Draft June 2012.


In Celebration of Psalm Nineteen:
God's handiwork in Creation

Chapter 13
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 orders) 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 packages?

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 classes?

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 Creation Narrative

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 picture emerges.

(2) A correlation between this timeline of novel innovations and the specific genetic or regulatory changes 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 unsequenced;

b. The difficult task of identifying the functions of the sequenced genes and the association into gene packages. Most genes and gene products operate 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 unknown

A fundamental difficulty is that the end result of genetic change is 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 traditional tree 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 evolutionary theory.

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 anticipation of greater insight, but the present we must be frustrated in our desire to complete the creation narrative.

* Consider, for example, the "old" narrative about convergent evolution 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 brain.

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 Carboniferous ages 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 sources
01. 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 amounts of  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 this
02. [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 conifer families.
• Cretaceous -- Angiosperms take over from gymnosperms. Explosion of angiosperms about 115 Ma.
• Cenozoic (after KT extinction 65.5 Ma) to Present -- Diversification of angiosperms;
        Origin of Grasses (Family Poaceae -- monocots) "the most important of all plant families to human economies" [Wiki];
        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 follows Margulis.

Non-Vascular plants
(Subkingdom Bryata, Phyla Pl-1 to Pl-3)

Pl-1 Bryophyta
. Mosses.

Pl-2 Hepatophyta
. Liverworts. Non-vascular.

Pl-3 Anthocerophyta. Hornworts. Non-vascular.

Vascular plants
(Subkingdom Tracheata, Phyla Pl-4 to Pl-12)

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.

Pl-4 Lycophyta
. Lycopods -- club mosses.

Pl-5 Psilophyta. Whisk Ferns. There is no fossil record of this phylum.

Pl-6 Sphenophyta. Horsetails.

Pl-7x Seed Ferns (Extinct) -- the First Seed Plants.

Pl-7 Filicinophyta -- true ferns.

Seed plants
Phyla Pl-8 to Pl-12.
"the seed, which is one of the most dramatic innovations during land plant evolution."

Pl-8 Cycadophyta -- Cycads. Cycads are gymnosperms -- "naked" seed plants;

Pl-9 Ginkgophyta -- Ginkgo tree. There is only one extant class, the common Japanese Ginkgo Balboa.

Pl-10 Coniferophyta -- ConifersGymnosperms [= "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 "evolved?"

Pl-11 Gnetophyta.

Margulis: "The oldest gnetophyte fossil dates from the Triassic" (245 Ma).

Pl-12 Anthophyta [= "Flower Plant"] -- Angiosperms [= "Seed Vessel"].

"Key innovations are rarely simple features, rather, they may involve a complex suite of changes."

This phylum is the flowering plants.

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 supply

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
(furrow or pore for passage of sperm)
Pollen with three colpi
Flower parts in multiples of three Flower parts in multiples of four or five
Major leaf veins parallel Major leaf veins reticulated - form a network
Stem vacular bundles scattered Stem vascular bundles in a ring
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 present
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 angiosperm seeds."

Pollen. Fossilized 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].

Misc. Pollen
Figure ??
Miscellaneous Pollen

Seeds.  The seed is 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)

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.

Seed Germination
Figure ??
Seed Germination: Monocot and Dicot

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 characteristic features.

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-daylily  Monocot Flowerparts
Figure ??
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
Figure ??
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 world."

family Fabaceae Dicot. Order Fabales.  The legumes. Many beans. "Third largest plant 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 elaborate process!

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 plants.

family Rosaceae. Dicot.
Order Rosales. Rosids. Roses, many berries, Apples, peaches, Cherries. Ca. 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 genome sequenced.

family Vitaceae (Vitidaceae). Dicot. Order Vitales. Grapes
        The oldest (grape?) vine leaf http://steurh.home.xs4all.nl/engplant/esezwijnr.html. 60 Ma.

family Magnoliaceae.    magnolia, Tulip tree. Order Magnoliales a Magnoliid. [Thot to be a basal angiosperm]




* Fossil Sunflower, 62.5 Ma. Also See Science Magazine, 24 Sep. 2010 and Daily Mail (UK).

Fossil Sunflower
Fossil Sunflower
62.5 Ma
Huiterara Formation, Argentina

^n01  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? (2000).

^n02  See the Wiki Timeline of Plant Evolution.

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^n10  "Parallelism 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.") -- http://www.mobot.org/mobot/research/APweb/orders/amborellalesweb2.htm#Evolution

^n11  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.

^n12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777257/ 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."

Critical 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."

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Hans Steur, The Paleobotany Pages, The Evolution of Plants: A Concise report on the development of the flora. http://steurh.home.xs4all.nl/engplant/eblad4.html

P.F. Stevens, Angiosperm Phylogeny Website

See The Timetree of Life ed. Hedges, Kumar. Oxford Press (very expensive!)

Seed Structure http://www.seedbiology.de/structure.asp

Seed Evolution Webpage http://www.seedbiology.de/evolution.asp

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