Evolution Can Occur Much Faster Than Previously Thought (ox.ac.uk)

An anonymous reader writes: An Oxford study on chickens discovered that evolution can make significant changes to a genome in as little as 15 years. "For a long time scientists have believed that the rate of change in the mitochondrial genome was never faster than about 2% per million years. The identification of these mutations shows that the rate of evolution in this pedigree is in fact 15 times faster." Professor Greger Larson, senior author on the study, said, "Our observations reveal that evolution is always moving quickly but we tend not to see it because we typically measure it over longer time periods."

Comments

Old

[Smiddi]

See the Earth is only 4,000yrs old :)

Re:Old

[Opportunist]

Please, oh please give me one YEC who uses this as proof of young earth. I'd really, really love to see one YEC use evolution to support his model. It would make the whole bunk even more hilarious.

Not a huge surprise

[The Real Dr John]

The long term changes in DNA didn't always get there in a straight line. So measuring over a shorter time would indicate a faster rate of change. But interesting nonetheless.

Re:Not a huge surprise

[Michael Woodhams]

There are two issues here. One is that a single DNA site could mutate several times. If we only see the end points, it looks like only one mutation has occurred (or even zero, if it mutates back to where it started.) This is pretty easy to correct for. E.g. if you compare two sequences and they differ in 10% of sites, it is reasonable to think that 1% of sites have actually mutated twice. (That is a little oversimplified, but not by much.)

The other issue is that a DNA mutation can spread through part of the population, but then go extinct. If you measure over short time periods, you see these mutations, but over long time periods you don't. There are mathematical reasons to think this does not affect your measured mutation rates if the mutations are neutral (neither helpful nor harmful.) Look up "neutral theory of molecular evolution" for details. However, if they mutations are slightly deleterious, this can be an issue, but there are limits to what you can achieve with this mechanism. (I wrote a paper on that once.)

Re:Not a huge surprise

[Mr Z]

Let me see if I understand. By measuring over a long period, we're measuring the long term rate of mutation survival after applying selection pressure, and that could be noticeably different than the raw rate of mutation. Is that a correct summary?

Please go slowly with me. I'm an engineer, not a biologist, and I admit biology is not my strongest subject. I am actually curious, though.

I remember hearing that there are large sections of DNA in many living things that are effectively "junk DNA," or at least we think are junk DNA. By junk DNA, I mean DNA that doesn't code for any useful proteins or other molecules, and generally seems to take up space. (I'm skeptical that there is much that is really "junk," but bear with me.) If there really are large stretches of non-useful baggage, it would stand to reason that these sections would not be subject to selection pressure, and so mutations to these sections aren't directly subject to selection pressure, because they don't affect the fitness of the organism.

Is there a way to measure the mutation rates for different sites in the overall genome of a given organism, so that: (a) we can determine if some regions are actually junk because mutations to them do not affect organism fitness, and (b) can distinguish between the rate of mutation and the rate of mutation survival? (This question more or less assumes my understanding in the first paragraph is accurate.)

Re:Not a huge surprise

[Michael Woodhams]

Let me see if I understand. By measuring over a long period, we're measuring the long term rate of mutation survival after applying selection pressure, and that could be noticeably different than the raw rate of mutation. Is that a correct summary?

Yes, that is correct. The technical term for 'mutation survival' is 'fixation'. A mutation is 'fixed' once the entire population carries it. It is 'extinct' (unsurprisingly) when it no longer exists in the population. When it exists in part of the population it is 'segregating'.

There are huge amounts of DNA that have no known purpose and appear to be junk. This is over 98% in humans, but varies a lot between organisms. The junkness of this is under debate. My feeling is that much of it really is junk, but some of it has a function we don't yet understand. (Also, sometimes the function is simply "we need a certain amount of space between these two bits of non-junk". This has a clear purpose, but is 'junk' in that the DNA letters don't matter.)

This particular experiment is about mitochondrial DNA which has very little 'junk', and that which it does have probably at minimum has something like 'need this amount of space' function.

Yes, scientists do like using 'junk' DNA for phylogeny (making family trees of organisms) because it is (we think) not subject to selection. On the other hand, you need to find the corresponding junk regions in all your critters and sequence them. It is easier to identify corresponding genes, and often someone else (who cared about the genes themselves) has done the sequencing work for you. Often the choice is doing phylogeny on genes using only a computer, when phylogeny on junk DNA requires samples and a molecular biology lab. Another issue is time scale: the junk DNA mutates faster, so it is good for closely related species (e.g. 'apes') but for distantly related species (e.g. 'vertebrates') you need highly conserved sequences (genes). The junk DNA will have mutated so much that it is all noise, no signal.

Is there a way to measure the mutation rates for different sites in the overall genome of a given organism, so that: (a) we can determine if some regions are actually junk because mutations to them do not affect organism fitness

Yes, if we have diverse organisms and a good alignment of their DNA, we can look for 'junk' regions by how much mutation occurs where. (Actually it tends to be the other way around - we see islands of conserved sequence, and deduce therefore that they have a function. This isn't how genes are detected, as there are more sensitive gene-specific ways of doing this.)

and (b) can distinguish between the rate of mutation and the rate of mutation survival?

Only I think by comparing mutation rates over pedigree time scales (a few generations) with mutation rates over long time scales - which is what this paper addresses.

Re:Not a huge surprise

[Mr Z]

Thank you for the thoughtful and detailed response. I think I have a better understanding. (But, I'll always stay mindful of the Dunning-Krueger effect... ;-) )

BTW, this statement captures something I was trying to express more clearly than I stated it:

(Actually it tends to be the other way around - we see islands of conserved sequence, and deduce therefore that they have a function. This isn't how genes are detected, as there are more sensitive gene-specific ways of doing this.)

What I was trying to get at was that if a section of DNA performs some useful function, even if we don't know what it is, it'll tend to be preserved because selection pressure will tend to preserve it by "selecting out" individuals whose mutations tampered with it. The observed long-term mutation rate for any given point should in some sense be inversely related to that point's significance. (More significant => fewer mutations, likely by a function much more stark than just "1/x", where "x" is significance. Key proteins should have a really strong bias to remain unmodified in viable offspring, for example.)

I now have a slightly different question: You mentioned the rate of repeated mutations, where the same piece of DNA was mutated twice or more, sometimes back to its original state. Suppose the environment shifts, such that selection pressure would favor a certain set of mutations to adapt a species to that new environment, and then the environment shifts back. I'm thinking fairly long term, cyclic shifts such as ice ages and the like.

Would such cyclic shifts meaningfully affect the assumptions underlying the multiple mutation rate? You gave this example: "if you compare two sequences and they differ in 10% of sites, it is reasonable to think that 1% of sites have actually mutated twice." I realize you mentioned it was oversimplified. It jibes with a basic knowledge of statistics and statistically independent random variables. I guess what I'm getting at is that cyclic shifts that affect which mutations improve, decrease or are neutral with respect to fitness would imply at least some of the variables aren't independent.

I guess it comes down to what fraction of the mutations actually affect fitness with respect to these cyclic forces. I imagine it's a fairly small proportion relative to the total set of mutations whose fitness effects are completely orthogonal to those long-term cyclic changes. If that's the case, am I correct thinking the effect wouldn't be large?

I guess in general, if the total delta between two samples is still relatively small (10% in your example), any second order effect such as this could only affect that approx 1%, and so that already bounds the potential error from simplifying assumptions anyway.

Again, thank you for your helpful (to my understanding, at least) response.

Re:Not a huge surprise

[Michael Woodhams]

What I was trying to get at was that if a section of DNA performs some useful function, even if we don't know what it is, it'll tend to be preserved...

Yes.

Would such cyclic shifts meaningfully affect the assumptions underlying the multiple mutation rate?

I'd expect it to be a very minor effect. I'm not aware of anyone getting worried about this. It is a matter of statistics: if you're comparing 100,000 DNA sites, you don't care much if 50 of them behave weirdly in some fashion. If you successfully target 'junk' DNA for the comparison, it is not an issue.

A related effect is convergent evolution. Say two species of bacteria each colonize high temperature environment. Then certain mutations which are favoured in high temperature will likely occur in both of them. When we compare their DNA, this can make it look like they are more closely related than they really are. This is more of an issue in morphology (Darwin's finches, for example, or cormorants, which look very similar all around the world but turn out often not to be closely related) but it can happen at the DNA level too.

Re:Not a huge surprise

[Mr Z]

I'd expect it to be a very minor effect. I'm not aware of anyone getting worried about this.

Got it. With everything else you've explained, that makes sense.

A related effect is convergent evolution. Say two species of bacteria each colonize high temperature environment. Then certain mutations which are favoured in high temperature will likely occur in both of them. When we compare their DNA, this can make it look like they are more closely related than they really are.

Ah, that also makes sense.

I thank you again for the informative responses. You've expertly escorted me up to (or possibly even well past) the edge of my competency. :-) I've certainly enjoyed the trip.

It's truly a fascinating topic, but for me to really get much more out of it, I think I need to do some homework to learn more about what's already known. There's only so much a generically analytic mind can do w/out learning what's already known in the field.

Thanks again.

Re:Not a huge surprise

[Michael Woodhams]

I could have spent the effort debating the creationists. This was much more fun.

Re:Not a huge surprise

[The Real Dr John]

Great discussion. I don't want to over-complicate, but we would be remiss if we didn't bring up the fact that some "junk" DNA is not junk at all, even if it is "non-coding" (does not encode for a protein product). The original concept of genes is that they have "exons" and "introns", where the exons code for parts of a protein product, and the introns get snipped out during the process of generating RNA from DNA. But some of the so-called junk DNA generates different kinds of RNA rather than standard "messenger RNA" or mRNA. For example they have found what are called microRNAs, small nucleolar RNAs and others. These tend to modify how other RNAs function (messenger RNAs and transfer RNAs which link base pairs to amino acids in ribosomes) etc. So there are many levels of complexity and mutations can happen in any of these different DNA regions thus affecting not just protein structure (when an exon is mutated) but also how gene regulation occurs (e.g., when microRNA regions are mutated). It will be interesting to see in the future if more "junk" DNA turns out to be doing something unique.

http://phys.org/news/2010-10-j...

http://www.evolutionnews.org/2...

Re:Not a huge surprise

[Anonymous Coward]

I'll post as AC because I haven't posted in a long time and honestly can't remember my username:

Evolutionnews, in spite of the name, is not a very good source (to put it mildly) when it comes to learning about evolutionary thought or the theory of evolution itself. It is a site run by proponents of Intelligent Design, so I'd take anything they write with a grain of salt.

Phys.org and other scientific news sites are much better choices, of course.

Re:Not a huge surprise

[Anonymous Cow Ward]

In addition, some DNA that doesn't make RNA at all (as far as we know, anyway) is important for regulating other pieces of DNA, which can be pretty far away.

Fossils

[The Evil Atheist]

Well considering that for the longest time, fossils were our main source of viewing evolution through time, of course it would seem to be slow. Who knows how many speciation events happen and die off before being able to leave a mark in the fossil record.

Re:Fossils

[Ol Olsoc]

God knows.

Leave the Flying Spaghetti Monster out of this, lest ye be smote by his noodly appendage.

Re:Fossils

[Ol Olsoc]

And he reached out towards me with his noodley appendage and ..... SLURP .... ahh well, so much for that....

Your reward of beer volcanos and fine hookers awaits you, brother. Rejoice!

Re:Fossils

[lhowaf]

Is "besmote" etymologically related to "bespoke?"

Re: Fossils

[The Evil Atheist]

Irrelevant to the point I'm making.

Re: Fossils

[Rei]

Yes it is. It's data about where there is no data. Example:

Bob: I firmly believe there is rabid gorilla loose somewhere in this city..
Jane: I just searched my home. There's no evidence of a gorilla.
Bob: The absence of evidence is not evidence of absence!
Jane: I just searched 100 homes. Still no evidence of a gorilla.
Bob: The absence of evidence is not evidence of absence!
Jane: I just searched 10% of the town. Still no evidence of a gorilla.
Bob: The absence of evidence is not evidence of absence!
Jane: I just searched 95% of the town. Still no evidence of a gorilla.
Bob: The absence of evidence is not evidence of absence!

Jane has a shortage of data about the presence of a gorilla. But the lack of finding data despite active search is itself very valuable data.

Re: Fossils

[Anonymous Coward]

How did Jane search the town? How does she know that when she moved from one area to another the gorilla didn't move into the area she just searched and is now claiming is gorilla-free?

Your example lacks credibility. It is representative more of an ideology than science.

Consider the arguments used by the Greeks to dismiss Aristarchus of Samos's heliocentric theory of the solar system:

Aristarchus: I believe the earth orbits the sun.
Greeks: If the earth orbits the sun, we would have evidence of parallax motion of the stars. We have searched for parallax motion of the stars, but we can't find any evidence, 100% of the times we tried.
Aristarchus: Absence of evidence is not evidence of absence.

In this case, Aristarchus was right. How do you know Jane is not in the same predicament as the Greeks?

Re:Fossils

[Ol Olsoc]

Is "besmote" etymologically related to "bespoke?"

It is derived from the early Sumerian endearment "Cacasmacked".

Re: Fossils

[The Evil Atheist]

Still not relevant to the point I'm making.

Re:Fossils

[Ol Olsoc]

As you mock, He laughs at you, and STILL loves you, LOL. No, God is not Cuthulu, he doesn't have appendages. Myself, I don't have problem with believing in the theory of evolution and believing in God. See, God, is outside of time, and hence He sees beginning, now, and end. A second to God is a thousand years... God can use the laws of nature, He made them! So when you read Feynman's Lectures, you know what, God made those laws and He doesn't change. So, when the preacher online starts harping about science, remind him that the same God that created all also created the physical laws that allows that internet stream of his Sunday service, and that God is constant. The same physical laws apply everywhere, because God made those laws, and God doesn't change!

My parents and grandparents might accuse you of apostacy, but they would be certain that you sir, are going to hell. And that's the problem.

So whic of the thousands of Gods is the right one, and how were you lucky enough to be born to the right group that knows the right one? He doth work in mysterious ways it would seem. So you can rejoice at your good luck.

Re: Fossils

[Michael Woodhams]

How did Jane search the town? How does she know that when she moved from one area to another the gorilla didn't move into the area she just searched and is now claiming is gorilla-free?

It is still evidence. If Jane's search and the gorilla's location are uncorrelated, then if there exists a single gorilla, having searched 95% of the town once, the number of gorilla sightings Jane would get would be a Poisson distribution with mean 0.95. In this case, she will have zero sightings about 40% of the time, so the evidence is not yet very convincing, but once Jane has searched the town all over 5 times and not sighted a gorilla, the evidence is strong that there is no gorilla (p value 0.007.)

Re: Fossils

[blue trane]

Too many assumptions. The absence of gorilla sightings assumes the gorilla is in a place people can see it, that people will report sightings truthfully, that Jane questioned everyone.

Your example ignores the Aristarchus problem. Your measurements might not be sensitive enough.

Thus absence of evidence is very plausibly not evidence of absence.

Re:Fossils

[Michael Woodhams]

Fossils are not relevant here. The methodology of this study, and of the studies over long time periods it is comparing to, are both from DNA sequencing, not fossils.

Re: Fossils

[blue trane]

Did Jane forget to look in the zoo? The gorilla could be "loose" in the zoo, out of its cage. Therefore the gorilla is "loose in the city."

96% of the universe is unexplained by physics. Yet we make claims of absolute certainty based on the 4% we can see. There is a lot of evidence that the absence of evidence is not evidence of absence.

Aristotle never saw an artery that had blood in it, therefore the absence of evidence of blood proved to him that arteries carried air.

How can you argue with Aristotle's 100% evidence of absence?

Re:Fossils

[alreaud]

No brother, that's the difference between Charismatic and Southern Baptist, LOL... ;-) Think about it, "Thousands of Gods"? If we're but a resemblance of them, then what does a committee do? I was impressed that of all of the scientific disciplines, astronomers seemed to be most likely to be of the faith. Why? Because, IMHO, they work with the "big" picture. A committee didn't create what they see in the Hubble Deep Field... A lot of my thought of it comes out of physics and quantum mechanics. Non-locality, a photon doesn't experience time (do the math), etc. If one can wrap their mind around an ever present NOW encompassing past, present, and future, then one can start to perceive the operating sphere of God.

Re:Fossils

[The Evil Atheist]

Try reading again:

Senior author Professor Greger Larson said: 'Our observations reveal that evolution is always moving quickly but we tend not to see it because we typically measure it over longer time periods. Our study shows that evolution can move much faster in the short term than we had believed from fossil-based estimates. Previously, estimates put the rate of change in a mitochondrial genome at about 2% per million years. At this pace, we should not have been able to spot a single mutation in just 50 years, but in fact we spotted two.'

The reason why mitchondrial measurements used long time frames was because of the mindset carried over from fossil estimates. The senior author himself says so in this quote from the article.

Re: Fossils

[Michael Woodhams]

OK, Jane has evidence for the absence of a certain class of gorilla (highly visible gorillas.) She has placed constraints on the properties of any gorillas in the town (that they not be highly visible.) She can't say anything useful about presence or absence of ninja gorillas.

Re:Fossils

[Barsteward]

aaahhh,,, isn't delusion delusional.....

Re: Fossils

[Barsteward]

the gorilla would have shat somewhere or probably in a few places

Re: Fossils

[Dragonslicer]

She can't say anything useful about presence or absence of ninja gorillas.

Great, now I won't be able to sleep for a week.

Re:Fossils

[Ol Olsoc]

If one can wrap their mind around an ever present NOW encompassing past, present, and future, then one can start to perceive the operating sphere of God.

As well as develop a sense of personal incredulity.

You are welcome of course, to your own beliefs. But really, it's only manufacturing your god in your own image. There are billions of others in this world who believe quite fervently in their version of god, and they are equally as likely to be correct as you are. People who have violent tendencies tend toward a god of violent tendencies, people who are materialistic opt for a god that rewards them with material goods. People who enjoy forcing others to do as their god demands have a tendency to have a god who justifies their conformity based aggression. And people who believe in live and let live have their version of god, but are always at risk of being eliminated by the violent god followers or not allowed to practice their faith by the everyone must conform god people.

Me? I just believe in being excellent to others. If at the end of my life, that isn't enough, well then to hell with me.

Re: Fossils

[blue trane]

There are still infinite hypotheses that would account for Jane's absence of evidence not being evidence of absence. Bob, the original claimant, could be cleaning up the gorilla poop. Or the gorilla poop could be in a park and easily confused for dog poop. Jane can only report her results and give her opinion; but that's all it is, scientifically, her opinion on the absence. There are infinite possibilities that her absence of evidence is not evidence of absence.

There is no evidence that gravitons exist; yet that is not taken as evidence of absence by physicists.

There was no evidence that the Higgs Boson existed for 40 years; that was not taken as evidence of absence.

Basically the idea that absence of evidence is evidence of absence is an opinion, not science. As the saying goes opinions are like assholes, everyone has one, and it stinks.

Re:Fossils

[Ol Olsoc]

Grow up.

For the FSM said thusly, "Beware the Christian zealot, for they are unexcelled ad dishing it out, but woefully meager in taking it."

Re: Fossils

[Spottywot]

Between the wonderful explanations of evolution and DNA at the top of the comments and you guys making me laugh, I proclaim 'Slashdot not dead!'

Re:Fossils

[RockDoctor]

Well considering that for the longest time, fossils were our main source of viewing evolution through time,

Considering that one of the major pieces of evidence used in Darwin's original "extended argument" ("On the Origin of Species", in case you don't get the reference) was the experience of contemporary animal husbandry (farmers not being the most fancy-prone of people, but understanding very well the financial value of breeding better stock animals) as well as the variation of animals bred by "fanciers" (pigeon breeders, dog breeders, etc), then I think you will struggle to support that argument. In fact, if you were to read the book (why go to a summary or a re-presentation, when the original is renowned for being well and clearly written. And out of copyright.), you'd find that Chapter 1, after the Introduction, goes under the title of "Variation under domestication and under nature."

Geological and palaeontological information doesn't get a mention until chapters 6 to 9 (the numbering varies between editions) and isn't a major plank at all. In fact, the peculiarities of the geological record presented more problems for the theory initially than support. However as time continued and our knowledge of the geological record got better (without much corresponding improvement in biological knowledge), the relative amount of palaeontological data had improved, and things like Marsh's phylogeny of horses (from Eohippus to modern Equus) did indeed become icons of evolutionary presentation. But that wasn't until the late 1870s, nearly 20 years (and I think 8 or 9 different editions) after the publication of OTOOS.

Re:Fossils

[The Evil Atheist]

Darwin's work heavily depended on Lyell's ideas of geology, including the idea that geological time is slow. So it doesn't matter if it doesn't get a mention until later chapters. The book was written to make a convincing argument so that it was hard to deny (hence starting of with artificial selection), not list things in order of importance.

Re:Fossils

[RockDoctor]

... Hmmm, a fair enough point. Darwin was actually sent the later volumes of Lyell's "Principles" while he was out on the beagle (I think he had the first volume when he boarded the Beagle).

however he was very cautious in his application of geological evidence - bearing in mind that he was a Fellow of the GSL (same as Lyell, and me) long before he published OTOOS, and was a student of Sedgwick. Even given the paucity of geological data in his time, he was well aware of the seemingly problematic abruptness of the Cambrian Explosion. (Wasn't Sedgwick the one who named Cambrian, and then participated in the "Devonian dispute" which was resolved by the erection of the Ordovician and Silurian periods. Changes in fossil fauna were a critical part of that debate, though the concept of a "mass extinction" wasn't really in the air at the time.

Nothing new here

[BarbaraHudson]

Nobody has thought for decades that evolution is a slow continuous process. Rather that it has periods where nothing much happens, then there's a spurt of changes, then another period of calm.

Pick the right time interval and duration and you can see either one or the other, as you want. Great way to make data fit your favorite theory :-)

Re:Nothing new here

[Anonymous Coward]

Just like human history. In my lifetime we went to the moon, after that not much happened.

Re:Nothing new here

[Rei]

According to something I read on Slashdot, since then we've all become cows. Which would now that I think about it be pretty compelling evidence of rapid evolution.

Also, moo.

Re:Nothing new here

[Michael Woodhams]

I think you're talking about punctuated equilibrium, which is about phenotypic change (change in body shape/size/colour/function etc.) I think punctuated equilibrium is somewhere between controversial and discredited, but it is not my field so I'm not sure.

In this case, we are talking about evolution at the level of DNA, which is commonly thought to be a continuous process with rate being nearly constant. https://en.wikipedia.org/wiki/...
The limitations of the molecular clock are what are being argued about in the academic debate that this paper is part of.

Re:Nothing new here

[BarbaraHudson]

Consider that the average human has between 60 and 200 mutations. And that even traits that are harmful, such as juvenile diabetes and sickle cell anemia, are successfully passed on. Sure, sickle cell anemia provides some protection against malaria, but what possible advantage can type 1 diabetes confer, aside from high sugar content fractionally lowering the freezing point of blood? Kind of outweighed by kidneys and eyes going bad, nerve damage, and extremities developing ulcers that turn gangrenous if not treated?

But us mutating into cows? That's udder nonsense :-) Though all the guys trolling anonymously mutating into bulls would explain all their bullsh*t ... still, anything's better than being a sheeple.

Re:Nothing new here

[BarbaraHudson]

Any change that doesn't result in a "change of body shape/size/colour/function etc" isn't going to be selected for or against unless and until the environment changes. Then it may prove to be either beneficial, detrimental, a bit of both, or neutral. Even then, it's a crapshoot. Blue eyes are a recent recessive mutation that carries with it a three-fold increased risk of glaucoma, as well as other diseases. Being left-handed comes with its' own problems, such as increased risk of ptsd and psychosis (weird fun fact: the majority of transsexuals are left-handed). And yet both persist.

Re:Nothing new here

[BarbaraHudson]

Mutations that are neutral in one environment will "pop out" when the environment changes. When there's a drastic environmental change, all these environmentally-neutral changes that have accumulated can suddenly be selected for or selected out due to the new environment.

Go back in time and take a selection of dogs and dump them in Newfoundland. Very quickly, those that are less able to handle cold will be out-bred, and those who do not have thick black coats with two layers, so that they can even get warm enough to dry out in the middle of winter on a summer day, are going to be at a serious disadvantage. And since surface area (and heat loss) to body mass is higher in smaller dogs, the largest will have the best chance of surviving and breeding. Since the culling process in such a harsh environment would be extremely rapid, it won't take too many generations to produce a line of dogs that are large, black, two-layer coats, and resistant to cold. Any dogs that were not born with one or more of these traits would probably not live long enough to breed.

This also affects their behaviour. Newfies can afford to be easy-going dogs because there aren't too many threats to them in nature - they can kill a horse.

Re:Mutation only, not evolution

[viperidaenz]

The chickens with mutations were kept for further study and their genes live on.
The other chickens are thrown away.

There appears to be a survival advantage.

This needed proving?

[Dereck1701]

Domesticated animals have changed significantly in the past few few decades let alone the past few thousand years. Modern broilers (meat chickens) can't even self procreate due to the changes but also grow from chicks to food in a couple months. Dairy cattle are another example, Today 9.3 Million dairy cattle produce 59% more milk than 25.6 Million cattle produced in the 40s. This isn't limited to animals, grain producing plants have significantly changed since the 30s, corn specifically has went from around 25 bushels per acre in the 30s to over 140 bushels per acre today. Anyone with even a passing knowledge of farming could have told you this. It should be noted though that while these plants/animals work well for modern farming, most would almost certainly go extinct after a few years without human care due to their extreme specialization (grain production, milk production, meat production, egg production etc).

Re:This needed proving?

[burtosis]

The article is about mitochondrial DNA, which to use a computer analogy, is closer to the operating system than features of software as you describe.

Re:This needed proving?

[Impy the Impiuos Imp]

Speaking of software, the math undergirding the understanding of evolution, exploring the gradient descent space of organism fitness, shows a rapid descent into local minima areas (similar to the dent of the heavy ball in the rubber gridwork in gravity science shows). This would predict the fits and starts as slow changes finally detect another low area and the benefits of more adaptation slide it right in i.e. change at that point is rapid as many small changes polish off the adaptation.

The angle of the local fitness space is basically the same as the actual real world fitness pressure (survival and reproduction).

Re:Selective Breeding

[rossdee]

When did chickens get to the Americas then?

Re:Mutation only, not evolution

[Oligonicella]

Not one single biological trait conferring a survival advantage was detected.

That's not the criteria for evolution.

Evolution is an optimization algorithm

[tempmpi]

The mechanisms for Evolution itself should also be under selective pressure. I would expect that traits, that allow for a quicker adaption to a changed environment, are a huge improvement of fitness. One example seems to be sexual reproduction as this allows for mixing of different sets of traits and allows sexual selection. But there should be other mechanisms as well. Random mutation seem to be quite ineffective, mechanisms that cause more specific mutations with a higher likelihood of increasing the fitness should be possible.

Re:Evolution is an optimization algorithm

[Opyros]

https://en.wikipedia.org/wiki/Evolvability

Happens even among human populations

[Anonymous Coward]

Within 15 years, Europe will not have any more white people.

Re:Happens even among human populations

[PPH]

Within 15 years

We've told you a million times: Don't exaggerate.

Re: Happens even among human populations

[mbeckman]

But they will still be people.

Re:Happens even among human populations

[The Evil Atheist]

How do you measure whiteness of people (not necessarily skin colour)?

Re:Mutation only, not evolution

[the gnat]

We've never observed evolution yet

Wrong

some scientists only assume it from observed differences in the fossil record.

Not "assume", "infer", and anyway decades of molecular biology, genetics, and genomics have proven at least as useful as fossils. My favorite example here.

Re:Light article, bad summary.

[myowntrueself]

15 years? The researchers observed 2 SNPs in a population of chickens over 50 years; which is "15x faster" than the previous estimate of 2% evolution every million years. There also wasn't much selection on these chickens, as they were lab chickens, so even less-fit mutations would persist. One SNP was non-synonymous (meaning it results in a codon change), and one SNP was synonymous (no codon change).

I'm not seeing where they got "Significant changes in 15 years" out of the article.

Interestingly, theropods (which Chickens evolved from) evolved very rapidly themselves.

Also, bird (and probably dinosaur) DNA and chromosomes works a little differently to mammals. Birds can be split down the middle with one half being male, the other female. Mammals can't do that (because hormones). Also female birds can produce offspring without males. Turkeys do this fairly regularly, all the offspring are male.

Birds work differently to mammals.

Re: Mutation only, not evolution

[Anonymous Coward]

Evolution defined: The theory of evolution by natural selection, first formulated in Darwin's book "On the Origin of Species" in 1859, is the process by which organisms change over time as a result of mutations in heritable physical or behavioral traits. Mutations that allow an organism to better adapt to its environment help it survive and have more offspring.

Re:Light article, bad summary.

[PopeRatzo]

Here's a better summary for you, after the chili I ate last night, there are now 80% less bacteria in my gut but those that remain are entirely new species never before seen.

If you ate the same chili I did, they won't be in your gut for long.

Wrong measure

[AK Marc]

There's a common misconception that fear can cause your hair to turn white. It's wrong, but true. What happens is that your hair us going white. It's 10% white, and nobody notices. 30% white and people can see it clearly, but don't point it out. But when you are at 30% white and have a strong fear event, you can have some hair fall out. The hair that falls out is disproportionately non-white. So it gives the appearance of a sudden whitening of your hair, caused by fear.

And my first thought on this was the same thing. Random mutation is long-term. But when a selection event happens, the "hidden" trait isn't created, but selected for. There is no "evolution", but a selection pressure that reveals the previous mutation as a preferential trait, making it appear to happen suddenly and revealed by the "cause" but not actually caused by the "cause".

Re:Wrong measure

[Anonymous Coward]

simply semantics.
You literally just explained how someones hair turned white.

No one was ever saying that your hair would immediately turn white at the moment of trauma.

I got a patch of white hair after a near death experience just about 10 cm2.
had nothing to do with my hair falling out immediately, but in that patch of skin it's grown white ever since. I noticed about 2 months after the event and thought I had paint in my hair.

Re: Wrong measure

[mbeckman]

That's a great analogy!

Re:Wrong measure

[dotancohen]

And my first thought on this was the same thing. Random mutation is long-term. But when a selection event happens, the "hidden" trait isn't created, but selected for.

Based on that logic, the elephant statue was already in the marble block before Leonardo began carving, and he just removed everything that wasn't elephant.

Re:Wrong measure

[The Evil Atheist]

Random mutation is long-term. But when a selection event happens, the "hidden" trait isn't created, but selected for. There is no "evolution", but a selection pressure that reveals the previous mutation as a preferential trait

That IS evolution. What else do you think is meant by evolution by natural selection?

Re:Wrong measure

[AK Marc]

Most people speak about it like the new mutation dominates much quicker. Why would they say that they are finding evolution happens faster than they thought if they already thought what you assert?

Re:Wrong measure

[The Evil Atheist]

There's nothing about evolution that says any trait must "dominate". The very minimum it needs to be is non-recessive.

Re:Wrong measure

[AK Marc]

You seem to be arguing with the implications of the article, not me. Yet you contradict me because you feel the need to argue about it with someone.

Re:Wrong measure

[dotancohen]

Actually, my comment was based upon a quote from Leonardo himself, in which he stated that he simply removed everything that wasn't elephant. It was my way of agreeing with the OP even if his argument sounds ridiculous.

Re:Wrong measure

[The Evil Atheist]

No, you have clear misconceptions about evolution. The article is fine.

Re:Wrong measure

[AK Marc]

Ah, so the "You are wrong" without explanation or reason is the best way to demonstrate that point.

Re:Wrong measure

[The Evil Atheist]

I already explained why you are wrong. Twice. You're the one who tried to deflect with your previous comment.

Re:Selective Breeding

[AK Marc]

http://lmgtfy.com/?q=chickens+...

So..

[willworkforbeer]

Their understanding of this phenomenon is slowly... well, you know.

Re:Mutation only, not evolution

[Anonymous Coward]

The study did not observe evolution. Not one single biological trait conferring a survival advantage was detected. All that was observed were two mutation of unknown origin. The authors surmise "paternal leakage", but nobody really knows the source of the mutations. The act of mutation itself was not observed. It was only detected by comparing samples over a long time span.

This is similar to what astronomers' do when they "blink" star fields -- switching between early and late images to make any change easy to pick up visually. When a change is picked up, the astronomer knows nothing about the cause, only that the change occurred.

But here we are, science and media over-reaching. The researchers themselves asserting that evolution is happening, and happening faster than before. We've never observed evolution yet -- some scientists only assume it from observed differences in the fossil record.

Why do scientists feel the need to over-reach in their conclusions? I can only guess. Funding, probably.

We have not only observed Evolution, we have taken it into our own hands in many ways. Consider the many breeds of dogs, all of them 100% of dogs are descended from Wolves. Human beings created dogs from wolves through selective breeding.

You are 100% wrong when you say we have not observed evolution.

Re: Mutation only, not evolution

[Anonymous Coward]

Selective breeding is not evolution. First, it's not random and undirected, a requirement for evolution. Second, it creates no new traits. Selective breeding can only select among traits already existing in the genome.

Human-directed gene splicing is not evolution either. It's intelligent design.

Re: Mutation only, not evolution

[mbeckman]

Wolves and dogs are the same species. Wolves and dogs are interfertile, meaning they can breed and produce viable offspring. In other words, wolves can interbreed with any type of dog, and their offspring are capable of producing offspring themselves. While it's likely true that men domesticated dogs from wolves, no additional functions were added to create a dog. Rather, functions were subtracted from wolves to produce dogs.

An essential aspect of evolution is that it is a random processing, not the result of conscious decisions by another organism.

Re:Mutation only, not evolution

[DRJlaw]

We've never observed evolution yet -- some scientists only assume it from observed differences in the fossil record.

Who is "we," kimosabe? Because the repeated emergence of antibiotic resistance, for example, is observed evolution. Then, if you're going to hang your hat on supposed horizontal gene transfer for antibiotic resistance, there's that niggling problem of emerging resistance to antimalarial drugs...

You-we may never have observed evolution, but medical-we certainly has.

Re: Mutation only, not evolution

[blue trane]

"it's not random and undirected, a requirement for evolution."

Counterpoint, by J. B. S. Haldane:

"Teleology is like a mistress to a biologist: he cannot live without her but he's unwilling to be seen with her in public."

Background information, link to paper.

[Michael Woodhams]

The paper is here but it is probably paywalled. (I have institutional access, so I'm not sure what that link will do to people who don't.)

This is part of an ongoing debate about rates of evolution. To a large extent it was kicked off by a 2005 paper by Simon Ho et al. (Ho is second author on this paper.) They observed that estimates of mutation rates derived from studies over short time periods are much higher than mutation rates derived from studies over long time periods. Short time periods are up to a few thousand years, e.g. comparing populations that have been separated by for a few thousand years, or ancient DNA compared to modern DNA in the same species, or multigenerational studies over a few years or decades such as this one. Long time periods are from comparing species whose common ancestor is typically millions of years ago.

This apparent acceleration in mutation rates is controversial.

I'm going to read the paper now, so I may have more to say later.

Re:Background information, link to paper.

[Michael Woodhams]

I've read the (mercifully short) paper now.

A long-running experiment started with a single population of chickens, and has been selectively breeding half for high body weight and the other half for low body weight. The full pedigree is known (mothers and fathers) over 40-50 generations. In addition, the two populations have been cross bred, for 8 generations.

Two mitochondrial mutations were detected in the low weight half of the population, both in one maternal lineage out of four major maternal lineages in that half of the population. However, one of the mutations also occurs in a few individuals from one of the other maternal lines in the low body weight half. They ascribe this to paternal leakage of mitochondrial genome, and can trace it back to a single mating. (This is covered in the supplementary material, which I haven't read.)

They have used the cross-bred population to investigate whether the mutations cause low body weight, but did not find any evidence that they do.

This experiment gives a mutation rate of 3x10^-7 mutations per site per year, with 95% confidence 4x10^-8 to 1x10^-6. (The rate comes from the observation of just two mutations, so the confidence interval is large.) By comparison, rates derived over time periods of 1 to 10 million years are around 1x10^-8.

It looks to me like a useful result, but the statistics aren't good enough to say that this experiment by itself proves the time-varying-rates hypothesis.

Re:Background information, link to paper.

[RichMan]

Have they factored in epigenetics into this? Where the gene is there but not expressed. Seems to me a lot of generation to generation adaptation can be explained by epigenetics and simply brining out already present factors.

The whole "15 years" thing in the summary should be in generations. That is like forever in botfly generations, yet nothing in land tortoise generations.

Re:Background information, link to paper.

[Michael Woodhams]

No, the paper has nothing about epigenetics. They are looking only at mitochondria which I believe is not affected by epigenetics. I don't think mitochondria can function without all of their genes. They are actually looking directly at the DNA - the mutations really did happen, because they are observing them at the most fundamental level. There is nowhere for them to 'hide'.

The experiment covers about 50 generations. (Or, more accurately, they are piggybacking off an existing experiment that has been running for 50 generations.)

Re:Background information, link to paper.

[140Mandak262Jamuna]

I'm going to read the paper now, so I may have more to say later.

Pontificating without reading the paper with a mere cursory glance at the title and guessing what the paper ought to say based on my prior biases produces very interesting threads of conversation.

Re:Mutation only, not evolution

[rahvin112]

We have better than 2 dozen scientifically confirmed speciation events fully documented and available in the literature in the less than 200 years we've been watching.

Evolution is a fact. There are entire branches of biological sciences based on it that would not be viable sciences without the existence of evolution. Those branches of science have a direct effect on you several times a year and one day they might cure your cancer. To deny evolution denies the reality around us every day.

Re: Evolution is more general

[blue trane]

But there is direction to evolution.

See for example https://mechanism.ucsd.edu/tea...

Ernst Mayr on Teleology

"Consider the following statement: 'The Wood Thrush migrates in the fall into warmer countries in order to escape the inclemency of the weather and the food shortages of the northern climates'. If we replace the words 'in order to' by 'and thereby', we leave the important question unanswered as to why the Wood Thrush migrates. The teleonomic form of the statement implies that the goal-directed migratory activity is governed by a program. By omitting this important message the translated sentence is greatly impoverished as far as information content is concerned, without gaining in causal strength." Mayr (1974)

Re:OH YAY more aspies

[Anonymous Coward]

Gravity is also a theory. Santa Claus is very real. As real as God. I believed in Santa until the age of 5, God -- 25. I cannot explain the discrepancy.

Re:Mutation only, not evolution

[Michael Woodhams]

Not one single biological trait conferring a survival advantage was detected.

True, but that wasn't what they were looking for.

The authors surmise "paternal leakage", but nobody really knows the source of the mutations.

False. The paternal leakage was as well as detecting the mutations (and detection was enabled by the mutations.) It is not put forward as an explanation.

We've never observed evolution yet

False. Evolution in HIV adapting to evade drug therapy can be seen in time series of samples taken from a single patent (and this has been replicated many times.)

Re:OH YAY more aspies

[Anonymous Coward]

Selective breeding is simply a matter of guided evolution.

In the wild, environmental pressures (food availability, etc.) 'select' traits suited to surviving said pressures at least until breeding age.
In selective breeding, environmental pressures (people) select traits, and attempt to get them to pass on through breeding.

The genetic mechanism is identical for both, only the method of 'selection' differs. Both are examples of evolution, though the latter rarely goes so far as to split off into a new species, because the desired traits tend to coalesce long before that.

Re: Evolution is more general

[mbeckman]

But teleology is just a wishful philosophy, like the selfish gene. It's not causation and adds nothing to cause-and-effect empirical science. .

Re:mitochondrial mutation = evolution?

[Michael Woodhams]

So this seems to just be another study showing the trickiness of using that 'clock'.

I agree except for the word "just". Yes, very much one of the things they are saying is that the molecular clock may have quirks, and failing to account for them will lead to error. (Whether this quirk is one which can be accounted for accurately isn't addressed in this paper, they are trying to establish that the quirk does in fact exist.) But it is more interesting that that, being a pedigree study over a large number of generations, and having a well documented case of paternal leakage. The only pedigree study I've been involved in was over a single generation.

Re:OH YAY more aspies

[Anonymous Coward]

Oh, and the 'different races' among humans are *also* examples of evolution.

Lighter skinned 'races' have less melanin, because in less sunny climates, they get less ultraviolet light from sunlight, which inhibits the production of Vitamin D. Melanin blocks ultraviolet light, so people with lower concentrations of melanin in their skin, produce Vitamin D more easily in those climates. Shortages of vitamin D cause all sorts of health issues, leading to reduced suitability for individuals with darker skin. As a result, people with genetics for lighter skin survived to reproduction age more often, and the trait was passed on more successfully to the point that it became the dominant (most common) trait over time.

Closer to the equator, on the other hand, darker skin has its own advantages (less susceptible to sunburns, for example), and remained the dominant trait in the sunnier climates (Africa, Australia, etc.).

Vitamin D is currently gotten mostly through our diet, so the environmental effects of skin color are drowned out these days.

Re: Mutation only, not evolution

[mbeckman]

HIV is a virus. It's not alive, and hence can't "survive". Viruses are DNA clockwork mechanisms that can't reproduce without hijacking a host cell, and thus can't enter the realm of biological evolution, which aims to explain the origin of life, not clocks.

Already known in humans

[gringer]

We have already observed recent mitochondrial evolution in the human population, with a few mutations specific to Polynesian populations that must have arisen during radiative settlement a few hundred years ago:

http://dx.doi.org/10.1371/jour...

Re: Mutation only, not evolution

[Michael Woodhams]

Viruses meet all the requirements needed for evolution to apply to them.

Re: Evolution is more general

[blue trane]

Why isn't it causation? Mutations can be seen as models of the future, predictions.

From wikipedia:

Evolution largely hoards hindsight, as variations unwittingly make "predictions" about structures and functions which could successfully cope with the future, and which participate in a process of natural selection that culls the unfit, leaving the fit to the next generation. Information accumulates about functions and structures that are successful, exploiting feedback from the environment via the selection of fitter coalitions of structures and functions. Robert Rosen has described these features as an anticipatory system which builds an internal model based on past and possible future states.

Teleology is more than wishful philosophy; as Haldane noted, it's essential to biology. The wishfulness comes in trying to deny teleology.

Re: Mutation only, not evolution

[the biologist]

https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment

E. coli evolved to eat a new chemical (citrate). It developed a new enzyme to do it. E. coli was previously defined as not being able to eat citrate. By the former definition, it has evolved into a new species.

How is antibiotic resistance a loss of function? Troll better, please.

Re: Mutation only, not evolution

[the biologist]

Name one of your tons of failed predictions of evolution. Be careful, I'll be able to tell if you're blaming a failed prediction of some not-evolution theory on evolution.

Re: Mutation only, not evolution

[the biologist]

There is no requirement for something to be alive for it to evolve.

The requirements for a system to evolve are pretty simple:
1. Some aspect of it must reproduce.
2. During reproduction, a "child" is similar to the "parent".
3. Sometimes traits change randomly.
4. Death happens.

Systems well outside the domain of conventional biology can experience evolution.

Re: Mutation only, not evolution

[the biologist]

Also... evolution does not in any way seek to explain the origin of life. You're thinking of abiogenesis, a distinctly not-evolution area of study.

Re: Mutation only, not evolution

[the biologist]

Several of them are listed here: http://www.talkorigins.org/faq...

Re: Mutation only, not evolution

[the biologist]

An essential aspect of evolution is that it is a random processing, not the result of conscious decisions by another organism.

What you've just described is in no way an essential aspect of evolution. It isn't even part of evolution. If some change in a population is the result of concious (or unconcious) decisions by another organism... evolution has still happened.

Re:Mutation only, not evolution

[labnet]

What I don't understand, is if it takes so many generations for a mutation that may or may not do anything, how do you explain complex functions that require thousands of beneficial mutations before the new functionality actually causes a survival benefit. I can't see how it would ever happen.
It's like throwing match sticks on a floor hoping one day it makes a sentence. You may after billions of attempts get a letter, but you will never achieve a whole sentence when those partial non beneficial mutations that are yet to form a beneficial structure are mutated back out again.

Re: Mutation only, not evolution

[the biologist]

Selective breeding is not evolution. First, it's not random and undirected, a requirement for evolution. Second, it creates no new traits. Selective breeding can only select among traits already existing in the genome.

Evolution isn't random and undirected. Random mutation paired with non-random selection results in evolution in the way it is conventionally thought of. Selective breeding changes the populations being selected, so does result in evolution.

Re:Mutation only, not evolution

[Anonymous Coward]

It's like throwing match sticks on a floor hoping one day it makes a sentence. You may after billions of attempts get a letter

Weird, I seem to always get an "I" on my first attempt with a single match...

Re: Evolution is more general

[mbeckman]

Also from Wikipedia (https://en.wikipedia.org/wiki/Teleology):

"Contemporary philosophers and scientists are still actively discussing whether teleological talk is useful or accurate in doing modern philosophy and science."

If they're still discussing whether teleology is "useful or accurate", it seems doubtful that it actually is essential to biology.

Re: Mutation only, not evolution

[the biologist]

The authors of the paper are talking about evolution, not "Darwin's evolution". We don't hold Darwin as a figurehead. He had some good ideas, but we've learned much since then.

Re:Mutation only, not evolution

[Barsteward]

Thrown away? not KFC'd?

Re: Mutation only, not evolution

[mbeckman]

I'm not the one asserting that evolution is a fact. The person making the positive assertion has the burden of proof. The challenger is not obligated to prove the negative (e.g. evolution is not a fact).

I always get to this point with evolutionists. They claim proof, but never deliver. That means they lose.

Re: Mutation only, not evolution

[Barsteward]

"evolution is a religion" you must be one of the potential Republican presidential candidates.....

Re: Mutation only, not evolution

[Barsteward]

Have you been playing with your name to create a handle for /. Is your name really Michelle Bachmann?

Re: Mutation only, not evolution

[mbeckman]

Name-calling is the last bastion of the man without an argument.

Re: Mutation only, not evolution

[mbeckman]

By that definition, a quartz crystal evolves.

Evolution requires adding information content. There is no evidence that viruses (or any actually living things) increase information content between generations. Mutations have only been observed to reduce complexity, and thus information content.

Re: Mutation only, not evolution

[NoOneInParticular]

I think you've got your emphasis wrong. Darwinian evolution explains the origin of species, not the origin of life. Given that life exists, Darwin explains that adaptation, speciation and the diversity of life we witness on Earth will necessarily happen. From a Darwinian perspective it truly doesn't matter whether there is "conscious" control or not, species interacting with each-other lead to differential survival rates in these species, and therefore evolution of traits that help with survival.

Humans and chickens are in a symbiotic relationship. We use them for food, they use us for getting more chicks. So chickens will evolve to be more tasty (because we select them that way), while we evolve to digest chickens more effectively and become less sensitive to the diseases they carry (because they select us this way). That we perceive to be in charge and are doing this "consciously" (whatever that means) is irrelevant from an evolutionary perspective.

Re: Mutation only, not evolution

[mbeckman]

When Charles Darwin published The Origin of Species he avoided discussing the origin of life. However, reading other texts by Darwin, and correspondence he exchanged with friends and colleagues, reveals that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from pages he pulled from his private notebooks, Darwin was convinced that âoethe intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbableâ.

Re:Selective Breeding

[NoOneInParticular]

Apparently, civilization is part of the chicken's environment now. To compare: ants have selectively bred greenfly to the point where the greenfly cannot poop unless an ant milks them. Have the greenfly not evolved? Have the ants?

Re: Mutation only, not evolution

[dave420]

And your childish misrepresentation of the facts, frequent confusion of "evolution" and "the theory of evolution", and willful ignorance of the accurate prediction made by the theory of evolution are the first bastion of an idiot with an axe to grind. Were you abused by a biologist as a child? Maybe one killed your Pa?

Re: Mutation only, not evolution

[Anonymous Coward]

Evolution, on the other hand, requires a gain of functional systems for bacteria to evolve into new bacterial kind, and ultimately, higher organisms.

Evolution doesn't go to the direction of higher complexity but to the direction of higher rate of survival. In this context it would be very much better to talk about eukaryotes instead of bacteria just avoid getting embarrassed in the inter-tubes.

Re:Mutation only, not evolution

[Anonymous Coward]

Thrown away? not KFC'd?

Obviously not, because they weren't mutants.

Re: Mutation only, not evolution

[DRJlaw]

However, mutation and natural selection have only been seen to result in bacteria with defective proteins that have lost their normal functions.

Citation needed. Antibiotic resistance plasmids do not cause the normal proteins of the bacterium to become non-functional. They add capabilities to organisms that did not have those capabilities before.

Also, producing more of a protein does not equal "defective proteins." Genetic upregulation of protein expression is still a mutation.

You honestly have no idea what you're talking about, and it's very evident to the rest of us.

Re:Mutation only, not evolution

[burtosis]

What I don't understand, is if it takes so many generations for a mutation that may or may not do anything, how do you explain complex functions that require thousands of beneficial mutations before the new functionality actually causes a survival benefit. I can't see how it would ever happen. It's like throwing match sticks on a floor hoping one day it makes a sentence. You may after billions of attempts get a letter, but you will never achieve a whole sentence when those partial non beneficial mutations that are yet to form a beneficial structure are mutated back out again.

You understand correctly. It is extremely rare if non-existent for even small non functional changes. All changes have some intermediate functional state. You can have horizontal transfer in some cases, but this does not imply you get a free lunch, nor does an inactive or 'junk' sequence acquiring an advantage.

It's also beneficial to note that with organisms like bacteria, over long periods of time, it's not billions of attempts, not trillions, not quadrillions. It surpasses quintillions of attempts for a single species and all it takes is one success to fix it in a population. It's a massively parallel process and just because humans often are extremely poor at conceptualizing it, that does not invalidate reality.

Re: Mutation only, not evolution

[mbeckman]

Another name-caller! This behavior just weakens your argument. I suggest you stick to facts in evidence.

Science has closely studied two genera of bacteria to gain an understanding of antibiotic resistance: Escherichia and Salmonella. While driven by expediency -- many people become ill from these organisms, so antibiotic resistance can be easily observed -- researchers have looked for, but not found, the smoking gun of evolution in antibiotic resistance. In speaking about Escherichia in an evolutionary context, France’s renowned zoologist, Pierre-Paul Grassé, observed (and here's your citation):

...bacteria, despite their great production of intraspecific varieties, exhibit a great fidelity to their species. The bacillus Escherichia coli, whose mutants have been studied very carefully, is the best example. The reader will agree that it is surprising, to say the least, to want to prove evolution and to discover its mechanisms and then to choose as a material for this study a being which practically stabilized a billion years ago (Pierre-Paul Grassé, Evolution of Living Organisms, New York: Academic Press,1977, p. 87).

Although E. coli allegedly has undergone a billion years’ worth of mutations, it still has remained “stabilized” in its “nested pattern.” While mutations and DNA transposition have caused change within the bacterial population, those changes have occurred within narrow limits. No long-term, large-scale evolution has occurred.

He goes on to say:

"Mutations, in time, occur incoherently. They are not complementary to one another, nor are they cumulative in successive generations toward a given direction. They modify what preexists, but they do so in disorder, no matter how... As soon as some disorder, even slight, appears in an organized being, sickness, then death follow. There is no possible compromise between the phenomenon of life and anarchy." (1977, pp. 97-98 )

James F. Crow, head of the Genetics Department at the University of Wisconsin and an expert on genetic mutations, states it even more emphatically:

"Almost every mutation is harmful, and it is the individual who pays the price. Any human activity that tends to increase the mutation rate must therefore raise serious health and moral problems for man." (James F. Crow, "Ionizing Radiation and Evolution," Scientific American, vol. 201, September 1959, p. 138).

and elsewhere...

"A random change in the highly integrated system of chemical processes which constitute life is almost certain to impair it-just as a random interchange of connections in a television set is not likely to improve the picture." James F. Crow (Professor of Genetics, University of Wisconsin), "Genetic Effects of Radiation," Bulletin of the Atomic Scientists, no. 14, 1958, pp. 19-20

I can provide many, many more citations of biologists and biochemists not finding evolution in antibiotic resistance. Can you provide any citations where evolution has been proven?

Faster evolution a trait?

[Codeyman]

Couldn't faster evolution develop as a trait, to evolve out of certain situations? If so, it is entirely possible that the earlier rate of evolutionary growth was correct and what we should be looking at is rate of rate of evolution.. but maybe rate of rate of evolution is also changing, in which case we should be looking at rate of rate of rate of evolution.. but maybe....

This has been known for decades

[JohnStock]

Flies/ frogs and other small lifeforms have been shown to evolve on much shorter timescales than 15y

Re: Evolution is more general

[Anonymous Cow Ward]

Evolution does not cover the origin of life. It covers life's diversification after life existed.

Re: Mutation only, not evolution

[Anonymous Cow Ward]

No - Darwin's title is more properly interpreted as "how species came about", which does not mean "how life came to be". Oftentimes, organisms grow more complex over time, but not always.

Re: Mutation only, not evolution

[Anonymous Cow Ward]

And yet, regardless of what Darwin did or did not believe, the modern theory of evolution does not address the origin of life. Abiogenesis is its own thing, and involved substantially less evidence and more guesswork.

Re: Mutation only, not evolution

[Anonymous Cow Ward]

Speciation in a vertebrate. You may also find this website educational.

Re:Mutation only, not evolution

[viperidaenz]

I assumed there was a rule against using medical experiments as food, but I could be wrong.

Re: Evolution is more general

[blue trane]

Why do so many birds have such varied and bright feathers?

One teleological explanation is that birds are influencing their own genes. Birds decide which feathers and colors they want to have. They set a goal and evolution follows.

Re: Mutation only, not evolution

[blue trane]

Ask the Fukushima residents about extraordinary claims requiring extraordinary evidence.

The evidence for a tsunami on the scale that occurred was not extraordinary, so the reasoning went that such an extraordinary event would not occur.

Yet once the event happened, the probability that it happened went to 1.

The reasoning behind "extraordinary claims require extraordinary evidence" is basically saying that your priors are so close to 1 almost no evidence will change your mind. See Cromwell's Rule...

Re:Mutation only, not evolution

[labnet]

Thats a naive statement. A light sensitive cell is not one mutation. Even to sense light and have that connect to a decision making system is a again thousands of unrelated mutations finally forming a functional structure.

Re:Mutation only, not evolution

[labnet]

Hi mbeckman,
It was interesting to see you were initially modded to about 4 insightful, and now -1 troll.
I though your comment was good. It is almost like evolution is a religion that cannot tolerate any amount of critique or debate.
Very Sad.

Re: Mutation only, not evolution

[mbeckman]

I said "ultimately" evolution seeks to explain the origin of life. It hasn't a clue yet, but it's run down many blind alleys (Miller/Urey, for example). no evolutionist thinks that there is any other explanation for life than random chance. They just can't come up with a workable hypothesis. However, ask any evolutionary scientist if he thinks devine creation is a reasonable explanation for the origin of life, and you'll hear a resounding "No. Evolution will, though."

Re:Mutation only, not evolution

[labnet]

I appreciate your considered reply; but it does sound non sensensical.
If I took the linux kernal, and made copy errors every so often, you are saying I would eventually get a 3D image processing library? And that all those copy errors wouldn't increase system entropy?

Re: Mutation only, not evolution

[mbeckman]

I asked rahvin112 to "Name one of your dozen proofs of speciation, and one instance where modern medicine depends upon evolution being a fact." I'm still waiting for him/her, or anyone, to put up.

Apparently, the evolutionist have chosen "shut up".

Re: Mutation only, not evolution

[mbeckman]

The Stebbins theory you cite is not an example of speciation. It's an example of a hypothesis that has very little evidence supporting it. Certainly no direct scientific observation. The absence of data is not data.

Re: Evolution is more general

[mbeckman]

Evidence? Experiments? Data? Anything concrete? I don't think so.

Re: Evolution is more general

[blue trane]

Try and make species without some kind of goal in your simulation.

Re: Mutation only, not evolution

[blue trane]

There is some conscious selection, some goal, that individuals of a species are exercising when they reproduce or choose whom to reproduce with. A bird might be wrong when choosing a mate based on colors, colors may not indicate the best traits for survival. The birds make choices, based on their own internally-defined goals, which may or may not agree with what you think they should choose based on your criteria of how evolution progresses.

Re: Evolution is more general

[mbeckman]

Precisely.

Re: Mutation only, not evolution

[mbeckman]

The Slashdot editors have unlimited mod points. Usually they are not so obvious :)

Re: Mutation only, not evolution

[Anonymous Cow Ward]

I'd really like to see you ask an evolutionary scientist about their opinion on the start of life. Divine creation is not a reasonable scientific explanation for the origin of life, because it's not scientific in the slightest. It's possible that's how life actually started, but it's not a reasonable scientific explanation. Moreover, evolution right now does not seek to explain the origin of life. It may in the future, but that seems unlikely.

Re: Evolution is more general

[blue trane]

https://en.wikipedia.org/wiki/...

Teleonomy is closely related to concepts of emergence, complexity theory,[13] and self-organizing systems.[14] It has extended beneath biology to be applied in the context of chemistry.[15][16] Some philosophers of biology resist the term and still employ "teleology" when analyzing biological function[17] and the language used to describe it,[18] while others endorse it.[19]

Re: Mutation only, not evolution

[Anonymous Cow Ward]

I named one proof of speciation. We've also seen it in bacteria numerous times (including, yes, gain of function!). However, speciation is expected to be a long process, based on the mutation rate we see in DNA. It's not surprising that we don't have many examples in larger organisms. As for modern medicine - proteins and processes conserved by evolution are the reason a lot of antibiotics and antiviral medicines work (and yes, while viruses aren't "alive" in the conventional sense, they do replicate and are under selective pressure, and thus can evolve). Evolution is the reason animal models for disease are informative, but not perfect. Evolution is the reason we test some things in monkeys, and why they give us more accurate results than mice do. Evolution is why bacteriophages could be an excellent way to combat antibiotic-resistant bacteria, but regulatory processes have (somewhat understandably) hampered that. Evolution is the best explanation we have for why muscle physiology is so well conserved, and why a lot of mammalian physiology is conserved across species. Evolutionary principles have guided some really neat antibacterial and antiviral compounds that look promising. In short, evolution has had an enormous impact on modern medicine.

Before I spend any more time on this "debate" - are you actually willing to change your mind? So many people who don't believe in evolution aren't. No amount of evidence is enough to convince them. Are you one of them, and if not, what evidence would you need?

Re: Mutation only, not evolution

[Barsteward]

i wasn't name calling, just trying to find a reason for your ideas

Re: Mutation only, not evolution

[Anonymous Cow Ward]

It's well-supported by anatomy, physiology, and genetic studies, but okay. Here are some examples of speciation in plants and other insects, with more references. I do still encourage you to look at this site.

Re: Evolution is more general

[blue trane]

You shouldn't discount it and say everything is directed by pure chance.

What is pure chance, anyway? There must be a goal to get a purely random distribution. Particles don't have random distributions; there is something deciding what puts them in one state or another. Somewhere there is a goal.

Re: Mutation only, not evolution

[mbeckman]

This is an interesting paper, but is addressing the question of new species creation by changing the definition of what a species is.They say as much in their introduction:

Although approximately 150 years have passed since the publication of On the origin of species by means of natural selection, the definition of what species are and the ways in which species originate remain contentious issues in evolutionary biology. The biological species concept, which defines species as groups of interbreeding natural populations that are reproductively isolated from other such groups, continues to draw support. However, there is a growing realization that many animal and plant species can hybridize with their close relatives and exchange genes without losing their identity.

I'm asking for evidence of speciation where genuinely new species have evolved, based on the classical definition of species as inter-breeding populations.

Re: Mutation only, not evolution

[Anonymous Cow Ward]

When you say you want evidence, do you mean direct observation, or genetic, physiological, and fossil evidence? And since you want to use the inter-breeding population definition, I assume you're only looking for evidence in living things that sexually reproduce?

Re: Mutation only, not evolution

[NoOneInParticular]

I think the difference about a scientist and a religious person about the origin of anything is essentially similar. The scientist will say: "it just happened", the religious person will say "God". They mean the same thing.