I. Schrödinger and Morse Code

    In 1943, Erwin Schrödinger gave a famous series of lectures at Trinity College in Dublin, Ireland, where he speculated about the physics of biology.  He proposed two main ideas, which will be discussed briefly.

order from order

order from disorder

The flow of Genetic Information:
 

 

LEGEND

• DNA codes for the production of RNA.
• RNA codes for the production of protein.
• Protein does not code for the production of protein, RNA or DNA.
• The end.

However, the "Central Dogma" has had to be revised a bit.  It turns out that one CAN go back from RNA to DNA, and that RNA can also make copies of itself.  It is still not possible to go from Proteins back to RNA or DNA, and no known mechanism has yet been demonstrated for proteins making copies of themselves.
 

 

    There are two aspects in which Schrödinger's order from disorder also play an important role in biology:

"negative entropy" - where an organism uses the energy obtained from burning food to offset the cost of storing information in the form of DNA, RNA, and protein sequences.

 

self-organisation - this is the process by which complex systems can spontaneously appear.  It is based on non-linear systems, far from equilibrium, and hence difficult (if not impossible) to predict, although some aspects can be modelled.

"What is Life?" by Erwin Schrödinger (Cambridge University Press, 1944)

"What is Life? The Next Fifty Years - Speculations on the Future of Biology" (edited by Michael P. Murphey and Luke A.J. O'Neill, Cambridge University Press, 1995.)

"At Home in the Universe - The Search for the Laws of Self-organization and Complexity", by Stuart Kauffman (Oxford University Press, 1995).
 

The DNA sequence contains several different types of information:

1. The DNA sequence can code for an amino acid sequence for proteins

2. The DNA sequence can code for an RNA sequence

tRNA

rRNA

snRNA

telomeraseRNA

other RNAs

3. The DNA sequence can code for protein binding sites
 
 
4. The DNA can code for architectural information

intrinsic DNA curvature

nucleosome positioning

5. The DNA can code for structural / stability information

transcription initiation

origins of replication

mutational "hot spots"

 
 

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The RNA sequence also contains several different types of information:

1. The mRNAs can contain several different levels of information:

specifies amino acid sequence for proteins

localisation signals for WHERE the protein will be made

stability signals to determine HOW MUCH protein is made

splice sites

editing sites

2. The tRNAs code for the genetic code - same in all living organisms (n.b. diff. in mitochondria)
 
 
4. The rRNAs code for the structures of ribosomes

intrinsic DNA curvature

nucleosome positioning

5. Other RNA/protein complexes have important biological functions

RNA template for teleomerase enzyme - necessary to prevent cancer

snRNAs necessary for mRNA splicing

snoRNAs are small nucleolar RNAs.

The PROTEIN sequence contains several different types of information:

1. The protein sequence can code for an "active site" for enzymes

2. The protein sequence can code for structural roles:

microtubules

myosin

collagen

etc.

3. The protein sequence can code for ion channels/pumps
 
 
4. The protein sequence can code for localisation information

within the cell

extra-cytoplasmic

5. The protein sequence can code for modification sites

 

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In 1977, Fred Sanger and colleagues in Cambridge, England, sequenced the first bacteriophage (phi-X174, 5386 bp long), for which he later won the Nobel prize.  Although this was a dramatic improvement over the conventional methods, this was still very slow, compared to the amount of information in a single human cell.

About a decade later, the human genome project was launched; this was an international effort, and the U.S. alone would pay about $200,000,000 per year for 20 years!  Most of this investment was in technology to speed up sequencing, which in fact has been realised.  Within a year, it is likely that it will be possible to read the entire DNA sequence of a human cell, in a few hours.
 
 

 

 The human genome project has also had a major influence on the rest of biology, as other organisms are being sequenced as goals towards the ambitious end of the 3,000,000,000 bp (or so) nucleotide sequence for the human genome.  In particular, the sequencing of complete bacterial genomes is revolutionizing the field of microbiology.   Presently, bacterial genomes are being sequence at a rate of slightly faster than one new genome every month!  As technology improves, this rate will increase.  It is estimated that within the next two years, we will know the complete genomic sequence of most major pathogenic bacteria.
 
 

What is "genomics"?

Genomics is simply the study of complete genomes.  More recently, genomics has meant the analysis of the complete DNA sequence of an organism's genome.  This field wasn't really possible until the publication of the genome of Haemophilus influenzae in 1995.

Proteomics is simply the study of the complete set of proteins encoded by a particular organism.

  Bacteriophage lambda has a genome of about 50,000 bp.  If you were to print the entire sequence out, with roughly 25,000 bp per page, it would take about 2 pages.  (The sequence would be in a very small font, and you could barely read it!)

The yeast Saccharomyces cerevisiae was the first (and only so far) eukaryote to be sequenced.  The yeast genome would occupy a thin volume of about 500 pages, or roughly twice the thickness of the E.coli volume.  I should mention that recent genetic analysis of the complete yeast genome has found that it likely has arisen from a duplication event - that is, yeast came from a more primitive organism which contained only half the number of chromosomes.

The first "animal" to be sequenced is likely to be the nematode C.elegans, which is about 100,000 bp long. The plant Arabidopsis thaliana is also being sequenced, and it is about the same size.  Both of these genomes are likely to be completed within the next year or so.
 
 

FINALLY, the human genome, by comparison, is quite large.  Using the same analogy as above, the human genome would fill 80 volumes!
 
 

 

 A List of Genomes that have been Completely Sequenced:
(so far, as of 1 Sept., 1998) 
 
 

A list of microbial genomes which are being sequenced and are presently searchable through TIGR:
 

 

This is based in part from data from The Institute for Genomic Research.  For more information click on the TIGR logo.

There are presently more than  100  organisms (including humans), whose genomes are in the process of being sequenced....
 
 

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