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Blood Test of 4 Biomarkers Predicts Death Within 5 Years

robbyjo Re:Correlation != Causation (104 comments)

Oh the classical correlation != causation meme! Read the f***ing paper first and understand the arguments!

You should understand WHICH 4 biomarkers they are testing: VLDL, Albumin, Citrate, and Alpha-1 acid glycoprotein. If these four are high, chances are the metabolism behind these four indicators has been wrong for DECADES and is hardly reversible. It makes sense, therefore, to predict 5-y mortality rate with these 4 biomarkers. Sure the prediction isn't perfect, but boy are they good indicators of someone health just as fasting blood glucose, blood pressures, cholesterols and other measurements!

So, just quit this kneejerk correlation != causation reaction already and understand the science behind it!

about 9 months ago
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Spoiler Alert: Smart Kids Become Successful Adults

robbyjo Re:Correlations (256 comments)

> Open articles. Ctrl-F "Controling" No results. Close tab. Nothing of value.

It does. It is abbreviated as "RGSC" on the article. Look at Figure 2 to see the model graphically and you see that RGSC is featured prominently on the top. Also, if you look at Table 2, the authors acknowledge the link between SES of origin AND math / reading abilities. But this paper shows that the math & reading abilities at 7 years old do predict mid-life SES above AND beyond the SES of origin.

about a year and a half ago
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Researchers Achieve Storage Density of 2.2 Petabytes Per Gram of DNA

robbyjo Major challenge: Retrieval and storage (136 comments)

Okay, storing is "solved". How about retrieval? Especially random access retrieval that are simple and fast (relatively speaking) that allow such storage medium to be practical? Certainly not DNA sequencing that can take weeks to complete?

The second problem: DNA denature and fragment at room temperature. Certainly a -80C lab freezer for storage wouldn't be practical.

Third problem: DNA secondary and tertiary structure. The coding scheme must also solves the problem of DNA tendency to make secondary structure (like hairpin) or tertiary structure (like super-coil) that can hamper reading / access to the information. I think this is the reason why the storage uses short sequences. But short DNA sequences like the one proposed (~100 bp, from the figure) could still make such structures.

about 2 years ago
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A Few Million Monkeys Finish Recreating Shakespeare's Works

robbyjo Re:It's a cheat. (186 comments)

Then, it's not really monkeys. It's more of monkeys with an oracle. That oracle thing made a whole world of difference.

more than 3 years ago
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Fake Names On Social Networks, a Fake Problem

robbyjo What constitutes a "real" name? (283 comments)

What constitutes a "real" name? Take a look at Sun Yat-Sen, for example. Which one do you think is THE real name? The original name? Baby name? Genealogy name? Courtesy name? School name? Eventually, Sun Yat-Sen was famed in China because of the pseudoname he used in Japan. And Yat-Sen itself is a school name.

more than 3 years ago
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Bitcoin Mining Tests On 16 NVIDIA and AMD GPUs

robbyjo GUIMiner is most likely optimized for AMD cards (403 comments)

The performance of GPU-based codes is highly dependent on the video cards. I highly doubt the dismal performance of NVIDIA cards. I think the authors most likely optimized the kernel code to AMD cards. This is evident when you look at the CL kernel code and you see that there are so many hardwired constants and fixed arrays (aligned to 128 ints or longs). Moreover, the authors GUIMiner don't seem to take advantage of NVIDIA's more local workthreads (compared to AMD's).

I'd say that declaring AMD a victor is premature.

more than 3 years ago
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Ask Slashdot: How To Encourage Better Research Software?

robbyjo Re:Not going to happen (104 comments)

Does "agile" software development allow scrapping 100% of the code and radically change the spec (and thereby everything else) every about 6 months just because of new scientific publication? It may sound extreme, but this often happen in research. If we take time to "structure" our code, before we know it, we have to redo it all over again. We do use libraries like GSL, BLAS, ATLAS, etc. to make our lives easier. These won't change, but whatever we build on top of these often get scrapped at regular basis. So, we really don't have incentives to "beautify" the code.

more than 3 years ago
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Ask Slashdot: How To Encourage Better Research Software?

robbyjo Not going to happen (104 comments)

Not only that most researchers are not proficient in programming language, they shape their codes more like prototypes so that they can modify the codes easily as the science progress. Conventional programmers will be frustrated with this approach since they want every single spec set in stone, which will never happen in research setting since research progresses very rapidly and specs can change dramatically in most cases. If you can set the spec in stone, it is usually a sign that the field has matured and is getting transitioned to engineering-type problems. Once the transition happens, it's no longer research, it's engineering. Then you can "make the code better".

more than 3 years ago
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Catching Exam Cheats With a Spectrum Analyzer

robbyjo Re:Exams in other cultures (210 comments)

In Ancient China, imperial exam was literally game-changing. The stake is high; it was virtually the only way peasants could become noblemen. Therefore, people did whatever it took to be successful. This system was copied and adapted to some degree in ancient Japan, Korea, or Vietnam. Hence similar attitude also pervades in these countries.

more than 3 years ago
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Chinese Written Language To Dominate Internet

robbyjo Re:Not necessarily popular with the Chinese, eithe (535 comments)

I think you should learn a bit into Chinese language and characters to understand how indispensable the characters really is. Consider English example of "bat", "bet", "bad", "bed", which are voiced very similarly. If spoken by non-native speakers with heavy accent, these words may be confused with "pat", "pet", or "pad". (Even in English, some accent-heavy people pronounce "pen" and "pin" identically!) A Chinese analog would disambiguate with "baseball bat" instead of just "bat" and so on. The problem is that such situation is much worse in Chinese than in English and it occurs even in daily use. This is why that most words are represented by two characters. Note that the pairing does not introduce new characters and thereby not adding to the "grinding". It's just adding new complexity to the language. Reading newspapers would require only about 4,000 characters (out of about 100K total) with about 300 tone-syllable combinations, giving about 13 of each left for disambiguation. Knowing about 2K is enough for daily conversation. Mind you these are still common use, including in formal signs or speeches. This is NOT uncommon as you've claimed.

Also, in Chinese, using more refined characters would show your erudition, politeness, or even social status. Politeness can mean everything for Chinese. So, you see, language isn't restricted for informational purposes only. It can also convey mood, politeness, formality, etc.

Note that new words are formed by juxtaposing two or more characters in an unusual way. With each character giving its individual meaning, the people could guess the meaning of the new word. If the people are deprived of the character and, say, have to read the pinyin, the meaning wouldn't be as obvious. Example: Xi3 yi1 = laundry becomes xi3 yi1 ji1 = washing machine. If the people don't know the characters, the meaning of xiyiji isn't immediately obvious. This fact makes Chinese language very intuitive and even facilitates learning. Children in China cope with this complexity pretty well. Their literacy rate is 97% in 2010.

The barrier of entry is as much as East Asian people learning English. Chinese and English are two completely different languages. For East Asian people, such barrier isn't as much, akin to the barrier of entry for learning French for English-speaking people.

Therefore, Chinese characters are indispensable.

more than 3 years ago
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An Interview With C++ Creator Bjarne Stroustrup

robbyjo Re:Is C++ ever the right tool for the job? (509 comments)

Yes. C++ (and Java) are indispensable for scientific software. In scientific software, the spec is ever changing as the science progresses and hence the flexibility to morph the programs as needed and maintainability are of paramount importance. On the other hand, we need the speed.

Some of these can be resolved by invoking ready-made C libraries and then called in higher level languages such as Python or R or Matlab. However, in many occasions, this luxury isn't available (e.g., Markov Chain Monte Carlo simulations or custom EM algorithm).

more than 3 years ago
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Chinese Written Language To Dominate Internet

robbyjo Re:Not necessarily popular with the Chinese, eithe (535 comments)

If you look at the wiki URL I cited, you'll immediately notice the problem. Chinese language IS a very terse and highly economical language with many symbols, sounds, and tones. In speech, people *disambiguate* words by pairing the words with "word-complements" (I don't know what they're called) to achieve the intended meaning. HOWEVER, the pairings are limited to daily use. Even then, there are still ambiguities. Take, for example, the word "shishi" in Pinyin. You get 23 matches. Even if you add tones, you STILL have ambiguities. If you look at the word list, they're not rare, right? If I say (in Pinyin) "shi4shi4 nan2 liao4", what does it mean? Is it "affairs of the world are hard to guess"? Or "everything is hard to guess"? Or "the state of the affair is hard to guess"? Or "affair of this world is hard to abandon"? In this situation, people disambiguate even further by putting in more "word-complements". Note that the phrase is a common complaint! It is so context specific.

Also, languages are NOT limited to spoken language. How about poems? Stories? Formalities? Jokes? Puns? If the words are written, especially in poems or terse narrative, they can be paired in almost every way and can create a very very powerful poem or narrative. Or puns! Oh man! There are so many puns based on this very fact.

Now, can you say that Chinese character is dispensable again?

more than 3 years ago
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Chinese Written Language To Dominate Internet

robbyjo Re:Not necessarily popular with the Chinese, eithe (535 comments)

You seem to look at Chinese words from Japanese perspective. Correction:
1. Chinese characters are logogram.
2. Classical Chinese is mainly monosyllabic, while Modern Chinese is mainly disyllabic for disambiguation purposes. See: http://en.wikipedia.org/wiki/Lion-Eating_Poet_in_the_Stone_Den
3. Chinese characters *are* indispensable. Pinyin or other romanization techniques (plus tones) simply cannot convey the same meaning as the original characters, though you can guess. Remember that Chinese language is tonal and tones for one character can change depending on the other word(s) it is paired with. Even with the tonality marks, there are still ambiguities remain in the romanized version of the words. The same problems occur in other "simplification" or "phonetic abugidas" (e.g., bopomofo). Tonality does not exist in Japanese. See the wiki URL above.
4. Since Chinese characters are indispensable, you have to sight-read them. Yes, some phonetic clues do show up, but not always lead you to the right one. Also, there are false friends, alternative spelling (even worse in Japanese), and one dot or one slash difference may make dramatic differences in sound.

more than 3 years ago
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NASA's 'Arsenic Microbe' Science Under Fire

robbyjo Re:Papers and Questions (152 comments)

Why can't these scientists just take the samples and redo the experiments *the right way* (and defend it) to see whether it is indeed a methodological error? If it is a methodological error, the result will go away. Why whining?

more than 3 years ago
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NASA's 'Arsenic Microbe' Science Under Fire

robbyjo Re:Papers and Questions (152 comments)

Actually, an easy fix would be getting the sample from the said lake OR from the scientists themselves, and then redo the experiment to see whether they can reproduce the result. Why whining, right?

more than 3 years ago
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US District Judge Rules Gene Patents Invalid

robbyjo Re:Natural Resource (263 comments)

Even for a new allele, say a SNP, its combination is only A, C, T, or G. Unless they can show that it is highly unlikely that the patented modification would occur naturally, any new alleles should be patent free. And heck, they can't compare the chance with pure random chance since we know that mutations / gene modifications do not occur randomly either. Claiming so would be very hard.

New treatment may or may not be patentable as well. If the treatment involves a naturally occurring sequence from other people (I'm thinking of siRNA and the likes), they can't patent the sequence either. They can only patent the method to synthesize it. Even then, if the method is in fact a naturally occurring method (i.e., that's how the body of human or other creatures does it), then they can't patent it either.

more than 4 years ago
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Science and the Shortcomings of Statistics

robbyjo It's a tough situation (429 comments)

Actually, it's a tough situation. There is no real life experimental data can 100% fit the assumptions of commonly used statistical models. Real life data is messy. There is some degree of simplification. In addition, resorting to whiz-bang fancy methods that "fit" the real data may not be easily interpretable. Ease of result interpretability is what medical scientists want. There are other issues as well, such as computing time, equations derivability, etc.

In addition, many many medical scientists use statistics as a tool to filter things (e.g. candidate genes, target enzymes, treatments, etc). In this case, 100% accuracy is not really important. Once the scientists narrow down the genes, they can test the validity directly in either test animals or real people.

more than 4 years ago

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