I got a Freestanding question that basically asked:
Which of these is a way to classify an organism as a eukaryote?
A. It is able to reproduce sexually
B. It has a mechanism for intron splicing
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The answer was B. However, I really don't agree with this answer because the explanation states that bacteria reproduce sexually via conjugation... which I'm pretty sure doesn't meet the criteria for sexual reproduction. Additionally, Archaea have introns, so you can't choose B. Likewise, I chose A. Anyone have any help?
​
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Side note: Wikepedia on bacterial conjugation "Classical E. coli bacterial conjugation is often regarded as the bacterial equivalent of sexual reproduction or mating since it involves the exchange of genetic material. However, it is not sexual reproduction, since no exchange of gamete occurs, and indeed no generation of a new organism: instead an existing organism is transformed."
https://en.wikipedia.org/wiki/Bacterial_conjugation#:~:text=coli%20bacterial%20conjugation%20is%20often,the%20exchange%20of%20genetic%20material.&text=coli%20conjugation%20the%20donor%20cell,often%20a%20plasmid%20or%20transposon.

Sorry if this isn't the sub for this, I'll move it somewhere else if necessary.
When I was in high school, I wrote a short story with the premise that there had been a civilization of sapient aquatic beings on Earth about 2.4 billion years ago, which descended from anaerobic methane-producing archaea and were destroyed by the Great Oxygenation Event. (A few of these beings managed to survive in stasis until the modern day through a soft sci-fi plot device, but that's not relevant to this post.)
I was thinking of creating a sequel to/expansion of the original idea, but unfortunately, I didn't know much about designing plausible speculative organisms, so when coming up with the "Shoalers" (As I called them.) I mostly just threw together all the cool terms I had learned from grade 11 biology class and by skimming wikipedia pages in order to make them as weird as possible, without concern for how well all the different traits fit together. I still don't really know that much, but I now know enough to know some aspects of the Shoalers' biology are a bit implausible.
Fortunately, my past self's laziness is somewhat helpful, as I didn't define any of the Shoalers' evolutionary history beyond the fact that they descended from methanogenic archaea that had convergently evolved multicellularity, which gives me complete freedom when deciding how they could have plausibly evolved all their implausible traits.
So, I was wondering if I could have some help coming up with broad explanations for why the Shoalers are the way that they are, hopefully with only minimal retconning of the traits I had previously established them as having.
Here's the information about the Shoalers I established in the short story. I'd rather not retcon any of it, unless it's completely unsalvageable:

• The Shoalers have a triradially symmetrical body shaped like a cylinder, which tapers into a single long flexible tail. They have no distinct head, but have a head-like cluster of organs at the anterior end of their body, consisting of three equidistantly-spaced "arms" which each have five "fingers", three toothless mouths (Three mouths?!?) near the base of each arm, and a single massive compound eye (which can see in nearly every direction except in the direction of the optic disk, because of the Shoalers' semitransparent skin.) between the three mouths. Adults can range from about 1.5 to about 3 meters in length, and from about 0.5 to about 1.75 meters in diameter.
  
• Shoalers are primarily filter-feeders, (I think the idea is that they simultaneously suck up food and move around by inhaling water through their mouths, filtering out food, and then expelling it through three funnels further down their body? I never actually established how they propel themselves, now that I think about it.) but are also capable of photosynthesis, collecting sunlight through a dense coating of hair-like setae on their tail. (I really don't understand why I added this detail. Maybe at some point in my research I got confused and assumed that methanogens had to be autotrophic, and then assumed that if they were autotrophs they had to be photosynthetic? I didn't really understand the chemistry behind different forms of respiration. I still don't, really.)
  
• Shoalers have thin and porous skin, and breath through cutaneous respiration. (Why would I do this??? Did I think a 3-meter-long active sapient organism that relies fully on anaerobic respiration wasn't implausible enough, so I had to make it passive anaerobic respiration too???)
  
• A species of bioluminescent single-celled prokaryotes lives within the Shoalers' skin, which they are (somehow) capable of altering the colour and brightness of. Shoaler languages are based on bioluminescence and body language, rather than sound.
  
• Internally, the Shoalers loosely resemble echinoderms, despite being unrelated. (That's literally all I said about their internal organs. I'm thinking I might just give them a water vascular system and otherwise ignore this statement.)
  
• Shoalers have no biological sexes and reproduce asexually.
  
• They're called "Shoalers" because they evolved to congregate in massive shoals as a defense against predation. As a relic of this instinct, Shoalers that have not interacted with other Shoalers recently tend to become rapidly anxious - Imagine how you would feel if you were locked in a tiny pitch-black room for X amount of time, and you will pretty much understand how a Shoaler would feel if left alone for the same amount of time.
  

The following information about the Shoalers isn't explicitly stated in the story I wrote, but I came up with during the process of writing the story or in the years afterwards. It can be retconned away, but it'd be nice to keep it if possible, I guess:

• Shoalers continue to live in large "Shoals" (Capital S because it's now a unique socio-biological phenomenon rather than just them swimming together.) of about 15-30 individuals, which have evolved from a temporary anti-predator adaptation into a kinship group sort of analogous to an extended family or a small clan. Members of a given Shoal live in close proximity to each other, and coordinate their actions through informal consensus or, more rarely, deference towards a respected individual or group of individuals within the Shoal. While humans consider human society to be made up of individuals who may belong to different groups, Shoalers consider Shoaler society to be made of up of Shoals who are in turn made up of individuals. (e.g. A Shoaler democracy would probably operate under the principle of "One Shoal, one vote", and in most Shoaler languages, the term for "individual" might literally translate as "Shoal-appendage".)
  
• Shoalers give live birth to about 70-80 young, which are about 2 centimeters long and non-sapient. These young are immediately abandoned by their parent, and about 95% percent of them die within their first two years of life. After reaching 2 years old, at which point a juvenile Shoaler is about as intelligent as a 4-year-old human, they are usually adopted by a nearby Shoal, whose members collectively raise and educate them.
  
• Shoalers have a symbiotic relationship with a coral-like prokaryotic colonial organism which evolved to shed small pieces of its body into the water to attract Shoalers and other related filter-feeders, who would then unwittingly spread the colonial organism's larvae (disguised amongst the particulate) to new places. The Shoalers underwent a societal revolution similar to the agricultural revolution when they learned to domesticate this organism as both a source of food and a construction material, using scaffolds and pruning to grow it into the shape of buildings.
  

So, I guess my questions would be:

• Is the high concept of the story - That unbeknownst to humanity, multicellular life first evolved in the anoxic oceans of the Neoarchaen, culminating in a civilization of sapient obligate anaerobes, before it was all destroyed by the Great Oxygenation Event - plausible in of itself? Is methanogenic respiration efficient enough to support a large multicellular organism? Is it plausible that humanity would have never stumbled on fossil evidence of these lifeforms, as long as they were all soft-bodied?
  
• Why would large, motile organisms like the ancestors of the Shoalers develop triradial symmetry over bilateral symmetry, and why wouldn't they be outcompeted by organisms with a bilateral symmetry and/or secondarily evolve bilateral symmetry themselves? On one hand, a three-sided cylindrical body is pretty close to the "torpedo" shape converged upon by fast aquatic animals like sharks and dolphins, and I could see it providing a situational boost to maneuverability since they would never have to rotate very far to point two of their limbs in a given direction, but on the other hand, I can't see any advantage to retaining a triradial body that would outweigh the benefits of either specializing one of the three limbs as a dorsal fin/something else and adapting the other two limbs into pectoral fins, or just not expending the energy to grow a whole-ass third limb that's probably redundant most of the time.
  
• Speaking of which, why and how the hell would they develop three different mouths? I'm thinking if their one big eye and brain are located in-between the mouth's three respective digestive tracts, that would explain why they don't slowly move towards each other and merge into one (cf. the size constraints on a cephalopod's donut-shaped brain.) but that doesn't explain why one hasn't grown larger and become the main mouth while the other two become vestigial, or why such a bizarre and inefficient system would develop in the first place.
  
• Is having one big compound eye implausible? What kind of compound eye would work best?
  
• Now that I think about it, I never established what their three limbs were originally used for, before the sapient Shoalers emerged and repurposed them for tool-use. Maybe rather than locomotion (which they would achieve through jet propulsion and/or their tail) the Shoaler's ancestors originally used their three limbs to catch food, developing "fingers" on the ends to either better restrain prey or provide a larger surface area for filter-feeding, as well as muscles for curling the limbs inwards in order to transfer food to their mouths, then a reef-dwelling species made these limbs more dexterous in order to use them to rapidly change speed and direction by pulling on and pushing off the structures of the reef, with the Shoalers finally adapting them in order to manipulate tools. Is that at all plausible?
  
• How do I explain their ability to perform photosynthesis? I was thinking of explaining it as the result of an endosymbiotic relationship between the Shoalers and an anaerobic photosynthetic microorganism, (perhaps even the same one they use to bioluminescence?) akin to the emerald sea slug, but I don't know if that makes any sense - It seems unrealistic to me that this extremely specific trait would just so happen to evolve in the one lineage that also developed sapience, so presumably its a feature of a much larger clade of which the Shoalers are just one member, and I don't know how plausible it is to have a significant portion of the animal-analogue species supplement their food supply with photosynthesis instead of wholly specializing as either heterotrophs or autotrophs.
  
• How the hell do creatures that large survive using passive respiration, and why haven't they developed a better solution? I don't even have the beginnings of an idea of how to explain this one.
  
• How would they control the bioluminescent microorganisms in their body with enough sophistication to use them to communicate?
  
• Why wouldn't the ancestors of the Shoalers have ever developed sexual reproduction? My only idea is that they could have some sort of ability to exchange genetic material akin to bacterial conjugation, sidestepping the genetic diversity issues inherent to asexual reproduction. I'm hesitant about that idea though, if only because it seems like a roundabout way of giving them the ability to reproduce sexually without calling it sexual reproduction.
  
• Is it realistic that a filter-feeder as large as a Shoaler would develop shoaling behaviour? The only aquatic animals I can think of that are comparable in size and swim together in big groups are dolphins and orcas, and they're hunters, not filter-feeders.
  
• Is their weird hybrid of r-strategist and K-strategist reproductive strategies, where they abandon their young for two years and then spend lots of energy raising the survivors, at all realistic? One obvious issue is the fact that there's seemingly no incentive for Shoals to adopt and raise new juvenile Shoalers, since they likely have no genetic relationship with each other - I was thinking a solution to this might be to say that newly-adopted Shoalers receive genetic material from the Shoal that adopts them, making the adoptee's future offspring descended from both the Shoal that birthed them and the Shoal that adopted them, and providing an evolutionary incentive for their adopter Shoal to raise and protect them. Is that at all plausible?
  
• Is the weird pollinator-into-domesticator symbiotic evolution between the Shoalers and the colonial organism they use as a crop and building material plausible?
  
• Are their any unrealistic elements to the Shoalers that I haven't realized are unrealistic (Or that I just forgot to mention) that need to be dealt with somehow? How should I deal with them?
  

Consider plasmid F. Plasmid F (for "fertility") is a plasmid, which is a small loop of DNA a few thousand base pairs in length. Plasmid F is found in Escherichia coli.
Now, plasmids are just loops of DNA. They do some things that living things do (reproduce, regulate their reproduction) but just as the bacterial chromosome is not alive, nor are plasmids.
Plasmid F contains in its code a set of instructions to generate an object called a "sex pilus" (I swear I didn't come up with the name) that is a long, thin tube that sticks out of the cell. This swings around until it contacts another cell that doesn't contain plasmid F and then it conjugates. For plasmid F, the plasmid (a single strand of it) is transferred from the donor (male) cell to the recipient (female) cell. (This stuff was worked out in the 1950s and 1960s so the terminology is not very P.C.)
OK. So that's plasmid F and we accept that plasmids are genetic elements, they can reproduce and transfer themselves from cell to cell, but they are not alive any more than the far more complex bacterial chromosome is.
So now let's move it along a step. Suppose that a mutant of plasmid F comes along and it codes for a sex pilus that is unusually long (stop snickering). This pilus is long enough to contain the entirety of plasmid F! And then in a second mutation, this "extra long pilus" plasmid F now comes up with a pilus that completely detaches from the donor cell and floats around freely in the medium until it finds a recipient cell and then transfers itself in.
Well, guess what? This hypothetical double-mutant plasmid F has now become a virus. And yet...it didn't suddenly become a living thing. It is still a plasmid, just one that can float around freely.
And that is why viruses are not alive.

Hello, I'm a biology student who loves the game and based on the following evidence I have drawn a few conclusions, but before I get into those, yes I know it's just a game and yes I know I'm reading too deep into it, but I did this for fun and wanted to share:
Supply drops are a sign of existing infrastructure. Or maybe it's automated with no one flying it, remaining in service after all other services have died off or been shut down.
Zombies don't freeze in the cold and need to rest, so they are alive.
The infection affects humans and other animals, so the infection is zoonotic.
Anti-biotics help cure the infection. So the infection is not a virus, but rather a bacteria.
The infection spreads via bites. sratches, and lives in the blood.
The bacteria who closely matches all these mentioned criteria is Capnocytophaga. A bacterial disease that lives in dog's mouths spreads through saliva, most often via bites. The bacteria, if given the right circumstances can infect the blood and can progress to become systemic. The only reason it rarely is a lethal hazard is due to how slow it reproduces....DUN DUN DUUUUUUUUN
Patient Zero monologue:
"'UN imposes sanctions on anti-biotics as rise of superbugs poses worldwide crisis'
And that's how the end began. That one headline forced the entire scientific and medical community to scramble like roaches on bathroom tile. Antibiotics had been our go-to cure for so many ailments, but all of a sudden our go-to was forced into being a last resort. Antibiotics could only be prescribed if there was a lethal threat. So what then? What would people be prescribed for their stomach ache? Or, god forbid, someone has to deal with a stuffy nose? The horror.
Millions of dollars went into funding genetic research. It was the most promising foe to face the villainous bacteria.The most effective technique was dubbed, 'Conjugation Elimination.' If you don't know, conjugation is the act of a bacteria piercing another bacteria, with a special part called a pilus, that injects a copy of genetic material. The recipient bacteria is then able to utilize that material. In simpler terms, bacteria 1 stabs bacteria 2 with a sillystraw and blows a load into bacteria 2, now bacteria 2 is genetically different than it was before. Conjugation Elimination takes advantage of this event by designing bacteria with the pilus, but that transfers two different genes. One gene to posses the pilus and one gene that inhibits reproduction. Before long, the mass population of bacteria in a host would be incapable of reproduction and die off.
Pretty soon this was the ultimate technique to cure all things bacteria related. And it was a fortune if you didn't have insurance. We lucky few who's government had decided health was a privilege had to pay arm and leg for these treatments. Damn pharmaceuticals were all over patenting specific bacteria treatments.
It all seemed so easy. All you had to do was inject some DNA into a bacteria cell and you had a cure. How could you mess that up? How could I have made this...It was easy for the most part to get everything I needed to do my own genetic engineering. It started off as me making some E-coli glow or making a bacteria explode when it came in contact with water. And then Arrow got sick, he was a bit older, sure, but he was my dog. I figured he had a Capnocytophaga bacterial infection in his mouth. No problem, I've made E-coli glow, I could recreate Conjugation Elimination. It may have been a felony to conduct genetic engineering without a permit, but all I needed to know were the genetic sequnces for the pilus and the gene that inhibits preproduction. Easy...Days spent in my dimly lit at-home lab, hunched over my microscope, sweat pooling in the optic lenses as my shakey hands forced a syringe into each bacteria cell. All for Arrow. Finaly I had a full batch, so I injected the modified bacteria into his left flank. All I had to do was go to sleep and awake to see my efforts being paid off. I was asleep before my head even hit the pillow. I was so exhausted.
I just remember some surreal fever dream-like images from that night's sleep. Everything was red, and I remember feeling so hungry that I would eat anything. I was so excited to see Arrow back in his prime. But what I saw made my heart fall to the floor. The injection site was blistering and putrid. My poor Arrow had a think yellow slime-like foam coming from his mouth as he lay in the exact position I left him. His breathing was eradic and extremely elevated. What had I done? I must have done something wrong with the gene to inhibit reproduction. It must have increased reproduction at least ten fold. In my horror and sorrow I pet his head, pushing his ears back, his eye piercing my sole as if he was asking me, 'why?' I grabbed a near by rag to wipe away the slime from his mouth. And before I could react, he bit me, his canines went clean through my palm.
I screamed and tried prying my hand free from the slimey grasp that was Arrow's mouth. I ran to my room as fast as I could and shut the door behind me. I could hear Arrow clawing away at the wood of my door. So I just sat there back against the door, terrified of my own dog and of what I had done.
I couldn't call for help, or else I could face prison time. I've been here for hours now trying to devise a plan to somehow make it out of here alive without hurting my dog anymore. But my vision is getting blurry, my fingers are tingling, and my mucus is so thick I can barely breath. I'm so sorry Arrow. What have I done?"

Multiplies; but never breeds, Uses air; but never breathes.
Consumes much; will never eat, Often measured by its heat.

I know single-celled organisms can reproduce asexually, but when a cell in a multicellular organism divides is that considered asexual reproduction too? Bonus points for sources.

Wanted to share my list of mnemonics that I found helpful for the MCAT. Many of these are from SDN but some are my own. I apologize in advanced for the crude and offensive ones but this often helps recall.
If there's any mnemonics you use for MCAT topics not on here please share!
 

Beta vs. alpha carbohydrates

alpha = trans/down, beta = cis/up bow down to alpha, beta beat me up  

Sympathetic vs. parasympathetic

Sympathetic = fight or flight, parasympathetic = rest & digest Paraplegics do a lot of sitting & resting (this is bad I'm really sorry but it works)  

Electronegativity trend

FONCLBRISCH F > O > N > Cl > Br > I > S > C > H  

Diatomic elements

BrINClHOF  

Water soluble compounds

NAG SHAm Nitrates (NO3^-) Acetate (CH3CO2^-) Group 1 metal cations (Li, Na, K, Cs, Rb) Sulfates (SO4^2-) except with PMS Castro Bar Halogens except with PMS Ammonium (NH4⁺) PMS = Pb (Lead), Mercury (Hg), Silver (Ag) Castro Bar = Ca (Calcium), Str (Strontium), Ba (Barium)  

Acid classifications

Increasing nuance/complexity when in alphabetical order. Arrenhius = acid forms H3O⁺ & base forms OH^- in water (most elementary definition). Brownsted-Lowry = acids donate protons (H⁺) and bases accept them. Lewis = acids accept electron pairs and bases donate them.  

La Chatelier's principle and equilibrium

When K & Q are in alphabetical order the arrow points to the direction the reaction will go to re-establish equilibrium. K > Q then reaction will go right, increasing product concentration. K < Q then reaction will go left, increasing reactant concentration.  

Anterior pituitary hormones

FLAT PEG Follicle-stimulating (FSH) Luteinizing (LH) Adrenocorticotropic (ACTH) Thyroid stimulating (TSH) Prolactin Endorphins Growth hormone (GH)  

Lysogenic vs. lytic virus lifecycle

Viral DNA incorporated into host genome and just replicated not transcribed (dormant) Lysogenic is a longer word so it takes longer (dormant)  

Retrovirus

retrovirus has RNA reverse transcriptase Two r's in retrovirus: RNA reverse (transcriptase)  

Nerve fibers & location in spinal cord

Sensory afferent, motor efferent, dorsal (towards back) afferent, ventral (towards front) efferent SAME DAVE  

Period of a pendulum

T = 2π√(L/g) pendulum on her period sits on a toliet (L) and g comes out like circumference of a circle (2π*r)  

Calcium hormones

Calcitonin: calcium into bones Parathyroid: rids bone of calcium  

Pyramidines

cytosine, thymine (RNA equivalent uracil) Have y's in them  

Deviations from Hardy-Weinberg Equilibrium

Mutations, migration, drift, non-random mating, selection Maggie May Does Not Smoke  

Cell cycle

Growth phase 1, S phase (DNA synthesis/replication), Growth phase 2, Mitosis, Cytokinesis Go Sally Go Make Children!  

Cell division

Prophase, Metaphase, Anaphase, Telophase PMAT  

Chordate traits

Dorsal nerve cord, notochord, pharyngeal slits, postanal tail Do Not Pinch People  

Embryogenesis

Morula, Blastula, Gastrula Must Be Good  

Fat soluble vitamins

Vitamins D, E, K, A DEKA  

Hormones that increase blood glucose

Somatotropin (growth hormone), thyroid hormones (T3 & T4), epinephrine, norepinephrine, glucagon, glucocorticosteroids, immunoglobulins STENGGI ferengi like sweet blood  

Path of sperm

Seminiferous tubules, epididymis, vas deferens, ejaculatory duct, urethra, penis SEVEN UP  

mRNA post-processing

Exons Expressed, Introns in the trash  

Taxonomy

Kingdom Phylum Class Order Family Genus Species King Philip Came Over For Gold & Silver  

White blood cells

Neutrophils, lymphocytes, monocytes, eosinophils, basophils Nobody Likes Me Eating Badgers  

Valence electrons

H likes to gain 1 e- to be stable, O 2, N 3, C 4 HONC 1234  

Ecell site of redox

Reduction at cathode, oxidation at anode REDCAT ANOX  

State functions

volume (V), Gibb's free energy (G), pressure (P), enthalphy (H), internal energy (E), entropy (S), temperature (T), potential energy (U), density (D) VG PHESTUD  

Basic amino acids

histidine, arginine, lysine HAL  

Cardiac cycle

systole = contraction, diastole = relaxation I Contracted a Cyst  

Diverging lens image

diminished, upright, virtual DDUV  

Acidic cations

Al, Fe, NH4, Zn, Cu, Be, Cr A Fact No Zebra Could Be Creepy  

DNA order

DNA is read 3'-5' left to right like we read. But is synthesized 5'-3' largest to smallest just how a pyramid is built.  

Bacterial conjugation

sexual reproduction in bacteria like a conjugal visit  

Pancreas hormones

insulin, glucagon, somastatin I GLUed ON SOMe TATs to my pancreas

I need to teach a demo class for a job interview. It is 40 minutes and the audience 9th graders at a gifted and talented school. The subject I have been asked to cover is bacterial reproduction, both sexual and asexual.

1. What major points should I hit?
2. Any cool activities/ labs/ demos I can do?

I was thinking about talking about how fast bacteria can grow and some everyday effects of that (stinky socks etc) before talking about asexual reproduction and conjugation, transformation and transduction.
Any suggestions or overall advice is welcomed.

A

Adnate - Where the gills or tubes under the cap of a fungus are perpendicular to the stipe or stem at the point of attachment
Adnexed - Where the gills or tubes under the cap of a fungus sweep upwards before being attached to the stem
Aerial mycelium - Hyphal elements growing above the agar surface.
Agar - An extract from a seaweed used to solidify media. The agar used in mushrooms cultivation is usually available in powder form
Agaric - A term describing mushrooms and toadstools having gills beneath a cap that is connected to a stipe or stem
Alkaline - Having a pH greater than 7.
Annulus - A ring of tissue left attached to the stem of a mushroom or toadstool when the veil connecting the cap and stem ruptures as the young fruitbody develops.
Antibiotic - A class of natural and synthetic compounds that inhibit the growth of or kill other microorganisms.
Ascomycetes - A group of fungi that have in common that they produce their sexual spores inside specialized cells (asci), which usually contain eight spores.
Aseptic - Sterile condition: no unwanted organisms present
Aseptic technique - Also sterile technique. Manipulating sterile instruments or culture media in such a way as to maintain sterility.
Autoclave - Basically a big pressure cooker, sometimes operating at higher pressure than 15 PSI, thus achieving sterilization temperatures above 250?F.
Axenic - Not contaminated; gnotobiotic: Said esp. of a medium devoid of all living organisms except those of a single Species

B

Bacteria - Unicellular microorganisms that may cause contamination in culture work. Grain spawn is very easily contaminated with bacteria. On the other hand there are some bacteria that are needed for the fruiting of agaricus. These are present in the casing soil.
Basidiomycetes - A group of fungi which produce their spores externally on so called basidia. Often four spores are produced per basidium. Many basidiomycetes show clamp connections on their hyphae, ascomycetes never do. Most mushrooms are classified as basidiomycetes, whereas most molds are ascymycetic.
Basidium (pl. basidia) - A cell that gives rise to a basidiospore. Basidia are characteristic of the basidiomycetes.
Biological efficiency - The definition of biological efficiency (BE) in mushroom cultivation is: 1 pound fresh mushrooms from 1 pound dry Substrate indicates 100 % biological efficiency. This definition was first used by the agaricus industry to be able to compare different grow setups and Substrate compositions. Note that this is not the same as true thermodynamic efficiency. The BE of Psilocybe cubensis is easily somewhere in the range of 200%uFFFDbr>
Birthing - Removing the fully colonized growth medium (like a cake from its jar) from whatever container it was kept in for colonization purposes and placing in an environment conducive to fruiting.
Bolete - A group of fungi having tubes rather than gills beneath the cap
Brown Rice Flour (BRF)- Ground brown rice. Many cultivators grind their own brown rice in a coffee grinder.
Buffer - A system capable of resisting changes in pH even when acid or base is added, consisting of a conjugate acid-base pair in which the ratio of proton acceptor to proton donor is near unity. An example is gypsum, which is an additive that increases a material's pH while helping to buffer it, or keep it within a desriable (and higher) pH range.

C

CaCl2 - Calcium chloride (Brand names: Damp-Rid, Damp-Gone, Damp B Gone, Damp Away). See desiccant.
CaCO3 - See calcium carbonate.
Calcium sulfate - CaSO4. See gypsum.
Carbon dioxide - CO2. A colorless, odorless, incombustible gas. Formed during respiration, combustion, and organic decomposition.
Carpophore(s) - Commonly known as "mushrooms", the reproductive organs of the true body of the fungus, formed by the web of mycelium that colonize a substrate.
Casing - Some mushrooms need a covering layer of soil with a specific microflora for Fruiting. Casing materials include peat and vermiculite; additives include calcium carbonate, calcium hydroxide (hydrated lime) and crushed oystershells.
CaSO4 - Calcium sulfate. See gypsum.
Cellulose - Glucose polysaccharide that is the main component of plant cell walls. Most abundant polysaccharide on earth, and common source of nourishment for cultivated fungi.
Clone - A population of individuals all derived asexually from the same single parent. In mushroom cultivation placing a piece of mushroom tissue on agar medium in order to obtain growing mycelium is called cloning. This is not strictly related to the colloquial notion of cloning, and is simply a manipulation of the natural asexual reproduction system of fungi.
CO2 - See carbon dioxide
Cobweb mold - Common name for Dactylium, a mold that is commonly seen on the casing soil or parisitizing the mushroom. It is cobweb-like in appearance and first shows up in small scattered patches and then quickly runs over the entire surface of the its substrate.
Coir - Coco coir. A short coarse fiber from the outer husk of a coconut. Used as a casing ingredient. Brand names include Bed-A-Beast .
CVG aka Coir Verm Gypsum- This commonly used acronym is one of the most commonly used substrates for growing Psilocybe Cubensis. CVG can be sterilized or pasteurized unlike other substrates that would otherwise require pasteurization and can't be sterilized with the intention of spawning to bulk in open air. Coir, Coir Verm, Coir Gypsum, and Coir verm gypsum are all usable combinations.
Colonization - The period of the mushroom cultivation starting at Inoculation during which the mycelium grows through the Substrate until it is totally permeated and overgrown.
Compost - Selectively-fermented organic material. Compost is one desirable substrate for mushrooms, but may vary in its components.
Coniferous - Pertaining to conifers, which bear woody cones containing naked seeds. Relevant in mushroom hunting.
Contamination - Undesired foreign material (contaminants), frequently organisms, in a growing medium. Often the result of insufficient sterilisation or improper sterile technique.
Cottony - Having a loose and coarse texture. Referred to a growth pattern of some fungi species or strains.
Culture - A sample of a given (generally desired) organism. In mycology, mushroom mycelium growing on a culture medium.
Culture medium - The material upon which a culture is developed. Micro-organisms differ in their nutritional needs, and so large number of different growth media have been developed, PD(Y)A (potato dextrose(yeast extract) agar) and MEA (malt extract agar) can be used for most cultivated mushrooms.

D

Deciduous - Trees and plants that shed their leaves at the end of the growing season. Relevant in mushroom hunting.
Desiccant - An anhydrous (moistureless) substance, usually a powder or gel, used to absorb water from other substances. Two commonly used dessicants are calcium hydroxide and silica gel. Dessication permits mushrooms to be preserved for extended periods.
Dextrose - A simple sugar used in agar formulations. Synonymous with glucose.
Dikaryotic mycelium - Contains two nuclei and can therefore produce fruiting bodies.
Diffusion - The movement of suspended or dissolved particles from a more concentrated region to a less concentrated region as a result of random movement on the microscopic scale. Diffusion tends to distribute particles uniformly throughout the available volume, given enough time, and occurs more rapidly at higher temperatures.
Disinfection - To cleanse so as to destroy or prevent the growth of microorganisms, usually referring to rubbing or spraying the surfaces one wants to disinfect with lysol, diluted bleach solutions or alcohol.

E

Endospore - A metabolically dormant state by which some bacteria become more resistant to heat, chemicals, and other adverse conditions. Given the proper conditions, they will reactivate (germinate) and begin to multiply. Many bacterial endospores cannot be destroyed at boiling temperatures. This is important to mycologists because grains contain a high number of dormant endospores, though rice often contains few to none; thus, many grains must be pressure cooked to achieve sterilization, whereas brown rice flour may simply be boiled.
Enzyme - A protein, synthesized by a cell, that acts as a catalyst for a specific chemical reaction.

F

Fermentation - Anaerobic (oxygen-less) decomposition. In mushroom cultivation, this often relates to composting. Easily-accessible nutrients may be degraded by micro-organism, making a substrate more selectively beneficial to the desired fungus. Unwanted fermentation may occur if the composted substrate is still very 'active' after inoculation or if thick layers or large bags are used. The latter may lead to low-oxygen conditions in parts of the substrate. Mushrooms are aerobic, meaning they need oxygen, while some undesirable bacteria thrive in anaerobic conditions.
Field capacity - Content of water, on a mass or volume basis, remaining in a soil after being saturated with water and after free drainage is negligible. Described as the state achieved when one can squeeze a handful of substrate or casing material hard, only to have one or two drops emerge.
Flow hood - A fan-powered and HEPA-filtered device that produces a laminar flow of contam free air. The air moves across the workspace allowing for open sterile work without the hassle and inconvience of a glove box.
Flush - The sudden development of many fruiting bodies at the same time. Usually there is a resting period between flushes.
Fractional sterilization - A sterilization method used to destroy bacteria and spores in preparation of grain spawn (rye, wheat, birdseed) requiring no pressure cooker. In this case, the jars fitted with a filter are boiled or steamed at 212?F (100?C) for 30 min in a covered pot, three days in a row. Between the boiling steps the jars are best kept warm, around 30?C, to allow the remaining endospores to germinate. The basic principle behind this method is that any resistant bacterial spores should germinate after the first heating and therefore be susceptible to killing during the subsequent boilings.
Fruiting - The process by which the mycelium produces fruiting bodies, or mushrooms, for the purpose of spore propagation (sexual reproduction).
Fruiting body - A mushroom. The part of the mushroom that grows above ground.
Fruiting chamber (FC) - A enclosed space with high humidity and fresh air exchange where mushrooms may fruit under proper conditions.
Fungicide - A class of pesticides used to kill fungi.
Fungus - A group of organisms that includes mushrooms and molds. These organisms decompose organic material, returning nutrients to the soil.

G

G2G - See grain-to-grain transfer. Inoculation of grain by already colonized grain.
Genotype - The set of genes possessed by an individual organism.
Geolite - One of several brand names/varieties of clay aggregate medium (also known as LECA for light expanded clay aggregate). It is a lightweight, porous substrate with excellent aeration.
Germination - The spreading of hyphae from a spore
Gills - The tiny segments on the underside of the cap. This is where the spores come from.
Glovebox - A glovebox is a device used to Isolate an area for work with potentially hazardous substances or materials which need to be free from direct contact with the outside environment for any reason. Most gloveboxes are small, tightly enclosed boxes having a glass panel for viewing inside and special airtight gloves which a person on the outside can use to manipulate objects inside.
Glucose - See dextrose.
Grain-to-grain transfer - The inoculation of grain with already-colonized grain. This procedure involves exposing uncolonized, sterilized grain, and so is prone to contamination. As such it should only be performed with a glove box, laminar flow hood, or similar device.
Gypsum - Calcium sulfate, CaSO4. A greyish powder often used in spawn preparation. It prevents the clumping of the grain kernels and acts as a basic pH buffer.

H

H2O2 - See hydrogen peroxide.
Hay - Grass that has been cut, left to dry in the field and then baled. It is fed to livestock through the winter when fresh grass is not available. The color of hay is greenish-grey. Not synonymous with straw.
HEPA - High Efficiency Particulate Air filter. A high-efficiency filter used in flow hoods.
Hydrogen peroxide - A clear aqueous solution usualy available in concentrations from 3%uFFFDo 30%uFFFDEasily decomposed into water and oxygen by enzymes like catalase, which is found in desirable mushrooms but not in many bacteria. This makes it capable of selectively destroying some competitors, and a tool sometimes used in cultivation. The mycological use of peroxide was the focus of a popular cultivation guide by Rush Wayne.
Hypha(e) - Filamentous structure which exhibits apical growth and which is the developmental unit of a Mycelium.

I

In vitro - From the Latin, in glass, isolated from the living organism and artificially maintained, as in a petri dish or a jar.
Incubation - The period after inoculation (preferably at a temperature optimal for mycelial growth) during which the Mycelium grows vegetatively
Inoculation - Introduction of spores or spawn into substrate
Isolate - A strain of a fungus brought into pure culture (i.e. isolated) from a specific environment

J

K

L

Lamellae - The gills of a mushroom
LC - See liquid culture
Lignin - A complex polymer that occurs in woody material of higher plants. It is highly resistant to chemical and enzymatic degradation. The white rot fungi are known for their lignin degrading capability.
Limestone - See calcium carbonate.
Liquid culture - A culture of mycelium suspended in a nutritious liquid, for use as an inoculant.

M

Magic mushroom - Any of a number of species of fungi containing the alkaloids psilocybin and/or psilocin. Common species are the 'liberty cap' (Psilocybe semilanceata) and Psilocybe cubensis, though there are dozens of others.
Maltose - Malt sugar, used in agar formulations.
Martha - Refers to a fruiting chamber based on a Martha Stewart-brand translucent vinyl closet.
MEA - Malt extract agar.
Metabolism - The biochemical processes that sustain a living cell or organism.
Multispore - Refers to an inoculation where multiple germinations and matings occur due to the use of various spores, as in a spore solution (e.g. spore syringe) and as opposed to an isolate. Liquid cultures may sometimes be called multispore (though they contain no spores) if they were produced from a spore solution, rather than an isolate.
Mycelium - The portion of the mushroom that grows underground. Plants have roots; mushrooms have mycelium. Mycelium networks can be huge. The largest living thing in the world is a single underground mycelium complex.
*Mycorrhiza# - A symbiotic association between a plant root and fungal hyphae.

N

O

Overlay - A dense mycelial growth that covers the casing surface and shows little or no inclination to form pinheads. Overlay directly results from a dry casing, high levels of carbon Dioxide and/or low humidity.
Oyster shells - See calcium sulfate.

P

Parasitic - Fungi that grow by taking nourishment from other living organisms.
Pasteurization - Heat treatment applied to a Substrate to destroy unwanted organisms but keeping a reduced concentration of favorable ones alive. The temperature range is 60?C to 80?C(140?F-175?F). The treatment is very different from sterilization, which aims at destroying all organisms in the substrate .
PDA - Potato dextrose agar.
PDYA - Potato dextrose yeast agar.
Peat - Unconsolidated soil material consisting largely of undecomposed, or only slightly decomposed, organic matter accumulated under conditions of excessive moisture. Used as casing ingredient in mushroom culture.
Perlite - Perlite is a very light mineral, often found next to the vermiculite in gardening stores. It has millions of microscopic pores, which when it gets damp, allow it to 'breathe' lots of water into the air, aiding in humidification, which is beneficial to fruiting. Peroxidated agar - Agar made with H2O2 for the purpose of retarding contamination by bacteria and new mold spores. Not suitable for use with ungerminated mushroom spores, only live mycelium. See also: hydrogen peroxide.
Petri dish - A round glass or plastic dish with a cover to observe the growth of microscopic organisms. The dishes are partly filled with sterile growth medium such as agar (or sterilized after they have been filled). Petri dishes are used to produce isolates.
PF - Psylocybe Fanaticus. The original spore provider and originator of the PF-Tek, one of the original home growing techniques on which many others are based.
pH - A measure to describe the acidity of a medium. pH 7 is neutral; higher means Alkaline, lower Acidic
Pileus - The cap of a mushroom.
Pinhead - A term to describe a very young mushroom, so-named for the pin-sized developing cap.
Polyfill - A polyester fiber that resembles synthetic cotton. Found at fabric stores, Wal-Mart, arts & craft stores. Also used as a filter medium for aquariums (filter floss). Used as a jar lid filter in preparation of grain spawn and for other filtration purposes.
Pressure cooker - A pot with a tight lid in which things can be cooked quickly with steam under higher pressure. The reason for it is that at 15 PSI (pound per square inch) pressure the water boils at a higher temperature (250?F, 121?C) than at ambient pressure.(212?F, 100?C). In mushroom cultivation used to thoroughly sterilize substrates and agar media.
Primordium - The initial fruiting body, the stage before pinhead
Psilocybin, Psilocin - Hallucinogenic organic compounds found in some mushrooms.
Pure culture - An isolated culture of a micro-organism, uncontaminated with others. Pure cultures are essential to the production of spawn because it is sensitive to contamination.

R

Rhizomorph - "Root-like". An adjective used to describe the appearance of the mycelium of some mushroom strains. Rhizomorphic mycelium is taken as a sign of fast colonization and qualities desirable for fruiting.
Rice cake - Many of the growing methods involve making a 'cake' of brown rice flour( BRF ), vermiculite and water, and injecting it with mushroom spores. Not a rice cake like you'd buy in a supermarket!
Rye - A hardy annual cereal grass related to wheat. Lat.:Secale cereale. In mushroom cultivation rye grain is used as spawn medium.
Ryegrass - A perennial grass widely cultivated for pasture and hay and as a lawn grass. Lat.:Lolium perenne. Seeds used as Substrate for P. mexicana and P. tampanensis.

S

Saprophyte - A fungus that grows by taking nourishment from dead organisms
Sclerotium - A hard surfaced resting body of fungal cells resistant to unfavorable conditions,which may remain dormant for long periods of time and resume growth on the return of favorable conditions.
Secondary metabolite - Product of intermediary metabolism released from a cell, such as an antibiotic.
Selective medium - Medium that allows the growth of certain types of microorganisms in preference to others. For example, an antibiotic-containing medium allows the growth of only those microorganisms resistant to the antibiotic.
Simmer - To cook just below or at the boiling point.
Slant - A test tube with growth medium, which has been sterilized and slanted to increase the surface area
Spawn - Culture of mycelium on grain, sawdust, etc., used to inoculate the final substrate, or bulk.
Spawn run - The vegetative growth period of the mycelium after spawning the substrate to bulk.
Species - Fundamental unit of biological taxonomy. Generally spoken, two individuals belong to the same species if they can produce fertile offspring
Spore print - A collection of spores taken from a mushroom cap, often collected on sterile card stock, aluminum foil, or some other flat surface.
Spore syringe - A solution of spores collected in a syringe, usually scraped from a spore print under sterile conditions. Several companies will sell you ready-to-use spore syringes for a few pounds/dollars. This site has links to, or address for, many of the most reputable of these companies.
Spores - Means of sexual reproduction for mushrooms and many other fungi. Comparable to a plant seed, save that spores combined sexually with one another after germination; there are no "male" and "female" spores as with seeds and pollen or sperm and eggs, but compatability is complicated. Spores are microscopic, and any visible clump of spores is in fact a collection of many thousands or millions of spores.
Stamets, Paul - The owner of Fungi Perfecti and mushroom guru. The co-author of The Mushroom Cultivator and many other helpful books.
Stem - The stipe or stalk of a growing mushroom.
Sterilization - Completely destroying all micro organisms present, by heat (autoclave, pressure cooker) or chemicals. Spawn substrate always has to be sterilized prior to inoculation.
Stipe - The stem of a mushroom at the top of which the cap or Pileus is attached
Strain - A genetic line considered to have common traits, usually identified for artificial selection by humans. Many strains have geographical names (e.g. Ecuador, Texan, Aussie), but point of natural origin is not necessarily the source of the name. Remember that strains are a human notion; vendors often differentiate between stocks that are not visibly different to everyone, but which have been perceived to have different characteristics, whether visual (e.g. the Penis Envy strain), chemical (as in strains perceived to have high potency), or behavioral (relating to the mushroom's response to environment, colonization speed, et cetera).
Straw - The dried remains of fine-stemmed cereals (wheat, Rye, barley...) from which the seed has been removed in threshing. Straw has a golden color.
Stroma - Dense mycelial growth without fruiting. Stroma occurs if spawn is mishandled or exposed to harmful petroleum-based fumes or chemicals. It also occurs in dry environments.
Substrate - Whatever you're using to grow the mushrooms on. Different varieties of mushroom like to eat different things (rice, rye grain, straw, compost, woodchips, birdseed). Different techniques involve infecting substrates with anything from spores, to chopped-up Mycelium, to blended mushroom.

T

Tek - Short for technique. Often prefaced with something to tell you what type of tek; e.g. PF-Tek, for Psylocybe Fanaticus Technique, one of the original home growing techniques on which many others are based.
Terrarium - A small enclosure or closed container in which selected living plants, fungi and sometimes small land animals, such as turtles and lizards, are kept and observed.
Tissue culture - Tissue cultures are the simplest way to obtain a mycelial culture. A tissue culture is essentially a clone of a mushroom, defined as a genetic duplicate of an organism. The basic procedure is to sterilely remove a piece of the mushroom cap or stem, and place it on an agar plate. After a week to ten days, Mycelium grows from the tissue and colonizes the agar. Great care should be taken to select a fruiting body of the highest quality, size, color, shape or any highly desired characteristic.
TiT - "Tub in Tub", refers to an incubator consisting of 2 plastic tubs and an aquarium heater.
Trichoderma - A common green mold.
Trip - What happens when you eat the finished product, if you are cultivating hallucinogenic varieties. With psilocybes, a trip tends to last from three to six hours. May range from mild visual effects and lightly enhanced perceptions, to a totally altered state of consciousness. Generally, this can be controlled to some degree by mindset, setting and dosage. Read some of the trip reports to get an idea of what other people have experienced before experiencing hallucinogens. Please always remember, although many of the effects seem to be experienced by many different people, you're going to have your trip, not someone else's.
Tyndallization - See fractional sterilization

U

Umbonate - Used to describe a cap with a raised central area above the point where the stipe meets the pileus

V

Veil - When a mushroom is growing, the edges of the cap are joined to the stem. As the mushroom grows larger, the cap spreads and the edges tear away, often leaving a very thin veil of material hanging from the stem.
Vermiculite - A highly absorbent material made from puffed mica. Used in rice cakes to hold water, and to stop the cake being too sticky. The mycelium likes room to breathe and grow.

W

WBS - Wild bird seed. Millet-based birdseed; used as spawn and Substrate in mushroom cultivation.

Z

Zonate - Marked with concentric bands of colour. Refers to the appearance of mycelium of some mushroom species on agar, for instance P. mexicana.

Given a population (colony) of bacteria, all offsprings are essentially clones of their parents, how will they speciate? Is it still meaningful to use terms like sympatric or allopatric speciation? Without sexual reproduction, gene flow occurs only in instances of bacterial transformation or conjugation, but as far as I know these are not strictly intraspecific. So at what point is bacterial speciation complete?

Organisms of many species are specialized into male and female varieties, each known as a sex.[1] Sexual reproduction involves the combining and mixing of genetic traits: specialized cells known as gametes combine to form offspring that inherit traits from each parent. Gametes can be identical in form and function (known as isogamy), but in many cases an asymmetry has evolved such that two sex-specific types of gametes (heterogametes) exist (known as anisogamy). By definition, male gametes are small, motile, and optimized to transport their genetic information over a distance, while female gametes are large, non-motile and contain the nutrients necessary for the early development of the young organism. Among humans and other mammals, males typically carry XY chromosomes, whereas females typically carry XX chromosomes, which are a part of the XY sex-determination system.
The gametes produced by an organism determine its sex: males produce male gametes (spermatozoa, or sperm, in animals; pollen in plants) while females produce female gametes (ova, or egg cells); individual organisms which produce both male and female gametes are termed hermaphroditic. Frequently, physical differences are associated with the different sexes of an organism; these sexual dimorphisms can reflect the different reproductive pressures the sexes experience.
Contents [hide] 1 Evolution 2 Sexual reproduction 2.1 Animals 2.2 Plants 2.3 Fungi 3 Sex determination 3.1 Genetic 3.2 Nongenetic 4 Sexual dimorphism 5 See also 6 References 7 Further reading 8 External links Evolution
Main article: Evolution of sexual reproduction It is considered that sexual reproduction in eukaryotes first appeared about a billion years ago and evolved within ancestral single-celled eukaryotes.[2] The reason for the initial evolution of sex, and the reason(s) it has survived to the present, are still matters of debate. Some of the many plausible theories for the appearance of sexual reproduction include: the creation of variation among offspring, to spread advantageous traits, the beneficial removal of disadvantageous traits, and that sex evolved as an adaptation for repairing damage in DNA. (See the evolution of sexual reproduction.)
While there are a number of theories, there are two main alternative views on the evolutionary origin and adaptive significance of sex. The first view assumes that sexual reproduction is a process specific to eukaryotes, organisms whose cells contain a nucleus and mitochondria. In addition to sex in animals, plants, and fungi, there are other eukaryotes (e.g. the malaria parasite) that also engage in sexual reproduction. On this first view, the adaptive advantage that maintains sexual reproduction (in competition with asexual modes of reproduction) is the benefit of generating genetic variation among progeny. Furthermore, on this view, sex originated in a eukaryotic lineage. The earliest eukaryotes and the bacterial ancestors from which they arose are assumed to have lacked sex. For instance, some bacteria use conjugation to transfer genetic material between cells; and while not the same as sexual reproduction, this also results in the mixture of genetic traits. The reason that bacterial conjugation is not the same as sexual reproduction is that the numerous genes necessary for conjugation are not located on the bacterial chromosome, but on small circular DNA self-replicating parasitic elements called conjugative plasmids. Thus, conjugation arises from an adaptation of parasitic DNA for its own transmission.[3]
The second alternative view on the evolutionary origin and adaptive significance of sex is that sex existed in early bacteria as the process of natural transformation, a well studied DNA exchange process still in existence in many present day bacterial species (see Transformation (genetics)). Transformation involves the transfer of DNA from a donor to a recipient bacterium. Recipient bacteria must first enter a special physiological state, termed competence, to receive donor DNA (see Natural competence). The numerous genes necessary for establishment of competence are located on the bacterial chromosome itself. Thus the process of transformation is likely beneficial to bacteria, and can be regarded as a simple form of sex. In general, competence is induced under stressful conditions, such as nutrient limitation and exposure to DNA damaging agents, as reviewed by a number of authors.[4][5][6] Sex, on this view, was present in the earliest single-celled eukaryotes because they were descended from ancestral bacteria capable of transformation. Sex was maintained as an adaptation for repairing DNA damage (see Evolution of sexual reproduction). In particular, meiosis the key stage of the sexual cycle of eukaryotes, in which genetic information derived from different individuals (parents) recombines, was likely derived from the analogous, but simpler, genetic information exchange and DNA repair process that occurs during transformation in bacteria[7][8][9][10] (and also see Meiosis, section: Origin and function of meiosis). Thus, by this view, sex appears to have evolved in bacteria as a way of repairing DNA damages induced by environmental stresses, was maintained through the prokaryote/eukaryote boundary, and continued to evolve in higher multicellular eukaryotes, in part, as a DNA repair process.
What is considered defining of sexual reproduction in eukaryotes is the difference between the gametes and the binary nature of fertilization. Multiplicity of gamete types within a species would still be considered a form of sexual reproduction. However, no third gamete is known in multicellular animals.[11][12][13]
While the evolution of sex itself dates to the prokaryote or early eukaryote stage, the origin of chromosomal sex determination may have been fairly early in eukaryotes. The ZW sex-determination system is shared by birds, some fish and some crustaceans. Most mammals, but also some insects (Drosophila) and plants (Ginkgo) use XY sex-determination. X0 sex-determination is found in certain insects.
No genes are shared between the avian ZW and mammal XY chromosomes,[14] and from a comparison between chicken and human, the Z chromosome appeared similar to the autosomal chromosome 9 in human, rather than X or Y, suggesting that the ZW and XY sex-determination systems do not share an origin, but that the sex chromosomes are derived from autosomal chromosomes of the common ancestor of birds and mammals. A paper from 2004 compared the chicken Z chromosome with platypus X chromosomes and suggested that the two systems are related.[15]
Sexual reproduction
Main article: Sexual reproduction Further information: Isogamy and Anisogamy
The life cycle of sexually reproducing organisms cycles through haploid and diploid stages Sexual reproduction in eukaryotes is a process whereby organisms form offspring that combine genetic traits from both parents. Chromosomes are passed on from one generation to the next in this process. Each cell in the offspring has half the chromosomes of the mother and half of the father.[16] Genetic traits are contained within the deoxyribonucleic acid (DNA) of chromosomes—by combining one of each type of chromosomes from each parent, an organism is formed containing a doubled set of chromosomes. This double-chromosome stage is called "diploid", while the single-chromosome stage is "haploid". Diploid organisms can, in turn, form haploid cells (gametes) that randomly contain one of each of the chromosome pairs, via meiosis.[17] Meiosis also involves a stage of chromosomal crossover, in which regions of DNA are exchanged between matched types of chromosomes, to form a new pair of mixed chromosomes. Crossing over and fertilization (the recombining of single sets of chromosomes to make a new diploid) result in the new organism containing a different set of genetic traits from either parent.
In many organisms, the haploid stage has been reduced to just gametes specialized to recombine and form a new diploid organism; in others, the gametes are capable of undergoing cell division to produce multicellular haploid organisms. In either case, gametes may be externally similar, particularly in size (isogamy), or may have evolved an asymmetry such that the gametes are different in size and other aspects (anisogamy).[18] By convention, the larger gamete (called an ovum, or egg cell) is considered female, while the smaller gamete (called a spermatozoon, or sperm cell) is considered male. An individual that produces exclusively large gametes is female, and one that produces exclusively small gametes is male. An individual that produces both types of gametes is a hermaphrodite; in some cases hermaphrodites are able to self-fertilize and produce offspring on their own, without a second organism.[19]
Animals Main article: Sexual reproduction in animals
Hoverflies engaging in sexual intercourse Most sexually reproducing animals spend their lives as diploid organisms, with the haploid stage reduced to single cell gametes.[20] The gametes of animals have male and female forms—spermatozoa and egg cells. These gametes combine to form embryos which develop into a new organism.
The male gamete, a spermatozoon (produced within a testicle), is a small cell containing a single long flagellum which propels it.[21] Spermatozoa are extremely reduced cells, lacking many cellular components that would be necessary for embryonic development. They are specialized for motility, seeking out an egg cell and fusing with it in a process called fertilization.
Female gametes are egg cells (produced within ovaries), large immobile cells that contain the nutrients and cellular components necessary for a developing embryo.[22] Egg cells are often associated with other cells which support the development of the embryo, forming an egg. In mammals, the fertilized embryo instead develops within the female, receiving nutrition directly from its mother.
Animals are usually mobile and seek out a partner of the opposite sex for mating. Animals which live in the water can mate using external fertilization, where the eggs and sperm are released into and combine within the surrounding water.[23] Most animals that live outside of water, however, must transfer sperm from male to female to achieve internal fertilization.
In most birds, both excretion and reproduction is done through a single posterior opening, called the cloaca—male and female birds touch cloaca to transfer sperm, a process called "cloacal kissing".[24] In many other terrestrial animals, males use specialized sex organs to assist the transport of sperm—these male sex organs are called intromittent organs. In humans and other mammals this male organ is the penis, which enters the female reproductive tract (called the vagina) to achieve insemination—a process called sexual intercourse. The penis contains a tube through which semen (a fluid containing sperm) travels. In female mammals the vagina connects with the uterus, an organ which directly supports the development of a fertilized embryo within (a process called gestation).
Because of their motility, animal sexual behavior can involve coercive sex. Traumatic insemination, for example, is used by some insect species to inseminate females through a wound in the abdominal cavity – a process detrimental to the female's health.
Plants
Flowers are the sexual organs of flowering plants, usually containing both male and female parts. Main article: Plant reproduction Like animals, plants have developed specialized male and female gametes.[25] Within most familiar plants, male gametes are contained within hard coats, forming pollen. The female gametes of plants are contained within ovules; once fertilized by pollen these form seeds which, like eggs, contain the nutrients necessary for the development of the embryonic plant.
Pinus nigra cone.jpg Pine cones, immature male.jpg Female (left) and male (right) cones are the sex organs of pines and other conifers. Many plants have flowers and these are the sexual organs of those plants. Flowers are usually hermaphroditic, producing both male and female gametes. The female parts, in the center of a flower, are the carpels—one or more of these may be merged to form a single pistil. Within carpels are ovules which develop into seeds after fertilization. The male parts of the flower are the stamens: these long filamentous organs are arranged between the pistil and the petals and produce pollen at their tips. When a pollen grain lands upon the top of a carpel, the tissues of the plant react to transport the grain down into the carpel to merge with an ovule, eventually forming seeds.
In pines and other conifers the sex organs are conifer cones and have male and female forms. The more familiar female cones are typically more durable, containing ovules within them. Male cones are smaller and produce pollen which is transported by wind to land in female cones. As with flowers, seeds form within the female cone after pollination.
Because plants are immobile, they depend upon passive methods for transporting pollen grains to other plants. Many plants, including conifers and grasses, produce lightweight pollen which is carried by wind to neighboring plants. Other plants have heavier, sticky pollen that is specialized for transportation by insects. The plants attract these insects with nectar-containing flowers. Insects transport the pollen as they move to other flowers, which also contain female reproductive organs, resulting in pollination.
Fungi Main article: Mating in fungi
Mushrooms are produced as part of fungal sexual reproduction Most fungi reproduce sexually, having both a haploid and diploid stage in their life cycles. These fungi are typically isogamous, lacking male and female specialization: haploid fungi grow into contact with each other and then fuse their cells. In some of these cases the fusion is asymmetric, and the cell which donates only a nucleus (and not accompanying cellular material) could arguably be considered "male".[26]
Some fungi, including baker's yeast, have mating types that create a duality similar to male and female roles. Yeast with the same mating type will not fuse with each other to form diploid cells, only with yeast carrying the other mating type.[27]
Fungi produce mushrooms as part of their sexual reproduction. Within the mushroom diploid cells are formed, later dividing into haploid spores—the height of the mushroom aids the dispersal of these sexually produced offspring.
Sex determination
Main article: Sex-determination system
Sex helps the spread of advantageous traits through recombination. The diagrams compare evolution of allele frequency in a sexual population (top) and an asexual population (bottom). The vertical axis shows frequency and the horizontal axis shows time. The alleles a/A and b/B occur at random. The advantageous alleles A and B, arising independently, can be rapidly combined by sexual reproduction into the most advantageous combination AB. Asexual reproduction takes longer to achieve this combination, because it can only produce AB if A arises in an individual which already has B, or vice versa. The most basic sexual system is one in which all organisms are hermaphrodites, producing both male and female gametes—this is true of some animals (e.g. snails) and the majority of flowering plants.[28] In many cases, however, specialization of sex has evolved such that some organisms produce only male or only female gametes. The biological cause for an organism developing into one sex or the other is called sex determination.
In the majority of species with sex specialization, organisms are either male (producing only male gametes) or female (producing only female gametes). Exceptions are common—for example, in the roundworm C. elegans the two sexes are hermaphrodite and male (a system called androdioecy).
Sometimes an organism's development is intermediate between male and female, a condition called intersex. Sometimes intersex individuals are called "hermaphrodite"; but, unlike biological hermaphrodites, intersex individuals are unusual cases and are not typically fertile in both male and female aspects.
Genetic
Like humans and other mammals, the common fruit fly has an XY sex-determination system. In genetic sex-determination systems, an organism's sex is determined by the genome it inherits. Genetic sex-determination usually depends on asymmetrically inherited sex chromosomes which carry genetic features that influence development; sex may be determined either by the presence of a sex chromosome or by how many the organism has. Genetic sex-determination, because it is determined by chromosome assortment, usually results in a 1:1 ratio of male and female offspring.
Humans and other mammals have an XY sex-determination system: the Y chromosome carries factors responsible for triggering male development. The default sex, in the absence of a Y chromosome, is female. Thus, XX mammals are female and XY are male. XY sex determination is found in other organisms, including the common fruit fly and some plants.[28] In some cases, including in the fruit fly, it is the number of X chromosomes that determines sex rather than the presence of a Y chromosome (see below).
In birds, which have a ZW sex-determination system, the opposite is true: the W chromosome carries factors responsible for female development, and default development is male.[29] In this case ZZ individuals are male and ZW are female. The majority of butterflies and moths also have a ZW sex-determination system. In both XY and ZW sex determination systems, the sex chromosome carrying the critical factors is often significantly smaller, carrying little more than the genes necessary for triggering the development of a given sex.[30]
Many insects use a sex determination system based on the number of sex chromosomes. This is called X0 sex-determination—the 0 indicates the absence of the sex chromosome. All other chromosomes in these organisms are diploid, but organisms may inherit one or two X chromosomes. In field crickets, for example, insects with a single X chromosome develop as male, while those with two develop as female.[31] In the nematode C. elegans most worms are self-fertilizing XX hermaphrodites, but occasionally abnormalities in chromosome inheritance regularly give rise to individuals with only one X chromosome—these X0 individuals are fertile males (and half their offspring are male).[32]
Other insects, including honey bees and ants, use a haplodiploid sex-determination system.[33] In this case diploid individuals are generally female, and haploid individuals (which develop from unfertilized eggs) are male. This sex-determination system results in highly biased sex ratios, as the sex of offspring is determined by fertilization rather than the assortment of chromosomes during meiosis.
Nongenetic
Clownfish are initially male; the largest fish in a group becomes female For many species, sex is not determined by inherited traits, but instead by environmental factors experienced during development or later in life. Many reptiles have temperature-dependent sex determination: the temperature embryos experience during their development determines the sex of the organism. In some turtles, for example, males are produced at lower incubation temperatures than females; this difference in critical temperatures can be as little as 1–2 °C.
Many fish change sex over the course of their lifespan, a phenomenon called sequential hermaphroditism. In clownfish, smaller fish are male, and the dominant and largest fish in a group becomes female. In many wrasses the opposite is true—most fish are initially female and become male when they reach a certain size. Sequential hermaphrodites may produce both types of gametes over the course of their lifetime, but at any given point they are either female or male.
In some ferns the default sex is hermaphrodite, but ferns which grow in soil that has previously supported hermaphrodites are influenced by residual hormones to instead develop as male.[34]
Sexual dimorphism
Main article: Sexual dimorphism
Common Pheasants are sexually dimorphic in both size and appearance. Many animals and some plants have differences between the male and female sexes in size and appearance, a phenomenon called sexual dimorphism. Sex differences in humans include, generally, a larger size and more body hair in men; women have breasts, wider hips, and a higher body fat percentage. In other species, the differences may be more extreme, such as differences in coloration or bodyweight. In humans, biological sex is determined by five factors present at birth: the presence or absence of a Y chromosome, the type of gonads, the sex hormones, the internal reproductive anatomy (such as the uterus in females), and the external genitalia.[35]
Sexual dimorphisms in animals are often associated with sexual selection – the competition between individuals of one sex to mate with the opposite sex.[36] Antlers in male deer, for example, are used in combat between males to win reproductive access to female deer. In many cases the male of a species is larger than the female. Mammal species with extreme sexual size dimorphism tend to have highly polygynous mating systems—presumably due to selection for success in competition with other males—such as the elephant seals. Other examples demonstrate that it is the preference of females that drive sexual dimorphism, such as in the case of the stalk-eyed fly.[37]
Other animals, including most insects and many fish, have larger females. This may be associated with the cost of producing egg cells, which requires more nutrition than producing sperm—larger females are able to produce more eggs.[38] For example, female southern black widow spiders are typically twice as long as the males.[39] Occasionally this dimorphism is extreme, with males reduced to living as parasites dependent on the female, such as in the anglerfish. Some plant species also exhibit dimorphism in which the females are significantly larger than the males, such as in the moss Dicranum[40] and the liverwort Sphaerocarpos.[41] There is some evidence that, in these genera, the dimorphism may be tied to a sex chromosome,[41][42] or to chemical signalling from females.[43]
In birds, males often have a more colourful appearance and may have features (like the long tail of male peacocks) that would seem to put the organism at a disadvantage (e.g. bright colors would seem to make a bird more visible to predators). One proposed explanation for this is the handicap principle.[44] This hypothesis says that, by demonstrating he can survive with such handicaps, the male is advertising his genetic fitness to females—traits that will benefit daughters as well, who will not be encumbered with such handicaps.
See also
Sex and gender distinction References
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Arnqvist, G. & Rowe, L. (2005) Sexual conflict. Princeton University Press, Princeton. ISBN 0-691-12217-2 Alberts B, Johnson A, Lewis J, Raff M, Roberts K, and Walter P (2002). Molecular Biology of the Cell (4th ed.). New York: Garland Science. ISBN 0-8153-3218-1. Ellis, Havelock (1933). Psychology of Sex. London: W. Heinemann Medical Books. xii, 322 p. N.B.: One of many books by this pioneering authority on aspects of human sexuality. Gilbert SF (2000). Developmental Biology (6th ed.). Sinauer Associates, Inc. ISBN 0-87893-243-7. Maynard-Smith, J. The Evolution of Sex. Cambridge University Press, 1978. External links
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