Great stuff
Now then, I'm off to stock up on bacillus subtilis just in case one of these cave dwelling Jurassic super dino-bacteria spawn up here in the light.
It's the one with camel poo in the pocket.
Bacteria found deep inside a cave that has had scant exposure to the outside world for at least four million years share some of the same antibiotic-resisting traits that other bugs are supposed to have developed in response to modern medicines. That’s the finding of a new research article, Antibiotic Resistance Is Prevalent …
Considering that even the newest antibiotics are from soil bacteria in the first place, it's not surprising that other bacteria have always evolved counter measures to survive.
Otherwise the only surviving bacteria today would be similar to the streptomyces family. This family of bacteria alone produce two-thirds of the today's available antibiotics.
Exactly right. Most human pathogens live in or on humans and were not exposed to antibiotics for a long time before the 20th cent. That's probably why the early antibiotics were so successful. We are, in effect, breeding them back to their wild ancestors by re-introducing them to the chemical warfare that goes on in the soil - and has done for over a billion years!
Is this a joke?
I've recently encountered a few quite fundamentalist Christians trying to make a distinction between Evolution (because evolution is *bad*) and Natural Selection (as something which doesn't create anything new, and therefore doesn't challenge the maker-power of God)... but I'm only just noticing how widespread this nonsense is becoming.
Would you care to define your terms, just to check you're on the same planet as the rest of us?
Isn't it that variation plus natural selection affects the frequency of particular versions of genes (and combinations of them?) Making natural selection more of a mechanism driving evolution.
(As *somebody* said, arguing with a creationist is like playing chess with a pigeon - it knocks the pieces over, craps on the board and flies home to its flock to claim victory.)
Natural selection is one mechanism that drives evolution. For evolution to occur natural selection needs to operate on a genetically diverse population with different fitnesses. So, for example random mutation or DNA copying error may generate a population of bacteria with resistance to a particular antibiotic. In the absence of that antibiotic, the resistant bacteria's mutation may be deleterious - it may grow more slowly, for example. However in the presence of the antibiotic, it will be the fittest bug - out-competing its breathren to become the dominant variety.
So evolution is a product of two mechanisms; one that generates diversity, the other that selects the 'fittest' individuals from this diverse population.
We are pleasantly surprised because our understanding of the world has increased. We learn from our discoveries and reapply them to things we already knew about. We now have new tools to understand antibiotic resistance and its acquisition. These are all surprising things.
Creationists? They aren't surprised because they are learning nothing. They already have their calcified worldview to which they will adapt every new thing to fit, and nod sagely with each fresh confirmation that 'god did it that way' and shake their heads sadly at those who don't understand.
Being unable to understand the intersection of natural selection and evolution though? That's a new one to me. "Like evolution but god did it", I presume?
@ Anonymous Coward 15
They're not replying to him - they're responding to the "Anonymous Coward" who said "In shock news... not everything is for your amusement. As new discoveries are made, evolutionists are surprised. Creationists... not so much. Plenty of natural selection, not much evolution."
Was that slipped in to see if we were awake/actually reading the article? Or do we have unique antibiotic properties?
Anyway, the findings demonstrate (to me anyway) that bacteria naturally have antibiotic properties and that's about all. Maybe they were so common because the isolated communities have been fighting it out for so long.
So does it work like this?
a) There are loads of naturally occurring bacteria, some of which are susceptible to antibiotics, others are resistant
b) These bacteria have reproduced for millennia, using humans and other species as breeding grounds
c) The antibiotic susceptible ones have been by far the more widespread, outcompeting the resistant ones
d) 70 years ago we waded in with antibiotics, and started hitting out at the susceptible ones in their key breeding grounds (firstly humans, then other species)
e) The anti-biotic resistant ones have found their competitors' population falling, and have started to spread out into the extra space.
b) It's a little wider in scope than just "These bacteria have reproduced for millennia, using humans and other species as breeding grounds"
Bacteria as a whole do not rely on humans or other animals, or more correctly just other forms of life, as breeding grounds - that's what viruses do. In broad terms bacteria can reproduce on their own, viruses use other organisms to reproduce however like all things there are various varieties that tend to bend these rules. Bacteria may happen to inhabit animals but are to be found lurking pretty much everywhere, it's just that animals produce a lot of waste of all forms and therefore can harbour quite nice environments for many bacteria to live.
This is aside from a lot of symbiotic relationships that have developed between bacteria and higher forms of life - for example humans can't survive without any bacteria and some of those that live in or on us are so specialised that they're largely unique to humans. This doesn't necessarily mean that they rely on us to survive just that we're their preferred environment - after all they need to be able to survive outside their animal environment hosts to spread.
One of the reasons that bacteria have adapted so rapidly to man-made antibiotics is that they have a large store of 'junk DNA' to call upon... just like you might have something in your cobwebby shed that 'might just come in handy' one day. It's much like 'delete' on your harddisk changing the index, but not the actual ones and zeros.
When their resistance to such-and-such a compound became redundant, it is more likely that the index was lost to mutation (since their was no selection pressure on it), rather than the genes for the resistance. Fast forward thousands of years, and it only takes a few mutations to restore their resistance, since all that needs to happen is for the index to be reinstated and the gene patched up, rather than rebuild the whole gene from scratch (through the process of natural selection of random mutations).
Sorry, to clarify:
One would imagine that over the many eons, chemical compounds similar to many of ones we use today as antibiotics have cropped up from time to time, produced by other bacteria and organisms as part of their ongoing chemical arms-race. Used and ambandoned, as they cease to be effective. The arms race moves on, and the compound ceases to be a part of the bacteria's environment. Immediate resistance might be lost (why waste the resources?), but many of the genes responsible live on in 'junk DNA'- but just not being used.
But yeah, what happened to the idea of fighting bacteria with 'phages' (viruses)?
So the obvious move is to *find* them.
The fact these bacteria have retained this resistance suggests *either* its still useful (because the bugs that excrete these poisons are still somewhere in the environment *or* there is no evolutionary pressure *not* to conserve their genes.
BTW the full theory of evolution requires both natural selection and *mutation*
Those of a theological bent can rationalize the 1st bit (species wipe each other out because they are just better at it than others) under the usual "It's all part of God's plan."
However the 2nd bit (introducing multiple random new species) is more troublesome to them. You seem to be dealing with a dithering God who keeps changing their mind. That does not sit well with the usual omniscient and omnipresent deity image.
Having worked with a number of IT staff I'd say some of them are quite capable of harboring (and excreteing) chemicals unknown to medical science.
"In other words, bacteria are already good at battling antibiotics, so it’s not entirely safe to assume anthropogenic antibiotics have created an evolutionary hothouse that forces bacteria to defend themselves."
FAIL at logic.
The bacteria population is NOT good at battling antibiotics at least by default otherwise there wouldn't BE any antibiotics.
The bacteria population BECOMES BETTER at battling antibiotics otherwise there wouldn't BE more antibiotics-resistant strains right now.
This "BECOMING BETTER AT" evidently comes from evolutionary pressure on the bacteria population. It doesn't come from God's Own Farts.
This is what "evolutionary hothouse that forces bacteria to defend themselves" MEANS.
Whether ancient bateria have activated genes to pump the molecules to the outside of their fatty surface is neither here nor there. It just means that modern bacteria probably can just fallback tio already-present genes, leading to better survivial in the hothouse.
The entire paragraph beginning "In other words" is an authorial interjection. It does not follow from what the previous paragraph quotes of the study, and is explicitly contradicted by the quotes from the study in the subsequent paragraph, so it is not a valid simplification at all; it is a non-sequitur that falls into the very trap of inferring too much from the data that the authors explicitly warn against.
Agenda much?
"The bacteria population is NOT good at battling antibiotics at least by default otherwise there wouldn't BE any antibiotics".
Hmm, let's see if I've got this straight...
"The zebra population is NOT good at battling lions at least by default otherwise there wouldn't BE any lions".
Nah, doesn't work for me. Although I suppose a lot does depend on that sublimely unquantified "good at".
"The bacteria population BECOMES BETTER at battling antibiotics otherwise there wouldn't BE more antibiotics-resistant strains right now."
The bacteria don't become better at battling antibiotics. Random mutations occur and those mutations that permit the new strains to function/live in the presence of antibiotics.
1) Bacteria thrive in current environment. Random mutations occur that introduce different attributes. One might have the effect of allowing the bacteria to be better able to survive in the presence of antibiotics. In the current antibiotic-free environment, they are not as successful as the original strain and their numbers are kept low.
2) Antibiotics are introduced to the environment which kills most/all of the original strain. The new strain is not affected by the antibiotics and now, with few of the original strain of bacteria to compete with are now able to reproduce to greater numbers and become the new dominant strain.
Mutations happen all of the time, but only the ones that give the species a better chance of surviving to reproduce survive. Even in man's genes there are a lot of dominant and recessive genes. The recessive ones are still there (good and bad) just waiting for the right opportunity.
I have to wonder how isolated this cave is really? Its certainly not hermetically sealed. For example, the earth is teeming with airborne (and waterborne) bacteria. Give them a few years and they will spread. They are incredibly pervasive. In which case, Horizontal gene transfer could easily explain antibiotic-resisting traits.
i.e. "Horizontal gene transfer is the primary reason for bacterial antibiotic resistance"
http://en.wikipedia.org/wiki/Horizontal_gene_transfer
Also even if it is hermetically sealed (which I extremely doubt) these aspects we interpret as antibiotic-resistance could easily evolve in different combinations in nature multiple times (For example, Convergent Evolution).
http://en.wikipedia.org/wiki/Convergent_evolution
Therefore antibiotic-resistance could simply be an example of Convergent Evolution where the old bacteria adapt to the evolutionary stress of exposure to antibiotics in the same way modern bacteria adapt.
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I think the issue that some people have with "Evolution" is that the term is overloaded, in classical mathematical terms.
Evolution through Adaptation occurs, where new generic material is not created, is seen in the world, and is demonstrated in a lab, using the Scientific Method.
Evolution, suggested by some to be a process where new (properly working) genetic material is created from nowhere through mutations, has not been demonstrated in a lab, using the Scientific Method.
Natural Selection has been observed and has been simulated by intelligent humans for thousands of years through Selective Breeding, to create variations on an initial kind (i.e. Animals migrating to an area not thriving, Native Americans liking curly hair having relations with Africans for offspring benefit, breeding out height of dogs, breeding in colors of horses, etc.)
There are some people who just feel that if something can not be demonstrated in a lab, through the Scientific Method, it is not science.
"Evolution, suggested by some to be a process where new (properly working) genetic material is created from nowhere through mutations, has not been demonstrated in a lab, using the Scientific Method."
Nonsense.
This is a variation of the "spontaneous generation" routine. IRL a fair number of genetic studies (EG Fruit fly larvae) and plant and yeast improvement programmes work by exposing *large* samples of the raw material to mutagens, classically strong poisons or radiation.
Most die.
The *rest* have their DNA disrupted (to differing degrees) which when internal repair mechanisms attempt to fix the damage result in new *variations* of the original organisms IE *mutants*.
Might be better, might be worse. Natural selection will sort them out.
Evolution is a process that operates on *statistically* large groups of organisms and generally the researchers only report the *successes*
In evolutionary terms a billion deaths are *nothing* provided a breeding group survives and re-populates the niche.
Sorry all those cute Walt Disney nature films are basically BS. The good survive, the bad get eaten.
"There are some people who just feel that if something can not be demonstrated in a lab, through the Scientific Method, it is not science."
Am I to take it that you think astrophysics is not a science, then? I've certainly never seen a lab big enough to house a galaxy....
"it’s not entirely safe to assume anthropogenic antibiotics have created an evolutionary hothouse that forces bacteria to defend themselves."
Sigh, and thus we are once again invited by El Reg to believe that scientific knowledge is just something someone assumed one day.
The fact that bacteria can evolve to be antibiotic-resistant by perhaps switching existing genes on, rather than by developing new genes, has absolutely no bearing on the question of whether or not those bacteria are in fact evolving to become antibiotic-resistant. A misunderstanding of the mechanism of a phenomenon does not disprove the phenomenon itself.
Ummmm - what we use as antibiotics actually occur naturally. They are what one species of bacteria use to ensure that they survive in an environment where another species is competing for the same resources. It is, therefore, remarkably unsurprising that there are antibiotic-resistant bacteria extant in the historical record. They are, in fact, evidence *for* evolution, not against.
Indeed. When resistance is lost, many of the genes responsible reside in 'junk DNA'. The resistance can be reinstated by a relatively small mutation.
When you 'delete' a file from your harddisk, you only delete the index entry. It is easy to conceive of a data error to the index restoring your file (a corruption of a few bits), rather than a simultaneous corruption of thousands of bits resulting an identical file popping into existence.
If people are put off by Dawkin's manner, give Stephen J. Gould a go. He's the one in The Simpsons who takes money from Lisa to perform tests a fossil 'angel', but instead keeps the cash and runs away!
If you actually read what Darwin wrote, evolution is not a theory at all, evolution is the observed fact (i.e. Species change over time - a fact based on mountains of evidence). Natural selection was then the theory to explain the observed fact.
As discussed earlier, seeing as many antibiotics are derived from bacteria, then some bacteria will already have an awareness of antibitoic compounds
A lot of antibiotics are derived from non-bacterial sources as well. Many plants (and animals) produce natural antibiotics - don't forget that one of the most famous antibiotics is derived from a fungus - Penicillin comes from the Penicillium fungi.
It's all part of ongoing battles between species - one organism produces a defence mechanism against another, the other then changes slightly to work around this and then the process starts again. The process is made considerably more "interesting" (as in complex as hell) when it involves multiple competing organisms...
Er, no. It's just that things are more complicated than we first expected. Which itself we should expect. Please see comments above.
"There are more things in heaven and earth, Horatio, Than are dreamt of in your [our] philosophy"
An analogy would would be all the hype around the sequencing of our genome: After we sequenced it, we discovered that it wouldn't give us all the answers; we would have to get to the bottom of 'protein folding' first. Why? Well, an adaptive coding system like DNA is full of sub-routines and switches... one piece of DNA can do different things dependant on context... bits of it get 'compressed'... all sorts of tricks. No great surprise, when you think about it.
Since there are so many informed comments on this here forum, I'd like to ask a question concerning evolution and caves. When ever I watch a documentary regarding a species that has evolved to live in zero light conditions, typically in a cave, these mostly have no skin pigmentation.
Now I know that skin pigmentation would be of no benefit for a creature living in the deep dark; however, I have never been able to figure out what the selection mechanism would be for this to be the end result. Any explanation given seems to be in the form of an evolutionary narrative such like "the creature does not need it". This, to me, does not answer the question as it does not explain what evolutionary pressure is applied so that a pale 'emo' version of a species has an advantage over a more colourful one.
I've half an idea that the answer may concern energy usage in marginal environments with the assumption that skin pigmentation production is too costly.
Any ideas on this would be appreciated.
Wondered that myself in the past as well. It's an interesting question and as it's common across multiple separate locations and diverse species there's likely to be at least one common reason.
Not producing skin pigmentation is probably a good answer, as with no need to do it for mating display or protection from harsh radiation (sunlight) it's likely to cease to be a selection factor. Instead selection would favour those best able to make do in these marginal environments and if a paler specimen needs less energy and nutrients it is likely to be better able to survive and reproduce compared to others.
Also there may have been some part way place, gloomy but not dark, where being darker in colour was a distinct disadvantage, possible mates can't see you as you blend into the background. So in the gloomy zone the dark individulas live at the well lit end and the pale individuals live at the dar end, add a few million years and we have 2 different species. Marginal areas, like tidal zones, put all sorts of interesting survival pressure into play.
Well, in a pitch dark cave there would be no selection pressure to keep the skin dark and UV proof. Any albino-like mutations would remain uncorrected. And that is assuming there is merely zero cost to having pigment.
If there is a cost to producing pigment that gives zero benefit, no matter how small a cost, the pigment will be lost over the ages.
For example, experiments on guinea pigs show that the pigmented areas of their skin is more susceptible to frost bite, thus supporting anecdotal observations regarding soldiers in the Korean War. Melanin is the pigment common to most animals other than spiders.
Much of evolution is about tiny advantages over many, many generations.
As has been pointed out, our use of antibiotics is simply us taking advantage of a long-running chemical arms race.
But also, a lot of "pathogenic" bacteria are perfectly happy out in the wild world and can make a living in soil, on plants or wherever, so it is unwise to assume they are highly limited in their choice of habitats. They are tough little so and so's and can even make a living in caves!
Enterococcus faecalis (which I much preferred as Streptococcus faecalis) seems very happy living on grass - and is a major ingredient of silage innoculants.
And while I am on the subject of name changes, I have my suspicions about some of those prettily named bugs in up-market yoghurt - remember the old Japanese yoghurt slogan - "A pure culture from the gut of an Octogenarian Bulgarian peasant". From the days when they thought that the right gut fauna could make you live for ever. They should have called it "After Many a Summer"
Does this mean if we can find the trigger which allows the bacteria to "fall back" to those ancient resistance genes we can simply inhibit that with a small molecule and make penicillin work again?
Either that or dig up the Russian phage therapy work as these seemed to work better than the best antibiotics at the time.
AC/DC