The call to alter already wrote to the Ref, this requires a write-lock on 
the ref (see LockingTransaction.java/doSet).  After that it sleeps a while 
and gets to its commit phase.  The other transactions retries in the 
meantime.  Consider the following code, which introduces some atoms for 
counting the retries

(defn tz []
  (let [rr (ref 10)
        a1 (atom 0)
        a2 (atom 0)]
    (println "Starting future")
    (future
     (dosync
      (swap! a1 inc)
      (alter rr + 100)
      (Thread/sleep 8000)))
    (println "Sleeping a bit")
    (Thread/sleep 1000)
    (println "Another dosync")
    (time
     (dosync
      (swap! a2 inc)
      (ref-set rr 1)))
    [@rr @a1 @a2 (.getHistoryCount rr)]))

user> (tz)
Starting future
Sleeping a bit
Another dosync
"Elapsed time: 7001.554 msecs"
[1 1 71 0]

Note, how the 71 retries nice fit the approximately 7 seconds left and the 
100 miliseconds time-out (LOCK_WAIT_MSECS)  for the lock used in 
LockingTransaction.java/tryWriteLock.

Transactions with significantly different run-times should be avoided, 
although there is some point at which older transactions will get their 
turn.  This could be another explanation of the effect.  Take a look at the 
barge-function in LockingTransaction.java

Hope this helps,
Stefan 

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