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Comment: Today, I would never have learned programming (Score 5, Insightful) 608

by jw3 (#47414751) Attached to: Normal Humans Effectively Excluded From Developing Software

I got my first computer in 1986; I was 13, and it was a ZX Spectrum with a build-in BASIC interpreter. When you switched on, you could start away programming. In fact, the computer came with a little book with programming examples and little games. I spend countless hours typing in listings that I found in newspapers. To even load a simple game you had to enter a command.

Since then, I learned C, tcsh, C++, bash, Perl, much later also Python and R. It was a step by step process, and I would never have started it (and became what I am now, that is, computational biologist) if not for this one computer with the BASIC interpreter.

I have kids now, and they have Android tablets. The sheer power, their parameters and their capabilities are overwhelming. I don't know how many instances of a ZX Spectrum emulator I could run on one of these, a thousand?

But even though they run on a system that is related to the system I am using every day, I would not know how to write a program for them to save my life. In theory, I know how I would approach it, I even set up once an Eclipse environment once, but I never got to even start a Hello world program. If I were 13, I would not even know that I can write a program myself.

It is amazing, but I think that actually, my kids will have a much harder time to learn programming than I had, and they will get much less fun in return...

Comment: Novel, it is not (Score 3, Interesting) 85

by jw3 (#47271895) Attached to: The Game Theory of Life

John Maynard Smith introduced the game theory to evolutionary biology in the early 70's. It was a breakthrough at that time, however today it is scarcely news. Evolutionary biology, and in especially population genetics has been a highly mathematized discipline ever since before WWII, when it was developed by Fisher, Wright and Haldane. Later you had Hamilton and Maynard Smith. It is nice that computer scientists noticed that something exciting is going on here, but don't fall for press releases and insubstantiated claims.

Comment: They got it all wrong (Score 1) 634

by jw3 (#46965429) Attached to: Why Scientists Are Still Using FORTRAN in 2014

Speaking as a scientist with 20+ years of experience in programming: we are unlikely to choose a programming language based on its elegance, ideas behind etc. Two primary factors are (i) who else is using a given language and (ii) what libraries for that language are out there. For example, exactly 0 of the languages mentioned in the original article are used by statisticians. Haskell might be cute to write a generic program with, but in R or SPSS I have all the cutting-edge statistical tools I need for my work.

Comment: No, they did not (Score 4, Informative) 109

by jw3 (#45984187) Attached to: World-First Working Eukaryotic Cell Made From Plastic

Again, the press release is misleading. Worse, it fires back on the real and great accomplishment by suggesting it is something that it is not.

The scientists managed to squeeze key enzymes into different minuscule compartments of a cell-like structure. That in itself is fascinating and a great achievement; but that doesn't make an eukaryotic cell. It does not replicate; it does not synthesize the lipid-like structures; it lacks a cytoskeleton and a complex organization; the reactions going on are few and very simple. It is as much an eukaryotic cell as a neural net algorithm is a working brain.

However, it has working enzymes within little bubbles within other bubbles, which can be called "compartmentalization", a feature of eukaryotic cells that distinguish them from bacterial cells.

Nonetheless, this is a considerable achievment that has both a practical side and is a working model with potential to make in vitro experiments helping to understand the processes that go on in the real cells.

Comment: Am I missing something? (Score 2) 134

by jw3 (#43893943) Attached to: Pi to Go: Hot Raspberry Pi DIY Mini Desktop PC Project

"fully enclosed mini desktop computer that could be taken anywhere without the need for cabling or setup"

So, basically, a laptop?

Seriously -- how is that news? People have been doing it for years now. Here is a random google link from 2012: http://blog.parts-people.com/2012/12/20/mobile-raspberry-pi-computer-build-your-own-portable-rpi-to-go/

Comment: Re:Dr. Fred Klenner cured polio with Vitamin C (Score 2) 105

by jw3 (#43801207) Attached to: Scientists Find Vitamin C Kills Drug-Resistant Tuberculosis

The problem is that anything above 400mg / day gets quickly removed from our organism. So no, we are not chimps (and btw, chimps also can't synthesise vitamin C naturally), and our organisms know pretty well how much vitamin C is needed.

Pauling specifically believed that overdose of vitamin C can prevent cancer. It was a very interesting hypothesis, and it was very important to test it. However, several large prospective studies undertaken in the 80's have, unfortunately for all of us, falsified that claim.

Klenner's observations from the 30's-50's have also not been confirmed by any kind of systematic study.

Comment: Re:I take 6 grams a day (Score 3, Informative) 105

by jw3 (#43801171) Attached to: Scientists Find Vitamin C Kills Drug-Resistant Tuberculosis

6000 mg vitamin C daily, not counting vitamin C in the food? That is a lot. Consult your physician and be very, very cautious about suggesting medical advice if you are not prepared to take moral and financial responsibility for it. Yes, vitamin C is important. Yes, increased intake of vitamin C has been show to have several health benefits, including reduced stroke and cardiovascular disease risks, especially in smokers. However, "increased intake" means "well below 1g/day".

6000 is 30-100 times the recommended daily dose. Although studies indicate that vitamin C intake at 2-4 g/day may not have large adverse effects (1), one has to be extremely cautious when recommending supplementing your diet by a 100x of a daily dose. The fact that you don't experience any adverse effects such as kidney stones (at least yet) does not mean that a person reading your comment will not suffer from that either.

Apart from the problems with the digestive tract, vitamin C can hamper endurance in physical exercises (2). Moreover, vitamin C not used by the organism (which requires as little as 100-200mg / day) is excreted (3). For that, it is metabolised to oxalic acid, which in turn can cause kidney stones (4 and the references therein). So yes, although problems with vit. C overdose do not seem to be common and are not comparable to overdoses of some other vitamins, at 6g/d saying that "C can't hurt" is very risky (especially as supplements can contain other vitamins as well, and the fat soluble vitamins A, D, E and K can cause severe adverse effects -- vitamine poisoning -- when overdosed).

The highest risk-free level of daily intake for vitamine C has been recently proposed to be 1000 mg (1g) (5, 6). People, before you install some shady software someone recommends at a biology-oriented website, ask your IT friend for advice. Before your follow medical advice from Slashdot, consult your physician.

"Rational by choice."

Prove it. Read the evidence based medical studies rather than trusting and spreading anecdotes.

(1) http://onlinelibrary.wiley.com/doi/10.1111/j.1753-4887.1999.tb06926.x/abstract
(2) http://ajcn.nutrition.org/content/87/1/142.short
(3) http://ajcn.nutrition.org/content/69/6/1086.short
(4) http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2362.1998.00349.x/full
(5) http://jama.jamanetwork.com/article.aspx?articleid=189543
(6) http://www.pnas.org/content/93/8/3704.short

Comment: Why is M.tb. a problem and other clarifications (Score 4, Informative) 105

by jw3 (#43800529) Attached to: Scientists Find Vitamin C Kills Drug-Resistant Tuberculosis

Mtb is an intracellular pathogen. It invades our cells, the very same cells that are supposed to kill bacteria (the macrophages). This is why treatment of TB takes six months. Vitamin C, at a dosage lethal for Mtb as described in the article, cannot be used to kill the bacteria in our cells. The importance of the article is that it identifies a potentially intereseting difference between Mtb and other bacteria.

As for vitamin C, this is not some kind of a miraculous drug; it is just a co-enzyme required for a few particular reactions in our metabolic pathways. We, humans, are mutants, we lack the ability to synthetise vitamin C -- along with our cousins, the monkeys, although most animals do synthetise it on their own. Lack of vitamin C impedes the metabolism. However, only little of the co-enzyme is needed, and once vitamin C is no longer a limiting factor, it has barely an effect.

Think about that in terms of a network. If your wireless router is extremely slow, buying a new one will increase the speed of your connection. But what good is a super fast wifi router, if the outgoing connection runs at 10Mbit?

Vitamin C is also an antioxidant, and this is why some people (quite incorrectly) think that taking large doses of vitamin C are beneficial. However, there are two forms of this compound, L-ascorbate (vitamin C) and D-ascorbate; both are antioxidative, but only one is a co-enzyme. D-ascorbate, however, shows no beneficial effects.

Big pharma has not much interest in preventing the use of vitamin C in Mtb treatment. Mtb drugs are cheap, generic, and effective; the main reason why Mtb is a problem for much of the world is lack of fast and cheap diagnostic tools. You see, 2 billions (2e9, one third of worlds population) are infected with Mtb, and of these, only 10% will develop tuberculosis during their lifetime. However, we don't know which, why, and when. Also, when a person falls ill, it is not a quick process like a flu; rather than that, a person starts feeling unwell, caughing and becomes infectious over weeks before she finally decides to see a doctor. Here is a review article I wrote on TB and biomarkers: http://www.ncbi.nlm.nih.gov/pubmed/23181737 (full text behind a paywall, unfortunately).

Pauling believed that taking large doses of vitamines will prevent cancer and took large amounts of vitamin C throughout his life. In 1994, he died of prostate cancer.

Comment: Bad news for you (Score 1) 228

by jw3 (#43099671) Attached to: Ask Slashdot: Advice For Summer Before Ph.D. Program?

Counting from the start of my PhD program, I have spent over 15 years doing science (biology) -- most of my grown-up life. I'm still doing science, it's my life. And what I have to say to you, young padawan, is not nice.

You are about to do the most thrilling (awesome, exciting, depressing, frustrating, crazy, fulfilling, everything at once) thing on Earth, you will be doing bloody science, and you think about getting ...new hobbies? New interests? All that in a fashion of someone shopping for a new T-shirt? (ah, skydiving, seems nice, I'll take a pair).

How will you come up with ideas for your research if you have not enough curiosity and interest in the world around you, and you have to fish for interests / hobbies on Slashdot? This is how your question sounds for me: "I just got an apprenticeship at NASA, can someone give me an idea for a new hobby? 'cause I have none". If you need to ask a question like that, then better ask yourself whether PhD in science is really what you want.

Apart from that, if you already have anything that you like to do with your free time, plus you have some kind of relationship (or plan to have one), plus you will take your science seriously, you will have barely any time to pursue "new hobbies / interests". Go and read http://www.phdcomics.com/.

And get out of my lawn.

Comment: Re:Some clarifications (Score 3, Informative) 77

by jw3 (#42724973) Attached to: Mutations Helped Humans Survive Siberian Winters

This reasoning is a fallacy.

You can make precisely the same argument about the last common ancestor between humans and chimps, or the last common ancestor of humans and neandertals. In a general context, chimp brain is as complex as ours. Yet evolution happened in between, we can track it, and we can see that it did in fact modify the cognitive functions of that ancestor; chimps are not humans. And hell, even the developmental machinery that makes an egg develop into an adult vertebrate is complex and interdependent, and if what you are quoting were true, one would expect all vertebrate life remain at the stage of a fish.

The actual reason might be much more mundane: the initial small population of modern humans expanded so rapidly that any resultant genetic differences between populations are the result of neutral evolution (like genetic drift) rather than natural selection. This is also why genetic diversity is inversely correlated with geographic distance to Africa. Essentially, we are all still this same small initial population, but we expanded like a balloon, taking down - directly or indirectly - any other populations that might have existed at times (like the neandertals, denisovians and many, many other hominins).

Comment: Re:Dairy for 25k years? (Score 2) 77

by jw3 (#42724055) Attached to: Mutations Helped Humans Survive Siberian Winters

It is off topic, but the ability to digest lactose as adults evolved somewhere between 5,000 and 10,000 years ago. The greatest ability to digest lactose as adults is clustered in the Arabian peninsula, southern Iran and Pakistan, far western Africa, and northern Europe (southern Scandinavia, Iceland, Ireland, Great Britain, Denmark, northern Germany, and northern France). I couldn't tell you though if the genetics are the same but it seems unlikely given the geographical clustering.

Yes, it is the same mutation you are talking about. The associated mutations (or "snips", SNP -- single nucleotide polymorphisms) are all the same, even in the West African tribes, and are thought to be of a common origin.

However, there actually is a known case convergent evolution of lactase persistence, fully described in this Nature Genetics paper: http://www.nature.com/ng/journal/v39/n1/full/ng1946.html . The authors analysed genotypes of East African pastoral tribes where lactase persistance is also widely spread, and found several alternative mutations in the same regulatory region. The most common of these mutations is thought to be ~ 7000 years old.

Comment: Re:Arterial plaque? (Score 1) 77

by jw3 (#42723977) Attached to: Mutations Helped Humans Survive Siberian Winters

Of course not only in the mitochondria. Reactive oxygen species are also one of the first lines of defense against bacteria; macrophages generate reactive oxygen in the phagosomes - when macrophages ingest a live bacterium, it then becomes surrounded by a membrane, forming a phagosome. It is best explained with a picture: http://textbookofbacteriology.net/Phago.jpeg

Next, the phagosome changes into what is called phagolysosome, which is like a death cage for the bacterium. All sorts of nasty enzymes and molecules get injected in this space, including enzymes producing reactive oxygen species.

However, immune cells can also release oxygen directly into bloodstream. Given the cytotoxicity of ROS, this is like detonating nukes in your blood vessels, and can result in collateral damage. However, this stuff totally happens. Neutrophils can undergo a sort of harakiri, releasing DNA-bound bacteriocidal proteins in form of a sticky NET ("Neutrophil Extracellular Traps"). Proteins in NET generate extracellular ROS. It's a bit like gutting yourself and strangling the enemy with your own intestines.

So yeah, our own immune system produces ROS when it is fighting bacteria. The desired effect is local and limited to bacteria, but collateral damage is known to exist, and antioxidants can help to contain it.

That said, the hypothesis is not even that (a proper hypothesis), but more like a vague idea: how could you test it scientifically?

Somebody ought to cross ball point pens with coat hangers so that the pens will multiply instead of disappear.

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