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    Feed the Geek: Biology Basics.

    Dear Readers - please do not reply to this post. If you have feedback or critique concerning content pm me, this is more than welcome - there is a lot for me to get through and this thread will get far too long otherwise. Genuinely interested in all feedback, especially concerning errors in my text.

    Dear mods - if I could PLEASE have this thread to myself for a few months I could get a very nice bio basics tutorial happening.

    Learning about learning.

    This first post is to introduce me and my aims here, and help you through this thread and other stuff you might encounter in the links and posts of this forum.

    The internet has made it possible to get a great education at home – or fill your head up with shit.

    I wound up at university due to my lifelong love of nature and obsession with marijuana. Growing was outdoor, then aquaponics, then organics and now organic no till. The quest for knowledge, and the ability to share this knowledge have sustained me with energy for a time, but I realized after a long struggle with my ego that all my eclectic bits of knowledge weren’t doing me that much good, I was an authority on fuck all, and a lot of what I’d learnt from the internet (including this and other weed forums) was crap. I was getting frustrated with my lack of discernment and my lack of a life. I needed to go back to school. I needed critical thinking skills, and to learn to separate crap from cake.

    I’ve included a lot of descriptions of words used in biology - it’s as much learning another language as it is learning a science. You may find it helpful to keep another tab open with Wikipedia and examine the new words as you go to help understanding. Spurr has posted a helpful glossary resource it would be good to familiarize yourself with as well. I make no apologies for appearing in any manner patronizing, I am merely trying to give everyone a reasonable chance of grasping the material at hand. Sometimes having things spelt out can be irritating, I know it is for me, but often when we already ‘know’ something, we miss half the learning associated with it. If you feel you are being talked down to check your ego in at the door. If this is simple to you, great! You don’t need it. Perhaps you could be writing an article instead. It was only a short space of time ago most of this was unknown to me.

    Botanical nomenclature: Words in italics like Amanita muscaria are names of an animal, plant, microbe, or fungi - in this case a fungi. The two parts of the name describe genus (Amanita) and species (muscaria). A. muscaria is the same name but now it is abbreviated - this form may be used after the name has been introduced in full. Amanita sp. is an amanita, but species is unknown or unnamed. Amanita spp. (note two p’s in spp.) is a more general term including all known amanita species in the context given. Only the genus and species names are given in italics. When handwritten, the two words are Underlined individually as writing in italics is difficult.

    Why would this level of detail be important? Well, say you go mushroom picking… Amanita muscaria is Fly Agaric, containing a drug. Amanita sp. could be a drug (A. muscaria), it could be delicious food (A. caesarea), or a deadly poison Death Cap (A. phalloides). Amanita spp. could be all of the above, or more, or none of the above according to the context.

    Names ranking higher than genus are typically not italicized. From the bottom to top ‘ranking’ the system covers: species, genus, family, order, class, phylum, kingdom and domain.

    Why would all that detail interest you? Well, each step of the name gives details about the organism. By the time you get down to genus you know a lot about an organism already. Eg: Amanita muscaria.

    Domain: Eukarya - an organism whose cells contain complex structures enclosed within a membrane.

    Kingdom: Fungi – all have extracellular digestion and cell walls that contain chitin.

    Phylum: Basidiomycota - can be recognized by distinctive fruiting bodies, or by the formation of an anatomical hyphal feature - the clamp connection.

    Class: Agaricomycetes – this is under debate for proper classification right now so I leave it to the geeks to finish their arguments and give us a definition. DNA testing is moving a lot of fungi about from previously ‘defined’ classifications.

    Order: Agaricales – Gilled mushrooms.

    Family: Amanitaceae - usually found in woodlands. They emerge from an egg-like structure formed by the universal veil.

    Genus: Amanita - The genus Amanita contains about 600 species of agarics including some of the most toxic known mushrooms found worldwide. This genus is responsible for approximately 95% of the fatalities resulting from mushroom poisoning, with the death cap accounting for about 50% on its own.

    Species: muscaria - The quintessential toadstool, it is a large white-gilled, white-spotted, usually deep red mushroom, one of the most recognizable and widely encountered in popular culture. Several subspecies, with differing cap colour, have been recognised to date. Genetic studies published in 2006 and 2008 show several sharply delineated clades which may represent separate species.

    As you see, a lot of information is derived from knowing an organism’s classification. This is a valuable tool in biology, try it sometime with a species you want to learn about. Enter the name in wiki, then on the right hand side a box with the classifications comes up. Click on Domain, learn what it is, when satisfied with that click the back button, then click on kingdom, learn some more, back button, etc… (almost) all of the A. muscaria information above was picked up in 5 minutes on Wikipedia plus tons of other information about the species and all the ranks it belongs to. Wikipedia is not allowed for scientific referencing, but a few of my professors use it for a source. My rule of thumb is, if the wiki article is a stub, or doesn’t have a lot of references, proceed with caution. Otherwise wiki is an awesome resource for learning. I crosscheck with other sources and check references if I have to be sure of something.

    Anyways, if it looks like a big word and it’s not in italics, it’s a big word. If it is in italics, it’s probably the name of something.

    The best way to learn things is in threes. Preview, study and review. By finding a new word, looking at the context and pondering the meaning… you preview the concept – what is it, how does it apply to what I know, do I know of any examples of this or is it new to me? Generate questions and thoughts on the unknown subject. Then, by reading on, either in the post or in another source for more information, you enter the period of study in which you have a receptive attitude towards the subject. Try to grasp the concept, do not worry if you do not at first, sometimes it takes retrospect, or more pieces of the picture, before things start to click. Then review… I find the review period is best after a rest from study, a cup of tea, or a sleep, but no longer than 24 hours after study or 60% of the information just vanishes. A review involves skimming back over the original text, rechecking your grasp of new terms, and having a think about how it fits in with other knowledge you have. Each round of reading and thought adds new synapse associations in your brain reinforcing the retention. Recent research shows even old farts like me can generate not only new synaptic pathways in the brain, but entire new brain cells. Never too old to learn new tricks even if, like me, you’re toasted most of the time you study. Writing notes, speaking terms out loud, putting on loud old school punk and jumping round the place with notes in front of me - all very effective at adding new neuronal pathways, reinforcing the learning process.

    I have an agenda: to promote knowledge for those who seek it that it might be applied to empower people to improve their circumstances long term.

    This leads me to ask myself a question – do I use this science knowledge to help myself practically? So far I’ve proved my soil doesn’t need N top ups so I saved myself money and had a good laugh at fert pushers expense, I recognize organisms that are useful to me - medicinal fungi and plants I never knew existed grow in my yard, food plants, fertilizer plants, N fixing trees, a whole array of useful environmental services at my disposal – all I needed was the knowledge. The garden is beginning to grow itself in places. I’ve learned to seed beets – wait for the second year – lol. It seems every day at uni I go AHHH, that’s why! Learning how plants grow I spot crappy pruning at the store when I buy plants, and avoid problems in future with branch crowding etc that I used to get. In the future I see myself being a very effective consultant applying a blend of many disciplines to sustainable food production systems. Do I think the education is worth it? Yes, because I have a goal, to educate and empower, to design sustainably - I’m going to put a dent in pollution and the purses of corporate pushers. As I stated before "The internet has made it possible to get a great education at home – or fill your head up with shit.". Every man and his dog is trying to sell something and they’ve learned to blog it and write ads that look like genuine articles. When you add to this the corporate influence on science, it’s easy to see why science can get a bad rap. It’s in many people’s personal interests to try and rubbish science or make rubbish science – to push their rubbish! Learn trusted sources, and learn their trusted sources.

    The reference materials for the following posts are all based from: Campbell, Biology, 8th Edition; Raven, Plant Biology, 7th Edition; plus notes from a series of lectures on plant biology - unless otherwise referenced in individual posts. Raven is the best option for those interested in plant biology if you’ve done a bit of pre-university biology you should be fine with it. Any biology student, formal or informal, will also find Henderson’s Dictionary of Biology to be an invaluable resource. Good resources are crucial for learning. Be fussy about what you read and view, research and discuss it.

    I hope you enjoy this material as much as I enjoy putting it together.
    I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
    My tomatoes make me completely delusional.

    I'm going to make it a point to say how awesome you are for referencing the Campbell bio book. That book is simply the best general biology book out there. Thumbs up to you sir. Me likey references.


      In the beginning…

      The Earth is 4.5 Billion years old, give or take a few days. For 600 million years there was nothing but meteoric bombardment. Imagine that. Every morning you get up and draw the curtains, bombardment again, can’t go out. Turn on the news – bombardment, the weather, more freakin bombardment, for 600 million years nothing but bombardment happening till finally, one side must have surrendered or something, and the bombardment stopped. Somewhere shortly after this time life poked a figurative cilia up, some single celled, suspected anaerobic, self replicating assembly of organic molecules, and life was born.

      Evolution is the overarching theme to all of biology and ties it all together. Still hotly debated to this day, yet evolution has withstood scientific testing thousands of times in a myriad of different ways and consistently proves true. We have thousands of missing links today, and more being uncovered all the time. Science does not suppose on the existence or non existence of god however; science deals with what is testable, like the age of the planet, and the DNA that ties all of life together. How life actually originated we still do not know exactly, but we have got close...

      Urey and Miller’s 1952 experiments mimicking early Earth’s conditions yielded many organic compounds including amino acids, sugars, lipids, and precursors for nucleic acids. These are the building blocks for life. More on this and experiments that followed the original can be found here:

      Craig Venter earlier this year copied out the DNA for an organism on a computer and then machines assembled the entire genome which was transferred into another cells ‘empty shell’ which was then “booted up” and transformed into the organism the code was written for… “We report the design, synthesis and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including “watermark” sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.”

      We can form most of the hardware in a lab (pre-cells), and we can now write the software (DNA) for entire organisms in the laboratory. What we cannot yet do, is connect the dots between the two, how did life first get it’s ‘spark’, how did a pre cell become a bacteria? We don’t yet know. It’s incredibly complex, but that’s not stopped us before.

      Bacterial conjugation and plasmid transfer vectors (in a future post, or look it up now) explain a lot about how DNA can be moved about from single celled organism to organism and as DNA codes for things, it also explains in part how such a variety of bacterial life forms can be found.

      Among the single cells that existed very early on our planet, a new group came to prominence about 3.5 billion years ago – these organisms made oxygen. Many of the anaerobes died off, some were out of reach of oxygen forming the pockets of archaean extremophiles we find and speak of in awe today. A suspected cyanobacteria was the cause of this oxygen, photosynthesis had begun to change the planet.

      Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
      Craig J. Venter et al.
      I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
      My tomatoes make me completely delusional.


        Origins of Land Plants.

        NOTE: Aquatic 'plant' looking species, including seaweeds, are not plants, they are algae. Some terrestrial plants have submerged root zones. Some plants are thus aquatic. I think of them more as aquatic/terrestrial and perhaps someone might be able to define this better for me. Fully submerged ‘plants’ are typically algae. Nature however, tends to present exceptions to every rule we set to describe it.

        The first land plants are thought to be descendants of a charophycean green algae (CGA) that had a mycorrhizal partnership with a zygomycete fungi.

        CGA is found amongst both phytoplankton and freshwater biofilms, also an assortment of terrestrial habitats including tree bark and desert surfaces. Currently, six extant (still alive today) groups of CGA are recognized. Of these six the Charales are getting much attention. Charales are an order of freshwater algae. A fascinating thing one can do with a Charale is get a slice of it fresh and put it under the microscope and observe the cytoplasmic streaming. This is rapid movement of the cytoplasm and contents around the algae’s cells. Amazing to watch. Oxygen weed works perfectly. Plenty of other freshwater 'plants' (algae!) will too.

        CGA and plants share several features. Chlorophyll a as the primary photosynthetic pigment, and chlorophyll b and carotenoids as accessory pigments. They also store starch inside of their chloroplasts whereas other photosynthetic organisms deposit it outside. Plants and a few species of green algae are also the only organisms that form a phragmoplast (bits in centre of cell that become cell plate) and cell plate (central structure that is created during cell division, becomes cell wall between new cell and old) during mitosis (asexual cell division making exact copies). Recent studies of gene content, intron content (pieces edited out of genes as they are made in the nucleus), gene order and insertions/deletions in coding areas show the charales to be sister to a clade (an organism and all its descendants) including, amongst others, land plants. (Turmel, 2006, 2007). What this means is Charales and land plants shared a common ancestor, one branch becoming the freshwater algal ancestor, another becoming the ancestor of land plants.

        Zygomycete fungi: A common example is Rhizopus stolonifer (bread mold). They are mostly terrestrial in soil or on decaying organic material. Some are parasites of plants, insects, and small animals, while others form symbiotic relationships with plants. Amongst the plants they form mycorrhizal partnerships with are the Bryophyte Phylum, the most simple form of terrestrial plant.

        It is considered that fungi made land first. Plants themselves only arrived on land around 475 million years ago. This lends the question, what was the fungal diet? Lichen (algal or cyanobacteria/fungi partnerships) are known to consume mineral rock, while fixing atmospheric nutrients and water. Animals had been around for 125 million years prior to land plants, and bacteria a good 3 billion years before that. Shorelines where organic matter like algae and animals was lifted up in tides would have provided initial habitat for microbial invasion of the land. I suspect somewhere in the rotting weeds of a damp river or lake shore after flooding a zygomycete and charophycean algae that had previously joined forces in water managed to survive the land. However it happened, plants came to be on the land, and once again the planet was changed profoundly.

        The Chloroplast Genome Sequence of Chara Vulgaris shed light into the closest green algal relatives of land plants. Turmel, M & Lemieux, C 2006. Mol. Biol. Evol. 23: 1324-1338.

        The Green Algal ancestry of land plants as revealed by the chloroplast genome. Turmel, M. Pompert, J.F. Charlebois, P. Otis, C & Lemieux, C. International Journal Of Plant Science 168: 679-689.
        I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
        My tomatoes make me completely delusional.


          Backtracking a bit.

          Before we get onto plants. Plants are Eukaryotes, which came after Prokaryotes, how did we go from one to the other?

          Prokaryotes: Including the domains Bacteria and Archaea. Single celled organisms. They have no membrane bound organelles (organs inside of a cell), they do have ribosomes (read mRNA code and synthesize proteins) but these are smaller in size than in Eukaryotes. They lack a cell nucleus and nuclear envelope (double membrane surrounding nucleus) rather having a nucleoid region within the cytosol (liquid within cells). Division is by binary fission (asexual reproduction). Variety in these organisms is due to mutation (huge numbers and fast generational turnover make the relatively low occurrence of mutation a major contributor to variety in prokaryotes) and several other means including direct cell – cell conjugation, plasmid and viral vectors.

          Eukaryotes: Single celled (eg: protists) or multiple celled organisms (eg: plants, fungi and animals) consisting of cells with membrane enclosed organelles, a clearly defined nucleus with nuclear envelope, and mitotic (asexual, making identical copies) and meiotic (sexual, leading to genetic recombination) division.

          How eukaryote cells arose from prokaryote cells has long been under study. The theory of fusion held weight for a long time, that phagocytosis (one cell engulfing another as seen by amoebae) occurred to a cell which was protected from digestion, but made useful metabolites. The digested cell found metabolites it could use, and symbiosis over time ‘fused’ the two (or more) life forms as one.

          An interesting seemingly related but not so relevant aside: Elysia chlorotica is a sea slug that engulfs algae and keeps plastids from the algae plus some DNA for itself. It also has photosynthetic DNA in its own genome, possibly from previous digestion of photosynthetic organisms. The result is a photosynthetic sea slug that can greatly reduce eating or even cease to eat entirely! It is not entirely sea slug though, some of its plastids are algal. Foraminifera (amoeboid protists) exist as single celled animals with several species also ingesting and using algal photosynthetic equipment, some of these have been recorded to grow in biomass photosynthetically without need for further ingested nutrition. This ‘evidence’ is not valid to the origins of eukaryotes though, however interesting it is. These are eukaryotes utilizing eukaryotes. And furthermore, they do not reproduce the plastids, their young must graze their own. How did the prokaryotes eventually give rise to eukaryotes?

          Last week was published findings by scientists (Devos, Reynaud) that may have put paid to the fusion theory, and suggest an intermediate or 'missing link' cell existed all those billions of years ago. PVC bacteria, members of which are commonly found in today's sewage treatment plants or acid bogs, represent an intermediate type of cell structure. "The structure of PVC suggests that it is an ancestor of a 'missing link' cell which connected prokaryotic to eukaryotic cells along an evolutionary path all those billions of years ago," says Devos.

          There may have been several paths from A to B. I look forward to further research, specifically the molecular phylogeny of these intermediate organisms.

          Intermediate Steps.
          Damien P. Devos and Emmanuel G.Reynaud.
          Science 26 November 2010: Vol. 330 no. 6008 pp. 1187-1188 DOI: 10.1126/science.1196720
          I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
          My tomatoes make me completely delusional.


            Diploid and Haploid.

            The easiest way to explain this is in this forum is by mentioning a third state – triploid. Triploid weed plants have 3 instead of 2 sets of chromosomes.

            Diploid: (2n) = 2 sets of chromosomes.

            Haploid: (n) = 1 set of chromosomes.

            When tracking sexual life cycles of plants the chromosomal number is expressed with either the terms diploid and haploid or the (n) and (2n) format which is common on diagrams especially. Or both the words and abbreviations are interchanged at will…

            Alternation Of Generations.

            All plants undergo complex sexual life cycles involving the production of both spores and gametes. This is known as the alternation of generations.

            Sporophytes produce spores. The sporophyte plant is diploid (2n) but the spores they produce are haploid (n) due to sexual recombination called meiosis. The spores (n) from sporophytes (2n) grow into gametophytes (n) which are either male (n) or female (n).

            Gametophytes produce gametes - sperm and eggs. Gametes (n) fuse together in fertilization to become a diploid (2n) zygote (fertilized egg). The zygote (2n) grows out into an embryo (2n) and eventually the sporophyte plant.

            Thus we have the alternation of generations:

            Sporophyte -> Spores -> Gametophyte -> Gametes -> Sporophyte -> ……

            Most plant structures we view today are sporophytes. Large diploid structures like vegetables and cannabis, the trees we climb and graze and build with, all visibly sporophytes. The gametophytes are reduced, some to such an extent it takes a microscope to find them. But they are there.

            Plants have undergone a lot of changes through time. 400 million years ago the largest plants were only two feet high and 20 foot fungi dominated the landscape. It wasn’t for another 55 million years that plants really started to come into their own.

            Prehistoric mystery organism verified as giant fungus.
            I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
            My tomatoes make me completely delusional.



              The following picture depicts a lichen Lichenomphalia umbellifera growing on the stems of sphagnum moss, the major building block of peat moss.

              Lichens are not plants. A lichen is a symbiotic partnership between a fungi (mycobiont) and algae or cyanobacteria (photobiont). Many lichens resemble simple plants but L. umbellifera is fairly rare in nature and shows clearly the fungal component of the relationship. Some lichenologists refute these are lichen at all, but they fit the classification. This is a Basidiolichen. A basidiomycetes fungi mycobiont with algal photobiont granules where the stem meets with the sphagnum moss.

              The oldest established lichen fossil is around 400 million years old and plant fossils predate this by 75 million years. But in May 2005 evidence was presented in Science in Yuan, Xiao and Taylor’s report: Lichen-Like Symbiosis 600 Million Years Ago. “The fossil record of fungi and lichens is scarce. Here we report the discovery of lichen-like fossils, involving filamentous hyphae closely associated with coccoidal cyanobacteria or algae, preserved in marine phosphorite of the Doushantuo Formation (between 551 and 635 million years old) at Weng'an, South China. These fossils indicate that fungi developed symbiotic partnerships with photoautotrophs before the evolution of vascular plants.”

              Here are some more typical rock eating lichens.

              Previously I mentioned the first plants were thought to be a charophycean green algae in a mycorrhizal partnership with a zygomycete fungi. Much like lichens then, these ancestral plants.
              I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
              My tomatoes make me completely delusional.


                I think this one belongs up top also. Nice work Mr. Fista.



                  Thanks V. Worked pretty hard on trying to make this interesting and informative. I'm more interested in getting stickies in my garden but throwing this up top should make it easier for those dipping their toes in this forum.

                  Edit: My apologies for letting personal opinion into this science thread. Hope you folk are enjoying it so far. I'll replace this post with something interesting before too long.
                  I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                  My tomatoes make me completely delusional.


                    Bryophytes: Hornworts, Liverworts, Mosses.

                    The evidence is compelling that plants evolved from charophycean green algae and that plants all share common ancestry. Bryophytes are the simplest or least complex group of plants; and are thought to share the link between charophycean algae and vascular plants. The bryophytes consist of three divisions of plants: Liverworts, Hornworts, and Mosses.

                    Photo Above: Bryophytes are unique amongst plants in that the gametophyte is the dominant generation. The plant you observe is a gametophyte (makes gametes, remember). The thin stalks that grow out of the moss with small bulb like tips are the spore producing sporophytes. The sporophyte is parasitic and entirely dependent on the gametophyte, the sporophyte is typically not photosynthetic.
                    • Bryophytes lack vascular tissues xylem and phloem but some mosses have hydroid and leptoid cells that can transfer water and nutrients respectively.
                    • Bryophytes do not have root systems; they attach to the substrate with rhizoids: elongated single cells or filaments of cells. Rhizoids are typically only anchors to the substrate, absorption of inorganic ions and water occurs directly through the gametophyte.
                    • Bryophytes sperm (male gametes) have flagella and need water so they may swim to the egg. This feature is also shared by ferns.

                    A generic life cycle of Bryophytes is pictured below.

                    Archegonia are female sexual organs that produce eggs on a gametophyte. Antheridia are male organs producing sperm also on a gametophyte. These sexual organs may be on the same gametophyte (monoecious – one house eg: hermaphrodite) or on separate gametophytes (dioecious – two houses). The sporophytes spores are borne on the sporangia. Note that meiosis occurs and the spores are haploid from a diploid parent. Note above the line is diploid (2n) and below is haploid (n). Reread alternation of generations (post 6) to help understanding of the picture.

                    Liverworts: Hepatophyta.

                    Typically inconspicuous but capable of generating large mass in the correct conditions, liverworts are the simplest of all plants and may comprise a group of their own. Liverworts are unique in that they lack stomata and a cuticle. They also typically lack specialized conducting cells (a very few genera are found to have water conducting strands). Liverworts can be either leafy or thallose.

                    The leafy liverworts are well represented in the tropics and in areas of specifically high rainfall and are also widely scattered in temperate zones. Liverwort leaves generally consist of a single layer of undifferentiated cells that lack a thickening midrib. Spore dispersal in all liverworts involves dehiscence – the drying out of elaters, which are part of the sporangium’s structure, which generates tension until something breaks/detaches/rapidly unfurls and disperses the spores. In the photo below a leafy liverwort (left) is compared to a moss with midribs in its leaves (right).

                    Pictured below is a thallose liverwort. These are non-leafy and described as simple or complex in accordance with the number of cell layers but the terms can be misleading when examining the plants further - some ‘complex’ liverworts are far simpler that other ‘simple’ liverworts. Typically complex liverworts have many small openings present on the surface of the plant allowing gas exchange below the surface layer of cells. Many liverworts can reproduce through fragmentation – broken off pieces grow into clones. Also, the small cups you see pictured below are gemma cups. Inside of these are small balls called gemma. These can be washed out and may grow into a gametophyte. This asexual reproduction of gametophytes from gemma happens in addition to fragmentation and the alternation of generations.

                    Hornworts: Anthocerophyta.

                    Hornwort gametophytes might seem to resemble thallose liverworts but these plants show a distinct lineage. Hornworts, unlike liverworts, have stomata. And most hornwort cells contain only one large chloroplast, unlike other plants which have many smaller chloroplasts in their cells. The sporophytes contain a meristem – an actively dividing area of growth that continues as long as conditions are favorable – many sporophytes of hornworts elongate for prolonged periods of time. The sporophyte is also green, having chloroplasts and photosynthetic capability unlike the ‘typical’ bryophyte sporophyte.

                    Mosses: Bryophyta.

                    Many plants identified as mosses are not mosses at all. Reindeer moss is a lichen, club moss and Spanish moss are vascular plants, and sea moss and Irish moss are algae. The actual mosses are composed of three classes: Bryidae (‘true’ mosses), Sphagnidae (peat mosses) and Andraeidae (granite mosses).

                    Constituting a diverse group of somewhere between 9000 and 15000 species - again molecular evidence is generating debate as to actual classification numbers versus double ups etc. We can definitely say there are a lot of mosses.

                    Mosses, like lichens, are very sensitive to pollution and many species are not present in populated areas. In the wild they dominate much of the terrain in the far north and south and in many other places above the treeline. Mosses survive extreme Antarctic cold and desert heat, many species remain alive for years without water, recovering growth quickly when water finally arrives. Some can be found on salt splashed rocks on the seashore, but none are truly marine.

                    Below is pictured an accumulation of moss.

                    To be continued...
                    I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                    My tomatoes make me completely delusional.


                      Mo’ Mosses.

                      More Mosses: Division Bryophyta.

                      All moss gametophytes have two distinct phases as the protonema (see moss life cycle picture in previous post) and the leafy gametophyte. In true mosses, the protonema cells are in a single layer, and the branching resembles filamentous green algae. Leafy gametophytes develop from bud like structures on the protonema. In some mosses the protonemata (plural) persist and assume the major photosynthetic role, and the gametophytes are minute. Protonemata are characteristic of all mosses, some liverworts, but not hornworts.

                      The True Mosses: Class Bryidae.

                      The true moss gametophyte is leafy and typically upright rather than flattened as in the leafy liverworts. Three initial ranks of leaves after axial twisting resemble a spiral arrangement - like phyllotaxy, but instead the stem twists. Not so apparent in some aquatic mosses. In many species the stems of gametophytes and sporophytes have a strand of water conducting hydroid cells (dead when mature, become empty and thus useful as a pipe). In some genera, leptoids – living food conducting cells, surround the hydroids.

                      Cushiony mosses (below and above). Gametophytes are erect and little branching, usually bearing terminal sporophytes.

                      Feathery Mosses. (below) Plants are creeping, leaves typically branched often superficially resembling ferns, often hanging as epiphytes from trees.

                      The Granite Mosses: Class Andreaeidae. (below)

                      Occurring in mountainous or arctic regions, often on granite rocks, the genus Andreaea consist of only about 100 species. The gametophytes closely resemble true mosses but the sporophyte lacks a true seta (stem) and is raised instead on a stalk of gametophyte tissue, the pseudopodium. The spore release mechanism also differs from other mosses with 4 ‘slits’ (vertical lines of weaker cells among stronger cells) that open widely when the capsule is dry, releasing windborne spores, and closing when it is moist. A second genus found in Alaska, Andreaobryum, has one (discovered) species. It has a sporophyte with a true seta, and its capsule splits to the apex.

                      The Peat Mosses: Class Sphagnidae.

                      Diverging from the main line of moss evolution very early, the genus Sphagnum holds approximately 350 species of mosses. The gametophyte stems bear clusters of branches, often five per node, resembling a ‘mop like’ head. The plants form bright green or reddish clumps in boggy ground. The leaves lack midribs and consist of large dead cells surrounded by a narrow band of green, or red, living cells. The dead cells are what gives sphagnum it’s water holding capacity (20 times the dried weight), the pores and thickenings in these readily fill with water. In living plants the dead cells keep them turgid.

                      Sphagnum sporophytes are also distinctive with spherical red to blackish brown capsules raised on a pseudopodium which is part of the gametophyte as with the granite mosses.

                      An estimate of 1% of the worlds soil (1/2 the land mass of the United States) is peat bog. Peat bog can have a pH as low as 4 due to sphagnum releasing H+ ions and altering their environment. Peat is the accumulation of sphagnum, as well as sedges, grasses, reeds and other plants that grow with sphagnum. Recent experimentation and microscopy by IC Mag member Microbeman shows peat is also loaded with microbial life.

                      I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                      My tomatoes make me completely delusional.


                        My apologies I've had no updates for ages. I've been busy with university summer school. Now I'm going on holiday, then university again. In ~ 3 months I will be sitting down to give this thread a decent bunch of additions. Till then I'm just too busy to do it justice as I want to keep the quality high. Bear with me, this thread is by no means forgotten.

                        Hope you've enjoyed it so far.
                        I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                        My tomatoes make me completely delusional.


                          Very nice read!

                          I've learned much in an initial skim of it,... I'll read it again and again when in a slightly better state of mind for sure!

                          Keep up the good posting!
                          I'm NOT a botanist, but I play one on the internet

                          If anything posted by this user has offended you,.. please unread it


                            This is very interesting! Thanks MrFista. I await your return!

                            'I don't want to believe, I want to know.' -Carl Sagan


                              WOW , This is really a great synopsis of basic biological breakdown of the early stages in soil development. Thanks for compiling this info, it refreshes the mind on principles all growers should have a basic knowledge of.

                              thanks again and lets see some more !!
                              California prop 215 medical Grower
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