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Mathematics and Visualization

Hamish Carr · Christoph Garth

Tino Weinkauf Editors

Topological
Methods in Data
Analysis and
Visualization IV
Theory, Algorithms, and Applications
Mathematics and Visualization

Series Editors
Hans-Christian Hege
David Hoffman
Christopher R. Johnson
Konrad Polthier
Martin Rumpf
More information about this series at http://www.springer.com/series/4562
Hamish Carr • Christoph Garth • Tino Weinkauf
Editors

Topological Methods
in Data Analysis
and Visualization IV
Theory, Algorithms, and Applications

123
Editors
Hamish Carr Christoph Garth
University of Leeds Department of Computer Science
Leeds, United Kingdom Technical University of Kaiserslautern
Kaiserslautern, Germany

Tino Weinkauf
School of Computer Science
and Communication
KTH Royal Institute of Technology
Stockholm, Sweden

ISSN 1612-3786 ISSN 2197-666X (electronic)

Mathematics and Visualization
ISBN 978-3-319-44682-0 ISBN 978-3-319-44684-4 (eBook)
DOI 10.1007/978-3-319-44684-4

Library of Congress Control Number: 2011944972

Mathematics Subject Classification (2010): 00A66, 57-04, 54-04

© Springer International Publishing AG 2017

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Cover illustration from Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simula-
tions by A. Gyulassy, A. Knoll, K. Chun Lau, B. Wang, P.-T. Bremer, M. E. Papka, L. A. Curtiss and
V. Pascucci. By courtesy of the authors.

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Preface

Since Helman and Hesselink’s landmark paper on vector topology in 1989, topolog-
ical analysis has formed an increasingly important part of scientific visualization.
This is not only because it opens up novel forms of understanding but also because
as our data has increased past terascale, machine analysis necessarily substitutes
for laborious human inspection of visualizations. More and more, one can argue
that data analysis precedes rather than succeeds visualization and that topological
analysis is one of the key approaches given its strong mathematical underpinnings,
precise answers and verifiable outcomes.
From its early starts in vector field topology, topological visualization has
expanded to embrace analysis of scalar fields in the form of contour trees,
Reeb graphs and Morse-Smale complexes, analysis of abstract graphs and high-
dimensional data and, most recently, analysis of multivariate fields through Jacobi
sets, Reeb spaces and the joint contour net, linking with the mathematical field of
fibre topology in the process.
Topological visualization is, however, not concerned only with the topological
computation per se. One of the strongest features of the community is its focus on
the full range of theoretical understanding, algorithmic advances and application
work, all of which are represented in this volume.
Starting in 2005, biennial workshops have been held on topological visualization
in Budmerice (2005), Grimma (2007), Snowbird (2009), Zürich (2011), Davis
(2013) and Annweiler (2015), where informal discussions supplement formal
presentations and knit the community together. Notably, these workshops have
consistently resulted in quality publications under the Springer imprint which form
a significant part of the working knowledge in the area.
In the most recent workshop (2015), at Kurhaus Trifels in Annweiler, Germany,
bivariate analysis, Reeb spaces and fibre topology increased in importance, anchored
by keynotes from Professor Osamu Saeki (Kyushu), one of the leaders in fibre topol-
ogy, and Professor Kathrin Padberg-Gehle (Lüneburg), who works on computational
methods for nonlinear dynamical systems.
Of the 23 papers presented at TopoInVis 2015, 20 passed a second-round review
process for this volume. In addition, Professor Saeki contributed a survey of the

v
vi Preface

relevant fibre topology to this volume for the benefit of the community, which we
expect to shape approaches to data visualization in future years, and a further paper
was contributed directly to this volume.
We have grouped this paper in Part I with the two most closely related papers.
Of these, one deals with multi-modal analysis in a particular application domain
(atmospheric impacts of volcanic eruptions). The other deals with joint contour nets
(a quantized approximation of fibre topology) and their relation to analysis based on
Pareto set analysis.
We have then collected papers relating to high-dimensional data in Part II. Here,
the first paper applies scalar field topology to optimization problems, based on the
common description of optimization as a search landscape. In contrast, the second
paper discusses algorithms for computing and visualizing merge trees (one of the
principal forms of scalar analysis) in high-dimensional data. These are grouped with
a paper that considers the relative quality of different measures applied to reduce the
dimensionality of the data.
Part III then collects papers that use scalar topology in relatively low-dimensional
spaces (i.e. three-dimensional space). Here, the first paper compares similarity
between scalar fields, using histograms as summaries of geometric information
to supplement the underlying topological analysis. The second paper is more
applied in nature, as it addresses a practical domain problem—how to track
diffusion of ions into a battery material, using Morse-Smale analysis, to identify the
potential diffusion channels. Lastly, the third paper addresses the inverse problem
of (re-)constructing a scalar field from a known Morse-Smale complex.
Where Part III deals with scalar fields, Part IV considers vector and tensor
fields. Here, while the broad strokes of the analysis are well-understood, actual
computation of topological invariants has a number of practical problems. At the
heart of these is the tension between formal mathematical expression of continuous
models and practical numerical computation. The papers in this part therefore
primarily address issues of discontinuity and degeneracy in the analysis process.
Of these, the first paper deals with issues at the boundary of flow fields through
computation of escape maps, while the second computes similarity measures
between nearby integral curves to detect regions of shared behaviour. A third paper
extends existing ideas for decomposition of vector fields, in order to underpin
a future generation of algorithmic approaches, while a fourth paper extends
existing mathematical analysis of tensor fields as a preliminary to developing new
techniques.
Part V then considers a theme common to many of the newest approaches—
indirect detection of topological features to avoid the numerical problems of early
methods. Here, the goal is to detect coherent structures in a variety of contexts and
use them as the basis of the visualization. The best known techniques for this use
finite time Lyapunov exponents (FTLEs), and three of these papers extend these
techniques, while the fourth considers related computations.
In the first paper on FTLEs, they are used to detect regions of topological change
as a scalar field, which is then subjected to a second round of topological analysis
to detect ridge features. The second paper builds on the observation that not all
Preface vii

topological boundaries are equally important and maps secondary evaluations to

these boundaries to aid in interpretation. The third paper considers an orthogonal
but crucial issue—the effect of approximation on this form of analysis. Lastly, the
remaining paper considers alternate measures of topological importance, replacing
FTLEs with stochastic computations based on transfer operators.
The last part, Part VI, is devoted to papers that are more explicitly about
algorithms or software engineering. Here, the first paper is about the selection
of thresholds for topological analysis, while the second considers the software
instruction necessary for practical deployment of topological techniques. A third
paper looks at improving the computation of merge trees in a distributed setting,
while the last paper considers knotted graphs, an area of topology not previously
represented in the TopoInVis community.
We note that these areas have followed a common pattern in development—
initially, there were only one or two papers published on flow topology, but over
time, they expanded and triggered the development of the TopoInVis workshop.
Later, new techniques were introduced, in particular the detection of coherent
structures using finite-time Lyapunov exponents, and we now see this separating
as a related but different topic.
Equally, the first TopoInVis workshop did not involve a significant amount of
scalar topology, but this area has increased over time and is represented primarily
in Parts I and II, since Reeb and Morse analyses are sufficiently well-developed to
justify two distinct areas. This growth then triggered developments in analysis of
high-dimensional data: hence Part V.
It is therefore encouraging to see the development of fibre topology and
multivariate analysis as an emerging theme in topological visualization, as it shows
that the pattern continues. Equally, we have started to see work submitted on the
peculiar software engineering challenges of topology, and we expect this theme to
develop further in future.
As with any workshop, however, the measure of quality is not the breadth of
the papers, nor the number of people attending, but whether new ground is being
broken. Here, the pattern of development is clear, and we confidently look forward
to additional themes emerging in future TopoInVis workshops.
We would like to thank all of the participants in TopoInVis 2015, as well as
Springer, for their continued support and look forward to further developments in
all of these areas.

Leeds, UK Hamish Carr

Kaiserslautern, Germany Christoph Garth
Stockholm, Sweden Tino Weinkauf
Contents

Part I Topology-Based Analysis of Multi-Variate Data Sets

Theory of Singular Fibers and Reeb Spaces for Visualization . . . . . . . . . . . . . . 3
Osamu Saeki
Topology-Based Analysis for Multimodal Atmospheric Data
of Volcano Eruptions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 35
Alexander Kuhn, Wito Engelke, Markus Flatken,
Hans-Christian Hege, and Ingrid Hotz
A Comparison of Joint Contour Nets and Pareto Sets . . .. . . . . . . . . . . . . . . . . . . . 51
Lars Huettenberger, Christian Heine, and Christoph Garth

Part II Topological Techniques for High-Dimensional Data

Visualizing Topological Properties of the Search Landscape
of Combinatorial Optimization Problems .. . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 69
Sebastian Volke, Dirk Zeckzer, Martin Middendorf,
and Gerik Scheuermann
Computing and Visualizing Time-Varying Merge Trees
for High-Dimensional Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 87
Patrick Oesterling, Christian Heine, Gunther H. Weber,
Dmitriy Morozov, and Gerik Scheuermann
Agreement Analysis of Quality Measures for Dimensionality
Reduction . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 103
Bastian Rieck and Heike Leitte

Part III Scalar Field Topology

Fast Similarity Search in Scalar Fields using Merging Histograms .. . . . . . . 121
Himangshu Saikia, Hans-Peter Seidel, and Tino Weinkauf

ix
x Contents

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery

Materials Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 135
Attila Gyulassy, Aaron Knoll, Kah Chun Lau, Bei Wang,
Peer-Timo Bremer, Michael E. Papka, Larry A. Curtiss,
and Valerio Pascucci
Piecewise Polynomial Reconstruction of Scalar Fields
from Simplified Morse-Smale Complexes . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 151
Léo Allemand-Giorgis, Georges-Pierre Bonneau,
and Stefanie Hahmann

Part IV Vector and Tensor Field Topology

Topological Extraction of Escape Maps in Divergence-Free
Vector Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 171
Ronald Peikert, Gustavo Machado, and Filip Sadlo
Compute and Visualize Discontinuity Among Neighboring
Integral Curves of 2D Vector Fields. . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 187
Lei Zhang, Robert S. Laramee, David Thompson, Adrian Sescu,
and Guoning Chen
Decomposition of Vector Fields Beyond Problems of First
Order and Their Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 205
Wieland Reich, Mario Hlawitschka, and Gerik Scheuermann
Maximum Number of Degenerate Curves in 3D Linear
Tensor Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 221
Yue Zhang, Yu-Jong Tzeng, and Eugene Zhang

Part V Coherent Structures

Hierarchical Watershed Ridges for Visualizing Lagrangian
Coherent Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 237
Mingcheng Chen, John C. Hart, and Shawn C. Shadden
Finite Time Steady 2D Vector Field Topology . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 253
Anke Friederici, Christian Rössl, and Holger Theisel
Comparing Finite-Time Lyapunov Exponents in Approximated
Vector Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 267
Stefan Koch, Sebastian Volke, Gerik Scheuermann, Hans Hagen,
and Mario Hlawitschka
Transfer Operator-Based Extraction of Coherent Features
on Surfaces . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 283
Kathrin Padberg-Gehle, Sebastian Reuther, Simon Praetorius,
and Axel Voigt
Contents xi

Part VI Software and Algorithms

ADAPT: Adaptive Thresholds for Feature Extraction .. .. . . . . . . . . . . . . . . . . . . . 301
Peer-Timo Bremer
Efficient Software for Programmable Visual Analysis Using
Morse-Smale Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 317
Nithin Shivashankar and Vijay Natarajan
Notes on the Distributed Computation of Merge Trees
on CW-Complexes .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 333
Aaditya G. Landge, Peer-Timo Bremer, Attila Gyulassy,
and Valerio Pascucci
Computing Invariants of Knotted Graphs Given by Sequences
of Points in 3-Dimensional Space . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 349
Vitaliy Kurlin
 Part I
Topology-Based Analysis of Multi-Variate
Data Sets
Theory of Singular Fibers and Reeb Spaces
for Visualization

Osamu Saeki

Abstract This is a survey article on singularity theory of differentiable maps with

applications to visualization of scientific data in mind. Special emphasis is put on
Morse theory on manifolds with boundary, singular fibers of multi-fields, their Reeb
spaces, and their topological transitions.

2000 Mathematics Subject Classification (MSC): Primary 57R45; Secondary

57R35, 58K15, 68U05, 65D18

1 Introduction

This is a survey article on singularity theory of differentiable maps, which focuses

on their singular fibers and Reeb spaces. The author will try to explain those
materials which may help researchers in the visualization community to use them
for their own purposes. Therefore, for many of the statements, theorems, etc.,
their rigorous proofs are not given in this article, and instead the author will try
to give appropriate references. Furthermore, some of the results might have little
importance from a mathematical point of view, basically because they are classical
and/or well known to mathematicians in general. However, the author will try to
include them as long as they can play important roles in visualization of scientific
data. Surprisingly, many of the important results that will be explored in this article
are quite new in singularity theory. Some of the problems treated in this article are
being investigated in singularity theory as central issues. This means that problems
in the visualization community may lead to interesting problems or sometimes
essential solutions in singularity theory.
The contents of the article are as follows. In Sect. 2, we review the theory of
generic scalar fields, namely, Morse functions. As this is widely known to the

O. Saeki ()
Institute of Mathematics for Industry, Kyushu University, Motooka 744, Nishi-ku,
Fukuoka 819-0395, Japan
e-mail: saeki@imi.kyushu-u.ac.jp

© Springer International Publishing AG 2017 3

H. Carr et al. (eds.), Topological Methods in Data Analysis and Visualization IV,
Mathematics and Visualization, DOI 10.1007/978-3-319-44684-4_1
4 O. Saeki

visualization community in general, we will try to cover issues which might not be
so popular. Special attention is paid to Morse functions on manifolds with boundary,
since in many situations, data sets are given on a bounded domain in Euclidean
spaces which have boundary. We also describe the deformation of Morse functions,
from the view point of the simplification of the Reeb graph.
In Sect. 3, we review the singularity theory for generic multi-fields, which are
called stable maps in singularity theory. We will see that Morse theory can be
extended naturally to some dimension pairs, but not to all cases, at least theoretically.
In Sect. 4, the theory of singular fibers of differentiable maps is explained.
Mathematically, a fiber is a map around a given pre-image and it contains the
information of nearby pre-images. This is why it is important for grasping the
topological transitions of pre-images, which is essential in visualization.
In Sect. 5, we explain the concept of Reeb space of a given multi-field. This is
the straightforward generalization of Reeb graph for a scalar field. We will see that
several structure theorems are already known in singularity theory. In fact, once
you have a classification of singular fibers, a structure theorem then follows. Some
topological transitions of Reeb spaces are also presented with the simplification of
Reeb spaces in mind.
In Sect. 6, we will give several open problems related to singularity theory
and visualization of singular fibers. We will also explain how the visualization
techniques can be useful in singularity theory itself. We will give several examples
of ongoing projects in this direction as well. We end this paper by summarizing
the impact of such singularity theoretical results and techniques on computational
topology and visualization.
Throughout this paper, all manifolds and maps between them are differentiable
of class C1 unless otherwise indicated. A manifold is closed if it is compact and
has no boundary. The symbol Dk denotes the unit disk in Rk .

2 Morse Functions

2.1 Functions on Manifolds Without Boundary

Let us first consider scalar functions on manifolds without boundary. Let N be a

closed manifold of dimension n, n  1, and consider a smooth scalar function
f W N ! R. For a point p, let dfp W Tp N ! R denote the differential of f at p, where
Tp N denotes the tangent space of N at p. This is a linear map defined as follows. For
a tangent vector v 2 Tp N, the value dfp .v/ is the derivative of f in the direction of v
at p. We say that p is a critical point of f if dfp is the zero map. This is equivalent to
the following: for local coordinates .x1 ; x2 ; : : : ; xn / of N around p, we have

@f @f @f
. p/ D . p/ D    D . p/ D 0:
@x1 @x2 @xn
Theory of Singular Fibers and Reeb Spaces for Visualization 5

For example, if p attains a local minimum or maximum of f , then it is a critical

point, since the partial derivatives of f at such a point necessarily vanish.
Definition 2.1 For a critical point p 2 N of f , let us take local coordinates
.x1 ; x2 ; : : : ; xn / around p. Then the n  n symmetric matrix
 
@2 f
Hf . p/ D . p/
@xi @xj 1i;jn

is called the Hessian of f at p. We say that the critical point p is non-degenerate if

det Hf .p/ ¤ 0. It is not difficult to see that this is independent of a choice of local
coordinates.
The following lemma is fundamental (for example, see [24, 25]).
Theorem 2.2 (Morse Lemma) If p 2 N is a non-degenerate critical point of f ,
then there exist local coordinates .x1 ; x2 ; : : : ; xn / of N around p such that f is locally
expressed as

f .x1 ; x2 ; : : : ; xn / D ˙x21 ˙ x22 ˙    ˙ x2n C c; (1)

where c D f .p/ is a constant.

In the above theorem, the number of negative signs appearing in (1) is called
the index of the critical point p. The Morse Lemma implies that the differential
topological behavior of f around a non-degenerate critical point is completely
determined by its index.
Definition 2.3 A smooth function f W N ! R is a Morse function if its critical
points are all non-degenerate, and their f -values are all distinct.
As a corollary to the Morse Lemma, we see that a non-degenerate critical point
is isolated in the set of all critical points. In particular, if N is closed, then a Morse
function has only finitely many critical points.
Theorem 2.4 Any smooth function f W N ! R can be approximated arbitrarily
well, including partial derivatives, by a Morse function.
Thus, in many situations, we may assume, at least theoretically, that a given
function is a Morse function. Even if it is not, we can approximate it by a Morse
function by perturbing it arbitrarily slightly. For a computational technique for
perturbation which is very useful in practical situations, called the simulation of
simplicity, the reader is referred to [10].
Definition 2.5 Let f W N ! R be a smooth function. For a real number r 2 R, we
say that it is a critical value of f if there exists a critical point p 2 N of f such that
r D f .p/; otherwise, a regular value.
6 O. Saeki

N R

Fig. 1 Example of level sets: one can observe a topological change of level sets as the value in R
passes through a critical value

By the implicit function theorem, we see easily that for a regular value r, the
pre-image f 1 .r/ is a smooth submanifold of dimension n  1 of N, as long as it
is non-empty (for example, see [26]). Based on this observation, we introduce the
following notion.
Definition 2.6 For a real number r 2 R, the set

f 1 .r/ D fp 2 N j f .p/ D rg

is called a level set of f .

An example of level sets is depicted in Fig. 1.
The following theorem implies that a topological transition of level sets never
occurs around a regular value.
Theorem 2.7 Let f W N ! R be a smooth function on a closed manifold N. Suppose
that the closed interval Œa; b  f .N/  R contains no critical value of f . Then, there
exists a diffeomorphism h W f 1 .Œa; b/ ! f 1 .a/  Œa; b such that h.x/ D .x; a/ for
all x 2 f 1 .a/, and that the following diagram is commutative:
h
f 1 .Œa; b/ ! f 1 .a/  Œa; b
f & .p2
Œa; b;

where p2 is the projection to the second factor.

Furthermore, the topological transitions of level sets of a Morse function can be
described by using the Morse Lemma. If p is a non-degenerate critical point of index
, then the transition of level sets is locally described around p by

x21  x22      x2 C x2C1 C x2C2 C    C x2n D "

Theory of Singular Fibers and Reeb Spaces for Visualization 7

Fig. 2 Example of local level set changes for dimension 3: the top half corresponds to the case of
a critical point of index 1 or 2, while the bottom half corresponds to the case of index 0 or 3

for " 2 R with j"j sufficiently small. The other parts which sit outside of a
neighborhood of p do not change topologically in a sense similar to that in
Theorem 2.7. Examples for the case n D 3 are depicted in Fig. 2.
Definition 2.8 For a real number r 2 R, we call the set

Nr D fp 2 N j f .p/  rg

a sub-level set of f .
Note that if r is a regular value, then the corresponding sub-level set is a smooth
manifold whose boundary is the level set.
Suppose that a Morse function f is given. Starting from a real number r0 strictly
less than the minimum of f , let us consider the topological transition of the sub-
level sets Nr . Then, according to Theorem 2.7, its topological transition occurs near
a real number r only if r is a critical value of f . Furthermore, if p is a critical point
with value r, then by using the Morse Lemma, we can show that NrC" , with " >
0 sufficiently small, is obtained by attaching a -handle to Nr" , where  is the
index of the critical point p. A -handle is an n-dimensional disk of the form D 
Dn attached to @Nr" along @D  Dn . In this way, we get a so-called handle
decomposition of the manifold N [24].
On the other hand, if we look at the transitions of the homotopy types of the
sub-level sets, then we get a decomposition of N as a CW complex [25].
For more details about handles, the reader is referred also to [12, Chap. 6]. An
application of handle decompositions for morphing 3D shapes has been explored in
[35].
Let us now define the Reeb graph of a Morse function.
Definition 2.9 Let f W N ! R be a Morse function on a closed manifold. Then,
each level set of f has finitely many connected components. Contracting each such
component to a point, we get a space Rf . More precisely, two points x; x0 2 N are
equivalent if they lie in the same component of a level set. This is an equivalence
relation, and the quotient space of N with respect to this equivalence relation is
8 O. Saeki

N R

qf f¯

Rf

Fig. 3 Reeb graph of the height function f on the torus: the original function is decomposed into
the composition of the quotient map qf and the function fN defined on the Reeb graph. The vertices
of Rf are the qf -images of the critical points of f

denoted by Rf , which is endowed with the quotient topology of N. Let qf W N ! Rf

denote the quotient map. By definition, we have a natural map fN W Rf ! R such that
f D fN ı qf . Such a decomposition of f is sometimes called a Stein factorization [20].
Please note that, by definition, the quotient space Rf is a topological space.
In fact, it is not difficult to show, with the help of Theorem 2.7, that Rf is a 1-
dimensional cell complex, or a graph: for each critical point p, its image qf .p/ is a
vertex of Rf . For this reason, the space Rf is very often called the Reeb graph [28].
An example of a Reeb graph is depicted in Fig. 3. We warn the reader that a vertex of
Rf may have degree two if the manifold is non-orientable or has dimension greater
than or equal to three.

2.2 Functions on Manifolds with Boundary

So far, we have considered Morse functions on manifolds without boundary.

However, in many practical situations, scalar functions are defined on a manifold
with non-empty boundary, such as a region in Rn with smooth boundary. In this
subsection, we review the theory of Morse functions on manifolds with boundary.
For details, the reader is referred to [14, Sect. 3] or [2].
Let N be a compact manifold with boundary and f W N ! R a smooth function.
There are two types of critical points. One is a usual critical point, i.e., a point p 2 N
Theory of Singular Fibers and Reeb Spaces for Visualization 9

such that the differential dfp W Tp N ! R vanishes. We call such a point p a (usual)
critical point of f . Note that such a point p may lie in the interior as well as the
boundary of N in general. The other is a critical point of the restricted function
f@ D f j@N W @N ! R. Such a point is called a boundary critical point of f . Note that
a critical point of the second type necessarily lies on the boundary @N. Note also
that a usual critical point on @N is a boundary critical point, while the converse is
not true in general.
The following lemma is well-known.
Theorem 2.10 (Morse Lemma along Boundary) Let f W N ! R be a smooth
function defined on a manifold with boundary. If p 2 @N is not a usual critical point
of f , but is a non-degenerate critical point of f@ , then there exist local coordinates
.x1 ; x2 ; : : : ; xn / of N around p such that
(1) fxn  0g corresponds to N, and fxn D 0g corresponds to @N,
(2) f is locally expressed as

f .x1 ; x2 ; : : : ; xn / D ˙x21 ˙ x22 ˙    ˙ x2n1 ˙ xn C c; (2)

where c D f .p/ is a constant.

Examples for the case n D 2 are depicted in Fig. 4.

Fig. 4 Boundary critical points of functions defined on surfaces with boundary: the top half
represents x21 C x2 , while the bottom half represents x21 C x2
10 O. Saeki

Definition 2.11 A smooth function f W N ! R defined on a manifold with

boundary is a Morse function if
(1) it does not have a usual critical point on the boundary,
(2) every critical point of f in Int N is non-degenerate,
(3) every critical point of f@ D f j@N is non-degenerate, and
(4) the critical values of f and f@ are all distinct.
It is easy to verify that the critical points and the boundary critical points of a
Morse function f are all isolated. As we are assuming that N is compact, f has only
finitely many critical and boundary critical points.
Then, the same approximation theorem as Theorem 2.4 holds also for functions
on compact manifolds with boundary.
A real number r is a critical value of f if there exists a critical point or a boundary
critical point p of f such that r D f .p/. Otherwise, it is called a regular value. Note
that if r is a regular value, then the level set f 1 .r/ is a smooth submanifold of N
of dimension n  1 with boundary [26]. In this case, we can also show that f 1 .r/
intersects @N transversely along the boundary and that @. f 1 .r// D f 1 .r/ \ @N.
Then, the same product theorem as Theorem 2.7 for functions on compact
manifolds with boundary also holds.
Such a theorem implies that a topological transition of level sets or sub-level
sets occurs only around critical values. Note that these values may be the critical
values of the function f@ D f j@N . Therefore, in practical applications, one needs to
look for boundary critical points, or sometimes one may need to distinguish usual
critical values from boundary critical values. This should be carefully treated, since
a topological transition merely implies that the relevant value is either a critical
value or a boundary critical value, and in some cases, a boundary critical value may
have no importance.
Remark 2.12 As in the case where N has no boundary, if we pass through a usual
critical value of a Morse function, then the topology of the sub-level set necessarily
changes. On the other hand, if we pass through the value of a boundary critical point,
then the topology of the sub-level set changes if and only if the gradient vector of f
at the boundary critical point points “inward” [14]. See Fig. 5.
With the help of the product theorem (cf. Theorem 2.7), we can show that the
space Rf of a Morse function f defined on a compact manifold with boundary is
again a 1-dimensional cell complex, or a graph, which is called the Reeb graph of
f . The vertices are the qf -images of critical points and boundary critical points. The
structure of such Reeb graphs for scalar functions defined on compact surfaces with
boundary is studied in [5, 33].
Theory of Singular Fibers and Reeb Spaces for Visualization 11

Fig. 5 Topological transition R

of sub-level sets may not N
occur even if we pass through
a boundary critical value. In
inward
this example, f 1 ..1; a/
is diffeomorphic to
f 1 ..1; b/, while
c
f 1 ..1; b/ is not
diffeomorphic to f
f 1 ..1; c/
b

outward a

2.3 Deformations of Morse Functions

The following deformations of Morse functions are well known: birth-death of a

pair of (usual) critical points, and birth-death of a pair of boundary critical points.
We also have a birth-death of a usual critical point near the boundary.
The first one refers to a 1-parameter family ft W N ! R, t 2 I, of smooth
functions, where I D ."; "/ and " > 0 is very small, with the following
properties:
1. ft is a Morse function for t ¤ 0,
2. there exists a coordinate neighborhood U in N such that ft does not depend on t
on a neighborhood of N n U,
3. on a smaller open set V with V  U, ft is given by

ft .x1 ; x2 ; : : : ; xn / D x31 ˙ tx1 ˙ x22 ˙    ˙ x2n

with respect to some local coordinates .x1 ; x2 ; : : : ; xn /.

Mathematically, this can be regarded as a path in the space of functions C1 .N; R/
which crosses a “codimension 1 non-Morse stratum” transversely at one point. Note
that this transition creates a pair of critical points of adjacent indices, or eliminates
such a pair.
A birth-death of a pair of boundary critical points is described in a similar
fashion. This is locally described by

ft .x1 ; x2 ; : : : ; xn / D x31 ˙ tx1 ˙ x22 ˙    ˙ x2n1 ˙ xn ;

where fxn  0g corresponds to N and fxn D 0g corresponds to @N.

12 O. Saeki

Fig. 6 Birth-death of a usual critical point near the boundary: in the middle figures, the encircled
dots are usual critical points and are, at the same time, boundary critical points. The two functions
on the left have only a boundary critical point, while the two on the right have both a boundary
critical point and a usual critical point in the interior

A birth-death of a usual critical point near the boundary is locally described by

ft .x1 ; x2 ; : : : ; xn / D ˙x21 ˙ x22 ˙    ˙ x2n1 C txn ˙ x2n :

For n D 2, this deformation is locally depicted in Fig. 6.

We have other types of generic transitions: crossings of critical values. These
deformations do not create nor eliminate critical points, but they interchange the
values of two (usual or boundary) critical points.
In the course of the above deformations, a topological transition of Reeb graphs
may occur as follows if the manifold has no boundary (see also [7]).
Theorem 2.13 If a topological transition of the Reeb graphs for a generic defor-
mation of Morse functions on a closed manifold of dimension n  2 occurs, then it
is one of the transitions locally described in Fig. 7 (or their upside down versions).
Note that in Fig. 7, (1) and (2) correspond to birth-death of a pair of critical
points, where in (1), one of the critical points is a local minimum or a local
maximum. The other three correspond to crossings of critical values. Note also that
the indices of the relevant critical points have certain restrictions. For example, for
(1) and (2), their indices are adjacent, while for (4), they must be 1 and n  1.
The reader should be careful, since not all transitions are realizable. For example,
the transition (2) from the right to left is always possible if n  3. More precisely,
given a Morse function whose Reeb graph has a subgraph as in the right hand side of
(2), then one can construct a generic 1-parameter deformation of the given function
Theory of Singular Fibers and Reeb Spaces for Visualization 13

(1) (2)

(3) (4)

(5)
Fig. 7 Possible transitions of Reeb graphs for generic 1-parameter deformations of Morse
functions on closed manifolds near a given parameter: these are local descriptions, and the part
lying outside of these graphs does not change during the deformation

to another Morse function whose Reeb graph is locally of the form as in the left hand
side of (2). However, for the resulting graph, the transition (4) from the right to left
cannot be applied. This is because after the birth of a pair of critical points, they
are so involved with each other that their values cannot be interchanged to make a
crossing of critical values.
We can also prove that the transition of Fig. 7 (1) is always possible. More
precisely, if the Reeb graph of a Morse function contains one of the two graphs
in the figure as a subgraph, then we can deform the given Morse function by passing
through a birth-death exactly once so that the resulting Morse function has the Reeb
graph obtained from the original one by replacing the subgraph with the other graph
in the figure. This gives a theoretical justification for simplification of a Reeb graph
for visualization purposes that uses the topological transition described in Fig. 7 (1).
The above theorem can be proved by using a result on local structures of Reeb
spaces of generic maps into the plane [19]. (For the definition of a Reeb space, refer
to Sect. 5.1.)
14 O. Saeki

3 Stable Maps

3.1 Notion of Stable Maps

Let N be a smooth manifold and f W N ! Rm a multi-field: in other words, we have

a set of m scalar functions fi W N ! R, i D 1; 2; : : : ; m, such that f D .f1 ; f2 ; : : : ; fm /.
In this section, we survey the singularity theory which studies such a set of m smooth
functions at the same time, and not individually.
For a straightforward generalization of the theory of Morse functions to the
case of smooth maps into Rm , we need a theorem similar to the Morse Lemma.
However, in singularity theory of differentiable maps, it is known to be very difficult
in general. Therefore, we adopt the following definition.
Definition 3.1 Denote by C1 .N; Rm / the set of C1 maps N ! Rm equipped with
the Whitney C1 topology (for details, see [13]). A smooth map f W N ! Rm is
called a C1 stable map, or a stable map for short, if there exists a neighborhood
U.f /  C1 .N; Rm / of f such that every map g 2 U.f / is C1 equivalent to f
[13], where two maps f and g 2 C1 .N; Rm / are C1 equivalent if there exist
diffeomorphisms  W N ! N and W Rm ! Rm such that f ı  D ı g.
This means that even if one perturbs a stable map slightly, we end up with a map
which behaves exactly the same as the original map up to diffeomorphisms of the
domain and the range. This is the origin of the terminology “stable”.
We can also define the notion of a C0 stable map by replacing diffeomorphisms
by homeomorphisms in the above definition.
Let S1 .N; Rm / (or S0 .N; Rm /) be the subspace of C1 .N; Rm / that consists of
all C1 (resp. C0 ) stable maps. By definition, both of them form open subsets of
C1 .N; Rm /. Mather [22] showed that if N is compact, then S1 .N; Rm / is dense in
C1 .N; Rm / if and only if the dimension pair .n; m/ lies in the so-called nice range.
In other words, if .n; m/ is in the nice range, then every smooth map N ! Rm can
be approximated arbitrarily well by a C1 stable map. On the other hand, Mather
[23] showed that if N is compact, S0 .N; Rm / is always dense in C1 .N; Rm /. Hence,
every map can always be approximated by a C0 stable map.
For example, for .n; m/ D .8; 6/, S1 .N; Rm / is never dense in C1 .N; Rm /.
Remarkably, for the 4-dimensional complex projective space CP4 viewed as a real
8-dimensional manifold, there exists no C1 stable map CP4 ! R6 [1]. In fact,
there are uncountably many equivalence classes of “generic” singularities for these
dimensions, and a theorem like the Morse Lemma cannot be expected.
On the other hand, it is known that every dimension pair .n; m/ with m  5 or
m  2n  1 is in the nice range (see [13, 22]).
Theory of Singular Fibers and Reeb Spaces for Visualization 15

In the following, for a smooth map f W N ! Rm , we denote by S.f / the set of

points p 2 N such that the differential dfp W Tp N ! Tf .p/ Rm has rank strictly less
than minfn; mg, where the differential is the linear map associated with the m  n
Jacobian matrix of f at p with respect to some local coordinates around p and f .p/.
The set S.f / is called the singular point set or the Jacobi set of f , and a point in
S.f / is called a singular point of f . The singular point set S.f / is often denoted by
J.f / in the visualization community (see [6]). Note that when n  m, the notation
J.f / encodes the behavior of multiple Morse functions in the sense that it collects
the points where the gradient of the m Morse functions are linearly dependent.

3.2 Characterization of Stable Maps for Specific Cases

Although theorems like the Morse Lemma do not exist in general for multi-
fields, for some specific dimension pairs .n; m/, we do have such theorems. In the
following, if we say that a map is stable, then it means that it is C1 stable.
In the function case, the following is known.
Theorem 3.2 Let N be a closed n-dimensional manifold, n  1. Then a smooth
function f W N ! R is stable if and only if it is a Morse function. In particular, the
dimension pair .n; 1/ is always in the nice range.
The above theorem means that the notion of a stable map generalizes the notion
of a Morse function in a reasonable sense.
Let us introduce the following notion.
Definition 3.3 Let fi W Ni ! Rm , i D 0; 1, be smooth maps with dim N0 D
dim N1 D n. For singular points pi 2 Ni of fi , i D 0; 1, we define that they have
the same singularity type if for some open neighborhoods Ui of pi and Vi of fi .pi /
and diffeomorphisms  W U0 ! U1 and W V0 ! V1 with  .p0 / D p1 and
.f0 .p0 // D f1 .p1 / such that the following diagram is commutative:

Note that the Morse Lemma claims that a non-degenerate critical point of a
function has the same singularity type as the critical point of a quadratic function
˙x21 ˙ x22 ˙    ˙ x2n .
Let us now consider the case m D 2. Let f W N ! R2 be a smooth map of a
closed n-dimensional manifold, n  2.
16 O. Saeki

Definition 3.4 A point p 2 S.f / is a fold point if f can be expressed by

f .x1 ; x2 ; : : : ; xn / D .x1 ; ˙x22 ˙ x23 ˙    ˙ x2n /

with respect to appropriate local coordinates around p and f .p/. In other words, p has
the same singularity type as the above polynomial map. Similarly, a point p 2 S.f /
is a cusp point if it has the same singularity type as the map

.x1 ; x2 ; : : : ; xn / 7! .x1 ; ˙x32 C x1 x2 ˙ x23 ˙    ˙ x2n /:

We denote by F.f / the set of fold points of f , and by C.f / the set of cusp points. It
is easy to verify that F.f / is a smooth 1-dimensional submanifold of N, while C.f /
is a discrete set of points.
For the case of n D 2, see Fig. 8. See also [9].
Then the following characterization of stable maps is known.
Theorem 3.5 (Whitney [38]) A smooth map f W N ! R2 is stable if and only if
the following conditions are satisfied.
(1) Every singular point is either a fold point or a cusp point.
(2) The restriction f jF.f / W F.f / ! R2 is an immersion (i.e. a non-singular curve)
with normal crossings: i.e. for every point q 2 R2 , the pre-image .f jF.f / /1 .q/
consists of at most two points, and if it consists of two points, then the images
of the differentials at the two points are linearly independent in Tq R2 .
(3) f .F.f // \ f .C.f // D ;.
(4) The restriction f jC.f / is injective.

S( f )

fold cusp
Fig. 8 Fold and cusp points for the case n D 2: these are the singularities that can appear for
stable maps of surfaces into R2
Theory of Singular Fibers and Reeb Spaces for Visualization 17

Let us now consider the case m D 3. Let f W N ! R3 be a smooth map of a

closed n-dimensional manifold, n  3.
Definition 3.6 A point p 2 S.f / is a fold point if it has the same singularity type as
the map

.x1 ; x2 ; : : : ; xn / 7! .x1 ; x2 ; ˙x23 ˙ x24 ˙    ˙ x2n /:

A point p 2 S.f / is a cusp point if it has the same singularity type as

.x1 ; x2 ; : : : ; xn / 7! .x1 ; x2 ; ˙x33 C x2 x3 ˙ x24 ˙    ˙ x2n /:

A point p 2 S.f / is a swallowtail point if it has the same singularity type as

.x1 ; x2 ; : : : ; xn / 7! .x1 ; x2 ; ˙x43 C x1 x23 C x2 x3 ˙ x24 ˙    ˙ x2n /:

We denote by F.f / the set of fold points of f , by C.f / the set of cusp points, and by
ST.f / the set of swallowtail points. It is easy to verify that F.f / and C.f / are smooth
2- and 1-dimensional submanifolds of N, respectively, while ST.f / is a discrete set
of points.
Theorem 3.7 A smooth map f W N ! R3 of a closed n-dimensional manifold N,
n  3, is stable if and only if the following conditions are satisfied.
(i) Every singular point is either a fold point, a cusp point, or a swallowtail point.
(ii) The singular point set S.f / is a smooth 2-dimensional submanifold of N under
the above condition. Then, for every r 2 f .S.f //, f 1 .r/ \ S.f / consists of
at most three points and the map f jS.f / around f 1 .r/ \ S.f / is equivalent to
one of the six maps whose images are as described in Fig. 9: .1/, .2/ and .4/
correspond to 1, 2 or 3 fold sheets, respectively, .3/ corresponds to a cusp
point, .5/ represents a transverse crossing of a cuspidal edge as in .3/ and a
fold sheet, and .6/ corresponds to a swallowtail point.

4 Singular Fibers

4.1 Concept

Let f W N ! Rm be a smooth map of a closed n-dimensional manifold, n  m  1.

In this section, we mainly consider the case with m  2, i.e. the case of a multi-field.
Definition 4.1 For a point r 2 Rm , the set f 1 .r/ D fp 2 N j f .p/ D rg is called
the fiber of f over r. In particular, when m D 1, this notion coincides with that of a
level set.
18 O. Saeki

(1) (2) (3)

(4) (5) (6)

Fig. 9 Possible local configurations of the image of f jS.f / in R3 for a stable map f W N ! R3 of a
closed n-dimensional manifold N, n  3

In fact, in singularity theory, we use the terminology “fiber” in such a way that it
contains more information than just the pre-image as follows [29].
Definition 4.2 Let fi W Ni ! Rm be smooth maps of n-dimensional manifolds,
i D 0; 1. For ri 2 Rm , we say that the fibers over r0 and r1 of f0 and f1 ,
respectively, are equivalent if for some open neighborhoods Ui of ri in Rm , there
exist diffeomorphisms ˚ W .f0 /1 .U0 / ! .f1 /1 .U1 / and ' W U0 ! U1 with
'.r0 / D r1 which make the following diagram commutative:

When r 2 Rm is a regular value of f , we call f 1 .r/ a regular fiber; otherwise, a

singular fiber.
For example, the following is well known [29].
Theorem 4.3 Let f W N ! R be a Morse function on a closed surface N. Then the
fiber over each critical value in R is equivalent to one of the three types of fibers as
depicted in Fig. 10.
Theory of Singular Fibers and Reeb Spaces for Visualization 19

(1)

(2)

(3)

Fig. 10 List of equivalence classes of singular fibers for Morse functions on closed surfaces. For
each horizontal arrow, the left hand side depicts the neighborhood of the pre-image of a critical
value, and the arrow represents the map as a height function. Thus, for example, the function
in (1) has exactly one local extremal point as a critical point, but the corresponding pre-image
may not be connected and may have several circle components consisting of regular points whose
neighborhoods are diffeomorphic to a cylinder. The component of the neighborhood containing a
critical point is diffeomorphic to a disk for (1), a 2-sphere with three disks removed for (2), and a
Möbius band with a disk removed for (3). In particular, singular fibers of type (3) never occur if
the domain surface is orientable

4.2 Ehresmann Fibration Theorem

In the following, a map is proper if the pre-image of a compact set is always

compact.
Theorem 4.4 (Ehresmann Fibration Theorem [11]) Let f W N ! Int Dm be a
proper submersion of an n-dimensional manifold N (possibly with boundary) into
the interior of the m-dimensional disk with n  m such that f j@N W @N ! Int Dm is
also a submersion if @N ¤ ;. Then for the center 0 of Int Dm , the pre-image f 1 .0/
is a compact .n  m/-dimensional manifold with boundary, and for an arbitrary
diffeomorphism h W f 1 .0/ ! F onto a manifold F, there exists a diffeomorphism
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clever; the Gordian knot of every question might easily be solved in
this way.
Bearing in mind that the question we are now trying to solve is
this, “What is the evidence afforded by Geology, as to the history of
creation, and in what way does the geological age of the world affect
the supposed statement of Scripture, that the world is only 6,000
years old?” I reply thus, and I prefer to use the words of others rather
than my own, lest it should be supposed that I am introducing mere
novelties of opinion on this subject:—“That the first sentence in
Genesis is a simple, independent, all-comprehending axiom to this
effect; that matter, elementary or combined, aggregated only or
organized, and dependent, sentient and intellectual beings have not
existed from eternity, either in self-continuity or in succession: but
had a beginning; that their beginning took place by the all-powerful
will of One Being, the self-existent, independent and infinite in all
perfection, and that the date of that beginning is not made known.”
These are the words of Dr. Pye Smith,[123] of whose name as an
authority, both in matters of science and philology, no one need be
ashamed.
Dr. Redford says, “We ought to understand Moses as saying,
indefinitely, far back, and concealed from us in the mystery of eternal
ages, prior to the first moment of mundane time, ‘God created the
heavens and the earth.’”
“My firm persuasion is,” says Dr. Harris, “that the first verse of
Genesis was designed by the Divine Spirit to announce the absolute
origination of the material universe by the Almighty Creator, and
that it is so understood in the other parts of Holy Writ; that, passing
by an indefinite interval, the second verse describes the state of our
planet immediately prior to the Adamic creation; and that the third
verse begins the account of the six days’ work.”
Dr. Davidson, in his “Sacred Hermeneutics,” says,—“If I am
reminded, in a tone of animadversion, that I am making science, in
this instance, the interpreter of Scripture, my reply is, that I am
simply making the works of God illustrate His word in a department
in which they speak with a distinct and authoritative voice; that it is
all the same whether our geological or theological investigations have
been prior, if we have not forced the one into accordance with the
other. And it may be deserving consideration whether or not the
conduct of those is not open to just animadversion who first
undertake to pronounce on the meaning of a passage of Scripture,
irrespective of all appropriate evidence, and who then, when that
evidence is explored and produced, insist on their à priori
interpretation as the only true one.”
But I quote no more: such are some of the eminent theological
contributions to this department of science:—satisfactory in this
respect, that a fair interpretation of Scripture does not require us to
fix any precise date, much less the inconsiderable one of six
thousand years, as the period of the earth’s formation.
Geology teaches the same thing.—Of the various formations that
compose the earth’s trust, to the ascertained extent of ten miles,
suppose we select two,—the Old Red Sandstone and the Chalk
formations. Laborious and scientific men have been at the pains to
calculate the gradual increase of some of these now proceeding
deposits,—such as the Deltas, in course of formation at the mouth of
the Nile, and at the gorges of the Ganges; and they find that the
progress of the depth of increase is exceedingly small,—probably not
more than a foot in many years. Mr. Maculloch, a name standing
very high for accurate investigation, states, from his own
observation, that a particular Scottish lake does not form its deposit
at the bottom, and hence raise its level, at the rate of more than half-
a-foot in a century; and he observes, that the country surrounding
that lake presents a vertical depth of far more than 3,000 feet, in the
single series of the Old Red Sandstone formation; and no sound
geologist, he hence concludes, will, therefore, accuse the computer of
exceeding, if, upon the same ratio as the contiguous lake, he allows
600,000 years for the production of this series of rock alone.
A last instance which may here be adduced, of the apparent length
of time required for the construction of a particular rock, offers itself
in the Chalk formation. The enormous masses of this rock,
presenting their tall white precipices in such simple grandeur to our
view, might well excite our astonishment at the periods which would
seem needful for their collection and deposition, even if they were
mere inorganic concretions of calcareous matter. But what shall we
say when the investigations of the microscope have lately revealed to
us that these mountains of chalk, instead of being formed of mere
inert matter, are, on the contrary, mighty congeries of decayed
animal life,—the white apparent particles, of which the chalk masses
are composed, being each grain a well-defined organized being, in
form still so perfect, their shells so entire, and all their characteristics
so discoverable, as to cause no doubt to naturalists as to the species
in the animal economy to which they belonged. How justly does Sir
Charles Lyell, who in his “Elements” records at length this surprising
discovery, exclaim,—
“The dust we tread upon was once alive!”

“Look at the lofty precipices which lay naked a slight section of the
Chalk at the Culvers, or the Needles in the Isle of Wight, or the still
loftier Shakspeare Cliff at Dover, and let the mind form a conception,
if it can, of the countless generations of these minutest of living
creatures it must have required to build up, from their decayed
bodies and their shelly exuviæ, layer on layer, those towering masses
thus brought to our view. Who shall dare to compute the time for this
entire elaboration? The contemplation almost advances us a step
towards forming a conception of infinitude.”[124]
I need not dwell longer on the antiquity of the globe:—Geology and
Scripture present no conflicting testimonies on this subject. Our
interpretation of Scripture has, undoubtedly, been modified; but the
living Word itself abideth, in all its grandeur and purity, for ever.
And “the time is not far distant when the high antiquity of the globe
will be regarded as no more opposed to the Bible than the earth’s
revolution round the sun and on its axis. Soon shall the horizon,
where geology and revelation meet, be cleared of every cloud, and
present only an unbroken and magnificent circle of truth.”[125]
The reader shall not be detained so long on the second point of
inquiry, which is
II. “Was death introduced into the world before the fall of man?
and if it was, how are the statements of Scripture, on this question, to
be explained?” To this I have replied by anticipation, that, in my
opinion, death, upon a most extensive scale, prevailed upon the
earth, and in the waters that are under the earth, countless ages
before the creation of man. Into the proof of this position allow me to
go very briefly, although I am well aware that I run the risk of
incurring the charge of heterodoxy, when I state my full conviction,
that death, as well as the world, was pre-Adamite. The general
impression is the contrary; but general impressions are not always
right:—“general impression” is a very unsubstantial ghost to deal
with, very like that cant phrase we spoke of at the beginning of this
lecture,—“the intelligence of the age.” “General impression” has it,
that death was not pre-Adamite; that there was no death before the
fall; and that, to say the contrary, is, at least, to tread on very
dangerous ground. In vain does Geology—“now happily a true
science, founded on facts, and reduced to the dominion of definite
laws”—lay bare the Silurian rocks, and discover even there extinct
forms of life in exquisitely beautiful preservation. In vain does
Geology, after showing us the fossil trilobite and coral, unfold the
volume of the Old Red Sandstone, and show us there the fossil
remains of fish—so perfect that we might imagine them casts rather
than fossils. In vain does Geology open its vast Oolitic system, and
show us there other forms of extinct life in fossil insects, tortoises,
mighty saurians, and huge iguanodons. In vain does Geology lay bare
the Chalk, with its marine deposits; and the Tertiary formation, with
its enormous theroid mammalia, far surpassing in size the largest
animals we are acquainted with. In vain are all these fossil remains
exhibited imbedded in the earth; and in vain do we search, amidst all
these, for one fossil remain of man, or one fossil vestige of man’s
works. The easy, the cheap, the unreflective answer is, “Oh! these
things were created there, or else Noah’s flood left them there.”
Of course, we can fall back upon a miracle as having done all this;
but to have recourse to miracles when no miracle is recorded, is just
to shake our faith in that all-inspired testimony, that supernatural
Book, the existence of which is the great miracle of time. But there
are the fossils! How did they come there if the forms of animal life,
once inhabiting those remains, had not previously lived and died?
Created! What? Created fossils? Then why not, when the Almighty
created man, did he not create, at the same time, some skeletons of
man, and place them in the earth, as he put skeletons of trilobites,
fishes, reptiles, and mammals there? Our common sense and
reverence both reject the idea. As to the puerile notion that Noah’s
flood put them there, did not Noah’s flood overwhelm man as well as
animals? and as the bones of man are as durable as the bones of
animals, how is it that we never meet with a fossil human skull or
thigh bone, or house?
 We believe that death was a part of the divine plan of God’s
creation; that death is a law of all organic life—a necessary law and a
most benevolent provision; that the living structure of all animals
derives its substance from dead organic matter. We believe that,
altogether apart from human sin, preceding and successive
generations must be the order of being; for if there were no death,
animals would soon pass beyond the limit of provision sufficient for
nutritive support, or of localities for suitable habitations. We believe
that if there had been no death prior to man’s sin, it would involve
the supposition that all animals were herbivorous; whereas, even the
little ladybird cannot live without its meal of aphides; and, so
believing, we find our faith in Scripture deepened when, seeing on
every hand the extensive proofs of death, we find man, the moment
he lost his lordship and proud eminence, and reduced himself
voluntarily to the condition of animalism, immediately brought
penally within the influence of that law of death, whose existence he
must have recognised in the death of animals from the first day of his
creation.
Does any one reply, “This is contrary to Scripture?” I ask them
what Scripture teaches that the death of animals is the result of
man’s sin?—rather would not Scripture sanction the thought that
death was a part of the divine plan of God’s creation, and that the
certainty of man’s transgression was the reason for giving this
constitution to nature? True, Milton sings, in his noble poem, that
will live as long as the English language lives—
“Of man’s first disobedience, and the fruit
Of that forbidden tree, whose mortal taste
Brought death into the world, and all our woe:”

but we are not obliged to call the Paradise Lost our Bible; or to quote
Milton as a physiological authority, although the prevalence of the
opinion that death was not pre-Adamite, and a good deal of theology
besides, is more of Miltonic than of Scripture teaching.
I leave this branch of my subject far before it is exhausted: so far
from that, each of the three points enumerated might easily be
expanded into a lecture; and I can only hope that my brevity in
treating these topics will not be misconstrued into a desire to shirk
any of the difficulties with which their investigation is surrounded.
 III. I come, lastly, to the question of the Noachian Deluge, and
shall again repeat my own words: “What was the character of the
Noachian Deluge?—was it partial or universal? and what are the
apparent discrepancies, in this case, between science and the Bible?”
And I have added to this my belief that the Noachian Deluge was
quite partial in its character, and very temporary in its duration: that
it destroyed only those animals that were found in those parts of the
earth habitable by man, and that it has not left a single shell or fossil,
or any drift boulders or pebbles, or any other remains that may be
traced to its action.
Very briefly we shall try and prove this; and perhaps the most
popular way will be the best remembered,—only that the reader will
bear in mind that this little book does not pretend to exhaust the
subject, but only to realize the idea expressed at the beginning of this
chapter. Presuming, that all have in their recollection the Scriptural
account of the Noachian Deluge, instead of quoting words with
which all are familiar, I will only remark, as the basis of my
illustrations, that rain descended, and probably the ocean
overflowed, for forty days; that the waters lay upon the land, and
covered them one hundred and fifty days; that at the end of that time
they began to subside, and that in twelve months and twenty-seven
days they were gone from the face of the earth, and the Noachian
family liberated from the ark.
The question is, was this flood universal, and were all kinds of
animals preserved in the ark? To which my answer, as involving my
belief, is this, that the flood was local, and that only the animals
peculiar to Armenia were provided for in Noah’s ark.
“Oh! but the Bible says it was universal,” says everybody. Yes; but
that, you know, is just the question between us. The terms “all the
earth” seem to imply universality, but they do not necessarily involve
this. “All countries came to Egypt to buy corn;” certainly not all the
world literally, but all the surrounding countries. So there were once
dwelling at Jerusalem devout Jews “from out of every nation under
heaven;” but not literally out of every nation, for the names of the
nations are immediately given, and we find the nations to have been
a few between Egypt and the Black Sea, and between Italy and
Palestine. There are many other illustrations of a similar character:
these will suffice: I only adduce these to show that at the beginning
Scripture does not oblige us to consider “all” as meaning “every one;”
or to understand literally “all the inhabitants of the earth” as
meaning every creature.
Now, looking at the structure and composition of the earth’s crust,
especially its fossiliferous rocks, I am driven to one of three
conclusions, each of them involving difficulty, I acknowledge, but the
one that involves the least is, of course, the most preferable. Either I
must admit—
1. That the fossils in these rocks were all deposited in order and in
succession, without injury, through a crust of rocks ten miles in
thickness, during twelve months’ violent diluvial action:
2. Or that they were all deposited there during the 15,000 or
16,000 years that had elapsed since the creation of man prior to the
Deluge; that is, supposing the creation of man and the creation of the
earth to have been synchronous. Or, lastly, which theory I accept—
3. That the date of the earth’s physical being is unknown to us, and
that the fossiliferous rocks were deposited in decades of ages before
the creation of man.
For, on the other hand, let us suppose the flood to have been
universal, in the strict and literal sense of the term; then let me
suggest some of the consequences and difficulties of such a theory.
1. One consequence would be that some remains of man or of his
works would have been found; but nothing of this kind has occurred.
Even Armenia has been geologically examined, and no human
remains have been found; and surely man’s bones would last as long
as the shells of a trilobite or terebratula?
2. And, secondly, the organic remains, the fossils themselves,
would have been found confusedly heaped together; whereas, the
remains in the crust of the earth are as carefully arranged as the
contents of a well-ordered cabinet. We know always to a certainty
what fossils will be found in any rock before we examine that rock.
3. Besides which, some, at least, of the organic remains found
ought to correspond with existing beings and species: yet the
contrary is the case, except only a few fossils found near the surface
of the earth, in that portion of the earth’s crust occupied by the
tertiary system.
 Nor is this all. Consider the vast difficulties the universal flood
theory has to contend with, all of which are removed by the theory
we have adopted.
1. There is the quantity of water required. If all over the earth the
water rose twenty-two feet six inches above the tops of the highest
mountains, the quantity of water required would be eight times the
whole quantity of water now existing. Where all this could have come
from first and gone to afterwards, are prodigious stumbling-blocks.
Of course we can resort to miracle; but this is not the way to get rid
of difficulty in a manly and honest spirit.
2. Then consider the number of animals the ark must have
contained. There are 1,000 species of mammalia, 5,000 species of
birds, 2,000 species of reptiles, and 120,000 well-ascertained and
distinct species of insects. Do we pretend that all these were housed
and fed for nearly thirteen months in a vessel that was only 450 feet
long, 75 feet broad, and 45 feet high; and that such a vessel contained
room for them, and their food, besides that of man, for such a long
period. The little toys of Noah’s ark are certainly pretty, but very
mischievous, and most of the popular notions of the flood have
grown up from our nurseries as much from the use of this toy in this
case, as from the reading of Paradise Lost in the other: and the result
is, the Bible is made responsible for it all.
3. Then consider the subsequent distribution of animals: the polar
bear and the tropical elephant, the ferocious tiger and a young fawn,
going out together in order, and without violence: of course we can
suppose another miracle to repress passions and violence. Besides
which, in addition to the fauna, the animal kingdom, we must ask
what became of the flora or vegetable kingdom during this period, if
the flood were universal? We have at least twenty-five botanical
provinces, with their peculiar and numberless farms of vegetable life;
what became of them? Were they preserved in the ark, or under the
water?—for such questions must be answered by those who charge us
with inconsistency in attempting to reconcile the facts of science with
the words of Scripture. And as a last difficulty, (suggested first, I
believe, by Dr. Pye Smith, and which I shall therefore state in his
words, lest it should seem that I use “plainness of speech,”) let us
look at the descent from Ararat out of the ark, into Armenia, with all
these animals, birds, insects, plants and trees. “That mountain is
17,000 feet high, and perpetual snow covers about 5,000 feet from
its summit. If the water rose, at its liquid temperature, so as to
overflow that summit, the snows and icy masses would be melted;
and on the retiring of the flood, the exposed mountain would present
its pinnacles and ridges, dreadful precipices of naked rock, adown
which the four men and the four women, and with hardly any
exception the quadrupeds, would have found it utterly impossible to
descend. To provide against this difficulty, to prevent them from
being dashed to pieces, must we again suppose a miracle? Must we
conceive of the human beings and the animals as transported
through the air to the more level regions below; or that, by a miracle
equally grand, they were enabled to glide unhurt adown the wet and
slippery faces of the rock?”
Such are some of the difficulties and some of the consequences
that must flow from an acceptance of any other theory than the one I
have proposed: that the flood was partial in its character, extending
only over the habitable parts of the earth; and that it was so
temporary in its character as not to have left a single trace of its
influence visible on rock or fossil.
I have thus endeavoured to suggest points of reconciliation
between the accepted facts of Geology and the recorded statements
of Scripture; and if this slight contribution be accepted as an aid to
faith, and a proof of candour on my part to meet those who linger on
the border land of doubt, my purpose will be fully answered.
Let me add, in the words of Chenevix Trench—words uttered in the
University of Cambridge not long since: “May we in a troubled time
be helped to feel something of the grandeur of the Scriptures, and so
of the manifold wisdom of that Eternal Spirit by whom it came; and
then petty objections and isolated difficulties, though they were
multiplied as the sands of the sea, will not harass us. For what are
they all to the fact, that for more than 1,000 years the Bible
collectively taken, has gone hand in hand with civilization, science,
law—in short, with the moral and intellectual cultivation of the
species, always supporting and often leading the way? Its very
presence as a believed book, has rendered the nations emphatically a
chosen race; and this, too, in exact proportion as it is more or less
generally studied. Of those nations which in the highest degree enjoy
its influences, it is not too much to affirm that the differences, public
and private, physical, moral, and intellectual, are only less than what
might be expected from a diversity in species. Good and holy men,
and the best and wisest of mankind, the kingly spirits of history
enthroned in the hearts of mighty nations, have borne witness to its
influence, and have declared it to be beyond compare the most
perfect instrument and the only adequate organ of humanity: the
organ and instrument of all the gifts, powers, and tendencies, by
which the individual is privileged to rise beyond himself, to leave
behind and lose his dividual phantom self, in order to find his true
self in that distinctness where no division can be,—in the Eternal I
am, the ever-living Word, of whom all the elect, from the archangel
before the throne to the poor wrestler with the Spirit until the
breaking of day, are but the fainter and still fainter echoes.”

M. CLAY, PRINTER HEAD STREET HILL.

 1. Whewell’s Astronomy and Physics, p. 48.
2. From παλαιός, ancient, and ζωόν, life; ancient-life period.
3. Hughes, Physical Geography. 3d ed. p. 21.
4. Hughes, Physical Geog. p. 22.
5. Dr. Pye Smith.
6. As Chimborazo in South America, 21,414; Ararat, 16,000; Dhawalagiri, in
the Himalayas, 28,000 feet above the level of the sea; compared with which what a
mole-hill is Vesuvius, only 8,947 feet; or Blue Mountain Peak, 8,600, or even Mont
Blanc, that monarch of mountains, which is 15,816 feet above the sea!
7. Hughes, p. 16.
8. Chambers’ Rudiments of Geology, p. 71.
9. These wells are so frequently spoken of as to need no explanation, further
than to remind the reader that they are so called from having been first introduced
in the province of Artois, the ancient Artesium in France.
10. The deepest Artesian well is the famous one in the Plaine de Grenelle,
Paris. This well yields 516 gallons a minute; its temperature is 81° Fahr.; and its
depth is nearly 1,800 feet.
11. How truly hieroglyphics—sacred carvings; (ieros, sacred, glupho, I carve;)
and in this sense there is a holier meaning than Shakspeare could have dreamt of
in his well-known lines, when applied by the geologist to his researches:—

“And this our life, exempt from public haunt,

Finds tongues in trees, books in the running brooks,
Sermons in stones, and good in everything.”

12. And I may say, my friend also, to whom, during my residence in Jamaica, I
was frequently indebted for contributions on natural history to the Jamaica
Friendly Instructor, of which I was Editor.
13. A Naturalist’s Sojourn in Jamaica, by P. H. Gosse, Esq. pp. 496–7.
14. So called because of its grained or granular appearance.
15. First brought from Syene, in Egypt.
16. Feld-spar, written also felspar, a compound of feld, field, and spar.
17. See Ansted’s Ancient World, p. 21.
18. Memnon, or Ramesis. This famous head is in the British Museum; the
body is of greenstone, the head of syenite, and the bust one continuous mass.
19. From dis and integer. The separation of the whole parts of a rock, without
chemical action, by means of the light, the air, or the rain, is called disintegration.
 20. Lieut. Portlock on Geology, p. 93.
21. Ansted’s Geology, Descriptive and Practical, vol. ii. pp. 290, 291.
22. Ansted’s Geology, p. 291.
23. As the ancients did not know or use the compound metal brass, though
bronze was common amongst them, we must in this verse, and all others in which
the word “brass” is used, understand it to mean copper.—Hughes’ Scripture
Geography, Art. Geology of Palestine, p. 133.
24. Murray’s Hand-book for Cornwall, p. 199.
25. Ansted, vol. ii. p. 418.
26. Whewell, Anniversary Address to Geol. Society, 1839.
27. In Memoriam.
28. Dr. Pye Smith says 140,000 feet.
29. See a valuable map of fossils published by the Christian Knowledge
Society.
30. Trilobite: treis, three, and lobos, a lobe; having three lobes.
31. Bridgewater Treatise, vol. i. p. 396.
32. A fossil shell allied to the Argonauta and Carinaria.
33. “Man has no tail, quantum mutatus; but the notion of a much-ridiculed
philosopher of the last century is not altogether without foundation; for the bones
of a caudal extremity exist in an undeveloped state in the os coccygis of the human
subject.” Poor man!—Vestiges of Creation, p. 71.
34. Sedgwick, p. 216, “On the Studies of the University of Cambridge.”
35. “My School and Schoolmasters,” by Hugh Miller.
36. “Old Red Sandstone; or, New Walks in an Old Field;” by Hugh Miller, p.
48.
37. “By mind, by hand, and by hammer.”
38. “Old Red Sandstone,” p. 66.
39. Ichthyolite: ichthus, a fish, lithos, a stone: fossil fish, or the figure or
impression of a fish in the rock.
40. “Old Red Sandstone,” pp. 41, 42.
41. “Old Red Sandstone,” p. 69.
42. From akanthos, a thorn, and pterugion, the fin.
43. From malakos, soft, and pterugion, the fin.
 44. 1. Ganoid, from ganos, splendour, because the scales are coated with a
bright enamel.
45. 2. Placoid, from plax, a plate; sometimes large, sometimes reduced to a
point; e.g. shark.
46. 3. Ctenoid, from kteis (gen. ktenos, a comb); scales jagged like a comb.
47. 4. Cycloid, from kuklos, a circle; scales smooth and simple: e.g. salmon,
&c.
48. From kephalē, the head; aspis, a buckler.
49. Coccosteus, from kokkos, a berry, and osteon, a bone.
50. “Old Red Sandstone,” p. 86.
51. Pterichthys: pteron, a wing, and ichthus, a fish.
52. “Old Red Sandstone,” pp. 80, 81.
53. Osteolepis: osteon, a bone, and lepis, a scale.
54. Operculum, the flap which covers the gill.
55. “Old Red Sandstone,” p. 111.
56. “Vast quantities:” let any reader go and turn over the non-bituminous
shale lying on the waste heaps of every coalpit, and he will see that this is no
exaggeration.
57. Capillus Veneris.
58. Corruption of arrière-dos, a fire-place. See a view and description of one
in “A Visit to Penshurst,” in Howitt’s “Visits to Remarkable Places,” Second Series.
59. Juicy and soft, as peas, beans, plantains, bananas, &c.
60. “Ancient World,” pp. 76, 77.
61. This may seem strange at first; but I have journeyed through tropical
forests that realized completely this sketch, so far as stillness and silence are
concerned. A modern and most accomplished naturalist says of a Jamaica virgin
forest, “Animal life is almost unseen; the solitude is scarcely broken by the voices
of birds, except that now and then the rain-bird or the hunter (large cat-tailed
cuckoos that love the shade) sound their startling rattle, or the mountain partridge
utters those mournful cooings which are like the moans of a dying man.”—Gosse’s
Jamaica, p. 198.
62. From κάλαμος (calamus), a reed.
63. Ansted’s “Ancient World,” p. 82.
64. Mesozoic: i.e. middle life period; mesos, middle, zoos, life.
65. The Religious Tract Society.
 66. Lyell’s “Manual of Elementary Geology.” Postscript, p. 13.
67. Ansted’s Geology, vol i. p. 306.
68. Ichnites; from ichnon, a footstep, and eidos, like.
69. Ornithos, a bird, and ichnon.
70. Marsupial, from marsupium, a pouch; animals of the fourth order of
Cuvier, that have a pouch in which the young are carried.
71. Batrachian, from batrachos, a frog; animals in Cuvier’s fourth class of
reptiles.
72. Cheir, the hand, therion, a wild beast; a wild beast with a foot like a hand.
73. From labyrinthus, a labyrinth, and odous, a tooth; so called from the
labyrinthine structure of the tooth.
74. In some cases we find, corresponding to a set of footmarks, a continuous
furrow, presumed to be the impression of a tail dragged along the sand by the
animal while walking.
75. Ansted’s Ancient World, pp. 125–127.
76. Knight’s Cyclopædia of Arts, &c.
77. Quarterly Review, May, 1852. Article on Roger de Coverley.
78. This is a corruption, we are inclined to think, of the word “layers;” one of
those provincial corruptions of the Queen’s English that get stereotyped.
79. Buckland’s Bridgewater Treatise. pp. 351, 352.
80. A fossil bivalve, allied to the oyster, and very abundant in the secondary
strata.
81. Belemnite, from belemnos, a dart, and so called from its arrow-headed
shape.
82. Saurian, from sauros, a lizard, the name by which the great family of
lizards is designated.
83. From ichthus, a fish, and sauros, a lizard; so called from its resemblance to
both.
84. Heteroclite; heteros, another, and klitos, inclining; a word applied to any
thing or person deviating from common forms.
85. Very unlike the alligator, whose eyes are placed at a considerable distance
behind the nose.
86. From pleiōn, more, and sauros, a lizard; because it is more like a lizard
than the Ichthyosaurus.
87. Mantel’s Fossils of the British Museum, p. 341.
 88. This formation is sometimes called the Jurassic system.
89. Lyell’s Manual of Elementary Geology, p. 12, ed. 1852.
90. “So vast an expanse!” Mr. Darwin traced coral reefs in the Pacific, 4,000
miles long and 600 broad. Between the coasts of Malabar and Madagascar there is
a chain of coral reefs, called the Maldives and Laccadives, 480 miles long and 50
miles wide. On the east coast of Australia there is an unbroken reef of 350 miles
long; and between Australia and Guinea, coral reefs extend 700 miles in length.
Truly the coral animals, like the “conies,” are a “feeble folk,” but their habitations
survive our proudest monuments.
91. Hugh Miller’s First Impressions, pp. 203, 204.
92. Brash is s Wiltshire word for short or brittle; and thus a quick-tempered,
irritable person, is said to have a brashy temper.
93. Geology for Beginners (Weale’s Series), p. 147.
94. Juke’s Popular Geology, pp. 42–44.
95. From krinos, a lily, and eidos, like; lily-shaped animals of the Radiated
division, forming a link between the animal and vegetable world.
96. From trochos, a wheel; wheel-shaped crinoideans.
97. From pteron, a wing, and dactulos, a finger; the wing-fingered animal.
98. The term Weald or Wold is the old Saxon for our present Wood; and now,
altered by pronunciation, is found in connexion with many words and names of
places: e.g. Waltham (Weald-ham), the wood house or home; Walthamstow, the
wood house store, and so on. Thus it is that words are “fossil poetry.”
99. Alison’s description of South America, in History of Europe (Article, South
American Revolution); vol. viii.
100. “Our disposition is, and has been, not to multiply miracles after the sort
in which this has been done by many more zealous than wise friends of revelation.
In all cases we allow the miracle without question, which is distinctly claimed to be
such in the Scriptures, and where the circumstances clearly indicate that a miracle
was necessary,—we say ‘necessary,’ because we are persuaded that the Almighty
has almost invariably chosen to act through natural agencies, and under the laws
which he has imposed on nature, whenever they are adequate to produce the
required result. We believe it is one of the beautiful peculiarities of the Bible, that it
has none of those gratuitous and barren wonders, which form the mass of the
pretended miracles which the various systems of false religion produce.... For our
own part, we do not wish to hear of small miracles, which leave us doubtful
whether there be any miracle at all. If we are to have miracles, let them be
decidedly miraculous, and let not our veneration for the Divine character be
offended by exhibitions of the Almighty, as laying bare his holy arm to remove the
small remaining difficulty which theorists leave him to execute.”—Dr. Kitto’s
Biblical History of Palestine.
 101. We have a fine specimen before us which we brought from Demerara,
answering well to Gosse’s description of the iguana found in Jamaica. “In the
eastern parts of the island the great iguana (Cyclura lophoma), with its dorsal
crest, like the teeth of a saw, running all down its back, may be seen lying out on
the branches of the trees, or playing bo-peep from a hole in the trunk.” It is
considered a great delicacy by many, but it never seemed Christian food to us, and
we never ventured to provoke our palate with a taste.
102. Enaliosaurians are sea lizards, such as those found in the Lias; and
deinosaurians are terrible lizards, such as those found in the Wealden.
103. Ansted’s Ancient World, pp. 164–168.
104. Just published by Bohn, in his valuable “Scientific Library;” a marvel of
cheapness and value.
105. Since writing the above we have met with the following, which proves that
this origin of chalk is not so fabulous as some think it:—“Lieut. Nelson, Mr. Dance,
and others have shown, that the waste and débris derived from coral reefs
produces a substance exactly resembling chalk. I can corroborate this assertion
from my own observations, both on some very white chalky limestones in Java and
the neighbouring islands, which I believe to be nothing else than raised fringing
coral reefs, and on the substance brought up by the lead over some hundreds of
miles in the Indian Archipelago, and along the north-east coast of Australia, and
the coral sea of Flinders,”—Juke’s Physical Geology, p. 263.
106. We take the origin of the word Folkstone to mean, that that old town was
once built of the brick that may be made of the galt: it was the folk’s-stone.
107. “The Religion of Geology,” &c., by E. Hitchcock, LL.D. &c. p. 70.
108. Mantell’s “Geological Excursions,” p. 145.
109. Richardson, p. 391.
110. Under-borne rocks; upo, below, and ginomai, to be formed.
111. Middle life period: mesos, middle, and zoos, life.
112. Recent-life period: kainŏs, recent, and zoos, life.
113. Juke’s Practical Geology, p. 265.
114. Lyell’s Manual of Geology, pp. 97, 98.
115. Ansted’s Geology, vol. ii. p. 14.
116. Even Hitchcock’s good book is sadly disfigured and damaged, by trying to
make geology prove too much. How can geology teach or suggest sin and the
resurrection?
117. British Quarterly, Feb. 1852.
118. Owen’s British Fossil Mammals and Birds, p. 255.
 119. Mantell, pp. 477–479.
120. Mantell, p. 471.
121. The skeleton is not more than 150 years old, and is probably one of an
Indian who fell in war; and has been covered with carbonate of lime, held in
solution in some spring.
122. Hugh Miller’s “First Impressions of England and its People,” p. 362.
123. No sooner did geology give signs of being able to speak from her
subterranean abode, and say something new about the history of this old world,
than Dr. Smith was among the foremost of the geologists, intent upon the
interpretation of these mysterious, and at first incoherent sounds. At times the
sounds seemed unscriptural, but his faith never failed; at other times it seemed in
confirmation of Scripture, and he was filled with delight. There were sepulchres
older than what he had accounted the era of death, and he must solve the mystery.
Mineralogy, to which from his youth he had given considerable attention, became
to him history more ancient than that of Moses, and poetry more fascinating than
that of Homer. His minerals became books of wonderful tales; his fossils, before
riddles of nature, the pictures of things in ancient worlds. The earth was a land of
monuments, and the rock which before seemed nothing more than the solid
masonry of the foundation on which men might build their dwellings, became the
enduring chronicle of the millions of years in which extinct ages had risen,
flourished and decayed. From that time he suffered no discovery of the geologists
to escape his attention; and every valuable book upon the subject in English,
German, or French, contributed its supplies to mitigate his insatiate craving after
further information.
Dr. Smith had another reason for devoting a large proportion of his time to
geological studies. The new science had something to say about Holy Scripture. It
threatened, as many understood its first ambiguous words, to contradict the book
of Genesis.
Whatever affected theology was of supreme importance in the estimation of
the Homerton professor. Having full confidence in the truth of God’s word, he was
sure that nature and revelation, however they appeared to superficial observers,
could not be really at variance. In that confidence he patiently listened to every
word the new science had to say about the creation of the world. To him belongs
the honour, in the opinion of the most eminent geologists, of having relieved their
science of every appearance of hostility to Scripture. Of his book on this subject,
Dr. Mantell said, “It is, indeed, the dove sent out from the ark of modern geology;
and it has returned with the olive branch in its mouth.”—British Quarterly, Jan.
1854. Art. Dr. Pye Smith.
124. Gray’s Antiquity of the Globe, pp. 57–59.
125. Hitchcock, p. 70.
 August, 1854.

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