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Comment Re:How could the Earth heat it? (Score 1) 96

I've shown the claim is implausible, not impossible. I'd be interested to see what evidence there is to support it.

I don't see the need for the claim from an evolutionary point of view: there is no reason I am aware of to suppose that current tides are insufficient to drive organisms to evolve into terrestrial niches.

Comment Re:How could the Earth heat it? (Score 1) 96

What happened 4 billion years ago is not the point - the claim was made in the context of the 'conquest' of the land by multicellular life, which was only about 0.5 billion years ago (not 1 billion, as I used in my analysis, and so tides were likely only about 15% higher then.) I agree that tidal conditions were very different four billion years ago, and that my linear extrapolation would not apply so far back.

10% (for a billion years, or 5% for 500 million) is a small enough change in distance that we wouldn't expect the recession rate to have changed a lot over that time. This is a somewhat weak point in my argument - the recession rate of the moon is largely dependent on how many Bay of Fundys there are in the world, so the current rate may not be typical. However the argument is strong enough to place the burden of proof on those making the claim: you claim an effect an order of magnitude greater than simple analysis allows for. Show evidence for these tides, or a well founded model which predicts these tides (at the required time.)

Comment Re:How could the Earth heat it? (Score 5, Interesting) 96

1 billion years ago the Earth had 100 to 1,000 foot tides as the Moon and the Earth were much closer

My initial response is "I don't think so." My second response is to calculate, so here goes:
Current distance to moon = 384,400 km = 4 x 10^8m
Current rate of increase in distance to moon = 3.8 cm/year = 4 x 10^-2 m/year.
If this rate were constant over a billion (10^9) years, then a billion years ago the distance to the moon was 4 x 10^-2m/year*10^9year = 4 x 10^7 m closer, or 10% closer. Tidal effect strengths are inverse-cube in distance, so a billion years ago, lunar tides would have been about 30% larger than now.

This doesn't come close to "100 to 1000 foot tides."

Comment Re:I could be missing something (Score 3, Informative) 96

As seen from the moon, the Earth is only about two degrees across, so the proportion of projectiles blocked by it would be miniscule. Even that small effect is reduced (possibly beyond zero) by 'gravitational focusing': projectiles which come towards the moon from the direction of the Earth which would otherwise have missed can be deflected by Earth's gravity such that they hit. (And this happens more often than projectiles that would have hit being deflected so they miss.)

Here is a paper I found on gravitational focusing.

Comment Re:So which is it? (Score 1) 115

This is a quibble, but non-volatile RAM has only been the Holy Grail since about 1970. Prior to that, magnetic core memory was the standard RAM technology and is non-volatile. (To quibble the quibble, for a short period of time Williams tubes were the state-of-the-art (indeed, only) RAM, and they are volatile. Alan Turing played with Williams tubes.)

Comment Re:Not a huge surprise (Score 4, Informative) 208

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...


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.

Comment Re:Not a huge surprise (Score 5, Informative) 208

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.

Comment Re:Background information, link to paper. (Score 1) 208

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.)

Numeric stability is probably not all that important when you're guessing.