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What is the brain? 

Larry W. Swanson 

M.D. Baker – Axonal flip-flops and oscillators V IEWPOINT 

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U. S. A. 97, 5616–5620 

From a structural perspective, there are ten basic parts of the vertebrate CNS that are almost 

universally agreed upon.These parts have been grouped in at least five different ways corresponding 

to five different theories about its basic plan or architecture.Two classical models that remain 

popular today are derived from (1) comparative anatomy and the body’s segmental organization, 

and (2) comparative embryology and the neural tube’s transverse and longitudinal organization. 

A new approach is concerned with deciphering the genetic program that assembles the 

nervous system during embryogenesis; how it will correspond to the other models remains to 

be determined. The simplest current model to explain the organization of the mammalian 

nervous system involves a segmental trunk that mediates reflex sensory–motor functions, and 

suprasegmental cerebral hemispheres and cerebellum. 

Trends Neurosci. (2000) 23, 519–527 

‘…anatomy should not be bound by any rule but ought to 

change as frequently as dissections are begun.’ Nicolaus Steno 

(1669) 1 

‘The terminology of the brain is in great confusion.’ C. Judson 

Herrick (1915) 2 

TWO YEARS AGO, Gorica Petrovich and I wrote an 

essay for this journal entitled ‘What is the amygdala?’ 

3 Not surprisingly, it raised broader, even more 

obvious and important questions that we seldom 

pause to think about in this relentlessly reductionistic 

day and age, including, what are the basic parts of the 

brain, or even more to the point, what do we mean by 

the word ‘brain’ itself? An overview of how some of 

the major contributors to the neuroanatomical literature 

have addressed these questions over the centuries 

has revealed two surprising insights that may be worth 

sharing. First, my understanding (and I doubt if I am 

alone in this) of the brain’s basic parts goes back to 

dogmatic, essentially undocumented statements in 

recent textbooks, and similarly, the precise meaning of 

certain terms such as ‘brainstem’, ‘basal ganglia’, and 

‘cerebrum’ has never been entirely clear to me, 

although I usually have not worried too much about 

it. Second, even though the nomenclature nightmare 

referred to by Herrick 2 in the quote at the beginning of 

the article certainly has not gone away 4 , there is actually 

a great deal of information embedded within the 

confusion. On one hand, we will see that there are on 

the order of ten generally agreed upon parts of the vertebrate 

CNS (ignoring disputes about what they are 

called), and on the other hand these parts have been 

grouped in at least five different ways, constituting five 

‘theories of brain architecture’, to use Baer’s 5 insightful 

phrase. Because there seem to be no compelling reasons 

for choosing among these theories or models at 

the present time, they provide a set of fresh ways to 

consider the basic plan of the CNS – especially important 

long-term goals of developmental and systems 

neuroscience. The subject of regional neuroanatomy 

might seem irrelevant to molecular and cellular neuroscience, 

until one comes to view the function of a gene 

0166-2236/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S0166-2236(00)01639-8 TINS Vol. 23, No. 11, 2000 519 

Acknowledgements 

The author is 

grateful to Hugh 

Bostock for 

innumerable useful 

discussions and 

Matthew Kiernan 

for his comments 

on the manuscript. 

This work was 

supported by the 

MRC. 

Larry W. Swanson 

is at the 

Neuroscience 

Program, The 

University of 

Southern 

California, Los 

Angeles, 

CA 90089-2520, 

USA.

V IEWPOINT 

‘Brain’ 

(c. 4200 BC) 

L.W. Swanson – Brain architecture 

Dual brain 

(c. 340 BC) 

Aristotle 

or neuron in terms of its role within a particular neural 

system or part of the brain. This brings us back to the 

two questions posed at the beginning of this review. 

CNS nomenclature in antiquity 

From one perspective, the history of neuroanatomical 

nomenclature can be traced back more than 6000 

years (Fig. 1). An equivalent to the English word 

‘brain’ is found in an Egyptian manuscript composed 

~4200 BC (Ref. 6), although its most famous occurrence 

is in the Edwin Smith Surgical Papyrus (a 1700 BC copy 

of an Egyptian manuscript composed some 1500 years 

earlier), where 13 cases of skull fracture caused by 

war injuries are discussed 7–10 . In approximately 340 BC 

Aristotle published the first surviving account of brain 

dissections 10 . He distinguished the parencephalon or 

small brain (cerebellum in Latin) from the encephalon 

or large brain (cerebrum in Latin), which extends 

down through the back as the spinal marrow (the 

marrow of the back bone or vertebral column; our 

spinal cord). This was the first theory or model of CNS 

architecture and consisted of three parts based on the 

simplest gross anatomical criteria, that is a small brain 

attached to a large brain, which in turn is attached to 

a spinal marrow (Fig. 2a). This dual (large and small) 

brain model was followed unaltered for about 1800 

years, until the work of Vesalius, described below. 

Before progressing to the European Renaissance it 

is important to note that Aristotle started the unenviable 

tradition of ambiguous terminology in 

neuroanatomy referred to by Herrick 2 . Aristotle used 

exactly the same word, encephalon, in two very different 

ways: first, in its oldest sense, as the ‘marrow’ of 

the skull, and second, as a name for his ‘large brain’. 

As with all such ambiguities, the meaning of a specific 

example of the word can only be inferred from its context, 

which is a crucial problem today because keywords 

with more than one meaning might be used 

(without context) for database queries. 

Interestingly, this ambiguity was recognized, and 

even dealt with, very quickly in classical antiquity. As 

Galen noted 10 , in approximately 290 BC the founder of 

human anatomy, Herophilus, might have proposed 

the unequivocal term enkranon for the neural contents 

of the skull compared with Aristotle’s specialized 

use of ‘encephalon’ for the large brain. Unfortunately 

520 TINS Vol. 23, No. 11, 2000 

Willis 

1644 

Varolio 

1573 

Vesalius 

1543 

Malpighi 

1672 


Edinger 

1908 

1980s 

Segmental 

Segmental 

Segmental 

Developmental 

Evolutionary 

Genomic 

trends in Neurosciences 

Fig. 1. Evolutionary history of major theories on regional organization of the CNS. In the 16th and 17th centuries there 

was an ‘explosion’ of theories regarding the basic regional or topographic organization of the CNS after the ‘dual brain’ 

account of Aristotle was introduced in classical antiquity (~340 BC). Two new classes of theory, evolutionary and genomic, 

were added in the 20th century; the former has had little substantial influence, whereas the latter is, just now, maturing. 

this useful distinction never caught 

on. From an early time, however, 

careful anatomists began to speak of 

the ‘brain proper’ (or the cerebrum 

proper or the encephalon proper) 

when referring to Aristotle’s large 

brain, and the ‘brain’ or ‘brain in 

general’ when referring to the 

neural contents of the skull. 

Incidentally, a curious tradition has 

evolved in English (which probably 

dates back to 1755 and the publication 

of Samuel Johnson’s great 

dictionary 51 ), where frequently the 

part of the CNS in the skull is 

referred to as the encephalon or 

brain, whereas the large brain is 

referred to as the cerebrum. Once 

one is aware of ambiguities associated 

with definitions and uses of 

the words ‘brain’, ‘cerebrum’ and 

‘encephalon’ it is amazing how often their meaning is 

unclear when reading the literature carefully. 

The Renaissance explosion of models: segmental 

and developmental 

With the publication in 1543 of his truly revolutionary 

masterpiece, De Humani Corporis Fabrica 52 , 

Vesalius codified Renaissance anatomy, which was 

based on two principles: direct observation instead of 

reliance on classical texts, and use of the new, naturalistic 

art to illustrate results (his principal artist, Kalkar, 

was in all probability from Titian’s studio). Similar to 

Aristotle, Vesalius proposed a tripartite division of our 

CNS, but this time the parcellation was based on much 

better structural analysis that now included a consideration 

of the nerves 17 . At the core of Vesalius’s description 

was the dorsal medulla, which corresponds to our 

spinal cord, medulla and pons (Figs 2,3). He extended 

Aristotle’s ‘spinal medulla’ up into the cranium 

because the whole structure is associated with a series 

of major paired nerves beginning rostrally with our 

trigeminal nerve, and thus excluding the ‘atypical’ 

nerves associated more rostrally with the eye and olfactory 

apparatus. Vesalius attached his version of the 

large brain (now the Latin cerebrum instead of the 

Greek encephalon) to the rostral end of the dorsal 

medulla or ‘trunk’ (derived from Willis, see below), and 

the small brain (now the Latin cerebellum instead of 

the Greek parencephalon) to the dorsal aspect of the 

trunk, just caudal to the cerebrum (Fig. 2). 

This was the first example of a general class of 

model wherein a central trunk that generates ‘segmental’ 

nerves is associated with two ‘suprasegmental’ 

structures, the cerebrum and cerebellum, as specifically 

articulated at the close of the 19th century by 

Meyer 53 . Based on the origin of regularly spaced nerve 

pairs, Vesalius was able to escape from the all too easy 

convention (advocated by Galen and still common 

today) of dividing what we call the CNS into a part 

within the skull and a part within the vertebral column 

(brain as a whole and spinal cord, respectively). 

Nevertheless, the double meaning of the word 

cerebrum referred to in the preceding section was evident 

even in his text. For example, at the beginning 

of chapter four in Book VII, Vesalius wrote: 

‘Dissectionum professores, universum cerebrum in anterius,

quod cerebrum, & in posterius, quod cerebellum vocant: 

deinde anterius in dextrum & sinistrum dividere resolent…’, 

which Singer 17 has translated as ‘By professors 

of dissection the brain is customarily divided into an 

anterior part, which they call ‘cerebrum’, and a posterior, 

the ‘cerebellum’, the anterior (being divided) 

into right and left’. Note that Singer has used ‘brain’ 

instead of ‘cerebrum’ at the beginning of the sentence 

(even though Vesalius used cerebrum), and in the title 

of his book, Vesalius on the Human Brain 17 . 

Thirty years later, in 1573, Varolio (who discovered 

the pons, or more accurately, our middle cerebellar 

peduncles) came up with a second interpretation of 

where the trunk ends rostrally 26 . He showed the trunk 

extending all the way to the base of the cerebral hemispheres 

(thus including our interbrain or diencephalon), 

and he referred to the whole trunk as the 

spinal marrow rather than the dorsal marrow of 

Vesalius (Figs 2,3), which was probably an unfortunate 

choice because the rostral end is not within the spinal 

column; that is, the term is obviously inaccurate. 

The final variant of the ‘segmental’ model from 

this era appeared in the first book devoted exclusively 

to nervous system structure and function, 

Willis’s classic Cerebri Anatomie, where the word neurology 

was first used 34 . Willis extended the trunk 

even farther rostrally, to include what he identified 

and named the striate body (the non-cortical part 

of the cerebral hemisphere, Fig. 3 and Table 1). 

However, he introduced a major new division: the 

part of the trunk in the skull he referred to by the 

synonyms oblong marrow, medullary stem and 

medullary trunk – in distinction to the part of the 

trunk in the spinal or vertebral canal (the spinal marrow). 

So accordingly, there were oblong and spinal 

divisions of the marrow or trunk. This advance contains 

an initial concept of a ‘brainstem’, although 

this term does not appear to have been used until the 

19th century (Table 1). Note that the first definition 

of the medulla oblongata (oblong marrow) included 

what today we call the basal ganglia/cerebral nuclei, 

interbrain, midbrain and hindbrain. Essentially, 

Willis pointed out that the cranial nerves arise from 

the oblong marrow, whereas the spinal nerves arise 

from the spinal marrow. 

Willis provides another classic example of how 

nomenclature can become confused for no apparent 

reason. Since the time of Galen our superior and inferior 

colliculi (corpora quadrigemini, tectum) had been 

referred to as the testes and nates (buttocks), respectively. 

However, Willis inexplicably reversed this, 

despite what would seem to be an unforgettable explanation 

of Galen’s terminology by Vesalius 17 , ‘This part 

of the cerebrum graphically represents the two nates 

connected together. But since the upper part even 

more resembles the testes because of that gland (the 

pineal) which is like a penis, the Ancients, who traditionally 

trained youths in the home in verbal distinctions, 

called that part DIDYMOS. We, imitating them, 

name it testes or gemelli. Since in the hind and lower 

part of this body is placed the orifice of the passage 

from the third ventricle to the fourth, and since this 

orifice has some resemblance to the anus, and since in 

the hind part of this area there is a transverse linear 

impression separating the upper parts from the lower, 

the Ancients as I believe, gave to this region the name 

GLOUTION (GLOUTOS � buttock)’. 

L.W. Swanson – Brain architecture V IEWPOINT 

Malpighi (who proved Harvey’s model of the circulation 

of the blood by discovering the capillary connection 

between arteries and veins, and is considered 

the founder of histology) provided the final classical 

model of CNS organization in 1672 (Ref. 37), based on 

embryology in the chick (Figs 2,3). He described and 

beautifully illustrated how at very early stages of 

development the nervous system seems to be associated 

with a plate-like structure that is broad rostrally 

and tapers caudally. Then, one can see three sequential 

vesicles or swellings in the broad rostral area that 

corresponds to the future brain. Finally, there is a 

series of five sequential vesicles in the brain region, 

with the most rostral vesicle actually being paired, the 

developing eyes lying on either side of the second 

vesicle (which he seems to have associated with the 

optic thalamus of Willis, our interbrain), and the third 

vesicle (which he called the cristate vesicle and thus 

discovered our midbrain) also being paired. How Baer 

named the same vesicles in a way that is still followed 

today is considered below, but the important point 

here is that Malpighi discovered a fundamental transverse 

organization of the neural tube, and thus, presumably, 

of the adult CNS. 

In summary, by 1672 there were three general models 

of CNS organization: the dual brain model of 

Aristotle; the segmental model of Vesalius, Varolio, and 

Willis; and the embryological model of Malpighi. By 

this time, six basic parts of the CNS had been identified, 

although the definition of several of them varied with 

different authors. These parts included the cerebrum, 

striate body (basal ganglia/cerebral nuclei), optic 

thalamus (interbrain), cristate vesicle (midbrain), 

cerebellum, and spinal or dorsal marrow (spinal cord). 

How these three models evolved will now be examined. 

The dual brain model 

Aristotle’s basic model of a small or posterior brain 

attached to a large or anterior brain, which in turn is 

attached to the spinal marrow or cord, exerted a considerable 

influence well into the 19th century, but is 

now largely forgotten. Nevertheless, a crucial part of it 

has survived in a convoluted way, caused mainly by 

the pioneering work of Vieussens 13 , who in 1684 was 

the first to begin subdividing and then extending 

Willis’s corpora striata, which he called the corpora 

striata inferiora (essentially the anterior striate bodies). 

Because he used Aristotle’s model, he went on to 

describe Willis’s optic thalamus (interbrain) as the corpora 

striata superna posterior (essentially the posterior 

striate bodies), and the rest of the ‘brainstem’ (our 

midbrain and hindbrain) as the corpora striata media. 

Many years later the influential neuroanatomist, 

Reil 10,15 referred to the first two divisions as the great 

cerebral nucleus, with an anterior part (Willis’s striate 

body) and a posterior part (Willis’s optic thalamus, our 

interbrain). Then, only a year later in 1810, the even 

more influential neuroanatomical work of Gall and 

Spurzheim 16,59 referred to the same features as the great 

cerebral ganglion, with its anterior and posterior parts. 

By 1876, Ferrier 36 would refer to the great cerebral 

nucleus or ganglion as the basal ganglia, the first reference 

to this term that I have found thus far. It remained 

for the majority of leading 20th-century neuroanatomists 

to restrict the term ‘basal ganglia’ (‘basal 

nuclei’) to its original meaning, the corpus striatum 

of Willis, that is, the basal nuclei of the cerebral 

TINS Vol. 23, No. 11, 2000 521

V IEWPOINT 


Segmental 

Developmental 

Striate 


Antiquity to end of the 17th century 

(classical) 

ENCEPHALON 

Cerebrum (cortex) 

body 

INF 

T N 

Vesalius (1543) 17 

CEREBELLUM 

522 TINS Vol. 23, No. 11, 2000 

DORSAL MARROW 

SPINAL MARROW 

Varolio (1573) 26 , Aranzi (1587) 27 

Optic 

thalamus 

N 

T 

Encephalon (brain) = 

encephalon (proper) 

PAR- 

+ parencephalon 

ENCEPH. 

Cerebellum 

(cortex) 

Willis (1664) 34 

SPINAL MARROW 

Aristotle (c. 340 BC) 10 , Mondino (1316) 10 , Berengario (1523) 11 , Dryander (1536) 12 

CEREBRUM 

CEREBRUM 

Terminal vesicle 

[Optic Cristate 

thalamus] vesicle 

Cerebrum (brain) = 

cerebrum (proper)+ 

cerebellum 

CEREBELLUM 

Cerebellar 

vesicle 

Malpighi (1673) 37 

Oblong marrow, 

medullary stem/trunk 

Spinal marrow 

Brain vesicles and spinal medulla 

(transverse divisions) 

Spinal medulla 

Fig. 2. Neuroanatomical nomenclature. The main ways of subdividing 

the CNS are shown in the column on the left. Note that the dual brain 

and segmental models involve a large and a small brain attached to a 

central core of variable length, whereas the developmental model features 

a rostrocaudally arranged series of vesicles. In the early 20th-century, 

evolutionary models were introduced and towards the end of the 

century a genomic approach began to emerge. By now there are at least 

ten basic parts or regions that are widely accepted (disregarding nomenclature 

debates that are usually of a theoretical nature). These parts are 

shown in the small diagram to the right, without imposing any assumptions 

about how they are grouped. By illustrating their topographic relationships, 

they have a very specific meaning and they can be used to 

compare and describe any of the other schemes in this chart. The flatmap 

shows the right side of the CNS, with rostral to the left and caudal to the 

right; its construction is discussed in Ref. 50. Abbreviations: cereb., cerebral; 

cereb. ped., cerebral peduncle; corp. Quad., corpus quadrigemina; 

d. thalamus, dorsal thalamus; epi., epithalamus; gang., ganglion; hypothal., 

hypothalamus; INF, infundibulum; m., metathalamus; Met., 

metencephalon; Myel., myelencephalon; N, nates; PARENCEPH., parencephalon; 

pars mam. hypo., pars mammillaris hypothalamus; p. opt. 

hypo., pars opticus hypothalamus; Rhombenceph., rhombencephalon; 

SYN, synencephalon; T, testes; teg., tegmentum; tel. imp., telencephalon 

impar; thal., thalamus; vent. thal., ventral thalamus. 

Cerebral cortex 

(hemispheric ganglion) 

Anterior 

cereb. Posterior 

gang. 

cerebral 

ganglion 


Cerebellum 

Striate 

corp. 

quad. 

body Optic 

thalamus Cereb. 

pedun. 

Pons Medulla 

N 

T 

Haller (1781) 18 , Bell (1802) 19 , Leuret and Gratiolet (1839–57) 20 , Kölliker (1854) 21 , Luys (1865) 22 

Cereb. 

pedun. 

Cerebellum 

Pons 


Great cerebral ganglia 

(cerebral nuclei, basal ganglia) 

Primitive, medial, ascending 

(cerebral) ganglion 

Spinal cord 

Vieussens (1684) 13 , Monro (1783) 14 , Reil (1809) 15 , Gall and Spurzheim (1809) 16 

Reichert (1859) 28 , Schwalbe (1881) 29 

Cerebrum (cortex) 

body 

18th to mid-19th century 

(late classical) 


Striate 

body Optic 

thalamus 

Striate 

Optic 

thalamus 

Endbrain 

FOREBRAIN 

corp. 

quad. 

corp. 

quad. 

Midbrain 

MID- 

BRAIN 

Cerebellum 

(cortex) 

Ann. 

Prot. 

Pons Medulla 

Longet (1842) 35 , Ferrier (1876) 36 

Interbrain 

corp. 

quad. 

Cerebellum 

Baer (1837) 5 , Edinger (1885) 38 

CTX 

Cerebellum 

Pons 

Medulla 

Cerebrum 

Spinal marrow 

Cerebrum 

Brain stem 

Spinal marrow 

Brain stem 

Spinal marrow 

HINDBRAIN 

Pons Medulla SPINAL MARROW 

L/D 

R C 

M/V 

BG TH 

HY 

T 

TG 

CB 

P M 

Major Regions 

SP 

BG, basal ganglia (cerebral nuclei) 

CB, cerebellum 

CTX, cerebral cortex (pallium) 

HY, hypothalamus 

M, medulla 

P, pons 

SP, spinal cord 

T, tectum 

TG, tegmentum 

TH, thalamus


Anterior 

cereb. Optic thal. 

gang. 

Tuber cinereum 


Cerebellum 

Pons Medulla 

Cerebellum 


Cerebral (central) ganglion 

Central tubular gray matter 

Spinal cord 

Meynert (1872) 23 , Gaskell (1889) 24 , Dejerine and Dejerine-Klumpke (1895) 25 

rhinencephalon 


Late 19th to early 20th century 

(modern–histology) 

Cerebellum 

corp. Met. 

m. quad. RHOMBENCEPH. 

thalamus 

pars cereb. Pons 

p. opt. 

Myel. 

mam. ped. H T 

hypo. hypo. 

I S 

M U S 

His (BNA, 1895) 39 

Cerebrum = 

forebrain + midbrain 

Sulcus limitans 

(adds longitudinal organization 

to transverse divisions) 

sulcus limitans 

SPINAL MEDULLA 

basis 


tel. 

epi. 

tectum 

teg. 

hypothal. S Y 

N 

d. thalamus 

vent. thal. 

imp.I S THMUS 


Contemporary 

Spinal marrow 

Bechterew (1900) 30 Carpenter and Sutin (1983) 31 , Nauta and Feirtag (1986) 32 , Williams (1995) 33 


Brain stem 

Cerebellum 

Striate 

Optic thal. 

corp. 

quad. 

body 

Tuber cinereum 


Pons Medulla 

T R U N K 

Ann. 

Prot. 

Herrick (1915) 2 

Cerebral cortex Cerebellum 

(cortex) 

Striate 

corp. 

m. quad. 

thalamus 

Pons 

pars cereb. 

Medulla 

body 

p. opt. mam. 

hypoth. hypo. ped. 

p a l l i u m 

corpus striatum 

striate body 

epi. 

epi. 

Archencephalon 

p a l l i u m 

basis 


tel. 

imp. 

epithal. 

d. thalamus 

vent. thal. 

corp. 

quad. 

Ahlborn (1883) 42 , Kingsbury (1920) 43 

Ann. 

Prot. 

Brain stem 

tectum 

Met. Myel. 

Spinal cord 

teg. 

hypothal. S Y Deuterencephalon & spinal cord 

N 

(prechordal) 

Palaeëncephalon (old brain) 


Neopallium 

Archepallium 

C E R E B R U M 

C E R E B R U M 

Spinal cord Brainstem 

Spinal cord 

p a l l i u m 

Cerebellum 

Crosby et al. (1962) 40 , Nieuwenhuys et al. (1998) 41 

p a l l i u m 


Edinger (1908) 46 , Kappers (1909) 47 MacLean (1990) 48 

p. opt. 

hypoth. 

Spinal cord 

epi. 

Met. Myel. 

Cerebellum 

corp. Met. 

m. quad. 

thalamus 

pars cereb. Pons 

p. opt. 

Myel. 

mam. ped. 

hypoth. hypo. 

corpus striatum 

CB 

CB 

Forebrain 

Kupffer (1906) 44 , Kuhlenbeck (1967–1978) 45 


Hindbrain 

Neomammalian 

SPINAL MEDULLA 

Paleomammalian 

Paleopallium Reptilian 

Hox-2.6 (e12.5 mouse) 

Wilkinson et al. (1989) 49 

TINS Vol. 23, No. 11, 2000 523 


Segmental 

Developmental 

Genomic Evolutionary

V IEWPOINT 

(a) 

(b) 

(d) 


(c) 

(e) 

hemisphere (Table 1). At the same time the meaning of 

‘cerebrum proper’ was being greatly restricted to the 

cerebral hemispheres (Table 1), leading to the demise of 

the dual brain model. As an interesting historical footnote, 

in 1836 Solly60 introduced the term ‘hemispheric 

ganglion’ to refer to the cerebral cortex, in an effort to 

provide a complement to Gall and Spurzheim’s ‘great 

cerebral ganglion’ (later, the basal ganglion). 

Segmental models 

The evolution of these models – essentially consisting 

of a trunk generating regularly spaced paired 

nerves, and suprasegmental cerebrum and cerebellum 

– is complex and only a broad overview will be given 

524 TINS Vol. 23, No. 11, 2000 


Fig. 3. Pioneering illustrations of CNS topography. (a) In this drawing, Vesalius (1543) 17 

illustrates his concept of the human dorsal medulla – essentially a trunk that generates a 

regular series of paired nerves, beginning rostrally with the trigeminal nerves (labeled 3 and 4 

at the far left) and ending caudally with a 30th pair of spinal nerves at the far right. The region 

between A and B is what we know today as the pons and medulla (5 is the facial nerve; 6 is 

cranial nerves IX–XI; and 7 is the hypoglossal nerve); that between B and H is what we know 

as the spinal cord. (b) Thirty years later, Varolio 26 illustrated the base of the human brain and 

showed the spinal medulla (labeled 1–3 on the left side or top; and labeled a,b on the right 

side or bottom, rostral is to the left) as extending all the way to the base of the cerebral hemispheres, 

just caudal to what is obviously the optic chiasm. (c) Shortly thereafter, Willis 34 

extended the trunk even farther rostral to include what he identified and named the striate 

bodies (labeled A in this dorsal view of the sheep brain, which has been rotated so that rostral 

is to the left). This figure beautifully illustrates the entirety of what Willis referred to (leaving 

aside the cerebellum, T and s, which was bisected and pulled to either side) as the oblong marrow, 

medullary stem, or medullary trunk. (d) A lateral view of the right half of a chick embryo 

after four days of development as drawn by Malpighi 37 . Using His’s later terminology, the following 

parts of the neural tube seem clear: E indicates the paired telencephalic vesicles, D the 

diencephalic vesicle, F the optic cup and choroid fissure, A the mesencephalic vesicle, B the 

metencephalic vesicle, and C the myelencephalic vesicle. (e) Illustration of how Edinger 46 

viewed the mammalian neëncephalon as being added on top of the lower vertebrate paleëncephalon, 

basically at the rhinal fissure, which extends caudally from the olfactory bulb at the 

far left. Some of the figures have been lightly retouched so that the labels are clearer. 

here (Fig. 2). The Vesalian model was refined in the late 

18th century by Haller18 who divided the cerebrum 

sequentially into cerebral cortex, striate body, optic 

thalamus, and the corpora quadrigemini and cerebral 

peduncle, which together form our midbrain. Caudal 

to this, he was the first to distinguish clearly between 

the pons and medulla as we now refer to them, 

although he was somewhat obscure about the larger 

part of the CNS that they should be placed within. One 

of the last major anatomical analyses based on the 

Vesalian model was published by Meynert23 in 1872. It 

took advantage of the histological methods that had 

been introduced earlier in the century. Essentially, he 

introduced an innovative, longitudinal way of thinking 

about the brainstem by dividing the traditional 

posterior cerebral ganglion into a dorsal zone, which 

he called the optic thalamus proper (our thalamus), 

and a ventral zone, the tuber cinereum (our hypothalamus). 

He included the optic thalamus proper and 

the corpora quadrigemina in the true posterior cerebral 

ganglion, and included the tuber cinereum, cerebral 

peduncle (our ventral midbrain or tegmentum), pons, 

medulla, and spinal cord in what he called the central 

tubular gray matter, which was responsible for generating 

all of the motor nerves. 

Here, for the first time, we can recognize ten basic 

parts of the CNS that are common to virtually all 

modern gross anatomical descriptions: cerebral cortex, 

basal ganglia/cerebral nuclei, thalamus and hypothalamus, 

tectum and tegmentum, pons, medulla, 

cerebellum, and spinal cord (in modern terms). 

Willis’s basic model of a brainstem stretching from 

the corpus striatum rostrally to the medulla caudally 

was refined by the addition of Haller’s subdivisions35,36 , 

and in Herrick’s2 final major reincarnation by the addition 

of His’s embryonic schema (see below). 

It is Varolio’s basic model that has remained popular 

today, refined by division of the central trunk into a 

brainstem part, generating the cranial nerves and a 

spinal cord part, generating the spinal nerves31,32 . Haller’s 

subdivisions of the brainstem have usually been applied 

to this model, see for example Ref. 30, although in a 

rather idiosyncratic way, Reichert28 and then Schwalbe 29 

included the cerebellum in the brainstem (Table 1). 

Developmental models 

The great Baer has the distinction of having provided 

simple, descriptive names (Fig. 2) for the embryonic 

brain vesicles first identified by Malpighi (see 

above), and for demonstrating 5 that these vesicles are 

probably common to all vertebrates. These contributions 

have had a profound influence and lasting value. 

He recognized three primary vesicles (in English, forebrain, 

midbrain and hindbrain), and five secondary 

vesicles (in English, the forebrain vesicle divides into 

endbrain and interbrain vesicles, and the hindbrain 

vesicle divides into hindbrain, consisting of cerebellum 

and pons and afterbrain vesicles). The actual subdivisions 

were quite similar to Haller’s scheme, proposed 

a few years earlier, so a number of equivalent 

synonyms were generated, for example, optic thalamus 

and interbrain, and endbrain and cerebrum 

(Fig. 2). By the mid-19th century, writers using the 

dual brain, segmental, and developmental models of 

CNS organization were using each others nomenclature 

for subdivisions almost interchangeably. What 

was different was the way they grouped the various

TABLE 1. Historical overview of the meaning of some common gross anatomical terms for parts of the CNS 

Common gross Modern scheme of basic subdivisions Selected refs 

anatomical terms 

Cerebral Basal Inter- Mid- Hind- Cere- Spinal 

cortex ganglia brain brain brain bellum cord 

subdivisions. The Malpighi–Baer model was unique 

because it viewed the basic plan of the brain in terms 

of three rostrocaudally arranged swellings, in contrast 

to suprasegmental cerebrum and cerebellum attached 

to a trunk generating the cranial and spinal nerves. 

The final major variation of the Malpighi–Baer 

model was provided by His towards the end of the 

19th century. He described 61 a longitudinally oriented 

limiting sulcus that divides the right and left halves of 

the developing neural tube into a dorsal alar plate 

(which, at least initially, is sensory in function) and a 

ventral basal plate (which, at least initially, is motor in 

function). Subsequently, the question of where to 

place the rostral end of the limiting sulcus has generated 

endless and unresolved controversy, although 

His himself placed it at the optic chiasm in the 1895 

‘Basle Nomina Anatomica’ (BNA), an ‘official’ tabulation 

of anatomical nomenclature 39,62 . In some ways 

the original BNA taxonomy of brain parts is less satisfactory 

today than the older and simpler scheme of 

Baer. For example, His divided the endbrain (telencephalic) 

vesicle into pallium, rhinencephalon, and 

corpus striatum, the latter of which he extended to 

include all of the hypothalamus except for the mammillary 

bodies (even though the hypothalamus, 

including the preoptic region, is derived from the 

third ventricle neuroepithelium). In addition, His 

included, between the midbrain and hindbrain, a narrow 

isthmus vesicle whose components in the adult 

mammal have never been identified satisfactorily. 

Nevertheless, His’s basic model has had a profound 

and lasting influence, see for example Ref. 41, mainly 

because it makes a distinction between dorsal, sensory 

regions of the CNS and ventral, motor regions. 

Analysis of this combined structural and functional 

approach would require another essay, but by way of 

introduction it very nicely complemented the brilliant 

earlier work of Magendie 63 and of Luys 22 and 

Meynert 23 . Magendie showed experimentally that the 


Cerebrum (proper) X X X X X Aristotle10 , Vieussens 13 1684, Monro 14 1783, Reil 15 1809 

X X X X Vesalius17 1543, His 39 (BNA 1895), Herrick 2 1915 

X X X Müller54 1843 

X X Varolio26 1573, Reichert 28 1859, Nauta-Feirtig 32 1986 

X Willis34 1664, Ferrier 36 1876 

Cerebral hemisphere X X Baer 5 1828, Herrick 2 1915, Nauta-Feirtig 32 1986 

X Willis34 1664, Ferrier 36 1876 

Cerebral or basal X X X X Vieussens 13 1684, Reil 15 1809, Gall-Spurzheim 16 1810 

nuclei or ganglia X X X Meynert23 1872 

X X Ferrier36 1876 

X Herrick2 1915, Crosby et al. 40 1962, Nauta-Feirtig 32 1986 

Cerebellum X Aristotle 10 , universal since antiquity 

Brainstem X X X X Baer 5 1828, Herrick 2 1915, Ranson-Clark 55 1959 

X X X Obersteiner56 1888, Carpenter-Sutin 31 1983, Nauta-Feirtig 32 1986 

X X X X Reichert28 1859, Schwalbe 29 1881 

X X Jacobsohn57 1909, Olszewski-Baxter 58 1954, Williams 33 1995 

Spinal cord X X X X Varolio 26 1573, Aranzi 27 1587 

X X Vesalius17 1543, Malpighi 37 1672 

X Aristotle 10 , universal since 18th century 

dorsal roots carry sensory information into the spinal 

cord, whereas the ventral roots carry motor information 

out of the spinal cord. Luys and Meynert 

suggested that sensory information travels up dorsal 

regions of the neuraxis on route to the cerebral 

hemispheres, whereas motor information leaving the 

hemispheres takes a more ventral route. 

A clear alternative to the Malpighi–Baer model was 

proposed by Ahlborn in 1883 (Ref. 42). Based on an 

examination of lamprey development, he proposed 

that the hindbrain, similar to the spinal cord, develops 

adjacent to the notochord and is thus epichordal, 

whereas the forebrain and midbrain (Vesalius’s cerebrum) 

develop rostral to the notochord and are thus 

prechordal. This idea was supported by Kingsbury43 , 

who showed conclusively that the definitive, histologically 

defined embryonic floor plate does not extend rostral 

to the hindbrain–midbrain junction. Assuming that 

the notochord and floor plate are essentially co-extensive, 

this would support a prechordal derivation of the 

midbrain and forebrain. By contrast, Kupffer published 

an exhaustive review of his own work and that of 

others in 1906 (Ref. 44), concluding that the midbrain 

is epichordal. He used the terms deuterencephalon for 

supposed epichordal parts of the brain, and archencephalon 

for supposed prechordal parts, an interpretation 

that has been followed by Kuhlenbeck45 . 

Unfortunately, the exact rostral limit of the notochord 

and its precursor remains problematic, partly because of 

the uncertain nature of the so-called prechordal plate. 

Evolutionary models 

All of the models discussed so far are based on comparative 

anatomy and embryology, with an emphasis 

on mammals, and even humans. However, it was 

inevitable that phylogenetic models would be proposed 

after the publication of Darwin’s The Origin of 

Species in 1859 (Ref. 64). Interestingly, they did not 

appear until approximately the turn of the century, 

TINS Vol. 23, No. 11, 2000 525

V IEWPOINT 


and then had only a brief, disruptive life, undoubtedly 

because relatively small amounts of reliable information 

about non-mammalian brain circuitry were 

(and are) available. In spite of this, the main intellectual 

stimulus came from Edinger (see Ref. 46), who 

proposed a distinction between palaeëncephalon (old 

brain) and neëncephalon (new brain). According to 

this model (Figs 2,3), part of the brain is common to 

and essentially unchanged throughout all vertebrates, 

and is responsible for all of the sensory–motor reflexes 

and purely instinctive behaviors necessary for survival. 

This is the palaeëncephalon, which constitutes 

the entire fish brain. During the course of subsequent 

evolution, a new layer is added, the neëncephalon, 

which corresponds to the cerebral pallium. This is tiny 

in amphibians, a little bigger in reptiles, considerably 

larger in birds and huge in mammals. According to 

this model, brain evolution took place in a geological 

fashion by the addition of strata. 

Edinger’s young colleague, Kappers, soon elaborated 

this basic idea dividing the pallium into three successively 

evolved regions47 : the oldest or paleopallium 

(essentially the primary olfactory cortex), archipallium 

(more or less Ammon’s horn or the hippocampus), and 

neopallium (all the rest, Fig. 2). In addition, he divided 

the corpus striatum (basal ganglia/cerebral nuclei) into 

three parts: the paleostri-atum (globus pallidus), archistriatum 

(amygdala), and neostriatum (caudate nucleus 

and putamen) 65 . Omitting details, this line of thinking 

led to designations like paleo-, archi- and neothalamus; 

and paleo-, archi- and neocerebellum (see Ref. 45). It 

has had very little influence on contemporary neuroscience 

and the basic connectional principles that it 

rested on almost a century ago have not been borne 

out (for example, that almost all sensory inputs to the 

pallium of fish and amphibians are inevitably olfactory) 

41,45 . Instead, most contemporary evolutionary (i.e. 

comparative) thinking seems to be based on the embryological 

models discussed above (see Refs 41,45). All 

that remain of this model (except for MacLean’s triune 

brain concept48 ; Fig. 2) are the constantly used, basically 

inaccurate, terms neocortex and neostriatum. It is 

telling that Elliot Smith, who actually introduced the 

concept of ‘neopallium’ in 1901 (Ref. 66), wrote a strenuous 

disclaimer less than a decade later67 . 

Genomic models 

Molecular genetics is breathing new life into developmental 

and evolutionary models of brain organization, 

although it is premature to start placing the results into 

a historical perspective. The ultimate goal is to decipher 

and understand the genetic program that assembles the 

neural tube, in part by analysing spatiotemporal patterns 

of gene expression throughout development and 

establishing their functional significance. Once important 

sets of genes are identified, their expression patterns 

could be compared to the many structural patterns illustrated 

in Fig. 2, and eventually this approach should 

provide criteria for helping to decide which, if any, of 

the many structural arrangements suggested thus far 

best represent the basic plan of the CNS (Ref. 68). 

Furthermore, it might be possible to infer how these 

genomic programs, with their constituent genes, 

evolved over the ~400 million years of vertebrate existence 

69 – and perhaps to determine whether 19th-century 

attempts (see Ref. 24) to homologize the invertebrate 

and vertebrate CNSs have any validity 70 . To date, the 

526 TINS Vol. 23, No. 11, 2000 

best example by far of this approach is the partly overlapping 

patterns of Hox gene expression in the developing 

vertebrate hindbrain49 , where they correlate to the 

appearance of the long-known finer subdivisions called 

rhombomeres (see Ref. 45). 

Overview 

This review has focused narrowly on the history of 

attempts to enumerate the major parts of the adult 

vertebrate CNS – an exercise in classical regional or 

topographic structural analysis, identical to enumerating 

the major parts of the body: head, neck, trunk, tail, 

upper limbs and lower limbs. The conclusion seems to 

be that there are at least ten basic parts that, after centuries 

of research, almost everyone now agrees on 

(ignoring disputes about exactly what they are called, 

and where their borders are placed): (1) a dorsal cerebral 

cortex or pallium; (2) ventral or basal cerebral 

nuclei or ‘ganglia’ [(1) and (2) forming the cerebral 

hemispheres or cerebrum]; (3) a dorsal thalamus; (4) a 

ventral hypothalamus [(3) and (4) forming the interbrain], 

(5) a dorsal tectum, (6) a ventral tegmentum 

[(5) and (6) forming the midbrain], (7) a cerebellum, 

(8) a pons, (9) a medulla, and (10) a spinal cord. 

By contrast, there are at least five different theoretical 

frameworks for grouping or arranging these ten 

basic parts (and many more variations on the basic 

themes; Fig. 2), and it is doubtful that there are compelling 

reasons at this stage for adopting one particular 

scheme. Therefore, the time does not seem ripe to 

propose here yet another unifying hypothesis or 

model based on essentially the same data. 

Nevertheless, it is worth observing that there have 

been no serious attempts to present a comprehensive, 

modern systems model of CNS organization. 

Reconsidering the gross anatomy analogy, the 

regional account is traditionally complemented with a 

systems account. Thus, in addition to the various 

topographically arranged parts or regions listed above, 

the body is described as having skeletomotor, circulatory, 

digestive, respiratory, reproductive, immune, 

endocrine and nervous systems. One’s initial thought 

might be that the systems approach is more useful 

than the topographic, but from a broad functional 

perspective this is not strictly true. The hand is used, 

for example, to write with. For the upper limb to perform 

this behavior the skeletal system acts as a series 

of levers that are moved by the muscles, which in turn 

are controlled by nerves directed from the CNS. The 

vascular system supplies oxygen and nutrients to the 

tissues in the limb, the immune system fights infections 

in this part of the body, etc. One important reason 

why the basic organization of the nervous system 

remains mysterious is that a consensus enumeration 

of its functional systems has not been achieved. 

Ultimately, a profound understanding of what the 

brain is and how the brain works will be based on an 

integrated view of its topographic and systems organization. 

This has been accomplished for most of the 

body, partly explaining why the reductionistic molecular 

biology approach is so powerful. However, the 

nervous system remains problematic: the nature of its 

organizing principles as a system is an unsolved problem 

that can only hinder the rational search for ways 

to cure the many diseases that strike within it. 

Finally, note in Fig. 2 that the tripartite model first 

proposed by Varolio in 1573 remains the simplest for

mammals, refined only by a subdivision of the central 

trunk into brainstem and spinal cord. Perhaps a systems 

model based on the fundamental organization of 

connections within and between these three parts 

might be a useful way to start. The profound question 

really is not ‘what is the brain?’ but rather ‘what are 

the basic parts of the nervous system and how are they 

interconnected functionally?’ 

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