There was a delightfully curious little creature called “Opabinia” (a stem-arthropod) living on the Cambrian sea-floor up until a little over 500 million years ago. It had a clawed feeding proboscis and no fewer than five eyes: arguably a more complex arrangement of visual apparatus than present-day crustaceans. Had Opabinia been able to compare itself with organisms that would succeed it, might it have “viewed” itself as “higher” in certain respects than two-eyed crustaceans – which were just starting to evolve in the Cambrian? When humans use the words “higher” and lower” to describe organisms it reflects an obsession with regarding the temporal passage of evolution as towards “higher” complexity in all respects, and perceiving recent branches in the “tree of life” as “higher” than older ones.
It's an old problem, and it affects BioEssays and other journals, as recently pointed out . Perhaps that's because it's almost been accepted as a linguistic “short-hand” for what is really meant. But as I increasingly ask “what is really meant?”, I increasingly realize that there are simple ways of expressing oneself correctly. Rigato and Minelli  note that this involves more than merely replacing “lower” and “higher” with “primitive” and “advanced”, or “plesiomorphic” and “apomorphic”. “Basal”, instead of “lower”, also can't be used ; and “Complex”/“Simple” should be used with great care (so-called “simple” organisms can have complex attributes and vice versa) and specificity of meaning. However, we should never be tempted back to “higher”/“lower” by fear that the real concepts are difficult to express: they require an important change in perspective, alright, but linguistically they are simple (some examples later).
No serious biologist can disagree with the argumentation against the concept of the progression of life expressed by “higher”/“lower” and instead for “tree thinking” and the concept of common ancestors. As I perceive it, the “higher”/“lower” trap is set by our concentration on the organism rather than the phenotype, or trait, and the process that produces it. This is particularly evident in papers discussing a feature of an organism or group of organisms. A perspective shift from concentrating on the organisms' “place” in an evolutionary “hierarchy” towards concentrating on the process of evolution and pressures involved in producing traits makes solutions to our problem appear as if by magic. Some representative examples with shifts of perspective follow:
From whole organism to phenotype:
Before: Key developmental genes are conserved between primitive and higher organisms. After: Key developmental genes are conserved between organisms that have very different body plan complexity.
Note here that “complexity” can be justified because it is applied to a feature of the organism rather than the organism as a whole.
From organism to evolutionary process:
Before: How evolution added regulatory modifications in higher animals… After: How regulatory modifications were acquired during animal evolution…
From generalization to specificity:
Before: …important for complex nervous system function in higher organisms. After: …important for complex nervous system function, as has evolved in certain animal lineages.
But often the way out of the “trap” is nothing short of naming the group of organisms of relevance, e.g. “decapods” or “eutherian mammals” etc., thus accurately informing the reader.
Essentially, the organism is the unit of selection, but not that of evolution. Different parts of the organism evolve at different rates – some in concert, others rather more independently – and in response to different biotic and abiotic “pressures” and “limitations”. This is the thought-bridge between understanding tree thinking (and common ancestors) and being able to describe the evolution of creatures in the correct terms. For it helps us to imagine why, for example, the eye of a mantis shrimp is – in one sense – more complex than that of a human: 16 distinct rhodopsins, in contrast to four. Opabinia became extinct as an entire organism, no matter how many eyes it had; but many of the genes and features that it shared with other organisms are still with us today, still evolving and branching into new organisms via common ancestors.