Mitochondria - are they really separate organisms that once merged into eukaryotic cells?

Mitochondria - are they really separate organisms that once merged into eukaryotic cells?

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Theoretically, mitochondria are said to be a separate organism that is concerned with its own life and its own processes. In fact, it even duplicates individually. I know a similar question is here but I have something else apart from that to ask.

  1. Is the presence of their own DNA/RNA - like compound justify or prove that the mitochondria was once a separate living organism?
  2. If the mitochondria is indeed a separate living organism, then how is it controlled by the nucleus? Or is it not? Logic would suggest that since mRNA exists in the mitochondria separate from DNA in the nucleus, they have their own control over how they behave.
  3. Often, living organisms working together have to have some sort of payment system. For example, bacteria in the body provide Vitamin K and other breakdown vitamins, and in return the body gives it a suitable home to live in. Is there any such business occurring between the individual cell and the mitochondria? Does it keep some nutrients for itself? If not, what is its mode of nutrition?
  4. In effect, cells did exist before mitochondria joined the party. Is there any way to at least have a feasible hypothesis on why and how the cells bonded with the mitochondria or how the cells even existed in the first place without the presence of and organnelle that can break down food and convert it into energy?
  5. Why do mitochondria have their own membrane? And that too folded? Is that to increase the surface area available for the electron transport chain, or is it for simple compactness?
  6. Why does the mRNA in our bodies always exactly match the mRNA of our mothers and only our mothers? Can any genetic mutation change this fact?
  7. Is it possible, that a mitochondrion can somehow escape the cell and start performing its life otherwise?
  8. mRNA would suggest that mitochondria make their own proteins / at least some basic amino acids. If there are any such proteins, are they utilized for the cell? Or are they used for cellular respiration? Or are they kept by the mitochondria for there own means?

I will appreciate all answers!, SmallDeveloper (a.k.a SmallScientist :) )

EDIT : Basically, I am asking 3 things:

  1. Were mitochondria really separate organisms once?
  2. If so, how do they get their nutrition?
  3. How did cells exist before mitochondria came along?

  1. Yes. But it is incorrect to call mitochondria an organism now.
  2. Most of their genes were lost and are now encoded in the nuclear genome
  3. It gets most of its metabolites
  4. It is not known. See the other post for details.
  5. Why membrane: I guess you know that. Why folded: you guessed right.
  6. Only ovum donates mitochondria and other cytoplasmic factors. Sperm just provides the haploid genome.
  7. No
  8. Most of them are key respiratory enzymes

40 Interesting Mitochondria Facts: Structure, Function, mtDNA

By now you must have understood at least one thing – we are going to produce facts about each and every component of a cell – be it animal cell or a plant cell. We have already covered Cell Membrane facts and we have also covered Cytoplasm facts .

It is now time to move on to other components of a cell. So, we have decided to start with Mitochondria facts. Mitochondria is popularly known as the POWERHOUSE of a cell. But why so? Let us find out!

While we will obviously answer that question, we will also ponder on various other questions that are usually connected with this essential cell organelle. Let us begin…

Name MitochondriaOriginated from two Greek words – Mitos and Chondros. Mitos means thread and Chondros means granule
ColorBrownish red – only part of cell that is colored
Size0.5 micron to 1 micron in animal cells
Present InBoth Animal and Plant cells
Present InAll Eukaryotic cells
GenomeMitochondria has it own Genome and DNA
mtDNAMitochondrial DNA is circular
CapabilityCapable of self dividing when needed


Based upon data accumulated from sluggish decaying radioactive isotopes, Globe is thought to have formed around 4. 55 billion years back. From this time of origins, a continual procedure for geological and physical change has occurred, which created conditions leading to the origin of life about 4 billion years ago. Life is considered to have undergone the procedure of evolution, defined as 'DNA series change and the inheritance of that change, often under the selective stresses of the changing environment. ' (1) Microfossil data suggests that unicellular eukaryotes arose on Earth about 2 billion years back, after the development of an oxic environment and the technology of breathing metabolism in cyanobacteria. This timing infers that the availability of oxygen was a sizable effect on the biological evolution that led to the introduction of Eukarya. (1)

"The defining attribute of eukaryotes is the occurrence of your well-defined nucleus within each cell. " (2) Typical eukaryotic skin cells contain a membrane bound nucleus and organelles enclosed by an outer plasma membrane these organelles are organised into compartmentalised structures that have their own function(s) within the cell, often working with other organelles to complete vital biological functions. This compartmentation in skin cells is essential in organisms as it allows differing compositions of nutrition to exist inside each compartment instead of outside, creating perfect conditions for biochemical reactions to occur. (3) The dissimilarities between eukaryotes and prokaryotes are shown in Stand 1:

Mitochondria are membrane-bound organelles within the cytoplasm of all eukaryotic skin cells and are most concentrated in skin cells associated with energetic operations, such as muscle skin cells which constantly require energy for muscle contraction. The two surrounding membranes that encompass a mitochondrion differ in function and composition, creating specific compartments within the organelle. The exterior membrane is regular in appearance and made up of protein and lipids, in around equal measure, whilst the outer membrane contains porin proteins making it more permeable. The internal membrane is merely widely permeable to oxygen, water and skin tightening and it contains many infoldings, or cristae, that protrude into the central matrix space, significantly increasing the surface area and offering it an unusual shape. As can be seen in Physique 1, mitochondria contain ribosomes and also have their own hereditary materials, mitochondrial DNA (mtDNA), independent from the nuclear DNA. (4)

Mitochondria will be the rule sites of ATP creation- in an activity known as oxidative phosphorylation. Products of the Krebs routine, NADH + H+ and FADH2, are carried forwards to the electron carry chain (ETC) and are oxidised to NAD+ and Gimmick, liberating hydrogen atoms. These hydrogen atoms break up to produce protons and electrons, and the electrons are passed down the ETC between electron companies, dropping energy at each level. This energy is utilised by pumping the protons into the intermembranal space triggering an electrochemical gradient between the intermembranal space and the mitochondrial matrix. The protons diffuse down the electrochemical gradient through specific channels on the stalked allergens of the cristae, where ATPsynthase located at the stalked particles, supplies electronic potential energy to convert ADP and inorganic phosphate to ATP. In mammalian cells, enzymes in the interior mitochondrial membrane and central matrix space carry out the terminal periods of blood sugar and fatty acid oxidation along the way of ATP synthesis. Mitochondria also play an important role in the regulation of ionised calcium mineral concentration within cells, largely because of the ability to accumulate substantial amounts of calcium. (3)(5)

Chloroplasts are membrane-bound organelles found within photosynthetic eukaryotes. Chloroplasts are encircled by a two times membrane, the outer membrane being regular to look at whilst the internal membrane contains infoldings to form an interconnected system of disc-shaped sacs called thylakoids. These are often arranged directly into stacks called grana. Enclosed within the internal membrane of the chloroplast is a fluid-filled region called the stroma, formulated with water and the enzymes necessary for the light-independent reactions (the Calvin routine) in photosynthesis. The thylakoid membrane is the site of the light based mostly reactions in photosynthesis, possesses photosynthetic pigments (such as chlorophyll and carotenoids) and electron carry chains. Chloroplasts, like mitochondria, contain ribosomes and their own independent DNA (ctDNA), which is central to the idea of endosymbiosis. The composition of a typical chloroplast is shown by Amount 2:

Radiant energy is caught by photosynthetic pigments and used to excite electrons in order to create ATP by photophosphorylation. The light based mostly reactions occur in the thylakoid membrane (Photosystem II or P680) and eventually, these reactions produce the ATP and NADPH necessary for photosynthesis to keep in the stroma (where Photosystem I or P700 is located). A series of light 3rd party reactions happen within the stroma producing sugars from carbon dioxide and normal water using ATP and NADPH.

The most backed hypothesis (put forward by Lynn Margulis) for the origin of the eukaryotic cell is that of endosymbiosis which is suitably called as 'symbiosis occurs when two different species benefit from living and working alongside one another. When one organism actually lives inside the other it's called endosymbiosis. '(6) The endosymbiosis hypothesis expresses that 'the modern, or organelle-containing eukaryotic cell evolved in steps through the steady incorporation of chemo-organotrophic and phototrophic symbionts from the site Bacteria. ' In other words, chloroplasts and mitochondria of modern-day eukaryotes arose from the secure incorporation into another type of cell of any chemoorganotrophic bacterium, which underwent facultative aerobic respiration, and a cyanobacterium, which carried out oxygenic photosynthesis. The beneficial association between the engulfed prokaryote and eukaryote could have given the eukaryote an edge over neighbouring skin cells, and the idea is usually that the prokaryote and eukaryote lost the capability to live individually. (1)

Oxygen was a key point in endosymbiosis and in the surge of the eukaryotic cell through its creation in photosynthesis by the ancestor of the chloroplast and its own utilization in energy-producing metabolic procedures by the ancestor of the mitochondrion. It really is well worth noting that eukaryotes underwent immediate evolution, most probably because of their capability to exploit sunlight for energy and the higher yields of energy released by aerobic respiration. Support for the endosymbiosis hypothesis are available in the physiology and metabolism of mitochondria and chloroplasts, as well as the composition and sequence of these genomes. (1) Similarities between modern-day chloroplasts, mitochondria, and prokaryotes relative to eukaryotes are shown in table 2:

Mitochondria - are they really separate organisms that once merged into eukaryotic cells? - Biology

Evidence for endosymbiosis

Biologist Lynn Margulis first made the case for endosymbiosis in the 1960s, but for many years other biologists were skeptical. Although Jeon watched his amoebae become infected with the x-bacteria and then evolve to depend upon them, no one was around over a billion years ago to observe the events of endosymbiosis. Why should we think that a mitochondrion used to be a free-living organism in its own right? It turns out that many lines of evidence support this idea. Most important are the many striking similarities between prokaryotes (like bacteria) and mitochondria:

    Membranes — Mitochondria have their own cell membranes, just like a prokaryotic cell does.

When you look at it this way, mitochondria really resemble tiny bacteria making their livings inside eukaryotic cells! Based on decades of accumulated evidence, the scientific community supports Margulis's ideas: endosymbiosis is the best explanation for the evolution of the eukaryotic cell.

What's more, the evidence for endosymbiosis applies not only to mitochondria, but to other cellular organelles as well. Chloroplasts are like tiny green factories within plant cells that help convert energy from sunlight into sugars, and they have many similarities to mitochondria. The evidence suggests that these chloroplast organelles were also once free-living bacteria.

The endosymbiotic event that generated mitochondria must have happened early in the history of eukaryotes, because all eukaryotes have them. Then, later, a similar event brought chloroplasts into some eukaryotic cells, creating the lineage that led to plants.

The Unique Merger That Made You (and Ewe, and Yew)

A t first glance, a tree could not be more different from the caterpillars that eat its leaves, the mushrooms sprouting from its bark, the grass growing by its trunk, or the humans canoodling under its shade. Appearances, however, can be deceiving. Zoom in closely, and you will see that these organisms are all surprisingly similar at a microscopic level. Specifically, they all consist of cells that share the same basic architecture.

These cells contain a central nucleus—a command center that is stuffed with DNA and walled off by a membrane. Surrounding it are many smaller compartments that act like tiny organs, carrying out specialized tasks like storing molecules or making proteins. Among these are the mitochondria—bean-shaped power plants that provide the cells with energy.

This combination of features is shared by almost every cell in every animal, plant, fungus, and alga, a group of organisms known as “eukaryotes.”

Bacteria showcase a second, simpler way of building a cell—one that preceded the complex eukaryotes by at least a billion years. These “prokaryotes” always consist of a single cell, which is smaller than a typical eukaryotic one and bereft of internal compartments like mitochondria and a nucleus. Even though limited to a relatively simple cell, bacteria are impressive survival machines. They colonize every possible habitat, from miles-high clouds to the deep ocean. They have a dazzling array of biological tricks that allow them to cause diseases, eat crude oil, conduct electric currents, draw power from the Sun, and communicate with each other.

Still, without the eukaryotic architecture, bacteria are forever constrained in size and complexity. Sure, they have their amazing skill sets, but it’s the eukaryotes that cover the Earth in forest and grassland, that navigate the planet looking for food and mates, that build rockets to Mars.

Why It Pays to Play Around

The 19th-century physicist Hermann von Helmholtz compared his progress in solving a problem to that of a mountain climber “compelled to retrace his steps because his progress stopped.” A mountain climber, von Helmholtz said, “hits upon traces of a fresh. READ MORE

The transition from the classic prokaryotic model to the deluxe eukaryotic one is arguably the most important event in the history of life on Earth. And in more than 3 billion years of existence, it happened exactly once.

Life is full of complex structures that evolve time and again. Individual cells have united to form many-celled creatures like animals and plants on dozens of separate occasions. The same is true for eyes, which have independently evolved time and again. But the eukaryotic cell is a one-off innovation.

Bacteria have repeatedly nudged along the path towards complexity. Some are very big (for microbes) others move in colonies that behave like single, many-celled creatures. But none of them have acquired the full suite of crucial features that define eukaryotes: large size, the nucleus, internal compartments, mitochondria, and more. As Nick Lane from University College London writes, “Bacteria have made a start up every avenue of eukaryotic complexity, but then stopped short.” Why?

The transition is arguably the most important event in the history of life on Earth.

It is not for lack of opportunity. The world is swarming with countless prokaryotes that evolve at breathtaking rates. Even so, they were not quick about inventing eukaryotic cells. Fossils tell us that the oldest bacteria arose between 3 and 3.5 billion years ago, but there are no eukaryotes from before 2.1 billion years ago. Why did the prokaryotes remain as simple cells for so damn long?

There are many possible explanations, but one of these has recently gained a lot of ground. It tells of a prokaryote that somehow found its way inside another, and formed a lasting partnership with its host. This inner cell—a bacterium—abandoned its free-living existence and eventually transformed into the mitochondria. These internal power plants provided the host cell with a bonanza of energy, allowing it to evolve in new directions that other prokaryotes could never reach.

If this story is true, and there are still those who doubt it, then all eukaryotes—every flower and fungus, spider and sparrow, man and woman—descended from a sudden and breathtakingly improbable merger between two microbes. They were our great-great-great-great-. -great-grandparents, and by becoming one, they laid the groundwork for the life forms that seem to make our planet so special. The world as we see it (and the fact that we see it at all eyes are a eukaryotic invention) was irrevocably changed by that fateful union—a union so unlikely that it very well might not have happened at all, leaving our world forever dominated by microbes, never to welcome sophisticated and amazing life like trees, mushrooms, caterpillars, and us.

I n 1905, the Russian biologist Konstantin Mereschkowski first suggested that some parts of eukaryotic cells were once endosymbionts—free-living microbes that took up permanent residence within other cells. He thought the nucleus originated in this way, as did the chloroplasts that allow plant cells to harness sunlight. He missed the mitochondria, but the American anatomist Ivan Wallin pegged them for endosymbionts in 1923.

These ideas were ignored for decades until an American biologist—the late Lynn Margulis—revived them in 1967. In a radical paper, she made the case that mitochondria and chloroplasts were once free-living bacteria that had been sequentially ingested by another ancient microbe. That is why they still have their own tiny genomes and why they still superficially look like bacteria. Margulis argued that endosymbiosis was not a crazy, oddball concept—it was one of the most important leitmotivs in the eukaryotic opera.

The paper was a tour de force of cell biology, biochemistry, geology, genetics, and paleontology. Its conclusion was also grossly unorthodox. At the time, most people believed that mitochondria had simply come from other parts of the cell. “[Endosymbiosis] was taboo,” says Bill Martin from Heinrich Heine University Düsseldorf, in Germany. “You had to sneak into a closet to whisper to yourself about it before coming out again.”

Margulis’ views drew fierce criticism, but she defended with equal vigor. Soon she had the weight of evidence behind her. Genetic studies, for example, showed that mitochondrial DNA is similar to that of free-living bacteria. Now, very few scientists doubt that mergers infused the cells of every animal and plant with the descendants of ancient bacteria.

“[Endosymbiosis] was taboo,” says Bill Martin. “You had to sneak into a closet to whisper to yourself about it before coming out again.”

But the timing of that merger, the nature of its participants, and its relevance to the rise of eukaryotes are all still hotly debated. In recent decades,origin stories for the eukaryotes have sprouted up faster than old ones could be tested, but most fall into two broad camps.

The first—let’s call it the “gradual-origin” group—claimed that prokaryotes evolved into eukaryotes by incrementally growing in size and picking up traits like a nucleus and the ability to swallow other cells. Along the way, these proto-eukaryotes gained mitochondria, because they would regularly engulf bacteria. This story is slow, steady, and classically Darwinian in nature. The acquisition of mitochondria was just another step in a long, gradual transition. This is what the late Margulis believed right till the end.

The alternative—let’s call it the “sudden-origin” camp—is very different. It dispenses with slow, Darwinian progress and says that eukaryotes were born through the abrupt and dramatic union of two prokaryotes. One was a bacterium. The other was part of the other great lineage of prokaryotes: the archaea. (More about them later.) These two microbes look superficially alike, but they are as different in their biochemistry as PCs and Macs are in their operating systems. By merging, they created, in effect, the starting point for the first eukaryotes.

Bill Martin and Miklós Müller put forward one of the earliest versions of this idea in 1998. They called it the hydrogen hypothesis. It involved an ancient archaeon that, like many modern members, drew energy by bonding hydrogen and carbon dioxide to make methane. It partnered with a bacterium that produced hydrogen and carbon dioxide, which the archaeon could then use. Over time, they became inseparable, and the bacterium became a mitochondrion.

There are many variants of this hypothesis, which differ in the reasons for the merger and the exact identities of the archaeon and the bacterium that were involved. But they are all united by one critical feature setting them apart from the gradual-origin ideas: They all say that the host cell was still a bona fide prokaryote. It was an archaeon, through and through. It had not started to grow in size. It did not have a nucleus. It was not on the path to becoming a eukaryote it set off down that path because it merged with a bacterium. As Martin puts it, “The inventions came later.”

This distinction could not be more important. According to the sudden-origin ideas, mitochondria were not just one of many innovations for the early eukaryotes. “The acquisition of mitochondria was the origin of eukaryotes,” says Lane. “They were one and the same event.” If that is right, the rise of the eukaryotes was a fundamentally different sort of evolutionary transition than the gradual changes that led to the eye, or photosynthesis, or the move from sea to land. It was a fluke event of incredible improbability—one that, as far as we know, only happened after a billion years of life on Earth and has not been repeated in the 2 billion years since. “It’s a fun and thrilling possibility,” says Lane. “It may not be true, but it’s beautiful.”

I n 1977, microbiologist Carl Woese had the bright idea of comparing different organisms by sequencing their genes. This is an everyday part of modern biology, but at the time, scientists relied on physical traits to deduce the evolutionary relationships between different species. Comparing genes was bold and new, and it would play a critical role in showing how complicated life like us—the eukaryotes—came to be.

Woese focused on 16S rRNA, a gene that is involved in the essential task of making proteins and is found in all living things. Woese reasoned that as organisms diverge into new species, their versions of rRNA should become increasingly dissimilar. By comparing the gene across a range of prokaryotes and eukaryotes, the branches of the tree of life should reveal themselves.

They did, but no one expected the results. Woese’s tree had three main branches. Bacteria and eukaryotes sat on two of them. But the third consisted of an obscure bunch of prokaryotes that had been found in hot, inhospitable environments. Woese called them archaea, from the Greek word for ancient. Everyone had taken them for obscure types of bacteria, but Woese’s tree announced them as a third domain of life. It was as if everyone was staring at a world map, and Woese had politely shown that a full third of it had been folded underneath.

These two microbes look superficially alike, but they are as different in their biochemistry as PCs and Macs are in their operating systems.

In Woese’s classic three-domain tree, the eukaryotes and archaea are sister groups. They both evolved from a shared ancestor that split off from the bacteria very early in the history of life on Earth. But this tidy picture started to unravel in the 1990s, as the era of modern genetics kicked into high gear and scientists started sequencing more eukaryotic genes. Some were indeed closely related to archaeal genes, but others turned out to be more closely related to bacterial ones. The eukaryotes turned out to be a confusing hodgepodge, and their evolutionary affinities kept on shifting with every new sequenced gene.

In 2004, James Lake changed the rules of engagement. Rather than looking at any single gene, he and his colleague Maria Rivera compared the entire genomes of two eukaryotes, three bacteria, and three archaea. Their analysis supported the merger-first ideas: They concluded that the common ancestor of all life diverged into bacteria and archaea, which evolved independently until two of their members suddenly merged. This created the first eukaryotes and closed what now appeared to be a “ring of life.” Before that fateful encounter, life had just two major domains. Afterward, it had three.

Rivera and Lake were later criticized for only looking at seven species, but no one could possibly accuse Irish evolutionary biologist James McInerney of the same fault. In 2007, he crafted a super-tree using more than 5,700 genes from across the genomes of 168 prokaryotes and 17 eukaryotes. His conclusion was the same: Eukaryotes are merger organisms, formed through an ancient symbiosis between a bacterium and an archaeon.

The genes from these partners have not integrated seamlessly. They behave like immigrants in New York’s Asian and Latino communities, who share the same city but dominate different areas. For example, they mostly interact with their own kind: archaeal genes with other archaeal genes, and bacterial genes with bacterial genes. “You’ve got two groups in the playground and they’re playing with each other differently, because they’ve spent different amounts of time with each other,” says McInerney.

They also do different jobs. The archaeal genes are more likely to be involved in copying and making use of DNA. The bacterial genes are more involved in breaking down food, making nutrients, and the other day-to-day aspects of being a microbe. And although the archaeal genes are outnumbered by their bacterial neighbors by 4 to 1, they seem to be more important. They are nearly twice as active. They produce proteins that play more central roles in their respective cells. They are more likely to kill their host if they are mistakenly deleted. Over the last four years, McInerney has found this same pattern again and again, in yeast, in humans, in dozens of other eukaryotes.

This all makes sense if you believe the sudden-origin idea. When those ancient partners merged, the immigrant bacterial genes had to be integrated around a native archaeal network, which had already been evolving together for countless generations. They did integrate, and while many of the archaeal genes were displaced, an elite set could not be ousted. Despite 2 billion years of evolution, this core network remains, and retains a pivotal role out of all proportion to their small number.

T he sudden-origin hypothesis makes one critical prediction: All eukaryotes must have mitochondria. Any exceptions would be fatal, and in the 1980s, it started to look like there were exceptions aplenty.

If you drink the wrong glass of water in the wrong part of the world, your intestines might become home to a gut parasite called Giardia. In the weeks that follow, you can look forward to intense stomach cramps and violent diarrhea. Agony aside, Giardia has a bizarre and interesting anatomy. Itconsists of a single cell that looks like a malevolent teardrop with four tail-like filaments. Inside, it has not one nucleus but two. It is clearly a eukaryote.

But it has no mitochondria.

Mitochondria (left) are domesticated versions of bacteria (right) that now provide the cells of every animal, plant and fungus with energy. Shutterstock

There are at least a thousand other single-celled eukaryotes, mostly parasites, which also lack mitochondria. They were once called archezoans, and their missing power plants made them focal points for the debate around eukaryotic origins. They seemed to be living remnants of a time when prokaryotes had already turned into primitive eukaryotes, but before they picked up their mitochondria. Their very existence testified that mitochondria were a late acquisition in the rise of eukaryotes, and threatened to deal a knockout blow to the sudden-origin tales.

That blow was deflected in the 1990s, when scientists slowly realized that Giardia and its ilk have genes that are only ever found in the mitochondria of other eukaryotes. These archezoans must have once had mitochondria, which were later lost or transformed into other cellular compartments. They aren’t primitive eukaryotes from a time before the mitochondrial merger—they are advanced eukaryotes that have degenerated, just as tapeworms and other parasites often lose complex organs they no longer need after they adopt a parasitic way of life. “We’ve yet to find a single primitive, mitochondria-free eukaryote,” says McInerney, “and we’ve done a lot of looking.”

With the archezoan club dismantled, the sudden-origin ideas returned to the fore with renewed vigor. “We predicted that all eukaryotes had a mitochondrion,” says Martin. “Everyone was laughing at the time, but it’s now textbook knowledge. I claim victory. Nobody’s giving it to me—except the textbooks.”

I f mitochondria were so important, why have they only evolved once? And for that matter, why have eukaryotes only evolved once?

Nick Lane and Bill Martin answered both questions in 2010, in a bravura paper called, “The energetics of genome complexity,” published in Nature. In a string of simple calculations and elegant logic, they reasoned that prokaryotes have stayed simple because they cannot afford the gas-guzzling lifestyle that all eukaryotes lead. In the paraphrased words of Scotty: They cannae do it, captain, they just don’t have the power.

Lane and Martin argued that for a cell to become more complex, it needs a bigger genome. Today, for example, the average eukaryotic genome is around 100–10,000 1 times bigger than the average prokaryotic one. But big genomes don’t come for free. A cell needs energy to copy its DNA and to use the information encoded by its genes to make proteins. The latter, in particular, is the most expensive task that a cell performs, soaking up three-quarters of its total energy supply. If a bacterium or archaeon was to expand its genome by 10 times, it would need roughly 10 times more energy to fund the construction of its extra proteins.

It was as if everyone was staring at a world map, and Woese had politely shown that a full third of it had been folded underneath.

One solution might be to get bigger. The energy-producing reactions that drive prokaryotes take place across their membranes, so a bigger cell with a larger membrane would have a bigger energy supply. But bigger cells also need to make more proteins, so they would burn more energy than they gained. If a prokaryote scaled up to the same size and genome of a eukaryotic cell, it would end up with 230,000 times less energy to spend on each gene! Even if this woefully inefficient wretch could survive in isolation, it would be easily outcompeted by other prokaryotes.

Prokaryotes are stuck in an energetic canyon that keeps them simple and small. They have no way of climbing out. If anything, evolution drives them in the opposite direction, mercilessly pruning their genomes into a ring of densely packed and overlapping genes. Only once did a prokaryote escape from the canyon, through a singular and improbable trick—it acquired mitochondria.

Mitochondria have an inner membrane that folds in on itself like heavily ruched fabric. They offer their host cells a huge surface area for energy-producing chemical reactions. But these reactions are volatile, fickle things. They involve a chain of proteins in the mitochondrial membranes that release energy by stripping electrons from food molecules, passing them along to one another, and dumping them onto oxygen. This produces high electric voltages and unstable molecules. If anything goes wrong, the cell can easily die.

But mitochondria also have a tiny stock of DNA that encodes about a dozen of the proteins that take part in these electron-transfer chains. They can quickly make more or less of any of the participating proteins, to keep the voltages across their membranes under check. They supply both power and the ability to control that power. And they do that without having to bother the nucleus. They are specialized to harness energy. Mitochondria are truly the powerhouse of the eukaryotic cell. “The command center is too bureaucratic and far away to do anything,” says Lane. “You need to have these small teams, which have limited powers but can use them at their discretion to respond to local situations. If they’re not there, everything dies.”

If intelligent aliens did exist, they would probably have something like mitochondria, too.

Prokaryotes do not have powerhouses they are powerhouses. They can fold their membranes inwards to gain extra space for producing energy, and many do. But they do not have the secondary DNA outposts that produce high-energy molecules so the central government (the nucleus) has the time and energy to undertake evolutionary experiments.

The only way to do that is to merge with another cell. When one archaeon did so, it instantly leapt out of its energetic canyon, powered by its new bacterial partner. It could afford to expand its genome, to experiment with new types of genes and proteins, to get bigger, and to evolve down new and innovative routes. It could form a nucleus to contain its genetic material, and absorb other microbes to use as new tiny organs, like the chloroplasts that perform photosynthesis in plants. “You need a mitochondrial level of power to finance those evolutionary adventures,” says Martin. “They don’t come for free.”

Lane and Martin’s argument is a huge boon for the sudden-origin hypothesis. To become complex, cells need the stable, distributed energy supply that only mitochondria can provide. Without these internal power stations, other prokaryotes, for all their evolutionary ingenuity, have always stayed as single, simple cells.

The kind of merger that creates mitochondria seems to be a ludicrously unlikely event. Prokaryotes have only managed it once in more than 3 billion years, despite coming into contact with each other all the time. “There must have been thousands or millions of these cases over evolutionary time, but they’ve got to find a way of getting along, of reconciling and co-adapting to each other,” says Lane. “That seems to be genuinely difficult.”

This improbability has implications for the search for alien life. On other worlds with the right chemical conditions, Lane believes that life would be sure to emerge. But without a fateful merger, it would be forever microbial. Perhaps this is the answer to the Fermi paradox—the puzzling contradiction between the high apparent odds that intelligent life would exist elsewhere among the billions of planets in the Milky Way, and our inability to find any signs of such intelligence. As Lane wrote in 2010, “The unavoidable conclusion is that the universe should be full of bacteria, but more complex life will be rare.” And if intelligent aliens did exist, they would probably have something like mitochondria, too.

T he origin of eukaryotes is, by no means, a settled matter of fact. Ideas have waxed and waned in influence, and although many lines of evidence currently point to a sudden origin, there is still plenty of dissent. Some scientists support radical notions like the idea that prokaryotes are versions of eukaryotes that evolved to greater simplicity, rather than their ancestors. Others remain stalwart devotees of Woese’s tree.

Writing in 2007, Anthony Poole and David Penny accused the sudden-origin camp of pushing “mechanisms founded in unfettered imagination.” They pointed out that archaea and bacteria do not engulf one another—that’s a hallmark of eukaryotes. It is easy to see how a primitive eukaryote might have gained mitochondria by engulfing a bacterium, but very hard to picture how a relatively simple archaeon did so.

This powerful retort has lost some of its sting thanks to a white insect called the citrus mealybug. Its cells contain a bacterium called Tremblaya, and Tremblaya contains another bacterium called Moranella. Here is a prokaryote that somehow has another prokaryote living inside it, despite its apparent inability to engulf anything.

Still, the details of how the initial archaeon-bacterium merger happened are still a mystery. How did one get inside the other? What sealed their partnership—was it hydrogen, as Martin and Müller suggested, or something else? How did they manage to stay conjoined? “I think we have the roadmap right, but we don’t have all the white lines and the signposts in place,” says Martin. “We have the big picture but not all the details.”

Perhaps we will never know for sure. The origin of eukaryotes happened so far back in time that it’s a wonder we have even an inkling of what happened. Dissent is inevitable uncertainty, guaranteed.

“You can’t convince everyone about anything in early evolution, because they hold to their own beliefs,” says Martin. “But I’m not worried about trying to convince anyone. I’ve solved these problems to my own satisfaction and it all looks pretty consistent. I’m happy.”

Ed Yong is an award-winning science writer. His work has appeared in Wired, Nature, the BBC, New Scientist, the Guardian, the Times, Aeon, Discover, Scientific American, The Scientist, the BMJ, Slate, and more.

This article originally appeared in our “Mergers & Acquisitions” issue in February 2014.

CPS Biology!

After reading the article about reading Lynn Margulis, I have to disagree with my so-called cousin. I agree that there isn’t a direct evolutionary link between prokaryotes and eukaryotes like those between other related organisms, but that doesn’t mean prokaryotes were not involved in the development of eukaryotes. My “cousin” might disagree with me on that because the way in which eukaryotes were involved may not be found in any other example of evolution. The theory that argues this is called the Serial Endosymbiotic Theory (or SET). The Serial Endosymbiotic Theory states that eukaryotic bacteria came about by certain prokaryotic bacteria engulfing other prokaryotic bacteria that could metabolize well or photosynthesize, for example, in their cell membranes and forming a symbiotic relationship with them. These simpler prokaryotic bacteria that had good metabolisms or could photosynthesize, over generations, became the eukaryotic organelles like the mitochondria or chloroplasts (respectively). The Serial Endosybiotic Theory also challenges another one of ID’s counter-arguments, namely, the flagellum. Intelligent Design claims that the flagellum is such a complex organelle that there could not have been more simpler versions of it on a host cell that survived long enough to reproduce. While some scientists point to underdeveloped flagella on some bacteria to disprove this, the SET argues that the eukaryotic flagellum is another organelle that evolved from a prokaryotic symbiote. That, and the fact that eukaryotic and prokaryotic bacteria’s flagella have very different structures, led Margulis to try to have the eukaryotic flagellum labeled by a different name the undulipodium.

This cousin of mine must not see Margulis' SET theory in such a black and white perspective. Although he/she has a valid point, there are explanations of the SET theory that contradict his/her statement. For instance, eukaryotic cells evolved through a SERIES of symbiotic partnerships. These "series" can arguably be the intermediate steps which he claims the evolution lacks because this modifications occurred as a series of "discrete events". Later on these series evolved into three different kinds of organelles: chloroplasts, mitochondria and flagella. The first two prokaryotic organisms were simple photosynthesis bacteria and fermenting bacteria. These later became prokaryotes that were aerobic. The prokaryotes would detoxify oxygen through respiration. This development of repsiration set the stage for the evolution of eukaryotic cells as these new cells would also be able to detoxify oxygen. Today, if one is to examine both free living bacteria and eukaryotic cells, they will find many similarities between the two. These similarities prove that there were intermediate steps. The evidence Margulis presented through when establishing the SET theory contradicts my cousin's statement.

Although irreducible complexity would seem like a strong argument towards intelligent design, Margulis' SET theory can contradict it. SET shows that eukaryotic cells, cells presumed to be the most basic life form in biology, actually "evolved" from the symbiosis of several prokaryotic cells. Margulis theorized that small, photosynthetic or energy producing prokaryotes, over time, as cells reproduced these undigested "cells within cells" and became more common, they came to be considered key energy producing organelles such as chloroplasts or mitochondria. This shows that eukaryotic cells could, in fact, be "reduced" to simpler elements, having evolved through time.
One living example of an intermediary stage of this form of evolution is the ciliate Strombidium Purpureum that houses a photosynthetic and respiratory bacteria symbiotically living inside of it. Living in an anaerobic environment, similar to earth's early atmospheric stages, the ciliate receives energy from this bacteria in the form of ATP, used in many cellular functions of Eukaryotic cells.
Lastly, SET theorizes that the flagella found in eukaryotic cells also arose from the symbiosis of two cells. Spirochetes, cells that use a corkscrew motion to for mobility, may have fuse with other cells, to develop the uniquely eukaryotic flagellum. Although this theory still needs to be researched and refined further, it would appear that my cousin needs to do some research about the substantiated Serial Endosymbiotic Theory.

The irreducible complexity argument that my "cousin" uses to prove intelligent design is utterly disproven by the endosymbiosis article by Lynn Margulis. This argument of intelligent design revolves around the basis that a direct evolutionary link needs to be found between cells that didn't have mitochondria and cells that did have them. Serial Endosymbiotic theory answers this claim (by partially bypassing it as well). The well-accepted theory states that prokaryotic bacteria engulfed other prokaryotic bacteria that were better at photosynthesis or the production of ATP. Most of the time, the engulfed prokaryotic cells would have been digested, but in some cases, for unknown reasons, the two cells would have a tense relationship, the smaller energy producing cell existing inside the larger one. In return, the larger cell provided protection. This partnership would have proven to have enough benefits that the cells that had said partnership would have better chances at survival and would have enabled those cells to have greater odds at reproducing: by the process of natural selection, those cells, with that symbiotic relationship with their smaller partner, would have become more and more commonplace. Over time, the smaller, energy-producing prokaryotic cell located in the larger cell would have lost unnecessary functions and have become completely dependent on its host-it would have merged. Likewise, the larger host cell would have become completely dependent on its smaller partner to supply it with energy. This argument answers the argument of irreducible complexity because it shows that evolution of mitochondria and chloroplasts (via regular means) did not necessarily occur: symbiosis could have led to the same thing, and in fact was more likely. Incredibly complex organelles didn't have to evolve-maybe they were imported instead. This argument therefore takes out the irreducible complexity argument, which is based on the premise that it is impossible for very complicated and precise cell parts to have merely evolved "by chance."

I wouldn't agree with the long-lost cousin because there is too much extra evidence that helps to show it happened through evolution. The way I see it, intelligent design is only an excuse for something that we don't know exactly how it happened. In other words, when something happens that we can't explain with sufficient evidence, but we still need a reason for it to have happened, people "blame"/ attribute the occurrence of this confusing subject on God.
Something such as the flagella (a concept which doesn't have much evidence to back up its evolution) might be acceptably and understandably thought of as coming from intelligent design. This is only because it is something that doesn't seem to have enough evidence backing up its evolutionary process (or lack of one). I think that part of the reason it is acceptable (to me at least) for someone to think of these things as coming from intelligent design is that there is no other reason to explain a happening like this, but people need something so that they can base other science off of something. Personally, I wouldn't use Intelligent Design to explain anything, but I can see why someone would.
The case of the eukaryotic cells versus prokaryotic cells does not seem to me like a case of Intelligent Design. There is so much evidence and scientific support that shows why and how these types of organisms can be so profoundly different from one another and have basically no middle ground in between. The fact that the SET states that eukaryotic bacteria were formed by one prokaryotic bacteria "eating" another prokaryotic bacteria shows that there is obviously no way there could have been a middle ground because the eukaryotic bacteria came from the prokaryotic bacteria directly. This seems to me like sufficient evidence in favor of natural evolution (and not Intelligent Design).

Unlike many of the people who have responded thus far, I actually have cousins in Alabama, and I'm sorry to say that they are not taught Intelligent Design in schools like we steriotypically think here in the Bay Area. But no matter. If this hypothetical situation did arise I would respond that my cousin was correct to think that there are few to no intermidiates between prokaryotic cells and eukaryotic cells. However, Lynn Margulis provides us with a theory to bridge the gap that isn't an intelligent designer. She proposes that serial endosymbiotic theory explains the developement of eukaryotic cells. and he has gather a large array of evidence to support her claim. SET, her theory, suggests that eukaryotic cells developed from a beneficial partnership between two prokaryotic cells. This partnership began when one of the cells "ate" the a second cell but the second cells was able to avoid being digusted by the predetor cell. Thus, the two cells began to coexist. Some of the partnerships were beneficial for the two cells involved. An example of this is the when a predetory prokaryote cell ate an anaerobic prokaryote. The anaerobic prokaryote (precursor of the mitochondria) helped the predetory cell survive in an oxygene rich enviroment, and the anaerobic prokaryote was provided fuel and protected from outside attack by its host. As time progressed, the two cells became so interdependent that they lost the ability to survive without each other. The anaerobic prokaryote lost its ability to do the metobolic functions the host cell did and the host cell needed its partner to detoxify the oxygene gas in the air. Thus, the precursor of the eukaryotic cell was born out of these partnerships. There are no intermidiates because none of the prokaryotic cells developed organelles on there own. Instead, these organelles were created by partnerships between two cells. I have one last observation I feel obliged to point out. It is that at most southern family gatherings (although I can only speak for my own family) contraversial topics like this are avoided like the plague.

Especially after having read the essay about SET, I would definitely disagree with this long-lost cousin. even before having read the article, I believed simply labeling a complex body part etc. as a result of intelligent design was a "simple way out." Just because at the moment there's no explanation for how an extremely complex structure came to be by evolution doesn't mean that there is no possible scientific explanation.
But now, having read about SET, I think that there is definitely some pretty legitimate proof that it is no Intelligent Design at work with eukaryotic cells. Margulis' work provided a very compelling argument for the evolutionary development of extremely important organelles in the cell, such as the mitochondria and the chloroplasts. The idea "irreducibly complex" eukaryotic cell is completely undermined, because Margulis provides the explanation for the development of such structures. For example, the mitochondria must have been extremely archaic prokaryotic bacteria at some point in time, and became parasitic. When the first photosynthetic cells began to photosynthesize, releasing into the atmosphere oxygen, a highly reactive gas. Prokaryotes tired to adapt, (very few) some hid in the most "unoxygenated" areas they could find, while many others used these parasitic mitochondria that used oxygen to help keep these cells alive. (To explain it extremely simply)
So, with such a clear contradiction of what my cousin claimed, at least for the mitochondria, the chloroplasts, and potentially the flagellum my cousin's assertion that ID is responsible for the eukaryotic cell is completely inaccurate.

Well George, it is interesting that you feel these eukaryotic cell structures support Intelligent Design because I happen to have just read an article about this very subject quite recently. One part of your argument is quite valid. Thus far there have been no fossils found to prove the existence of intermediary steps from simple prokaryotic cells to the seemingly perfectly adapted structures contained within plant, animal and fungal cells today. However, Lynn Margolis has proposed a theory to the scientific community, which explains how evolution could even still have created these organelles. Serial Endosymbiotic Theory, or SET, is based upon the primary idea that ancient cells could have evolved to include photosynthesizing and metabolizing bodies rather rapidly, due to external pressures in their ecosystems. The SET argues that this evolution could have been the product of a changing environment billions of years ago, as well as the emergence of special symbiotic relationships between larger cells and smaller, more specialized, ones. Margulis explains that early on cells may have consumed or were invaded by smaller bacteria-like cells but not have been able to fully digest them. Instead, these smaller cells would share a mutually-beneficial relationship with the host cell, trading their detoxification for the production of sugar cells and protection offered by larger cells. And George, surely you can see that soon this relationship because not just helpful, but mandatory, as each partner started to rely on the other for survival. Soon, structures like these small bacteria were necessary in larger cells and as such the cells evolved. Just to make sure you believe me, I’ll give you a few pieces of evidence that Margulis uses to back up the SET. First, she examines structures such as chloroplasts and mitochondria, and finds that these complex organelles actually contain pockets of DNA similar to that found in archaic (and also some modern) bacteria. This points to the idea that these structures were once their own separate organisms. As to why this relationship would have developed in the first place, Margulis explains that billions of years ago a certain group of organisms started creating oxygen, a dangerously reactive gas. In order to cope with this harmful substance, cells would have needed to pair up with cells that could turn this gas into something useful. So do you see now George? Even complicated biological structures can be explained logically through studying the history of the organisms. Evolution really isn’t as impossible as you think it is.

The idea of Intelligent Design that my long-lost cousin is contradicted by Lynn Margulis's theory, SET. If someone was looking for a way to "prove" Intelligent Design to be correct, pointing out the lack of intermediaries between prokaryotic cells and eukaryotic cells might be a first choice, because the lack of intermediaries might show irriducible complexity. However, SET contradicts this idea. In SET, some prokaryotic bacteria "ate" or engulfed another prokaryotic bacteria. While some of the bacteria was digested, some was not. The undigested bacteria and the bacteria that swallowed it formed a symbiotic relationship. The outer bacteria provided protection, and the inner one helping with the oxygen. Eventually the symbiotic relationships became neccesary for the cells to survive. The inner cells became organelles. Because the cells combined instead of one cell slowly changing, there would not be intermediates between prokaryotic and eukaryotic cells. So, this idea is not evidence for irriducible complexity or ID.

To respond to my long lost cousin, I would counter his/her assertions that eukaryotic cells are a good example of ID, meaning that eukaryotic can’t have evolved from previous cells due to their irreducible complexity, with Margulis’ SET. According to Margulis, eukaryotic cells evolved through a series of symbiotic partnerships which involved prokaryotic cells. The process consisted of prokaryotic bacteria engulfing other prokaryotic bacteria that carried out photosynthesis or ATP production better. Normally, the smaller cell would have simply been digested, but some times, it continued to live inside its host. After some time, the small engulfed cell and the larger host cell became mutually dependent on one another. Eventually, their partnerships were so beneficial, that those that had the partnerships survived, and by natural selection, became more popular. Her theory states that smaller cells lived inside the larger host cells and eventually evolved into the energy producing organelles such as mitochondria and chloroplasts. Thus, Margulis’s theory proves that eukaryotic cells could be broken down into smaller, simpler molecules with the help of time. This disproves the assumption of my cousin that eukaryotic cells are an example of something so complex that it couldn’t have evolved.
-Callie Roberts

I disagree with my cousin that eukaryotic cells are too complicated to have been developed through traditional evolutionary means and are therefore evidence for intelligent design. My cousin believes that the sharp distinction between eukaryotic cells and prokaryotic cells is too great to be explained by gradual changes, however, SET explains this sharp distinction through a series of discrete events. According to Margulis's theory, eukaryotic cells were developed through a number of symbiotic relationships between smaller bacteria and several different types of host prokaryotic cells. The partnership between the host cell and the invading bacteria developed into three different organelles. There are also similarities between the free-living bacteria and the organelles found inside a eukaryotic cell. For example, the eukaryotic flagella have a method of swimming similar to that of spirochetes.

I understand my cousin's thoughts that there are no intermediates, however I would have to disagree with what he said. In Lynn Margulis' essay on how cells evolved the SET theory is introduced. SET is the Serial Endosymbiotic Theory. This theory has many parts that cause eukaryotic cells to not be an example of irreducible complexity. The SET theory states that eukaryotic cells evolved through a series of symbiotic pernerships. These partnerships involved many different kinds of prokaryotic that would eccentially eat smaller prokaryotic cells, evolving eventually into three kinds of organelles. These different organelles are mitochondria, chloroplasts, and flagella. These steps in evolution supposedly were a series of "discrete events". One example of SET is the evolution of mitochondria, which is found in almost all eukaryotic cells. According to Margulis, small respiring bacteria could burrow through cell walls of their prey and go into their cytoplasm. Sometimes this killed either the host or the parasite, but other times the two managed to survive. Each one benefited differently from their coexistence. The paraiste required oxygen, and allowed its host to survive in oxygen rich environments that the host had once not been able to survive in. Sometimes the parasite also gave some of its ATP to the host. The host then provided sugar and other organic molecules to act as fuel for the aerobic respiration. Eventually the two became more and more dependent on each other, and their once "opportunistic parasitism evolved into an obligatory parnership." Eventually the small respiratory bacteria evolved into the mitochondria of eukaryotic cells. Other examples she has are of the Choloplast and the flagella.
Because of the research Margulis did and the article I read about her I definatly disagree with my cousin, however I would be willing to hear out his opinions and have a scientific debate with him.

If my cousin were to look closely at Margulis' studies of prokaryotes versus eukaryotes,I'm sure s/he would come to understand why Margulis established her theory of SET. Prokaryotes are dissimilar to eukaryotes, and a lot less complicated. However, it is evident that the combination of prokaryotes could have resulted in a mutually beneficial relationship, and the reproduction of a complicated eukaryote. Just because for instance, the mitochondria of present eukaryotes, could not exist as separate entities from the rest of the organism, does not mean that a long time ago, those were not merely organelles, but separate organisms that could metabolize very well. And these prokaryotes were swallowed up by others, eventually becoming inseparable/unable to reproduce independently. I would have to disagree with my cousin, and say that eukaryotes are a good example not of ID, but of organisms forming symbiotic relationships over the course of time.

Although my "cousin's" arguement is logical in the sense that there are few (or no) visible intermediate steps between prokaryotes and eukaryotes, it does not make much sense to say that this means that eukaryotes are a prime example of ID. According to Lynn Margulis, the SET is clear evidence that eukaryotic bacteria exist due to prokaryotes consecutivley consuming other prokaryotes, thus eventually learning to coexist and developing into complex forms of their pervious selves (aka eukaryotes). This process fits the definition of evolution better than that of intelligent design, and therefore does not favor my cousin's position on the matter, because it is a series of unprovoked events which eventually led to a new species of organisms (eukaryotic bacteria).

Eukaryotic cells are definitely not an example of irreducible complexity, and cannot be used to defend the claims of Intelligent Design. First of all, there is no strict evidence that points to the fact that there are no intermediates between prokaryotes and eukaryotes. It is more likely according to Lynn Margulis and the SET, that prokaryotes and the organelles of eukaryotes, which developed as smaller prokaryotic cells, eventually came together to form the earliest eukaryotic cells. One example is the mitochondrion, which has been shown in earlier forms to contain protein-building ribosomes and DNA similar to that of bacteria. Also, the first prokaryotic cells were anaerobic, so when oxygen began to become abundant, they were almost driven to extinction, but when they engulfed or were invaded by other aerobic bacteria such as the mitochondrion, they realized that instead of ingesting it, they could create a symbiotic relationship in which the mitochondria used the oxygen to provide energy for the cell. This must have kept going until the cell engulfed other prokaryotic bacteria such as chloroplasts and established a symbiotic relationship with them. These small, respiring bacteria began to lose the metabolic functions that were provided by the host cells, explaining how they evolved into the organelles they are now, dependent on the cell as a whole.

First off, the fact that it is my cousin would automatically spur an argument about who is right. If he/she (we'll go with she) thinks that irreducible complexity shows strong evidence that ID is correct, then naturally I have to argue that she is completely incorrect. Sure she may be a biology student in college, but I am a biology student at College Prep and I had to read Lynn Margulis' essay so I have much evidence to argue with. If my cousin started off by saying that eukaryotic cells are irreducibly complex because there were no intermediate steps between prokaryotes and eukarytoes, then I would counter by saying "nuh uh". Lynn Margulis' SET states that prokaryotes essentially ate other prokaryotes, and that since there were now two cells living together it was a eukaryote. Of course I would be proud of my answer and ask why she thought eukaryotes were irreducibly complex. Like usual, she should most likely respond with "because I said so". I would then begin to smash her argument explaining why eukaryotes were not irreducible complex: SET argues that prokaryotes came together in and developed a symbiotic relationship (one where both prokaryotes depended on the other to survive). Margulis thought this because she observed prokaryotes that had very similar traits to select parts of eukaryotes. One example of this is a very simple energy producing cell. She thought that this simple cell was engulfed by a different cell and those cells worked together for better living. She thought this type of process eventually evolved into what is now a mitochondria or chloroplast (metabolizer and photosynthesizer). Just like evolution, Margulis concluded that those "irreducibly complex" cells were not so irreducible. Odd and random occurrences once again could be attributed to the evolution of a species, even if they seem unable to work without every single characteristic. As always, my cousin would have nothing left to argue for her statement, and would conclude with a "so?"

Dear Cousin,
The reason that there are no intermediates between the simple prokaryotic cell and the complex Eukaryotic cell is explained by Lynn Margulis’ Serial Endosymbiotic Theory. If you assume that the complexity of a Eukaryotic cell evolved in the fashion dictated by Darwin, then yes, there should be intermediate steps. However, as you stated already dear cousin, there’s a distinct lack of these intermediate phases of development. In Serial Endosymbiotic Theory (SET), it’s put forth that the organelles within a eukaryotic cell didn’t develop through natural selection, but instead were simpler prokaryotic cells that were enveloped by eukaryotic cell. These photosynthetic parasites were sometimes digested, but sometimes they would develop a mutually beneficial relationship with their host in some cases, these parasites would even become required for the host’s lifecycle. Eventually, the parasites would lose their metabolic function, and the respiratory bacteria would eventually evolve into the mitochondria of today’s prokaryotic cells. If you take this theory into account, it makes sense that there are no intermediate forms a mitochondrion, once it has lost metabolic function, can no longer function outside the host cell.

Although the theory of irreducible complexity would seem to support an argument such as intelligent design, the theory of SET would seem to disprove it. The theory of SET states that complex Eukaryotic cells were formed via evolution, just like everything else. The lacking intermediaary steps my cousin is talking about do exist, she just doesn't understand them. The intermediary steps are that prokaryotic cells engulfed other simple prokaryotic thus creating a more complex cell. Eventually, this process created the complex eukaryotic cell. Some evidence Lynn Margulis gives for this theory is that DNA can be found outside the nucleus in chloroplasts and the mitochondria. This points to the cells once being separate. The theory of SET explains scientifically, what you and other proponents of ID say can not.

Although my cousin is correct in saying that eukaryotic cells display a high level of complexity, he is incorrect in assuming that this complexity can only have been created through Intelligent Design. I would explain to my cousin that the reason for this complexity lies in Lynn Margulis's theory of serial endosymbiosis. The basic idea of this theory, also known as SET, is that eukaryotic cells evolved by consuming smaller prokaryotic cells which were indigestible and thus remained within the larger cell. The two cells quickly formed a symbiotic relationship, as one provided food for the other in return for the necessary nutrients for respiration. The smaller cells evolved to be very important parts of their host eukaryotic cells, and they became known as cell organelles. Two key examples of eukaryotic organelles are mitochodria and chloroplasts. Mitochondria provide the cell's ATP, or energy, and chloroplasts photosynthesize, using the sun's light as energy for the larger eukaryotic cell. So, my cousin should understand that a eukaryotic cell is complex because of the organelles that are needed for its survival. They did not just one day appear within the cell but in fact, they were capable of living independantly. Once they became a part ot a larger cell, though, they formed an important relationship which is the basis for Margulis's theory.

Things are rarely proven in science, instead most scientific principles are theories, and although they are only theories they are widely accepted and have yet to be proven wrong. Currently, the Serial Endosymbiotic Theory, as its name suggests is a theory, whereas Intelligent Design is not. The fact that there are no predecessors to today’s modern eukaryotic cells is not necessarily proof that they must a product of intelligent design either. As cells that had not engulfed other smaller cells would be competing for the same necessities of survival but at a serious disadvantage. These other cells, predecessors lacking the smaller cells (that would later evolve into organelles), would likely be facing a rising population of the evolved cells fighting over the same resources, driving them to extinction and removing evidence of the links between the ancient and modern cells. Furthermore there is also a good deal of evidence supporting that at one point in time many of the organelles in modern cells were once individuals cells themselves and were consumed by the larger cell. For example several organelles in modern eukaryotic cells have a double membrane, which would suggest that at one point in time they were separate cells. Moreover Mitochondria and Chloroplasts have their own sets of DNA and reproduce separately from their host cells. So as you can see, eukaroytic cells are not necessarily and example of irreducible complexity infact it is likely that they are a result of evolution through consumption as suggested by the SET.

While my cousin is entitled to their opinion, he or she has clearly failed to realize that the Serial Endosymbiotic theory proves that there were evolutionary changes through symbiotic relationships including a prokaryotic cell which disproves using eukaryotic cells as an example of irreducible complexity. According to Margulis, 4 billion years ago the simplest cell was a globule of water that was surrounded by enzymes and enclosed a couple genes. Eventually the prokaryotic cells used their metabolism without needing oxygen. With the photosynthetic fabrication of oxygen gas and following the evolution of respiration we have the basis of evolution of eukaryotic cells. The mitochondria were the initial to experience evolution. It is important to note that only plants and some protists contained chloroplasts which means that chloroplasts must also have evolved. The evolution of eukaryotic cells also involves the flagellum. My cousin does claim that there are no intermediate forms to show the evolution of eukaryotic cells which shows that these eukaryotes are irreducibly complex. However, the intermediate forms vanished, which lead to few eukaryotic cells gaining the ability to swallow food particles. This proves that the cells became predators and they needed to consume organisms. Consequently, this caused different cells to create a new shielding exterior wall that differed from prokaryotic cells. This is why my cousin can not claim that eukaryotic cells are prime examples of irreducible complexity.

I think i would have to disagree with you, Mr. long lost cousin. Although you are right in saying that scientists have not found intermediate steps between prokaryotes and eukaryotes, Margulis's Serial Endosymbiotic Theory (SET) shows us that eukaryotes aren't an example of irreducible complexity. Margulis's SET theory proposes that one prokaryotic cell engulfed another, without completely digesting it. This resulted in a beneficial partnership between the two cells, each cell helping the other survive in their environment. Over time, the cells became so dependent on each other, that they were unable to separate, resulting in a eukaryotic cell. The reason there aren't any intermediate steps is that the organelles weren't developed by the prokaryotic cell, but by the combination of the two cells. Have fun with your biology studies cuzz

If my long lost cousin were to tell me that he fells this way about evolution then I would explain to him Lynn Margulis’ SET theory and how it disproves his belief in irreducible complexity among prokaryotic and eukaryotic cells. Although Lynn Margulis has provided substantial evidence that suggests that prokaryotic cells evolved into eukaryotic cells I can see how someone could be confused by SET. For example, there is no fossil evidence that shows the intermediate steps of the eurkaryotic evolution. However, SET is widely excepted by the science world and there have been no experiments that would suggest that it is not correct. SET says that simple prokaryotic cells formed symbiotic relationships with other prokaryotic cells, thus, over time, creating completely separate cells that were eukaryotic. The mitochondria, the first organelle to be formed was created by parasitic bacteria invading a larger cell and burrowinginto it. Mostly the bacteria or the cell that it invaded were killed when this happened, but sometimes they were able to work together. In time the cell and the parasitic bacteria created a mutually beneficially relationship. During time this relationship grew stronger as the mitochondria relied on the original cell more for metabolic functions and as oxygen increased in the Earth’s atmosphere the cell relied on the respiratory functions of the bacteria more. This is the earliest form of eukaryotic cell. Several more parts of cells developed in a similar way, including flagella and chloroplasts. As I have said some people find it hard to believe this theory on account of the lack of fossil evidence, however accounting ID for the development of eukaryotic cells is, to me, an easy way out of a difficult problem, SET on the other hand provides a scientific explanation that I find far more convincing.

If a cousin of mine were to give Eukaryotic cells as an example of irreducible complexity then I would explain how although there is no direct evolutionary link between eukaryotic cells and prokaryotic cells, like there are in most other cases of evolution, Lynn Margulis’ serial endosymbiotic theory (SET), gives us a very good explanation of how a prokaryotic sell could evolve into an eukaryotic cell. It started when one bigger Eukaryotic cell ate a smaller one, however for some reason the smaller cell was not digested. What happened was the cells formed and uneasy relationship. The smaller cell produced excess ATP and the larger cell provided the smaller one with protection. When the cells divided they divided at the same time to that the relationship continued. This was the origin of the mitochondria. Scientist have also found DNA in the mitochondria, which supports the claim that at one point it was its own cell. Another way that one part of Eukaryotic cells developed was when cells started photosynthesizing. Because this added huge amount a oxygen to the environment, many species died of oxygen poisoning. However some cells developed ways to deal with the increasing amount of O2, other cells were eaten by the cells that could survive and just like the ATP producing cells formed an uneasy relationship with the cells that have consumed them. The larger cells then had the ability to do photosynthesis and could survive in oxygen rich environment. Finally the cells became so dependent on each other that they had to have this relationship to survive. Through many random occurrences like these we finally got the eukaryotic cells we have today.

My "cousin's" would not be relevant to the evolution of eukaryotic cells, according to Lynn Margulis' theory. If eukaryotic cells were indeed irreducibly complex, than if one were to remove any one part of it, it would not be able to function. But the Serial Endosymbiosis Theory says that at one point, eukaryotic cells did not have some of the organelles, such as the mitochondria. So if eukaryotic cells were indeed irreducibly complex, than these precursors to the modern version would not have been functional, and therefore would not have survived to reproduce and evolve. Back to my "cousin's" argument that there are no intermediate stages between prokaryotic and eurkaryotic cells.
According to SET, there were some intermediate steps, such as those right after one cell engulfed another. So my "cousin's" claim is not true according to SET.

Well. one reason that there are no existing intermediates between very simple prokaryotic cells and the much more complex eukaryotic cell is that they would have died off because natural selection would have favored the more complex eukaryotic cells. According to Lynn Margulis, eukaryotic formed through symbiotic partnerships involving several different kinds of prokaryotic cells. The smaller cells invaded the larger partner and they evolved into three different kinds of organelles: mitochondria, chloroplasts, and flagella. Each cell using the benefits of the other and creating an efficient complex cell (a prokaryotic cell). Although it may be hard to believe, we know that partnerships exist today. I would tell my cousin that prokaryotic cells are not an example of intelligent design that they evolved from several kinds of prokaryotic cells "eating" one another to form a symbiotic partnership and forming various organelles.
Helen M

I would say to my cousin that although there is no direct evidence there are a lot of theories that argue their point very well. Lynn Margulis's theory (SET) about the evolution of eukaryotic cells poses a good argument on how it could have happened. She says that over time cells engulfed other cells and together they formed a symbiotic relationship. Gradually more components were added. Also, when cells combined with other cells those could be argued as being the intermediate steps but as they got new organelles the older cells could have died off due to natural selection, which would leave no intermediate steps for us to find. There is some evidence of intermediary stages still alive today, the Strombidium Purpureum contains a photosynthetic bacteria inside of it. They have a symbiotic relationship. Also, just because their is not as much evidence for the evolution of eukaryotic cells as their is for evolution of other species doesn't mean that some higher being had to have made it. I would disagree strongly with my cousin.

Although my cousin's assertion that eukaryotic cells are a prime example of irreducible complexity may at first seem to be strong evidence for his idea of Intelligent Design, Lynn Margulis' endosymbiotic theory can strongly contradict it. Both Intelligent Design and the Serial Endosymbiotic Theory (SET) say that eukaryotic cells were not the result of gradual evolutionary changes, explaining why there are no intermediates between simple prokaryotic cells and complex eukaryotic cells. However, Intelligent Design cannot explain for why the mitochondria and chloroplasts have their own separate DNA, while SET can. According to SET, the DNA, RNA, and ribosomes found in mitochondria and chloroplasts are remnants of the protein-building machinery of the ancient free-living bacteria that had parasitically entered the host cell, established a symbiotic coexistence, and together evolved to become the mitochondria organelles of today's eukaryotic cells.
-Sterling Watson

My long lost cousin's beliefs that eukaryotic cells show examples of ID would probably be backed by the fact that there are no proof of any intermediaries. However, Lynn Margolis' theory of endosymbiosis and cell evolution show examples that counteract this idea. The endosymbiotic theory is that eukaryotic cells evolved alongside prokaryotic cells through a system or symbiotic relationships. An example of endosymbiosis is when one prokaryotic cell is enveloped by another cell. The eukaryotic and prokaryiotic cells combined, forming a beneficial partnership. After time, the two cells became highly dependent on one another, and the prokaryote could no longer perform metobolic functions of the host cell, and the host cell was reliant on it's partner to detoxify the oxygene gas in the air. After time and through forms of natural selection, the two became inseparable, forming a more efficient eukariotic bacteria. Due to this scientific evidence, my cousin's original perspective on the evolution of the eukaryotic cell has been disproved.

“I’m sorry cuz, but you are totally wrong. Eukaryotic cells most likely evolved from prokaryotic cells, as described by Lynn Margulis, a scientist from the 70’s. In her theory, which is called SET, or Serial Endosymbiotic Theory, she explains that what most likely happened was a big prokaryotic cell devoured a little prokaryotic cell. At this time oxygen was just starting to come into the atmosphere, an only a few cells had developed respiration, which allowed them to move into oxygen-rich places. When the big cell ate the little cell, it became a symbiotic relationship, since the little cell allowed the big cell to move into places full of oxygen and the little one could feed off of what the big one ate. The little cell is today’s mitochondria, which contains its own set of DNA. Scientist’s know today that this “eating” can happen since the Bdelbribrio cell does it today.
Later on, some of these cells containing the mitochrondria…since these cells would survive better there would be a lot of them… ate a photosynthetic cell, which, in the same way, developed into a chloroplast. Chloroplasts also have their own sets of DNA. Scientist’s are also sure that this could happen because the cell Paramecium bursaria is playing host to a green algae cell today. The algae shares the sugar it produces with the Paramecium cell. These two cells can exist independently if we pull them apart. So, cuz, tell me this, if a being invented the eukaryotic cell, why would he/she/it put DNA in multiple places inside the cell.
As for there being no intermediary cells between simple prokaryotic cells and complex eukaryotic cells, it is only more proof for the whole eating thing… if eukaryotic cells had evolved then there would probably be some intermediary cells that are part prokaryotic and part eukaryotic. Cuz, ID just doesn’t hold up to scientific evidence that show how the eukaryotic cell really came into existence.”
-Danielle Glass

After reading the essay on Lynn Margulis and SET, I would have to strongly disagree with my cousin though prokaryotic cells and eukaryotic cells do have major differences, even the idea of irreducible complexity cannot prove they were separately created by an intelligent creator. However, SET can prove, through a series of evolutionary developments, how they came to exist the way they do today. The first organisms were very simple prokaryotic cells that lived in water and fed on organic material created by chemical reactions in the Earth. Soon, they evolved to photosynthesize as the organic molecules’ population (their food source) began to decrease. When new oxygen-excreting bacteria evolved, these primitive cells were mostly wiped out, except for the few that changed to detoxify oxygen by changing it into water molecules. This new development, respiration, led to the evolution of eukaryotic cells mitochondria were the first organelles to evolve. They survived by burrowing their way into prokaryotic cells and establishing a symbiotic relationship, creating the beginnings of a primitive eukaryotic cell. Clearly, SET can prove that there are indeed intermediary steps between prokaryotic and eukaryotic cells, while intelligent design cannot.

The argument that no intermediate steps between prokaryotic and eukaryotic cells evolutionarily disproves the theory of evolution ignores the unique way in which eukaryotic cells evolved. Endosymbiotic theory, the belief that eukaryotic cells began as symbiotic relationships amongst several prokaryotic cells, is able to justify the theory of evolution more than satisfactorily. It points to the existence of independent strands of DNA in mitochondria and chloroplasts as evidence that these structures were once independent cells, which were either engulfed by larger cells or burrowed past their cell membranes into the cytoplasm. At that point, if both cells survived the process, they would form a symbiotic relationship, with the inner cell creating energy for both of them and protecting the outer sell from the dangers of oxygen, and the outer cell capturing the molecules both needed for respiration. Eventually, each of these cells would become dependent on the other, needing the other cell’s function to survive, and the first eukaryotic cells were born.

If my long lost cousin Billiffany (I can't decide if I want my cousin to be a girl or a boy and as a result she/he is stuck with this name which is a combination of Billy and Tiffany. Poor poor Billifany.) were to read all these comments left by my classmates I'm sure that my cousin would probably think that we were all complete idiots for not believing in the theory of Intelligent Design, or maybe Billifany might even be convinced by our arguments. Nonetheless I can't help but feel frustrated that ID has once again come up in our discussions even though everyone is entitled to their own opinions and deductions. Even so, I still have trouble understanding why people would rather trust some Guy sitting on a cloud up in the sky than in a theory that has a bunch of supporting evidence. However, I suppose that it's a different subject, or maybe it isn't.
Although there are still some “blind spots”, areas that lack enough evidence, in Lynn Margulis's serial endosymbiotic theory (SET) I still believe that SET provides us with an adequate theory that explains the development of eukaryotic cells. SET suggests that eukaryotic cells are the result of a partnership between two prokaryotic cells. Margulis states that it all began when a prokaryotic cell “ate” another prokaryotic cell and for some reason the second cell avoided being digested by the host cell, so the two began to coexist, one inside the other. This coexistence, though probably very difficult at first, proved to be very beneficial to both cells and in the end they became too dependent on one another and relied heavily on each other to survive. As a result, Margulis argues, the two prokaryotic cells evolved so that they were permanently together. This makes logical sense right Billifany? And because the two cells combined with one another instead of one cell shifting and changing, thus it’s reasonable that no one has found any intermediates of this process. Eukaryotic cells exist not because some high and mighty power decided one day that they should exist but through a wonderfully complicated but logically satisfying process called SET. Ponder that cuzo Billifany.

This cousin of mine clearly needs to learn more about SET. The Serial Endosymbiotic Theory contradicts his or her arguments concerning eukaryiotic cells. Though the link between prokaryotes and and eukaryotes isn't evident in the same way as it is in other organisms, it is still present. This is because the evolution was largely based upon the formation symbiotic relationships with other species, rather than simply mutations of a single species. Many Eukaryotic bacteria arose from certain prokaryotes ingesting others. The symbiosis between the two prokaryotes gave them useful abilites such as photosynthesis, or improved metabolism, and over time, the sybiotic relationship evolved from two prokaryotes working together, into a single functioning eukaryote, as the two components became increasingly dependent upon eachother.

Both SET and ID is based on the idea that there are no intermediate steps between very simple prokaryotic cells and much more complex eukaryotic cells. However, ID does not have any evidence to back up the idea that eukaryotic cells are too complex to have evolved from simpler organisms. In contrast, Lynn Margulis and SET provide lots of evidence proving that eukaryotic cells can be broken down into simpler molecules. SET argues that eukaryotic cells evolved through series of symbiotic partnerships between two different kinds of prokaryotic cells. For example, smaller respiring cell invaded a larger cell that gave the larger cell protection against oxygen and in return, the host cell provided fuel for aerobic respiration. Over time both cells became dependent on each other and a mandatory partnership became key. Eventually the invading respiratory bacteria evolved into the mitochondria of today’s eukaryotic cells. The cells that now had mitochondria had higher metabolic rates than prokaryotic cells and as a result were able to grow and ‘eat’ smaller cells. These smaller cells inside the big cell then became semi-independent and evolved into chloroplasts. This is why today we see similarities between living bacteria and eukaryotic organelles. Thus, according to these similarities that back up SET eukaryotic cells can essentially be traced to simpler organisms. Due to all this evidence that supports SET I would have to disagree with my cousin.

I would only agree with my long lost cousin on the matter that there are no intermediate steps between the simply prokaryotic cell and the complex eukaryotic cell. As far as this being an example of irreducible complexity, I would have to disagree.
Lynn Margulis's theory "SET" provides a very good explanation to why there are not any intermediate steps and why the eukaryotic cell is not an example of irreducible complexity. SET states that eukaryotic cells evolved from symbiotic partnerships between prokaryotic cells. Early prokaryotic cells that fermented and photosynthesized were happy that there was barely any oxygen because an abundace would have put an end to them. However, when the amount of oxygen started to grow, most of these anaerobic cells died, some retreated to places with almost no oxygen, but most importantly some evolved to be able to detoxify oxygen. This is what enabled the evolution of eukaryotic cells. Margulis's SET states that a respiring parasite, would invade an anaerobic prokaryotic cell. Most of the time, one of the partners would die, but some of the time they would both find a way to coexist. Once they learned to live together, they could benefit from each other: the respiring parasite would take care of the oxygen allowing them to live where-ever they wanted, and the anaerobic cell would provide the parasite with the fuel it needed to respire. And eventually, the two partners became extremely dependent on each other and the parasite evolved into the mitochondria that eukaryotic cells have today. This shows that there should not be any intermediate steps between a porkaryotic cell and eukaryotic cell because it was not ONE cell that evolved over time, it was a partnership.
This explanation of the creation of organelles disproves the idea of irreducible complexity, and sorry long lost cousin.

If eukaryotic cells had just shown up, they would have shown irreducible complexity. However, something such as bactiria is not irreducible complex, and that is what started the prosses of evotution of eukaryotic cells. They started out of two diffrect kinds of bactiria that were very compatable. The host bactiria instead of killing or being killed by the invasive bactiria would have lived with it, and would have been able to live in situation it normally couldn't have, such as in an enviornment with oxegen. Or the invasive bactiria would keep the bactiria alive because it would recive sugers or organic subsances. Eventually, over hundreds of years, the invasive bactiria would lose certain qualities, becoming something very similer to microcondria or other organnels. If enough bactiria over time had invaded other bactirias and then lost some of their original qualities, we could get a eukaryotic cell as it is today.

My dear cousin from Alabama makes a valid point when he argues that there is no evidence that illustrates the evolution of prokaryotic bacteria to eukaryotic bacteria. However, when he claims that the organelles of eukaryotic bacteria are irreducibly complex, he fails to understand that they need not have evolved into their current state, but could have existed as independent bacteria prior to being consumed by a fellow prokaryote. Said Alabamian cousin is correct in saying that if the prokaryotic bacteria had evolved according to the sequence laid out by Darwin, we should be able to find the intermediary steps easily. However, instead of the more ‘normal’ process of random mutation, eukaryotic bacteria evolved by consuming ENTIRE prokaryotes. Over time, the swallowed prokaryotes’ special capabilities would have integrated completely with those of the host bacteria.

Lynn Margulis’ Serial Endosymbiotic Theory (SET) states that eukaryotic bacteria evolved by swallowing prokaryotic bacteria with highly specialized skills, such as generating ATP. Instead of digesting the bacteria for food, as they normally would, the ‘swallower’ prokaryote and the ‘swallowed’ prokaryote developed a symbiotic relationship in which the larger bacteria provided shelter while the smaller one focused on its skill, such as producing energy. Over time, the two bacteria’s systems become so closely integrated that they can no longer survive without each other. Natural selection would have favored these eukaryotic bacteria that were more efficient than their eukaryotic counterparts, which is why today’s prokaryotic bacteria contain the result of those symbiotic relationships.

I would have to say that my cousin is only making this claim that eukaryotic cells are an example of irreducible complexity because he (his name is Charles) has not read Lynn Margulis's essay on the evolution of cells, unlike all of us, which is why have an edge and can say that his claim is a false one.
Lynn Margulis's main argument in her essay, the serial endosymbiotic theory (SET), argues that eukaryotic cells are the result of endosymbiosis, which is where in this case one prokaryotic cell would get engulfed by another prokaryotic cell, and they would symbiotically live together. But although this theory does have some holes in it, it still provides a good explanation for the development of eukaryotic cells. After the one cell engulfed the other, the smaller one would avoid being digested, and they would live together. This relationship proved to be beneficial to both cells and they basically relied on one another to carry on. Margulis argues that these two prokaryotic cells evolved in this way so that these two cells were permanently bonded, to form a eukaryotic cell.
But in terms of there being no intermediate steps, one might argue that cells' combining could be the intermediate steps. But as these cells that ate other cells obtain new organelles and resources, the older ones would probably have died off because of natural selection, as these new megasupercells were better suited to survive now, which would get rid of all the intermediate steps we could have found.
In conclusion, Charles is a bit silly in saying that eukaryotic cells are examples or irreducible complexity. And also, even though their evolving is not quite like normal evolution (where organisms evolve very slowly, generation after generation), it is a different process where the evolutionary steps occurred as a series of discrete events, thus we have the named this theory the Serial Endosymbiotic Theory. So ha, Charles.

Although I can sort of see where they are coming from, I disagree with my cousins. I think if you are too lazy to really think about it and try to understand things like the Eukaryotic cells having Intelligent Design as an options is helpful. However if you read carefully Lynn Margulis' essay chapter thing she actually seems to give sufficient evidence proving the evolution of Eukaryotic cells by natural selection. SET or Serial Endosymbiotic Theory says that Eukaryotic cells came from Prokaryotic bacteria "eating" or sort of surrounding other Prokaryotic bacteria, this means that Eukaryotic cells didn't just pop in to existence, there had to be some kind of middle area where the Prokaryotic bacteria slowly transformed into the Eukaryotic cells. So even if this theory is not completely true or a few small details change it still proves that there was in intermediate step and that there is no irriducible complexity to the cell and that it wasn't Intelligent Design.

SET presents a clearly supported explanation for the development of the much more complex, compartmentalized Eukaryotic cells-my cousin’s explanation of this development using ID pales in comparison to the well warranted argument of SET. The first step in the development of much more complex eukaryotic cells was the existence of the simple prokaryotic cells-those that used fermentation to gather the ATP they needed. Later new bacteria developed that used solar power to gather their energy, but they still did not need oxygen. However, The next type of organism to develop used photosynthesis, and split water molecules in the processes, releasing lots of oxygen into the environment. While many of the prokaryotic cells died because the oxygen created too toxic an environment for them to survive in, some developed respiration technology, thus enabling them to continue existing. Following this, some of the respiring organisms invaded the non-respiring ones, and became attached inside the cytoplasm. In some cases, the parasite was destroyed by the host organism, but in others, they developed a coexistence with benefits to each. The organism that respired made it possible for the host to live in environments that had a lot of oxygen, and donated its ATP to the host cell. In exchange, the host cell donated a variety of organic molecules for the parasite to use for its photosynthesis process. As time progressed, the partnership between the host and the parasite developed into a dependence on one another. Additionally, the development of chloroplasts can be explained in a similar fashion. After the relationship between the host cell and what evolved to be the mitochondria developed, the carnivorous cells ate a smaller photosynthetic cell. Instead of fully digesting it though, the host cell and the smaller cell established a partnership and eventually evolved into chloroplasts. Clear examples of this phenomenon exist in other places throughout nature-indication that it is not simply ID at work. An example of this is the host cell Paramecium Busaria and the parasitic cell Chlorella. The two can exist independently, but if the host cell has the chance, it will eat but not fully process the Chlorella, thus establishing a partnership of endosymbiosys.

I will have to disagree with your ideas about eukaryotic cells being irreducibly complex. While you say that there are no intermediary steps between Prokaryotes and Eukaryotes, I would have to disagree. Even though we have not found a perfect match in the lineage of prokaryotes and eukaryotes, I am confident to say that Lynn Margulis' Serial Endosymbiotic Theory is a very solid idea. Looking back at Darwin's Theory of Evolution makes SET look very promising. SET is the idea that early on in Earth's history, bacteria evolved into different forms of bacteria and later into certain prokaryotic cells with certain abilities. Certain bacteria, such as respiring parasites, dug themselves into other prokaryotes. This action combined the two cells creating a prokaryote carrying the abilities of both the parasite and original cell. With this combination, Margulis argues that the cell would be better fit to survive in its habitat and possibly evolve into a predator. This would later help it absorb other cells and evolve even further. SET's argument for Prokaryotic evolution explains the idea of intermediary steps between Prokaryotes and Eukaryotes. These steps show us how cells the Prokaryotic cells could have adapted to their environments and evolved to later become the complex functioning parts of the Eukaryotic cell. Different cells could have evolved with traits to respire, photosynthesize, etc. and would later specify themselves in other cells and become organelles.

My stubborn cousin has no idea what he/she is talking about. Obviously he/she has not heard of Lynn Margulis and her theory of SET. While my cousin claims that a lack of intermediate steps between simple prokaryotic cells and complex eukaryotic cells proves ID, Lynn Margulis has found abundant information stating otherwise. Her theory became SET, or Serial Endosymbiotic Theory. It states that Eukaryotic cells were able to evolve through endosymbiosis, the burrowing of a bacterial parasite into the cytoplasm of another bigger host cell. The bacterial parasite is capable of respiration, a function that had evolved due to the photosynthetic production of oxygen gas. These aerobic parasites would find larger anaerobic host cells to infiltrate and protect them from oxygen gas in return for fuel. This new endosymbiotic cell later evolved into the mitochondria, chloroplast and the flagellum. All of which are organelles present in eukaryotic cells. Basically, photosynthesis and respiration allowed the evolution of all eukaryotic cells. So, the energy producing mitochondria organelle evolved from small, respiring, free-living bacteria which was then engulfed by a larger predator cell which continued the process of evolution. The photo-synthesizing Chloroplast organelle evolved in the same way but can only can be found in plant cells. The process of endosymbiosis can easily account for the intermediate steps that proponents of ID claim don't exist. Unlike the mitochondria and the chloroplast, Margulis fails to provide any concrete evidence towards her theory of the flagellum's evolution. Supporters of ID claim that the eukaryotic flagellum is a perfect example of an irreducibly complex organelle. Margulis claims that the eukaryotic flagellum differs so tremendously from the prokaryotic flagellum that it should be renamed "undulipodium". She believes that the eukaryotic flagellum evolved from spirochetes. An example she uses to illustrate undulipodium's similarity to the spirochete is the spirochete's presense in cockroaches and how similar they are to eukaryotic flagellum. Although this isn't significant proof, ID's beliefs fail to offer any proof. All of this shows that there was in fact an intermediate step of evolution between prokaryotic and eukaryotic cells. ID fails because of its frail support and Margulis' well substantiated theory.

Sorry this is Lydia period 6. I really can't get my school account to work.

Although it is true that complex eukaryotic cells probably could not evolve on their own to create organelles like mitochondria from useless blobs, Lynn Margulis' SET theory shows that those organelles could evolve outside of the cells from early prokaryotes and then form a symbiotic relationship with simple eukaryotes, eventually leading to the cells in each of our bodies today. Although this theory was originally rejected by the scientific community, it is now widely accepted. There is a lot of evidence for SET, such as the fact that mitochondria and chloroplasts reproduce differently from the cells they are a part of, or the similarity between their structures and those of early prokaryotic cells. The fact that these organelles cannot survive outside of the cells they are a part of does not mean anything. Lichens are another example of two different living things cooperating to form one structure which would not function without the other component.

Be that as it may, my dear cousin, your argument for the irreducible complexity of eukaryotic cells has a bit of a void. You argue that since there is no intermediary organism in existence between prokaryotic and eukaryotic cells, eukaryotic cells cannot have evolved from their prokaryotic counterparts. Here, cousin, is where you are mistaken. There was no series of small changes leading up to, say, mitochondria, which are unique to eukaryotic cells. According to SET, or Serial Endosymbiotic Theory, which was laid out by biologist Lynn Margulis in the late 1960's and early 1970's, a prokaryotic cell consumed another smaller prokaryotic cell, but for some reason did not digest it. The ingested cell most likely was good at producing ATP, which is the main energy source for cells. The larger cell offered the smaller protection and did not digest it, and the smaller cell produced ATP for the larger. Thus, a symbiotic relationship was formed. When the larger cell underwent mitosis, so did the smaller, and two "double cells" were created. It is because of this process that there are no intermediate steps between prokaryotic and eukaryotic cells, because it is impossible for a cell to be partly consumed by another. I appreciate all your contributions to the family, cousin, but in this area I believe I have you beat.

Though I respect my Alabaman cousin's beliefs, I do not believe that eukaryotic cells are irreducibly complex and would happily show him my copy of the essay on Lynn Margulis’s theory. According to the Serial Endosymbiotic Theory, various types of prokaryotic cells underwent evolutionary changes over a period of a couple billions years by means of symbiotic alliance amongst each other. The process involved the smaller party attacking the larger party and together evolving into three critical organelle species including mitochondria, chloroplasts, and flagella. SET argues that this started happening approximately 2.5 billion years ago when the sudden abundance of oxygen produced by photosynthetic bacteria provoked surviving prokaryotes to develop respiration systems. This lead to the onset of eukaryotic organelle development, starting with mitochondria. Little bacteria with respiration abilities became parasites to bigger anaerobic prokaryotes, and their interaction eventually caused the small bacteria to morph into mitochondria, which is found in almost all eukaryotic cells today. The overwhelming, though at times admittedly controversial, body of evidence that includes the example I discussed vigorously support the theory that eukaryotic cells are not irreducibly complex, but were involved in an extensive evolutionary process.

I would tell my cousin that there actually is a plausible evolutionary connection between the prokaryotes and the eukaryotes. The SET theory explains that the parasitic bacteria of the prokaryotes found their way into the prokaryote. She believes that the main cause of this occurance was the evolution of cyanobacteria, which created oxygen. Margulis claims that the bacteria that were unable to function with oxygen (anarobic bacteria) were forced to seek refuge within the prokaryotic cells. Over time, the bacteria lost many of it's once necessary traits that were made unecessary by it's new location, such as "metabolisin functions". The prokryote also began to rely on the bacteria for it's survival. Hence, the bacteria evolved into some of the important organelles of a Eukaryote. Therefore, the concept of "irreducable complexity" of a eukaryote is not entirely true. Thanks to Margulis, there is reason to believe that with the help of some bacteria, the some prokaryotes evolved into more complex cells.

After learning about endosymbiosis, everything my cousin says becomes rubbish to me. There is no irreducible complexity, the only thing is that now, with a eukaryotic cell, we simply have two bodies instead of one. According to Lynn Margulis' theory of SET, the evolution of the eukaryotic cell took place when one cell engulfed another, offering the smaller one protection from other cells, and in return receiving another source of energy. Margulis' statement is quite solid with the exception of one gap: why didn't the cell just digest the other?
Next, by following with this theory of SET, an intermediate step could not have been possible. When the other cell engulfed the other, it just happened. Boom. And we now that each body came from different origins because the appearance of DNA in the mitochondria, or chloroplast. Next, the intermediate steps can be seen in the similarities between the two different kinds of cells. When the eukaryotic cell developed DNA, ribosomes, cytoplasm, and a membrane, all those can be seen as the intermediate steps in the evolution of the eukaryotic cell. BYAH cousin - you wrong

After reading the essay on Lynn Margulis and SET, I would strongly disagree with my cousin. Although it may seem at first that a eukaryotic cell is irreducibly complex, there is much evidence found in SET to show that these cells indeed did evolve to become how they are today. First of all, SET is described as a "series of discrete events" that led to the formation of the eukaryotic cell, showing that it evolved to become as complex as it is now. There is evidence that the eukaryotic cell did evolve from basic prokaryotic cells, where one prokaryote parasite burrowed into another cell through the cell wall. Although the host or the parasite was killed most of the time, sometimes they would coexist. Mutual benefits stemmed from this partnership, and eventually, the cells became so dependent on each other that they could no longer survive on their own, creating a complex eukaryotic cell. The bacteria that had invaded eventually evolved into the mitochondria. This explains why mitochondria have their own DNA, and SET also provides a logical explanation of the evolution of the eukaryotic cell. Eukaryotic cells can indeed be broken down into smaller parts, disproving my cousin's idea that eukaryotic cells are irreducibly complex.

If my cousin from alabama said that to me i would first wonder why he was talking to me about biology, then i would point out the SET. i would say to my cousin that the reason why eukaryotic cells have no intermediates with prokaryotic cells is b/c some prokaryotic cells may have engulfed one another,developed a symbiotic relationship, and evolved to depend on each other so much that they became one. This idea that symbiotic prokaryotic cells evolved into eukaryotic cells contradicts his statement. If SET is right, there would be no place for intermediates between prokaryotic and eukaryotic cells.

I don't agree with my cousin. Eukaryotic cells aren't a good example of irreducible complexity. Although my cousin argues that a cell as complicated as the eukaryotic cell could not have evolved from some other cell, like the prokaryotes, SET doesn't argue that it does. Lynn Margulis does point out that eukaryotic and prokaryotes are too dissimilar to have been "related". What she does say is that different prokaryotes "swallowed" each other. Somtimes, the prokaryote host would not survive this living situation, but at others they would form symbiotic relationships where they use eachother's strengths to work together. Over time, these prokaryotes that combined sucessfully made different, more complex cells. So, although it is true that there is a "gap" in the evolutionary process, it's because it wasn't really one species evolving, but instead simply simpler cells forming symbiotic relationships and changing/strengthening/complexifying over time.

Unfortunately for my cousin, evidence of steps between prokaryotic and eukaryotic cells exists. However, the intermediates challenge our basic, incremental-change understanding of evolution. Instead, the changes were sudden but successful.

In the 1970s, Lynn Margulis revolutionized both evolutionary and cellular biology, which had little in common, by claiming that mitochondria had evolved from a once-separate prokaryote. Serial endosymbiotic theory (SET) describes the co-evolution of two organisms--beginning when one burrowed into (or was engulfed by) another, leading the first to become parasitic. The new life form had an advantage over its simpler peers, as the ancestral mitochondria could respirate--create ATP (energy for cells) by taking in oxygen--a nifty trick in an environment increasingly filled with oxygen gas. (This was due to the evolution of photosynthetic bacteria, which released the gas as a byproduct.)

Evidence for SET includes the structural similarities between mitochondria and prokaryotes, and a genome separate from the cell's nucleus.

Margulis's theory gave biology more than one intermediate--she pointed to chlorophasts, found only in plants, as another organelle created from endosymbiosis.

I could mention flagellum, but due to the controversy over its evolution, I think I won't give my cousin space to contradict me.

My dear cousin from Alabama (I wonder if Alabama has a booming Filipino population?). It is true that there are no proven intermediates between the simple prokaryotic cells and the much more complicated eukaryotic cells. But there is in fact evidence to support claims of the evolution of the eukaryotic cells. Margulis’ theory, SET, is based on the idea that older cells could have developed photosynthetic and metabolic bodies. She states that larger cells may have either consumed or been invaded by smaller cells similar to bacteria. This would often kill either the smaller or larger cell, but sometimes they would both survive. Instead of the larger cell digesting the parasite, they would develop a mutually beneficial relationship. The larger cell would protect the smaller cell and provide it with sugar cells in exchange for ATP. Eventually the process that came from this relationship became necessary to the survival of the larger cells and the parasites. While some prokaryotes attempted to adapt or hide themselves in unoxygenated areas, the cells would eventually begin to evolve into one cell and make the relationship permanent.
Margulis backs her theory up by examining organelles such as mitochondria or Flagella. These organelles have concentrated areas of DNA similar to DNA found in archaic bacteria, demonstrating that these pockets were once their own cells. With all of this evidence, my cuz from the south, I respectfully disagree with your statement that eukaryotic cells are an example of irreducible complexity. Their evolution can be explained with scientific evidence and logic. Tell aunt joe that I hope her cold gets better.

I would respond to my cousin’s belief that eukaryotic cells are an example of ID by explaining the endosymbiotic theory. Lynn Margulis’ theory provides a link between prokaryotic cells and eukaryotic cells. According to Margulis, the first bacteria were anaerobic photosynthetic bacteria and fermenting bacteria. However, eventually aerobic photosynthetic bacteria evolved, and their production of oxygen, which was toxic to the other bacteria, forced the anaerobic varieties either to hide out in oxygen-poor regions (and become today’s archaebacteria) or to become aerobic. The anaerobic-turned-aerobic bacteria managed to do this by turning oxygen back into water and energy, developing a system of respiration. These bacteria then became parasites and forced their way inside the larger, anaerobic bacteria. However, this turned out to be a mutualistic relationship the parasite shared the energy it produced, and the host provided the sugars and other molecules that the parasite needed. Additionally, the formerly anaerobic host could now survive in an oxygen-rich environment. Eventually, the photosynthetic parasites evolved into mitochondria. Some of these eukaryotic cells grew large enough to become predatory. Part of their diet would have consisted of cyanobacteria, which could have evolved into the chloroplasts in plants.

SET would then refute my cousin’s thinking that eukaryotic cells are irreducibly complex. The theory shows that there is a way for these complex cells to have evolved naturally without the aid of an intelligent designer.

I completely disagree with my cousin's statement. The statement that eukaryotic cells are irreducibly complex is false. Eukaryotic cells did in fact come from prkaryotic cells. This can be explained by Lynn Margulis' Serial Endosymbiotic Theory, or SET. Set states that Eukaryotic cells through a series of symbiotic relationships between prokaryotic cells. The series can be intermediate steps. Later on these symbiotic relationships will add three organelles to the prokaryotic cells, which will make them become eukaryotic cells. Proving that eukaryotic cells are not irreducibly complex There are many examples in nature supporting Lynn Margulis' theory. Long ago when there were only prokaryotic cells. There was little oxygen in the world, and it was toxic to most living organism. Then when oxygen became more and more abundant, Organisms that used oxygen to survive started to form. The organisms that used oxygen would engulf the other and the other way around. Now the organisms that once thought of oxygen as poison, can now live in an environment with it around. These two cells formed what is called a Endosymbiotic relationship. And through a discrete series of this, eukaryotic cells were formed. SET also challenges another example supporting ID, flagellum. ID theorists claim that the flagellum has no other simpler versions, so it is irreducibly complex. But SET argues that the eukaryotic flagellum was made up of spirotches to create a new organelle. Since Margulis believed that the prokaryotic and eukaryotic flagellum have different structures, the eukaryotic flagellum was called undulipodium. These are examples that prove Eukaryotic cells are not irreducibly complex, and were created through a series of symbiotic relationships.

I would argue with my long lost cousin that Intelligent Design is not a scientific theory and if he or she wants to believe in God, he or she can practice that belief outside the scientific world. If he/she is a Biology student, he/she should understand that Intelligent Design cannot be proven and evolution can, also, I would hope that he/she has read Lynn Margulis' writings. If my cousin wants a career in Biology, he/she should not have such a biased view. Intelligent Design may be regarded as a scientific theory by some but it is not believed by the greater scientific world.

I would explain to my cousin about the essay on the SET theory. Lynn Margulis' Serial Endosymbiotic Theory theory states that prokaryotic cells engulfed other prokaryotic cells which turned into eukaryotic. This was the intermediate step they didn't just appear. I think that is definitely enough proof for me and should be for my cousin.

After learning about Margulis's Serial Endosymbiotic theory, I would disagree with my cousin's assertion based on the theory of endosymbiosis, a better theory than intelligent design for the explanation of the evolution of eukaryotes from prokaryotes. Though slightly bizzare (it almost says that some organisms swallowed other organisms which in turn became organelles), the evidence is overwhelming, and the theory is logical. The endosymbiotic relationship is one that benefits both parties involved, creating an unique evolutionary occurence - that of a rapid change, as opposed to the theory of autogeny, the slow gradual evolution of an organism. The main piece of evidence for endosymbiosis is that the DNA of the various elements of the cytoplasm vary from the DNA of the nucleus and the cell itself. However, they co-evolved in a mutually beneficiary relationship, and they are slowly becoming the same organism. Another argument for intelligent design is the flagella, which Margulis explains in her works. The flagella was thought of as a prime example of irreducible complexity, being so built on its various interdependent features that the absence of any one of them would cause a lack of functioning. However, Margulis links it to a spirocheaete, a type of bacteria that causes diseases but evolved to help a cell move. Finally, I would tell my cousin that Intelligent design is fighting a loosing battle because it keeps having to alter its theories to pave way for new discoveries in science.

While there is no direct evolutionary chain between prokaryotic and eukaryotic cells, there is evidence that organelles within eukaryotes could have evolved from a prokaryotic cell with a similar function. At some point in their evolution these prokaryotes were consumed by a larger prokaryotic cells, but instead of being broken down by the larger cells, they formed a symbiotic relationship with the larger cells. An example of this is the chloroplast, which probably originated as a photosynthesizing cell, but when consumed, the larger cell used the photosynthesizing property of the smaller cell. Eukaryotes are not an example of irreducible complexity because there were intermediate steps, but they were between prokaryotes and organelles and not between prokaryotes and complete eukaryotic cells.

I would tell my cousin that eukaryotic cells are not an example of irreducible complexity. Irreducible complexity is an argument used as proof of existence of an Intelligent creator. However, science does have a theory for the evolution of eukaryotic cells. While there aren't intermediates between prokaryotes and eukaryotes, there are very clear links between these cells that explain the evolution of Eukaryotes in Serial Endosybiotic Theory (SET). At one point life was made of prokaryotic cells, but through evolution some of these prokaryotes developed the ability to photosynthesize, produce ATP etc. When engulfed by other prokaryotes, they formed a symbiotic relationship where the engulfed bacteria performs its special function for the predator while the predator protects the engulfed cell. Through evolution, because these cells survived better with the symbiotic relationship, these engulfed bacteria became organelles in the prokaryotes giving way to eukaryotic, complex cells. This is supported with scientific evidence that found traces of DNA in organelles like mitochondria that prove they could have once stood on their own as prokaryotes prior to joining with the cell. There is also fossil evidence where biologists found eukaryotic cells without mitochondria and endoplasmic reticula. This proves that the evolution of eukaryotic cells is not an example of irreducable complexity because their origin can be explained with substantial, scientific evidence.

After reading the article on Lynn Margulis, I would have to strongly disagree with my so-called cousin. My cousin may not see Margulis' theories as I do, but to argue his point of Intelligent design he would have to bypass all the research that has been done about Serial Endosybiotic Theory (SET). Although the Eukarotes are incredibly complex, they can not be a "prime" example of ireducible complexity because they did not evolve from nothing to what they are today overnight. They took many stages to being the cells they are today. Margulis' research and theory show that Eukaryotes as well as Prokaryotes once used photosynthesis, and stages later evolved to respirating. Again, this didn't just occur overnight, steps works taken for the cells to evolve in the ways they did. So my cousin could only argue against Serial Endosybiotic Theory (SET) and in favor of Intelligent Design if he completely ignored Margulis' research. Margulis' theory correctly showed that Eukaryotes and Prokaryotes evolved over millions of years and that there is always a possibility of something smaller.

This cousin is clearly incorrect, as Margulis states that eukaryotic cells evolved using several types of prokaryotic cells in a symbiotic evolution. While they may not be directly related, her SET theory shows that they do have some relation. The only part that gets a bit iffy is when she discusses the spirochetes, where there is no evidence to how they could have possibly been evolving the same.

I, for one, am an individual who is able to accept and aknowledge both the Intelligent Design theory and the theory of evolution. I believe that life was divinely inspired and was set into motion with the ability to adapt and evolve with its surroundings. Disreguarding personal beliefs, I, from a scientific standpoint believe that "my cousin" is wrong. Intelligent Design, scientifically speaking, is not responsible for every known organism. It seems as proponents of scientific theory only implement it when there is something that they cannot readily explain scientifically. That being said, after reading Margulis's essay, the evidence supporting eukaryote's evolving from prokaryotes are overwhelming. Eukaryotes are NOT of irreducible complexity. We can see how evolution has caused simple prokaryotes to engulf other prokaryotes with different abilities (such as better metabolisms and the ability to photosythesize) which have formed organelles like mitochondria and chloroplasts. This is Margulis's theory called Serial Endosymbiotic Theory (SET). My cousin is wrong for stating that there are no intermediates between Eukaryotes and Prokaryotes. Marulis's SET theory proves it.

I would have to agree with Manasi. I feel that the irreducible complexity argument, when used in reference to prokaryotic and eukaryotic cells is a really easy way to explain the transformation without looking at the actual chain of events which enabled the change. If you break down the whole process, and look at Margulis' SET theory, there arises a completely logical and scientific explanation for the advancements of the prokaryotic cell.
The SET theory that Margulis explains shows that after surrounding a smaller prokaryote, the larger prokaryote benefits from the engulfed cell's advantages while the smaller too does from the host's return. With the new advancements the cell is more functional. So through not one, but many of these joint partnerships the prokaryotic call is able to become eukaryotic.
So with this in mind I would respond to my cousin's comment by stating that if they were to look harder there are steps between the prokaryotic and eukaryotic cells. And that these steps are the continual entrance of prokaryotic cells into another, creating a new third call, then repeating later in the third type of cell evidently continuing the evolution process. So ID is not the only explanation.

Nonsense, my dear cousin. Science has indeed found intermediates to link prokaryotes and eukaryotes. The predominant theory, generally accepted, is that organelles like chloroplasts and mitochondria were cells in their own right, absorbed by the ancestors of today's eukaryoric cells. They existed in a symbiotic relationship, and over time the host and the symbiont became one. The process is referred to as endosymbiosis. I am afraid, my dear cousin, that your arguments are as bunk as the one I sleep in (actually, though, I sleep in a bed). And so is Intelligent Design.

If one of my many cousins from Alabama was smart enough to be a college biology student and was arguing that eukaryotes can't have evolved from the more simple prokaryote merely because there is no evidence thus far that proves the existence of imtermediary steps between the two, then I would laugh and explain how the Lynn Margulis essay might prove him wrong. If he/she was arguing that the eukaryote is a prime example of irreducible complexity and there is no way a prokaryote could have evolved to become a eukaryote, then in a way I could agree because it didn't exactly require evolution. According to Murgulis' Serial Endosymbiotic Theory (SET), eukaryotes are the result of an ancient prokaryote eating, or engulfing, another prokaryote and, for some reason, it did not digest it. The second, engulfed prokaryote existed inside of the other and a symbiotic relationship emerged in which the inner bacteria provided protein etc. while the engulfing cell provided protection etc. Eventually the two cells became dependant on each other to survive and reproduce (which they could only do as one cell, not seperate).
From this came the eukaryote, and so although my cousin was partially right in saying that eukaryotes did not directly evolve from another cell in the most common form of evolution, he/she should not have ruled evolution out completely.

I would kindly respond as so:
Long lost cousin, whose name I cannot recall, you are terribly mistaken to believe that eukaryotic cells are a good example of Intelligent Design for there is a theory that does explain the appearance of this complex organism through evolution. This theory is Lynn Margulis’s serial endosymbiotic theory. It is hard to believe that eukaryotic cells just suddenly burst into existence therefore, Margulis explained that the cells were composed of two prokaryotic cells: one inside the other, coexisting. For example, as the air continued to contain increasing amounts of oxygen, bacteria that could easily take in the oxygen and produce ATP nestled into another bacteria. In some cases, the two formed a symbiotic relationship and eventually depended so much on each other that without their partner, they could not function and died. This parasite bacteria evolved into the mitochondria. The same goes for chloroplasts although these bacteria only appeared in plant and protist cells. Scientific evidence supports the SET, showing that the DNA of mitochondria and chloroplasts is similar to bacterial sequences instead of other eukaryotic ones. Also, we cannot dismiss the fact that they reproduce by dividing like bacteria. Therefore, my cousin, you must understand that eukaryotic cells are not an example of irreducible complexity. I won’t hold your obviously wrong beliefs against you so why don’t we go get something to eat I’m starving. (Yes! Midnight snack!!)

According to my cousin, there are no intermediates between very simple prokaryotic cells and the much more complex eukaryotic cells. As a result, eukaryotic cells are an example of irreducible complexity. However, based on the SET, eukaryotic cells are the result of prokaryotic cells absorbing each other. This is a better example of evolution than intelligent design because the prokaryotic cells become more and more dependent on each other. They "evolve" from two prokaryotes into one eukaryote as opposed to prokaryotes and eukaryotes already existing without any relation because of intelligent design. The SET gives the explanation to how eukaryotes came to be with evidence. For example with the mitochondria, there are no intermediates because the prokaryotes have already evolved into one and have been reproduced as one.

After reading the essay about Lynn Margulis, I would have to dis agree with my cousin. Lynn came up with the idea that prokaryotic cells developed into Eukaryotic cells.There are many difference between the cells and I can understand my cousins point of view. In the essay Lynn shows that there are intermediate steps to go from Prokaryotic to Eukaryotic. To prove this she talked about the development of the mitochondria and the chloroplast. The chloroplast was a product of the rare cases where the bigger cell didn't digest the Chloroplast but rather engulfed it, and used it to made a super cell. This is true for the mitochondria as well. The prokaryotic cells that were very simple but specialized in something like creating energy, they were engulfed instead of digested. Prokaryotic cells also changed in ways that allowed them to function in oxygenated areas. Bacteria used a host cell, and share its ATP that creates oxygen, in return the Host cell would provide sugar to allow it to continue to make oxygen which would help areobic respiration. The evidence in the essay would lead me to believe that there was a development from prokaryotic to Eukaryotic. Unfortunately i have to disagree with my cousin but i can't disagree with the facts

Well cousin, I must say that I would have to disagree with your argument of eukaryotes being of irreducible complexity. According to the serial endosymbiotic theory the development of eukaryotes occurred through a series of discrete events. A prokaryote parasite would burrow into another cell and invade its cytoplasm, often times killing either parasite or its host but in some cases a coexistence was formed. This partnership between the two would have mutual benefits. The parasite’s respiration would allow the cell to survive in areas that it would have previously been unable to and cell would provide fuel for the parasite’s aerobic respiration. Eventually through the process of natural selection the parasites would evolve into mitochondria. It is speculated that some of these new cells grew larger and became capable of eating smaller cells like cyanobacteria. In some cases the cyanobacteria may have resisted digestion and evolved into chloroplast. According to the SET theory there would have been no intermediates, so this would not be a very good example of ID.

Well, i agree with my cousin there are no intermediates between very simple prokaryotic cells and the much more complex eukaryotic cells but this does not mean that eukaryotic cells are proof of irreducible complexity. It can always be difficult to try to convince a believer of intelligent design that there is proof that something else caused evolution and not a higher intelligence. I think that if my cousin read Lynn Margulis' article then she might change her mind about her belief that eukaryotic cells are a prime example of irreducible complexity. If my cousin read this article then she would learn about the Serial Endosymbiotic Theory. This theory states that eukaryotic cells were created when some prokaryotic bacteria "ate" other prokaryotic bacteria that was able to metabolize or photosynthesize. And so this realtionship caused the simple prokaryotic bacteria to eventually become eukaryotic organelles. This theory would explain to my cousin that in fact eukaryotic cells are examples of irreducible complexity.

To logically prove to my cousin that he or she was wrong, I would explain the Serial Endosymbiotic Theory (SET) to him/her as proof of how prokaryotes and eukaryotes were connected. The first step of this process was the evolution of prokaryotic cells to be able to photosynthesize and produce oxygen, a development which led to the ability to respirate and produce ATP. Next, small, respirating bacteria began to invade larger prokaryotic cells. The bacteria would grant oxygen and ATP to the cell in exchange for sugar to use as energy. As the oxygen in the air increased and the cells depended more on the bacteria for survival, the bacteria developed into mitochondria. I would here remind my cousin that that cases similar to that of the bacteria and the cells occur nowadays. Sometimes these mitochodria-filled cells absorbed other, smaller cells with the ability to photosynthesize. The small cells probably evolved into chloroplasts. Finally, the eukaryotic flagella (or as Margulis calls them, undulipodium) may have evolved from the bacteria called spirochetes. The undulipodium's axial filaments are quite similar to the spirochetes' microtubules. Scientists have also discovered several cases of motility symbiosis including the Mixotricha whose spirochetes were thought to be flagella for a long time. I would hope that my cousin, when faced with such scientifically-supported theories, might reconsider his/her opinion on the validity of "Intelligent" Design.

I'd like to start by responding to Alice's note of her cousins in Alabama. I too have cousins in Alabama, though they are more like these fictional long lost cousins - I have never met them. They are both highly educated (many have PhD's and MD's) but are proponents of ideas such as intelligent design. One PhD cousin is trying to prove that parts of the bible were written by Adam and Eve. These stereotypes are less distant than one might think.
Now, if this long lost cousin from Alabama were to cite the development of eukaryotes from prokaryotes as an example of irreducible complexity I would point her towards Lynn Margulis' Serial Endosymbiotic Theory (SET). I would call her attention to certain organelles inside of prokaryotic cells - the mitochondria for example - that have their own separate DNA. The distinction between prokaryotes and eukaryotes is the presence of organelles with specific tasks enclosed in their own membranes. This DNA found in some organelles is evidence of these intermediaries that she was denying the existence of. If these organelles have their own DNA, then at some point they were probably separate cells. If one prokaryotic cell engulfs another, I would explain to her, then the two may be able to work in symbiosis until the the interior cell evolves to the point of complete dependency on the outer cell. Cells that engulfed other cells with useful properties such as metabolisms or the ability to photosynthesize would survive to reproduce.

I'd like to start by responding to Alice's note of her cousins in Alabama. I too have cousins in Alabama, though they are more like these fictional long lost cousins - I have never met them. They are both highly educated (many have PhD's and MD's) but are proponents of ideas such as intelligent design. One PhD cousin is trying to prove that parts of the bible were written by Adam and Eve. These stereotypes are less distant than one might think.
Now, if this long lost cousin from Alabama were to cite the development of eukaryotes from prokaryotes as an example of irreducible complexity I would point her towards Lynn Margulis' Serial Endosymbiotic Theory (SET). I would call her attention to certain organelles inside of prokaryotic cells - the mitochondria for example - that have their own separate DNA. The distinction between prokaryotes and eukaryotes is the presence of organelles with specific tasks enclosed in their own membranes. This DNA found in some organelles is evidence of these intermediaries that she was denying the existence of. If these organelles have their own DNA, then at some point they were probably separate cells. If one prokaryotic cell engulfs another, I would explain to her, then the two may be able to work in symbiosis until the the interior cell evolves to the point of complete dependency on the outer cell. Cells that engulfed other cells with useful properties such as metabolisms or the ability to photosynthesize would survive to reproduce.

I would have to correct my cousin because although there are no intermidiates that we can see between prokayotic and eukaryotic cells, there is a way to explain their evolution.

In SET, the idea is that prokaryotic cells engulfed other prokaryotic cells. Instead of consuming them, the bigger cell would allow the inner cell to operate in a symbiotic relationship. Over time and generations, they would lose together and their cells would form together to form certain organelles within the over-arching membrane. This might be the hardest issue that I'd have to press with my cousin because they would most likely wonder at why the prokaryotic cell did not simply comsume the other cell for energy.

This directly clashes with the idea of irreducable complexity because it can be traced back at how these organisms first evolved because if it is a process of evolution, then it would not be irreducibly complex.

How about a brief response after that three page one from last time?

To quote a well-known and well-respected fellow evolutionary biologist, “Eukaryotic cells are definitely not an example of irreducible complexity, and cannot be used to defend the claims of Intelligent Design.” (Dr. Nikhil Rajapuram, author of Why My Cousin’s Theory of ID is Wrong) As Dr Rajapuram states in his book, the Serial Endosymbiotic Theory (SET) proposed by American microbiologist Lynn Margulis says that mitochondria and chloroplasts arose from certain prokaryotes, which established mutually beneficial (aka symbiotic) relationships with the earliest eukaryotes. In the distant past, these free-living prokaryotes were consumed by those hungry eukaryotes, but managed to survive somehow within the larger cells. The autotrophic prokaryotes proved useful to their hosts because they produced glucose through photosynthesis. The heterotrophic prokaryotes also were useful because they could generate the energy (ATP) for the host. The host in turn provided protection for the engulfed prokaryotes. Over time, the autotrophic prokaryotes developed into chloroplasts and the heterotrophic prokaryotes developed into mitochondria. These organelles still contain their own DNA, and their own ribosomes, which contribute to this theory.

However, my cousin’s refusal to believe me is not without reason (litotes). Besides mitochondria and chloroplasts, there’s no other clear evidence of other major traits or transitions that can be attributed to symbiogenesis. Thus, SET can’t contradict my cousin’s belief in ID by too much.

(Sorry, Robbie, I decided not to be pro-ID it would have taken too much time)

I would not agree with my “cousin”, and say that eukaryotic cells are a good example of intelligent design. Intelligent design states that things become what they because of a higher being, like God. However, it seems highly unlikely to me that “God” could have created anything, especially something this complex. Instead, I would be more likely to agree with Darwin’s theory of natural selection. The theory that the eukaryotic cell was created slowly by cells coming together and the unneeded being “thrown away” is a much more logical approach (in my opinion) to this subject. To further emphasize my opinion, the Serial Endosymbiotic Theory also states that eukaryotic cells evolved from a series of symbiotic partnerships involving many different kinds of prokaryotic that would consume smaller prokaryotic cells. This eventually involved into three kinds of organelles which are mitochondria, chloroplasts, and flagella. Supposedly, these steps in evolution were a series of "discrete events". Mitochondria (found in most eukaryotic cells) are an example of Serial Endosymbiotic Theory. This goes to show that the small bacteria found in cells evolve to become more fit the need of the cell.

I would not agree with my “cousin”, and say that eukaryotic cells are a good example of intelligent design. Intelligent design states that things become what they because of a higher being, like God. However, it seems highly unlikely to me that “God” could have created anything, especially something this complex. Instead, I would be more likely to agree with Darwin’s theory of natural selection. The theory that the eukaryotic cell was created slowly by cells coming together and the unneeded being “thrown away” is a much more logical approach (in my opinion) to this subject. To further emphasize my opinion, the Serial Endosymbiotic Theory also states that eukaryotic cells evolved from a series of symbiotic partnerships involving many different kinds of prokaryotic that would consume smaller prokaryotic cells. This eventually involved into three kinds of organelles which are mitochondria, chloroplasts, and flagella. Supposedly, these steps in evolution were a series of "discrete events". Mitochondria (found in most eukaryotic cells) are an example of Serial Endosymbiotic Theory. This goes to show that the small bacteria found in cells evolve to become more fit the need of the cell.

I would respect my cousin point of view but i would present him with Lynn Margulis paper of "The Evolution of Eukaryotics Cells". I think this would help him make a more balanced decision, he would be more informed about alternative theories. Some of the arguments of the Serial Endosybiotic Theory challenge the ideas of Intelligent design in a very straight forward way. For example the ID theory claims that the flagellum is so complex that there were no simple versions of this organelle but SET reveals that there are some underdeveloped flagella on other ancient bacteria. I would invite my cousin to take a look at the article because it exposes the weaknesses of the ID theory with logical series of modifications in the different cells.

The cousin arguing that because there is no evidence of slow intermediate evolution from simple prokaryotic cells to complex eukaryotic cells with mitochondria and other organelles. One widely accepted theory says that instead of a slow evolution of different organelles (which has no fossil evidence to back it up) isn't the only way in which the organelles came to serve important functions in a cell. Instead, the organelles, like the mitochondria, were present, freely, outside of the cell. Then, through endocytosis, a larger cell would "eat" the smaller cell (mitochondria). It just happened that having a mitochondria inside of a cell proved beneficial to the reproductive success of the cell and from then on, the new cells would have mitochondria.

Because the mitochondria had evolved separately from the cell, there would be no fossil evidence of an evolving mitochondria inside of the cell. This explains the seeming suddenness of the appearance of larger, more complicated cells.

Well…my cousin’s theory isn’t completely wrong. However, Margulis’s theory of SET makes more sense because it has more physical evidence. For instance, Marqulis says that eukaryotic cells have evolved from a series of symbiotic partnerships involving different kinds of prokaryotic cells. Meaning that these multi-celled organisms must have evolved from something less complicated (i.e. prokaryotic bacteria). Because she has proved that there is some type of intermediate stage that eukaryotic cells have evolved from, there is no way to show that these cells have just popped out of nowhere or from a higher being. This being said, the theory of SET shows that these cells are not a product of irreducible complexity or of ID. In the SET theory, a prokaryotic bacteria “eats” or engulfs another prokaryotic bacteria. The “undigested” bacteria creates a symbiotic relationship. The outer bacteria provides protection, while the inner bacteria bring oxygen to the cell. This relationship becomes essential to the cell’s survival.

my cousin, while a biology student, may need to do some continued reading before earnign their degree, I think. As vast as the gulf between eukaryotic and prokaryotic cells is, it is not at all insurmountable for the powers of natural selection. Lynn Margulis' work expanding the Serial Endosymbiotic Theory (SET) goes a long way towards showing that. The gradual, symbiotic relatioship that the theory states may have developed between some prokaryotic cells could easily, with time and circumstances, have produced the kind of cells that would become full eukaryotic cells, and continue evolving form there into the massive diversity of eukaryote life we see today. The many organelles of eukaryotes can often be explained with the aid of prokaryote symbiants, with such illustriously "irreducible" examples as the mitocondria and flagellum. So, no, whilwhuvqse the verison of SET put worth in the Margulis article may not be entirely complete, it does seem sufficient to disavow any notions of an irreducibly complex gap between the two.

After having understood the basis for endosymbiosis and "the evolution of eukaryotic cells," I would have to agree with my cousin's assertion. He is correct in his argument that eukaryotic cells display a high level of complexity. However, he is incorrect in his assumption that intelligent design is the basis for this complexity. The explanation of this complexity can be found in Lynn Margulis's theory of endosymbiosis, SET. The idea of this theory is as follows. Eukaryotic cells evolved by consuming small, digestible, prokaryotic cells that remained in the cell. The two cells learned to grow symbiotically, one provided energy while the other provided protection. The smaller of the two cells, mitochondria, provides the cell's main source of ATP energy. Over time, the host cell engulfs a chlorplast which performs photosynthesis to provide the eukaryotic cell with another form of energy. In conclusion, this cousin needs to understand that in no way was the evolution of eukaryotic cells spontaneous. Organelles are the primary reasons for a eukaryoitc cell's existence, which is the basis for Lynn Margulis's theory of endosymbiosis.

Upon finishing that unnecessarily large article, i would have to go ahead and disagree with my Alabama grown cousin. hehe, Alabama.
simply because a part of the body is very complicated does not mean it should be labeled as an irreducibly complex result of the "theory" of intelligent design. If everybody took this "simple way out" than no scientist would ever get anything done, but instead whenever they hit a wall they would label it a result of intelligent design and move on.
The reason that there are seemingly no intermediate steps between the simple prokaryotic cells and the multi fascited eukaryotic cells is that symbiotic relationships would occur much more rapidly than most evolutionary processes. After mitochondrea and the first anearobic bacteria formed their symbiotic relationship the mitochondrea lost its metabolic functions as they would be provided by the cell and as such was no longer able to survive by itself. what had started as a case of opportunistic parasitism evolved into an obligatory partnership. Some evidence that supports this claim is that a cell that had its mitochondrea experimentally taken out cannot reproduce them on its own. Margulis SET theory also challenges the the theory that the flagellum is also a product of intelligent design. Margulis argues that the flagellum had actually evolved from a prokaryotic symbiote and differs from the flagellum of prokaryotes to such a degree that it should be called an undulipdium.
With many smaller experiments pointing towards Marguli's SET, the previously separate studies of cellular biology and evolution theory have been linked together in a way that should dissuade anybody from buying into the notion that anything, including eukaryotic cells, is a product of intelligent design.

Robert Gorter, MD, PhD, is emeritus professor of the University of California San Francisco (UCSF)

Bacterias and other micro-organisms play a crucial role in making life possible on earth No bacterias, no life!

Dr. Robert Gorter: “This article tries to give an overview of the development of bacterias and other micro-organisms and by tracing them back to the earliest stages of evolution and how early bacterias got incorporated into living cells that compose all complex animal organisms up to men. Mitochondria are a perfect example of an early form of a bacteria that was incorporated into a plant or animal cell. Mitochondria, the so-called “powerhouses” of cells, are unusual organelles in that they are surrounded by a double membrane and retain their own small genome. They also divide independently of the cell cycle by simple fission. Mitochondrial division is stimulated by energy demand, so cells with an increased need for energy contain greater numbers of these organelles than cells with lower energy needs (in case of body builders)”

Louis Pasteur (1822-1895) was renowned for his discoveries of the principles of vaccination, microbial fermentation and pasteurization. He is remembered for his remarkable breakthroughs in the causes and preventions of diseases (hygiene)

When Louis Pasteur discovered the pathogens (bacterias and micro-organisms that make us sick) and the principles of sterilization (pasteurization) and hygiene, life expectancy jumped up and quality of life increased significantly.

In modern times, a certain phobia has been developed and has become main stream: an abnormal and persistent fear of bacilli (bacteria). A phobia is an unreasonable and excessive sort of fear that causes avoidance and panic. Phobias are a relatively common type of anxiety disorder in most societies.

Dr. Robert Gorter: “The sterile world people live in industrialized nations pay a prize: increasingly, the incidence and prevalence of severe allergies and autoimmune diseases are documented due to the fact that the immune system is no longer trained by minor infections which are accompanied by fever. Also, the consequent vaccinations against childhood diseases at very early age are associated with decline in overall cellular immune functions, making the adult more vulnerable for malignancies.”

Intracellular Symbioses

Metabolic co-evolution in cooperative symbioses between animals and intracellular bacteria

In this article, Robert Gorter , et. al. wants to give three examples how in evolution various forms of “primitive” live join and compose complex organisms and the biodiversity as we know it. And how Mother Nature can rapidly respond to huge, man-made catastrophes.

Robert Gorter: “About ten to twelve million years ago, a population of African apes diverged down two paths. One lineage gave rise to the gorilla family. The other eventually split again, producing one branch that led to the development of the humans (Homo sapiens) and another that forked into chimpanzees and into bonobos. This is the story of our recent evolutionary past, as far as it is physical.”

It is also the story of some families of microbes living in our guts.

We have tens of trillions of bacteria and other microbes in our guts—at least ten for each of our own human cells that compose the body. Some species within this microbiome are passers-by, which we pick up from our food and our environments. But others are much older companions and they are our best friends, passed-on to us by breast feeding by our mothers and direct family members.

Although orangutans may consume leaves, shoots, and even bird eggs, fruit is the most important part of their diet. They live predominantly in trees

Gorillas are ground-dwelling, predominantly herbivorous apes that inhabit the forests of central Africa

They are the largest living primates. The DNA of gorillas is highly similar to that of humans, from 95–99% depending on what is counted, and they are the next closest living relatives to humans after the chimpanzees and bonobos.

Chimpanzees are one of two exclusively African species of great apes that are currently extant

Native to sub-Saharan Africa, both are currently found in the Congo jungle. Classified in the genus Pan, they were once considered to be one species. However, since 1928, they have been recognized as two distinct species: the common chimpanzee (P. troglodytes) lives north of the Congo River and the bonobo (P. paniscus) who live south. Based on genome sequencing, the two extant Pan species diverged around one million years ago. The most obvious differences are that chimpanzees are somewhat larger, more aggressive and male dominated, while the bonobos are more gracile, very peaceful, and female dominated.

Andrew Moeller, evolutionary biologist at the University of California, Berkeley, USA, found that there are a few groups of human gut bacteria whose history pre-dates humanity. Their ancestors lived in the guts of ancestral apes, and as those ancient animals diverged into modern species, the microbes did, too. In technical terms, they evolved into simpler ones, if you drew out their family tree, you’d get ours for free you could reconstruct the evolution of apes simply by comparing the right bacteria in their bowels.

Bacteria are prokaryotes, which consist of a single cell with a simple internal structure

“Some of the bacteria in our gut are derived from very ancient lineages that have been passed down through the primates for millions of years,” says Moeller. “They’re like our genes in that sense.”

Robert Gorter: “Many animals utilize nutritionally-inadequate diets but survive by associating with symbiotic bacteria inside their own cells and that are restricted to specialized insect cells known as bacteriocytes. Bacteriocytes are invariably transferred from parent to offspring (vertical transmission) and overproduce key nutrients that supplement the inadequate diet of their animal host.”

Currently, investigations are conducted world-wide into how the function of the symbiotic bacteria and the host bacteriocyte are structured for nutrient exchange. We apply metabolic models and experimental approaches, informed by genomic, transcriptomic and proteomic data, to establish how essential amino acid overproduction by the symbiotic bacteria is sustained and scaled to host demand.

The whitefly Bemisia tabaci, displaying the symbiotic bacteria Portiera (Cy3, red) and Hamiltonella (Cy5, green) in the insect bacteriocytes. FISH micrograph by Hong Wei Shan

Our research concerns both symbioses with a single bacterial partner (e.g. Buchnera in aphids) and symbioses in insects with multiple intracellular symbionts. We are finding that the metabolic capabilities of the bacteriocytes are exquisitely tuned to the nutritional requirements and products of the symbiotic bacteria, including functions that compensate for the loss of metabolism-related genes in the bacteria. In some symbioses, such as the whitefly Bemisia tabaci, the synthesis of certain essential amino acids (e.g. lysine) involves reactions coded by genes horizontally transferred from other bacteria to the insect genome.

Robert Gorter: “Buchnera lacks genes for the biosynthesis of cell-surface components, including lipopolysaccharides and phospholipids, regulator genes and genes involved in defense of the cell. These results indicate that Buchnera is completely symbiotic and viable only in its limited niche, the bacterium. Buchnera is a close relative of Escherichia coli.

Co-speciation between animals and microbes is fairly common. Aphids, those sap-sucking banes of gardeners, carry Buchnera in them, which provide them with essential nutrients that are missing from their meals. Their alliance was formed between 180 and 250 million years ago, when the dinosaurs were just starting out, and their fates have been entwined ever since. The family trees of aphids and Buchnera strains are also perfect matches.

A Petri dish with cultured bacteria’s which usually from colonies when grown in a dish

That’s kind of a special case, though. Buchnera lives inside the cells of its host only, and nowhere else. It would not survive outside a living cell of a host animal. It is also strictly passed from mother to offspring via egg cells. Co-speciation was almost a foregone conclusion. Our gut bacteria have no such constraints. They live freely within the ecosystem of our bowels. They can move vertically from parent to child, but also horizontally from peer to peer. It’s much less obvious that they should have co-speciated with us at all.

Howard Ochman: Department of Integrative Biology, University of Texas at Austin Evolutionary Biology, Evolutionary Genetics, Molecular Evolution

In 2010, Howard Ochman found hints that they might. He was the first to show that a family tree constructed using the microbiomes of apes mirrored the one drawn from their own DNA. So, for example, the microbiomes of three chimp subspecies were more similar to each other than to bonobo microbiomes, and more similar to bonobo microbiomes than to human ones.

But Ochman just looked at microbiomes as a whole. Moeller, his graduate student at the time, decided to look for particular species and strains of bacteria whose histories match our own. Moeller relied on a large bank of stool samples, collected from wild apes in Cameroon, Tanzania, and the Democratic Republic of the Congo, and from wild humans living in Connecticut.

Robert Gorter: “Andrew Moeller found many examples of co-speciation within two families of bacteria that are common in our guts—the Bacteroidaceae (“BACK-tuh-roy-DAY-see-ay”) and the Bifidobacteriaceae (“BIH-fih-doh-BACK-tee-ree-AY-see-ay”). Some of the co-speciating microbes, like Bacteroides vulgatus, are familiar to researchers others are a mystery, and haven’t even been named yet.”

But it’s not as if the entire microbiome is co-speciating neatly, or even most of it. “There are some bacteria that seem to track their host lineage perfectly and others that don’t seem to care which host they’re in—they’re just jumping around,” says Moeller. For example, one lineage had jumped from chimps to gorillas, and another recently moved from humans to chimps.

Britt Koskella, University of California, Berkeley, USA, is an evolutionary biologist seeking to understand how interactions and symbioses among species generate and maintain much of the diversity on earth

Still, this study “shows clear potential for the co-evolution between humans and their gut microbiome,” says Britt Koskella, an evolutionary biologist at the University of California, Berkeley, who was not involved in the study. “It also raises interesting questions about how modern human behavior, such as cleanliness and changes in diet, might be altering those tight associations and leading to increased health problems, like allergies and cancer.”

Robert Gorter: “Koskella is talking about the hypothesis, popularized by Martin Blaser, that we are inadvertently evicting longstanding bacterial partners from our bodies. Moeller certainly found some evidence for this. He showed that some lineages of co-speciating bacteria are present in gorillas, chimps, and bonobos, but their counterparts are missing from Western guts (although some still exist within people living in rural Malawi).”

That raises two important questions:

Firstly, “why are these microbes disappearing?” Dr. Robert Gorter and others have blamed the trappings of modern life, including wanton use of antibiotics and an obsession with sanitation. That’s possible, but in a previous study, Andrew Moeller showed that the diversity of the human gut microbiome has been falling for a very long time it’s lower among human hunter-gatherers than chimps or gorillas, and then still lower still among Western city-dwellers. “I think it probably started when humans started cooking our food,” he says. “Immediately, you’re going to lose some ability to host a complex consortium of bacteria, because you don’t need them anymore.”

Secondly, “Are these lost groups doing important things in chimps and bonobos, which we’re not getting?” Moeller asks. Some would argue that these microbes must have been doing something important, given their long history with us. Robert Gorter: “likely, they helped to digest our food or calibrate our immune system, and perhaps their absence partly explains why chronic inflammatory and autoimmune diseases (and also cancer?) are on the rise.

It’s a compelling idea, but a speculative one. We still don’t really know how these ancient microbes are affecting us, or vice versa. Which means, according to Katherine Amato, from Northwestern University, that we can’t strictly claim that we’re co-evolving with them. “Do these patterns of co-speciation matter to us in the grand scheme of natural selection?” she asks. “Does having the wrong strain make individuals less reproductively successful?” Jessica Metcalf, from the University of Colorado in Boulder, has similar questions. “What do bacteria that co-diversified with their hosts have in common?” she asks. “And are they more important to their hosts than ones that were acquired through the environment?”

“When we start to be able to answer these questions is when things will really get exciting,” says Amato. To do that, she thinks researchers will need to look at the entire genomes, to see if changes in the microbes correlate with new traits or abilities in their hosts. They’ll also need to move outside the apes and think about monkeys, lemurs, and other primates. “Searching for patterns among only four host species may be over-simplifying aspects of the story,” she says.

Mitochondria (red) from heart muscle cell of a rat. Nearly all our cells have these structures. Credit: Thomas Deerinck, National Center for Microscopy and Imaging Research

Mitochondria are specialized structures unique to the cells of animals, plants and fungi. They serve as batteries, powering various functions of the cell and the organism as a whole. Though mitochondria are an integral part of the cell, very strong evidence shows that they evolved from primitive bacteria which were incorporated very early on in cells of primitive life.

All living organisms are built with one fundamental brick: the cell. In some cases, a single cell constitutes an entire organism. Cells contain genetic material (DNA and RNA), and they carry out essential functions, such as metabolism and protein synthesis. Cells are also capable of self-replicating. However, the level of organization varies within the cells of different organisms. Based on these differences, organisms are divided into two groups: eukaryotes and prokaryotes.

Plants, animals and fungi are all eukaryotes and have highly ordered cells. Their genetic material is packaged into a central nucleus. They also have specialized cellular components called organelles, each of which executes a specific task. Organelles such as the mitochondria, the rough endoplasmic reticulum and the golgi complex serve respectively to generate energy, synthesize proteins and package proteins for transport to different parts of the cell and beyond. The nucleus, as well as most eukaryotic organelles, is bound by membranes that regulate the entry and exit of proteins, enzymes and other cellular material to and from the organelle.

Individual mitochondria are capsule shaped, with an outer membrane and an undulating inner membrane, which resembles protruding fingers. These membranous pleats are called cristae, and serve to increase the overall surface area of the membrane. When compared to cristae, the outer membrane is more porous and is less selective about which materials it lets in. The matrix is the central portion of the organelle and is surrounded by cristae. It contains enzymes and DNA. Mitochondria are unlike most organelles (with an exception of plant chloroplasts) in that they have their own set of DNA and genes that encode proteins.

Prokaryotes, on the other hand, are single-celled organisms such as bacteria and archaea. Prokaryotic cells are less structured than eukaryotic cells. They have no nucleus instead their genetic material is free-floating within the cell. They also lack the many membrane-bound organelles found in eukaryotic cells. Thus, prokaryotes have no mitochondria.

Mitochondria Function

The main function of mitochondria is to metabolize or break down carbohydrates and fatty acids in order to generate energy. Eukaryotic cells use energy in the form of a chemical molecule called ATP (adenosine triphosphate).

ATP generation occurs within the mitochondrial matrix, though the initial steps of carbohydrate (glucose) metabolism occur outside the organelle. According to Geoffrey Cooper in “The Cell: A Molecular Approach 2nd Ed” (Sinauer Associates, 2000), glucose is first converted into pyruvate and then transported into the matrix. Fatty acids on the other hand, enter the mitochondria as is.

ATP is produced through the course of three linked steps. First, using enzymes present in the matrix, pyruvate and fatty acids are converted into a molecule known as acetyl-CoA. This then becomes the starting material for a second chemical reaction known as the citric acid cycle or Krebs Cycle. This step produces plenty of carbon dioxide and two additional molecules, NADH and FADH2, which are rich in electrons. The two molecules move to the inner mitochondrial membrane and begin the third step: oxidative phosphorylation. In this last chemical reaction, NADH and FADH2 donate their electrons to oxygen, which leads to conditions suitable for the formation of ATP.

Dr. Robert Gorter: “Logically, mitochondria multiply when a the energy needs of a cell increase. Therefore, power-hungry cells have more mitochondria than cells with lower energy needs. For example, repeatedly stimulating a muscle cell will spur the production of more mitochondria in that cell, to keep up with energy demand. Logically, mitochondria multiply when the energy needs of a cell increase. Therefore, power-hungry cells have more mitochondria than cells with lower energy needs. For example, repeatedly stimulating a muscle cell will spur the production of more mitochondria in that cell, to keep up with energy demand.”

A secondary function of mitochondria is to synthesize proteins for their own use. They work independently, and execute the transcription of DNA to RNA, and translation of RNA to amino acids (the building blocks of protein), without using any components of the cell. However, here too, there are differences within eukaryotes. The sequence of three DNA nucleotides U-A-G (uracil-adenine-guanine) is an instruction for translation to stop in the eukaryotic nucleus.

Origins of mitochondria: The Endosymbiont Theory

In her 1967 paper, “On the Origins of Mitosing Cells,” published in the Journal of Theoretical Biology, scientist Lynn Margulis proposed a theory to explain how eukaryotic cells along with their organelles were formed. She suggested that mitochondria and plant chloroplasts were once free-living prokaryotic cells that were swallowed up by a primitive eukaryotic host cell.

Lynn Margulis’ hypothesis is now known as the “endosymbiont theory.” Dennis Searcy, emeritus professor at University of Massachusetts Amherst, explained it as follows: “Two cells began to live together, exchanging some sort of substrate or metabolite (product of metabolism, like ATP). The association became mandatory, so that now, the host cell cannot live separately.”

Even at the time that Margulis proposed it, versions of the endosymbiont theory were already in existence, some dating back to 1910 and 1915. “Although these ideas are not new, in this paper they have been synthesized in such a way as to be consistent with recent data on the biochemistry and cytology of subcellular organelles,” she wrote in her paper. According to a 2012 article on mitochondrial evolution by Michael Gray in the journal Cold Spring Harbor Perspectives in Biology, Margulis based her hypothesis on two key pieces of evidence. First, mitochondria have their own DNA. Second, the organelles are capable of translating the messages encoded in their genes to proteins, without using any of the resources of the eukaryotic cell.

Already in Berlin in 1906 and during the following years, the German scientist Rudolf Steiner pointed out that earlier, more primitive life forms merged anatomically as well as functionally (physiologically) and building the anatomy of new, higher-developed organisms guided by evolutionary dynamics (but not ad random) which then developed into the biodiversity as we know today.

Genome sequencing and analyses of mitochondrial DNA have established that Margulis was correct about the origins of mitochondria. The lineage of the organelle has been traced back to a primitive bacterial ancestor known as alphaproteobacteria (α-proteobacteria).

Robert Gorter: “Despite the confirmation of the mitochondria’s bacterial heritage, the endosymbiont theory continues to be researched. One of the biggest questions stays, ‘Who is the host cell?’”

The questions that linger are whether mitochondria originated after the eukaryotic cell arose (as hypothesized in the endosymbiont theory) or whether mitochondria and host cell emerged together, at the same time (this theory is strongly supported by Rudolf Steiner).

Bacteria: The First Responders to Oil Spills

This map shows the magnitude of the oil spill in the Gulf of Mexico

The toxic substance, composed of alkanes and aromatic hydrocarbons, posed a huge threat to the organisms that called the Gulf their home. Not only did the oil congeal on the surface, but it also settled into the ocean’s sediment. It spread literally everywhere.

In a desperate attempt to reverse the damage, dispersants were distributed alongside the oil. At that point in time, the scientific community and the cleanup crew were unaware that certain bacterial species had already appeared at the scene instead of fleeing it.

That’s right – among the estimated 1 trillion microbial species that inhabit the globe, several species of bacteria actually use their natural metabolic processes for good purposes. They can reduce the amount of oil waste spilled during disasters such as the Deepwater Horizon Spill.

In 2010, in an event now known as the Deepwater Horizon Spill, the Gulf of Mexico’s fragile oceanic ecosystem became severely polluted with approximately 4.9 million barrels of oil

In a recent publication written by a collaboration of researchers from The University of Texas Marine Science Institute, the University of North Carolina, and Heriot-Watt University, it was suggested that these bacteria have special genes which allow them to quickly adapt to environments with low nutrients.

Their gene sequencing, published in the journal Nature Microbiology, was done in order to further understand the relationship between toxic spills and bacterial function.

One bacteria species in particular, Neptuniibacter, had never before surfaced at an oil spill scene. Yet there it was – working closely alongside the more commonly present Alcanivorax to feast heartily on the oil.

Interestingly, the researchers found that over time the sudden rush of chemicals changed the complete structure of the microbial community in the area. When they returned to the spill site after one year, they noted that the bacterial communities had become more diverse over the time period.

The conclusions drawn from the research show just how adaptable the bacteria are. Their ability to modify themselves to fit a suddenly altered environment is a remarkable characteristic.

Unfortunately, oil spills are common in the Gulf, and elsewhere. But, luckily, bacterias native to the ecosystem are prepared and ready for action. Think of these small yet mighty organisms as first-responders to the scene of the accident. They assess the damage and do what they can to stabilize the area. Then, they call for backup.

“After the spill, all bacteria work(ed) together to efficiently degrade oil,” commented Nina Dombrowski, a post-doctoral researcher who contributed to the research.” Bacterial communities already present at the site of an oil spill respond(ed) in a rapid and efficient manner, becoming abundant during the spill and actively degrading oil compounds.”

As we get to know the significance of these microorganisms, we can promote understanding and conservation of the microbial world. This knowledge also provides us with helpful insight to reversing the damage done to marine ecosystems.

Composting: its importance and the role of bacteria and other micro-organism

Robert Gorter: “Bacteria are found in every living habitat on earth and play an essential role with regards to composting. In fact, without compost bacteria, there would be no compost, or life on planet earth for that matter. Beneficial bacteria found in garden compost are the “garbage men” of the earth, cleaning up trash and creating a useful product. In other words, they recycle almost anything that is bio degradable.”

Bacteria are able to survive extreme conditions where other life forms crumble. In nature, compost exists in areas such as the forest, where compost-enhancing bacteria decompose organic matter like tree and animal droppings but also carcasses. Putting beneficial bacteria to work in the home garden as well as in agriculture is an environmentally friendly practice that is well worth the effort.

Beneficial bacteria found in garden compost are busy breaking down matter and creating carbon dioxide and heat. The temperature of compost can get up to 60 degrees Celsius due to these heat-loving microorganisms. Compost-enhancing bacteria work around the clock and in all sorts of conditions to break down organic material. In tempered climates, during frost the composting processes are slowed down but not come to a complete stop.

Fungi plays important role as decomposing of complex plant polymers in soil and compost. Fungi include molds and yeasts, in compost they break down tough debris, enabling bacteria to continue the decomposition process once most of the cellulose has been exhausted. Fungi grows rapidly by producing many cells and filaments, and they can attack organic residues that are too dry, acidic, or low in nitrogen for bacterial decomposition. Saprophytes because they live on dead or dying material and obtain energy by breaking down organic matter in dead plants and animals. Fungi are mostly found during both mesophilic and thermophilic phases of composting. During higher temperature they live on outer layer of compost. Scytalidium thermophilum helps in growth of thermophilic fungus.10 Fungi favor an acidic pH range.


Actinomycetes are fungi resembled bacteria with filamentous. They are resistant to dry, acidic, or low in nitrogen for bacterial decomposition environment. Saprophytes because they live on dead or dying material and obtain energy by breaking down organic matter in dead plants and animals. Variety of Fungal Species are found during both mesophilic and thermophilic phases of composting. During higher temperature they like to live in the outer layer of compost.

Protozoa are one-celled microscopic animals. Mostly found in water droplets in compost but play a relatively minor role in decomposition. Protozoa obtain their food from organic matter in the same way as bacteria do but also act as secondary consumers ingesting bacteria and fungi.

Worms and other invertebrates are very essential in the overall composting or organic materials

Other Invertebrates

Ants make compost richer in phosphorus and potassium by moving minerals from one place to another. Springtails one of the most important invertebrates as they help in breaking down materials They chew on decomposing plants, pollen, grains, and fungi. They also like to eat nematodes and droppings of other arthropods and then clean themselves after feeding. Snails and slugs like fresh garbage so mostly found on top of compost pile. Centipedes are fast moving predators found mostly in the top few inches of the compost heap. They have formidable claws behind their head which possess poison glands that paralyze small red worms, insect larvae, newly hatched earthworms, and arthropods (mainly insects and spiders). Files are mostly found in mesophilic stage, they provide airborne transportation for bacteria. They also eat organic vegetation. Files larval phase (maggots) does not survive thermophilic temperatures.

Their incorporation into soil increases fertility (e.g. nitrogen fixers, nitrifiers, sulphur oxidizers), structure (e.g. exopolysaccharide producers), and can have other effects as a result of high activity and population levels, as well as through specific biochemical traits of the micro-organisms. Increased numbers of microorganisms in compost also have an indirect role in improving plant health. Microorganisms form symbiotic associations with plant roots and synthesize and excrete nutrients (amino acids, vitamins), plant growth hormones and chelators, alter physical conditions to optimize plant growth, and decompose or neutralize toxic substances. The majority of bacteria isolated from composts were Gram-negative.7 Microorganisms may affect negatively as they compete for oxygen, nutrient which can inhibit metabolic products. Optimal pH values for composting range from pH 5.5 to 8.0. Initial pH of composting are acidic which forms acid-forming bacteria. As pH starts to increase and becomes alkaline and finally drops back to near neutral as a result of humus formation.

Garden snails (Helix aspersa: Helicidae) on a compost heap feeding

Once decomposed, this rich, organic dirt is used in the garden and in agriculture to enhance existing soil conditions and improve the overall health of plants that are grown there.

Why Is the Nucleus So Important?

Of all eukaryotic organelles, the nucleus is perhaps the most critical. In fact, the mere presence of a nucleus is considered one of the defining features of a eukaryotic cell. This structure is so important because it is the site at which the cell's DNA is housed and the process of interpreting it begins.

Recall that DNA contains the information required to build cellular proteins. In eukaryotic cells, the membrane that surrounds the nucleus — commonly called the nuclear envelope — partitions this DNA from the cell's protein synthesis machinery, which is located in the cytoplasm. Tiny pores in the nuclear envelope, called nuclear pores, then selectively permit certain macromolecules to enter and leave the nucleus — including the RNA molecules that carry information from a cellular DNA to protein manufacturing centers in the cytoplasm. This separation of the DNA from the protein synthesis machinery provides eukaryotic cells with more intricate regulatory control over the production of proteins and their RNA intermediates.

In contrast, the DNA of prokaryotic cells is distributed loosely around the cytoplasm, along with the protein synthesis machinery. This closeness allows prokaryotic cells to rapidly respond to environmental change by quickly altering the types and amount of proteins they manufacture. Note that eukaryotic cells likely evolved from a symbiotic relationship between two prokaryotic cells, whereby one set of prokaryotic DNA eventually became separated by a nuclear envelope and formed a nucleus. Over time, portions of the DNA from the other prokaryote remaining in the cytoplasmic part of the cell may or may not have been incoporated into the new eukaryotic nucleus (Figure 3).


Evidence that mitochondria and plastids arose from ancient endosymbiosis of bacteria is as follows:

  • Both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (in being circular and in its size).
  • They are surrounded by two or more membranes, and the innermost of these shows differences in composition from the other membranes of the cell. The composition is like that of a prokaryotic cell membrane.
  • New mitochondria and plastids are formed only through a process similar to binary fission. In some algae, such as Euglena, the plastids can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell. In such a case, the plastids will not regenerate.
  • Much of the internal structure and biochemistry of plastids, for instance the presence of thylakoids and particular chlorophylls, is very similar to that of cyanobacteria. Phylogenetic estimates constructed with bacteria, plastids, and eukaryotic genomes also suggest that plastids are most closely related to cyanobacteria.
  • DNA sequence analysis and phylogenetic estimates suggests that nuclear DNA contains genes that probably came from the plastid.
  • Some proteins encoded in the nucleus are transported to the organelle, and both mitochondria and plastids have small genomes compared to bacteria. This is consistent with an increased dependence on the eukaryotic host after forming an endosymbiosis. Most genes on the organellar genomes have been lost or moved to the nucleus. Most genes needed for mitochondrial and plastid function are located in the nucleus. Many originate from the bacterial endosymbiont.
  • Plastids are present in very different groups of protists, some of which are closely related to forms lacking plastids. This suggests that if chloroplasts originated de novo, they did so multiple times, in which case their close similarity to each other is difficult to explain. Many of these protists contain "secondary" plastids that have been acquired from other plastid-containing eukaryotes, not from cyanobacteria directly.
  • Among the eukaryotes that acquired their plastids directly from bacteria (known as Primoplantae), the glaucophyte algae have chloroplasts that strongly resemble cyanobacteria. In particular, they have a peptidoglycan cell wall between their two membranes.
  • These organelles' ribosomes are like those found in bacteria (70s).
  • Proteins of organelle origin, like those of bacteria, use N-formylmethionine as the initiating amino acid.

Analysis knocks down theory on origin of cell structure

Cilia inside the human trachea. Scanning electron micrograph.

( -- Understanding how living cells originated and evolved into their present forms remains a fundamental research area in biology, one boosted in recent years by the introduction of new tools for genomic analysis. Now, researchers at MIT and Boston University have used such tools to put what they say is "the last nail in the coffin" for one theory about the origin of a basic structure in the cell.

In the process, by illuminating a key step in the initial evolution of a basic structure that still exists in most cells in the human body, it may help researchers understand how some of these components work. These include parts of the neurons that make up our brains, sperm cells that determine fertility, and basic elements of cellular reproduction.

Many biologists have thought that three of the basic structures within the kinds of cells that make up all animals and plants -- called eukaryotic cells -- started out as separate, independent organisms. Then, at some point, these merged with other primitive cells to produce a symbiotic unit. But new evidence strongly contradicts that origin for one of those structures.

Eukaryotes are cells that have a nucleus within them: a membrane-surrounded kernel at the cell's center that contains its genetic material, DNA. These are the cells that make up virtually all of the complex, multicellular life on Earth, and they differ from the smaller, more primitive prokaryotes (bacteria and archaea), which have no such internal structure and whose DNA floats freely within their outer membranes.

The idea that the eukaryotic cell's nucleus originated as a separate organism, initially greeted with skepticism decades ago, is now a mainstream view though still not universally accepted. The process is known as endosymbiosis.

Similarly, other structures within such cells -- tiny subunits called mitochondria, which produce all of the cell's energy -- are now generally believed to have originated as separate organisms. And a third type of structure in eukaryotic cells, called cilia, the tail-like structures that enable them to move or to sense their environment, are also thought by many biologists to be yet another example of endosymbiosis.

But the new analysis by Hyman Hartman, visiting scientist in MIT's Center for Biomedical Engineering, and Temple Smith of Boston University, published in the April issue of the journal Cell Motility and the Cytoskeleton, provides strong evidence that this idea cannot be true for the origin of cilia. They found that genes that produce the cilia have unique characteristics that are not present in the kinds of simple cells that would have led to the symbiotic union. That suggests that cilia may have originated earlier, within the evolving cell, through a process that remains to be understood.

In short, these cell structures must not have arisen through mergers and acquisitions, as the other cell components were, but were developed in-house.

The paper describing the new findings was designated a "must read" by the Faculty of 1,000, an online service whose users select what they think are the most important research papers out of the scientific journals. Linda Amos, a biologist at the Medical Research Council's Laboratory of Molecular Biology in Cambridge, England, said she selected the paper for that recognition "because it suggests a likely route for a crucial step in the evolution of eukaryotes from prokaryotes."

Amos said others had suggested "that the cilium itself might have once been an independent free-swimming prokaryotic cell that a pre-eukaryote could have taken over in a similar way to the mitochondrion, by engulfing it." But the new research "makes it much more likely that the cilium with its complicated array of specialized dyneins [proteins] developed gradually within the same cell type that eventually itself became the ancestral eukaryote."

That development process, Hartman says, may be related to the evolution of mitosis, the process of cell division that is the basis of all plant and animal reproduction, and unraveling its origins could help in understanding this fundamental process.

"It's a big advance," he says. It provides "evidence for a very long history of something that was there before" the origin of the kind of cells that made all advanced life possible. If this analysis is confirmed, he says, "understanding the cilia is now going to become one of the great projects" for biologists to pursue.