An update of General physical laws ruling biology

Recently, a letter entitled “Physical Laws Shape Biology” was published in Science (8 February 2013, 10.1126/science.339.6120.646). The title of this letter is very similar to the one that I previously posted in my blog “General physical laws ruling biology” , but my post was not cited and the exact concept of laws might be different from the one that I posted and originally proposed more than 10 years ago during my oral presentation in an international academic meeting. At that time, most scientists thought my proposal as a science fiction, but it seemed that scientists have recently realized that problem and the similar topic was reviewed in a special issue at Science (12 October 2012, vol 338, issue 6104), including two reviews and two perspectives. Although these Science papers are still restricted to some specific disciplines and the overall vision of these papers is still limited as well as the approaches proposed by these papers might not really help to solve the general physical laws controlling biology as thought, it seemed that this direction is starting. It sounds interesting and exciting, but please be careful when examining the direction if interested.


WCTDS, a Web-server of Cell Type Discrimination System

WCTDS is a software for discriminating stem cell types and subtyeps based on DNA methylation biomarkers [Wang A, et al 2013 PLoS ONE 8(2): e56095]. Coded by Python, Django, R, Linux shell, and MySQL, WCTDS runs under Linux-Apache2 server.


Please click the link below to access WCTDS.


Thanks for your interest. Any suggestions and comments, please use the comment form below.


A web server for discriminating the cell types and subtypes of stem cells and somatic cells

A web server for discriminating the cell types and subtypes of stem cells and somatic cells

Recently I applied the hub identification concept from systems network theory to identify biomarkers and established an efficient system to discriminate the cell types and subtypes, A Quantitative System for Discriminating Induced Pluripotent Stem Cells, Embryonic Stem Cells and Somatic Cells . This system assumes that users do not have any background info of their cells for testing and they only have DNA methylation level data on given loci. The system would tell users the cell type and subtype info after running tests. Many computational works need to be done to reach that point.  To make the system practical, I have also developed a web service using Linux-based Apache server to make it easy applied to daily works without requiring any computational programming. This web service only requires the testing data (e.g. DNA methylation % level data) via uploading online and the computer software automatically takes care of the analysis and provides users the final results including the cell type and subtype info, figures and tables that detail the discrimination accuracy. The discrimination system and the web service would be expended to other areas like human diseases in the near future. I hope the web service available soon for public users once I find a way to support the server running. Keep checking if interested! Now avaialble

Biological laws – variable

Continuing..(please see my last post for an introduction)

We might need a couple steps to uncover the biological laws. Finding such laws is my missions, and it also might be the missions for biologists who might be interested in it. The core of the laws is the variables that can be used to describe the laws. I would keep posting this parts step by step as I think. Below is the general part.

For the long term, we would find the fundamental elements as variables for describing the basic general laws in biology.  We still do not know the fundamental elements in biology right now, but our understanding the biology evolve fast, from the morphological phenotypes to molecular phenotypes. With the DNA discovery, biology has gone through a molecular era. Recently we knew the functions of microRNAs and no-coding RNAs. We even start a trip to walk into the junk DNA (>98% genome) to identify the functions for them. All these sounds amazing, but they might not be the fundamental elements for controlling biology.  These fundamental elements might have already been known but have just been ignored or they are still concealing in our ordinary practices.  We have been limited by the conventional concepts in biology. After the theory of evolution  formulated by Charles Darwin, followed by DNA-based molecular biology, we have not got any real breakthroughs in biology.  We should find a way like fractal theory to decompose the biological complexity into a simple form and then develop a pattern finder like Chaos-based approaches to uncover the fundamental elements in biology. Once we know the fundamental elements, we could write a math equation to describe the biology. By then, we will know the principles of biological evolutions, aging, diseases, and so on.

….to be continued

General physical laws ruling biology

Anyou Wang

“Is there any physical law obeyed in biology? Something like the Newton’s motion laws? ” I asked this seemly naïve question in public a couple of years ago. Actually, this question arose when I read the fractal and chaos theory during my graduate study. Originally, I thought that chaos theory might help to solve this problem, but the simple chaos map sounds complex (e.g. Figure 1) and this topic is too complex. In order to get more talent and gifted scientists involved, I would post here an array of what I thought and what I got so far. Hopefully, this platform can accelerate the new discoveries in this area.

Figure 1. The chaos profiling of gene expressions derived from microarray.

First of all, I like to address why I believe there are general physical laws in biology. Almost anything in the universal obeys a certain physical laws, known or unknown to date. Of course, without exception, biology should obey some simple laws. This point might be too old to be posted here as it must be posted somewhere like historical books, but some people would still yell that biology is too dynamically complex to obey some physical laws. This argument sounds reasonable, but I should remind that object motions were also very complex around 200 years ago before Newton’s law discovery, even today, they are still very complicate because there are various types of objects and their motions seem chaos. However, Newton’s motion laws describe all motion obey the physical laws and the second law about the force and mass and acceleration (F=mdv/dt) should be familiar to most quantitative biologists since the ordinary differential equations are the most frequently used theory for describing the dynamic processes in the quantitative biology.

After googled the topic, I found the topic arose by a philosopher of biology and I did not have the materials in my hand, but I did not think that the real biological laws can be revealed by general philosophy. They should be solved by interdisciplinary, especially combinations of biology and mathematics.

Two excellent papers (Science 324, 81, and 85) described automating science might be interesting, but they might only be helpful in dealing with the detail components of biology and specific processes in biology and the real physical laws in biology might not be generated by simple math equation derivations. We need view biology as a whole object instead of components of an object.

For the Newton’s law, we learned that the most fundamental elements in objects are essential variables for describing the laws for the objects, but such fundamental elements in biology we can use them as parameters to describe the physical laws in biology remain unknown.

We have increased daily our biological knowledge in genetics and epigenetics from biochemistry and genomics studies. Recent developments in system biology and genome-wide profiling in genetics and epigenetics may accelerate our understanding biology in higher level, but we still have no ideas about the most fundamental elements controlling the biology. The physical laws for biology are not available until we know very well these most fundamental parameters in the whole biology.

…To be continued