Omission of 'FROM' ? diff between pgsql 7.4.1 and pgsql 8.1.4

hi
I am upgrading from pgsql 7.4.1 to pgsql 8.1.4. However, some of the application
queries won't run on the newer version of pgsql.
An example of the type of query is:

SELECT
protein_external_links.protein_id, external_links.external_id,
proteins.public_name
WHERE
protein_external_links.external_link_id = external_links.id and
protein_external_links.protein_id = proteins.id and
external_links.external_database_id != 8 and
external_links.external_id_type_id = 2;

on pgsql7.4.1 what tables need to be queried seems to be implicitly deduced from
the rest of the SQL without the need for a FROM clause.
However, on pgsql 8.1.4 the following error is given:
ERROR: missing FROM-clause entry for table "protein_external_links"

Is there some query optimization config setting I can set in pgsql 8.1.4 to fix
this problem rather than having to change the queries in the code? I've read
over the changes between pgsql 7 and pgsql 8 but nothing seems to stand out to
me as referencing this problem. Anyone with more knowledge that can point me in
the right direction?

Thanks
Kate