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Bates was a pioneer and lead linguist studying how the brain processes language. More specifically, Bates made significant contributions towards the fields of child language acquisition, cross-linguistic language processing, and aphasia, investigating the cognitive, neural, and social linguistic factors subserving these processes. With Brian MacWhinney, Bates developed a model of language processing called the competition model, which views language acquisition as an emergentist phenomenon that results from competition between lexical items, phonological forms, and syntactic patterns, accounting for language processing on the synchronic, ontogenetic, and phylogenetic time scales. She was a main proponent of the functionalist view of grammar, in that communication is the main force that drives language's natural forms. This view provides support for Bate's widely known perspective: the brain does not use specialized linguistic centers, but instead employs general cognitive abilities in order to solve a communicative conundrum. Much of her research provided evidence towards the core principles of empiricism and against the nativist school of thought, which made her a major player in the East Pole-West Pole divide of cognitive psychology and cognitive neuroscience.

Language Acquisition
In defense of communication functioning as a main force of language acquisition, she looked to the prelinguistic use of commands by infants that required them to develop and use social skills. She highlighted the reliance on pointing by infants in order to fill their need to communicate before they are able to speak. The child's ability to incorporate imperatives in their gestures in order to make a command or request was found in her research and shows the necessity of communication regardless of language. Bates also coined the term protoword, a word-like utterance made by prelinguistic children that has meaning (e.g. yumyum), but does not represent the adult-like form.

When discussing the time period where children begin to speak, Bates received a lot of attention for finding an overwhelming amount of nouns within the first 50 words of a native English speaker's vocabulary. Bates helped settle an ongoing debate among linguists who argued that a referential language style, characterized by the child's first 50 words containing mostly object labels, was a better strategy in developing language than a personal and socially expressive language style. She found that regardless of the strategy applied by the child, they learn words at the same rate. She did, however, find strong predictive power in the child’s vocabulary at 13 and 20 months old and their grammatical complexity at 2 years old. Bates finds that language learning comes from the neural plasticity in the brain; therefore, children can and are able to learn a language, even with brain trauma.

Neural Plasticity
Research in her lab also showed that adult aphasic patients' deficits were not specific to linguistic structures theorized to be localized to specific brain areas, nor were they restricted to the linguistic domain. Lesion sites overlap in the role that they affect speech fluency and complexity. Language is dependent upon basic cognitive processes such as memory, pattern recognition, and spreading activation. This perspective runs counter to the theory of Noam Chomsky, Eric Lenneberg, and Steven Pinker that language is a special stimulus that is processed by specific language modules in the mind such as the localization to the Broca's and Wernicke's areas.

Through her research, Bates demonstrated that neural plasticity allows children with damage to the right hemisphere or the left hemisphere to learn and apply language within a normal range of use. However, when children are matched in age, sex and socioeconomic status, their use is lower than that of children who did not suffer brain damage. The same study presented evidence that brain damage has permanent consequences on language use when incurred as an adult. In a comparative study on the Origins of Language Disorders, Bates found that the period between 0 to 5 years of age was important to the argument of neural plasticity as this suggests that reorganization in response to an injury occurs during this period. However, there are limits to brain plasticity. Despite the area that is damaged, whether it be right-frontal or left-frontal, it increases the risk for expressive language delay within 19 months to 30 months. This suggests that the left-frontal area isn't a unique region that encourages normal language development.