Communication packets error with MySQL

Hi,
I'm having a problem with executing a query on MySQL. It seems that I'm getting the communication packets error once in a while and I'm not sure whether the query is bad or the settings on the database server is bad. Could anyone give me an insight where to look after?
Thank you,
852825
MySQL: 5.1.41-3ubuntu12.7
JDBC: 5.1.12
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Got an error writing communication packets
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
     at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
     at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
     at com.mysql.jdbc.Util.getInstance(Util.java:384)
     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
     at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3562)
     at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3494)
     at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1960)
     at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2114)
     at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2696)
     at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2105)
     at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2264)

I've tried the community but no response so far. Any tips on where to look?

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Sat Oct 9 16:04:52 2010
WARNING: inbound connection timed out (ORA-3136)
Sat Oct 9 16:05:32 2010
WARNING: inbound connection timed out (ORA-3136)
Sat Oct 9 16:06:30 2010
WARNING: inbound connection timed out (ORA-3136)
Sat Oct 9 16:07:10 2010
WARNING: inbound connection timed out (ORA-3136)
Sat Oct 9 16:09:35 2010
Incremental checkpoint up to RBA [0x1d.1f9928.0], current log tail at RBA [0x1d.1f9a79.0]
Sat Oct 9 16:11:52 2010
WARNING: inbound connection timed out (ORA-3136)
Sat Oct 9 16:29:40 2010
Incremental checkpoint up to RBA [0x1d.1f9b87.0], current log tail at RBA [0x1d.1f9bf4.0]
~
Please help.

Communication packets error with MySQL

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