Posted 20 Decembe 2011

       

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

Chapter 8

The Third Genesis:
   
Creation of The Proper (Eukaryotic) Cell*

ca. 1.8 Ba


"An organic being is a microcosm, a little universe  formed of a host of self propagating organisms inconceivably minute, and as numerous as the stars in heaven."
 - Charles Darwin
Animals and Plants ii, p399 (1887)

NOTE: Ba (Ma) = Billions (Millions) of years before the present time.


The "Big Bang" Creation of Eukaryotes
The sudden appearance of eukaryotes at about 1.8 Ba, with no clear predecessors and with major structural and genetic changes, has been described as a "Biological Big Bang (BBB)"1. Not only do the eukaryotes appear on the scene suddenly and without warning or obvious predecessors, but even within the major classes of eukaryotes there is no clear line of antecedence -- no clear "archeotype." Indeed the eukaryotes appear to be examples of "reductive evolution" -- the ancestor appears to be more complex than the descendents. This is a recurring theme in the development of species.
"The origin of eukaryotes is a huge enigma and a major challenge for evolutionary biology."1.1  At root, the problem is twofold: first, there is a great chasm between the most complex prokaryote and the least complex eukaryote; and second, there are six major groups of eukaryotes, with no evident common ancestor1.2 -- which leads to the assertion that the "ancestor" must have been more complex than any existing eukaryote, and the present strains derived from that complex ancestor by reductive evolution -- see the box on reductive evolution. In summary, eukaryotes appear suddenly with no known ancestors, and the inferred ancestor was more complex than any eukaryotes that exist today! -- hence the remark that the Eukaryotes began in a  "likely 'big bang' of early eukaryote radiation." [ibid.]

"Even the most widely accepted notion that eukaryotes originated from prokaryotes is problematic because traits unique to eukaryotes, such as the nucleus, endomembrane system, cytoskeleton, and mitosis, are found in all taxa with no intermediate stages left as signposts of their evolution."
1.3

To confuse the issue even more, the genes of eukaryotes are "
an uneven mix of genes of apparent archaeal origin, genes of probable bacterial origin, and genes that so far seem eukaryote-specific, without convincing evidence of ancestry in either of the two prokaryote domains."1.4




Reductive Evolution
Reductive evolution refers to the concept that the ancestors of a given species are more complex than the descendents. The reduction of functionality seems to be a general (or at least a common) feature of species development. When this reduction reflects the elimination of redundant functionality, or elimination of an un-needed function, it is a plausible "advancement." But when the ancestors suddenly appear (or are inferred), with novel and complex features that then disappear in the descendents, reductive evolution contradicts some basic assumptions of evolution that argue for a progressive advancement in species complexity.

At the beginnings of modern geology, a number of early geologists remarked that the fossil record often began with the sudden appearance of a complex species which then evolved over time by losing functionality, so that the later appearances were more specialized and less complex than the ancestors. This phenomenon -- later termed Reductive Evolution -- was widely regarded by some early geologists as plausible evidence for a divine Creator because of the lack of fossil precursors, and as a counterpoint to the apparent general rule of progressive development (which is also clear in the fossil record)1.5. Perhaps the classic example of this is the trilobite, discussed in a later chapter, which appeared full-formed as one of the earliest animal fossils.

When Darwin's Theory of Evolution appeared in 1859, there was a wholesale movement towards the adoption of evolution by purely natural means. This meant, in effect, that the sudden appearance of novel classes was overlooked, "removed into a more distant and dimmer region" as Lydia Miller noted about 10 years later, in 1869. As she noted, the facts still remained but were de-emphasized.

Given the complex ancestor, one may construct a plausible chain of evolutionary events to explain reductive evolution: the elimination  of superfluous features (such as the eyes of blind cave fish) or the elimination of redundant and overlapping genes. Such change towards simplification  may be understood to be plausible and reasonable; but this reasoning does not explain a complex ancestor that appears to have no precedent. The usual "explanation" is the incompleteness of the fossil record, or the lack of hard parts which can be fossilized -- such as the exoskeletons of shellfish.

With the recent advent of detailed gene studies, one might have hoped that the problem of complexity of the first "proto-eukaryotes" might be solved, but such is not the case. Consider the following statement regarding the identity of the very earliest eukaryotes, summarizing a decade of intensive genetic research on the origin of eukaryotes:

There are therefore no grounds to consider any group of eukaryotes primitive... Rather it is becoming increasingly clear that most or perhaps all of them evolved from more complex ancestral forms by reductive evolution. Reductive evolution refers to the evolutionary modality typical of parasites: they tend to lose genes, organelles and functions when the respective functionalities are taken over by the host. So the archezoan (crown group) phylogeny seems to have been disproved, and deep phylogeny and the theories of the origin of eukaryotes effectively had to start from scratch.

The terminology in this quotation perhaps needs some interpretation:

• "no grounds to consider any group of eukaryotes primitive": The general groupings of (protist) eukaryotes do not exhibit a hierarchy of development from one of their own kind.

• "most ... evolved from more complex ancestral forms by reductive evolution.": all examples appear to come from an unknown, more complex ancestor, of unknown connection with existing prokaryotes (the presumed antecedents of the first eukaryote).

Part of the difficulty is that:

• Eukaryotes are a radical advance in organizational complexity over all prokaryotes

• All eukaryotes display a large package of genes that are unknown -- let alone separately existing -- in any prokaryotes.

• The genes that do appear to be shared with prokaryotes seem to be indiscriminately selected from both archaea and bacteria. There is no plausible scenario in which this might occur -- even given lateral gene transfer (LGT), which is well-established and demonstrated in the laboratory.

The difficulty is not in the reductive evolution itself, but in the implied complexity of the first ancestor -- the sort of thing that one would normally associate with a divine Creator.



A number of the early gelogists remarked on this apparent inversion of what one would expect. This is the sense of Hugh Miller's remark that "The magnates walk first" -- see below.

Buckland, Geology and Mineralology (2nd Ed. 1837) p.294 "[regarding fossil fish] a kind of retrograde development, from complex to simple forms, may be said to have taken place. As some of the more early Fishes united in a single species, points of organization which, at a later period, are found distinct in separate families, these changes would seem to indicate in the class of Fishes a process of Division, and of Subtraction from more perfect, rather than of Addition to less perfect forms. ... In no kingdom of nature, therefore, does it seem less possible to explain the successive changes of organization, disclosed by geology, without the direct interposition of repeated acts of Creation."

Hugh Miller, Foot-prints of the Creator, (3rd. Edition, 1858) p. 325 "We know, further, so far at least as we have yet succeeded in deciphering the record, -- that the several dynasties were introduced, not in their lower, but in their higher forms; that, in short, in the imposing programme of creation it was arranged, as a general rule, that in each of the great divisions of the procession the magnates should walk first." [See also the box.]


Edward & Charles Hitchcock, Elementary Geology (1860) p. 363 "Sixth Law. -- Complexity and perfection of organization as well as intelligence increase as we ascend in the rocks. This is true as a general fact; but in particular tribes we find the reverse, viz., retrogradation from a lower to higher, condition. 'All our most ancient fossil fishes,' says Professor Sedgwick,  'belong to a high organic type; and the very oldest species that are well determined, fall naturally into an order of fishes which Owen and Miller place, not at the bottom, but at the top of the whole class.' ... 'The Cephalopods, the most perfect of the molluscs, which lived in the early period of the world,' says D'Orbigny, 'show a progress of degradation in their generic forms. The molluscs as to their classes have certainly retrograded from the compound to the simple, or from the more to the less simple.'" p. 367 "Thirteenth Law -- Many of the fossil animals had a combination of characters which among living animals are found only in several diferent types or classes. Agassiz very appropriately calls such types Prophetic Types. For they form the pattern of animals that were to appear afterward."


Alexander Winchell, Sketches of Creation (1870). p. 314 "Nature has always issued her bulletins. It is a most interesting fact in the history of the animal creation that Nature advertised her plans in the very earliest creative acts. In our study of the relics of the primeval ages we do not find the grand and fundamental purposes of Infinite Wisdom unfolding themselves by degrees as type after type of organic life made its advent upon our planet. ...Nature had her plans, and these were mature in the very beginning. ... [315] [U]pon the very threshold of Paleozoic Time representatives of Radiates, Molluscs, and Articulates burst into multifarious being almost simultaneously. So nearly simultaneous was the appearance of each of these types, that all hypothesis of their genealogical succession is rationally precluded. ... [317] There is no successional relation between the four sub-kingdoms of animals, nor even between the several classes of the invertebrate sub-kingdoms; but among the orders of the several classes and the classes of the Vertebrates we find generally a progress from lower to higher in the order of introduction. But there is another principle, complementary to this, which needs to be united to it in order to present us with a true view of Nature's method. There has generally been a downward as well as an upward unfolding of each type from the central forms in which it was first embodied. Trilobites, the first representatives of the Crustacean type, belong indeed to the lowest group, but do not lie at the bottom of the group. The earliest reptiles were not the lowest of the Amphibians, but Labyrinthodonts, the highest Amphibians; Vertebrates began, not with the lowest fishes, but with a grade of fishes above the mean level of the type... We shall arrive, therefore, at the truest expression of the plan of Nature in reference to the succession of organic beings by saying that each type was first introduced at a nodal point, from which the stream of development proceeded in both directions...."

James Dana, Manual of Geology, (1896) p1031 "No successional lines among Insects appear to have passed between the higher tribes of Neuropters, Orthopters, Coleopters, Lepidopters, Hymenopters; but each was derived from some early [unwitnessed - dcb] comprehensive forms."

-- p.487 ""The Lower Cambrian species have not the simplicity of structure that would naturally be looked for in the earliest Paleozoic life. They are perfect of their kind and highly specialized  structures. No steps from simple kinds leading up to them have been discovered; no line from Protozoans up to Corals, Echinoderms, or Worms, or from either of these groups up to Brachiopods, Mollusks, Trilobites, or other Crustaceans. This appearance of abruptness in the introduction of Cambrian life is one of the striking facts made known by geology."






This chapter concerns the origin of the first single-celled Eukaryotes, called Protists01.5a. Protists preceeded plants and animals (multi-celled species) by about a billion years.

By 1.8 Ba bacterial life had existed on Earth for over 2 billion years. During this time the oxygen generated by bacteria changed the oceans and atmosphere from a reduced to an oxidized state. A pending crisis was about to arrive: up to this time waste oxygen was removed from the oceans and atmosphere by oxidizing minerals in the crust and dissolved in the ocean. But that sink for oxygen was rapidly being depleted and oxygen approached 20-25% of the atmosphere (a level that will remain steady from that point because of what came next).

During the millennia leading up to this time, critical biological material (the detritis of past life) had spread to every nook and cranny throughout the earth's surface and oceans. In particular, this included fixed nitrogen, which most species cannot prepare, and is required for the genetic molecules of all species. This distribution of biological material was necessary for the next development in life.

Tectonic plate movement began to create stable dry land, the material of the future continents. By 800 Ma or so, an equilibrium will be reached between the creation and erosion of continental material. However, the land was hostile to life: it was bombarded with intense cosmic and solar radiation; and this continued until the atmospheric oxygen slowly built up an ozone layer in the outer reaches of the atmosphere. That ozone layer would not be fully in place until about 400 Ma. Thus, between 1.8 Ba and about 400 Ma, all of life existed in the oceans, where the cosmic rays were to a large extent filtered out by ocean water and by the shelter of, for example, protective layers of stromatolite minerals.
 

At this point (~1.8 Ba) the proper (eukaryotic) cell suddenly appeared, without any known precedents. Its appearance was very timely: it used oxygen and so provided an efficient sink for excess oxygen. The oceans were now oxidized; most of the reduced minerals in the ocean and accessible portions of the earth's crust were now oxidized, and so reduced minerals could no longer provide a way to remove oxygen waste from the ocean water. Without a new way to use it, oxygen would reach levels that would choke out life -- which would recede to a sickly low equilibrium between life and its own wastes1.6. The eukaryotic cell solved that problem and led the way to the later development of multicellular life -- the plants and animals.


To say the eukaryotic cell is "much more complex" is not to imply that the bacterial cell is simple. In fact, as we saw in earlier chapters, even the simplest of bacterial cells is vastly complex. But if the bacterial cell is complex, the eukaryotic cell is much, much more complex. Because of this added complexity, the eukaryotic cell can only survive and propagate in an environment that has readily available supplies of food and other products of bacterial life: the tasks that the eukaryotic cell must carry out take so much effort that it requires these prepared sources -- together with an array of specialized organelles to prepare the cell's needs -- in order to keep up its pace of living. Even plants and other so-called autotrophs need organic food. For example, no eukaryotic cell (or most bacteria) is able to fix nitrogen, a laborious and energy-intensive task that was carried out by specialized bacteria over the two billion years since the first life appeared and that continues today. The product of that effort was an abundant supply of organic matter distributed throughout the earth -- almost all organic matter of whatever kind includes a supply of fixed nitrogen.

In addition, most advanced species of life, including all animals and many eukaryotes, are based on oxygen metabolism, and this required that the earth had to be changed from a strongly reducing environment to an oxidizing environment (the atmosphere, the  oceans and the earth's crust). That process occurred over the same two billion years, and ended up with a stable 20% oxygen atmosphere, and most reduced ocean salts oxidized and precipitated to form the major ore deposits.

Bacteria, the only life forms present to this point, did not have the basic design that is needed for complex life. A new cell type was needed, so radically different that it amounted to a new creation of life, which we call the Third Genesis02, the eukaryote cell. This occurred around 1.8 billion years ago. All plants and animals are made from eukaryotic cells. The eukaryotes at this time were protists -- single-celled eukaryotes.

The Eukaryotic Cell. The most visible distinction between bacteria and eukaryotes is the presence of a nucleus - think of the yolk of an egg (Figure 1). All eukaryotes have the genetic material - the DNA - in long strands called chromosomes, enclosed in a nucleus that is separated from the rest of the cell by a protective membrane. In contrast, prokaryotes - the bacteria - have looped DNA that is not separated from the rest of the cell. The nucleus protects the DNA from damage by contact with food or cell invaders. Passage of material across the nuclear membrane is controlled by ports formed of complex molecules that are designed to allow only certain kinds of material to pass.


DNA in proper cell
Figure 1
DNA in Prokaryotes and Eukaryotes
dcb

A second readily visible feature of eukaryotes is that they are generally larger and have more structure. Figure 2 is the paramecium, a single-celled eukaryote. This larger size and structural detail is due to the fact that all eukaryotes have a cytoskeleton which provides an internal structural support. Bacteria do not have a cytoskeleton and must be very small. All of the vi
sible plants and animals are eukaryotes.

paramecium-diag
Figure 2
Paramecium



 Carbonaceous-Foliage
Figure 2a
Cell Size Scale
Note relative size of Mars "fossils"


The nucleus and cytoskeleton are only a few of the features shared by all eukaryotes, which the following table summarizes.

Table 1
Common Features of All Eukaryotes

 Mitochondria
Mitochondria, sometimes called the "cellular power plants" are the reason why all eukaryotes are oxygen-breathers03. They "burn" oxygen (forming water) to produce ATP, the "batteries" universally used to provide energy for cell metabolism. Many bacteria also have mitochondria, but the eukaryote mitochondria are much larger and more advanced.

Mitochondrion
Figure 3
Typical Mitochondrion
Wiki
 
The mitochondria contain their own bacteria-like (circular) genetic material, and reproduce independently from the cell's own genetic material. This is one reason why biologists conclude that it originated as a bacterial cell which took up residence in an ancestral eukaryote.

Cytoskeleton
The cytoskeleton (Figure 4) is a unique feature of the eukaryotic  cell that provides a number of important features.
• Structural support throughout the cell's interior
• Internal transport network connecting all cell components


Cytoskeleton
Figure 4
Eukaryotic Cytoskeleton
Blue = nucleus; green  = microtubules; red = microfiliaments

There is no comparable structure to be found in bacteria; it leads to major improvements found only in eukaryotes:

1.  Another characteristic feature of the eukaryotic cell is the fact that it has internal structure. Bacteria come in only a few typical shapes that can be characterized as "balloon shapes" (Figure 5) that form as a result of turgid pressure. These shapes are what result when the surface membrane provides the only structure, and the shape is maintained by turgid pressure -- spheres, tubular shapes and spiral shapes. There is little or no internal structural support.

Bacterialshapes-Merc
Figure 5
Bacterial Shapes
Note: limited to balloon-like shapes "inflated" by osmotic (Turgor) pressure.
From the Merck Manual

In contrast, a proper cell has a cytoskeleton for internal structural support. The cytoskeleton allows the proper cell to assume a fantastic range of shapes and sizes (Figure 6), including sizes that are easily visible to the naked eye.


Ciliates
Figure 6
Ciliate Shapes (Eukaryotes)
Bar at right is 1 mm.
Source: P. Eigner
used by permission

2. The movement of food and waste in bacteria is limited to random diffusion. In eukaryotes these movements are controlled by a highly developed transport system moving along microtubules, which involves the Kinesin linear motor molecule.  See the Kinesin Transport Molecule box below. The consequence is that bacteria are limited in size to a maximum on the order of 10 µm, the practical limit of diffusion (Figure 7)3.1. In contrast, eukaryotic cells can be relatively very large.
Bacteria Size
Figure 7
Bacterial Size

Internal Membranes;
Nucleus
the logical order is: first the cytoskeleton, then nuclear membranes attached to the cytoskeleton, which in turn form the organelles including the most prominent visual one, the nucleus.

Internal membranes are used to provide a special local environment to conduct specialized tasks. An example in bacteria is the chloroplast of cyanobacteria used in photosynthesis. Eukaryotes make a much richer use of membranes, which form a number of specialized organelles that are joined by the cytoskeleton. The nucleus is the most visible organelle, bounded by a specialized membrane that uses special access ports to control traffic to the nucleus interior. Many other organelles also exist, each with its own specialized functions. Not all organelles (other than ribosomes and the nucleus) exist in every eukaryote.

The nuclear membrane is a double membrane.

The separation between transcription and translation
 ?? the cytoplasm outside the nucleus is structured by the cytoskeleton. So where does the genetic info go? Inside its own environment inthe nucleus. Doesn't therefore use (?) the transport mech of the cytoskeleton (so how does the mRNA etc move???)

Organelles
The organelles are small "factories" contained within the eukaryotic cell. Each organelle is bounded by a membrane to form a controlled microenvironment that specializes in a particular cell function. Figure 8 shows some of the organelles found in all eukaryotes. See the box on Organelles for a description of some of these organelles and their functions.

Eukaryote Membrane Structure
Figure 8
Eukaryote Membrane Structures


Chromosomes
All bacteria and archaea have circular DNA, in which the genetic information is contained in complementary strands of nucleotides forming the DNA "ladder". All eukaryotes have the DNA in chromosomes, each containing two complete copies of its complement of DNA. In the "condensed" (compact) state a chromosome appears in the diploid "X" form as shown in Figure 9. Chromosomes can also be a single (haploid) strand of DNA (a chromatid). In sexual reproduction, the egg and sperm are both haploid, and  they combine to form the diploid chromosomes in the fertilized egg.
chromosome
Figure 9
A Chromosome

Histones are proteins that assist in packing the DNA "spools around which DNA winds". Highly "conserved" proteins -- throughout eukaryotes and some archaea, but not found in bacteria. They are "spindles" that the dna wraps around so that it can be stored in compact form in the chromosomes. Chromatin is DNA + histones.

Protist chromosome numbers: amoeba 12 chromosomes; paramecium 50 chromosomes; some rhizopods reported to be as high as 1500.

Mitosis
cell duplication
All eukaryotes duplicate by a complex process called mitosis. This is a non-sexual form of duplication in which a parent cell divides into two eactly identical daughter cells. In prokaryotes, duplication is done by a different and simpler process called binary fission. In mitosis the parent first duplicates the chromosomes and then uses special cytoskeleton structure called the mitotic spindle to separate the new chromosomes to opposite sides of the cell, after which the cell divides using a process called cytokinesis.
Mitosis
Figure 10
Mitosis
green = mitotic spindle; orange = chromosomes;
blue = peroxisomes.

Multicellular species all begin as a single cell and grow by mitosis, which is also used for repair and replacement of cells in mature bodies.
Sex: Meiosis Sexual reproduction is by meiosis. It is associated with chromosomes, so no prokaryotes conduct meiosis, or can reproduce sexually. However bacteria can share dna between individuals through genetic recombination and in other ways that may achieve results comparable to sexual reproduction.

Meiosis is the stage of the sexual cycle in which a diploid cell, ordinarily having two complete sets of chromosomes, gives rise to haploid cells (gametes) each having one set of chromosomes.  Two such gametes arising from different individual organisms may fuse by the process of syngamy (fertilization) to generate a new diploid individual, thus completing the sexual cycle.

All eukaryotes except some members of the protist group excavata have meiosis
3.2.





Cell Signaling: is there something unique shared by eukaryotes?


Ubiquitin
Ubiquitin is a small regulatory protein (76 amino acids) found in all eukaryotes but entirely absent in prokaryotes. It directs protein recycling (programmed death) in the proteasome.

There is such a large difference between prokaryotes and eukaryotes that the creation of eukaryotes is virtually a total re-design, a new creation on a par with with the original creation of prokaryote life. For one thing, the simplest eukaryotes have over 10 times the DNA found in the most complex prokaryote04 and are physically much larger.

The first eukaryotic cells were single-celled (the protists), as bacteria are. Multicellular structures formed by bacteria are actually individual single-celled microbes that live together and may have some cell specialization such as the nitrogen-fixing heterocysts, and akinetes. But the structural and transport features of the proper cell have the potential for far more, and thus led in time to multi-celled species, and eventually to the visible, multi-cellular plants and animals.

This anticipation of future biological innovation is a characteristic of the creation of living species. In later chapters we will also discuss the formation of homeobox and development gene packages during the Cambrian explosion (about 550 Ma), which anticipated many innovations in animal life that would occur hundreds of millions of years later.

Protection of the genetic code.  All eukaryotes have the genetic material - the DNA - in long strands called chromosomes, enclosed in a nucleus that is separated from the rest of the cell by a protective membrane. In contrast, prokaryotes - the bacteria - have looped DNA that is not separated from the rest of the cell.

The nucleus protects the DNA from damage by contact with food or cell invaders. When the DNAs genes are copied prior to building the various proteins and other complex molecules of life, the genes are processed within the nucleus to remove un-needed information, and to correct copying errors.

It is hard to overemphasize how this contrasts with bacteria. The DNA of bacteria comes in constant contact with the cell contents, and as a result is subject to both random and deliberate changes in the DNA code itself. That is how viral infection works: a virus injects its genetic material into a bacterial cell, and the material then inserts itself into the cell's own DNA. From this point the cell begins to reproduce the virus, using the cell's own genetic machinery.

Bacteria are designed in this loose genetic way because one of the strong points about bacteria is the ability to respond to environmental changes by changing its genetic make-up. Bacteria can even share segments of DNA from other bacterial species, perhaps through snips of DNA that enter the cell as food. This is why bacterial species, such as the common E. Coli have so many different subspecies, both harmful and beneficial. One biologist, Lynn Margulis, argued that the concept of species is not really appropriate for bacteria because there is so much genetic variation. She notes: "Because bacteria that differ in nearly every measurable trait can receive and permanently incorporate any number of genes from each other or from the environment, the concept of 'species,' applicable to named eukaryotes, seems inappropriate for the Prokarya. For higher species, that advantage is overshadowed by the need to guard the genetic code's accuracy. The code is much more complex, and changes are very likely to be unwelcome. So for eukaryotes, the emphasis is on limiting changes in the code and controlling the accuracy when the code is copied. This work takes place within the nucleus.

More remarks along these lines will be made in the next chapter.

The Kinesin Transport molecules. In prokaryote cells, internal cell transport is accomplished by diffusion (see the box). In contrast to this, internal cell transport in eukaryotes uses the kinesin motor molecule in a "motorized" transport system  (see the box). The kinesin transport molecules are  designed to use electrostatic attraction to move two "legs" of the molecule along tubulin.


fractal

END NOTES

Alternative Splicing: "a process by which the exons of the RNA produced by transcription of a gene (a primary gene transcript or pre-mRNA) are reconnected in multiple ways during RNA splicing. The resulting different mRNAs may be translated into different protein isoforms; thus, a single gene may code for multiple proteins. Alternative splicing occurs as a normal phenomenon in eukaryotes, where it greatly increases the diversity of proteins that can be encoded by the genome ... Alternative splicing was first observed in 1977." This is a use of "junk" (non-coding) dna. Non-coding DNA seems to be restricted to Eukaryotes. (??) It seems to be a characteristic of Eukaryotes and is used in gene regulation (prokaryotes do not typically have non-coding dna). Cf "The C-Value Enigma."

In Eukaryotes, most DNA is noncoding -- that is, it does not code for genes that are translated to form proteins. Bacteria have, in general, much smaller amounts of noncoding DNA.

The junction of duplicated chromosomes is called the centromere (the attachment point for microtubules (the mitotic spindle attachment) during the separation of the chromosome strands during duplication. The centromere appears to be non-coding dna. About 95% of the human dna is non-coding.  See: http://en.wikipedia.org/wiki/Repeated_sequence_(DNA)  http://en.wikipedia.org/wiki/Eukaryotic_chromosome_fine_structure.

Dr. Ronald E. Hurlbert, Washington State University Microbiology 101/102 Internet text.   Chapter IX Microbial Exchange of Genetic Material. [MAY BE APPROPRIATE FOR EVOLUTION CHAPTER].


The Cytoskeleton
Structure in the "amorphous protoplasm"
   
When mid-19th Century biologists looked at cells through a microscope, they saw the cell protoplasm as an amorphous jelly. The prominent evolutionary proponent Ernst Haeckel viewed the protoplasm as the "life force" of living cells, and assumed that it, and therefore the essence of life, to be essentially simple05. However, by the end of the 19th century it was generally understood through numerous scientific investigations that there is much more structure and content to the protoplasm06.

The basic problem is the resolution of light microscopes which can only see things down to a dimension of a few microns -- the size of small bacteria. Therefore the elaborate structure within a bacterial cell was almost completely invisible.

The structural content of the "protoplasm" is built up of cytoskeleton threads that are only a few nanometers in diameter (a few molecules across), and can be viewed only with electron microscopes, first built in the 1940s. Even then, the essentially colorless threads can only be viewed if they were tagged with dyes or doped with heavy atoms such as gold.

The cytoskeleton performs a number of functions in the cell (see Figure 8): it provides:
• Structure, support and spatial organization;
• Food and waste transport between cell organelles and the cell wall;
• Contraction, dilation and movement;

Cytoskeleton Diagram
Figure 8
Functions of the cytoskeleton

The food and waste transport involves the Kinesin transport molecule which is a linear motor that carrys waste and food along the microtubules which connect the cell wall and all internal organelles. All eukaryotic cells have a microtubular organizing center
, the centrosome, near the nucleus, generally associated with the golgi apparatus. The centrosome is used to anchor the mitotic bundles during mitosis. See the video on cytoskeleton microtubules.


Organelles in Eukaryotes
One of the major features of the Eukaryotic cell is the presence of a number of organelles, which are sites where specialized activities take place. The organelles are enclosed membranes that isolate an "interior" which has the environment needed to carry out the specialized activity. from the general cell contents.

The idea of isolating part of the cell to perform a special function is not new with eukaryotes. The earliest cyanobacteria used such protected environments to conduct photosynthesis -- ATP synthase, for example, is a rotary motor embedded in a closed membrane with an acidic (high
H+) interior and is powered by the flow of H+ through the motor. In addition, nitrogen fixation in specialized cells (the heterocysts) also required the provision of a specialized (oxygen-free) local environment to drive the nitrogenase molecule.

Aside from photosynthesis, many other early bacteria also had mitochondria to produce ATP from oxygen. These bacterial mitochondria did not require the cytoskeleton network, because the bacterial cell was very small and relied on ordinary diffusion to distribute products to the "work site" where they were needed.
When the production rate or the transport time was too slow, the solution was to proliferate many mitochondria throughout the cell so that local needs could be met with local industry, so to speak. A similar thing happens in eukaryotes.

In eukaryotes, the cytoskeleton with its built-in transport system allowed the cells to support many more of these specialized membrane-bound "factories", the organelles, with the ability to move the raw materials, products and waste from specialized sites to the general cell.

organelles
Figure 6
Typical Eukaryotic Cell

Organelles found in all Eukaryotes
Organelle
Function
Remark
Nucleus
Contains DNA (chromosomes)
Site of transcription (formation of mRNA)
Nuclear Membrane has pores which restrict  entry/exit to mRNA after gene transcription from the chromosomes. Protein formation takes place  outside of the nucleus.
Nucleolus
Transcribe rRNA
Assemble Ribosomes
Ribosomes form proteins from mRNA (outside of the nucleus).
Mitochondria
Production of ATP (cell energy "batteries")
Self-replication with own circular DNA and ribosomes.
"Burns" Oxygen; waste is CO2. Converts ADP to ATP. Double membrane. Inner membrane has acidic interior to drive embedded ATP synthase. Appears to live within the eukaryote as if a symbiotic bacterium -- example of endosymbiosis?
Endoplasmic Reticulum
Rough ER: Protein translation and folding
Smooth ER: ???
RER has many ribosomes attached to outer membrane.

endoplasttic reticulum animation Protein Translocation
Golgi Apparatus
Protein modification, secretion
??
golgi apparatus -- and animation
Vacuoles
package food & waste;
Maintain stable cell environment (chemical, fluid, electrolytic, acidic balance).
Vesicles
Small sacks. May form spontaneously. Liposomes are prepared vesicles
Double membrane formed by lipids (hydrophobic tail; hydrophilic head). Used to transport food and waste (with Kinesin) , or as chemical reaction chambers.



























The Kinesin and Dynein Transport Molecules:
Molecular motors.
   

The Kinesin molecule transports food and wastes between the organelles of a eukaryotic cell, moving along microtubules of the cell's cytoskeleton (Figure 9).
 
031b-kinesin
Figure 9
Kinesin motor molecule
See the YouTube animation "Fantastic Vesicle Traffic"
 
Kinesin motors were first discovered by accident in 1981
by a Dartmouth professor, Robert D. Allen, when he used a television video camera to view squid nerve fiber under a light microscope07. By adjusting the image brightness it was discovered that details could be seen that are a tenth of the size that is normally visible in a light microscope, and for the first time, it was actually possible to see little objects moving along the nerve fiber. These turned out to be kinesin moving along microtubules.

The microtubules have a "polarity" which determines the direction in which the kinesin molecule moves. The "minus" ends in a centrosome. The kinesin move preferrentially in the "plus" direction along a microtubule (away from the centrosome), and the dynein molecule moves in the "minus" direction (towards the centrosome) between the endoplastic reticulum and the golgi apparatus
08.




Modes of Internal Cell Transport
Diffusion vs. Kinesin Transport
   
Bacteria rely on ordinary diffusion to move food and waste within a cell. Diffusion depends on random movement due to molecular collisions, and is typified by the dispersion of a dye in a beaker of water (Figure 10):

031c-diffusion
Figure 10
Diffusion





Eukaryotic Reproduction
Mitosis, Meiosis and Sexual Differentiation (dimorphism).
A bacterial cell reproduces by cell division.

Because eukaryotes have a cell nucleus and the DNA exists in chromosomes instead of the circular dna of bacteria, something more complex than the bacterial cell division is needed.
...
?ALL HAVE MITOSIS? MEIOSIS? NOT
?Are all chromosomes diploid (at some stage)?

http://www.emc.maricopa.edu/faculty/farabee/biobk/biobookmito.html
Eukaryotic chromosomes occur in the cell in greater numbers than prokaryotic chromosomes. The condensed replicated chromosomes have several points of interest. The kinetochore is the point where microtubules of the spindle apparatus attach. Replicated chromosomes consist of two molecules of DNA (along with their associated histone proteins) known as chromatids. The area where both chromatids are in contact with each other is known as the centromere the kinetochores are on the outer sides of the centromere. Remember that chromosomes are condensed chromatin (DNA plus histone proteins).
chromosome
Figure 11
Chromosome Mitosis
Showing microtubule (spindle fibers??) attachment points

Q: DO ALL EUK HAVE MITOSIS?
IS MITOSIS THE FIRST STEP IN MEIOSIS? OR ARE THEY ALTOGETHER DIFFERENT?
ARE ALL CHROMOSOMES DIPLOID AT SOME STAGE IN EXISTENCE? (CONTRA BACTERIA).
"All animals have a characteristic number of chromosomes in their body cells called the diploid (or 2n) number." -- all protists too???

Eukaryote cell cycle: do all go through a diploid as well as a haploid stage???
gametes are necessarily haploid -- ?one stage in meiosis??

Wiki: The only supergroup of eukaryotes which does not have meiosis in all organisms is excavata.
==>> ALL EUKARYOES HAVE MITOSIS(???) ==> PROBABLY UNIVERSAL - e.g. in multicellular ....
==>> ALL MULTICELLED EUKARYOTES HAVE MEIOSIS!(??)

Mitosis is the basis for formation of a multicellular body from a single cell (zygote), for growth in a multicellular species, and for cell replacement or regeneration in the event of damage.

?? All eukaryotes can reproduce by mitosis -- for example that's how multicellular species grow.
?? All (?) eukaryotes (except some single-celled excavata) can also reproduce by meiosis.




Eukaryotic Error Correction and Repair
A becterial cell reproduces by cell division.


ALL EUKARYOTES???

HOW COMPARE WITH BACTERIA?


ERROR CORRECTION?
Error-detecting and correcting schemes ensure the accuracy of the dna and rna copies. In bacteria, insertions and changes to the dna code occur frequently, because the dna is located in the cell cytoplasm and can come in contact with portions of dna derived from food and viruses. In addition the transcription of the bacterial dna is more prone to errors. Overall for a bacterial dna, transcription accuracy is on the order of one transcription error per ??? codons.  In contrast, overall transcription accuracy for a eukariotic cell is on the order of one error per billion codons. [CHECK]. This still results in about ??? errors per cell per second. [CHECK]



...




Eukaryotic Signalling and Cell Regulation
#
# Both are highly regulated by elaborate sensing systems ("chemical noses”) that make them aware of the reactions within them and the environment around them.


ALL EUKARYOTES???

HOW COMPARE WITH BACTERIA?




...




How do Mitochondria work?
Mitochondria are, in one sense, the key feature, next to the nucleus, of eukaryotes, because they are the "cellular power plants" -- they generate most of a cell's requirements for ATP -- that explain why eukaryotes use oxygen as a prime engine of metabolism. (??)

How do mitochondria use oxygen? redox reactions (oxidative phosphorylation).
http://en.wikipedia.org/wiki/Cellular_respiration
http://en.wikipedia.org/wiki/Electron_transport_chain

conversion of oxygen to water
Four membrane-bound complexes have been identified in mitochondria. Each is an extremely complex transmembrane structure that is embedded in the inner membrane. Three of them are proton pumps.
...





Introns and "Junk DNA"

distinction between dna that codes for genes and other dna.
Introns absent from bacteria, present in eukaryotes and some archaea.

Alternative splicing is widely used to generate multiple proteins from a single gene

Q: do all eukar dna code for genes? (prob not -- or maybe expression is suppresses? e.g. e coli genome is huge relative to what is actually xlated???

A becterial cell reproduces by cell division.

http://en.wikipedia.org/wiki/Noncoding_DNA
http://en.wikipedia.org/wiki/Intron
http://en.wikipedia.org/wiki/Alternative_splicing

ALL EUKARYOTES HAVE JUNK DNA???

Transcription & translation regulation?

HOW COMPARE WITH BACTERIA?
...
centromere teleomere -- essential parts of chromosome. Not coding to specific genes.

Jonathan Wells The Myth of Junk DNA (2011)





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ENDNOTES

  https://www.etap.org/demo/biology1/instruction3tutor.html
Prokaryotic cells have a cell wall composed of peptidoglycan (amino acid and sugar). Some eukaryotic cells also have cells walls, but none that are made of peptidoglycan.

The flagella in eukaryotic cells are different from the flagella in prokaryotic cells. Flagella are the structures that help cells move (scientists call it motility). The flagella in eukaryotic cells are composed of several filaments and are far more complex than the flagella in prokaryotic cells.

All cells have their genes arranged in linear chains called chromosomes. But eukaryotic cells contain two (or more) copies of every gene. During reproduction, the chromosomes of eukaryotic cells undergo an organized process of duplication called mitosis. You've learned about mitosis in several previous Lessons and you'll also hear more about it later.

=====

histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes.


http://en.wikipedia.org/wiki/Biological_membrane

How do mitochondria actually work?

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FOOTNOTES

* The background is the cytoskeleton of a proper (eukaryotic) cell.

 The Proper Cell
Figure ??
The Proper Cell.
The Background shows the cell cytoskeleton, a feature
(along with the nucleus) of eukaryotic cells. A plant and
animal cell are shown in the foreground. These will be
discussed in Chapter 9.


^n01  Koonin EV: The Biological Big Bang model for the major transitions in evolution. Biol Direct 2007, 2:21; and
Koonin EV: The origin and early evolution of eukaryotes in the light of phylogenomics Genome Biology 2010, 11:209. In the first reference, Koonin writes:

"Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla."

Some of the "cases in point" listed here form the "Geneses" discussed on this website and are the subjects of some of the Sharp Points. The second reference notes that "[t]he origin of eukaryotes is a huge enigma and a major challenge for evolutionary biology."

^n01.1 Koonin (2010) op. cit. He continues, "There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not. ... PhylogenomicReductive Evolution. reconstructions show that the characteristic eukaryotic complexity arose almost ‘ready made’, without any intermediate grades seen between the prokaryotic and eukaryotic levels of organization. ... it is becoming increasingly clear that most or perhaps all of them evolved from more complex ancestral forms by reductive evolution." Regarding the last comment see the box on Reductive Evolution.


^n01.2 The six major groups of eukaryotes are (from Wiki):

Excavata Various flagellate protozoa - the only group that does not have meiosis (sexual reproduction) in all organisms. Includes slime molds which have a life cycle that includes an amoeba-like multicellular aggregation phase.
Amoebozoa Most lobose amoeboids and slime moulds
Opisthokonta Animals, fungi, choanoflagellates, etc.
Rhizaria Foraminifera, Radiolaria, and various other amoeboid protozoa.
Chromalveolata Stramenopiles (or Heterokonta), Haptophyta, Cryptophyta (or cryptomonads), and Alveolata.
Archaeplastida (or Primoplantae) Land plants, green algae, red algae, and glaucophytes.

The problem is that all of these share the unique features of eukaryotes, but they have no apparent common ancestor. Some authors, however have named the Excavata as the ancesters of all eukaryotes: see Holt and Niles, Systematic Biology,  "The Taxa of Life". The systematics of Systematic Biology use the following clade classification system under the Eukaryotes:

Supergroup Uniconta
Animalia The Animal Kingdom: Develop from a Blastula. Together with fungi they form the Opisthokonta listed in the preceeding table

Fungi

Amoebozoae The Amoebozoa listed in the preceeding table.
Supergroup Excavata Euexcavatae The Excavata listed above. The excavate is a groove that runs longitudinally on the cell surface and  associated with at least one recurrent flagellum, which set up currents in the groove  to concentrate suspended particles and move them to a cytostome.

Discicristatae
Supergroup Chromalveolata Eukaryomonadae The references are to the bag-like sacs that underlie the cell membrane and that many taxa are pigmented (photosynthetic).
The Chromalveolata listed above

Heterokontae

Alveolatae
Supergroup Rhizaria
The reference is to the fine, filose, and often branching pseudopodia in this group. The Rhizaria listed above
Supergroup Archaeplastida
The reference is to this supergroup having the chloroplasts that came from a primary endosymbiosis with a cyanobacterium.
The Archaeplastida listed above.

Modern systematics such as are represented in these tables tend to make heavy use of genetic relationships that are inferred by DNA sequencing.

^n01.3  Gross and Bhattacharya, Uniting sex and eukaryote origins in an emerging oxygenic world Biology Direct 2010, 5:53 

^n01.4 Koonin (2010), op. cit.

^n01.5   Cf. David C. Bossard The Stones Cry Out IBRI RR 57 (2006. The geologic record sometimes shows the sudden appearance of a fully formed class of animals, followed by a regression in complexity from the earlier species, rather than a progression as one would expect.

William Buckland Geology and Mineralogy Considered with Reference to Natural Theology (2nd Edition, 1837)

[p. 312] The history of Chambered Shells tends further to throw light upon a point of importance in physiology, and shows that it is not always by a regular gradation from lower to higher degrees of organization, that the progress of life has advanced, during the early epochs of which geology takes cognizance. We find that many of the more simple forms have maintained their primeval simplicity, through all the varied changes the surface of the earth has undergone; whilst, in other cases, organizations of a higher order preceded many of the lower forms of animal life; some of the latter appearing, for the first time, after the total annihilation of many species and genera of a more complex character [emphasis added].

Edward Hitchcock, Religion of Geology and its Connected Sciences (1851)

[p. 255] "But a special appeal has been made on this subject to geology. The history of organic remains, it is thought, corresponds to what we might expect, if the hypothesis of development is true. In the oldest rocks we find chiefly the more simple invertebrate animals, and the vertibrated tribes appear at first in the form of fish, then of reptiles, then of birds, then of mammals, and last of all of man. What better confirmation could we wish than this gradually expanding series? ... But the tables are turned when we descend to particulars. ... for the onchus (a genus of fish) has been found in the ... lower silurian rocks [modern Ordovician -- dcb] of Bala. (¶) It is also a most important fact, that this fish of the oldest rock was not, as the development scheme would require, of a low organization, but quite high on the scale of fishes. The same is true of all the earliest species of this class ... the very oldest species that are well determined fall naturally into an order of fishes which Owen and Müller place, not at the bottom, but at the top of the whole class."

Hugh Miller, The Old Red Sandstone (7th Edition, 1858)

p. 40 "The argument is a very simple one. Of all the vertebrata, fishes rank lowest, and in geological history appear first. We find their remains in the Upper and Lower Silurians, in the Lower, Middle, and Upper Old Red Sandstone, in the Mountain Limestone, and in the Coal Measures ; and in the latter formation the first reptiles appear.* Fishes seem to have been the master existences of two great systems, mayhap of three, ere the age of reptiles began. Now fishes differ very much among themselves : some rank nearly as low as worms, some nearly as high as reptiles ; and if fish could have risen into reptiles, and reptiles into mammalia, wc would necessarily expect to find lower orders of fish passing into higher, and taking precedence of the higher in their appearance in point of time, just as in the Winter''s Tale we see the infant preceding the adult. If such be not the case —if fish made their first appearance, not in their least perfect, but in their most perfect state —not in their nearest approximation to the worm, but in their nearest approximation to the reptile —there is no room for progression, and the argument falls. Now it is a geological fact, that it is fish of the higher orders that appear first on the stage, and that they are found to occupy exactly the same level during the vast period represented by five succeeding formations. There is no progression. If fish rose into reptiles, it must have been by sudden transformation — it must have been as if a man who had stood still for half a lifetime should bestir himself all at once, and take seven leagues at a stride. There is no getting rid of miracle in the case — there is no alternative between creation and metamorphosis. The infidel substitutes progression for Deity ; Geology robs him of his god.

Hugh Miller, Footprints of the Creator
(3rd Ed. 1858)

[p. 307] "There is geologic evidence, as has been shown, that in the course of creation the higher orders succeeded the lower. We have no good reason to believe that the mollusc and crustacean preceded the fish, seeing that discovery, in its slow course, has already traced the vertebrata in the ichthyic form, down to deposits which only a few years ago were regarded as representatives of the first beginnings of organized existence on our planet, and that it has at the same time failed to add a lower system to that in which their remains occur. But the fish seems most certainly to have preceded the reptile and the bird; the reptile and the bird to have preceded the mammiferous quadruped; and the mammiferous quadruped to have preceded man."

[p. 308] "All the facts of geological science are hostile to the Lamarckian conclusion, that the lower brains were developed into the higher. As if with the express intention of preventing so gross a mis-reading of the record, we find, in at least two classes of animals, - fishes and reptiles, - the higher races placed at the beginning: the slope of the inclined plane is laid, if one may so speak, in the reverse way, and, instead of rising towards the level of the succeeding class, inclines downwards, with at least the effect, if not the design, of making the break where they meet exceedingly well marked and conspicuous."

Louis Agassiz, Contributions to the Natural History of the United States of America (1860), Vol I, p.

[Vol I, p.117] "Recent investigations in Palaeontology have led to the discovery of relations between animals of past ages and those now living, which were not even suspected by the founders of that science. It has, for instance, been noticed, that certain types which are frequently prominent among the representatives of past ages, combine in their structure, peculiarities which at later periods are only observed separately in different, distinct types. Sauriod Fishes before Reptiles, Pterodactyles before Birds, Ichthyosauri before Dolphins, etc. (¶) There are entire families, among the representatives of older periods, of nearly every class of animals, which, in the state of their perfect development exemplify such prophetic relations, and afford, within the limits of the animal kingdom, at least, the most unexpected evidence, that the plan of the whole creation had been maturely considered long before it was executed. Such types, I have for some time past, been in the habit of calling prophetic types. The Sauroid Fishes of the past geological ages, are an example of this kind. These Fishes, which have preceded the appearance of Reptiles, present a combination of ichthyic and reptilian characters, not to be found in the true members of this class, which form its bulk at present. The Pterodactyles which have preceded the class of Birds, and the Ichthyosauri which have preceded the appearance of the Crustacea, are other examples of such prophetic types. [emphasis added]"

Edward & Charles Hitchcock, Elementary Geology (1860),

p. 367 "Thirteenth Law.--Many of the fossil animals had a combination of characters which among living animals are found only in several different types or classes. Agassiz very appropriately calls such types Prophetic Types. For they form the pattern of animals that were to appear afterward."

Alexander Winchell, Sketches of Creation (1870).

p. 314 "It is a most interesting fact in the history of the animal creation that Nature advertised her plans in the very earliest creative acts. In our study of the relics of the primeval ages we do not find the grand and fundamental purposes of Infinite Wisdom unfolding themselves by degrees as type after type of organic life made its advent upon our planet. ...Nature had her plans, and these were mature in the very beginning."

James Dana, Manual of Geology, (1896)

p. 1031 "No successional lines among Insects appear to have passed between the higher tribes of Neuropters, Orthopters, Coleopters, Lepidopters, Hymenopters; but each was derived from some early [unwitnessed - dcb] comprehensive forms."

^n01.5a Protist is a term coined by Ernst Haeckel -- see Natürliche Schöpfungs-Geschichte - The History of Creation, p.200 (first published in 1868).

^n01.6 
Gross &
Bhattacharya op. cit. "Were eukaryotes forged by an oxygen crisis?"


^n02  The name is inspired by the book, How Life Began: Evolution's Three Geneses by Alexandre Meinesz (2008), although my enumeration of the "Geneses" is somewhat different. His three geneses are: bacteria, eukaryotic cells, and multi-cellular organisms.

^n03  Some authors speculate that eukaryotes were "forged by an oxygen crisis." (Gross and Bhattacharya Biology Direct 2010, 5:53) The "crisis" was the need to provide a sink for excess waste oxygen, as noted above.

^n03.1  The largest bacterium is Epulopiscium which lives in the gut of a tropical fish. Its size is 80 x 600µm. It appears to be able to survive despite the problems of diffusion because the medium is very rich in nutrients. [Schulz and Jorgensen, Big Bacteria, (2001).] Softpedia claims the largest is 700µm in length -- Epulopiscium. This bacterium solves the diffusion problem with 85,000 copies of its DNA, so all protein synthesis can be done locally.

^n03.2  See table at footnote #1.2.

03.3  ^n03.3  nn

03.4  ^n03.4  nn

03.5  ^n03.5  nn

03.6  ^n03.6  nn

03.7  ^n03.7  nn

03.8  ^n03.8  nn

03.9  ^n03.9  nn


^n04  Scott F. Gilbert, Developmental Biology, 5th Ed. p.5. See the Chart in the box Size Limits of Very Small Microorganisms in Chapter 6. The remark by Gilbert applies to plant and animal genomes, as compared with bacterial genomes.

^n05 Ernst Haeckel, The History of Creation (1876): Vol. I, On the Protoplasm Theory, p.99ff. [100] "protoplasm (the original slime) is the most essential (and sometimes the only) constituent part of the genuine cell." [p406] "the general explanation of life is now no more difficult to us than the explanation of the physical properties of inorganic bodies."

John Theodore Merz, A History of European Thought in the Ninetenth Century (1907-1914):  Vol. II. Chapter 10 "On the Vitalistic View of Nature" pp 444ff. The term "protoplasm" was coined by Hugo von Mohl in 1846 for the "visible but apparently structureless forms of cells and protoplasm."

^n06  George L. Goodale, Protoplasm and its History (Botanical Gazette Vol. XIV No. 335, Oct. 1889) Pdf (2.8 Megs) "Protoplasm is no longer regarded by any one in any sense as a comparatively simple substance. ... By better methods of staining, and by the use of homogeneous immersion [compound light microscope = DCB] objectives, the apparently structureless mass is seen to be made up of parts which are easily distinguishable. There has been, and in fact is now, a suspicion that some of these appearances, under the influence of staining agents, are post-mortem changes, and do not belong to protoplasm in a living state. But it seems to be beyond reasonable doubt that protoplasm is marvellously complex in its morphological and physical as well as its chemical constitution."

^n07 The description  by Pamela Clapp of the discovery of the Kinesin molecule neglects to note that Dr. Allen's wife Nina worked closely with him and participated in the discovery (or that the Allens were Dartmouth professors at the time of the discovery).

^n08 http://en.wikipedia.org/wiki/Microtubule_organizing_center. See the video Cytoskeletal Motor Proteins Part 1 Kinesin (43 min.), Part 2 Dynein (25 min.), Part 3 Mitosis (34 min.) narrated by Ron Vail, UCSF.

09   ^n09  n

10   ^n10  n

11   ^n11  n

12   ^n12  n

13   ^n13  n

14   ^n14  n

15   ^n15  n

16   ^n16  n

17   ^n17  n

18   ^n18  n

href="#n19">19   ^n19  n

20   ^n20  n


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REFERENCES


Bruce Alberts, et al. Essential Cell Biology: An Introduction to the Molecular Biology of the Cell (1998),
David C. Bossard, A Fit Place to Live. (2003)
David C. Bossard The Stones Cry Out IBRI RR 57  (2006). 
Wallace S. Broecker, How to Build a Habitable Planet (1985)
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
George L. Goodale, Protoplasm and its History (Botanical Gazette Vol. XIV No. 335, Oct. 1889) Pdf (2.8 Megs)
Ernst Haeckel, The History of Creation (1876): Vol. I On the Protoplasmic Theory, p.99ff.
Robert Hasselkorn, The Cyanobacterial genome core and the origin of photosynthesis (Proceedings of the National Academy of Sciences, 2006)
Dr. Ronald E. Hurlbert, Washington State University Microbiology 101/102 Internet text.
D. T. Johnston et al, Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age (Proceedings of the National Academy of Sciences, 2006)
Koonin EV: The Biological Big Bang model for the major transitions in evolution. Biol Direct 2007, 2:21
Koonin EV: The origin and early evolution of eukaryotes in the light of phylogenomics Genome Biology 2010, 11:209

Lynn Margulis and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The most recent edition of this work has been renamed Kingdoms and Domains (2009) by Lynn Margulis and Michael J. Chapman.
John Theodore Merz, A History of European Thought in the Ninetenth Century (1907-1914)
Harold J. Morowitz, Beginnings of cellular Life, Yale University Press, (1992).
J. Willliam Schopf, Cradle of Life: The Discovery of Earth's Earliest Fossils (1999).
Peter D. Ward &  Donald Brownlee, Rare Earth: Why Complex Life is Uncommon in the Universe. (2000)


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    Posted 20 Decembe 2011