Single-Celled Species' Genome As Complex As Ours?

An anonymous reader writes: "A new paper reports on the sequencing and analysis of the genome of a single-celled species known as Tetrahymena thermophila. This ciliate (like the Paramecium people look at in school) has some 27,000 genes, or nearly as many as humans. And despite existing as a single cell, this spcies encodes fantastic complexity and unusual features. For example, it has a primitive immune system that prevents the invasion of foreign DNA. Also, it is able to cordon off its germ cell lineage much as humans do with sperm and eggs. But Tetrahymena does this by having two nuclei within each cell, with one of the nuclei being held in reserve for sex. Basically, this species uses its genome complexity to function like a single celled chameleon, changing its shape and its properties in response to the changing environment. For example, when a new nutrient shows up in its neighborhood this species can build a kit to suck the nutrient in, degrade it, and turn it into cellular biomass quickly. Thus whereas humans use their genomic complexity in part to create a stable environment for the body, this species simply uses a genomic swiss army kit to make do with whatever environment it encounters."

Comments

Darwin All Over Again

[eldavojohn]

The funny thing about Origin of Species is that everyone immediately was pissed that Darwin had the nerve to say that we are descendents of monkeys.

Then a few years later, people were amazed that a simple worm has 20,000 genes. <sarcasm> How could it be that such a simple lowly creature has so many genes? Isn't more better? How could humans be beat? Blasphemy! </sarcasm>

And now it's 'news' that a single cell's genome has as many genes as a human's! When will we learn that the number of genes doesn't mean 'more advanced' or 'better off'? If this single celled organism's environment caused it to evolve more genes but physically change (seemingly) very little, why are we surprised?

Re:Darwin All Over Again

[|/|/|||]

Not only that, but "more advanced" and "better off" are completely arbitrary. Bacteria outnumber us a trillion to one - does that make them "better"? It all depends on your criteria!

Re:Darwin All Over Again

[BWJones]

The number of genes is not necessarily an indicator of sophistication. Also I should point out that as you allude to in your sarcasm, we humans are not the most sophisticated at all biological functions. For instance, the human eye is a much less sophisticated device than the eyes of other creatures such as birds, turtles and even many fish species who see in many more "channels" than we do with greater color discrimination (and they can often fix their retinas when damaged unlike us who suffer when AMD or retinal degenerative diseases hit us).

Re:Darwin All Over Again

[RsG]

Well, the main problem is the public perception that evolution produces "superior" species. This is rooted in a 19th century mentality that held to a notion that there were "upper" and "lower" life forms (which incidentally is a view that predates natural selection by a good many years, and is arguably not confined to the 19th century). When you talk about the views held by the average non-scientist regarding evolution, the most common perception is "survival of the fittest", with the implication that those that survive are somehow better objectively.

In actuallity, survival of the fittest implies fittness for a certain environment only. To borrow someone else's analogy, you can have the best gills in the pond and you'll still die off with the rest if the pond dries up.

The problem is really the human ego; we have an enourmously hard time accepting the idea that humans aren't innately special. We're intelligent, certainly, and we're unique, but then again every species that has a highly specialized survival strategy is unique.

Re:Darwin All Over Again

[RsG]

True, but the ability to adapt to alien (and I use the term very generally here) environments is not what our survival strategy entails.

Our survival is essentially rooted in toolmaking and inventiveness. There are other examples of species that employ tools, but none to the same degree that we do. Virtually everything that we need to survive, and everything that sets us apart, is rooted in this adaptation.

This is not the survival strategy of a generalist, it's the way of a specialist. We've got all our eggs in one basket. That basket has paid off in many unique and useful ways, which allow us to do things like survive in environments that are radically different from the ones we initially evolved in, but fundamentally we're still specialized.

The environment we're fit for is a technological one, rather than a geographic one.

Does this make us unique? Yep, but that's hardly an unusual affair for specialized animals. Does that make us intelligent? Hell yeah, but then we only consider intelligence/sapience so important because it's the only shtick we've got. There's a quote that goes something like "I used to think the mind was the most interesting part of a person - then I thought 'hey, wait, look who's telling me that'", which sums up our emphasis on brains quite nicely.

Re:Darwin All Over Again

[spun]

My criteria for "better" is the ability to set criteria for "better." Therefore I'm better than a bacteria. But maybe the bacteria have better criteria.

Re:Darwin All Over Again

[spun]

Come on, it's called "Intelligent" design, not "Frickin' Genius" design. The guy had like six days in which to do it all, of course he had to cut corners. What, do you think he's omniscient and omnipotent or something?

Re:Darwin All Over Again

[jc42]

They are certainly more highly evolved.

One of the standard tasks of teachers of biology courses is to disabuse the students of such notions. "Higher" and "lower" are value judgements that are biologically meaningless. Such terms might be appropriate in a religious context, but in a biological context they merely indicate cluelessness.

The "lowest" creatures on Earth have just as long an evolutionary history as ours, and are about as well-adapted to their niches as we are to ours. Single-celled organisms may be slightly better adapted, since they mostly have a shorter breeding cycle than we do. But given the universality of changing conditions, this generally doesn't mean a whole lot. The default assumption should be that most species are about equally well adapted to their niche. It takes evidence of special conditions to invalidate this.

Re:Darwin All Over Again

[jc42]

Bacteria don't have a space program. Therefore, they're fucked when the Sun expands. We're not.

Don't bet on this.

Back in the 1960s and 70s, there were a number of papers written by astronomers about the Earth's "dust tail", equivalent to a comet's tail, and made of particles of the outer atmosphere blown off by the solar wind. This was of some significance for long exposures in the part of the sky behind the tail.

The studies showed that the Earth's dust tail is mostly gases, but also includes small dust particles, including particles the size of bacterial spores. Further study showed that the upper atmosphere does in fact have a small number of such particles, including bacterial spores. More studies showed that many bacterial spores can survive conditions in space for a rather long time.

So the Earth is spewing a tail of gases, dust and bacterial spores into interplanetary space. The solar wind blows this outward. A small amount hits the outer planets (and "dwarf planets" ;-), but most of it escapes the Solar System.

This has probably been going on for 3 to 4 billion years. The Earth makes an orbit of the galaxy in about 220 million years. So we've made a dozen or more circuits of the galaxy, broadcasting bacterial spores the whole time. Calculations show that these spores by now have totally permeated the galaxy, and may have reached the Magellanic clouds, but probably not more distant galaxies.

There's a certain amount of conjecture here, of course. We don't actually know that bacterial spores are viable for the millions of years that it would take to reach other star systems. Few of them would ever encounter another planet where they could wake up and start living again. But over a few billion years, with a few billion spores per year (not much mass, really), small chances add up.

Some have suggested that this could be how life reached Earth. Google for the "panspermia" hypothesis for more information. There could well be other planets in the galaxy that are similarly broadcasting bacterial spores. Some of them could have been doing it for 12 billion years or so.

It's interesting to think about. Over billions of years, the Earth may not be as isolated as we might like to believe.

Evolutionary quagmire

[Tackhead]

> Tetrahymena does this by having two nuclei within each cell, with one of the nuclei being held in reserve for sex.

Hot.

> when a new nutrient shows up in its neighborhood this species can build a kit to suck the nutrient in, degrade it,

I like where this is goin'.

> and turn it into cellular biomass quickly.

Giggity giggity goo!

Tetrahymena

[in2mind]

Tetrahymena are non-pathogenic free-living ciliate protozoa. They are common in fresh-water. Tetrahymena species used as model organisms in biomedical researches are T. thermophila and T. pyriformis.

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

# of genes != complexity

[jbeaupre]

A most of you are aware, there is a lot of "junk" DNA mixed with genes. We're begining to learn that a lot of the "junk" is another form of coded instruction. Or to force fit an analogy for the Slashdot crowd, genes code for hardware, "junk" DNA codes for software. So equating the number of genes with the complextity of an organism is only part of the picture. Not as bad as equating the number of chromosomes with complexity (corn has more than humans, I believe). But still overly simplified.

Interesting

[Moby Cock]

I always find it odd that people think our DNA would be the most complex. It's really a rather stunning conceit. Single cell organisms have had millions of years to eveolve too, why shouldn't their DNA be as rich?

Darwin never said that

[MrFebtober]

Darwin had the nerve to say that we are descendents of monkeys.

I feel it's worth pointing out that no where in the Origin of Species does Darwin discuss human/great ape/primate evolution. I'm not even certain he used the word "evolution", but don't quote me on that. Also, no true evolutionary biologist has ever said that humans descended from monkeys. It's that whole common ancestor thing. Lot's of branches, not straight line.

Re:Darwin himself said it best

[RsG]

You do realize that the quote didn't say "organism", right? It specified "organ", which is a major difference in biology. Organs have pretty much zero to do with gene count, and in any case single celled organisms don't really have organs in the normal sense of the word.

What Darwin was saying was essentially that if an organ were encountered that could not have developed incrementally, then that would disprove his theory. People have tried to show that the eye meets this criteria, but we now know that light sensing organs can develop incrementally. Wings have also been brought up as a potential arguement, but are counteracted by examples of wing-like structures that serve some intermediate purpose other than flight.

Plus, gene count does increase incrementally, so even if Darwin had used the word organism, your answer would still be "no". Gene count is really pretty irrelevant as a measure of complexity, and in any case is easy to increase slowly over time with mutation.

Adaptability - an objective measure of superiority

[Pfhorrest]

In actuallity, survival of the fittest implies fittness for a certain environment only. To borrow someone else's analogy, you can have the best gills in the pond and you'll still die off with the rest if the pond dries up.

It's always seemed to me that there *is* an objective criterion for superiority in a species. Since we're judging superiority as fitness or the ability for a certain pattern (the genome) to continue propagating, then the superior species would be that one most able to overcome a greater variety of possible roadblocks to it's survival. To use your analogy, an amphibious fish, with watertight skin that can also breath air, would be objectively better by these criteria because it doesn't need the pond. It can live on land if need be.

In short, adaptability is what makes a species "superior". This is what has made homo sapiens the dominant large animal species on the planet - our intelligence has allowed us to adapt to damn near every (land) niche on the planet. Rats are a highly fit species for this same reason, as are cockroaches, and many fungi and microorganisms. All of these species are well-rounded and adaptable. (And by this criteria, this new species featured in TFA is likewise highly advanced). The one thing that I can see possibly giving mankind an edge up out of that group is our ability to radically change and even create environments around us, most notably including the ability to leave this planet of our own volition. (While some spores can survive in space, they couldn't just pack up and leave when the sun goes Red Giant on us all. We might be able to).

And since highly adaptable species are more fit to survive over longer periods of time, then evolutionary pressure *will* tend to select for them. And in that sense there is a sort of teleology to evolution: over time, as environments change back and forth and around to a variety of different extremes, the most flexible, adaptable, and generally well-rounded species will tend to outlive the rest. To survive in particular niches against competition from species specialized to those niches, they will have to become more capable in many areas as well; not simply jacks of all trades, but also aces of many.

You're certainly right that the old concepts of some sort of linear progression culminating in mankind are inaccurate. But that doesn't mean you have to deny any sort of progression, or any sort of objective criteria for discerning superiority or fitness between species.

Re:Try to Agree, not disagree

[PFI_Optix]

A creationist-friendly way to segue into evolution (I've seen this done, it works in most cases):

1) Start with an explanation of what science is. At its core, science is the ongoing effort to understand our world and the universe around it, how it works, and how it came to be. Specifically, science is intended to look at the world impartially and judge it only on proveable, repeatable observations. Science is the practice of observing facts and forming opinions based solely on those facts.

2) Define a scientific theory. It's not "just a guess". A true theory is supported by all the available facts, and can be used to predict further observations. When a theory is proven wrong, it is either modified (as evolution has been many times) or thrown out entirely.

3) Explain the basics of evolution. Point out that it describes a system of nature, and not just an order of progression. The theory of evolution is not the idea that man evolved from monkeys. The idea comes from the theory, but is not an integral part of it. Evolution at its most basic level is simply stated as "life changes".

I've put it this way before: Would you agree that every generation of humanity is somehow different than the last? That with each generation, some individuals never reproduce and some are far more successful (have more kids) than others? Does that not change the gene pool for the entire species? Every generation, the gene pool changes a little bit. When those changes are cumulative, that's evolution.

4) If the subject comes up, address the fact that evolution has never been meant as a direct challenge to any faith or belief. It is simply the best model for explaining the scientific observations available. It can be contradicted tomorrow, should sufficient observations be made.

Human eyes aren't optimized

[mangu]

the human eye is a much less sophisticated device than the eyes of other creatures

The human eye has a "design" error, in that the photosensitive layer is not in front, there are other cells above them. This means that the neurons that do the image processing functions in the retina must be transparent, and even so there is some absorption and scattering of light. Also, we have a blind spot in the retina where the optical nerve crosses the photosensitive layer.

In mollusks, OTOH, the outer layer of cells is the photosensitive one. The eye is more sensitive to light, has no blind spot, and allows for more data processing in the retina itself. That may be one of the reasons why octopuses are so good at camouflage, their eyes are very sensitive.

All this is one more argument for evolution and against the "intelligent design" theory.

Re:Human eyes aren't optimized

[BWJones]

The human eye has a "design" error, in that the photosensitive layer is not in front, there are other cells above them.......

Actually, the mammalian (human) eye is optimized for the metabolic loads it requires. It turns out that there is no higher area of metabolism in your body than there is at the photoreceptor/retinal pigment epithelium interface. It is a highly oxidative environment and evolutionarily, you need the apposition of the photoreceptors up against a layer of cells that can deal with the shed outer segments and the metabolic loads induced by rod photoreceptors. The other advantage is that you can snuggle the photoreceptors up to these cells that have a direct connection (diffusion) to a vascular layer. If it were backwards, the blood vessels would get in the way of the image formation and cast shadows.

In mollusks, OTOH, the outer layer of cells is the photosensitive one. The eye is more sensitive to light, has no blind spot, and allows for more data processing in the retina itself. That may be one of the reasons why octopuses are so good at camouflage, their eyes are very sensitive.

Octopuses, squid, and cuttlefish have fairly sophisticated retinas that is true and you are correct about their anatomy. However, they do not process the same metabolic loads that the mammalian retina does and thus do not require the same degree of buffering, care and feeding that mammalian photoreceptors do. You have to be careful about using "sensitive" to describe eyes as that descriptive is dependent upon lots of things. Typically in most retinas it has to do with the ability of the opsin to capture a photon and the cell the opsin is in to transduce that signal.

All this is one more argument for evolution and against the "intelligent design" theory.

Intelligent design (ID) really does not even factor into either argument. ID is a religiously/politically motivated belief, not a theory that can be tested.

Re:Human eyes aren't optimized

[TheRaven64]

The human eye is one of the worst designed pieces of equipment I have ever come into contact with. Here are some examples of things wrong with it:

• The majority of the sensors on it are completely overwhelmed in moderate light conditions, and are only useful at dusk.
• The resolution is very poor in the receptors that work in colour, and the high-resolution ones don't work at high light levels.
• The connection to the is seriously underspec'd (by a couple of orders of magnitude. Someone put a decimal point in the wrong place on the Intelligent Designs, perhaps?).
• The compression used to make up for the previous deficiency has serious bugs. These include the inability to properly transmit certain shapes, and the lack of absolute colour information. I wonder if our Intelligent Designer also worked on NTSC...
• As a previous poster mentioned, the connector for the uplink is badly wired and obscures the sensor.
• Very poor design tolerances. Only about 20% seem to be manufactured without any kind of defect.

If you've looked at the human brain recently, you will note that a volume similar to that of the eyes is dedicated to bug-fixes and work-arounds for poor design of the eyes themselves.

If the human eye is the best our Intelligent Designer can come up with, perhaps someone could point me in the direction of his Intelligent Bug-Tracking System.

Gene number...

[ktulus cry]

...isn't necessarily a representation of the number of actual protein products that a genome produces. Part of what makes humans so complex is the number of genes that produce multiple proteins. It isn't unique to humans, but is especially prevalent.

Beadle and Tatum's original hypothesis that "One gene encodes one enzyme" no longer holds true. Mechanisms such as alternative splicing and epigenomic effects (gene activation and silencing) can cause one gene to produce many isoforms, each which may be active differently between tissue types, and each which may have entirely different functions. Our 27,000 genes are quite possibly far more complex than another species 27,000.

Awwww

[Orange Crush]

It's like a microscopic MacGuyver . . .