( ( In ( simple organisms ) ) ( , ( ( the pacemakers ) ( ( are ( biochemical ( reaction loops ) ) ) ; ) ) ) )
(ROOT (S (PP (IN In) (NP (JJ simple) (NNS organisms))) (, ,) (NP (DT the) (NNS pacemakers)) (VP (VBP are) (NP (JJ biochemical) (NN reaction) (NNS loops))) (: ;)))
In simple organisms, the pacemakers are biochemical  reaction loops;
(ROOT (S (NP (JJ Biochemical) (NNS reactions)) (VP (VBP take) (NP (NP (NN place)) (PP (IN inside) (NP (NP (DT the) (NNS organisms) (POS ')) (NNS cells))))) (. .)))