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* Posts by MondoMan

335 posts • joined 8 May 2007

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Japan plans SEVEN satellite launches to supercharge GPS

MondoMan
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Pint

Re: "The corrected data is then compressed from 2mbps to 2kbps..."

"Really? 1000-to-1? It's not really very interesting data then is it?"

It's not the size, it's how you use it.

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MondoMan
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Facepalm

Is this just WAAS?

Is this perhaps just the super-accurate Japanese version of the US WAAS system? Essentially, a Differential GPS system broadcasting the corrections from a geostationary satellite?

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Most Americans doubt Big Bang, not too sure about evolution, climate change – survey

MondoMan
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Re: @ John Smith 19

You wrote a last throwaway:

"And of course there are the home countries of all those work visas coming into the US.

Japan, China, Singapore, S. Korea etc.

Not known for their Christianity, are they?"

Actually, South Koreans are well-known for the speed and intensity with which they have embraced Christianity.

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MondoMan
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Re: the questions

Very poorly written, so you've got to wonder about the skills of the authors of this survey, or whether they were trying to get a certain response.

For example, "The average temperature of the world is rising, mostly because of man-made heat-trapping greenhouse gases". While it's true that we are emitting an ever-rising amount of these gases, which should lead to more heat-trapping according to simple physics, it's also true that even the IPCC in its latest report has admitted that the average world temps have not risen during the past 10-15 years. So, the IPCC (and I along with them) would have to answer "Not at all confident" on this one.

Or, for a question supposedly designed to focus on the Big Bang: "The universe began 13.8 billion years ago with a big bang." Now, I'm a believer in the Big Bang theory, but have no idea whether the current estimate of the age of the universe is 10 billion years, 13.8 billion years, 15 billion years, or some other number in that general ballpark. I'd have to answer at best "Somewhat confidant" just because of the specific age issue.

Bottom line: good survey questions isolate a single issue at hand in each question -- they don't jumble multiple facts/issues as was done in many of these questions.

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Algorithm ramps up genetic computation

MondoMan
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Thumb Up

Re: not bad.... but..

@Grikath: "And it wouldn't show the actual level of expression, "

It *will* show the stead-state relative level of transcript abundance, which I know isn't the same thing, but tends to be related.

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MondoMan
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Boffin

Neato torpedo!

Perhaps this will help clarify the researchers' work:

DNA serves as the blueprint/instruction manual for the cell. However, the information in the DNA must be converted to other forms in order for it to perform any function, that is, to be "expressed". Thus, "gene expression" is just what function(s) are performed by an individual gene, and *how much* of that function is performed. The term is also used to refer to all the genes in the cell: all the functions being performed, and the level/amount of each function.

The cell uses many ways to regulate gene expression (to adjust the levels of different functions), most of which are difficult to measure and ascribe to a specific gene function when looking at all the functions of a cell. This paper is concerned with only the initial step of gene regulation -- "transcription". Transcription is simply the copying of modest stretches of DNA into sequence-identical working copies made of the similar molecule RNA. Essentially, it is like photocopying specific blueprint pages from the manual. Just as with a paper manual and photocopying, one simple way to get more use out of a single blueprint page in the manual is to make many photocopies of it. One can get a rough idea of what's being done on a project just by looking at all the photocopies in use there -- many copies of a given page or group of pages suggest much work on the function related to those pages, while a complete absence of a given page suggests no work currently being done on that function.

Similarly, collecting all the RNA transcripts from a group of cells, determining the sequence of each, and matching those up with the entire DNA genomic sequence allows one to infer which gene functions are in heavy use, light use, or unused. (Of course, given the other types of gene expression regulation, this will be an important, but partial, description of the gene expression in the cells.)

The researchers' new technique comes in the "...matching those up with the entire DNA genomic sequence..." step. Current bulk transcript sequencing techniques produce sequence fragments ("reads") on the order of 500 "letters" or "bases" long (DNA and RNA each have 4 possible letters). Since the entire genomic sequence in mammalian cells is about 3G bases long, and each cell typically has two copies, each transcript read must be aligned with 6G of genomic sequence. A simplistic sliding-comparison alignment algorithm would involve on the order of 10 to 1000 x 10^9 comparisons for just *one* transcript read; a proper experiment would involve mapping 10^6 or more reads so the number of comparisons (and compute time) rises rather rapidly!

By contrast, my understanding of the researchers' new technique is that they use a k-tuple approach which in principle requires compute time only linearly proportional to the total transcript read sequence lengths plus the 6 x 10^9 genomic sequence. The insight is that by breaking down the transcript reads into overlapping "tuples" of length k, and just counting how many times each k-tuple appears in the entire set of transcript reads, an expression "bar chart" can quickly be constructed on the genomic sequence.

For example, if one chose k=10, one would have 4^10 = 1048576 or approximately 1M possible 10-base-long tuple sequences. One would then go through all the (say, one million) transcript read sequences, producing about 500 tuples from each (500 bases average length, tuples offset by 1), or about 500M total. If the transcript read sequences were completely random, each of the 1M possible 10-tuples would have about 500 "hits". However, we know the sequences are NOT random, and in particular much of the genomic DNA will not be transcribed at all, so we expect many (most?) 10-tuples will show zero/few hits, and some more than 500.

To "read out" the results, one would just move along the genomic DNA sequence, shifting over one base at a time, and look up the transcript read hit count for the 10-tuple beginning at that position in the genomic sequence. While there might be short spurious peaks and valleys, in general, an expressed gene fragment would show up as a contiguous stretch of DNA where most positions showed roughly-equal levels of 10-tuple hit counts. The average hit count level would indicate the relative expression of that gene fragment.

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Liftoff! SpaceX Falcon 9 lifts Dragon on third resupply mission to ISS

MondoMan
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Alien

Soft landing's real use is on Mars

Elon has stated he wants to send a manned mission to Mars, which interestingly enough has no oceans for splashdowns and not enough atmosphere for parachutes all the way down.

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Red-faced LOHAN team 'fesses up in blown SPEARS fuse fiasco

MondoMan
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Pint

Re: glass vs blade fuse

The automotive-style standard and mini blade fuses I'm familiar are *much* harder to visually evaluate, and must be viewed from the side. The glass tubes are easy to evaluate from any angle, even if buried in a circuitry box. As a final bonus, they float if dropped in your beer.

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Borked Bitcoin bunker MtGox in administration: Lawyer seizes control

MondoMan
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Big Brother

This has all happened before

A few years ago, back when Bitcoin had soared and had hit the heady value of 30 USD (and when people still used graphics cards to mine BTC!), Mt Gox suffered an enormous theft, other large thefts/scams were in the news, and BTC dropped about 10x in value. Many proclaimed the end of Bitcoin and the press lost interest...

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Spy-happy Condoleezza Rice joins Dropbox board as privacy adviser

MondoMan
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Re: What did Rice do for DropBox or top people there to land a cushy deal

She was also provost of Stanford University for many many years; since Stanford founded and nurtures Silicon Valley, that's not a bad link to have on board.

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MondoMan
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Devil

Re: the Italian courts

The Italian courts are also retrying Amanda Knox yet again for a crime she didn't commit, even though they have the true perp convicted and in jail.

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MondoMan
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Devil

Re: internal contradictions were the only thing that brought down the Soviet Union...

Yes, just like with Lukashenko's Belarus.

Oh, wait.....

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In Australia, protesting against Brendan Eich will be a CRIME

MondoMan
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Megaphone

Re: Is this really a freedom of speech issue?

In the US, we tend to have an expansive view of free speech. If you can't contribute to support a political cause you believe in, your free speech is being limited, just as if someone stopped you from going around putting posters on notice boards, or paying for those posters, or paying for the taxi fare to pickup the posters, and so forth.

It's also worth noting that the legislative/legal issue is not about a right, it's about government recognition and support of a specific pre-existing social arrangement that it believes to have benefits for society as a whole. The government doesn't recognize marriages between very young people, or between more than two people, and so forth -- it's not technically a "right". The government (via the legislature, via the voters) decides what social arrangements it will officially recognize, and as long as there's some non-wacko reasoning behind it (even if many think that reasoning wrong), the courts don't get to over-rule the decision.

I'm glad that more and more people are realizing that government recognition of same-sex marriage has a positive effect on society and it seems a shame for some late-to-the-party zealots to single out someone's political contribution from 5 or 10 years ago without also attacking the others who did the same or similar, such as the Clintons and President Obama (those who pushed to impeach President Clinton and/or President Obama due to each's furtherance of the federal Defense of Marriage law are of course exempt from being called hypocrites here :) ).

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Get ready for software-defined RADAR: Jam, eavesdrop, talk and target ... simultaneously

MondoMan
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Linux

The TRUE reason they need to run at 100% duty cycle:

Otherwise, they'll quickly fail once the Chinese hackers start running their Bitcoin miners.

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El Reg's Deep Outback XP upgrade almost foiled by KILLER ARACHNIDS

MondoMan
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Pint

And I thought the American West was sparsely populated!

Here's hoping you don't run across the Night Rider...

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US judge tells Marvell to pay Carnegie Mellon Uni $1.5bn in patent fallout

MondoMan
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Re: There is a point...

If the Supreme Court refuses to hear the case, the case's most recent court judgment stands.

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Don't look at Maria's SQL, look at MY SQL, pleads Oracle

MondoMan
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Joke

SSDs

I used a stratified (sometimes also known as "sedimentary") filing system on my "solid state desk". The chief failure mode is when I spill my glass of milk on it...

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Can you tell a man's intelligence simply by looking at him? Yes

MondoMan
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FAIL

Bogus methodology

If you read the paper, they used a quadratic(!) model rather than a linear model for the correlation between facial attractiveness and IQ. Looking at their graph, not only are the data points clearly NOT forming anything like a parabola, but their computed parabola implies that past a certain point, more attractiveness would imply a *lower* IQ!

I guess the lesson is that given sufficiently noisy/scattered data, you can force it into any model you want.

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IBM PCjr STRIPPED BARE: We tear down the machine Big Blue would rather you forgot

MondoMan
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Is monitor really a shadow mask model rather than aperture grille?

Looking at the photo of the monitor screen, the vertical cutoffs of each stripe segment seem awfully sharp for it to be an aperture grille. I wonder if it's not really a fancy shadow mask, such as the "in-line" shadow mask example (labeled '21" TV CRT Display') shown in the Wiki entry for shadow masks:

http://en.wikipedia.org/wiki/Shadow_mask

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Byzantine Generals co-boffin Lamport bags CompSci's 'Nobel prize'

MondoMan
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Pint

Definitely a beer icon dude!

Reading through his pubs list (thanks for the link!), I am struck by the humor in his parenthetical descriptions of each publication or the circumstances of its creation. Academic IT in general seems to nurture more humorists than do fields such as biology, or perhaps it just doesn't frown on their work ...

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Seattle pops a cap in Uber and Lyft: Rideshare bizs get 150-driver limit

MondoMan
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Re: @stu4

The new law will require that Lyft/etc drivers be specially licensed and their cars inspected by the city, that the organizing company carry liability insurance that covers them while on duty. That should hopefully cover the tax/safety issues.

Customer recourse is notoriously poor even with the current Seattle taxi companies. The City Council has promised to improve current regulation of for-hire rides. We'll see what happens.

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MondoMan
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Re: Final Seattle vote was unanimous

Thx for the fixes!

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MondoMan
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Pint

Final Seattle vote was unanimous

http://blogs.seattletimes.com/today/2014/03/seattle-city-council-approves-lyft-uberx-and-sidecar-driver-caps/

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Previously stable Greenland glaciers now rushing to the sea

MondoMan
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Facepalm

Regarding the models

If these are the current models, they don't yet include physically accurate modeling of clouds (they parametrize them, but the real-life parameter values are still unknown), and didn't predict the recent loss of ice cover in the Arctic and the increase in ice cover in the Antarctic. I'm not sure I'd yet want to rely on them for predictions about the year 2100.

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BT caught in data gaffe drama: Whistleblower squeals over alleged email fail

MondoMan
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Re: intentionally wrong answers

But if the miscreant has access to the complete list of correct "wrong" answers (as above), the fact that they're wrong IRL doesn't help much. If you use sets of different wrong answers with different services, that will at least help firewall the pwning.

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Global Warming IS REAL, argues sceptic mathematician - it just isn't THERMAGEDDON

MondoMan
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Re: New Scientist overview

I checked it out -- as it's dated 2007, it turns out to be seriously out of date on some of the most controversial issues, such as the current so-called "hiatus" in global surface temps and the "Hockey Stick" controversy.

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MondoMan
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Childcatcher

Re: At what point...

I find it useful to compare predictions with what's happened in the recent past in order to gauge possible consequences. For example, we've measured the world's surface temps rising about 0.75C on average over the past 130 years, which includes both the 1900-1940ish warming and the 1975-2000ish warming. AFAIK, storms, flooding and so forth are not significantly worse today than in 1880.

If the *rate* of warming increased dramatically (say, 5x) over that seen in the past 130 years, I'd be much more concerned about taking *dramatic* and *immediate* action. As it is, it seems to me that another 10 years of research might really help clarify the situation (there's always the hope that the climate modelers might have figured out if clouds have net positive or negative feedback by then :) ).

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MondoMan
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Re: Orlowski supporting climate change is the REAL news

Ronny, if the climate system does indeed have a low sensitivity to added CO2 and other human-affected greenhouse gases, then the islanders will be fine for hundreds or thousands of years yet. Most of the other climate scientists we hear about in the news have been working on subfields with inherent massive unknowns/uncertainties that make them much less useful for current policy.

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MondoMan
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Re: Forth Byte.

I remember that one - Byte sure had nice cover art back in those days. But programming anything at all complicated in Forth messed up your head even more than HP RPN calculators!

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MondoMan
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Pirate

ecosystems and sensitivity

Ecosystems usually tend to be pretty robust; if they weren't, they'd die off the first time day became night or spring became summer.

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MondoMan
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Paris Hilton

Re: windpower not practical to reduce hurricane damage

Sadly, it's not to be believed by realists, since the modeled reduction in storm surge is as low as 7% even for a giant array of 86,000 (yes, 86 thousand!) wind turbines located in an offshore wedge to the SW of New Orleans. Of course, the storm also has to approach from the SW. Thus, "full" protection for New Orleans alone would require 500-600,000 (yes, half a million or more!) turbines.

Not sure how many would be needed to protect Paris...

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MondoMan
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Re: To the first AC:

"Averaged over all land and ocean surfaces, temperatures warmed roughly 0.85ºC from 1880 to 2012."

You've got the wrong units. According to data such as NOAA's (http://www.epa.gov/climatechange/images/indicator_downloads/sea-surface-temp-download1-2013.png), it's roughly 0.85 degrees F, not C. Your naive linear extrapolation to 1.5 degrees F of increase by 2100 is about 0.85 degrees C (strangely enough), which seems to fit well with Lewis' work reported in this story, and to be much lower than the 2+ degrees C warming you warned of without any calculations.

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MondoMan
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Joke

Re: Oooh, for a second, I thought this was going to be another Lewis article!

3 Dogecoins for a bag?

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Dell thuds down low-cost lap workstation for cheap frugal creatives or engineers

MondoMan
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Re: What's the point?

Isn't the HP220 a desktop, not a laptop?

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NASA robot plans mid-2020s trip: Europa. Wet, radioactive life forms (hopefully). Bliss

MondoMan
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Black Helicopters

Re: I'm not sure if I'm missing something here

Errr, wouldn't Putin be the one to go to "...to not worry about borders?" Surely he could find some extra billions dropped behind the Crimean sofa or rolling around the Sochi sledding track.

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'Polar vortex' or not, last month among the WARMEST Januaries EVER RECORDED

MondoMan
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Re: Rik, YOU get to choose what to write...

So I'm puzzled why you're touting one-month long averages, then discussing longer-term destructive weather as if it's somehow related. For example, as someone based in California, who is presumably drinking Hetch-Hetchy water, you should know that serious droughts are multi-year events because it takes years of low snowmelt to draw down California's extensive reservoirs. Yet, you write

"Here in the western US, we had the driest January since 2003 and the fifth driest on record for the lower 48 – and California governor Jerry Brown declared a drought state of emergency"

as if the former had something to do with the latter. You're better than that, Rik.

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Harvard student thrown off 14,000-core super ... for mining Dogecoin

MondoMan
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Alien

Alien Genome Mapping Project

Hey, if your bit of the work had included a genuine alien signal, you would have been hailed for creative use of resources!

Me, I'm just hoping the bodies frozen at Area 51 are *not* in a frost-free freezer. Bad stuff can happen when it periodically warms up to melt the frost...

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Google picks five teams to share $6 MEEELLION funding in Lunar X Prize

MondoMan
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Pint

vehicle names?

Presumably, they should all be tortoise-themed, as the (Jade) Rabbit currently has the lead in the race...

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Speaking in Tech: $65 JUST for internet and my ISP has the BALLS to throttle a service?

MondoMan
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Alert

Ms. Vela's "enthusiastic" vocabulary this week

Wow! I'm so used to bleeps (most of my podcasts are of normo-broadcast shows) that I was cringing every time, subconsciously expecting the language censors.

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MondoMan
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Aussie "horseless carriages"

Come on, we all know from the Mad Max movies that you've got some pretty badass "horseless carriages" out there!

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China confirms Jade Rabbit lunar rover has conked out

MondoMan
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Joke

Re: "Pilyugin"

And I thought you were going to make a tech support "have you checked if it is Pilyugin?" joke...

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MondoMan
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IT 0, LP 1 (but don't worry, it's not about climate change)

IT:

"Mars probe Curiosity dumped solar panels altogether in favor of a nuclear heart. That rover uses a basic nuclear power system to provide energy for getting around, but also to keep the rover warmish during nighttime periods. The reactor should outlast the rest of the rover's parts by years."

LP (in linked article):

"Curiosity will generate both heat and power from its Multi-Mission Radioisotope Thermoelectric Generator unit, build by the nuclear-space boffins of the Idaho National Lab. A radioisotope generator isn't a reactor - it doesn't use a chain reaction to accelerate fission in its plutonium. "

So technically, no "nuclear power", no "reactor", just natural radioactive decay...

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'Wind power causes climate change' shown to be so much hot air

MondoMan
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Surprised by RC's statement!

He writes:

...the effects are lost in the noise, or in the more cautious terminology of a scientist, the impacts of wind farms “remain much weaker than the natural climate interannual variability”.

The global surface temperature record is famous for its squiggliness (that is, for its interannual variability). Just about all reasonable folks also agree that this record's warming over the past century is much weaker than that interannual variability; however, I don't see anyone arguing as RC presumably would that that means the last century's warming is "lost in the noise".

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MondoMan
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Re: Urban heat island effects sadly not well-studied

Just wanted to note that urban heat island effects have NOT been well-studied for decades, or even one decade. Proper quantification and analysis of various effects on measured land surface temperatures has been signally lacking, with much hand-waving seeming to be its replacement if you actually read the papers that mention it. This may be due to the lack of a proper, organized government bureau doing the measurement and analysis, rather than the small, underfunded research groups that are in fact the maintainers of the temp indices. Imagine if we depended on a few poorly-funded and ill-equipped volunteer scientists to determine monthly employment numbers, factory utilization and similar economic stats! Wall Street/The City would be up in arms! It's a real shame that no one is willing to set up a proper climate statistics bureau that produces accurate, high-quality numbers that everyone can have confidence in.

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Bitcoin value plunges as Mt.Gox halts withdrawals and Russia says 'nyet'

MondoMan
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Why would anyone trust Mt Gox in the first place?

It's not like they have a track record of stability and security...

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Just as we said it would: HP clamps down on server fixers

MondoMan
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Re: Flashing new MBs to match old ones

Donn, just save a copy of the current BIOS image, and use that to flash any new replacement MB you need to swap in.

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'That was quick!': AT&T ends $450 T-Mobile poaching promotion

MondoMan
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TMob vs Sprint//////Crawl

All I know is that TMob's HSPA+ beats the pants off my old Sprint, even with WiMax. Plus, it's actually widely available here in Seattle,

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Gene boffins: Yes, you. Staring at the screen. You're a NEANDERTHAL

MondoMan
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Not 20%, rather 2% *per individual*

What the Reg hack didn't make clear here is that each modern individual's genome only has around 2% (roughly 0-4% range) of Neanderthal DNA. *Which* 2% varies from person to person; among the whole set of modern people sequenced (perhaps a few thousand?), all their Neanderthal DNA when grouped together comes from about 20% of the Neanderthal genome. Some parts of the Neanderthal genome are found again and again in different modern individuals, suggesting that they conferred some regional survival advantage over the African sequences that would otherwise be found in those locations.

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Google cleared to land in private terminal at Silicon Valley airport

MondoMan
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To Folsom?

Isn't that a prison?

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