Born in Taumarunui, Penny was educated at New Plymouth Boys' High School, before gaining undergraduate degrees in botany and chemistry at the University of Canterbury.
[16]: p.12 This research was significant because it suggested that modern eukaryote and prokaryote cells had long followed separate evolutionary trajectories, confirming "that evolution does not proceed monotonically from the simpler to the more complex".
[15] Penny told NBC News the results may have been surprising to some, but stressed that there was little evidence of the fusion theory explaining "the special genetic and cellular features of the eukaryotes".
They claimed the writers had "delivered biased opinions" that presented "an introns-early (and eukaryotes-first) view of early evolution that was current in 1980 and that was shown by conventional scientific criteria to be untenable over a decade ago".
They agreed it was "still premature to decide between introns first, early, or late...nevertheless, our primary conclusion is that there is good progress on understanding the complexity of the ancestral eukaryote cell".
The paper further attempted to resolve issues around "the relationships between clades and the timing of the evolution of birds", and based on the phylogenetic data, concluded that "seven Metave species do not share a common evolutionary history within the Neoaves".
[20] Resolution of controversies around the understanding of the evolutionary relationship between modern birds due to this polytomy at the base of the Neonaves, is the focus of later research in which Penny participated.
New developments suggested in this paper included reducing noise level and more accurate use of formulae to find predefined groupings in the optimal tree.
[22] One example, the extinct moa, closely related to the tinamou breed of birds from South America, according to Penny may have flown or "was blown, to New Zealand via Antarctica before it froze over".
However the researchers suggested that "the prevalence and preponderance of HCV [made] it a global health problem and accurate epidemiological data must underpin any effort to prevent transmission and control the virus".
[28] Penny told Kim Hill on RNZ in 2008, any model that couldn't be tested was not of "much use",[29] and a paper he co-authored in 1982 considered claims by Karl Popper that "Darwinism [was] not a testable scientific theory".
Penny contended that instead of using the tree of life concept, Darwin referred to his theory as 'descent with modification', which may have included the idea of an evolutionary tree but was technically more about cycles resulting from "hybridisation, endosymbiotic gene transfer, lateral gene transfer, recombination, lineage sorting, the complexities of genealogical relationships...[emphasising, for example]...the continuity between populations, subspecies, and sibling species".
[41] The 2007 annual report of the Institute of Molecular Biosciences noted that this award recognised "those persons who in any field of endeavour, have rendered meritorious service to the Crown and nation or who have become distinguished by their eminence, talents, contributions or other merits".
Peter Lockhart from Massey University said that Penny had made a "lifelong and lasting contribution to the study of molecular evolution...[and]...his work is characterised by great curiosity, intuition and a capacity to cross disciplines.
[4] Mike Steel, of the University of Canterbury, wrote in a tribute article in the New Zealand Science Review in 2009, that "Penny's formula [remained] the most remarkable closed-form expression for any class of phylogenetic trees in evolutionary biology".