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.)
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.
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.)
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.)
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.
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.
New privacy violating technologies come along every few years. Road network layouts last centuries. It would be very foolish to let privacy-attack-of-the-day heavily influence your road layouts.
Although people associate uranium with radioactivity, it is only very slightly radioactive (half life > 1 billion years), so if you don't assemble a critical mass the danger is actually chemical. (Heavy metals have a strong tendency to be toxic.)
Other posters have said that here we are dealing with plutonium-239, which has a half life of 24000 years. That is orders of magnitude greater activity (shorter life) than uranium. I've reached the end of my knowledge here - which is worse, is the radioactivity or the chemical toxicity of plutonium-239?
TFA suggests they are worried about radioactivity: "A main concern has been that the remaining plutonium was being allowed to degenerate into other radioactive components like americium, which emits gamma rays that travel farther and are hard to block" but concern is not always well founded, and reporters don't always get it right.
Can you give details of this Airbus demonstration flight crash? I think you've got a garbled version of Air France flight 296. The plane did refuse the pilot's command to raise the nose, but that was to prevent a stall. At the time this pilot/plane conflict occurred, the pilot had flown the plane into a state where a crash was inevitable.
Inspired by the United Airlines flight 232 (the DC-10 crash you cite), software has been written to control planes by differential thrust, and to do so better than people can. As I recall, it was deemed to expensive to put it into service. (I'm aware of two incidents since then when such software might have been used, and it probably would not have changed the outcome for either. Japan Airlines 123 likely was unlandable even with computer due to vertical stabilizer damage, and the DHL A300 damaged by a SAM at Baghdad in 2003 was landed successfully manually.)
I agree with you that "Main problem with computer control is trusting that the people writing the software properly anticipated all of the situations that could be encountered." However they don't need perfection - so long as they anticipate enough that computer-caused catastrophes are less common than human-caused catastrophes they prevent, it is a safety win.
I think there is a feet/meters confusion here. From the link in the AC post you're replying to, "... the 50-mile (80-kilometer) altitude used by US government agencies, including the FAA, for awarding astronaut wings." So AC meant 80km when they said 80K. I suspect (please correct me with details if I'm wrong) that you (reasonably) interpreted 80K as 80,000 feet and are saying Alan Shepard flew to 160,000 feet without it counting (by who?) as a space flight.
But the people who have the power to change the situation either don't know, don't think it is important, or don't care enough to act. Research like this can change one of the above.
"35 K is fine - I'm waiting for the 4wd trail rated version."
The model X ('crossover utility vehicle') is being launched sometime about now (I think a few hours ago.) As far as I know that is as close to 'trail rated' as they're currently planning to make. It probably has a price tag around $70k+ however. There is a 4wd version of the model S, so I expect model X will at least have that as an option, perhaps standard.
Mr Musk not only knows this, but changing this world in this way is Mr Musk's declared reason for founding Tesla Motors in the first place. The plan is to produce the Model 3 in a few years, which will have your 300km range, but current price is expected to be US$35k (neglecting government incentives for electric vehicles.)
What you're looking for is the Model 3 which does not yet exist, but has been Tesla's goal since inception. Everything we've seen up until now has been primarily done to gain experience and fund development towards the Model 3.
The Model 3 doesn't quite hit your targets - price US$35k, range 320km.
Lyme disease is bacterial, not viral. (Although maybe one day the methods used here will be able to be extended to the much larger genomes of bacteria.)
There are many people who will give bogus Lyme disease diagnoses. This might be what happened with your friend's wife. I haven't the knowledge or expertise to say more than 'it is a possibility'.
My understanding from a very quick skim of the paper (open access, here) is that they are not using microarrays. They have a mixture of a very large (2 million) number of probes to match DNA/RNA sequences of all known viruses which infect vertebrates. They use these to amplify viral sequences and then use normal high throughput DNA sequencing (Illumina, in this case) to see what they've got. They claim that it is sensitive to both DNA and RNA viruses (and all the variations - double, single stranded etc.) Being able to detect both DNA and RNA in a single test mildly surprises me, but I'm only slightly familiar with DNA sequencing technology, so maybe it isn't a big deal.
They do say "A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids." Perhaps that translates to say the microarray you talk about was used to make the 2 million probes.
As a complete aside, I'm a little surprised this isn't a Nature or Science paper.
An infrared cutting laser should be able to get in without completing any circuits. I'm not sure how portable they are (particularly in 1980.)
As well as an x-ray detector as an extra trigger, we could add temperature (detonate outside some range) and we could make the enclosure airtight and then pressurize (or depressurize) it and add a pressure trigger.
That is really cool, I didn't know about those. Thanks. For the sake of practicality, they'd probably be 600m from H. sapiens in the Ediacaran building, plus there'd be little sign beside the path from 'origin of life' to the main museum, at 2 km, to mark the correct location.
Wonderful - now all the scientific feuding over whether Amborella is the basal angiosperm can spill over into wiki edit wars.
(Amborella trichopoda is a New Caledonian flowering plant (angiosperm) with no close relatives. The deepest split in the angiosperm phylogeny may be Amborella splitting from everything else. Much ink and enmity has been spent on whether or not this is so. Here is a summary I found, although on a skim read I suspect it was written by a partisan.)
On my list of things to do should I ever inexplicably become astonishingly wealthy is to build a museum of phylogeny.
It would be a natural history museum, but with exhibits organized phylogenetically and the phylogeny would be represented by lines (mostly on the floor but branching out onto walls where needed) with a scale of something like 1 meter to 1 million years. (There would need to be an ongoing process of updating as scientific consensus changes.)
If you want to know how closely related you are to a chicken, you can walk it: start at H. sapiens, walk back to the mammal/dinosaur common ancestor, then forwards taking the correct paths until you reach G. gallus. The dinosaur part of the museum will be 65+ meters from the main part of the museum (representing the current day.) The main grounds of the museum will be about 550m long to cover Cambrian explosion to current day. About 3.5km away will be a much smaller museum about the origin of life. Somewhere in between will be a small museum about the origin of eukaryotes. At selected branching points on the phylogeny there will be metal cubes beside each branch, the volume of which are proportional to the now-living biomass descended from each branch.
There are some practical challenges in building this museum that I haven't worked out. Should I find myself with a few hundred million dollars and nothing better to spend them on, I'll give those challenges serious thought. (Or pay someone else to give them serious thought.)
How well do these systems work when their feedstock of CO2 is less than 0.5% pure (i.e. air)?
One of the niches they're looking to exploit is when renewable energy sources (primarily wind) are oversupplying so you can get your electricity very cheap or free (but only for a fraction of the time.) For this, they are going to be in competition with various industrial scale electricity storage technologies, which are not yet commercially viable in most situations, but are advancing and probably closer to viability than these technologies.
Slashdot Mirror
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.)
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.
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.)
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.)
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.
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.
New privacy violating technologies come along every few years. Road network layouts last centuries. It would be very foolish to let privacy-attack-of-the-day heavily influence your road layouts.
Although people associate uranium with radioactivity, it is only very slightly radioactive (half life > 1 billion years), so if you don't assemble a critical mass the danger is actually chemical. (Heavy metals have a strong tendency to be toxic.)
Other posters have said that here we are dealing with plutonium-239, which has a half life of 24000 years. That is orders of magnitude greater activity (shorter life) than uranium. I've reached the end of my knowledge here - which is worse, is the radioactivity or the chemical toxicity of plutonium-239?
TFA suggests they are worried about radioactivity: "A main concern has been that the remaining plutonium was being allowed to degenerate into other radioactive components like americium, which emits gamma rays that travel farther and are hard to block" but concern is not always well founded, and reporters don't always get it right.
Can you give details of this Airbus demonstration flight crash? I think you've got a garbled version of Air France flight 296. The plane did refuse the pilot's command to raise the nose, but that was to prevent a stall. At the time this pilot/plane conflict occurred, the pilot had flown the plane into a state where a crash was inevitable.
Inspired by the United Airlines flight 232 (the DC-10 crash you cite), software has been written to control planes by differential thrust, and to do so better than people can. As I recall, it was deemed to expensive to put it into service. (I'm aware of two incidents since then when such software might have been used, and it probably would not have changed the outcome for either. Japan Airlines 123 likely was unlandable even with computer due to vertical stabilizer damage, and the DHL A300 damaged by a SAM at Baghdad in 2003 was landed successfully manually.)
I agree with you that "Main problem with computer control is trusting that the people writing the software properly anticipated all of the situations that could be encountered." However they don't need perfection - so long as they anticipate enough that computer-caused catastrophes are less common than human-caused catastrophes they prevent, it is a safety win.
https://en.wikipedia.org/wiki/...
https://en.wikipedia.org/wiki/...
https://en.wikipedia.org/wiki/...
I think there is a feet/meters confusion here. ... the 50-mile (80-kilometer) altitude used by US government agencies, including the FAA, for awarding astronaut wings." So AC meant 80km when they said 80K. I suspect (please correct me with details if I'm wrong) that you (reasonably) interpreted 80K as 80,000 feet and are saying Alan Shepard flew to 160,000 feet without it counting (by who?) as a space flight.
From the link in the AC post you're replying to, "
But the people who have the power to change the situation either don't know, don't think it is important, or don't care enough to act. Research like this can change one of the above.
"35 K is fine - I'm waiting for the 4wd trail rated version."
The model X ('crossover utility vehicle') is being launched sometime about now (I think a few hours ago.) As far as I know that is as close to 'trail rated' as they're currently planning to make. It probably has a price tag around $70k+ however. There is a 4wd version of the model S, so I expect model X will at least have that as an option, perhaps standard.
Mr Musk not only knows this, but changing this world in this way is Mr Musk's declared reason for founding Tesla Motors in the first place. The plan is to produce the Model 3 in a few years, which will have your 300km range, but current price is expected to be US$35k (neglecting government incentives for electric vehicles.)
What you're looking for is the Model 3 which does not yet exist, but has been Tesla's goal since inception. Everything we've seen up until now has been primarily done to gain experience and fund development towards the Model 3.
The Model 3 doesn't quite hit your targets - price US$35k, range 320km.
"Oh look, a stampede, I think I'll join in and who knows, maybe I'll get to trample someone to death!"
That is so not what happened, whatever you may think. You have a severe case of bigotry.
Why hasn't this been moderated "troll" into oblivion?
Lyme disease is bacterial, not viral. (Although maybe one day the methods used here will be able to be extended to the much larger genomes of bacteria.)
There are many people who will give bogus Lyme disease diagnoses. This might be what happened with your friend's wife. I haven't the knowledge or expertise to say more than 'it is a possibility'.
Only if all the tests were for viruses.
My understanding from a very quick skim of the paper (open access, here) is that they are not using microarrays. They have a mixture of a very large (2 million) number of probes to match DNA/RNA sequences of all known viruses which infect vertebrates. They use these to amplify viral sequences and then use normal high throughput DNA sequencing (Illumina, in this case) to see what they've got. They claim that it is sensitive to both DNA and RNA viruses (and all the variations - double, single stranded etc.) Being able to detect both DNA and RNA in a single test mildly surprises me, but I'm only slightly familiar with DNA sequencing technology, so maybe it isn't a big deal.
They do say "A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids." Perhaps that translates to say the microarray you talk about was used to make the 2 million probes.
As a complete aside, I'm a little surprised this isn't a Nature or Science paper.
I was thinking along the same lines.
An infrared cutting laser should be able to get in without completing any circuits. I'm not sure how portable they are (particularly in 1980.)
As well as an x-ray detector as an extra trigger, we could add temperature (detonate outside some range) and we could make the enclosure airtight and then pressurize (or depressurize) it and add a pressure trigger.
I think there is a movie script in here.
That is really cool, I didn't know about those. Thanks.
For the sake of practicality, they'd probably be 600m from H. sapiens in the Ediacaran building, plus there'd be little sign beside the path from 'origin of life' to the main museum, at 2 km, to mark the correct location.
Wonderful - now all the scientific feuding over whether Amborella is the basal angiosperm can spill over into wiki edit wars.
(Amborella trichopoda is a New Caledonian flowering plant (angiosperm) with no close relatives. The deepest split in the angiosperm phylogeny may be Amborella splitting from everything else. Much ink and enmity has been spent on whether or not this is so. Here is a summary I found, although on a skim read I suspect it was written by a partisan.)
On my list of things to do should I ever inexplicably become astonishingly wealthy is to build a museum of phylogeny.
It would be a natural history museum, but with exhibits organized phylogenetically and the phylogeny would be represented by lines (mostly on the floor but branching out onto walls where needed) with a scale of something like 1 meter to 1 million years. (There would need to be an ongoing process of updating as scientific consensus changes.)
If you want to know how closely related you are to a chicken, you can walk it: start at H. sapiens, walk back to the mammal/dinosaur common ancestor, then forwards taking the correct paths until you reach G. gallus. The dinosaur part of the museum will be 65+ meters from the main part of the museum (representing the current day.) The main grounds of the museum will be about 550m long to cover Cambrian explosion to current day. About 3.5km away will be a much smaller museum about the origin of life. Somewhere in between will be a small museum about the origin of eukaryotes. At selected branching points on the phylogeny there will be metal cubes beside each branch, the volume of which are proportional to the now-living biomass descended from each branch.
There are some practical challenges in building this museum that I haven't worked out. Should I find myself with a few hundred million dollars and nothing better to spend them on, I'll give those challenges serious thought. (Or pay someone else to give them serious thought.)
You're right. I took 400ppm, turned it into 0.4 parts per thousand and then forgot the factor of ten for per-thousand to percent.
How well do these systems work when their feedstock of CO2 is less than 0.5% pure (i.e. air)?
One of the niches they're looking to exploit is when renewable energy sources (primarily wind) are oversupplying so you can get your electricity very cheap or free (but only for a fraction of the time.) For this, they are going to be in competition with various industrial scale electricity storage technologies, which are not yet commercially viable in most situations, but are advancing and probably closer to viability than these technologies.