Darwinian Evolution Considered As a Phase 313
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."
Capitalism? (Score:2, Interesting)
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.
Re:I realize scientists need a breakthrough (Score:4, Interesting)
Similar to the silly "nature versus nurture" debate, I think the key here is that for different critters, different types of evolution are significantly more dominant.
Re:It's still natural selection (Score:4, Interesting)
I wrote about this a while ago (Score:4, Interesting)
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.
Gene Synthesis (Score:4, Interesting)
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?
Re:Here's A Tip, Folks (Score:5, Interesting)
I'm not trying to take away anyone's "sense of wonder". I'm saying that horizontal gene transfer is one known way in which variation can occur. Remember, evolution requires only that there be variation in populations. For the most part, that variation will either be in allele frequency, but sometimes is also mutational, sometimes due to neutral drift, and probably with considerably less frequency due to horizontal transfer. It ain't new, and neither is trying to make a well known phenomena sound exciting and "paradigm shifting" by announcing it to the world.
Man, but I hate science journalism.
Re:Here's A Tip, Folks (Score:3, Interesting)
I think your confusing things here. Of course horizontal gene transfer can potential influence fitness. Evolution requires variability in traits. How exactly that variability gets there (mutation, mitosis, neutral drift, horizontal gene transfer) is the dirty details of evolution. However a trait makes it into a population, once its there, it can be fixed, and thus alter fitness.
Re:Original paper on arXiv (Score:4, Interesting)
http://arxiv.org/abs/q-bio/0702015 [arxiv.org]
Ok, I've read the original paper now, and it is almost as moronic as the New Sensationalist makes it out to be.
Their argument is analogous to the following claim:
I can stand on dry land, or I can swim in the water, but there is the broad swath of territory that is neither dry land nor water so deep I can do nothing but swim in it. Therefore, the concept of "land" (or "water") may actually be completely useless! Aren't we clever?
Scientists have a tendency toward various kinds of conceptual realism, where they think that there is exactly one way to properly understand the universe, and the entities picked out by that way are "real" and no others are. When they find a case that they can't crisply classify under the existing concepts there are two moves: the smart one, that refines existing concepts and introduces new ones to deal with the boundary cases; and the idiotic one, that claims that since the existing concepts don't deal well with the new case, they must not pick out anything "real" after all and should be thrown away.
That the biological species concept fails in various ways has been known for a long time. They are now pointing out that certain criteria that would normally be used to delineate individuals might also fail under some circumstances. To this I say: big deal. The biological species concept, like the concept of Newtonian mass, is still incredibly useful in understanding reality under a wide range of circumstances, which is all a scientist can hope for. If their new concepts--which they don't really offer--transform smoothly into the biological species concept in the appropriate circumstances I'll be interested. Otherwise, they're just gabbling.
Re:Well duh? (Score:5, Interesting)
I saw an article recently about a species of snail that has acquired the genes for making chlorophyll from the algae it eats. It hasn't yet acquired the genes to make chloroplasts, so it has to eat algae to get enough chloroplasts from the algae to allow photosynthesis to work, but after that it is capable of living with no food other than light.
So, obviously this is still ongoing, and on larger scales than microbes.
Re:I realize scientists need a breakthrough (Score:3, Interesting)
> The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense. I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect. Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species. Who knows, maybe our ability to digest some specific foodstuff (a foodstuff that we previously relied on a bacteria in our gut to help us digest/process) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time. Just an example.
You're crazy. Let's assume for the sake of argument that DNA from a bacterium will sometimes end up in a nearby human cell. Since the bacteria in your example live in your guts, they will share DNA with cells in your guts. These cells are not involved in procreation and therefore their 'mutations' will not be inherited and therefore they do not influence human evolution.
The only way to make this work (still assuming the DNA trading between human cells and bacteria is possible) would be if sperm or an egg somehow were to come in contact with bacteria from your guts. I don't think the whole 'ass-to-pussy' thing that I may or may not have accidentally stumbled upon at some point in my life while searching for, eeeeh, educative programming related articles is so widely practiced that it has a significant effect on human evolution ( except when you get a horrible infection and die :p ).
Re:Gene Synthesis (Score:5, Interesting)
There are instances of proteins evolving into something that does something different.
"Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species -- a shrew and a lizard -- giving each a venomous bite."
http://www.sciencedaily.com/releases/2009/10/091029125532.htm [sciencedaily.com]
Generally, what happens in these cases (where a protein evolved into a different protein with a different function) is that the original DNA sequence gets duplicated, and then one of the duplicates starts evolving (and the other copy continues to serve the same original function that it had earlier). One of the things that evolutionary biologists do is look at protein sequences and find similar sequences within the same organism. Very often, there's a tree-like structure showing multiple variations on a single protein within an organism. For example, humans have multiple copies/variations on the hemoglobin gene. They're either inactive or active at different phases in a person's life. Example:
"Fetal hemoglobin, or foetal haemoglobin, (also hemoglobin F or HbF) is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream."
http://en.wikipedia.org/wiki/Hemoglobin_F [wikipedia.org]
http://en.wikipedia.org/wiki/Hemoglobin#Types_in_humans [wikipedia.org]
There's also the case of the fish antifreeze that evolved from non-protein-coding DNA:
"Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA."
http://www.sciencedaily.com/releases/2006/04/060404090831.htm [sciencedaily.com]
Re:Original paper on arXiv (Score:5, Interesting)
Except that isn't true. Every one of the 64 possible 3 base sequences is a valid code for either an amino acid or a stop codon. Some viruses take advantage of this by overlapping protein coding regions, with different proteins being coded by reading in different frames. In eukaryotes, there are some genes that can code for proteins with very different sequence regions because an exon skipping splice variant results in a frame shift that codes for a completely different sequence.
A more significant complaint about the "This code is universal, shared by all organisms" quote is that it isn't universal. There are small differences in the genetic code between genomes. NCBI lists no fewer than 23 [nih.gov] different versions, but given that a tiny fraction of all species have been studied there are undoubtedly many more minor variants. An especially interesting case- and the place that difference in genetic codes were first discovered- is that human nuclear and mitochondrial sequences use slightly different genetic codes. The mitochondria even have their own distinct ribosomes.
Re:You raise an interesting point here (Score:5, Interesting)
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.
Re:I realize scientists need a breakthrough (Score:1, Interesting)
The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense. I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect. Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species. Who knows, maybe our ability to digest some specific foodstuff (a foodstuff that we previously relied on a bacteria in our gut to help us digest/process) was derived from genetic material that originally came from a bacteria that had the ability but was passed on to us a codon at a time. Just an example.
Actually, this does not make sense and I can't believe this was modded insightful. Other than the fact that the structure of genes in eukaryotes (with a complex intron/exon structure) versus prokaryotes (that usually have genes structured in operons) would prevent horizontal gene transfer from occurring, passing DNA codon by codon would never work in a probabilistic sense. The hope that moving small (i.e. 3 nucleotides) piece of DNA from one organism to another would land in a gene (which is less than 2% of the human genome) and then even land in a portion of that gene to cause a functional change (much less a positive functional change) is so infinitesimal it is absurd. Moreover, for these changes to be inherited, they would need to occur in the germ lines of a human, not in somatic cells. The location of germ line cells is kept bacteria-free under normal conditions, so no possibility of horizontal transfer.
Plus, any time you study an eukaryotic organism that has a unique ability to digest a non-typical food source (e.g. termites), it is the result of a symbiotic relationship with gut bacteria that produce enzymes (via their own genes) to digest the materials, not by DNA transfer.
This leads me to the question of whether or not our preoccupation with sanitization/sterilization of our own bodies might be having some detrimental effect on our EVOLUTION. Is our wiping out species, to the point of extinction, actually limiting the evolutionary process, in essence limiting variation in the exchange of genetic material?
No. At worst it creates open niches for infectious bacteria to inhabit, but no DNA transferring is lost.
Re:I realize scientists need a breakthrough (Score:1, Interesting)
Not that crazy. There is a lot of so-called junk DNA in our genome (as in: DNA without any known function), and I have heard before that many genetic researchers believe this junk DNA comes from viruses originally. I don't recall about bacteria leaving their mark in our genome, and considering viruses aren't much more than a chunk of DNA or RNA that likes to enter a host's cells it makes more sense to pick up some DNA from viruses than from bacteria.
How that virus DNA ended up in our genome I don't know, that was not mentioned, there are presumably theories about it but I haven't ever read about that. I would expect indeed that the only plausible way would be during conception of a baby. Or during production of egg/sperm cells.
Re:Here's A Tip, Folks (Score:3, Interesting)
Acquisition of a trait (by whatever means) would never amount to a significant percentage of the gene pool of an organism unless it proffered some usefulness.
Though a popular view, that's not true. Assuming 'trait' means an independent mutation, then that trait can go to fixation in a population by simple chance (the expectation is that this happens to 1/2N mutations). Also, genes that are physically near each other on the genome tend to be passed as a set. Therefore, it is likely that a completely neutral, or even slightly disadvantageous mutation, that happens to be near an advantageous mutation (or a mutation that won the mating lottery and is heading toward fixation) will also be propagated throughout a population. There are other more esoteric reason why this could happen too, but a strictly adaptationist view of evolution was dropped in the 60s.
Re:Capitalism? (Score:3, Interesting)
You read Darwin's Radio too huh?
Re:Here's A Tip, Folks (Score:1, Interesting)
Another way of thinking about horizontal gene transfer is that it's exactly like Darwinian evolution, but with the evolutionary units competing amongst themselves being the genes rather than the organisms. This is nothing new - this viewpoint was promulgated by Dawkins in "The Selfish Gene" back in the 70s.
Re:Well duh? (Score:4, Interesting)
Creationism is ridiculed because creationism is ridiculous. Such posts get modded up because people with mod points agree, whether on topic or not. It's not really worth a sociology paper or anything.
If you really want to defend creationism on /., I salute your bravery. If you are just trying to figure out why people do what they do, I wish you tremendous amounts of luck.
Re:Here's A Tip, Folks (Score:3, Interesting)
Man, but I hate science journalism.
While I simply try to keep myself up to date and absolutely don't work in the field, I remember having read about this (namely eukaryotes grabbing strands from viruses) years ago. As I recall the title at the time was more along the line of "viruses sharing dna with organisms may open new research avenues" or something along those lines. Anyway it didn't strike me as being especially sensationalist. Since then I keep an eye open for further news upon those lines.
OTOH, it seems that labs feel that they are in a race to be noticed so any time any of them has anything whatsoever that might be newsworthy, it always gets twisted into some kind of earth shattering event (and of course once one generalist publication starts doing it, others tend to follow). Of course most of the time nothing much comes out of it since that's the way research works (slowly). Apparently "The New Scientist" has some over-enthusiastic writers.