Posted on 01/14/2002 3:01:36 PM PST by Karl_Lembke
By Barry A. Palevitz
One of the enduring questions in biology is how eukaryotic cells arose from prokaryotic ancestors at least 2 billion years ago. Besides differences in genome organization, eukaryotic animals, plants, and fungi possess a much higher degree of cellular compartmentation in the form of membrane bound organelles than their distant bacterial and Archaean cousins. But how did such a plethora of cellular domains, each with a discrete role in metabolism, evolve?
To the extent that science proves anything, it answered the question for two eukaryotic organelles a long time ago. Mitochondria and chloroplasts evolved from endosymbiotic associations between an ancestral host cell and smaller prokaryotic partners. In the case of chloroplasts, the symbiont was a photosynthetic cyanobacterium; for mitochondria, most likely it was ana-proteobacterium.
The cytoplasm of eukaryotic cells is like chicken soup-it's chock full of organelles suspended like chunks of assorted vegetables and noodles in cytosolic broth. The broth also contains filaments of various dimensions that collectively comprise the cell's cytoskeleton. Like the bones of a large animal, the cytoskeleton provides a structural framework lending shape to cells and against which enzymatic 'muscles' work to elicit movement. That's how amoebae migrate, algae swim, stem cells divide, and cytoplasm streams relentlessly up, down, and across plant cells.
While the cytoskeleton is as much a hallmark of eukaryoticity as any mitochondrion or chloroplast, the origin of its filaments in deep time is more mysterious. Biologists assumed that genes for cytoskeletal proteins arose from prokaryotic precursors, but evidence in favor of the hypothesis was scarce, until recently.
Tubulin First on Stage
Microtubules comprise one component of the cytoskeleton responsible for a variety of movements including mitosis and meiosis. The 25 nm tubes consist of dimerica- and b-tubulin subunits that share about 40 percent sequence homology. Another form,y-tubulin, functions in microtubule formation.
But where did microtubules come from? It now appears that tubulins share a common ancestor with a protein called FtsZ, a key player in bacterial cell division.1 FtsZ is also present in plants, where it functions in chloroplast division,2 and a similar protein associates with mitochondria, at least in one alga.3 FtsZ polymerizes into filaments in the test tube in a process dependent on GTP. The same nucleotide is required for tubulin assembly into microtubules.1
Tubulins and FtsZ are clearly related, judging from similarities in three-dimensional structure. And although the proteins share only about 15 percent amino acid sequence identity overall, they're much more similar at the local level, particularly at the domain responsible for binding and cleaving GTP.4,5
Actin Into the Fold
Like the tubulins, actin-another essential component of the eukaryotic cytoskeleton-is a globular protein that binds nucleotide, in this case ATP. As actin monomers polymerize into 6-nm-wide microfilaments consisting of two helically wound protofilaments, the ATP, situated in a deep enzymatic cleft between two halves of the protein, hydrolyzes to ADP and inorganic phosphate.
It turns out that actin shares its ATPase domain with a family of proteins including hexokinase, the enzymatic kick starter of glycolysis, and several bacterial proteins. One of them is called MreB, a protein essential for generating or maintaining the rod shape of many bacteria. By examining structural similarities between eukaryotic actin and MreB from Thermotoga maritima, a research team at the Medical Research Council in Cambridge, England recently concluded that the two proteins are more closely related to each other than to other members of the family and undoubtedly share a common ancestor.6
The group showed that the three-dimensional shapes of actin and MreB are so similar they can be superimposed. The analogy with tubulin/FtsZ goes even further. Both proteins share considerable amino acid homology at several key sequences surrounding the ATP binding site, again situated deep in a cleft between two halves of the folded polypeptide chain.
Under the right conditions, MreB polymerizes into protofilaments that pair up lengthwise. The protein subunits are spaced about the same distance apart along the filaments as in polymeric actin, but MreB double filaments aren't nearly as helical.
The similarity between MreB and actin doesn't stop at structure and sequence. In a paper published earlier in 2001, a research group led by Jeffrey Errington at the University of Oxford, U.K. visualized MreB in the rod shaped cells of Bacillus subtilis using fluorescence and electron microscopy.7 MreB forms filamentous bands that encircle the cell in low helices, like reinforcing hoops. In an essay accompanying the Cambridge group's article, Duke University cell biologist Harold Erickson calculated that each band contains 10 protofilaments.8
When Errington's team genetically deprived cells of functional MreB, they became spherical. A search of genome databases showed that MreB is present in bacteria with nonspherical shapes, including rods. It's absent in spherical cocci. In other words, MreB has a cytoskeletal function. "I think it is quite convincing that MreB is the actin progenitor," says Erickson. "A key step, still unknown, going from bacteria to vertebrates is to develop a mechanism to make the double-helical actin filament from the single MreB protofilament structure."
More Acts to Follow
The story doesn't end with MreB; there's more to find out. Scientists want to know if MreB is also present in eukaryotes-associated with mitochondria and chloroplasts-as is FtsZ. According to Katherine Osteryoung, a plant biologist at Michigan State University in East Lansing who identified two FtsZ genes in the mustard plant Arabidopsis,2 "there's no obvious indication of MreB in plants that I've found or am aware of."
Actin normally functions along with the motor enzyme myosin to produce cellular motion, while microtubules utilize two other motor families called dynein and kinesin related proteins. Researchers now wonder whether MreB and FtsZ work in conjunction with bacterial motors. According to Erickson, "none have been turned up in genetic screens for cell division (or other activities), and none have been identified by sequence gazing. My bet is that kinesin and myosin evolved in eukaryotes, after the evolution of microtubules and eukaryotic actin filaments."
Still, Osteryoung is pleased with the latest results: "To someone interested in these issues, establishment of the prokaryotic origins of two major eukaryotic cytoskeletal proteins is enormously satisfying. I look forward to the day when evolutionary intermediates... from MreB to actin and FtsZ to tubulin, perhaps awaiting discovery in some obscure and primitive eukaryote, will more fully reveal the evolutionary steps by which key components of the eukaryotic cytoskeleton acquired their present-day structures and functions."
Barry A. Palevitz (palevitz@dogwood.botany.uga.edu) is a contributing editor for The Scientist.
References
Sorry to ruffle your feathers, but you did state your belief as declarations of fact (NO WAY..., etc.)
As for God using evolution to create - that's a tough sell. If we (man) are nothing more than upgraded monkeys, then there is really nothing special about us. But He says He made us in His image. He loves you and me, no matter if anyone else does or not.
Good comments. The answer is that when comparing related proteins from very different organisms the similarity can decrease to 15% or so, yet there is still a recognizable relationship based on structure and function. Using the design paradigm, rather than evolutionary one, it would be that the watchmaker used a phillips head screw in one case but a thumbtack in the other.
The ape and man were made with phillips head screws, maybe a little different in width or size, but very close. The bacteria does the same thing with a thumbtack. That's the analogy. The head and pin of the tack and the screws are different by a fair amount but there is still a conserved shape and function we can see. That is the 15%.
On the subject of sequence similarities, it can be tricky. There are amino acid comparisons (or protein sequence) and DNA sequence similarities. DNA (nucleic acid) codes for the amino acids and it takes three individual nucleic acids to code for one amino acid. There are more than one three letter codes for each amino acid as well (with one excpetion -- can the fundie evolutionite cultists answer the question which one? Probably not). This degeneracy of coding means that a peptide sequence can theoretcially be a 100% match, but the gene coding for them will not be.
For example, the three letter codes for valine are:
GTT
GTC
GTA
GTG
You'll note they all have GT as their first two bases.
So, one DNA sequence might be:
GTTGTTGTTGTT
and another
GTAGTAGTAGTA
Comparing them we have:
GTTGTTGTTGTT
GTAGTAGTAGTA
Red and blue being the bases that differ. Only 8/12 are identical. That means a DNA similarity of 67%.
But all the triplets code for valine, so it is a 100% match at the protein level.
No. Run some blasts or simple seq aligns with disparate proteins. You'll not get the right matches in many many cases.
Some random sequence might have a high match in an unconserved region and skew the alignment. And the differences in size always make it hard to know where to begin the alignments, where the gaps are.
heck, run programs with slightly different algorithms from different labs and you'll get different alignments and gaps etc...
Of course it is easy to line up two sequences and count matches. But if they differ by a lot there is a lot more to it than just slapping them next to each other.
Take for example a hypothetical protein with two transmembrane domains. One is in bacteria, the other mammals. The latter is 400 aa and the former 250. Line them up from their amino terminals and look at the matches -- it means nothing. I shouldn't have to have to tell you this.
Oh, lordy, tell me about it! But you're right, and that was my point - you can do a crude count and get numbers and compare them and you really haven't measured anything much. Before we really get an idea of the evolutionary implications (if any) of this sort of research we're going to have to know a great deal more about why things fold up the way they do and stick to what they stick to.
Nobel time prize for that.
This kind of recurrent objection to the plain evidence always makes me wonder about what self-esteem problems religious people suffer.
I mean - we've gone in just 6,000 years from unable to make written language to sending probes out of our solar system, unlocking the genetic code of life, probing the subatomic and mapping the galaxy. Not to mention whipping most diseases, hunger, increasing personal liberty, etc etc etc. Then there's all that philosophy, morality and ethics we've developed over the millenia that increasingly focuses on individual liberty rather than service to king or state.
Hell, I'm practically exploding with pride. If that doesn't make us pretty freaking special, I don't know what would.
Am I the only one thinking this?
They're basically looking for a pattern that's not already seen in nature - isn't that right, RA?
Not so much a pattern, but a type of signal not found in nature; narrowband CW. :)
As soon as one is found, though, it'll be carefully examined to see if there's any possible natural explanation for it.
Recall pulsars.
And Sagans hay vision as you call it, is based on statistical analysis, which is a pretty good science. Otherwise gambling wouldn't make the house money.
No, to say right NOW that there are no other intelligent civilizations out there besides ourselves, is just arrogance talking, not scientific proof. Besides, we are out on the edge of the galaxy, most stars are towards the middle of the galaxy, so it may be a while before we detect anyone else.
While we're looking at the statistics for the number of possible civilizations in the galaxy, we should also think about the window of opportunity for civilizations to make contact with other civilizations.
If the life span of a civilization is less than a million years, then our chances of detecting anyone else may be few and far between. There might be a hundred civilizations that have formed in our immediate neighborhood, but the most recent may have collapsed thousands of years ago. Any radio signals we might detect are now well out of reach....
I am certain that there are others out there, it's just a matter of time. Statistically, it's almost impossible for us to be alone in the universe.
I'm for hypothetically dissecting the mysteries of origins as far as possible, and yet I still wish to hold the mystery of creation dearly. Panspermia is a worthy contender, as is the quantum multiverse concept, at least to my ways of thinking at this time.
We find pieces that bear a strong family resemblance.
I've done a little study of my own. I found that a yugo shares many of the same functions as a Honda Civic. They both have four wheels, a motor, a steering wheel, a gas pedal, a brake, headlights, etc. In fact, I'm sure that they share more than a 15% homology.
I have concluded that long ago, a steel mill blew up and over billions of years, yugos evolved. After another billion years, Honda Civics have evolved from yugos. If we carry this evolution even farther, we get a Hummer!
Actually, up to the "steel mill blowing up", you're not too far off track. Cars can be classed in families, where certain models borrow features from others. The difference between automotive design evolution and Darwinian evolution is that different features will be adopted across lines of descent.
That is, if Subaru comes up with an ultrasound obstacle locator, and it's well accepted (selected for), Nissan, Toyota, Chevy, Ford, and BMW will all produce cars that have the same or a similar feature.
In the case of biological organisms, we can follow the spread of innovations and modifications only along lines of descent. We don't see, for example, one sea creature developing a lung, and the same design of lung appearing in the next model year in unrelated other sea creatures.
The problem with the "exploding steel mill" analogy is that we've never observed a steel mill explosion forming machined parts. We have seen complex molecules, including amino acids and nucleotide bases, form as the result of simpler compounds bashing together in a mixture.
All organisms share some sort of homology. If one function is to be performed (like the cleaving of GTP), it would make sense that God used a very similar-looking molecule to accomplish the task.
Why not identical? Why the millions of slight differences, arranged in a way that's beautifully explained by assuming millions of years of descent with slight modifications? Why not any of an effectively infinite number of other arrangements?
Evolution has an answer. IDIOTs don't.
While this article discusses protein similarities, the question still remains: what is the MECHANISM of the change? How long did it take? Is anyone in control of it?
Those are actually valid questions. Especially the first one.
I believe that God has taken these bits and pieces and put them together to create distinct organisms.
OK, how? By what mechanism did God take these bits and pieces and put them together? We've seen factories. We've watched them work. We've watched them being built and re-tooled. The only mechanism we've EVER seen putting simple organic molecules together into proteins and amino acids is the blind combining and re-combining in accord with the laws of physics and chemistry.
If you choose to believe that these laws were designed by a Designer who expected intelligent life as the inevitable result, be my guest. But this does not rule out naturalistic evolution.
These organisms all share the same building blocks and need to perform some of the same functions, so of course some of the molecules will look similar. This is analagous to the car example. A Honda Civic shares a lot of the same parts with a Honda Accord. It does not mean one "evolved" from the other, it means they had the same DESIGNER!
This argument would have a lot more weight if a Honda Civic and a Honda Accord DID have the same designer. However, I'll just bet you that they had different designers. (Indeed, there's a small chance that the two design teams had no members in common, but I wouldn't bet on that.)
In addition, I can pretty much guarantee that the Honda Civic and the Toyota Tercel had different designers. Do we assume a different God for each "kind" (whatever one of those is)?
Think about it. If God didn't design this world and its inhabitants so that they would be somewhat similar, it wouldn't function the way it does. Just because things have similarities does not mean that they were not designed that way on purpose. If God didn't use the same 20 amino acids to make up all the proteins in this world, we wouldn't be able to eat anything.
If all life hadn't evolved from a single common ancestor, it would't function the way it does. Living things wouldn't have the similarities and the slight differences we see if they hadn't undergone eons of descent with modification.
And we have the ability to break down amino acids into their component parts, and use these parts to build others as needed. All that's required in a human diet is eight "essential" amino acids. Cats require at least one extra -- taurine. Why didn't the designer simply set up all life to use the same basic "kit" of amino acids?
The design of this world is so intricate and ingenious that I am in awe. I can't reconcile the word "accident" with the things I see happening in the human body, let alone the interworkings of the world with its inhabitants and the inhabitants with each other.
Your privilege. Again, real scientists doing real work in the field don't care what you can or cannot reconcile.
Am I the only one thinking this?
I'm with you, brother!
In fact, your post & Aric2000's post about how we're on a rather insignificant planet off to the side somewhere suddenly reminds me of the Parable of the Talents. IIRC, the sons who invested their smaller endowments & made them grow impressed the father much more than the son who took his grand endowment & did nothing with it.
Any pride we humans feel about ourselves shouldn't depend on our ancestry per se. It should depend on what we do with the endowment we've been given. All morally healthy people approach life that way, IMO.
Indeed as we continue to cram more data into a frequency range, spread spectrum is the way to go. However, Radar and High-energy broadcasts are still required. Also if we spread out into the solar system, we will need hi power communications if were are to effectively communicate with many nodes. So a species may be noisy as radio develops, become quiet as the technology advances, and becomes noisy again as they expand into their solar system.
Count on it. :)
The problem is that this doesn't happen by accident. It involves learning and application of that knowledge by intelligent beings.
The problem with the "exploding steel mill" analogy is that we've never observed a steel mill explosion forming machined parts. We have seen complex molecules, including amino acids and nucleotide bases, form as the result of simpler compounds bashing together in a mixture.
We've also never observed a "big bang" forming planets, stars, or galaxies. Some folks just assume it happened. We've never seen a steel mill explosion forming machined parts because the laws of entropy would prevent it. Why can we then assume that an explosion of dirt would form biological machinery far more intricate and complicated than any machine we could build. Logic seems to have eluded the evolutionists.
Also, the only time we have seen aa's and nucleotides form from simpler molecules is when we (as intelligent beings) have manipulated the environment and introduced catalysts that we're not sure even existed.
Let's for the sake of argument assume that is was possible for nucleotides AND amino acids to form in earth's "primordial" environment. The problem you encounter then is that the nucleotides have to form an RNA molecule (at least that's the current theory, until it changes again with the wind) which is unstable unless coated with protein. Where's the protein? It hasn't been made yet. The RNA would have to quickly catalyze a reaction that put enough aa's together to form a protective coating before it denatured.
Too many things would have to happen simultaneously for this to occur. There are too many highly unlikely obstacles for this theory to overcome. Evolutionists seem to think that the ultimate catalyst is time, that given enough time even the most unlikely events could occur.
Why not identical? Why the millions of slight differences, arranged in a way that's beautifully explained by assuming millions of years of descent with slight modifications?
Because organisms need to live in a variety of habitats and environments. For a given function (GTP cleaving), it may be that each different arrangement gives the protein optimum function in different environments (pH differences, temperature differences, etc.). God also knew that the earth would change and that animals would need to adapt, so he made that possible by introducing as much variation as we see today.
By what mechanism did God take these bits and pieces and put them together? We've seen factories. We've watched them work. We've watched them being built and re-tooled. The only mechanism we've EVER seen putting simple organic molecules together into proteins and amino acids is the blind combining and re-combining in accord with the laws of physics and chemistry.
Factories are beside the point (except that they support my theory because it is intelligent life that runs and operates these things). The only reason we see these molecules forming from "blind" recombination is because we, as intelligent beings, put just the right chemicals, the right amounts of these chemicals, and the right catalysts into this mixture. We don't know what type of mixture existed in the past. Some assume that the mixture we used is the one that existed ONLY BECAUSE it is the mixture that worked. It proves nothing.
If you choose to believe that these laws were designed by a Designer who expected intelligent life as the inevitable result, be my guest. But this does not rule out naturalistic evolution.
No it doesn't. I never said it did. I'm just providing examples of how it *might not be* naturalistic evolution for the benefit of those who are so sold out to the idea of naturalistic evolution that their logic seems to have stopped functioning.
This argument would have a lot more weight if a Honda Civic and a Honda Accord DID have the same designer.
They did... HONDA.
In addition, I can pretty much guarantee that the Honda Civic and the Toyota Tercel had different designers. Do we assume a different God for each "kind" (whatever one of those is)?
All cars have the same designer: man. Intelligent beings. Some people do believe that there is a different god for each kind. I choose to believe that ONE God did all of this because He has written a book about it and I know beyond all doubt in my own heart that He is very much alive today. He has done some things in my life and in the lives of my friends that I can't even fathom. If you had the same experiences, you would know it too.
As far as the definition of a "kind" (when referring to organisms), a 3 year old could tell you that a dog is different from a cat is different from a horse. If you put a picture of a coyote, a bobcat, and a mule side by side, a child could tell you that they are different kinds. A child would also know that a coyote, a wolf, and a dingo are all the same kind.
If all life hadn't evolved from a single common ancestor, it would't function the way it does. Living things wouldn't have the similarities and the slight differences we see if they hadn't undergone eons of descent with modification.
What makes this statement any more valid than mine? We reach two different conclusions from the same evidence. Both are equally valid. Is it just because your view is more widely accepted? The earth was once thought to be flat, and those who said it was round were laughed at.
I'm not trying to disprove naturalistic evolution; I don't think either theory will ever by proven or disproven. I'm just trying to get the robots to recognize that there might be another option they should consider. We all know what happens when people ASS-U-ME things...
And we have the ability to break down amino acids into their component parts, and use these parts to build others as needed. All that's required in a human diet is eight "essential" amino acids. Cats require at least one extra -- taurine. Why didn't the designer simply set up all life to use the same basic "kit" of amino acids?
And we can break down cars (that were designed and created by intelligent life) into their component parts and put them back together to form different machines.
If God had made all creatures so that they would use the same "kit" of aa's, then the intricate food web we see would not exist. Nature would not function the way it does. Nature functions so well because organisms are able to find niches, and many niches are available based solely on the nutritional requirements of the organisms.
God is far more intelligent than you give Him credit for. When He is at His dumbest, He is still smarter than you and I.
Your privilege. Again, real scientists doing real work in the field don't care what you can or cannot reconcile.
So molecular biology is not a real science? I don't study evolutionary biology, but I am studying molecular biology, and I do work in the field. I don't have my Post-hole Digger (Ph.D.) yet, but I'm working on it.
You've made this point before and you'll need to explain it a little more. We see a lot of variation today. (And think of all the extinct variation represented in the fossil record!) Taking Adam as an example, I ask you, once again, if all the variation we see in humans today is collected in this one individual, what type of creature you imagine Adam was?
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