## January 14, 2010

### Going to Singapore

#### Posted by John Baez

Yay! My leave was finally approved!

It’s official!

My wife Lisa Raphals and I are going to Singapore from July 1st, 2010 to June 30, 2011.

She’ll be teaching at the Department of Philosophy at NUS — the National University of Singapore. I’ll be doing research at the CQT — the Centre for Quantum Technologies, which is right next to the math and physics departments on campus, but not precisely part of NUS.

It’ll be an adventure — Bali, Borneo, Malaysia and Sumatra will be right next door. And it’ll be a good chance to drastically change the direction of my research. If I thought I were going to live forever, I could easily enjoy spending a few millennia on constructive quantum field theory, and a few on nonlinear wave equations, and a few on quantum gravity, and a few on $n$-categories. But I’ve always expected to be here for a much shorter time — so I’ve never wanted to spend my whole life on any one of those projects. Better to explore a bit more of what life has to offer — even if, alas, it means doing a somewhat slap-dash job.

I’ve done a lot of highly theoretical stuff. So now I’d like to try my hand at some slightly more ‘practical’ endeavors. I’m sure I’ll still enjoy explaining math and physics. I guess that even counts as practical. I’m not sure how work on ‘quantum technologies’ will mesh with my growing urge to help save the planet. But that’s part of why doing something new is rejuvenating: you feel like a kid again when you don’t know exactly how things will work out!

Posted at January 14, 2010 5:30 PM UTC

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### Re: Going to Singapore

Congratulations!

Posted by: Toby Bartels on January 14, 2010 6:37 PM | Permalink | Reply to this

### Re: Going to Singapore

Congrats!

I just got back from a trip to Singapore. I loved it there :)

PS: Posting here at the n-Cafe didn’t work for me though, but maybe it was due to something at my specific hotel. At least I could read it.

Posted by: Eric on January 14, 2010 11:10 PM | Permalink | Reply to this

### Re: Going to Singapore

If I mysteriously disapppear in July, it means I can’t post to the $n$-Café from Singapore. If that happens, send out a rescue team.

But I’m not really very worried about that possibility. What I’m more seriously worried about is whether people at the $n$-Café will get annoyed if I start posting a lot about quantum technology — or worse, practical ideas about how to save the planet!

Since I don’t want to annoy people (at least, not very much), I might wind up starting another blog.

But no matter what happens, I’ll probably keep wanting to write This Week’s Finds, and posting that here.

Posted by: John Baez on January 15, 2010 2:40 AM | Permalink | Reply to this

### Re: Going to Singapore

Well I’ll certainly enjoy learning more about quantum technology. And over the last few years I’ve become a lot more “conscientized” (is that really a word?) about saving-the-planet (even posted a youtube song last month) but I definitely need to pull up my socks and get much more serious about it. I’m still rooting for the Joan Baez/ John Baez environmental double act to tour the world: the former sings the songs while the latter explains the science!

Posted by: Bruce Bartlett on January 15, 2010 2:04 PM | Permalink | Reply to this

### Re: Going to Singapore

Not simultaneously, I hope.

I’m glad you’re getting serious about this stuff. It takes time to change gears! Strong forces pull us towards familiar paths — what used to work. But the world is changing fast.

Posted by: John Baez on January 16, 2010 5:03 AM | Permalink | Reply to this

### Re: Going to Singapore

Have a great time!

Posted by: Tom Leinster on January 14, 2010 11:28 PM | Permalink | Reply to this

### Re: Going to Singapore

Have fun in Singapore. Also, it turns out that quantum technologies are important for the green revolution. I know this because I am a senior member of the MIT Energy Club and my two specialties are finance for the green sector and quantum physics for the green sector.

Here are two examples of what I mean:

1) Quantum nonlocal entanglement was recently established in biological systems for the first time ever in a paper on natural photosynthesis by M. Sarovar et al. (arxiv paper 0905.3787). If you google the phrase “quantum entanglement photosynthesis” you will first see various articles about how this discovery by Sarovar et al. could help lead to better PV (photovoltaic) solar cells.

I also think that quantum effects might help to make artificial photosynthesis more efficient, and various teams around the world are pursuing artificial photosynthesis technologies.

2) No one has yet figured out the correct way to calculate the potential theoretical maximum open-circuit voltage (Voc) for an organic polymer based PV solar cell (either for the tandem or non-tandem solar cells).

Posted by: Charlie Stromeyer on January 15, 2010 2:40 AM | Permalink | Reply to this

### Re: Going to Singapore

These are the kind of things I might like to think about! Thanks for the suggestions.

Posted by: John Baez on January 15, 2010 2:43 AM | Permalink | Reply to this

### Re: Going to Singapore

John, here are some more items for you to think about within this theme:

Most of the world’s organic based PV solar cells are polymer-fullerene solar cells. The polymers are conjugated (conducting) polymers with a high degree of quantum coherence [1]. The fullerenes are C60 or C70 molecules. (Btw, single molecule transistors such as C60 superconductors are promising candidates as quantum information processing devices [2]).

Now, it turns out that a single photon will more efficiently excite multiple electrons within bulk PbSe or PbS materials than in colloidal PbSe quantum dots [3].

Perhaps someone could find a way to make an ordered structure of PbSe or PbS bulk materials and then put into the pores an organic PV material. The main engineering challenges would probably be the surface tension, pore filling and adjusting the morphology within the tight confines of the pores.

Also, in today’s edition of the journal Science there is a very important paper [4] about an energy cost effective breakthrough initial step towards recycling waste CO2 from the atmosphere into something useful.

Finally, you might want to see these two excellent (albeit unrelated) papers about a first realization of doing quantum chemistry on a quantum computer [5], and about a highly efficient way to construct dye-sensitized tandem solar cells [6].

One of the authors of [5], A. Aspuru-Guzik, has even used category theory in teaching course(s) about quantum information and computation at Harvard University.

(You might even already know that quantum theory is the most accurate and thus most valid scientific theory there is, and that quantum theory already underlies 30% of U.S. GDP.)

[1] E. Collini and G.D. Scholes, “Coherent Intrachain Energy Migration in a Conjugated Polymer at Room Temperature”, Science v323(5912), pp.369-373 (2009).

[2] C.B. Winkelmann et al., “Superconductivity in a single-C60 transistor”, Nature Physics, 25 October 2009.

[3] J.J.H. Pijpers et al., “Assessment of carrier-multiplication efficiency in bulk PbSe and PbS”, Nature Physics 5, pp.811-814 (2009).

[4] Robert F. Service, “Catalyst Offers New Hope for Capturing CO2 on the Cheap”, Science v327(5963), p.257 (2009), and see the article to which this refers starting on page 313.

[5] B.P. Lanyon et al., “Towards quantum chemistry on a quantum computer”, Nature Chemistry, 10 January 2010.

[6] A. Nattestad et al., “Highly efficient photocathodes for dye-sensitized tandem solar cells”, Nature Materials 9, pp.31-35 (2010).

Posted by: Charlie Stromeyer on January 15, 2010 6:49 PM | Permalink | Reply to this

### Re: Going to Singapore

Yes, congratulations!

It’s an interesting question what to choose to work on, entering different points in a career. Something tempting me, but which would require a lot of effort, would be to try to understand the range of graphical languages used in systems biology. Our Centre for Reasoning reading group has taken a look at some of Cardelli’s work already. Next week we get to read an attempt to forge a common language for systems biology – Systems Biology Graphical Notation.

You’d expect huge overlapping with the graphical notation of other disciplines, perhaps the bond graphs mentioned in recent TWFs. To go beyond dabbling will take serious commitment.

Posted by: David Corfield on January 15, 2010 8:54 AM | Permalink | Reply to this

### Re: Going to Singapore

Thanks a lot for the link to this paper, David!

I hadn’t noticed the actual link at first, since it was a bit down the page you pointed us to. Here’s the center for all information on this graphical language:

This is exactly the sort of thing I’m interested in these days! As the authors write:

One can hardly imagine today’s electronics industry, with its powerful, visually oriented design and automation tools, without having first established standard notations for circuit diagrams.

These circuit diagrams, and bond graphs, are not just rough hand-wavy pictures: you can think of them as a precise notation for describing systems made of components that satisfy 2nd-order differential equations. As such, they deserve to be integrated into the rest of mathematics, and that’s what I’m busy doing now.

But there’s potentially a lot more mileage to be gained from doing this sort of work in an important subject where the notation is still a mess! As the article continues:

… Such was not the case in biology. Despite the visual nature of much of the information exchange, the field was permeated with ad hoc graphical notations having little in common between different researchers, publications, textbooks and software tools. No standard visual language existed for describing biochemical interaction networks, inter- and intracellular signaling gene regulation—concepts at the core of much of today’s research in molecular, systems and synthetic biology. The closest to a standard is the notation long used in many metabolic and signaling pathway maps, but in reality, even that lacks uniformity between sources and suffers from undesirable ambiguities.

They claim that their SBGN is ‘three orthogonal languages’.

Posted by: John Baez on January 16, 2010 10:36 PM | Permalink | Reply to this

### Re: Going to Singapore

There’s an amusing piece by Lazebnik about how biologists need to develop a graphical language as engineers have – Can a Biologist Fix a Radio? – or, What I Learned while Studying Apoptosis.

Posted by: David Corfield on January 17, 2010 12:16 AM | Permalink | Reply to this

### Brother, Can You Spare a Paradigm; Re: Going to Singapore

“… At some point, David said, the field reaches a stage at which models, that seemed so complete, fall apart, predictions that were considered so obvious are found to be wrong, and attempts to develop wonder drugs largely fail. This stage is characterized by a sense of frustration at the complexity of the process, and by a sinking feeling that despite all that intense digging the promised cure-all may not materialize. In other words, the field hits the wall, even though the intensity of research remains unabated for a while, resulting in thousands of publications, many of which are contradictory or largely descriptive. The flood of publications is explained, in part, by the sheer amount of accumulated information (about 10,000 papers on apoptosis were published yearly over the last few years), which makes reviewers of the manuscripts as confused and overwhelmed as their authors….”

Completely consistent with Thomas Kuhn’s Structure of Scientific Revolutions. Anomalies, Crisis, Revolution, New Paradigm.

Posted by: Jonathan Vos Post on January 17, 2010 1:43 AM | Permalink | Reply to this

### Dubious of the radio analogy

I’m a bit torn looking at that paper. I can see that a systematic (and hopefully graphical) notation would be of great use, if for no other reason than it might render brute force search feasible (my idee fixe). But I think the radio analogy confuses things because we already know only one set of concepts that make sense for circuitry. I think a better analogy would be considering a known low-level machine code in computers as the “already understood things” (analogous to, eg, “chemical reaction X occurs”, etc) and the task being to figure out concepts for understanding the behaviour of programs. We have various different conceptual frameworks for practically constructing understandable programs (ie, ignoring unversality of computation meaning they can in theory simulate each other) including procedural programming, object oriented programming, functional programming, logic programming, term-rewriting and more, each with their structuring concepts (eg, currying for functional languages). If I give you a host of converted-to-machine-code programs in some unknown framework (ie, pretend you’ve never heard of any of the above frameworks and I give you billions of examples from one particular one), the task of figuring out appropriate concepts and hence notation looks a lot harder and exploratory than the radio example. Still both possible and very, very desirable, but much harder.

Posted by: bane on January 17, 2010 6:06 AM | Permalink | Reply to this

### Re: Dubious of the radio analogy

The computer programming analogy reminds me to mention the unified modelling language (UML), which I did not before, because it’s hardly more than a distraction - I don’t think that it could be of interest to mathematicians…but I’ll let you make up your own mind:

UML was invented as a graphical language that helps modelling systems and processes before a significant part is realized as an object oriented software system. Certain types of diagrams can be used to generate e.g. Java program stubs and vice versa: There are tools that will take Java programs as input and generate e.g. object diagrams (I’m certain that there are tools for all well known object oriented programming languages, but Java is the only one where I used this round-trip myself). The big companies that I know of all have some “diagram-standard”, which means that every concept for a software system has to have certain types of diagrams - if you forget one you must have a good explanation or it won’t be approved.

Posted by: Tim vB on January 18, 2010 12:46 PM | Permalink | Reply to this

### Re: Dubious of the radio analogy

Tim, thanks for telling us about UML which I didn’t know about and which is interesting mathematically for this reason:

UML enables what are called UML state machines which generalize the concept of finite state machines (FSM) in an advantageous manner.

Another way to generalize FSM is via coalgebraic automata theory .

Either UML state machines and/or coalgebraic automata theory could be used to further generalize pattern theory which is the type of AI that the Fields medalist David Mumford is currently working on.

Btw, for John Baez, the main argument I have heard for why synthetic biology might have a relatively minor impact upon evolution is that synthetic organisms will be created for highly specialized purposes and thus are expected to lack the flexible adaptive qualities of populations of naturally evolved organisms, meaning that it might be tough for the synthetic critters to compete with natural critters.

Posted by: Charlie Stromeyer on January 18, 2010 6:18 PM | Permalink | Reply to this

### Re: Going to Singapore

I agree with Bane that Lazebnik’s paper is unfair to biologists.

Electrical circuits are designed by people, so it’s not surprising that people can take a radio and draw a circuit diagram that shows how it’s built from components, and write down a differential equation saying how each component works… and then, a differential equation saying how the whole system works.

Biological systems were not designed by people; they evolved. So, if we want to describe them in a reductionist way, we have to guess at the best way to divide them into ‘components’, and guess which interactions between these components are important and which can be neglected… and perhaps someday guess at some equations describing the components.

Depending on what we’re trying to do, one way around this problem is for people to design their own biological systems! I wrote about this in my August 20, 2005 diary entry:

This is called "synthetic biology". The First International Meeting on Synthetic Biology was held in the summer of 2004, with talks like "Rewiring cell signaling pathways", "Programming cells and synthetic gene networks", and "Biological property rights". But in fact, Thomas Knight has been teaching classes on synthetic biology for several years - back at my old grad school, MIT. The kids in these classes use a toolkit of standardized parts called Biobricks to build new biological systems. It’s sort of like building electrical circuits from resistors, capacitors, and transistors. They do this for fun during the Independent Activities Period — a kind of free-for-all that takes place each January between semesters.

Check out some of their projects! You’ll see stuff like:

The objective of the project is to design a bacteria that when cultured will produce a recognisable polka dot pattern in the culturing medium. Our design attempts to achieve this by hijacking the quorum sensing mechanism employed by bacteria such as Vibrio fischeri and more particularly in our case Pseudomonas aeruginosa used to regulate group behaviour. We are attempting to use the las/rhl quorum sensing system used by the latter, in conjunction with a heat trigger to cause small clumps of bacteria to turn on the LacZ colour expression gene and hopefully get a small selection of polka dots in a tasteful display of purple.

Some people will find this amusing. Some will find it exciting. Some will find it terrifying. I mainly just wish more people knew this kind of stuff is going on!

A while back I mentioned that scientists figured out how to expand the genetic code to create a new codon in E. coli bacteria. If you don’t know what that means, you won’t realize how far-out it is. The "letters" in DNA are grouped in "words" of 3 letters each, called codons, each of which serves as instructions to make a specific amino acid. A gene is a "sentence" built from these words, which creates a specific sequence of amino acids that get strung together to form a protein molecule. Since there are four letters - A, T, C, and G - there are potentially $4^3 = 64$ codons. However, a bunch of codons create the same amino acids, and some potential codons don’t get used at all. So in fact, most of the organisms on Earth only create 20 different amino acids. This leaves room for expansion - and scientists have created a new codon that lets Escherichia coli create an amino acid that’s not one of the usual twenty.

In an even more radical move, some other scientists have introduced new "letters" into the genetic code - that is, new base pairs besides the familiar A (adenine), T (thymine), C (cytosine) and G (guanine)!

When I read this, it reminded me of Greg Egan’s scary story "The Moat" in his book Axiomatic, where some radical secessionists genetically engineer themselves to have different base pairs and then… introduce a virus that kills off the rest of us? But, the original experiment came two years before Egan’s tale:

• S. A. Benner, S. E. Moroney, and C. Switzer, Enzymatic incorporation of a new base pair into DNA and RNA, Jour. Amer. Chem. Soc. 111 (1989) 8322–8323.

You can find a nice review of this and other work here:

Where will all this lead? Start imagining it now. Then read my October 27th entry.

Posted by: John Baez on January 17, 2010 9:01 PM | Permalink | Reply to this

### Re: Going to Singapore

Since I know many biologists in the Cambridge, MA area, I asked some of them if they thought that synthetic biology might or might not have a big impact on the future of evolution of life on Earth and they said it would likely be the least significant change compared to these four developments:

global climate change

stem cells engineering

genetic engineering

nanotechnology

Also, I don’t know if synthetic biology might even turn out to be as significant as various epigenetic changes combined. Speaking of evolution, here are some very weird new findings:

Even though prions lack a nucleic acid genome they still appear to evolve with some mutations according to a kind of Darwinian natural selection.

A green sea slug which can actually do photosynthesis. This is the first known photosynthetic animal! (Note that both plants and animals use the same chemistry for detecting CO2 molecules).

An epigenetic violation of Mendelian genetics.

Various apparent examples of Lamarckian evolution (including one discovered at MIT).

If anyone wants to know more about these evolutionary findings then I could post links to the relevant papers.

Posted by: Charlie Stromeyer on January 17, 2010 10:04 PM | Permalink | Reply to this

### Re: Going to Singapore

John expressed a thought in the form:

codons, each of which serves as instructions to make a specific
amino acid

Of course, codons don’t “make” (or “create”) amino acids—they simply code for them to be inserted (at that point) into a protein that is being built. The actual synthesis of the amino acids is a whole separate story.

Posted by: Tim Silverman on January 17, 2010 11:24 PM | Permalink | Reply to this

### Re: Going to Singapore

Thanks — duly fixed. When I first wrote that, could I have been under the delusion that amino acids were specially created as part of the process of sticking them together to form RNA? Dunno — that seems pretty stupid now. I think I’ve seen plenty of pictures like this:

By the way: a while ago I ran into a strange paper which tried to use Galois theory to explain the precise rules saying which codons code for which amino acids… or something like that.

It may have been this:

or it may have been this:

but neither of these look quite right. I don’t know why I’m mentioning it: was a fairly flaky attempt to solve what’s actually a famous puzzle. I guess it’s an example of how I wouldn’t want to apply math to biology! It would be cool if nature had evolved to a genetic code having some deep relation to the finite field with 64 elements, but it seems ‘too good to be true’.

Posted by: John Baez on January 18, 2010 1:11 AM | Permalink | Reply to this

### Re: Going to Singapore

The first graphic above doesn’t mention the crucial role played by microRNAs. Also, here is some valid mathematical biology you might want to know about:

RNA global conformation is defined mainly by topological constraints [1], and chromosomes are densely packed and folded without any knots or tangles into nuclei in the form of what are called “fractal globules” [2] which were initially deduced by reading a physics paper about Peano curves.

[1] M.H. Bailor et al., “Topology Links RNA Secondary Structure with Global Conformation, Dynamics and Adaptation”, Science v327(5962), pp.202-206 (2010).

[2] E. Lieberman-Aiden et al., “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principle of the Human Genome”, Science v326(5950), pp.289-293 (2009).

Posted by: Charlie Stromeyer on January 18, 2010 2:28 AM | Permalink | Reply to this

### Re: Going to Singapore

The second paper above, for example, is part of the field of systems biology. Category theorists could potentially play a useful role in this field which is what Taichi Haruna is trying to do. Here is one of Haruna’s recent abstracts which I cut and paste because I don’t know if there is a direct web link to it:

“An application of category theory to systems biology”

Taichi Haruna
Graduate School of Science, Kobe University

Abstract. “We discuss (i) a new analytical tool for directed networks and (ii) a new hypothesis on network motifs, through category theory. A network represented by a directed graph consists of a set of function-less nodes and a set of arcs between nodes. However, in real networks, nodes are not really function-less. For example, in transcription regulation networks or neuronal networks, we can find information processing in each node. It would be useful for further understanding of the real network structure if we succeed to obtain a formal representation including a function of a node such as information processing, which is usually neglected. Here we simply represent a function of a node as a directed graph representing information flow within nodes. In addition, we prepare another directed graph corresponding to an arc to represent how functions of nodes are related. Incorporating these materials into the Grothendieck construction in category theory, we obtain a graph transformation that transforms a network to its functional network. This transformation is a functor from the category of directed graphs to itself, denoted by L. L has its dual R (called the right adjoint to L in category theory). R is a transformation of forgetting function. We performed the transformation L to various real networks in the literature. We found a distinguishing global structure
common in the functional networks for the real networks by comparing them to suitable ensembles of random networks. Moreover, we obtained the condition when a directed graph G satisfies RL(G)=G. This equation means that all functional constraint appeared in L(G) is already incorporated in G itself. We make a new hypothesis on a network motif called bi-fan through this condition and our data analysis. Network motifs are local patterns found in real networks significantly more often than suitable ensembles of random networks. Among them, bi-fan is ubiquitously found in various real networks and is most over-represented. In the previous work, network motifs are considered locally both in their structures and functions. However, we discuss the possibility that the ubiquitous nature of bi-fan is explained in relation to the global feature of real networks by combining our data analysis and the mathematical condition RL(G)=G.”

Also, category theorists might play a useful role in the nascent field of quantum biology. There is an annual and legitimate conference devoted to this field called “QuEBS” which means “Quantum Effects in Biological Systems”.

I have previously speculated that this nanomagnetic technology [1] developed at the lab of Harvard physics professor Mara Prentiss might be used to study potential (nontrivial) quantum effects within cellular systems.

[1] R.J. Mannix et al., “Nanomagnetic actuation of receptor-mediated signal transduction”, Nature Nanotechnology 3, pp. 36-40 (2008).

Posted by: Charlie Stromeyer on January 18, 2010 4:55 PM | Permalink | Reply to this

### Re: Going to Singapore

Taichi Haruna’s PhD thesis is here (http://www.lib.kobe-u.ac.jp/repository/thesis/d1/D1004178.pdf), I think. (I have messed up trying to post links on this blog before). Its title is “Algebraic Theory of Biological Organization.”

[Fixed – DC]

Posted by: Eugene Lerman on January 18, 2010 5:33 PM | Permalink | Reply to this

### Re: Going to Singapore

John wrote:

I guess it’s an example of how I wouldn’t want to apply math to biology!

Along with a biologist friend, Albert Harris, at UNC, I’ve long held (as have others I’m sure), that one shouldn’t try applying (only) existing math to biology. The math used in physics is usually developed to do physics, cf. calculus.

Posted by: jim stasheff on January 18, 2010 1:26 PM | Permalink | Reply to this

### Re: Going to Singapore

Jim, there is at least one really good example which proves that your intuition is correct:

Back in the mid-1990s, it was shown that repetitive triangular patterns occur in the neuronal networks of the worm Caenorhabditis elegans.

Well, this finding in biology helped to inspire a new breakthrough result in combinatorics by M.E.J. Newman in his paper Random graphs with clustering .

Posted by: Charlie Stromeyer on January 18, 2010 9:45 PM | Permalink | Reply to this

### Re: Going to Singapore

There’s also Craig Venter’s plans for creating artificial lifeforms for various tasks in the very near-term (within months to years). What worries me a little about this is not the concept, but that the desire to make money as quickly as possible will cause careful regulatory scrutiny to be curtailed.

Posted by: bane on January 18, 2010 12:32 AM | Permalink | Reply to this

### Re: Going to Singapore

There seem to be many projects for developing artificial life — I listed a bunch in my October 27th 2005 diary entry.

Charlie wrote:

Since I know many biologists in the Cambridge, MA area, I asked some of them if they thought that synthetic biology might or might not have a big impact on the future of evolution of life on Earth and they said it would likely be the least significant change compared to these four developments:

global climate change

stem cells engineering

genetic engineering

nanotechnology

I’m no expert, but personally I suspect there won’t be a sharp line between ‘nanotechnology’, ‘synthetic biology’ and ‘genetic engineering’. There will be small artificial entities that act a lot like machines, small artificial entities that act more like organisms, and organisms that have been artificially modified. Some won’t reproduce, others will. We’ll need to be very careful about the ones that do! And knowing us, we probably won’t be careful enough.

One hopes that the organisms that already exist will be better adapted to ordinary conditions than the ones we create. But it may not always be true.

Even though prions lack a nucleic acid genome they still appear to evolve with some mutations according to a kind of Darwinian natural selection.

I didn’t know that. Information, please? I have a section on prions as part of my webpage on subcellular life forms. I think they’re really cool.

Speaking of the fuzzy line between synthetic biology and genetic engineering, check out the stuff on my subcellular life forms page about ‘Spiegelman’s monster’, if you don’t already know about that!

A green sea slug which can actually do photosynthesis.

There’s a picture of one in my January 1st 2009 diary entry, thanks to Mike Stay. The really cool part is that it eats algae and incorporates genes from these algae into its own DNA.

An epigenetic violation of Mendelian genetics.

Various apparent examples of Lamarckian evolution (including one discovered at MIT).

I mention a known form of Lamarckian evolution in my June 30th 2006 diary entry. It involves epigenetics: a mother can pass on traits she picked up during her life by doing histone methylation to her child’s embryo! Do you know more? I find this stuff fascinating.

Hmm, there’s a bit more about it here.

Posted by: John Baez on January 18, 2010 2:19 AM | Permalink | Reply to this

### Re: Going to Singapore

“Darwinian Evolution of Prions in Cell Culture” by J. Li et al. in Science, published online December 31, 2009.

Also, this is the best example of Lamarckian evolution I know of:

http://www.frontiersinzoology.com/content/6/1/7/abstract

Posted by: Charlie Stromeyer on January 18, 2010 2:57 AM | Permalink | Reply to this

### Re: Going to Singapore

Thanks a lot, Charlie!

By the way, if you type

<a href = “http://www.frontiersinzoology.com/content/6/1/7/abstract”>Bacterial feeding induces changes in immune-related gene expression and has trans-generational impacts in the cabbage looper (Trichoplusia ni)<a/>

Bacterial feeding induces changes in immune-related gene expression and has trans-generational impacts in the cabbage looper (Trichoplusia ni)

It’s a bit of work to type in a working link, but it greatly increases the chance that people will take a look.

(There are ways that take less work, but this particular way is easy to remember for anyone who knows a smidgen about webpages.)

Posted by: John Baez on January 18, 2010 4:03 AM | Permalink | Reply to this

### Re: Going to Singapore

A sytems biologist I know had the same reaction to Lazebnik’s paper – that it is unfair.

But perhaps one may make a fairer charge that they have rested content with influence diagrams when something more like a electrical circuit diagram is possible. The final diagram for CaMKII in synaptic plasticity here is starting to look like as intricate as a circuit diagram.

Posted by: David Corfield on January 19, 2010 11:58 AM | Permalink | Reply to this

### Re: Going to Singapore

That particular diagram of synaptic plasticity is not very realistic for two reasons:

1) The diagram claims to show what enables LTP (long-term potentiation), but we now know that LTP depends upon non-neurons called astrocytes [1] which are the most abundant type of glial cells in the human brain.

2) The diagram shows a role for glutamate which is the most common excitatory neurotransmitter in the mammalian nervous system, and glutamate is also a precursor for the inhibitory GABA. Well, it turns out that both glutamate and GABA can each communicate with cells non-synaptically too! See, for example, paper [2].

[1] C. Henneberger et al., “Long-term potentiation depends on release of D-serine from astrocytes”, Nature v.463, pp. 232-236 (2010).

[2] S. Olah et al., “Regulation of cortical microcircuits by unitary GABA-mediated volume transmission”, Nature v.461, pp.1278-1281 (2009).

Posted by: Charlie Stromeyer on January 19, 2010 12:39 PM | Permalink | Reply to this

### Re: Going to Singapore

For those of you who thought Lazebnik’s Can a Biologist Fix a Radio? unfair, you might like to try Cardelli’s Can a Systems Biologist Fix a Tamagotchi?.

Posted by: David Corfield on January 30, 2010 2:34 PM | Permalink | Reply to this

### Re: Going to Singapore

Can a Systems Biologist Fix a Tamagotchi?

Cardelli wants biologists to think about software as much as about hardware. Category theory has well known applications to programming, but these are to high-level structured programs, very different from the ad hoc low-level software that is DNA.

Posted by: Toby Bartels on January 30, 2010 5:25 PM | Permalink | Reply to this

### Re: Going to Singapore

FWIW, I didn’t think Lazebnik’s paper was unfair so much as that the radio analogy was an analogy that misled more that it illuminated given what (I think) he was trying to argue.

The Cardelli paper also seems to be avoiding talking about the main issue: in what manner can one best find (possibly approximate) high-level representation from a mass of data when one doesn’t know the concepts that representation embodies in advance. (Concepts implicitly creep in Cardelli’s paper at points, eg, when he talks about “stack traces”: how do we know tamagotchis aren’t programmed as a cellular automaton, where a stack trace doesn’t exist. Arguably this shows the difficulty of arguing from analogy to a “known” thing whilst pretending you don’t “know about it”.) As far as I can see, Cardelli is as much as anything arguing that there’s no “Royal road” discipline/methodology/whatever that will uniformly discern tamagotchi structure and that most approaches need to be pursued and incrementally build concepts and understanding.

Posted by: bane on January 31, 2010 11:20 AM | Permalink | Reply to this

### Tamagotchi

bane wrote:

Concepts implicitly creep in Cardelli’s paper at points, eg, when he talks about “stack traces”…

True, and I missed that! This has to be some kind of rank stupidity on my part, but it certainly shows that we are easily fooled by implicit, yet unwarranted, assumptions.

But I have to admit that I understood Lazebnik’s paper in a different way, namely that biologists are in need of a (graphical) language that allows to describe complicated systems and interactions, that impression came from Fig.3 of his paper, and less about how one should proceed to find the correct description of a given system in that language. But I have to admit that I did not think of the problem that one needs a concept of the systems one wants to describe before one can devise a language.

In the case of the Tamagotchi I would assume that it can be described by a series of UML diagrams. One notable criticism of UML is the inability to model different layers of abstraction: If you would succeed to model the Tamagotchi by UML diagrams - in the sense that it could be reproduced e.g. in the USA based on the model alone - most people will be unable to say what kind of system the model models (as one of my collegues liked to say:”Looking at an UML diagram in order to understand a software system is like looking at a globe through a straw - it’s impossible to get the overall picture”).

P.S.: The following part is a joke, right?

Q1: What differential equations does T. nipponensis obey? Hmm… Conclusion: Mathematical understanding fails.

Posted by: Tim van Beek on January 31, 2010 12:55 PM | Permalink | Reply to this

### Re: Tamagotchi

The following part is a joke, right?

I interpreted it as a limited conception of what constitutes ‘mathematics’, namely the stuff that a biologist would learn in school, only what leads to (and ends with) nonrigorous calculus and stats. Especially since ‘statistics’ is often taught in its own department, it’s easy to identify mathematics with differential equations.

But yes, it must be a joke, since Cardelli himself (a functional programmer and type theorist, among other things) knows better. (Unless he classifies everything discrete as ‘computer science’? Nah, he must know better.)

Posted by: Toby Bartels on January 31, 2010 5:19 PM | Permalink | Reply to this

### Re: Going to Singapore

And it’ll be a good chance to drastically change the direction of my research.

Since everyone else is congratulating, let me be the one to say: it’s also a bit sad. John Baez leaving categorical mathematical physics. It is a loss!

But, even though it took a long time to finally penetrate my skull, I suppose I understand the reasons now. And there is no point in forcing something if it is no fun anymore. But apart from all my best wishes to you and your wife, i’ll express this wish, half jokingly:

I wish after a year you’ll be sufficiently bored and relaxed from calculating the potential theoretical maximum open-circuit voltage for an organic polymer based PV solar cell that you come back with renewed energy to be yearning to think again about the abstract nonsense structure of the universe!

Posted by: Urs Schreiber on January 15, 2010 7:11 PM | Permalink | Reply to this

### Re: Going to Singapore

Urs wrote:

Yes. Thanks for saying that, Urs. It means more to me than all the congratulations.

It was painful to make this decision, and making it kept me busy for a long time. But now that it’s made, I’m looking towards a wide-open future, which makes me happy.

However, I doubt I’ll be able to completely quit ‘categorical mathematical physics’ — at least if you define it broadly enough.

For one thing, my current research on electrical circuits and related systems uses a lot of category theory. Ideally — in an optimistic scenario — I might succeed in getting engineers to realize that category theory is crucial for understanding the ‘bond graphs’ they use to model complex systems built from parts. And perhaps even biologists and people trying to understand ecosystems?

Also, Jim Dolan’s program of reformulating algebraic geometry using the language of ‘doctrines’ is picking up speed. This stuff is really beautiful: it’s so much simpler than the usual approach. I always enjoy talking to him, so there’s no way I’m going to stop doing that. In Singapore I can do it via Skype. And I hope to write more about this, someday.

Meanwhile, I am happy to know that categorical mathematical physics is in your capable hands.

Posted by: John Baez on January 15, 2010 7:50 PM | Permalink | Reply to this

### Re: Going to Singapore

Ah, good, then I can also say it’ll be rather sad if you leave this blog and this community. I can understand, though, that you’d want to move to greener fields after all this time; and, whatever you end up working on, I’m sure you’ll make it sound very interesting to us whenever you tell us about it.

Congratulations on opening this gate to a new garden, anyway, and best wishes to you and Lisa. I guess it’s a bit early to be saying bon voyage, but good luck!

Posted by: Tim Silverman on January 15, 2010 8:58 PM | Permalink | Reply to this

### Re: Going to Singapore

Thanks, Tim. I sure don’t want to lose touch with everyone here. Indeed, I hope to use my ‘pied piper’ talents to lure you all into doing beautiful things that also help save the planet. I just need to find out what those things are first.

And if anyone plans to visit Singapore while I’m there, drop me a line! Alissa Crans has already made plans to stop by… and some of Lisa’s friends want us to explore Thailand with them.

Posted by: John Baez on January 15, 2010 11:28 PM | Permalink | Reply to this

### Re: Going to Singapore

I am happy to hear of your move because it sounds exciting for you and Lisa. Being in Asia right now, Singapore in particular, is very exciting. There is vibrant optimism in the air about the future.

On the technical side, I am anything but sad as well. I never even considered that you’d leave ‘categorical mathematical physics’. I see it as though you are bringing categorical mathematical physics to more applied areas. That would be great!

For years, even before changing careers from applied physics to finance, I hung around this place because I always felt that computational physics could benefit from higher category theory. If space-time is an $n$-category, then surely a computer model of space-time should be an $n$-category as well. I also wished I (or better Urs!) could have a renewed look at our work on discrete differential geometry through the lens of category theory. Especially considering its close ties to Kahler differentials, universal differential envelopes, and synthetic differential geometry.

Now that I work in finance, I see all around me the opportunity to ‘categorify’ stuff. For example, I’ve mentioned before that it would be fun to look at a categorified Black-Scholes equation on loop space (or curve space) for modeling the yield curve.

While I was in Singapore, I tried to post these links (in regard to TWF 289):

This stuff is screaming for the attention of applied category theorists. I’d love to tie these topologies to Tom’s recent work on diversity.

Whether it is the environment, the economy, alternative fuels, quantum networks, whatever, any field can benefit from applied category theory so I’m excited to see where the new chapter takes you.

Posted by: Eric on January 16, 2010 2:20 AM | Permalink | Reply to this

### Re: Going to Singapore

Posted by: jim stasheff on January 16, 2010 2:15 PM | Permalink | Reply to this

### Re: Going to Singapore

Eric, here is another way that category theory might be involved in mathematical finance:

U. Montanari and J. Meseguer did important initial work on the connections between monoidal categories and Petri nets [1], and Y.Y. Du and others have written quite a few papers on the uses of Petri nets for finance (e.g., for dynamical stock trading systems).

Petri nets traditionally model discrete systems, but for at least the past decade there have been ‘hybrid Petri nets’ which model both discrete and continuous events.

I want to combine such hybrid Petri nets with Bayesian nonparametric statistics into a single system that can simultaneously handle discrete, continuous and probabilistic events, in part because when Emily Fox (now at Duke University) was at MIT she and her coworkers discovered a new way to use Bayesian nonparametric methods for discerning order within complex (complicated) systems, e.g., stochastic stock market volatility.

(As a side note which might interest you or John Baez, there is a quantum algorithm which offers an exponential speedup over classical algorithms for solving nonlinear ODEs [2].)

[1] S. Abramsky, “Petri Nets, Discrete Physics, and Distributed Quantum Computation”, in “Concurrency, Graphs and Models”, LNCS v.5065 (2008).

[2] S.K. Leyton and T.J. Osborne, “A quantum algorithm to solve nonlinear differential equations”, arxiv paper 0812.4423.

Posted by: Charlie Stromeyer on January 16, 2010 4:27 PM | Permalink | Reply to this

### Re: Going to Singapore

Eric wrote:

Being in Asia right now, Singapore in particular, is very exciting. There is vibrant optimism in the air about the future.

Optimism? That will be strange and interesting to experience. As you know, the mood in the United States, and especially here in California, is extremely dark. For example, I’m the chair of the library committee at UCR, and the budget for books was cut by 67% last year. My wife’s department decided to save money by disconnecting the phones in the professors’ offices! So when people talk about al Qaeda moving into “failed states”, we think “hello, Osama.”

On the technical side, I am anything but sad as well. I never even considered that you’d leave ‘categorical mathematical physics’. I see it as though you are bringing categorical mathematical physics to more applied areas. That would be great!

Yes, that would be great. I’m not sure how much overlap there is between working on quantum technologies, solving environmental problems, and doing beautiful math, and what I’ll do when they pull in different directions. But luckily, I can take it a day at a time and see how it goes. There’s certainly no shortage of things to explore!

Posted by: John Baez on January 16, 2010 4:04 AM | Permalink | Reply to this

### Re: Going to Singapore

John, there are some possible connections between these different topics in this sense:

Consider the basic problem of finding a vector x satisfying Ax = b for some given matrix A and vector b. This type of problem occurs in some of the science and engineering of energy systems.

There is now a new quantum algorithm [1] which enables a limited form of simulation for solving linear equations. More importantly, paper [1] proves that any quantum computation can be encoded into an instance of solving linear equations.

(20 years ago, F.W. Lawvere wrote that there are some interesting subtleties with systems of linear equations over distributive categories. Such categories are basically the same as polycategories, and these categories have been involved with both quantum physics and with linear logic [2].)

[1] A.W. Harrow et al., Phys. Rev. Lett. 103, 150502 (2009).

[2] See the recent work of Samson Abramsky, of Bob Coecke and of Peter Selinger.

Posted by: Charlie Stromeyer on January 16, 2010 2:15 PM | Permalink | Reply to this

### Re: Going to Singapore

Congratulations, again, and good luck in your new explorations! I, like others, will be sad to whatever extent you fade out of the “abstract nonsense structure of the universe” scene. You’ve done so much to help the subject already. But I definitely understand the urge to do new things, and the need to spend time on things that feel meaningful. (In general, I think the mathematical community could stand to be a little more understanding of people who leave it for other endeavors, for whatever reasons.) I’m glad you still plan to keep in touch!

Posted by: Mike Shulman on January 16, 2010 1:40 AM | Permalink | Reply to this

### Re: Going to Singapore

Thanks, Mike. You wrote:

In general, I think the mathematical community could stand to be a little more understanding of people who leave it for other endeavors, for whatever reasons.

I think the problem is that pure math is appreciated by so few people, and so beloved by those who do, that they feel it’s either a failure or betrayal of some sort to leave it.

I remember feeling somehow personally hurt when I learned (years after it happened) about Grothendieck’s decision to leave mathematics, or even Mumford’s decision to leave algebraic geometry for research on vision.

Why? I don’t know. Maybe I didn’t fully realize that someone may want to spend their finite lifespan on more than one thing. I wanted my icons to stay iconic! But I always knew that I wanted to do lots of things. In fact at a certain stage I had it all planned out: I would quit math at 40. But much later, around the age of 30, I heard about $n$-categories. They kept me quite busy for almost two decades. And now I realize that math is so broad that I can do almost anything while continuing to be a mathematician.

Do the rest of you plan to keep doing roughly the same type of work until you keel over, or a bunch of different things? David C., I know, has done quite a number of things under the header of ‘philosophy’.

Posted by: John Baez on January 16, 2010 7:15 PM | Permalink | Reply to this

### Re: Going to Singapore

David Mumford’s recent work has been in the area of pattern theory which is based upon finite state automata (FSA). Y. Venema generalized the ideas of FSA into what is called “coalgebraic automata theory” and then C. Kupke and others wrote various papers about this new more general theory.

I don’t really know anything more about coalgebraic automata theory, and thus it would not surprise me if it is somehow related to John Hunton’s or Tom Leinster’s ideas about coalgebraic topology.

Posted by: Charlie Stromeyer on January 16, 2010 10:14 PM | Permalink | Reply to this

### Re: Going to Singapore

As you all probably know, I haven’t changed fields
but the world around my field has sure changed.
cf. Gulliver versus Alice

Posted by: jim stasheff on January 17, 2010 1:46 AM | Permalink | Reply to this

### Re: Going to Singapore

I think of you as someone who cleverly adapted to changing times — your love of homological algebra and operads remained constant, but when homotopy theory and loop spaces went (temporarily) out of fashion and math inspired by physics became de rigeur in the 1980s, you were able to discover lots of new applications of these techniques.

I think of Graeme Segal as vaguely similar: in the 70’s he worked on loop spaces, but starting in the 80’s he caught the wave of string theory and worked on loop groups… and of course, conformal field theory.

It’s interesting to compare you two with another king of loop space theory: Peter May. I think of him as someone who stuck more closely to homotopy theory, not diving into the new wave of math inspired by physics. He stayed young in a different, more algebraic way: by staying at the cutting edge of spectra, model categories and more recently $n$-categories.

These are just the impressions of a cheeky youngster! I’d gladly be corrected.

Posted by: John Baez on January 17, 2010 2:16 AM | Permalink | Reply to this

### Re: Going to Singapore

Two months ago someone working in my office building retired, and I happened to be on the elevator with him as he was walking out with his lamp on his last day. He said, with a smile, something like “You know, they just honored me for 38 years of dedicated service, but actually I think it was more like inertia.”

I just retired myself, a little earlier than expected, and hastened by a recent hospitalization for something weird enough that the federal government is investigating. For my health I needed a fresh start away from that stressful old job, and I’m reevaluating everything from how I spend time with my dog to the mathematics I’m working on. I’ve been distracted for several months now by these events and a few other crises, and it has imposed a kind of forced vacation from mathematics that I’ve probably needed for some time, but would not have achieved due to inertia, and from which I should be able to return soon with fresh eyes.

More than a few excellent mathematicians have changed course. Good luck!

Posted by: Richard on January 17, 2010 4:36 AM | Permalink | Reply to this

### Re: Going to Singapore

Do the rest of you plan to keep doing roughly the same type of work until you keel over, or a bunch of different things?

To quote a great philosopher, I never make plans that far ahead.

Posted by: Mike Shulman on January 17, 2010 4:55 AM | Permalink | Reply to this
Read the post The Sacred and the Profane
Weblog: The n-Category Café
Excerpt: Contrasting two attitudes towards mathematics
Tracked: January 18, 2010 12:38 PM

### Re: Going to Singapore

As to Math and Computer Science at the frontier of Biology, see also Tim Gowers’ thread on

Polymath and the origin of life

Posted by: Jonathan Vos Post on January 18, 2010 6:37 PM | Permalink | Reply to this

### Re: Going to Singapore

Jonathan, thanks for this Gowers’ link, and there are others with very similar thoughts, i.e., last September there was a conference entitled Darwin Meets von Neumann .

Posted by: Charlie Stromeyer on January 18, 2010 8:42 PM | Permalink | Reply to this

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