One of the prime goals of cognitive scientists has been the understanding of the mechanisms underlying reading, at the heart of which is the relationship between graphemes and phonemes. In alphabetic scripts, such as English, the basic unit represented by a grapheme is essentially a phoneme (Venezky, 1970). A grapheme is defined as a letter or combination of letters that represents a phoneme. For example, the word thought contains seven letters and three graphemes (th, ough, t), representing three phonemes. The relationship between the orthographic and phonological forms of words varies across languages. In English the correspondence between spelling and sound is not transparent. A phoneme can be realised by many different graphemes and a grapheme can also be realised by many different phonemes (e.g., the letter a in late, sat, was, father etc )

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The deep orthography of English allows the existence of two kinds of words: regular words, which follow the rules of spelling-to-sound correspondence, and exception words, which break them. There is a large number of psycholinguistic studies devoted to the responses to these two kinds of words. It has been found that regular words take less time to be named than do exception words (e.g., Glushko, 1979; Gough & Cosky, 1977). For example, a group of trained phoneticians were presented with nonwords and asked to give all their possible phonemic transcriptions according to the rules of English (Gontijo, 1998). A high correlation was found between the number of times each pronunciation was given by the phoneticians. I am researching this with teachers: asking them to give possible pronunciation options for pseudo words, which is not dissimilar to the task they give children at the end of Year 1. As skilled readers can they calculate the possibilities, or have strategies to do so?  Sure, they can give the 'expected' pronunciation based on 'regular' correspondences but to teach children to read and spell they need a deeper understanding. This is what I go over in training.

Explicit phonics instruction is a ‘kick-start’ towards phoneme-grapheme awareness. Some of the phonics teachers I train think that knowing the GPC taught in the phonics program means children can decode words with ease. That is because they recognise words 'by sight' and it is not until they explicitly map words that they are reminded of the full range of correspondences used within the Universal Spelling Code.  

Take the word 'understand' - even if you use the orthographic mapping tool to see the graphemes understand you still have to figure out the phonemes how each grapheme is pronounced) 
It has nine graphemes (u-n-d-er-s-t-a-n-d) and, because they have many different pronunciations, produce a vast number of possible combinations. The total number of possible pronunciations for this word is at least 69,120
(8 x2 x2 x5 x4 x3 x9 x2 x2); see the grapheme–phoneme correspondences for the nine graphemes in the Spelling Clouds
eg u but united until language full revolution busy burial  (8)

n not drink (2)
d day education (2)
er water alternative adhered dossier clerk  (5)
s last was pleasure sugar (4)
t time initiate picture  (3)
a sat about father taken was fall many various orange (9)

With this word it would be quite easy to figure out with basic phonics, but were you  aware of the pronunciation options?
Probably not, as you recognise the word instantly (by 'sight') and didn't have to think about it much.
What if you had to read the word 'gallimaufry' - are  you sure about the pronunciation?   
This is why I SHOW children the phoneme element using Speech Sound Monsters. Once explored it's stored.

Phonics helps children when the graphemes map with the phonemes they have learned. What many teachers don't recognise is that children will try those, but often have to ignore those and use other clues, to 'get to' the word. They often use the very 'cues' teachers have been told not to encourage. The children that become skilled readers earlier - in spite of instruction - will figure out words, but 'track back' and adjust the mappings accordingly. This is an essential skill. Imagine if they had to try all the different combinations! - which they couldn't, as not taught them. So the 'kick-start' should be more about teaching children concepts than GPCs, and making the universal spelling code as VISIBLE as possible.  

 

As skilled readers, we hold words in our orthographic lexicon: the brain word bank. Three forms of the word need to be 'bonded' for it to be stored for instant recognition and easy retrieval: its phonological form (its pronunciation), its orthographic form (its spelling), and its semantic form (its meanings). This 'brain word bank' is crucial because of the possible challenges in pronunciation of words not already stored. Decoding can be laborious, consume a lot of working memory, and children might try to 'skip' it when it's difficult, resorting to guesswork, omitting words, or giving up altogether.

Some well-meaning adults provide children with 'irregular' words to learn as whole word units, especially when they observe the children struggling to decode words. These adults believe that memorisation will simplify the learning process, not realising that the brain isn’t ideally suited for this approach. Many children, given words in this manner, manage to subconsciously discern the three 'elements' (phonological, orthographic, and semantic forms). Without this subconscious processing, the words wouldn’t be effectively stored, and more crucially, the children wouldn’t be able to use these elements to recognise patterns in other words. A child might recognise a few hundred on flashcards but would struggle to recall the letters in the right order when writing, as they don't understand the role of each letter. Relying solely on memorisation also deprives children of the opportunity to develop a deeper understanding. 'Sight words' leant as whole words is an ineffective but very popular activity and, ironically, because they are actually very hard to memorise all manner of activities are designed to try to engage children and !
It is a lot less time consuming - and words are stored - when the three elements are the focus.

Sounds - Spelling - Meaning.  

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The orthographic mapping theory explain how skilled readers build an orthographic lexicon (Ehri, 2014). Orthographic mapping is the cognitive process by which children learn to recognise words without conscious effort (they don't need to decode the word as already stored) and to retrieve the word, to spell it correctly while writing. 

 Explicit phonics instruction acts as a ‘kick-start’ towards phoneme-grapheme awareness and orthographic mapping. However, teaching phonics explicitly does not automatically lead to the 'self-teaching' phase that is essential for children to become skilled readers. I provide them with as much information as possible: showing the graphemes (using the Code Mapping Tool), the phonemes (using the Speech Sound Monsters), and employing activities and books, such as '1,2,3 and Away!', to help them develop a broader vocabulary. The series offers a bridge towards independent reading. Even for children exposed to thousands of spoken words daily, nothing is as powerful for building vocabulary knowledge as deep reading. This 'visible' spelling code not only engages children but also bonds those three elements together really quickly ad the more words are stored, the more they recognise patterns and store more! By the time children start school they can have thousands of words stored, and children who have not started learning to read have more or less empty orthographic lexicons. We really need to train adults around the world, to offer this to ALL children.