Open Questions: Biology
See also: Exobiology --
Mathematics and biology
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.
- The discovery in the 1980s of the genes and proteins which control
the "cell cycle" -- the detailed process that cells go through in
dividing. Understanding of this process is crucial to figuring out
what goes wrong in cancer cells, and how to stop it.
- The identification, around 1990 by Carl Woese, of an entire new "kingdom"
of life forms -- the archaea --
in addition to bacteria and "higher" forms (like plants, animals, and
fungi). Archaea are as different (at the molecular level)
from the other forms as those forms are from each other.
- The gradual acceptance, over the last 25 years, of Lynn Margulis'
idea of endosymbiosis -- the theory that the more complex cells (called
"eukaryotes") which make up multicellular organisms originated when
simpler cells ("prokaryotes") of several types joined together in a
symbiotic union. This greatly improved the ability of cells to utilize
external energy sources in order to evolve significantly higher
- The continued accumulation of details about the astonishing complexity
of the mammalian immune system. These details paint a picture of a number
of processes that occur at the molecular level to help complex organisms
defend themselves against external parasites. They give us crucial
knowledge of how we may be able to assist this process with vaccines
and other new medicines.
- The working out -- which is still going on -- of the exact mechanism
by which a fertilized egg cell progresses from a single cell, to an embryo, to
a fully adult multicellular organism. One of the most amazing aspects of
this is that the mechanism is very similar in all multicellular organisms,
from plants on up to mammals. Many of the same (or similar) genes are
involved in organisms as dissimilar as insects and humans.
- The apparent confirmation since 1990 of the "out of Africa" theory of the
evolution of modern humans (Homo sapiens). Two distinct lines of
genetic evidence now point to the origins of our species only 100,000 or
200,000 years ago, somewhere in Africa.
- The publication in 2001 of the full sequence of the human genome.
Uncharacteristically, this project was completed much sooner than
originally envisioned, and lays the groundwork for even faster progress
in understanding how humans (and other organisms) grow, metabolize, and
(eventually) age and die.
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
A "reductionistic" theory is one which describes and explains some class
of phenomena by reference to existing facts and theories in some more
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
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
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
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
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.
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
- Good colledtion
maintained by the Harvard University Department of Molecular
and Cellular Biology. Emphasis is on molecular biology, evolution,
Yahoo Biology Links
- Annotated list of links.
- Categorized site directory. Entries usually include
Note that a number of general sites are listed in the
About.com Biology Links
- Categorized and annotated list of links.
- Large searchable directory of links, hosted by
- 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
- Directory of educational resources in biology and chemistry.
Molecular Biology's Search Engine
- A sophisticated search engine focused on biology and life
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
Top 20 Biology
- Good quality links arranged in categories, but without
California State University Biological Sciences Web Server
- Searchable database of life science resources. Lists are
available by research area or custom search.
- A "scholarly internet resource collection" for biological,
agricultural, and medical sciences.
BioScience Research Tool
- Annotated links to online biology tools and resources, in
- 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).
- A useful collection of educational information on biology,
dictionary of biology,
biology tutorials, and
Biology at About.com
- Extensive site covering all areas of biology. Contains
original articles and many
- 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.
- 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,
- 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.
- 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.
- "The Life Science Home Page". Contains a variety of resources,
external links, patent information, meeting announcements,
career aids, and discussion forums.
Surveys, overviews, tutorials
Unsolved problems in biology
- Article from
There is also a
"Wikibook" on the same topic.
- Article from
Biology basic topics,
List of biology topics,
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
Wikibooks: General Biology
- Textbook in the
Wikibooks collection. A work in progress, but already contains
much useful information.
The main sections are
Tissues & systems.
The University of Arizona Biology Project
- "An online interactive resource for learning biology". Some
of the topics featured include
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
- 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.
- Provides access to a large number of experts in various areas
of biology. Questions are posted and answered on the site, with
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.
- 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
Copyright © 2002-04 by Charles Daney, All Rights Reserved