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Submission + - An Excursion To Slashdot Terra Incognita: Hacking The Bible (christianitytoday.com) 1

An anonymous reader writes: Christianity Today reports, "From If someone releases a new API (code that lets applications interact with each other), or if Google unveils a new tool in beta, or if a new dataset is published online, it's a fairly safe bet that Smith will try to connect it to the Bible. In 2012, Stanford University published a Geospatial Network Model of the Roman World. Smith used it to calculate the time and cost of each of Paul's missionary journeys. The photo-sharing site Flickr lets users search by GPS coordinates, and he created a tool to feature contemporary photos of Bible places. Smith also used Flickr's API to look up each word in each Bible verse, grab the top 30 photos for each word, layer them on top of each other, and then take all the images from all the words in each verse and layer them on top of each other. That experiment didn't turn out well. Almost every verse just becomes a big orange blob. But it was an interesting idea. Smith's new idea isn't so innocuous. It's scary. And Smith knows it. But he loves it anyway. The Franken-Bible "There are about 30 modern, high-quality translations of the Bible in English," Smith announces to the BibleTech group. "Can we combine these translations algorithmically into something that charts the possibility space of the original text?""

Comment A lot of the same...and some I didn't see (Score 1) 531

My list:
-Vim (usually I'll go for a motif build of gvim).
-Links2 for a lightweight browser that works with many websites in text, framebuffer, and X11.
-Iceweasel (preferred) or Firefox for a full browser.
Chrom{e,ium} and Midori don't cut it; I liked a number of the features of Opera, but not everything. QtWeb is nice when it works but doesn't have enough security updates (WebKit has fixed several vulnerabilities since the last release).
-xli and fbi/ida for image viewers. (Yes, I use three: one for framebuffer, one for a quick view in X, and one for going through photos and making small adjustments).
-xpdf for a PDF viewer, preferably with a certain small patch.
It's fairly light, doesn't waste much screen, and has rectangular selection. Ever tried copy-pasting from a 2-column pdf that was output wrong?
-ksh (OpenBSD pdksh, ksh93, or mksh. NOT oksh.)
Floating point shell math as in ksh93 is nice.
-Ted for a word processor. Yes, it's almost forgotten, and it only edits RTF. But it displays RTF right, and writes RTFs that show up the same anywhere else. When you could end up using any version of Microshaft Office, Wordpad, OpenOffice/LibreOffice, Textmate, or even vde, that's nice.
-mpg123 is great for audio...
-ffplay or vlc for video
-Xiphos and libsword
-gcc, python, dc, groff/nroff and man.

Submission + - CDE 2.2.1 is released. (sourceforge.net) 1

idunham writes: Version 2.2.1 of the Common Desktop Environment was released on March 1, featuring several bugfixes/warning fixes/portability improvements, localization, and a new port. UTF8 support has been greatly improved, to go with a new Greek UTF8 translation; an en_US.UTF8 locale was also added. dtinfo now builds and works (at least on Linux and FreeBSD). The new NetBSD port expands the BSD support to the big 3: FreeBSD, NetBSD, and OpenBSD.

Comment Re:You've been snookered (Score 1) 170

Looks like an herbal product trade group; that said, I'd hesitate to describe this particular one as "crackpots".
I expect the "Botanical" would be better read as "Botanicals", which is very roughly "plants used for non-food purposes".
That disclaimer is virtually mandated by US laws.

Full disclosure:
I'm an ag major who comes down on the side of conventional agriculture. While I was still at the university, I knew some people (professors included) interested in "alternative medicine", partly because of the restrictions related to organic production.
My impression of alternative medicine is that it's a very mixed bag, with too much room for quacks in a field that could include legitimate work.

Comment Re:Difficult article (Score 1) 116

Besides criticizing Twitter, he praises newspapers.
Several of his points are good, but...

Random or structured search instantly possible (go directly to what you want without complexity or scan for higher level content without additional cognitive complexity. This type of information-seeking and process-switching is every site designer's dream although impossible to acheive.)

Um, what?
I can scan a newspaper page in probably 15-20 seconds (5-10 seconds for a very quick overview).
Then read the relevant section, in another 30 seconds or so.
Of course, a third of the stories require a reference to another page, which you must go fumble for to get a clue what they're talking about...

Meanwhile, I could have used Google, or pressed Ctrl+F or /, and found what I was looking for pretty quickly.

Overall, he manages to point in the general direction of problems, but making it into content that actually can be meaningfully applied is something he completely misses...
like all too many "UX designers".

Comment Re:Good luck keeping the genie in the bottle (Score 1) 215

Those who say that genetically modified products are safe are not necessarily saying that all GMOs are safe.

Genetic modification is a process which leads to a food with a different genetic profile than the original stock it came from.
It's quite possible to introduce a toxin this way, or an allergen; it's also possible to increase production of a vitamin, or to make a change that has no effect on the food portion. And it may be possible to reproduce the genetic code of a different species (which is what most of the de-extinction efforts are trying.)
And since it is a process, there is not necessarily any genetic or phenotypic characteristic in common between two GMOs.
So the obvious answer is to test everything and approve what is found to be safe.

Now, to finish the point, a genetically modified product has already been tested. Those who say that it is safe are not stating that it never should have been tested; they are saying that the testing was sufficient.

Comment Re:seems a bit strange (Score 1) 341

That said, why not make the agro businesses that make huge profits pay for unbiased testing in order to license the product?

The problem is that if they fund it, how do you ensure that the "third party" is unbiased?
And how likely are opponents of GMOs to consider it unbiased? I suspect that even if it did reduce the level of bias, you would hear as many people complaining that it can't be trusted. And perceptions may be as important as facts when it comes to getting the regulations changed.

...some pro-GMO person claims "Well our vitamin A rice".. but they neglect the "Terminating seeds" which reap huge profits for these companies.

There's a couple of things I'd like to point out:
1: If someone objects to all GMOs, they object to even the most beneficial ones. Vitamin A rice is a reasonable argument against those who want to ban GMOs. It's not a good argument against testing, but I've not seen it used that way myself.
2: If you are referring to the "terminator" traits where F2 is infertile rather than male-sterile lines, those have not been included in many seeds. In fact, the USDA currently does not list a deregulated corn or soybean terminator trait.
My understanding is that Monsanto had developed such a trait, which they intended to use to prevent accidental cross-pollination; but when people objected to it, they dropped it.

Male-sterile is quite different from the "terminator" trait; it prevents production of fertile pollen, so that a hybrid seed breeder does not need to hire people to go through the whole field and remove the male flowers from every plant that's supposed to be a female parent in the cross. It does not influence fertility of seeds.

But the reason for not saving and replanting seeds is that almost all seed is hybrid. This means that the second generation is likely to give you a level of variability that renders mechanized harvest impractical, as well as having lower productivity. And hand-harvesting corn is not something that pays off.

The FDA is swamped, sure. They don't need to be the testing company, they could be the gatekeepers for smaller independent companies to do testing. In other areas, like pharmaceuticals the cost of testing is assumed in the product. The same thing should be done with GMO foods, because the majority of the purposes are not altruistic but profit driven.

I did not mention cost as an issue because I'm well aware that there's quite a bit of testing in development of any crop.
I interned at Pioneer one summer collecting soil moisture measurements for drought stress trials, and they mentioned the scale of the testing.
A crop is usually tested for at least five years. Trials runs about $2000 per acre per year for corn, and there are always
several evaluations (resistance to pests, drought tolerance, nitrogen use efficiency, and so on) and they are replicated at 4-5 sites.

In pharmaceuticals, you still hear people claiming that there is bias, and once in a while you hear about trials that were tampered with.

Comment Re:'no definitive conclusions can be reached' (Score 1) 341

Don't forget about Lenape potatoes. Even if the study was correct, the same sort of problem has happened with conventional breeding.

"Plant-incorporated pesticides," to use the ag term, are not new pesticides. They are old ones in a new place.
For example: BT corn. It gets its name, and its effectiveness, from Bacillus thuringiensis, a bacterium that is a selective insect killer (different strains target different insects).
B. thuringiensis has long been used as an organic pesticide.
Pesticide resistance and tolerance are also not new traits; they come from species that were exposed to the pesticide and turned out to be resistant or tolerant.

The reason for the focus is that a farmer can lose most of his crop to certain major pests and diseases. It makes more sense to prevent crop loss while keeping yield potential constant than to increase yield potential 20% while still risking 80% of the crop.

Besides, that's not all that GMOs are developed for, though most are. Drought tolerance research has been in progress for a while, and at least one of the varieties has been approved.
And there's high lysine corn, high oleic acid soybeans, soybeans modified for improved yield, soybeans modified to produce stearidonic acid or have a better fatty acid profile, reduced nicotine tobacco, and reduced lignin alfalfa.

Comment Re:seems a bit strange (Score 1) 341

And I think you did not read that paper thoroughly, or have no clue how it applies to biological research as conducted today.

What Meehl describes is a two-part issue.

First, there's a problem with using the point null hypothesis (two numbers are equal) instead of a more general null hypothesis (two sub-populations are within natural variation of each other).
The problem is that the point null is always false in fact, so a sufficiently precise test is guaranteed to prove it false and is thus likely to support a directional theory about half the time.

The second issue is that of taking support for a statistical hypothesis as support for a larger non-mathematical theory.
Other theories may well predict the same outcome, so a favorable result does not prove your own theory.
The two combine to make a scenario where, given precise enough measurements, half the time you will find support for your pet theory.

Now, if you don't use statistical analysis, you are essentially setting p=.99 and using a point null hypothesis.

In agricultural and biological research, standard practice is to use the null hypothesis that the two groups are within a certain amount of variation of each other.
And this is not necessarily false, so problem #1 goes away.
Problem #2 is a psychological problem you can always run into.
But ignoring p-values will not solve anything.

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