Genetic testing for the masses (including myself): 23andme

Two years ago, I learned about 23andme.com, a company that does genetic testing for health, traits and ancestry. The idea is as follows: you send them a sample of your saliva (containing your DNA, I guess from cells in the mouth mucosa), they process it and check for specific genes. Then, they compare your genetic information with the currently known research about health (higher or lower chance of getting some diseases), ancestry (maternal and paternal) and genetic traits (color of the eyes, blood group).

It took me a while to decide and take the test: the idea of giving my DNA information to a private company, with information stored and available on the net, didn’t appeal me at all. Call me paranoid, but I can’t help it. I made some reputation checks with some trusted people I know, learned that the company has close ties with Google (a co-founder is Brin’s wife) and decided for it. The main push, however, was curiosity. In my genetic code it is written how my biological computer works, how it can break, and where it comes from. Too much to resist. After you place your order, they send you a sampling container, which is a test tube with a buffer solution in the cap.

What I found out is appealing: I learned that genetically I am a very healthy person, confirmed some hypotheses about my ancestors, and realized I have superpowers: I am immune to the most common strain of viral gastroenteritis. I left my genetic information in their database and, as long as I keep paying a small fee, they perform additional analyses on my sample for new genes. I keep receiving updates about new findings around once a month.

Do I recommend it? Yes and no. The most important point to keep into account is that, once you open the box of your genetic information, there’s no way back. What you learn may change forever how you see yourself, your past, your future and the future of your children. 23andme keeps you health information hidden to you unless unlocked manually. I didn’t even ponder a second about it, and clicked on all the “show my health information” buttons I could find. I cannot deal with not knowing, regardless how bad it can be. Knowledge may also allow to take action whenever possible, but for some conditions there’s not much to be done.

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The science of decay: beautiful BBC documentary

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More jaw-dropping advances in prosthetics

I already posted about advances in prosthetics some time ago, but this is beyond words. You may want to apply the wadsworth constant to the movie.

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The third eye of the iguana

Did you know that iguanas (and not only them) have three eyes ?

the feature is called Parietal eye, it is highly advantageous to spot the shadow of a predator coming from above, and it’s not unique to iguanas, but it can be found in frogs, lizards, sharks and other reptiles and fishes. In the Tuatara the eye is way more developed, but it regresses as the animal gets older. All these eyes can influence the pineal gland, apparently responsible for the circadian rhythm regulation.

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Pac-mecium and other games

This is a rather peculiar use of paramecia: by directing their preferential swimming movement by means of an applied electric field (a property called galvanotaxis) we can use them as player characters in videogames. I don’t expect this to become common gaming, though.

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Does chamomile really relax ?

ChamomileNothing says relax better than a peaceful evening in front of a steamy cup of chamomile. Since thousands of years, humanity uses it as a natural remedy for a large amount of ailments, most notably hypertension, sleeplessness and to ease a flu-dominated night, like in my case recently.

Moved by curiosity, I took some time investigating what is scientifically known about the therapeutic effects of chamomile and their mechanism of action. The results, I must say, are interesting and conflicting. Let’s examine what I was able to gather from around the internet and in a couple of scientific papers.

Chamomile is a class of plants whose main representatives, at least for infuse-making, are Matricaria recutita (German chamomile) and Chamaemelum nobile or Anthemis nobilis (Common Chamomile). It can be found wild or cultivated. Its flower is actually a composite daisy-like sprout. The flowers are the tiny yellow corollae forming the central bulb.

Chrysin

The pleasant fragrance the chamomile flowers produce arises from a large set of compounds (more than 120) including in particular sesquiterpenes such as chamazulene and alpha-bisabolol, flavonoids and flavanoids, like Chrysin, and many others. Most of these compounds are not present in free-form, but are bound to sugars through fragile bonds that can be broken easily, for example by heating.

Some research on the effects of these compounds has been performed. In particular, Chamazulene has been found to have antioxidant properties, together with matricin, alpha-bisabolol, and apigenin. Chrysin appears to show anxiolytic effect in laboratory rats (see also here and here) but nothing has been said for humans yet.

Chamazulene
Chamazulene

Other experiments show that chamomile can have small antibacterial effect on the gut’s bacterial population, both in human and rat. This finding, however, is a mere hypothesis to explain changes in the excreted substances.

So, it appears that chamomile does indeed have relevant activity, and for what concerns anxiolytic effects, some evidence exists. Despite this, The National Institute of Health page for chamomile reports insufficient evidence for most of the claimed therapeutical advantages of chamomile: the report is “C: Unclear scientific evidence for this use”, with only one case (“post-operation sore throat”) where a conclusion has been reached as “D: Fair scientific evidence against this use”. This is a very important example on how evaluation of pharmacological effectiveness is performed. Even when evidence supports presence of therapeutic effect from a given compound or preparation, only a set rigorous tests performed on human subjects allows to finally grant recognition of therapeutic effectiveness (or lack of it). In the case of chamomile, tests have been mainly performed in rats and mice. Even a single successful (or unsuccessful) human test is not enough to grant A (strong positive evidence) or F (strong negative evidence) grades in the Natural Standard grading scale. The grade C refers specifically to

      1. Evidence of benefit from >1 small randomized trials without adequate size, power, statistical significance, or quality of design by objective criteria, OR
      2. conflicting evidence from multiple randomized trials without a clear majority of the properly conducted trials showing evidence of benefit or ineffectiveness, OR
      3. evidence of benefit from >1 cohort/case-control/non-randomized trials AND without supporting evidence in basic science, animal studies, or theory, OR
      4. evidence of efficacy only from basic science, animal studies, or theory.

      Let’s examine the cases one by one.

      The first case occurs when tests result in positive evidence (it works) but the test is not “statistically significant” meaning that it has been performed on too few subjects: for something to be considered working, it must present an effect that occurs with some consistency. If you test a substance Foo on a single sick person, and he recovers, it does not mean that Foo is a cure. That person could have recovered just because he was lucky or strong enough to recover, regardless of Foo. A better test would be: treat 200 sick people with Foo, and take also 200 sick people with no Foo treatment, then compare the recovery rate in the two groups. If in the first group 180 people recover, while in the other only 20 recover, there’s definitely a good point in favour for Foo being effective in curing that sickness. Statistical analysis allows you to decide which numbers of people can be considered strong evidence or not enough evidence for Foo being an effective cure.

      The second case is when two or more tests produce conflicting results. For example if laboratory A sees a recover in its people using Foo, but laboratory B sees no recover. There could be many reasons for this. Improper testing could be one, and even if all tests are performed properly there could be additional factors we don’t know. Example: suppose that people at laboratory A had an unknown strong ease of recovery from that sickness (because they are immune for some biological reason), so the group without Foo medication recovers as well as the group without Foo. The conclusion for the laboratory A is that Foo has no effect, while laboratory B says that Foo has an effect. This is conflicting evidence, and must be resolved by checking more people, until a clear majority allows a unique conclusion to be drawn.

      The third case is when there is evidence for recover, but there’s no evidence from known science, animal studies or theory able to explain the observed phenomenon. This can lead to a scientific breakthrough if a new biological mechanism is found and explained, but until then, it is not possible to say anything about the pharmacological validity. This point also raises the difference from cohort case, control case, randomized or non-randomized trial. It would be an interesting discussion, but it goes a bit outside of my current knowledge, and I am determined to learn more about the details in the future.

      The fourth and last case is when evidence exists only because we infer it should work from what we known today of the human body’s mechanisms, but no actual test has been performed, or tests have been performed only on animals.

      In the case of chamomile, as of today we cannot confirm officially and with strong evidence on humans that a pharmacological effect does exists, because all tests have been performed on animals, with the very few human trials available still insufficient to draw significant conclusions. This does not mean that the effect does not exists.  It could exists, or it could not, and whatever the truth is we cannot put an approval stamp on it yet, because we haven’t tested enough. In agreement to the scientific method, unless something is demonstrated via evidence to hold, it is assumed not to hold. It’s like presumption of innocence in criminal trials: someone is assumed innocent until proven guilty from evidence. The other way around would be disastrous.

      Now, we can probably claim that the pure fact of preparing chamomile and enjoying its pleasant fragrance has a relaxing effect, but that would be a psychological effect triggering internal biochemical actions inside our body, finally leading to a relaxed mood. Mozart could have the same effect. The point is, from the pharmaceutical point of view, the correct answer (as of today) to the question “does chamomile really relax ?” is “some evidence exists that it does, but it’s still not enough to say for sure.”

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      The Arsenic bacterium. A case of bad scientific communication?

      As you probably heard in the news, two days ago everyone was ablaze for a mysterious announcement from NASA. Speculation started on how the new discovery would “impact the search for evidence of extraterrestrial life.” Someone found a habitable planet? Found a message with Seti@HOME? Discovered the primordial soup composition? The buzz resonated and amplified at every new passage, like in a Chinese whisperers game, speculations were born and distorted, sometimes by the lack of scientific knowledge of the message carriers, sometimes by a deliberate “science-fiction twist”. Now that the announcement has been made, it’s a big disappointment, a delusion… you name it.

      I’d like to propose to make a step back and see the thing from a bit of distance. Let’s analyze the facts. Life (from the tiny bacterium to a giant whale) generally uses six fundamental elements: Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, and Phosphorus. From these six elements, a large majority of the fundamental building blocks of life are created: DNA, Acetil CoA (a transporter molecule), ATP (for energy storage) and many, many others. Yes, some other elements are used, but they are in a tiny amount, and although this tiny amount is essential for life, it is really a pinch.

      On this planet, life managed to conquer places that are considered “extreme”. There’s a class of bacteria called “Extremophiles” which collects all those living under really unexpected conditions. For example, there are bacteria living in almost boiling water, or in very high concentration of acids. The “extreme” conditions are, however, in the eye of the beholder. For these bacteria, their condition is just the norm. For us, living in a scorching boiling hot spring, or in a poisonous acid well is “extreme”, as it would be extreme for them to live at 25 degrees of temperature in a neutral pH. In fact, they are well adapted to their niche. With the recent rise of techniques for biological analysis and sequencing, we are exploring more and more of these niches, and discover more and more bacteria (or communities of bacteria) well adapted to these niches.

      There is a lake in California called Mono Lake. It is one of those extreme places when it comes to conditions: high saline concentration and alcalinity makes it probably a very unpleasant place to take a bath. Fishes agree, and quickly give up and die, so the only thing that lives in that water are some shrimps, algae and bacteria. To complete the nice picture, it has one of the highest concentration of Arsenic, which is a poisonous substance to us, and in general to all organisms. As said before, any bacterium living in extreme conditions for us is classified as “extremophile”. GFAJ-1, the little bug announced by NASA rightfully belongs to the category, since it lives in the waters of the Mono Lake.

      The bacterium has proven really, really tough with respect to Arsenic tolerance. Grown in a lab with even higher concentrations of Arsenic and no Phosphorus at all, the bug decided to switch to Arsenic when it comes to inclusion in its fundamental components, replacing Phosphorus in DNA, ATP and so on. In practice, faced with a lack of a really important element such as Phosphorus, he said “screw that, I’m using Arsenic, it’s good enough for me”. This is really a novelty, but it is not revolutionary. It is just a very important finding, being the first time where life uses completely unusual strategies to continue thriving.

      Summing up, the content of this discovery is:

      1. for the first time, a different element (Arsenic) was experimentally seen as a substitute for another element (Phosphorus) to build fundamental biologically important molecules in-vivo.
      2. there’s no number 2

      Seriously, it’s a great finding, but that’s what the facts tell us. No aliens, no totally different life form on earth, no implications for space research… maybe just a little: we should not be so strict in assuming Phosphorus as so fundamental for life, given that it can be successfully replaced. We also should realize how resilient and adaptable is life when faced with harsh conditions.

      Excessive hype and broken dreams

      The announcement of the conference at NASA landslided a serious amount of speculation and hype. Maybe it was intentional, maybe it was just a mass craze triggered by unintentional circumstances. I cannot say. What is clear is a good amount of blog posts (1, 2, 3, 4, 5) pointed out the excessive hype, and the sheer disappointment that followed. This in turn fuels news fatigue. As I already pointed out in a previous post, this news fatigue in turns fuels misunderstanding, detachment and apathy towards new discoveries. We all want NASA to tell us: “listen, we got that call from ET” but seriously, it’s not how science normally works.

      So what’s the correct recipe ? What do you have to do and understand when you read or hear some scientific news, and how much weight do you have to apply? In my next post I will tell you simple rules on how to read scientific  news with a critical and realistic eye, directly from my experience on scientific papers. Stay tuned.

      Edit: I decided to postpone the continuation of the article for now. I already have a draft, but I am quite busy at the moment, and I have a very long queue of scheduled articles already. I may insert it in the queue, however.

      A Question/Answers site for Popular Science

      The kind folks behind StackOverflow, a free Question/Answers website for programming questions, recently decided to open new Q/A websites for many additional interesting topics, from wine tasting and cooking to mathematics. The fundamental requisite for such new sites to be opened is a rather strict community review and development of a critical mass of contributors and interested people. On area51.stackexchange.com the proposals are collected and evaluated by the community.

      I really enjoyed the proposal for a Popular Science Q/A site, and if the site is going to be opened, I will certainly be an active contributor. If you are interested, feel free to click on the link and then click “follow” on the proposal. This will largely increase the chances for such site to be opened. I am also positively interested and enthusiast for Q/A sites for Chemistry, Astronomy, Bioinformatics and, as a very old Dungeons and Dragons player, Role-Playing Games.

      Posted in Astronomy, Biology, Chemistry, Dissemination, Websites. Comments Off »

      Craig Venter programs a bacterium from scratch

      As you probably heard in the news, Craig Venter, the American biologist best known for starting up Celera Genomics and sequencing the human genome, achieved another big success. He created a fully working new bacterium, programming its DNA from scratch.

      Like a computer having hardware and software, a bacterium has a set of components that execute the software written in the DNA to create proteins. For quite some time, the strategy was to put small pieces of new DNA into full genomes, so to add a new piece of genetic code to synthesize a new protein, typically a pharmaceutical drug. For example, people with diabetes must periodically use insulin, a small protein which is normally produced by a fully functional pancreas. If the pancreas does not produce insulin, then diabetes arises. A solution is to inject insulin from outside, but this small protein must be produced somehow. The technique used to produce it is the Recombinant DNA: A small piece of DNA specifying the code to produce insulin was inserted into a normal bacterium (Escherichia coli, the same that lives in your gut). The altered bacterium duplicates, and millions and millions of daughter cells now produce the proteins their genetic code specifies for, like they were small chemical laboratories. Since specification for insulin has been introduced in their DNA, these millions cells also produce the precious insulin, which is then extracted, purified and sold for diabetes treatment.

      At the Craig Venter Institute, they went further. They didn’t add something new to a bacterium. They took all the DNA contained in one, throw it in the dumpster, put another DNA completely designed on a computer, and let it go. This has been done some time ago, but this artificial bacterium was not able to reproduce, until some time ago. Yesterday the paper has been finally published on Science: “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome“, marking the fact that the hardware (the mechanism that synthesize proteins) can be programmed at will by totally replacing the software (the DNA). In the most superior example of computer programming skills, the JCVI now controls a chemical computer. Venter walks the path of Wohler, once again demonstrating that life has nothing magic, but it is just a chemical system, obeying the rules of chemistry in a fascinating self-sustaining, self-replicating system made of order and chaos.

      What are the consequences of this achievement? What can we do with a totally programmable, reproductive chemical laboratory ? Well, it’s not that easy. Actually this achievement is great, a milestone that will probably earn Craig Venter the Nobel Prize very soon, but to go from this achievement to practical uses for humankind we are a bit far, although not that much far. Having such control will allow so endless possibilities that are almost difficult to imagine right now in their completeness, but we can start from:

      1. production of now expensive proteins to cure diseases, similar to the insulin case, reducing the cost and increasing the effectiveness of therapies.
      2. production of bacterial species able to consume and transform substances that are toxic for us
      3. bacterial species able to deliver a pharmacological payload near the source of the disease. Today we inject stuff in our body, for example to kill cancer, but we poison every single cell, even the good ones. What if a bacterial species is able to detect and attach to a tumor, and then start producing an anticancer drug right there ?
      4. production of electricity from biological sources. Take wood or sugar, let bacteria digest it and promote electricity creation (a so-called microbial fuel cell). It’s clean, renewable and easy to control. We already do something similar with Biosensors to evaluate the amount of glucose in blood.
      5. production of biofuels from garbage or pollutant, like used plastic.
      6. understand how a simple system like a bacterium works will give us the chance to understand more complex systems

      Yes, some will probably be scared at the idea of such inane level of control: biological weapons, superbugs… danger! danger!… but if you really stop for a moment, check some history, and think deep, you realize that biological warfare is nothing new: people in the middle ages threw corpses hit by plague beyond castle walls to kill the opponents via biological warfare; humanity does not need to create a powerful bacterium as a weapon: a large amount of them are already available in nature, ready to be harvested, and they could go straight on the tip of some rocket ! Being scared that this new technology could be used by mad, aggressive people as a weapon is not an issue. Again: the biological weapon is already out there, since the very beginning. This is the reason why biological weapon stockpiling and production has been banned since 1972 (Biological Weapon Convention) and only defensive research is allowed and pursued.

      In fact, if you think about it, understanding how bacteria work is actually the only way to find effective protection, and not only from human madness…There is a bigger menace out there to be worried about: the pure, crystalline natural cruelty, wiping thousands and thousands of species out with not a blink of compassion since 4 billions years. In 1918, the so called spanish flu wiped out 6% of the world population of that time. Six percent. We humans do not accept this harsh treatment from cruel nature, and we found a way to understand its mechanisms and use them at our own advantage. Our life today is twice as long and many times safer than the life of our ancestors, just 100 years ago: think about living in a world with no anesthesia, no penicillin, no anticancer drugs, no social security or medical assistance, with sounding remedies like skull trepanning, bloodletting, or Hirudotherapy.

      Are you really scared of the 21th century ? I’m not.

      Posted in Bioethics, Biology, Chemistry. Comments Off »

      Eight molecules that changed the rules of the game: Cisplatin

      Rule changed: revolutionized the treatment of cancer

      Cisplatin

      Cisplatin, formula [PtCl2(NH3)2] is a very simple compound of the precious metal platinum. It revolutionized the treatment of some types of cancer, in some cases with almost total chance of success, and it can be considered to full extent the “penicillin for (only some, unfortunately) cancer treatment”. (more…)

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