Open Questions: Biology

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See also: Exobiology -- Mathematics and biology

Introduction

Reductionistic and non-reductionistic theories

The principal open questions


Origins of life
Archaea and extremophiles
Evolutionary milestones
Evolutionary history of animals
Evolutionary theory
Human evolution
Molecular biology and genetics
Molecular evolution
Gene expression and regulation
RNA biology
Cell biology
Developmental biology
Microbiology
Systems biology
Protein chemistry and biology
Biochemistry
Biophysics

Recommended references: Web sites

Recommended references: Magazine/journal articles

Recommended references: Books

Introduction

Up until Watson and Crick worked out the structure of DNA in 1953 the life sciences had come to seem like a slow-moving, "mature" area of science in which most of the important discoveries had already been made and in which further progress was mostly a matter of filling in the details.

The last previous really significant advance had been Darwin's theory of evolution, published almost 100 years earlier, in 1859. Gregor Mendel published his ideas about genetics in 1866, but so obscurely that even Darwin did not know of them. It was not until about 1900 that Mendel's work was rediscovered and confirmed.

Generations of high school and college students came to think of biology as all about ickiness and sliminess (as in the dissection of frogs), or else as a routine, boring activity involving the collection and cataloging of endless cabinets of "specimens" of butterflies and moths in the dusty backrooms of natural history museums.

Watson and Crick, and the legions of molecular biologists who followed them, changed all that.

Progress after 1953 was slow at first. The "genetic code" wasn't completely deciphered until 1965 (by Marshall Nirenberg and others). Much of the next 20 years was occupied ferreting out details of how genes contained in DNA are actually transcribed and translated into proteins (which are the basic materials from which living things are constructed).

By the middle of the 1980s, discoveries -- which relied entirely on the knowledge of molecular biology already acquired -- were coming faster than ever. We started to learn some astonishingly basic facts about life itself -- which were surprising mainly in that they had remained mysteries for so long. Among these we might note:

So. It's clear that the life sciences today are anything but "mature" and slow-moving. In fact, research activity in the life sciences far exceeds that in other fields by a wide margin. Just a quick look at the table of contents of a prestigious journal such as Science that covers all fields of scientific research suggest that the life sciences are producing more new top quality results and findings than all other fields combined.

It's most unlikely this activity will be slowing anytime soon, either. Not only do we have (in such things as genome sequences) more data than ever before to study and analyze, but the questions that still remain unanswered (see below) are even more fascinating that those we've already addressed.


Reductionistic and non-reductionistic theories

A "reductionistic" theory is one which describes and explains some class of phenomena by reference to existing facts and theories in some more "fundamental" domain.

The nature of the chemical bond is a classic example. Properties of the chemical elements and of all compounds built from them (i. e., most common forms of matter) depend on the nature of bonds formed between the atoms of different types of elements. Chemists in the 19th century noticed many patterns in the way different elements behaved, and their work culminated in the periodic table proposed by Dmitry Mendeleyev in 1869. It was a splendid work of classification, but neither Mendeleyev nor any other chemist had the foggiest idea of why different elements had the chemical properties that they did.

Chemists observed that different elements tended to combine with each other in fairly predictable proportions, as described by the periodic table. They named the attachments that atoms formed with each other "chemical bonds", but they had no good theory to account for them. It was not until physicists had developed quantum mechanics in the 1920s that a viable theory of the chemical bond was possible. The resulting theory was largely the work of Linus Pauling in the 1930s. (Pauling later narrowly missed qualifying for his third Nobel Prize when he was beaten out by Watson and Crick in determining the structure of DNA.)

The theory of the chemical bond is a reductionistic theory because it explains purely chemical phenomena by means of facts and concepts from a completely different realm -- quantum physics in this case. Chemists never came up with even a plausible non-reductionistic theory of the chemical bond.

In contrast, Darwin's theory of evolution was thoroughly non-reductionistic. It describes and explains biological phenomena -- namely, the way in which different characteristics develop in different species over time -- in terms of other biological processes. Specifically, the processes of individual variation and natural selection.

The theory of evolution was hugely successful and quickly became the foundation of biology. It was successful, at any rate, as far as it went. It just happened not to be complete, because it didn't explain all relevant facts. For instance, it didn't explain why there were variations between different individuals of the same species, nor did it explain how these variations could be passed from individuals to their progeny. These observed facts simply had to be accepted as givens.

The situation is much the same as existed in chemistry before the theory of the chemical bond. Chemists knew that different atomic species behaved differently and obeyed quite precise rules of combination. But they had no idea of why this was. They could make good qualitative and even quantitative predictions of what would happen in a chemical reaction, but they couldn't explain the mechanism involved.

What we have learned in the last half century about molecular biology now enables us to formulate very good theories of many of the observational facts important in evolution which Darwin and his successors simply had to assume, but could otherwise only speculate about. These theories are reductionistic in nature, because they "reduce" biological phenomena to chemical ones.

The negative connotations of the words "reduce" and "reductionistic" bother some people. They shouldn't. Insofar as the theories in question are scientifically sound, they are simply doing their job -- to explain facts and observations which would otherwise be unexplained. The circumstance that certain biological phenomena are thereby "reduced" to chemistry is not to be lamented.

In fact, little of Darwin's theory of evolution, or other well-established non-reductionistic biological theories, for that mattter, is replaced by molecular biology. The different theories supplement each other well, and give a good metaphorical example of symbiosis. Each explains large parts of our overall knowledge which remains otherwise inaccessible.

This discussion is leading up to a point, and it is this: We are quite far from the end of the road in understanding what happens in evolution from a molecular point of view. Some of the most exciting research in biology today is concerned with how molecular biology is laying a firmer foundation for evolutionary theory, and in particular, how various biochemical processes of life have themselves evolved.

Take developmental biology, for example. This is the study of how the fertilized egg of a multicellular organism first develops into an embryo and then into a mature adult. It's quite an astonishing process, when you look into it. It turns out that what drives the process is the sequential unfolding of the expression of different sets of genes in the developing organism. This sequential process causes cells to encounter a series of chemical substances (mostly proteins), which in turn cause the expression of new genes in a chain reaction.

As already hinted, this process is very similar in organisms as different as insects and mammals. It is clear, therefore, that it is a process which has evolved in time. The study of how this process has evolved -- which is called evolutionary developmental biology -- will tell us a lot about why it now works the way it does.

But we can go a step further. The mechanism which controls when and how genes are expressed (i. e., interpreted to build corresponding proteins) is called "gene regulation". This mechanism turns out to have similarities in all forms of life -- from bacteria to humans. It has, therefore, also evolved. The study of this evolution will, likewise, tell us a lot about why it works the way it does.

And there is even a step beyond that. Many genes themselves are common to all forms of life (though usually with some changes). This makes sense, because once a gene has emerged that specifies a useful protein, it makes sense for nature to keep the gene (and the protein) around. Such genes are said to be "conserved". The genes, too, have therefore evolved. This particular field of study is called "molecular evolution".

At this point, the circle closes with itself. For it turns out that the process of molecular evolution -- i. e. change in DNA -- is sufficiently regular and predictable that it can serve as a kind of biological clock that measures time in units of eons. Not an exact clock, to be sure, but good enough that we can use it to estimate (however roughly) when different species (and families, and phyla) first diverged from each other. It allows us, in short, to attach rough dates to the genealogy of life on Earth. In particular, it is the means by which we believe the origin of H. sapiens to have occurred something like 150,000 years ago.

Understanding of biology at the molecular level thus serves a still quite intact theory of evolution at the macro level.


The principal open questions



Recommended references: Web sites

Site indexes

WWW Virtual Library: Biosciences
Categorized and annotated links.
Open Directory Project: Biology
Categorized and annotated links. A version of this list is at Google, with entries sorted in "page rank" order. May also be found at Netscape.
Biology Links
Good colledtion maintained by the Harvard University Department of Molecular and Cellular Biology. Emphasis is on molecular biology, evolution, immunology.
Yahoo Biology Links
Annotated list of links.
Galaxy: Biology
Categorized site directory. Entries usually include descriptive annotations. Note that a number of general sites are listed in the reference section.
About.com Biology Links
Categorized and annotated list of links.
Bio Netbook
Large searchable directory of links, hosted by L'Institut Pasteur.
Biosites
Large, searchable, hierarchically organized catalog of Internet resources in the biomedical sciences.
Biozone: Bio Links
Good collection of well-annotated links in many areas of biology. Maintained by Biozone International, a producer of resources for biology students and teachers.
Biology Online Directory of Life Sciences & Education
Links are well-annotated and organized into broad categories, but coverage is rather spotty.
BioTech Science Resources
Directory of links to Web sites and databases in molecular biology, chemistry, biochemistry, microbiology, ecology, and medicine.
BioChemLinks
Directory of educational resources in biology and chemistry.
Molecular Biology's Search Engine
A sophisticated search engine focused on biology and life sciences.
Cell and Molecular Biology Online
An informational resource of links for cellular and molecular biologists, by Pamela Gannon.
Martindale's Reference Desk: Bioscience & Biotechnology
Extensive, annotated list of links, unfortunately all on one large page.
Top 20 Biology
Good quality links arranged in categories, but without annotations.
California State University Biological Sciences Web Server
Searchable database of life science resources. Lists are available by research area or custom search.
InfoMine
A "scholarly internet resource collection" for biological, agricultural, and medical sciences.
BioScience Research Tool
Annotated links to online biology tools and resources, in various categories.
Geometry.Net: Biology
Provides results of Web searches for many biology topics.

Sites with general resources

University of Arizona Biology Learning Center
Contains a large variety of educational resources, such as a list of biology courses with online pages, the Biology Project, and the Student Biology Web (a series of Web sites constructed as class projects).
Biology Online
A useful collection of educational information on biology, including a dictionary of biology, biology tutorials, and external links.
Biology at About.com
Extensive site covering all areas of biology. Contains original articles and many external links.
Biointeractive
Good site with a variety of learning resources, including "virtual labs", animations, a virtual museum, and videos of science lectures. Produced by the Howard Hughes Medical Institute.
Access Excellence
A national educational program that provides high school biology and life science teachers access to their colleagues, scientists, and critical sources of new scientific information via the World Wide Web. Site features include a resource center and sections covering news, biotechnology, and health.
BioSci
A set of electronic communication forums, including Usenet news groups and electronic mailing lists, for use by biological scientists. Site includes complete archives and searchable index of forum messages.
BioTech
The site is really about biology and biochemistry in general, not just biotechnology. Principal resources include a searchable life science dictionary, information on bioinformatics, and external links to life science and chemistry resources.
SciWeb
"The Life Science Home Page". Contains a variety of resources, such as external links, patent information, meeting announcements, career aids, and discussion forums.

Surveys, overviews, tutorials

Unsolved problems in biology
Article from Wikipedia. There is also a "Wikibook" on the same topic.
Biology
Article from Wikipedia. See also Biology basic topics, List of biology topics, Organism.
Kimball's Biology Pages
An excellent online biology textbook by John W. Kimball, based on his popular hardcopy text. Best navigated like an encyclopedia/dictionary of biological terms. There's a lot here.
MIT's Biology Hypertextbook
Supplementary material for MIT's introductory biology course (7.01). The emphasis is on biochemistry, molecular biology, genetics, cell biology, and immunology.
Online Biology Book
An impressive piece of work by M. J. Farabee. Major topics include cells, genetics, plants, human biology, and biological diversity. There's also a fine glossary.
Wikibooks: General Biology
Textbook in the Wikibooks collection. A work in progress, but already contains much useful information. The main sections are Cells, Genetics, Classification, Evolution, Tissues & systems.
The University of Arizona Biology Project
"An online interactive resource for learning biology". Some of the topics featured include cell biology, developmental biology, immunology, and molecular biology.
Rediscovering Biology: Molecular to Global Perspectives
A professional development course for high school teachers. Covers mainly modern topics in biology, like molecular biology, developmental biology, and cellular biology. There is an online textbook, but the site also serves as a companion to a video series. Provided by Annenberg Media.
Serendip: Biology
A variety of educational articles and interactive exhibits.
The Tree of Life
This site presents the phylogeny of living things -- the hierarchical classification of life forms on Earth. It describes most of the major branches of the tree and provides numerous images, bibliographic citations, and external links.
PinkMonkey.com Biology Study Guide
Good, well-organized outline of the subject of biology. Provides definitions of the important concepts and a very condensed summary of the subject. Very good place to get an orientation to the subject.

Ask an expert

Scientific American Ask The Experts: Biology
Questions and answers on many different topics in biology. Most of the articles also have useful external links.
Allexperts: Biology
Provides access to a large number of experts in various areas of biology. Questions are posted and answered on the site, with responses archived.
ASU Ask A Biologist
Hosted by Arizona State University, this site is primarily intended to handle questions from students and teachers in grades K-12. But it has other useful features, such as good external links and articles about ASU biology research projects.
The Biology Page
A page hosted by The School Page which provides access to several experts who will reply to biology questions by email. There is no archive of answers, but the page does contain some external links.


Recommended references: Magazine/journal articles


Recommended references: Books

John Maynard Smith; Eörs Szathmáry -- The Origins of Life: From the Birth of Life to the Origins of Language
Oxford University Press, 1999
This very short book (for such a large topic) covers the history of life from its inception to the evolution of human language. The authors focus on "major transitions" in evolution, such as the origins of replication, the invention of the genetic code, the origin of prokaryotic and eukaryotic cells, the origins of sexual reproduction, and the transition to multicellular organisms. The treatment of such questions is used to survey much of biology in general.
Richard Fortey -- Life: A Natural History of the First Four Billion Years of Life on Earth
Vintage Books, 1999
The author is a paleontologist at London's Natural History Museum. His book is part history, part travelogue, part personal journal, but overall its subtitle describes it well. It's a good way to get an overview of much of biology, and the discursive style may help sustain interest for those who might think that reading about so many fossils is a bit dry and dustry.
John Maynard Smith; Eörs Szathmárt -- The Major Transitions in Evolution
Oxford University Press, 1995
The authors give a technical, yet accessible, survey of the key topics presented in their later, briefer book aimed at general readers (The Origins of Life). These topics are the evolutionary origins of the key innovations of life, including life itself, the genetic code, cells, eukaryotes, sexual reproduction, symbiosis, multicellular organisms, animal societies, and human language.
Christian de Duve -- Vital Dust: The Origin and Evolution of Life on Earth
Basic Books, 1995
de Duve is a 1974 winner of the Nobel Prize in biology and medicine. This book is a serious history and study of life from its origins to the present day. The history is explained in seven parts: the chemical origins, the emergence of RNA and the genetic code, the appearance of the first cells, the evolution of complex cells, the appearance of multicellular organisms, the (eventual) evolution of humans and the human brain, and the possible future evolution of life. Scientific details are carefully presented at each stage.
Michael P. Murphy; Luke A. J. O'Neill, eds. -- What is Life? The Next Fifty Years
Cambridge University Press, 1995
The book is a collection of papers from a celebration of the 50th anniversary of physicist Erwin Schrödinger's book What is Life? which foreshadowed the discovery of the structure and function of DNA. The papers, by leading biologists and physicists consider possible developments in the next 50 years for such problems of biology as the origins of life, the operation of the human brain, and the essential nature of life itself.

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