Draft June 2012.
In Celebration of Psalm
God's handiwork in Creation
Development of the Plant Classes*
|"If it weren't for
flowering plants, we humans wouldn't be here."
Remarks on the Animal and Plant Classes
|The description of the basic
plant and animal body plans -- the phyla -- which is the subject of
earlier chapters, is too general to convey a good understanding of the
creation narrative, which includes a great diversity beyond just the
variety of body plans01.
The classes (or
are the first level of refinement, and carry the narrative a step
further. When do they arise in the fossil record? What innovations are
required? Do these innovations require basic changes in the genetic
makeup or are they natural modifications of existing genes and gene
Of course the narrative goes on beyond even this level, but already
here the limitations of our present knowledge are daunting, and it
might hint of masochism to go much further. In particular, at present
the existence of many changes can only be pointed out; the way that
they came about is largely unknown: did the changes involve new gene
packages that were previously unknown, or were they "tweaks" of
existing genes, or of the regulatory structure? Why do so many of the
new innovations seem to spring up as "magnates" of the new
There is little doubt that many of the present gaps of understanding
will be filled in the coming decades and centuries, and I for one look
forward to these gains. At the same time the lack of deep insight into
how natural evolution works makes it difficult to understand the limits
of natural development.
|The (Temporary) End of the Secular
The science of cosmology is almost entirely the product of the past 60
years. It has formed the basis for the creation narrative presented in
this website. Our narrative is (nearly) at an end because we are now
hitting the frontiers of the mature parts of that narrative.
The main missing ingredients are these:
(1) A detailed timeline of the
principal innovations in living species (plants and animals). Thus far
only the most dominant peaks of this innovation can be discussed with
any degree of completeness. There are dozens, perhaps hundreds more
major -- perhaps astounding -- innovations yet to detail. Some may be
plainly visible, but (I suspect) many others hidden. We can see the
effects in the plants and
animals around us, but the deeper details of how and when they came
about are very sketchy. Major efforts to understand these innovations
are ongoing, but the field is so
vast it will be many decades, at least, before a reasonably rounded
(2) A correlation between this timeline of novel innovations
and the specific genetic or
that occurred to effect them. Ideally, one would like to see
a spreadsheet with the innovations listed together with the major
genetic changes that accompanied those innovations.
Several things delay the production of such a spreadsheet:
a. The relatively recent
development of the ability to sequence genes -- as a result there is a
natural logistic backlog of thousands of species that are as yet
b. The difficult task of identifying the functions of the sequenced
genes and the association into gene packages. Most genes and gene
collectively rather than singly. In addition, many genes perform more
than one function.
c. Many more genes are created and used during the normal execution of
gene expression -- understanding these "cryptic" genes and "biological
dark matter" is vital to understanding the overall genetic mechanisms,
yet they are largely unknown01a.
A fundamental difficulty is that the end result of genetic
only indirectly tied to the responsible genes -- first find the
dog, then identify the tail, and finally locate the wag. Life functions
are a rabbit-warren of indirect effects and causes.
(3) A specific narrative about the symbiotic
correlation between plant and animal (especially insect)
changes, and explanations of how this occurs in practice. One needs,
for example, to distinguish between so-called "convergent evolution"
(which is largely unexplained) and evolutionary development*.
(4) A detailed and accepted "tree
of life" based on genetic
relatedness. In the past decade there has been great progress in the
detailing of this tree of life using cladistics. But at present these
valuable investigations have not congealed into a single
generally-agreed storyline. Ultimately, one can
expect that a generally accepted tree based on cladism will replace the
based on physical similarity, that until recent decades has been the
main way that species relatedness has been inferred.
(5) Explain exactly how
such changes are recorded and implemented in
the genetic code or in gene regulation. There is overwhelming evidence
that it is NOT just a
matter of environmental pressure and "survival of the fittest": too
many changes occur too rapidly for that slow approach to gain traction,
particularly in higher species which often are associated with much
reduced rates of reproduction. This is the great unfinished business of
As a result of these limitations, the narrative as regards the
development of classes, orders and subdivisions below the basic body
plans (phyla and certain classes) is spotty. The future is bright with
greater insight, but the present we must be frustrated in our desire to
complete the creation narrative.
* Consider, for example, the "old" narrative about
in the octopus eye, versus the current view of evo-devo, that all eye
development in widely separated species uses the same highly-conserved
package of hox genes. This is not, of course, the full story of how
these changes occur, but it certainly is a change from the older view.
The intent of this chapter is to give a timeline for major innovations
in the plant phyla, particularly the angiosperms, and to describe these
innovations both as to what they achieve, the major molecular
innovations involved, and the genetic changes required to produce and
carry out these innovations.
In earlier chapters, the sort of treatment desired has been carried out
in some aspects of the central dogma, in the discussions of the
eukaryotic cell innovations, and to a very limited extent in some other
special topics (the development of stingers in the cnidaria, for
example), leading to a number of sharp points that have been noted at
the appropriate places.
Unfortunately, perhaps due to my own lack of comprehensive experience,
combined with what appears to be a very immature level of development
in the science that would allow such a discussion (after all, complete
genome sequencing has only been possible in the past decade or so),
this intent is difficult to carry off, and as a result this chapter is
unsatisfyingly incomplete, if not outright premature. Hence the
scarcity of sharp points -- I believe they are there, but they must
await further information.
I will therefore leave it incomplete -- as a marker, perhaps, for
future additions, posting whatever remarks I can glean from the
available information, in anticipation that more material
will become available.
The Creation Narrative carries
the development of life along two parallel paths: the animals and the
plants. In both cases, even the crude outline requires more detail than
a description of the phyla -- the body plans -- can provide. In the
case of animals, the needed details go at least to the next taxonomic
level, the classes, and in the case of the highest phylum, the
Chordata, and particularly the class of mammals, it is necessary to
describe things even further. To a lesser extent the same is true of
the plants. In particular, the angiosperms require more elaboration.
The History of Life: Development of
Food and Energy Stores. In one sense, one could characterize the
entire narrative of life as a need for adequate pre-positioned food,
and more recently, fossil fuel for energy. In the beginning, there was
no organic food,
particularly the essential fixed nitrogen. For this reason, a major
segment of the story of life on Earth could be characterized as a
scramble for an adequate supply of fixed nitrogen, which passes
on in the form of organic waste. Even the "autotrophic" plants
cannot survive without fixed nitrogen which must come (at least until
the invention of the Haber process) from the detritus of earlier
generations of life.
A characteristic of the advancement of life is that later life forms
uniformly require more energy. By the time the eukaryotes arrive, the
species can no longer generate enough energy to carry on their life
processes without substantial assistance from the environment. Thus,
to begin, eukaryotes need oxygen to carry on the higher levels of
metabolism as compared with bacteria. Indeed, the oxygen atmosphere is
itself the product of organic action developed over a very long time
and sustained by a high level of bacterial activity.
As the living species advance, the food requirements increase: mammals
require more prepared food (plants or other animals) than do lower
animals; angiosperms require more prepared food than do
gymnosperms, and so on. At the very top of the animal chain,
the human body expends about 25% of its entire energy budget on the
It is interesting, and once was remarked upon, that modern civilization
even carries this dependency on pre-positioned energy one step beyond
the food chain. The entire civilization now depends essentially on
fossil fuels, and until the time comes that nuclear power and other
non-fossil sources of energy take over, this condition will persist.
Thus one could (some early geologists and I do!) argue that the reason for the Devonian and
was that it was needed to provide the fuel for the modern industrial
revolution, and that for the next few centuries, the bulk of
civilization's energy needs will continue to come from various
pre-positioned and non-renewable fossil sources01. The miracle of the
recent shale-gas revolution is that the horizon for this dependency has
been pushed some centuries into the future.
In the case of plants, angiosperms require larger
food, particularly nitrogen, than do gymnosperms. This is a reason why
renewal of forests generally begins with groundcover and then with
gymnosperm trees (pines, etc.) and finally with angiosperm trees. On
the other hand (perhaps this is why they require larger amounts of
food), the leaves and other litter of angiosperms are higher in
nitrogen and food value, and they decay more readily, than the litter
of gymnosperms. The forest floor under gymnosperms is relatively free
of undergrowth, compared with the floor under angiosperms.
The general progression of plant growth on land is this02. [Figure ??]
• Devonian -- low plants, mostly fern-like, jungle-like growth to tall
jungle-like pith-centered trees (lycopods). Source of most shale gas.
• Carboniferous -- Continued growth of jungle-like pith-centered trees
in marshes and low areas;
early pine-like gymnosperms in
higher elevations. Source of most coal.
• Permian, Triassic, Jurassic -- woody trunked gymnosperms (conifers)
generally take over from pithy trunks.
Ancestors of many present-day
• Cretaceous -- Angiosperms take over from gymnosperms. Explosion of
angiosperms about 115 Ma.
• Cenozoic (after KT extinction 65.5 Ma) to Present -- Diversification
Origin of Grasses (Family Poaceae
-- monocots) "the most important of all plant families to human
Symbiosis between flowering
plants and insects.
Palynology: fossil record of pollen. Pollen is first found in
the fossil record in the late Devonian period.
apical meristems --- growth in length
lateral meristems --- growth in girth
The following nomenclature
The signature feature of the vascular plants is the invention
of the xylem to transport water, and
the phloem to carry nutrients (=
sap, the products of photosynthesis) throughout the plant.
-- club mosses.
Ferns. There is no fossil record of this phylum.
Ferns (Extinct) --
the First Seed Plants.
-- true ferns.
Phyla Pl-8 to Pl-12.
"the seed, which is one of the most dramatic innovations during land
Cycadophyta -- Cycads. Cycads
are gymnosperms -- "naked" seed plants;
Ginkgophyta -- Ginkgo tree.
There is only one extant class, the common Japanese Ginkgo Balboa.
Coniferophyta -- Conifers. Gymnosperms [= "naked seed"]
Usually 8 cotyledons.
Class Pinopsida Order Pinales:
all extant conifers.cedar, cypress, fir, juniper, larch, pine, redwood,
spruce, and yew. http://en.wikipedia.org/wiki/Pinophyta
"The conifers are an ancient group, with a fossil record extending back
about 300 million years to the Paleozoic in the late Carboniferous
period; even many of the modern genera are recognizable from fossils
60–120 million years old." "The world's tallest, largest, thickest and
oldest living things are all conifers. " "The mature pine seed
contains an uncurved embryo with many cotyledons. The embryo is
embedded in a nutritional tissue"
generally needle-like leaves.
==> "Fruits": Juniper berries, red cedar berries. Are they "gymno"?
Are they "cones"?
==> BOX: Remark on the many pharmaceuticals developed by plants --
most (?) of the poisons, drugs have plant origins (cyanide, digitalis,
warfarin, etc.). W/o these would our medicines ever have
Margulis: "The oldest gnetophyte fossil dates from the Triassic" (245
Anthophyta [= "Flower Plant"] -- Angiosperms [= "Seed Vessel"].
protected in a carpal enclosed in a fruit. This is a defining trait of
all angiosperms. Figure ?? shows the typical monocot
(field corn) and dicot (bean) seeds and their germination. Margulis
remarked that the angiosperm seed is
"one of the greatest evolutionary innovations." (p.457)
This phylum is the flowering
The leaves of angiosperms contains much more nutrition, and so
leaf-fall covers the ground under trees with a rich source of food for
undergrowth. This is in contrast with the pinacea which have less
developed leaves and consequently have a less nutritious food supply
that results in a sparse undergrowth. On the other hand, the pinacea
can generally survive on a sparser food supply, which is why they
generally form the first forest cover after a fire or other natural
disaster, angiosperm varieties of trees coming later with the
restoration of a food supply12.
There are two major sub-phyla: monocots and eudicots (dicots),
the characteristic distinction being whether the seed has one or two
cotyledons (seed-leaves), although the divisions have a number of
distinctive features as shown in the following table.
|Embryo with single cotyledon
||Embryo with two cotyledons
|Pollen with single colpus
or pore for passage of sperm)
|Pollen with three colpi
|Flower parts in multiples
||Flower parts in multiples
of four or five
|Major leaf veins parallel
||Major leaf veins
reticulated - form a network
|Stem vacular bundles
||Stem vascular bundles in a
|Root vascular bundles in a ring
|Root vascular bundles in middle
of the plant (tap root)
|Roots are adventitious
(arise from nodes in the stem)
|Roots develop from a
radicle in lower end of stem
|Secondary growth absent
||Secondary growth often
All Angiosperms have double
fertilization. In some (e.g. orchids) it is suppressed.
The double fertilization
produces endosperm. In some seeds it is absorbed into the cotyledons
during seed development (e.g. beans); in others it provides food to the
cotyledon during germination. "Sometimes the gymnosperm nutritive
tissue is also called
endosperm. However, it is preferred to reserve the term endosperm for
pollen provided the earliest fossil evidence of flowering plants. The
pollen typically has a highly configured hard shell which preserves
well (Figure ??). The pollen typically has a slit, called the colpus,
which allows passage of the sperm during fertilization.
The first fossil evidence of
angiosperms is fossil
pollen (early Cretaceous ca. 140 Ma -- note dicot pollen
characteristics below). earliest flowering plant fossil Koonwarra (120
Ma) [Margulis, p. 457].
The special feature of angiosperms
is that the seed is enclosed in a
tissue (derived from the ovary) that has nutritive value.
Actually there is a double provision: Within the seed is food for the
initial growth of the embryo (that is why seeds can be separated from
the rest of the enclosing tissue -- think apple seeds or peach pits
that are the seed itself.
Flowers. Both monocots and
dicots have beautiful flowers, and both have varieties that have
minimal, almost "cryptic" flowers. The conventional wisdom has it that
the dicots came first, even though they appear to be more complex, and
the first acknowledged specimens have cryptic flowers.
This means, from the viewpoint of evolution, that flowers for monocots
and dicots appear to have arisen independently, with different
Monocot flowers. Monocot flowers
include the very beautiful flowers of the Orchid, Lily and Iris
families. Figure ?? is a typical monocot flower, the Day Lily, in which
both the male (pollen-producer) and female (ovary) parts are included
in the same flower. Note the typical arrangement of 3 sepals (outer
layer) and 3 petals (inner layer). Other typical parts are indicated on
the right figure and in the insert. Note also the typical parallel
veins of the leaves.
The grass family (Poaceae) is an important family of
monocots that includes the grasses, corn (maize), and many feed grains
(wheat). The flowers of the grasses have no petals or sepals (in other
words, they don't have anything that looks like the conventional notion
of a flower). They do have clearly-defined male and female portions of
the plant, often located in separate parts of the plant -- for example
the male corn tassels and female corn ears.
Monocot flower (Day Lily)
(note 3 Petals & 3 Sepals);
note parallel leaf veins)
Dicot (Eudicot) flowers. The Dicots
form the larger sub-phylum of flowering plants. Dicot flowers typically
have four, five or more petals, but the number can reach much higher --
the marigold, daisy, sunflower (family Asteraceae, order
asterales -- the largest order of eudicots), and many other species.
Figure ?? shows
the flowers of a Clematis climbing vine. Note in this case that the
number of petals can vary on a single plant. This illustrates the fact
that the process of petal formation is quite different between monocots
and dicots. Note also the typical articulated leaf-veins11.[DESCRIBE]
Dicot flower (Clematis)
(6 and 8 petal flowers on the same plant
note network of leaf veins)
Various leaf fossils (Maple etc.) Oligocene ca 30 Ma.
family Asteraceae. Dicot.
Order Asterales. Sunflower family (asters, daisies). "Largest plant
family in the world"
family Orchidaceae. Monocot.
Order Asparagales. Orchid family. "Second largest plant family in the
Dicot. Order Fabales. The legumes. Many beans. "Third largest
family in the world" [Wiki]. Endosperm absorbed during seed
development. Legumes fix nitrogen through a symbiosis with bacteria in
root nodules. (SHARP POINT?) This is an
family Poaceae. Monocot.
Order Poales. The grasses. Cereal grains. The earliest fossil Poales
(pollen & fruit) date to the late Cretaceous (65.5 Ma). Corn genus
Zea. During the
Eocene large grassy plains came into existence 50 Ma Grasses
are ideally suited for grazing because the growing point is located
near the base of the plant or below ground rathern than at the plant
tip, unlike many other
family Rosaceae. Dicot. Order
Rosales. Rosids. Roses, many berries, Apples, peaches,
49.5 Ma. leaf fossils.
Oak = Rosid family Fagaceae order Fagales genus
Quercus. Hickory Genus Carya. Beech Genus Fagus.
Maple = Order Sapindales Family Aceraceae genus Acer
Dogwood = Order Cornales genus Cornus
mustard = Order Brassicales Family Brassicaceae.
Arabidopsis thaliana - smallest genome Genus Arabidopsis. First plant
family Vitaceae (Vitidaceae). Dicot.
Order Vitales. Grapes
The oldest (grape?) vine leaf
http://steurh.home.xs4all.nl/engplant/esezwijnr.html. 60 Ma.
magnolia, Tulip tree. Order Magnoliales a Magnoliid. [Thot to be
a basal angiosperm]
The Marcellus shale, and other formations that are associated with the
recent unconventional gas discoveries were laid during the Devonian Age
(ca. 350 Ma). The principal coal formations are from the Carboniferous
Age (ca. 250 Ma).
^n01a See Science
News Online Biological
Dark Matter (2002) and Tamburini & Mastromei, Do Bacterial Cryptic Genes Really Exist?
and convergence, homoplasy, are everywhere one looks, even
in early land plant evolution" (e.g. "The frequent reaquisition of
woodiness in clades that have become herbaceous" ... "Irish (2009)
suggests that features such as petals may evolve several times because
of the independent cooption of underlying gene regulatory networks.")
Plantain is a common lawn weed. It is a dicot, but has the peculiar
feature that some varieties have parallel leaf veins (like monocots)
while other varieties have reticulated veins that are typical of
dicots. The following figures illustrate the two varieties, which are
often found co-mingled in the same lawn.
[SHOW PLANTAIN WEEDS:
Frank Berendse1 and Marten Scheffer (2009) Ecol Lett. 2009 September;
12(9): 865–872. . "We propose that angiosperms due to their
higher growth rates profit more rapidly from increased nutrient supply
than gymnosperms, whereas at the same time angiosperms promote soil
nutrient release by producing litter that is more easily decomposed.
This positive feedback may have resulted in a runaway process once
angiosperms had reached a certain abundance." "angiosperms promote soil
nutrient levels by producing litter that is more readily
decomposed." "We hypothesize that gymnosperms do relatively well
under low nutrient conditions, and also maintain low nutrient levels in
the soil due to the nature of their litter. Angiosperms do not grow
well under such conditions but once they are present in sufficient
densities they enhance soil fertility through their litter implying a
positive feedback that might produce a runaway process once angiosperms
have reached a certain critical abundance."
transitions in nature and society
By Marten Scheffer (2009) Section 9.4 The Angiosperm radiation
p.175 "angiosperms need higher nutrient levels than the gymnosperms
that dominated before, whereas at the same time, angiosperms promote
soil nutrient levels by producing leaf litter that is more readily
decomposed. This implies a positive feedback that might produce a
runaway process once angiosperms reach certain abundance." [quoting
Frank Berendse] ... gymnosperms typically have a poor leaf litter. ...
"the ancient gymnosperms could thrive at low nitrogen concentrations
but were also keeping nitrogen contents in the soil low, because of the
kind of leaf litter they produced." ... "one can imagine a
gymnosperm-dominated world in which angiosperms have been suppressed
for a long time. However, once unleashed, they would become dominant in
a runaway process."
Hans Steur, The
Paleobotany Pages, The Evolution
of Plants: A Concise report on the development of the flora.
P.F. Stevens, Angiosperm
See The Timetree of Life ed. Hedges, Kumar. Oxford Press (very
Seed Structure http://www.seedbiology.de/structure.asp
Seed Evolution Webpage http://www.seedbiology.de/evolution.asp
Any comments or suggestions are welcome. Please email: firstname.lastname@example.org
Posted dd Mmmm 201?