Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.
This book vindicates my long-held view that biological objects do not act in isolation but interact with other things to make a living whole. It confirms my opinion that genes are not the master controllers of living things.
Furthermore, it showed me that systems occur at different physical scales (molecules, cells, organs, organisms, populations), that the systems at these scales influence each other, and that no scale is dominant. To understand biological/medical phenomena, including human consciousness, one must look at the (multi-scale) systems, not their individual components, in isolation.
Finally, I found it a lot of fun to read because it uses hypothetical stories to illustrate points. For example, silicon-based aliens visit Earth but fail to understand why certain things and people behave the way that they do.
What is Life? Decades of research have resulted in the full mapping of the human genome - three billion pairs of code whose functions are only now being understood. The gene's eye view of life, advocated by evolutionary biology, sees living bodies as mere vehicles for the replication of the genetic codes.
But for a physiologist, working with the living organism, the view is a very different one. Denis Noble is a world renowned physiologist, and sets out an alternative view to the question - one that becomes deeply significant in terms of the living, breathing organism. The genome is…
Of the various books available on this subject, I very much prefer this one because it makes it far easier to do systems biology.
First, it shows you how to view biological regulatory processes as a set of interacting components and their effect on each other. This alone can give clues to the behaviour of the system under different circumstances. However, it then goes on to show how these processes can be defined mathematically, which then enables us to get a quantitative view of what is going on.
When the predicted and observed numbers don’t match, we know that there is a gap in our knowledge and, hence, the place to discover new biology. Using this approach, I have.
... superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. - Nature
[This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology ... It assumes no prior knowledge of or even interest in biology ... One final…
This book turns on its head what I was taught about what controls metabolite flow through a pathway. It covers highly remarkable discoveries concerning which steps control changes in metabolite levels: those at the end rather than the start of pathways. This is amazing because it explains why decades of effort by bioengineers to overproduce particular metabolites was unsuccessful.
In response to a request from such a project, I explained how to block the inhibitory regulation by the early pathway step but added that, according to metabolic control theory, this would leave the end-product levels unchanged. I was correct on both counts! When my group later provided results from using a systems biology approach, they achieved their production target levels.
This is one of my most valued reference books, and I have referred to it many times.
With some explanatory text, it consists of a set of maps of biochemical pathways, differentiating between organism kingdoms, and includes how specific metabolites regulate the activity of particular enzymes. The pathways are very easy to find and easy to interpret. In contrast, the online equivalents can be difficult to interpret for a variety of reasons.
The book has the added advantage that it does not need a power supply or an internet connection and can be used in a far wider range of temperatures than computer hardware.
The pathways and networks underlying biological function
Now in its second edition, Biochemical Pathways continues to garner praise from students, instructors, and researchers for its clear, full-color illustrations of the pathways and networks that determine biological function.
Biochemical Pathways examines the biochemistry of bacteria, plants, and animals. It offers a quick overview of the metabolic sequences in biochemical pathways, the chemistry and enzymology of conversions, the regulation of turnover, the expression of genes, the immunological interactions, and the metabolic background of health disorders. A standard set of conventions is used in all illustrations, enabling readers to easily gather information and…
This book has been a companion for almost three decades.
Any bona fide bioinformatician will write some program scripts if only to reformat data in new and useful ways. Perl is not the most efficient or widespread scripting language, but it has the advantage of being highly flexible. It offers many ways to write a program to carry out a given task, so even computationally naive programmers can generate effective code.
Even though I am no longer actively developing software, I still have occasions when it is quicker to script something in Perl than do battle with larger apps.
When it comes to learning Perl, programmers consider this book to be the undisputed bible. You not only learn every nuance of this language, you also get a unique perspective on the evolution of Perl and its future direction. The 4th edition has been thoroughly updated for version 5.14, with details on regular expressions, support for UNICODE, threads, and many other features. Many Perl books explain typeglobs, pseudohashes, and closures, but only this one shows the motivations behind these features and why they work the way they do. It's exactly what you'd expect from its prominent authors: Larry Wall is…
Bioinformatics is in the space where biology, information science, and mathematics come together, while systems biology is an approach to biology/medicine that employs aspects of bioinformatics. Together, they bring biology to where physics was over a century ago: theory preceding laboratory/field experimentation. They use data and models to predict how biological processes work, prioritise which experiments should be done, and reveal knowledge gaps. This has applications across agriculture, medicine, and biomedical industries.
This book is written with upper school and young undergraduates in mind. It covers the basics of data collection/management (including image and text analysis), the tools to interpret data (computation, statistics, systems modelling, and AI), and the application areas in biology (molecules, cells, organs, and their regulation).
I am a Harvard- and MIT-trained physician-scientist, and I am drawn to research problems that bridge the basic and the practical – how a better understanding of cells and tissues can inform new therapies for cancer and other diseases. As children, we are all scientists – mini-hypothesis generators trying to make sense of the world. I suppose I never outgrew that curiosity. My list of best science books credits writers who bring to life the excitement that comes from looking at the natural world in a new way, a spirit that I try to emulate in my own writing. I hope you enjoy these books as much as I have!
Everybody knows that all animals—bats, bears, sharks, ponies, and people—start out as a single cell: the fertilized egg. But how does something no bigger than the period at the end of this sentence give rise to the remarkable complexity of each of these creatures?
FROM ONE CELL is a dive inside the cell and its evolutionary prerogatives to explain how these "endless forms most beautiful," as Charles Darwin called them, come about. Along the way, we learn about the scientific process, filled as it is with serendipity, as the story is told through the eyes of the scientists who informed…
From One Cell: A Journey into Life's Origins and the Future of Medicine
Every animal on Earth begins life as a single cell. From this humble origin, the nascent creature embarks on a risky journey fraught with opportunities for disaster-yet with astounding regularity, it reaches its destination intact. From One Cell illuminates this epic transformation-still one of nature's most mysterious feats-to show where we all come from and where we're going.
Through the eyes of the scientists unraveling the secrets of development, we see how all the information needed to build a human fits into a fertilised egg, and how the trillions of cells that emerge know what to become and where to…
