Recently my former group published one paper about the stability of complex food network in the journal ‘Science’. This is not my direction. But I am near enough to understand their ideas of research.

The basic question came from Robert May in the 70s. He found that there is a dilemma between the theory and the observation. People generally believe that the diversity in an ecological system makes it stable. But May showed it mathematically that with increasing connection links and interactive nodes, an ecological system will become more and more unstable. People with the experience of solving large nonlinear differential equations know that the system becomes more and more difficult to have steady states if the number of equations increase. So

Which is correct: our intuition or our model?

In this papery, they used a small trick before the simulation. If there is a steady state in a dynamic system, you can always re-scale the time for different variables to normalize one steady state to an unit vector = (1, 1, …, 1). Then you can do usual stability analysis around this point. Based on Monte Carlo sampling of different parameters, you will know how they effect the stability of the system around this steady state locally.

Using this half-analytical-half-numeric method, they generated 100 million food webs randomly and made a statistic how different factors effect the stability. They found that more connections and more species really de-stabilize the ecological system. That is, in a forest, if trees, birds, insects etc. form more connections and there are more species, the ecological system in this forest will be more inclined to collapse! (Really unintuitive?) The other conclusion is that the food web will be more stable if top predators like lions, tigers die fast, or they can eat more deer when deer population increases.

This kind of idea is actually not new. In 1960s, when Kauffman tried to study the gene regulatory network of the living organism, he did the same thing by creating millions of random networks since the real genetic networks would come decades later (He simply can not wait). Based on his statistics on all these random gene networks, Kauffman concluded that if we need an evolution in Life, we have to have our gene network at the edge of Chaos. That is, it is not either in deterministic system with the fixed number of steady states, nor in totally chaos without any steady states at all. It is just at this delicate zone in between.

Could this complexity analysis with large number of simulations will reveal more ‘emergent properties’ in Life? Let’s just wait and see.

Ref:

Recently a new search engine based on computable knowledge appears. It is called WolframAlpha, which cause quite a sensation in the media. Is a new rival for google is coming? New York Times have an article here.

Before WolframAlpha’s full launching this month, it accepted some applications to test its capability at first. I joined the preview test as a researcher of biological complex system.

It is really a big step for retrieving the knowledge in a more organized way than Google does. It has a huge curate database to avoid “Garbage In and Garbage Out”. It also takes advantage of powerful algorithms of Mathamatica language to do some quite intelligent computation, which is quite beyond Google’s ability. My test strategy is to start with some examples which need straight-forward computation, then the ones which demand a little bit more efforts.

Some pros with WolframAlpha

Some math and non-linear dynamic systems

I start with a slightly complicated integral.

integrate[Exp[-x^2]]

No problem. It is the field in which Mathemaica feels at home. It offers powerful mathematical computations for elementary users. After WolframAlpha appears, it may be no need for them to buy Mathematica any more.

Then I try some simple non-linear dynamic systems.

dx/dt=x*x-1,

It solves this nonlinear ODE well. The only problem, its sampling space is too small to locate the real attractor that is negative.

The similar problem happens to the similar problem with a higher order. It misses one negative attractor again.

dx/dt=-x*x*x+x

I want to know if WolframAlpha can find the bifurcation by varying parameter values in the equation. It is one of very important results to study nonlinear ODEs. Unfortunately, it only gives the analytical results and can NOT discuss the condition for the bifurcation.

dx/dt=r*x – x*x,

The worse thing is that it totally fails to produce any results when I input two-variable systems.

dx/dt=x + Exp[-y], dy/dt=-y

Now I change the gear to test its capability to do simple calculation of some facts. For example, If I want to compare the GDP of top 4 countries in the world, could WolframAlpha give what I want.

- GDP China , US, Japan, Germany

It did a pretty good job to gather the facts and do some plotting which help us to understand the trend of economical development of four countries.

Then we move to some social data from four countries:

- Divorce China , US, Japan, Germany

Then I tried with " internet Users Europe / US". It also give some satisfactory results and plotting. However, I am quite surprised that The same logic will not work such as comparing army population between China and US.

If I input “China army / US”, there is no results even “China GDP/US” is quite OK.

Some cons with WolframAlpha

When I try to ask some questions which are simple but need a little extrapolation. For example, I ask how many years China GDP can catch up with US if each keeps current economical growth rate.

“Years China GDP to catch up with US”

There is no answer. Then I try to give it some hind by giving future years.

China GDP / US in year 2050

It fails to give reasonable results as well.

WolframAlpha also notoriously lack of biological data. I tried to ask some questions without any computation. For example,

- translation rate of ribosome?

It should be 12 – 21 Amino Acids / second. No results from WolframAlpha.

- p53 protein complex numbers in human cell:

It should be 100 – 220 thousand / cell. Even some very simple facts are absent in its database.

- diameter of DNA

You can get the answer by asking the proton number Fe. But you will fail to get the atom number in Lysine.

Do you have some ideas to test WolframAlpha. Please let me know. :-)

When science is no longer a personal choice and individual career, an objective measure to evaluate researchers comes into beings to decide funding allocation and job promotion. However, how to build an objective measure, or whether it really exists, is becoming one of most debated topics among academical world. No matter you like it or not, it is there and grows like a child.

It starts from the number of publications, move to citations you have, then changed to Journal impact factors. Now a even newer version appeared in the latest issue of PNAS. You can read a really good discussion about all these measures and may inspire you to think more.

PNAS Editorial: The most influential journals: Impact factors and Eigenfactors?
http://www.pnas.org/content/early/2009/04/17/0903307106.short?rss=1

The website of Eigenfactor website:
http://www.eigenfactor.org/

What Eigenfactor is? here is from the articel:
" The Eigenfactor™ is now listed by Journal Citation Reports®. In practice, there is a strong correlation between Eigenfactors and the total number of citations received by a journal (2). A plot of the 2007 Eigenfactors for the top 200 cited journals against the total number of citations shows some startling results (Fig. 1). Three journals have by far and away the most overall influence on science: Nature, PNAS, and Science, closely followed by the Journal of Biological Chemistry. So, publish in PNAS with the full knowledge that you are contributing to one of the most influential drivers of scientific progress."

However, I like this comment best:

“The terrible legacy of IF is that it is being used to evaluate scientists, rather than journals, which has become of increasing concern to many of us. Judgment of individuals is, of course, best done by in-depth analysis by expert scholars in the subject area. But, some bureaucrats want a simple metric. My experience of being on international review committees is that more notice is taken of IF when they do not have the knowledge to evaluate the science independently.”

Anyhow, evaluation of science is a human process. It needs some human evaluation more than just one number.

Max Perutz: interview

A young man in his 17 claimed that only winning a Nobel prize can justify his career change from inheriting his father’s textile factory to studying Chemistry. A researcher spent 22 years to elucidate one protein’s structure, which has several thousands of atoms and was quite beyond any scientist’s imagination at that time. A man finally proved that oxygen carrying ability of Haemoglobin comes from its structure and relevant chemical bonds. A pioneering biophysicist finally earned his Nobel prize in 1962, and was the founder of the Laboratory for Molecular Biology in Cambridge, the birthplace of modern molecular biology. It is nobody but Max Perutz.

He also gave some useful tips how to run a scientifically active research group, how to choose a research topic and how to run a seminar to reward everybody.

I am quite surprized to find that this great man had a unforgetable experience of being in prison of citizens of enemy countries in Canada for several years during the World War II. Amazingly, he, united with other scientists, opened a prison university to give bright kids a education even in such a distressing time.

Since every living creature is living for its own purpose and benefits, it is very hard to believe that actually cooperation can naturally happen in nature. However, spontaneous cooperation is essential for the first multi-cellular organism to exit in the early history of life on earth. Why could we cooperate? How it comes into being. Martin Nowak gave a clear demonstration how it could happen in nature.

If you don’t know who Martin Nowak is, here is Wiki website

Here is his video lecture:

1) go to Britain royal society TV website

2) Search for key words “Why we cooperate”

Then you can see a online video of this lecture.

Every year our group will go to a small town named Oberwiesenthal in the south Germany for a group retreat. It is a yearly opportunity for people to chat with each other and give informal talks about their own research. It is also the time to have fun: going ski, hanging around in the bar and hiking in the mountains etc.

People complain that they don’t know each other’s research even they are next-door neighbors. Even everybody agrees that discussion with people in the same field will benefit each other, it is usually difficult to do so. So it is really eyes-opening for us to know what other guys are working on. Group retreat is a also a good to know guys around and paves the way for chatting during the coffee break later.

It is due to Kai’s efforts to record and edit a small piece of video during this holiday. You can find people reading physics book on the coach. People are thinking hard during the seminar. People are explaining their research about why bees can fly and how the fruit fly’s wing can grow etc. People are chatting in the bar. People are playing table tennis called Chinese game, which I have never played before as a Chinese :-)

Here you can have a glimpse what some young researchers’ holiday could be. :-)

Today I present a Physics Review Letter paper named “Cell fate as a high-dimensional attractor of a complex gene regulatory network” in the journal club of our group.

To my surprise, the response is quite polarized. For some people, they take for granted that cell types are attractors in gene network (maybe because that we are in the physics institute for complex system anyhow). They think that it is nothing more than just rewriting the biological facts in the physics language ( I don’t know how many biologists actually accept this hypothesis. It is more widely accepted that cell types arise from turning on the type-specific Transcription Factors). They also complained that the 2-gene cross-inhibition example is too simple to demonstrate the effects of high-dimensional gene regulation space. They demanded a clear mathematical formula for cell reprogramming in the gene network.

However, other people quickly recognized the importance of the paper and began to embrace this idea enthusiastically. We even begin to discuss how to build such a network. One guy even suggest the possibility to invite the author here for giving a talk by himself.

Maybe a good journal club presentation is not to get the consensus of everybody. Rather it can arise the true interests of the people.

There is an interesting story in one of Chinese classics - Zhuang zi, whose author influenced the Chinese intellectual’s way of thinking as much as Confucius did. A man had several monkeys at his home. He usually feed them four nuts at breakfast and three of them at dinner. However, one day he decided to have a change just for fun. He told those monkeys that instead of following the routine, he would give them three nuts in the morning and four at night. To his great surprise, all monkeys were very angry since they thought the owner did a trick on them and it was unfair. In our eyes, we human beings are much smarter than the monkeys to know that the total number of nuts is conserved. There is no point to argue against the change. However, we may be not that smart when we are dealing with much broader issues that this.

I have a good friend when I studied in the university. He is a voracious reader and would not be bothered to have alternative views. We usually debated a lot whether our society does make the progress with the development of the modern science and technology. He told me one of his stories when he was a teenager. Like the majority in his age then, he got addicted to some ‘happy’ drugs and spent every weekend in those disco bars for the whole night. You can not resist to it because it makes you feel so high. But the terrible thing is that afterwards you feel so exhausted but could not fell into sleep for a long time. It is simply unbearable pain. Finally he totally got rid of those drugs since he figured out a theory of it: the happiness is conserved. If you try to get more by using drugs, you have to pay back with enormous pains later.

In his view, the same tragedy is happening when we are claiming to make technical progress in our human civilization. We employ the powerful technology to exploit the resources on earth to satisfy our fanatical consumption according to the capitalism model. We keep our GDP growing each year. We keep on consuming more and more. People are asked to work harder and harder. Nobody stops and ask whether we are running into the right direction. The current financial crisis now is the bitter antidote for us. Maybe there is something conserved on earth and we should show some respect to the law of nature. We are not only consumers, but also the producers and contributors to the environment in which we are living. Everything will be changed if we could put it in a longer time scale.

This is what I am thinking after I read this story.

Albert Abraham Michelson is the first American to win Nobel prize. When he was asked why he wanted to do such a difficult job to measure the speed of light, he said:“It is just the great fun to do it.” Yes, for many scientists, it is the fun of being a craftsman of science which drive them so enthusiastic to do the research day after day, month after month, and year after year.

Freeman Dyson also thought that craftsman is really a interesting job. You use your hand or brain to make whatever you like. Unfortunately, the modern society after the industry revolution deprives this privilege from many people. They should love their jobs if they could do sth with their own hands. Now their jobs are taken by massive production and cold machine. Dyson said that in our time there are actually still two fields in which craftsman will be abundant: biological research and software making. Most biological experiments are still too complicated to be automatically performed. Really innovative Software also demand the creative minds and craftsmanship to make them work.

It is very true. In many times, doing research is just the right combination of right ideas and great craftsmanship. You need to be really a master-hand in either theoretic thinking, or doing experiments.

On March 17th, Apple company revealed its new iPhone operation system. You are really amazed how much a marvelous combination of software and bio-medical technique can go. Please have a look of follow youTube video:

Living things are much more than just packages of DNA. In fact, organisms interact with their genes and environment in a complex way, forcing biologists to question their assumptions about the nature of humanity.

Using live musical performances and scientific explanations, Denis Noble will describe how “the orchestra” is replacing “the selfish gene” as the way we think about life.