Monthly Archives: December 2011

precious metals

Still diving down, some pundits expect this to continue for the next few months. Yet most see a long-term uptrend, and view this as a correction at best.

So the way to buy in is to wait for the price to pierce some moving average to the upside, right?

Along with GLD, suggestions include silver weaton and great panther.

Also, gold mining stocks, which have been punished this year, could payout big.
Lots of hype at:

Some claim the silver/gold ratio should be 16:1 (currently it is ~40:1),
there is roughly 16 times more silver in the ground than gold, thus the silver price will eventually reach one-sixteenth the price of gold.
which implies silver is currently undervalued by 2/3rds

Ivanhoe Mines Ltd. (IVN:TSX; IVN:NYSE)
Hunter Bay Minerals Plc (HBY:TSX.V)

Platz– German pre-fab homes

Gorgeous design, efficient, and all the info is in german.

Zarges– when you want your stuff to get there safe

Euro– they don’t want a resolution

An eye-opening article by Jeff Miller

The Euro crisis will not be solved any time soon. Why not? Because politicians live off of crisis.

The EU cannot create wars (unlike certain other countries), so they do this instead, giving them the excuse to push through policies which would otherwise be impossible.

I should probably spend some time on Miller’s blog…

Britta Riley: A garden in my apartment

Britta Riley: A garden in my apartment

Wanted to grow her own food, in a NY city apartment. Started window gardens, which use hydroponics. She can grow a salad a week.

Hydroponic technology is rapidly being patened away from us. Her website is an open-source collaboration of designs and technologies, an effort to keep hydroponics in the public domain.

She calls it R&DIY, instead of R&D.

Annie Murphy Paul: What we learn before we’re born

Annie Murphy Paul: What we learn before we’re born

No surprizes here. The mother passes tons of information on the environment to her unborn fetus, which then adopts to it.

I post this in support of my theory that birthplace has huge determinants in one’s comfort zone, a comfort zone I have been living outside of for many too many years. Poor badger

Luis von Ahn: Massive-scale online collaboration

Luis von Ahn

The guy who came up with capchas. His next idea was to use them to digitally scan books. When you have two words, one is known to the computer and the other is the scan. Average the scan word over 10 respondants to get the “correct” interpretation.

His next project: Duolingo. You learn a language for “free”, and in the mean time translate the internet. The key is to average user interpretations to arrive at a correcdt translation.

My winter king

This is a poem by Astrid, about a snow leopard.

Come here my winter king.
Your breath makes the bells ring
One look from your eyes and I’m in love

Come now, I’ll leave my glove
I can stroke your soft winter fur
your jet black spots, and hear lovely purr.

Come here my winter king.

Molecular Clocks and the puzzle of RNA virus origins –Holmes 2003

Journal of Virology

Dr. Holmes investigates why phylogenetic dating of viral speciation implies that the major RNA virusus originated not more than 50,000 years ago, yet their hosts speciated many millions of years in the past.

One problem is the rate of replication, which is roughly 10^-3 subs/site/year (21), which further implies the average distance between any two sequences is limited to 500 years (since after 1000 years, every position will have mutated). Better to look at non-synonymous sites, assume the rate is 10^-5, and put the divergence at 50K years ago. Voiala.

So, do virus change their mutation rate? Is it because once adopted to their host species, they don’t drift very much? No. Adoptation does not give RNA a repair mechanism, and mutation at synonymous sites doesn’t slow down.

Perhaps different parts of the genome mutate at different speeds? Likely:

An important evolutionary by-product of these high mutation rates is a cap on genome size; genomes larger than ∼15 kb are rarely produced because of the “error threshold,” the generation of a prohibitive number of deleterious mutations (11). Since viral genome sizes are limited, sequence regions will encode multiple functions and individual mutations will often have pleiotropic effects, such as those influencing both cell tropism and immune evasion (1). This, in turn, may mean that there are relatively few evolutionary pathways that can be followed by RNA viruses; otherwise, at least one key function will be disrupted, so that mutations preferentially accumulate at that small proportion of sites that are free to vary. Supportive evidence for such a model is the frequency with which convergent evolution is observed for RNA viruses (4, 7, 13), as expected if only a limited number of evolutionary pathways are viable, and the evidence that RNA (37) and protein secondary structure (22) can act as constraints against sequence change.

Helpful to use a (skewed) gamma distribution to allow the rate to vary along the chromosone.

low α values (i.e., <1) mean that the sequence alignment is composed of both very quickly and very slowly evolving sites, and this appears to be true in most cases.

the three groups of flaviviruses, the mean d at these sites, corrected for multiple substitutions but without a gamma distribution, is ∼0.25 and is similar to the nonsynonymous distance estimated previously. The maximum likelihood estimate for the shape parameter of the gamma distribution for these data is highly skewed (α = 0.34). As expected, evolutionary distances increase if they are now estimated using this gamma model (mean d = 0.43), although not sufficiently to make a major difference to estimated divergence times, which only increase to a little over 20,000 years (again assuming a rate of 10−5 substitutions/site/year). However, more dramatic results are obtained if an even more skewed gamma distribution is used. If α = 0.1, then d increases to 2.3, so that maximum divergence times will be in the region of 100,000 years ago


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Silk road tor
Keepon robot