and economic reasons.

And, empires fell apart as a sort of national identity arose. But, now, there are regional identities that are stronger still, and cut along cultural lines.

So, are the Kosovars Albanian or Serbian? Neither. They are Kosovar, much like the Austrians are not German, but Austrian, or the French Swiss are Swiss, not French.

It'll be interesting to watch Kosovo form a real government and economy now that the question of their identity is resolved (at least for them). There's a lot a work ahead for them and the global economy was not set up for tiny states to prosper in.

Link: Frenzy greets the new Kosovo - The Boston Globe:

In a move that inflamed tensions in this volatile region, the ethnic Albanian government of Kosovo yesterday proclaimed the province independent from Serbia, forming a new and very troubled country in Europe.

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)