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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?

Comment: Re:Some clarifications (Score 1) 77

by jw3 (#42723845) Attached to: Mutations Helped Humans Survive Siberian Winters

Post scriptum: erratum and an additional explanation

"cognitive and brain development" -> "cognitive functions and brain development"

"gene is not important" -> gene itself might be important, but its precise sequence might not matter because different variants are able to fulfill the same function. The problem is that a synonymous mutation usually is not visible to natural selection, but that doesn't mean that a non-synonymous mutation is always visible; many non-synonymous mutations are effectively neutral.

Also note that the whole story works only for protein coding genes, because we can easily tell "important" (non-synonymous) from "non-important" (synonymous) changes. However, first of all there are many important genes which do not encode proteins, for example the regulatory microRNAs or structural RNAs. It is not easy to tell which mutations are neutral, and which aren't. Second, there are regulatory regions that can matter a lot; again, it is hard to tell which mutation will have an effect. For example, the famous lactase persistence mutation is a mutation in a regulatory region, not in the gene itself; it messes up the switch of the gene that all other mammals use to turn off lastase production in adult animals. It does not alter the sequence of the protein coding region.

Such cases can still be worked on, for example by looking whether there are mutations in regions that are otherwise conserved in other species. Unfortunately, this is nowhere as sensitive or specific as considering the dN/dS ratio.

Comment: Some clarifications (Score 5, Insightful) 77

by jw3 (#42723411) Attached to: Mutations Helped Humans Survive Siberian Winters

1. Just like the article says and unlike the Slashdot summary suggests, shiver-free thermogenesis is old and all mammals share it.

2. The researchers found traces of positive selection in a gene involved in shiver-free thermogenesis.

3. How do you look for traces of selection? A mutation in a DNA fragment coding for a protein can have two effects: either it changes the corresponding amino acid in the protein sequence (non-synonymous mutation), or it does not (synonymous mutation). This is because genetic code is redundant and different codons code for same amino acids, so a change from one codon to another does not have to change the protein. Synonymous mutations are assumed to be neutral for evolution (although they are not, not always).

Now, if you look at many possible variants of a gene and collect many different mutations, you can calculate whether the ratio of non-synonymous to synonymous mutations (called the dN/dS ratio) is (i) higher (ii) lower or (iii) quite like expected. Depending on the outcome of the test, you can say:

- if it is higher than expected, then there is a positive selection force at work (the gene is pushed towards change)
- if it is lower than expected, then we have a case of purifying selection; the gene is being actively maintained as it is, and any non-synonymous mutations are being removed from the population
- if it is neither lower nor higher, the gene is just not important

4. So, nice, you found that a gene related to non-shiver thermogenesis shows traces of positive selection. So what?

The answer is, not much. You do not always know which mutation was the one being selected. And even if you can pinpoint it, very often you will not be able to say what it actually does. So fine, you have a leucine replaced by arginine at position 186 in a protein chain; you might be able even to model the new sequence and see a delicate shift in the structure of the protein. How does it relate to the protein function? What has been modified or improved? No idea.

5. OK, why is that important? It is important because much of the genetic variability of the humans that we know is thought to have been fixated by genetic drift and other neutral evolutionary effects (like surfing the wave of colonization) - rather than selection. There are few examples of selection known. Light skin is one of them, and is thought to be an adaptation to the vitamin D deficiency caused by lack of sun at high latitudes. Mutation that keeps lactase being produced throughout life is another one. There were independent (convergent) events in both cases, by the way.

Look, humans are special. Special in the sense that humans are genetically extremely uniform, and the genetic differences between, say, native Australian, a blond-haired, blue-eyed Swede and a member of the Mbuti people from Africa are all together much smaller than between two chimpanzee individuals from groups living a few hundred kilometers apart. And moreover, these few mutations specific for some people but not for other seem to be more or less neutral in their character.

Finding differences that are *not* neutral, that are actually doing something is therefore an interesting thing. Notably, the few existing differences like that are linked to mundane things like metabolism or immune response (yes, some people are special because they don't fart after drinking milk, how is that for a superior race), and not, for example, to cognitive and brain development. The latter differences are found between humans and other primates.

Comment: Re:Kuhn is not everything (Score 1) 265

by jw3 (#42529415) Attached to: Does All of Science Really Move In 'Paradigm Shifts'?

The problem is that it does not describe very well how science has actually progressed, in the past or the present.

As mentioned, this is philosophy, not science, so it is hard to confront different and contradictory views.

For example, there will be some who will tell you that the popperian concept of falsification is one of the most influential ideas of the XX century, responsible for the dramatic progress in understanding of our world that happened in the XX century. Not least because of the statistical hypothesis-testing framework, and there is little doubt about the influence of XX century statistics on progress in science.

But yes, it does not fit the copernican revolution.

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