This is perhaps the most deceptively simple and important biological insight of this decade. As Huxley said of natural selection, "How extremely stupid not to have thought of that!"
http://blogs.discovermagazine.com/notrocketscience/2011/10/17/the-two-genome-waltz-how-the-threat-of-mismatched-partners-shapes-complex-life (http://blogs.discovermagazine.com/notrocketscience/2011/10/17/the-two-genome-waltz-how-the-threat-of-mismatched-partners-shapes-complex-life)
QuoteVirtually all complex cells – better known as eukaryotes – have at least two separate genomes. The main one sits in the central nucleus. There's also a smaller one in tiny bean-shaped structures called mitochondria, little batteries that provide the cell with energy. Both sets of genes must work together. Neither functions properly without the other.
Mitochondria came from a free-living bacterium that was engulfed by a larger cell a few billion years ago. The two eventually became one. Their fateful partnership revolutionised life on this planet, giving it a surge of power that allowed it to become complex and big (see here for the full story). But the alliance between mitochondria and their host cells is a delicate one.
Both genomes evolve in very different ways. Mitochondrial genes are only passed down from mother to child, whereas the nuclear genome is a fusion of both mum's and dad's genes. This means that mitochondria genes evolve much faster than nuclear ones – around 10 to 30 times faster in animals and up to a hundred thousand times faster in some fungi. These dance partners are naturally drawn to different rhythms.
This is a big and underappreciated problem because the nuclear and mitochondrial genomes cannot afford to clash. In a new paper, Nick Lane, a biochemist at University College London, argues that some of the most fundamental aspects of eukaryotic life are driven by the need to keep these two genomes dancing in time. The pressure to maintain this "mitonuclear match" influences why species stay separate, why we typically have two sexes, how many offspring we produce, and how we age.
The original essay is here: http://onlinelibrary.wiley.com/doi/10.1002/bies.201100051/abstract;jsessionid=38BD914A6F8A6CC1CEDA0BB17A6F51BF.d02t04
The mitochondrial-nuclear relationship is one of the oldest and most important aspects of eukaryote biology. The mitochondria, at one time free living bacteria, are internal obligate symbiotes of the eukaryotic cell. Not only that, but their bacterial genome is parsed down from thousands to thirteen; the rest of the management genes have been transferred to the nucleus, but are still necessary to make the electron transport chain work well and not leak free radicals all over the place. Therefore, there is heavy selection for the nuclear and mitochondrial genomes to be compatible, since free radicals (electrons without a nucleus) are high energy and dangerous to life. They cut through tissues, mutate DNA and generally wreck havock. When a mitochondria stops working correctly, it either kills it's host cell (general cell death), or turns off the self kill ability (cancers). This and telomere length on nuclear chromosomes are probably what causes aging, as the telomeres shorten, allowing more copy errors, and mutations and copy errors accrue in the mitochondrial genome. And this accelerates as the electron leak worsens, in a feedback cycle. Which would explain the quick degeneration rate of people with end life diseases. And since this relationship is directly related to longevity, fecundity, and gene compatibility, it's no wonder that evolution has selected very widely used reproductive aspect of two sexes (with mitos passed down by only one), because multiple lineages of mitochondria in a single cell would decrease the total compatibility. It also explains why organisms with high energy lifestyles, like bats and birds, have low fecundity, because only embryos with highly compatible mitonuclear matches would survive development; the leak threshold is lower, the efficiency necessarily higher. Conversely, rats have lower energy efficiency needs, so they have higher fecundity. This also brings up another point, that species with lower leak levels have longer lives; pigeons, for example, live much longer than rats.
These are all, I think, majorly important ideas and routes for research, especially when it comes to aging and life extension.
Interesting brain chew, Kai. Thanks. :)
Mind blown.
This is all really interesting - I didn't realize that the mitochondrial DNA evolve faster.. and I'm not sure I entirely understand why.
I would have guessed nuclear DNA evolves faster because it has more variance?
What does it mean that "nuclear and mitochondrial genomes cannot afford to clash"? in what ways do they clash?
Quote from: Cramulus on October 17, 2011, 09:43:29 PM
This is all really interesting - I didn't realize that the mitochondrial DNA evolve faster.. and I'm not sure I entirely understand why.
I would have guessed nuclear DNA evolves faster because it has more variance?
What does it mean that "nuclear and mitochondrial genomes cannot afford to clash"? in what ways do they clash?
To add to that, wouldn't sharing and mixing genetic material from two(or more) parents increase the likely-hood of new variations showing up, or does that restrict it by preventing genetic material that is too variant from creating a viable cell?
Do mitochondria reproduce within cells during the cell's lifespan?
Quote from: Cramulus on October 17, 2011, 09:43:29 PM
This is all really interesting - I didn't realize that the mitochondrial DNA evolve faster.. and I'm not sure I entirely understand why.
I think I figured it out. Mitochondria reproduce multiple times during an organisms life, whereas nuclear DNA only makes it out of the barn during reproduction.
GOT IT NOW!
(http://www.strangekidsclub.com/wp-content/uploads/2011/04/the_more_you_know1.jpg)
That's right, Cram, but remember it's only the mitochondria in the germ tissue that gets passed to the mother's offspring. So not a massive amount of times, but still more than nuclear DNA.
In what ways can they clash with the nuclear DNA?
Quote from: Donald Coyote on October 17, 2011, 09:56:34 PM
Quote from: Cramulus on October 17, 2011, 09:43:29 PM
This is all really interesting - I didn't realize that the mitochondrial DNA evolve faster.. and I'm not sure I entirely understand why.
I would have guessed nuclear DNA evolves faster because it has more variance?
What does it mean that "nuclear and mitochondrial genomes cannot afford to clash"? in what ways do they clash?
To add to that, wouldn't sharing and mixing genetic material from two(or more) parents increase the likely-hood of new variations showing up, or does that restrict it by preventing genetic material that is too variant from creating a viable cell?
Do mitochondria reproduce within cells during the cell's lifespan?
To answer your questions:
1. Nuclear and mitochondrial genes cannot afford to clash because this leads to mitochondrial innefficiency, which leads to leaky electrons, which leads to cell damage and mutation. The electron transport chain within the cristae walls of a mitochondrion is a finely tuned process. If you are familiar with cellular respiration, you'll know that organism that do not use oxygen in the synthesis of ATP (the molecule used to convey energy in cellular processes in just about every organism) have to do so by anoxic fermentation, and they get very little ATP from this process. This is in comparison to aerobic respiration, which from every glucose molecule not only generates two ATP from the anerobic glycolysis, but also 10 molecules of NADH+, which can generate ATP through the electron transport chain. This is nearly a 10-fold increase in efficiency.
The way the electron transport chain works is the electron from the NADH+ is passed intermembraineously through a series of protein gated channels that direct hydrogen ions out of the inner area of the mitochondrion. For every one NADH+, three hydrogen ions are directed out. (Note: after the electron is done passing it's energy off to the gated channels, it is donated to an oxygen (which causes a water molecule to be created), just to keep a free electron from making trouble). Now, this causes a hydrogen osmotic gradient; there are now more hydrogen molecules outside the inner area than within. This hydrogen gradient moving downslope through the cristae walls back into the inner area of the mitochondrion is what drives the major production of ATP from ADP.
Interestingly,
mitochondria have not retained all the genes to make this process work. They have some of the genes in the Electron Transport Chain, and all of the necessary bacterial tRNA genes, but none of the enzymes that run the citric acid cycle. Most of the necessary components have been, at some time in evolutionary history, donated to the nucleus of the cell; they are no longer stored in the mitochondrial genome. Therefore, to make aerobic respiration work, many of the components must be donated by the nuclear genome. You can see how important it is that these do not clash, then, as any component that lowers the efficiency will result in A) some lost energetic potential and B) a leaky electron transport chain which allows free radicals to escape. The components can clash in the sense that they are proteins, and proteins are folded structures of ammino acids, and if the folded structures do not fit together precisely, they do not work correctly on what ever purpose they are designed.
2. The hypothesis of mixing mitochondrial material being more inefficient, is because any one line of mitochondria isn't guaranteed to be a good match with every nuclear genome. Having only one mitochondrial lineage matched with one genome means that, if there is not a good match, that individual will not survive to maturity and will not reproduce, therefore that pairing will not continue in the population. If there are multiple lineages, then perhaps only one of those will be a good match, thus lowering the overall efficiency. Having only one mitochondrial lineage means that, if the pairing works, there aren't going to be problems of inefficiency from other involved pairings. Another reason could be that of aniosgamy, that is, that the gametes (egg and sperm generally) are significantly different in size. The sperm's mitochondria often doesn't even make it into the egg, and when they do, they are significantly outnumbered (1 million to several hundred) by the mitochondria of the egg, and are in a degraded state from the transfer.
3. Mitochondria do reproduce within cells over a lifetime; obviously copy errors in nuclear and mitochondrial DNA decrease respiratory efficiency over a lifetime. And while they reproduce generally at the same time as nuclear reproduction, they reproduce separately, the same way bacteria do, by fission. However, only the mitochondria in the germ layer tissue is passed to the offspring, and these generally reproduce only a small number of times compared to the rest of the tissues in an organism.
I should note, the other reason why mitochondrial DNA mutates faster is because it IS closer to the electron transport chain, and even in a high efficiency operation there will be some occasional leakage. mtDNA also doesn't have as robust repair mechanisms as nuclear DNA. The mitochondria can't even replicate or transcribe itself, because the genome doesn't retain a gene for DNApolymerase or DNAtranscriptase.
It's important to remember that when something works in biology, it tends to be conserved. Genetic diversity is all well and good if necessary to deal with a changing environment, but oxidative respiration was perfected a long time ago, and the cellular environment hasn't changed very much since then. Selection on pairings now is due to inefficiency that interferes with fecundity. Since diversity would just lower the efficiency in most cases, these things tend to be conserved. If it works, don't fix it (or break it, for that matter).
It's also interesting to think about how eukaryotic phototrophs (e.g. plants, algae) have to work well with not only mitochondria but also chloroplasts. And sometimes the chloroplasts have come to the lineage through secondary (organism 'eating' an alga that 'ate' a cyanobacteria) or even /tertiary endosymbiosis (organism 'eating' an alga that 'ate' an alga that 'ate' a cyanobacteria).
So, I was taking a break from studying biochem to read PD.com- and ended up reading Kai summarizing what I was supposed to be studying anyway. Although not a suitable substitute, I found it a rather entertaining happenstance.
Quote from: 'Kai' ZLB, M.S. on October 18, 2011, 05:50:43 PM
It's also interesting to think about how eukaryotic phototrophs (e.g. plants, algae) have to work well with not only mitochondria but also chloroplasts. And sometimes the chloroplasts have come to the lineage through secondary (organism 'eating' an alga that 'ate' a cyanobacteria) or even /tertiary endosymbiosis (organism 'eating' an alga that 'ate' an alga that 'ate' a cyanobacteria).
That's amazing. It's so complex, it
must have been designed by some higher power!
:asshat:
Quote from: LMNO, PhD (life continues) on October 18, 2011, 05:56:59 PM
Quote from: 'Kai' ZLB, M.S. on October 18, 2011, 05:50:43 PM
It's also interesting to think about how eukaryotic phototrophs (e.g. plants, algae) have to work well with not only mitochondria but also chloroplasts. And sometimes the chloroplasts have come to the lineage through secondary (organism 'eating' an alga that 'ate' a cyanobacteria) or even /tertiary endosymbiosis (organism 'eating' an alga that 'ate' an alga that 'ate' a cyanobacteria).
That's amazing. It's so complex, it must have been designed by some higher power!
:asshat:
Hah. Actually, the way we know that secondary and tertiary endosymbiosis has happened is from the remnants of the earlier organisms: in the form of earlier cell walls and membranes, photosynthetic pigments, and DNA. We can trace the lineages back through those leftovers from a not-quite perfect endosymbiosis. This is especially clear in the glaucophytes, a type of Archaeplastida algae (algae being a sort of catch all term for non-vascular photosynthetic organisms, comprising everything from cyanobacteria to diatoms to dinoflagellates to the semivascular charawort; it is not a real or natural group of organisms, it is polyphyletic, but it is a sometimes useful term) which has something across between chloroplasts and cyanobacteria. These cyanelles, as they are called, are more or less cyanobacteria in a state of partial endosymbiosis with the glaucophyte host organisms. Together with the Rhotophyta and the Viridiplantae (green algae plus land plants) they make up the Archeoplastida, which seem to all have gained their chloroplasts from a single endosymbiosis of a cyanobacteria over 1.5 bya. Though, there is some dispute whether this group is monophyletic or not. I tend to believe it is.
On a side note, I find the way the Eukarya tree is shaping out into 6 or 7 superkingdoms to be very interesting. These are:
- Archaeplastida: As above.
- Excavata: A group of unicellular flagellates, many of which have a excavation where the food cavity lies (classic example being Euglena (http://en.wikipedia.org/wiki/Euglena)
- Amoebozoa: A group of mostly unicellular organisms characterized by lobelike, cytoplasmic flow. Classic examples are Amoeba (http://en.wikipedia.org/wiki/Amoeba_proteus) and dog vomit slime mold (http://en.wikipedia.org/wiki/Dog_vomit_slime_mold)
- Rhizaria: A group of amoeboid unicellular organisms with filament or rod like pseudopods. There aren't really any classic laboratory examples of these; the Forameniferans (http://en.wikipedia.org/wiki/Foraminifera) are my favorite.
- Opisthokonta: Multicellular and unicellular organisms that when flagellate posess a single posterior flagellum. Includes the metazoans (all multicellular animals), fungi, and related groups.
- Chromalveolata: One or two groups, depending on who you ask, the Alveolates and the Stramenopiles or Heterokonts. The alveolates include cilliates (like Paramecium (http://en.wikipedia.org/wiki/Paramecium), dinoflagellates (like red tide (http://en.wikipedia.org/wiki/Red_tide)), and Apicomplexa (like Plasmodium (http://en.wikipedia.org/wiki/Plasmodium). The stramenopiles are several groups characterized by two, differently shaped, forward facing flagellae (a familiar but strange member of that group is diatoms (http://en.wikipedia.org/wiki/Diatom)). As stated above, these two are together or separate depending on who you ask.
Quote from: Kurt Christ on October 18, 2011, 05:52:04 PM
So, I was taking a break from studying biochem to read PD.com- and ended up reading Kai summarizing what I was supposed to be studying anyway. Although not a suitable substitute, I found it a rather entertaining happenstance.
Don't just trust everything I say, though. Same goes for your textbook, too. I've probably botched part of it.
Dear Kai:
You are very kind not to end your last post with a "pwned" macro. However, you probably should have.
"dog vomit slime mold" :lol:
Quote from: Cramulus on October 19, 2011, 01:00:40 PM
"dog vomit slime mold" :lol:
It looks like dog vomit, but apparently it's edible. Tastes earthy, like fungi, almost. Or so I've heard. I've seen some really neat time-lapse photography of individual slimes flowing.
Quote from: LMNO, PhD (life continues) on October 19, 2011, 03:14:01 AM
Dear Kai:
You are very kind not to end your last post with a "pwned" macro. However, you probably should have.
Why? :sad:
Well, I made some asshatted comment about ID, and you quite neatly and succinctly kicked it in the balls, thereby laying down what could be referred to as "pwnage".
In other words, "awesome post in response to a stupid joke".
this is off-topic, but it's a question for Kai
I watched a documentary which mentioned a particular kind of deep sea creature, and I'm trying to remember what it was called.
They are very very small, and look like little trees. They absorb particles from the surrounding water, and use those particles to build the twigs at the end of the "branches". Essentially they build themselves from their surroundings. They are somehow able to decide which particles to include and which to reject.
The narrator of this documentary mentioned that we have few definitions of intelligence which can't be applied to these simple creatures.
any idea what it was?
Ah - found it! It was "tree foraminifera". Werner Herzog talks about them in his documentary "Encounters at the End of the World"
(http://2.bp.blogspot.com/_L2UB67zlmHw/SiHgdwtDgGI/AAAAAAAAA5Y/rNYeab9S0EY/s1600/Notodendrodes+antarctikos_shawn.jpg)
found a website with the transcript:
QuoteAll that the divers had brought back from the ocean floor were a few spoonfuls of sand containing the strange single-celled creatures the scientists are studying here.
They are known as tree foraminifera, primordial single-celled organisms. They branch out in the shape of trees. The branches give off pseudopodia, microscopic false feet that gather and assemble grains of sand
into a protective shell around the twigs.
These are the pseudopodia that are secreted by foraminifera. They're long, thin, tendril-like projections.
What the foram does is it wakes up, sends out the pseudopods and then just grabs every particle in its environment and pulls them in toward its body. There's a certain pattern to the way that they sort the particles.
They can select particular grains out of everything in the environment and just end up with them.
They're beautiful masons. Could that be a very early appearance of intelligence?
- I say it with great care.
- Yeah, I have to say it with great care, too, because there are stories about how these particular organisms have fit into that debate.
Turn of the last century, for example, there was a scientist, a British scientist named Heron-Allen who, apparently, during one of the debates in one of the British societies was pointing out the fact that every definition of intelligence that was being formulated could be fulfilled by these single-celled creatures.
Borderline intelligence, yeah, at the single-celled level. I mean, it is a manifestation of the best of our abilities, really, the way that they build their shells. It's almost art.
That is a twig. You are being put on.
LIVING FUCKING TWIGS!!
:treefucker:
Quote from: Cramulus on October 25, 2011, 11:57:07 PM
LIVING FUCKING TWIGS!!
:treefucker:
KEEP FUCKING THAT
CHICKEN TWIG!
Diffusion-limited aggregates (http://en.wikipedia.org/wiki/Diffusion-limited_aggregation) look like trees. That's just what happens, for the same reason that a planet looks like a sphere. Not much intelligence involved.
If you tweak the parameters of when/where/what particles attach to the aggregate, it's very possible to get a more sparse tree-looking shape like in your picture, instead of the usual more dense feathery/moss like structure.
It's fucking awesome, though.
Additionally, DLAs are cool to simulate on a computar because they look pretty.
Quote from: Cramulus on October 25, 2011, 09:29:25 PM
this is off-topic, but it's a question for Kai
I watched a documentary which mentioned a particular kind of deep sea creature, and I'm trying to remember what it was called.
They are very very small, and look like little trees. They absorb particles from the surrounding water, and use those particles to build the twigs at the end of the "branches". Essentially they build themselves from their surroundings. They are somehow able to decide which particles to include and which to reject.
The narrator of this documentary mentioned that we have few definitions of intelligence which can't be applied to these simple creatures.
any idea what it was?
I'm going to respond to this and your other post together, Cram (to take up less room); this is fucking AWESOME. I knew that Foraminifera were fucking awesome, but I had never heard of this type before.
As for intelligence, I think all living things have it. By Antero Alli's definition, even bacteria and archaea can absorb, integrate and communicate information, or they wouldn't have survived. Proteins on the surface of the cells 'absorb' information from the surrounding environment; proteins and nucleic acids within the cell 'integrate' the information with the rest of the cell systems; and the result is information is 'communicated' back out into the environment via movement or whatever reaction the cell takes. The extent of intelligence is a measure of how much and how well the organism absorbs, integrates and communicates information about its environment.
But back to the foraminiferans. The 'roots' and 'twigs' are hollow tubes through which the fillamentous pseudopods move. All Rhizarians have these, kinda like an amoeba but the cytoplasmic flow is all stretched out and tentacle-like. The foramenifera in particular make shells kinda like diatoms, except out of calcium carbonate instead of silica, and they're pocked with pores where the pseudopods stick through. The tree foraminiferans remind me of caddisflies a bit. They use the sand tubes to protect so they can reach farther into the environment. And like caddisflies, they probably have some sensory mechanism for size ordering the particles. (ETA: or it's just fractal physics operating, as Zero said, which is just as cool)
I think there's a tendency to look at very small eukaryotes and compare them to bacteria, or little animals, but these are not bacteria, and they are certainly not animals, or plants, or any thing familiar to our ordinary experience. Rhizaria are their own kind of life, so alien to us; we're more closely related to fungi than to forams. They're only covered under the international code of /zoological/ nomenclature because we don't have a code for Rhizarian nomenclature, and we didn't even know how different they were when we first learned of them.
I mean, think of it this way. Think of all the different kinds of animals (metazoans); everything from sponges to insects and nematodes, to vertebrates. Now consider: Foramenifera is a division of life even OLDER than Metazoa, far more diverse in the past than now. It's a whole other kingdom. Whatever guidelines we're using as remarkable based on our metazoan experience just doesn't cut it.
that is really cool
man, imagine if they became the dominant form of life in this joint
Quote from: Cramulus on October 27, 2011, 04:42:56 AM
that is really cool
man, imagine if they became the dominant form of life in this joint
They were, at one point. Given the acidification of the oceans I'm thinking it's not likely. CaCO3 and acid do not mix well. There are about 275 thousand described species of forams, and only 4000 of those are alive today. The rest are known from their fossilized shells. Apparently it's a good profession for a paleontologist to hang out with oil rigs, because the foram species from a sample can tell what geological period the core is taken from.
As we're discussing crazy/cool behavior at the (near)microscopic level, check this out:
http://www.youtube.com/watch?v=br-YxeXWx6s
Professor Arthur J. Olson of the Scripps Research Institute demonstrates a 3D printed model of a virus that self assembles when shaken. Olson is head of the Molecular Graphics Laboratory, which uses 3D computer models, 3D printing, and augmented reality to create tools for life science researchers and educators.
between this and the solar system video, you are blowing my mind this morning, big T
Reading this article made me think about this thread and our discussion of alien beings living among us.
http://www.orionmagazine.org/index.php/articles/article/6474/
It's about octopuses. They're mollusks, which are Lophotrochozoans (http://en.wikipedia.org/wiki/Lophotrochozoa), one of the four major groups of bilaterally symmetrical Metazoa (the other three being Ecdyzoa, which includes nematodes, arthropods and other animals that molt, Platyzoa, which includes rotifers, and platyhelminths, among other things, and Deuterostomia, which includes echinoderms and chordates). Most Lophotrochozoans don't posess nervous systems, and most mollusks don't have anything as developed as cephlapods. We're separated by ~550 million years. So when we study octopuses, given their ability to absorb integrate and communicate information, we are trying to communicate with aliens.
Quote from: 'Kai' ZLB, M.S. on October 29, 2011, 10:05:25 PM
Reading this article made me think about this thread and our discussion of alien beings living among us.
http://www.orionmagazine.org/index.php/articles/article/6474/
It's about octopuses. They're mollusks, which are Lophotrochozoans (http://en.wikipedia.org/wiki/Lophotrochozoa), one of the four major groups of bilaterally symmetrical Metazoa (the other three being Ecdyzoa, which includes nematodes, arthropods and other animals that molt, Platyzoa, which includes rotifers, and platyhelminths, among other things, and Deuterostomia, which includes echinoderms and chordates). Most Lophotrochozoans don't posess nervous systems, and most mollusks don't have anything as developed as cephlapods. We're separated by ~550 million years. So when we study octopuses, given their ability to absorb integrate and communicate information, we are trying to communicate with aliens.
That was fascinating! I love octopuses.