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Darwinian Evolution Considered As a Phase
LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea. Woese and physicist Nigel Goldenfeld argue that, even in its sophisticated modern form, Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth. Woese and Goldenfeld believe that horizontal evolution led to the rise of the genetic code itself. "At the root of this idea is overwhelming recent evidence for horizontal gene transfer — in which organisms acquire genetic material 'horizontally' from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself."
I strongly suspect it isn't, nor was it ever, one type of evolution over the other, but a complex interaction between many environmental pressures where both types of evolution played a role.
Why are so many posts with factual errors modded up?
The first 2 parts of Spore are like Horizontal Evolution, and the later parts are all vertical.
It makes perfect sense. Clearly Will Wright is a genius.
For anyone familiar with the Red Queen Hypothesis ( http://en.wikipedia.org/wiki/Red_Queen ) this should be obvious.
While direct DNA transfer is not the component usually referred to by this "arms race," it is merely an extension of a known theory.
No one makes a big hype about this theory, because it doesn't say your grandfather was a monkey and piss off the religious nuts
So, would this "horizontal gene transfer" be like capitalism? Does it become a battle to see who can acquire the most and/or the best genes? Do you end up with winners for a while, until the losers get disgusted and start sparking genetic revolutions? Would Darwinian revolution be a happy meritocracy that arose as a kind of "compromise"?
However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving. It always implied to me that the organisms (as defined by its genetic code) were what did the surviving. If organisms enhance their survival by acquiring genes through means other than sex, this doesn't seem non Darwinian to me. It just seems like a deeper understanding of evolution.
The more intriguing possibility, with serious impliations for us humans, is "intentional evolution". In other words, organisms purposefully manipulating their own genes. That actually might be considered a radical enough change to give it a new name: Recursive Evolution.
I guess you could push horizontal genetic flow with viruses in the higher organisms, like us. In general however, horizontal genetic flow occurs between plants and bacteria because they have the molecular mechanisims for it. If anything it would suggest horizontal genetic flow was the first stage of evolution, with classic evolution taking over more so as time moved forward since higher organisms have a higher need to maintain genetic continuity due to specific and more complicated form. For instance you have chromosomal ploidy in plants because they follow a different evolutionary strategy: stay in place, but grow as much as possible to aquire resources. In this case genetic diversity may help. In the ambultory mammal however, it wants to retain a very specific morphology to keep doing what it does, therefore it maintains a more rigid genetic control and linear evolution.
"Men willingly believe what they wish." - Julius Caesar
You know, scientists just keep reforming their ideas until it conforms to observable reality. How can they expect anyone to believe what they say when they're just going to keep changing their minds?
I prefer my religion. It allows me to conform reality to my ideas.
I pass on my genes horizontally
Watch those corners
So does this explain why you can stick "random" genes into a completely different organism and gain traits that wouldn't arise normally? This seems like it'll be very useful in GE if the mechanics of it are explored more.
This really isn't entirely new; Dawkins' book The Selfish Gene is based around the idea that it's individual genes that are selected for, not organisms.
I am going to come over there and take all your stuff and I'm going to kill you and take your weapons and use them for myself!!!
If you're really nice and sweet I'll beat the crap out of you and then stick you in my kitchen to make food for me.
The second is referring to mitochondria not kitchen bitches.
I'd go on a Vegan diet but the delivery time from Vega is too long. --brownkitty
. . . you're better off doing it vertically.
Wearing running shoes.
And ideally permission of the farmer.
(beat)
What?
We've already known that evolution depends on both inheritance of genetic matter and mutation of genetic matter. This is a third mechanism for generating traits, but it stills falls under the umbrella of natural selection. If the change is beneficial, and leads to more offspring, the change will be selected for. Certainly worth study, and we may not have known the full scope of the phenomena, but it doesn't really contradict Darwinian evolution at all.
As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?
For those who do not care to register for that New Scientist, we still have arXiv... :)
http://arxiv.org/abs/q-bio/0702015
Paul B.
The notion that life probably started by weak, stochastic replication of families of similar molecules.
By weak, is meant that the replication of the molecule/structure is more imperfect from generation to generation
than in present day life, and so a class of similar molecules (life codes) is being continued through time
rather than a singular particular molecule (same genome).
If this origin theory were true, we would expect the replication capability (continued recreation of imperfect but still somewhat replication-capable molecules)
to be robust to change of DNA/RNA even today.
By stochastic, is meant that such imperfect replication is likely to only be stochastically successful in a huge population of the
initially highly approximate (i.e. weak) replicator molecules.
In other words, we would not expect this proto-life to be as reliable at being able to continue (or to always reliably grow by recruiting
surrounding matter into high-fidelity copies.)
So we might expect these proto-life molecule soups to initially just contain in some regions higher than expected probabilities,
stochastically, from time to time, of weak-replicator molecule classes.
Perhaps there is a binary threshold of replication probability and fidelity at which the process self-sustains reliably in the
generality of environment it finds itself in. Life catches fire, and cannot easily be stopped at its matter and energy recruitment
game from that point on.
Where are we going and why are we in a handbasket?
Here's a tip, folks. The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.
Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now. We know that particularly with prokaryotes, horizontal transfer happens, and that while more difficult with eukaryotes, can still happen (ie. endo-retroviral insertions). It is yet another facet of evolution, not some independent force.
The world's burning. Moped Jesus spotted on I50. Details at 11.
Horizontal transfer isn't really over, either - we still have retroviruses.
There have been some other interesting discoveries regarding horizontal gene transfer recently. For example, this PNAS paper looks at sea slugs that can photosynthesize by themselves -- http://www.pnas.org/content/105/46/17867.full.pdf). The sea slugs photosynthesize through a combination of harvesting chloroplasts from the algae they eat and via horizontal transfer of genes involved in photosynthesis from these same algae. This is a bizarre and amazing discovery which demonstrates how genes can move from plants and be incorporated in an animal genome.
"horizontal gene transfer - in which organisms acquire genetic material "horizontally" from other organisms around them, rather than vertically from their parents or ancestors."
Genetically modified foods are like the "artificial selection" equivalent of nature / natural selection - if the transfer of genes can happen from one set of species to another, then GM crops are kinds of an accelerated / selective version of this. If I were Monsanto or another big GM food company, I'd be looking to twist this into "Genetic material gets transferred to other species in nature, what's wrong with us doing it?"
Global warming and other natural disasters are a direct effect of the shrinking number of pirates - Gospel of the FSM
One of the big difficulties I have in understanding evolution is the process of gene syntheses. It seems reasonable that over time certain combinations of genes can win out over others, and certainly in bacteria you see this horizontal gene transfer happen all the time. You even see it in plants now thanks to genetic engineering, and before that you saw it in a more limited way thanks to viruses and cross-pollination and things like that. But all these things have to do with the transfer of genetic information between life-forms.
The question in my mind is where did all the genes come from in the first place. Proteins are complex macro-molecules. It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction. It's more of an all or nothing thing. It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason. Worse still, you can't (as far as we know) start with a working a protein and reverse-transcribe from it into a strand of DNA or RNA that could code for it.
What do you think?
Just why is it that ultra-conservative rants about God or racial superiority or anti-socialism are instantly modded off-topic, troll, and/or flamebait until they sink beneath the thresh hold and yet completely off-topic attacks on Creationism in every story even vaguely connected with biology or evolution get modded +5 insightful?
Same reason why at least someone will look favorably on the fact that you may have served pizza for desert, while you will be forever banished from the kitchen (and other places) if you serve up a pile of dung.
Both are off-topic, but while one still satisfies the basic requirements - the other is a pile of shit.
In the case of pizza - it is still food; in case of pointing out the errors of creationism - it is still a discussion about evolutionary theories, it only digresses towards pointing out the wrong ones.
Creationism and a plate full of dung - a pile of shit.
Mit der Dummheit kämpfen Götter selbst vergebens
Have Woese and Goldenfeld a brilliant new idea? All they're saying, I think, is that "parent" and "child" are the appropriate units of selection only when genes are passed vertically: from parent to child. They're suggesting that horizontal gene transfer is underrated as a historical evolutionary force.
Agree or not, it hardly undermines Darwin. Genes weren't known in the 19th century. Darwin didn't have a clue about genes, so we're gonna knock him for being "wrong" about it? I mean, was Jesus wrong about genes, too? It's anachronistic silliness.
Science is fundamentally dynamic. Any science that hasn't progressed in 150 years ain't doing too well. (Dear creationists: stop calling us "Darwinists." We've moved on.) I mean, The Origin came out in 1859, for crying out loud! Darwin was more brilliant, more insightful, and rightly more famous than I'll ever be. But if we both had to take a biology test right now, I'd kill him.
It is important to note that the idea the "science is about truth" is a common intellectual error of modern society. Science has nothing to do with finding truth or learning how the universe actually works or anything of the sort. Science is about building models of observable natural phenomena. The point of the models is to conform with what is observable and hopefully predict something that hasn't yet been observed, but which can then be tested and seen to work. Good science is about building models that work well, and refining models that don't. Poor science is about building models that sound like they ought to work but don't conform to observation. Really lousy science is about building models that can't be tested against reality and don't predict anything. Are you listening evolutionary psychologists? Take for example: "survival of the fittest" - This is a model for the mechanism by which one organism gets to spread its genes. It sounds perfectly plausible, almost indisputably sensible. But what does it mean? The key is the word "fittest". "Fittest" means best able to survive. So the model mechanism is really survival of the one ones that survived. Now it sounds trite and unhelpful, which it is. How do we know it's not "survival of the luckiest" or "survival of every n-th one"? We don't, but survival of the fittest is more appealing to our cultural sensibilities, so we go with that. If you remember that science is about coming up with ways to get your head around nature, rather than about figuring out what nature really is, then you don't get caught in the trap of "how can you trust science?" You only have to trust it as far as it is working for you, you don't have to build your world view on it.
Science is not the search for "truth". It's the search for an explanation. Unfortunately, it has become the new religion, people simply believe what some scientist says as gospel and, as you identified, are then frustrated and irritated if it is found to be incomplete or utterly false.
That is not how science is to be treated. Science does not have all the answers. Science is the search for those answers, not the answer itself. Science is not about believing, it is about doubting. About offering a theory and offering ways to test that theory. Especially the latter part is often overlooked by people. A good theory offers an angle to falsify it. I may state that at the center of a black hole is cake. Just to make all the Portal players happy. And while we're at it, before the big bang there was a flat world carried by a turtle. You cannot falsify either theory. You cannot test them. So they have to be true. Right? False! Both are non-theories. They have zero scientific value. At least until we somehow find ways to test them.
So presenting any theory that offers no vector of testing is, scientifically, worthless. Unfortunately, that's not easy to convey to people. They want explanations. And science cannot offer them. Science is not about certain answers. It is about questioning theories.
We used to have a Bill of Rights. Now, with the rights gone, all we have left is the bill.
You're right - religion and science are the same in one sense. They are guesses at what reality is.
The largest difference is that science acknowledges that it is a guess. A very educated guess, which yes yielded modern life as we know it. Religion tries to claim that it is the truth, and the only truth, and expects it's adherents to doggedly follow it's rules and values way beyond their useful context. To give you an example, a slashdot poster recently gave a ridiculously long opinion on whether pig meat cultivated in a lab would be kosher or not.
Now, religion in it's early days claimed to heal the sick, to make the blind see, and to allow the lame to walk again. It has never done any of these things. Science, on the other hand, has done all of these things and much more. I'll stick with the continued results of the scientific method. You can keep your bronze age mysticism.
It seems to me that one of the reasons journalism science is so bad, is that they believe (rightly or wrongly) that any article which appears to be saying "DARWIN WAS WRONG!" will sell more copies.
The article doesn't say that, obviously, but it at a cursory glance it could be perceived as that.