Darwin's Doubt I

Recently, I watched an interview with Stephen Meyer on Vimeo. In the interview, he discusses his latest book 'Darwin's Doubt'. Meyer is a member of the Discovery Institute and promotes the idea of 'Intelligent Design'. Now, I, as a molecular biologist, know for a fact that life is very poorly designed. Consider us, humans: we suffer backaches, headaches, joint pains, women run tremendous risk when giving birth and we need to wipe our asses after we poop. All results of piss-poor design. Our body plan doesn't suit our upright gait and our brains are too big. On the molecular level it gets even worse. Seemingly simple tasks are executed by hugely complex molecular machines and there's a lot of wasteful cycling of components. All this is easily explained from our origins. We gradually developed through evolution to become the diabolical master minds that we are today.

Since gradual evolution, through mutation and selection, is such a blatantly obvious process and such a beautiful and explanatory theory, I decided to read the book and try and discover what Meyer's problem with the theory of evolution was. I knew from the interview that he was wrong on many issues but Meyer struck me as too intelligent a man to be simply ignorant. He was clearly educated, so how could he be so wrong? I don't readily attribute to malice that which can be explained by ignorance, but perhaps he had a hidden agenda? Or was there something else to his theories?

Short answer: no. Meyer speaks with eloquence and authority about a subject he doesn't even begin to understand. In the next blog posts, I aim to enlighten my readers about Meyer's mistakes while I'll try to explain why he's wrong and what's the right way of interpreting the data. I fully understand that not everyone is a trained molecular biologist and so the intricacies of the evolutionary process may be hard to understand. Unfortunately, the headlines don't help you much, as the media frequently over-states the conclusions from scientific research. Even the actual research papers won't help you much, as scientists nowadays are inclined to over-state their conclusions too. It's understandable, since otherwise we can't convince journal editors or peer-reviewers to publish our work. Thus, the only way to really determine what can and can not be concluded from scientific research is to dig into the data and find out for yourself what they say. Data never lies (unless it's fabricated, but that's not so easily done anymore).

So is Meyer just ignorant then? Well, no, not really; he could have asked for an explanation of the data, so ignorance is no excuse. Fact is, as he reveals in the last chapter of his book, that he lives in mortal existential terror. He's simply afraid that is he wasn't created by some creator for some purpose, his life is meaningless and therefore worthless.

Since I was born and raised without religion and never felt the need for any gods in my life, this attitude always puzzles me a bit. Yet, I've have, through my travels, frequently encountered true believers who were simply afraid of divine punishment if they didn't fulfill their duties as good Christians, Muslims, Buddhists or what have you. This is perfectly understandable in rural areas where petty farmers are completely dependent on random natural forces for their existence. The only thing the can do is pray and hope their gods will listen. Yet, in modern society, this need for faith seems a bit redundant.

Why would your life be meaningless, unless there was a god who created you? Your life has as much meaning as you give it. The odds of you being alive today are negligible and yet, here you are! Bravo, I say! Now go and make the best of it. You'll never have another chance. It also doesn't really matter how you live your life, as long as you live it well. The only important thing is that everybody else has as much of a right to a good life as you do, so do well to others. Not for a divine reward, but simply out of respect. Is that so hard? Does that really require divinity?

In episode 20 of season 6 from Star Trek: The Next Generation, the Enterprise crew discovers a series of clues hidden in the DNA of distinct alien races that lead them to uncover that all of those races had a common ancestor. The figure in white is a projection of this ancestor revealing her message, as hidden in the DNA of humans, klingons, cardassians, romulans and some other spcies. It's a good episode!

Either way, Meyer doesn't want to preach in his book, so instead he constructs an elaborate argument on why Darwinian evolution can't explain the Cambrian explosion (the sudden appearance of many animal life forms in the fossil record some 540 million years ago) and that this must have been a creation event. He's careful not name his creator, lest he offend some god or another, I suppose, so I'll make a logical assumption that explains the creator: Life on Earth was seeded by an alien race who carefully programmed the DNA of early life forms to evolve into us today. This is how I chose to interpret the theory of intelligent design and it's a fair interpretation. Those aliens themselves, of course, evolved through random Darwinian mechanisms, but since the odds of this occurring are quite rare, they found themselves rather lonely. Thus they seeded some other planets with life, in the hopes of having someone to talk to eventually. Bit of a stretch, but it's also the plot of a Star Trek: The Next Generation episode and more likely than divine creation, so I'll go with it.

Over the next few posts, whenever I find the time and motivation, I'll go over Meyer's arguments and explain exactly how wrong he is (every single time). Nothing personal, of course, everyone is free to believe what they want to believe, but when they start telling lies on my turf, I get a little cranky. I won't tell you how to read your Bible either and I won't have you converting the innocent with pseudoscience.

What’s up with the bees?

No bees here!

Bees are dying and blogs are buzzing. A phenomenon called ‘colony collapse disorder’(CCD) has been decimating bee populations in North America and Europe. Bloggers are eager to put the blame pesticides, herbicides, GMO crops and mono-cultures, but what’s really going on? What’s this mysterious bee disease, what should we do to prevent it and should we be really worried? Will our crops fail and nations starve when the bees die out? Time to review the different facts and factors involved and see if we can make some sense out of all the buzzing.

Bees: who are they and why should we care?

First of all: not every bee is a honey bee but, in the context of CCD, honey bees are all we care about. It’s the honey bees that are dying. Solitary bees, carpenter bees, bumblebees and what not are not under threat. There are in fact almost 20.000 known species of bees . Yet, honey bees are important pollinators. By buzzing around and hopping from flower to flower they pollinate the flowers and this is essential for some plant species to bear fruit. Without pollination, we’d have no  apples, no pears, no grapes (and no wine), no kiwi’s and no cacao. The list goes on . Are honey bees the only pollinating species? Not at all. We won’t see the instant demise of all of our crops once the bees are gone. Honey bees are an important pollinating species, but far from the only species. Other insects pollinate too, such as bumblebees, hoover flies, midgets and even mosquitoes. In addition, animals such as humming birds and fruit bats pollinate many crops in regions where they’re abundant. Farmers tend to utilize honey bees to pollinate their crops, since it’s simple enough to put up a couple of hives in your orchard and their honey is a nice bonus, but they’re hardly essential. As far as I could find, only a few fruit crops appear to depend on pollination by honey bees alone, such as lemon and lime. Still, honey bees do put in a lot of effort in the pollination of many of our crops and crop-yields may very well be severely reduced without honey bees around. However, it’s a gross overstatement that our world would perish and our civilization collapse without the bees. Such overstatements sell movies, but don’t really help us much otherwise.   

Colony collapse disorder: what’s that then?

The sudden disappearance of all the worker bees from a hive is what causes a bee colony to collapse. No worker bees, no food, no hive. This is not a new phenomenon, though the name CCD was only coined in 2006. Entire bee colonies have disappeared since ancient times and this phenomenon has been labelled as “disappearing disease” or “spring dwindling” (Oldroyd, 2007). However, the rate of honey bee colony loss reported in particular since the 2006-2007 season, is quite unusual. What really happens in CCD is unclear. The bees don’t die at the hive, as such, they simply disappear. They fly out and never return to their hives. Do they get disoriented and lose their way? They fly out and die elsewhere? Nobody really knows. A number of causes have been proposed for this phenomenon, primarily infectious diseases and chemical contamination of the bees’ environment with pesticides and/or herbicides.

Infectious diseases

Bees, like any other living thing, are susceptible to a number of pathogens including mites, fungi and viruses. The most prolific bee-killer is the mite Varroadestructor. This mite has been spreading throug the world since the 1960s and has, in fact, been responsible for decimating bee colonies, including domestic honey bees and wild bees. However, chemicals have been developed that kill the mites, so called ‘miticides’ and, although the mite still infects virtually every colony, the infection is under control and rarely results in colony destruction loss (Oldroyd, 2007).  In addition, it seems that the mites have become less virulent while feral bee populations have mostly become resistant. Another likely candidate for an infectious disease contributing to, if not causing, CCD is a combination of a fungal and a viral disease. Invertebrate iridescent virus (IIV6) and the fungus Nosema caranae have been linked to CCD. However, the study identifying the IIV6 has later been called into question. Another pathogen associated with CCD is the parasitic phorid fly. This fly lies its eggs in life bees and when the eggs hatch the larvae eat the bee alive. Before the bee succumbs, the larvae control the bee turning the bee into a ‘zombee’. Such a scenario might explain why the bees of CCD colonies go missing since infected bees won’t return to the hive to die. However, further investigation into the role of the phorid fly is still pending and if you think you see a zombee you can help by catching it and reporting your find on the Zombee Watch site. Altogether, although CCD appears to be linked to an infectious disease, no clarity exists yet about the pathogen that may cause it.

Pesticides, herbicides and GMO crops

First, there’s absolutely no evidence that genetically modified crops are associated with CCD. To the contrary, in areas where high amounts of GMO crops are present, such as in Illinois, no cases ofCCD have been reported. The alarmist blogs have been blaming the herbicide Round-up, glyphosate, for the death of bees, but again, there’s no evidence for such claims. In fact, the latest research shows no effect whatsoever of glyphosate on bee health. The only substances that seem to affect bees negatively are the neonicotinoids used as pesticides. These compounds were designed as relatively safe insecticides to control pest-species that damage our crops. Initial studies showed little to no effect on foraging honey bees, that might ingest the compound through contaminated pollen. However, a concurrent study indicates that ingestion of the compound might render bees more susceptible to viral diseases. Thus, the neonicotinoids are still suspect and will remain so, pending further investigation. The E.U. has therefore banned the use of these substances for the time being.

Conclusions

We still don’t know for certain what’s causing CCD. A combination of factors seems likely. Over-all, the phenomenon appears to be pathogen-related and the parasitic phorid fly seems a likely cause. A loss of plant diversity may also be a contributing factor, as may certain chemicals in the environment that render the bees more susceptible to infection. However, bee populations are already seem to be recovering, bees are not exactly on the brink of extinction. I don’t think there’s a reason to panic, but it never hurts to be cautious. 

The Sense of Vaccines part III

Colored electron micrograph
of a dendritic cell

I hope I convinced you that vaccines work and that they're safe. They internet is full of these sort of sites, that give you false, unreferenced information about vaccine safety (in this case about the human papillomavirus (HPV) vaccine). They're against vaccines and will make the adverse effects sound worse than they are. However, without references and statistics, it doesn't mean anything that "many of the vaccine recipients were stricken with serious and life-threatening disabilities". How many? How serious? How are these disabilities linked to vaccination? How many women that were not vaccinated developed these disabilities? The truth can be found here and the original study here.

Scientists don't lie about such things; it's not in their interest at all. Their findings? "We found no statistically significant increased risk for the outcomes studied". They checked for the "life-threatening disabilities" mentioned on the first site and did not find them. They mentioned them because they checked for them, not because they found them as the alarmist site implies. What they did find were 5 cases of blood-clotting (venous thromboembolism; VTE) among 600,000 women studied (five in six-hundred thousand!) and all of these women were at high risk for VTE anyway, due to smoking, obesity, coagulation disorders etc. So yes, the HPV vaccine is safe as well. Only time will tell whether it will really protect against cervical cancer, though. It only prevents infection against 4 out of 30-40 strains of HPV, although these do include the ones responsible for 70% of the cases of cervical cancer.

Now that we have all that covered, I want to discuss how vaccines actually work. How does a vaccine make you immune to a disease and why should you have your baby vaccinated? Shouldn't a healthy diet of mother's milk and fruits later on be enough to protect your precious child? The key to understanding vaccination, or immunization, is the dendritic cells (see top left).

Dendritic cells are the first line of defense against anything invading your body that doesn't normally belong there. They're just tiny little cells and there aren't that many of them, but they do get around. These little cells are constantly on the prowl through your skin, the lining of your gut and well, all those places the inside of your body is likely to meet the outside world (you can use your imagination). They just spread their little tentacles everywhere and sample the environment, that's what they do all day, every day.

In the figure below I've illustrated what happens when a dendritic cell, on patrol in your skin, encounters an antigen (that is: a vaccine). In the left panel, the dendritic cell encounters just the antigen and is intrigued. In the right panel, the antigen is given with an adjuvant, an addition to the vaccine, that resembles a molecule commonly found when the body is infected, a pattern that dendritic cells are trained to recognize as a sign of trouble. The dendritic cell that encounters the antigen+adjuvant, isn't just intrigued, it is alarmed! As a consequence, it immediately migrates from the skin, through the lymphatic vessels to the lymph node.

Figure 1: A Dendritic Cell encounters Antigen

In the lymph node, our dendritic cell, loaded with antigen, meets with B cells and T cells to show his prize. B cells (and also T cells) form a very diverse mob and most of them are not at all interested in what our brave dendritic cell has to show. Each and every one of these cells is trained to only respond to one specific threat  and if that isn't the one our dendritic cell is carrying, the one we just got vaccinated against, they're simply not interested. I've illustrated this in figure 2, below.

Figure 2: Our Dendritic Cell meets with B cells in the lymph node

Now you will also understand why a vaccine with whole virus is better than a recombinant vaccine with only a small part of the virus: the odds of meeting a B cell that recognizes one the many different parts of a virus are simply bigger than meeting a B cell that just so happens to recognize only the one specific part you put in your vaccine.

When the dendritic cell and the B cell that recognizes the antigen meet, they form a stable interaction and dance around for a while. I don't just make this up, it really happens! Below, I've posted a cool movie that demonstrates this interaction in the lymph node of a living mouse. The dendritic cells are green, the T cells (in this case) are red. Notice how the dendritic cell meets with many uninterested cells until it finally forms a stable interaction with one cell.

I've mentioned B cells and T cells and both can be found in the lymph node, both are trained to recognize a very specific antigen (your B and T cells can basically recognize anything that is not 'you') and both interact with dendritic cells, but they have very different jobs. After B cells encounter the antigen they're were born to  detect, they multiply, change and start producing antibodies. The antibodies can recognize and stick to the exact same antigen the B cell knows and you can imagine that a ton of these antibodies binding to a virus are going to cause trouble for the virus. Any particle coated with antibodies, will in fact be 'eaten' and destroyed by the other cells of your immune system. T cell don't make antibodies but they can either help the B cells, activate the other cells of the immune system or even destroy infected cells (or tumor cells!) directly. Your lymph nodes swell up from all those T and B cells multiplying and getting active.

However, your immune system doesn't stay on red alert after each antigen you encounter! Otherwise you'd be constantly sick and feverish. Instead, when the infection is cleared and no dendritic cells come in anymore carrying fresh antigen, the immune system goes to sleep again. However, so-called 'memory cells' remain. They carry the memory of the infection they encountered, the memory too, of the vaccination. It is because of these memory cells that your immune system reacts much faster and much more effective to a second encounter with the same antigen. They awake and raise the alarm in hours, instead of days, when another dendritic cell comes in with despised antigen they knew before!

Memory cells can live a long time, but not forever. About 60 years is the life-span of a memory cell. That's why elderly people are again susceptible to diseases they had immunity against before. We don't really know why some infections and some vaccines give good immunological memory and others do not. Life vaccines generally work best and longest, but why? Research on that topic is, of course, ongoing. It is also good to realize that some vaccines wear off after 10 years or so. The pertussis (whooping cough; the 'P' in the DTP vaccine) vaccine, for example. Whooping cough is not lethal for adults, only really for infants, so it doesn't really matter for you. However, you can't transmit immunity that you don't have to your infants by breast feeding .
How does that work? Your immune system always makes some antibodies against everything you're immunized for. When you're pregnant, those antibodies are shared with the fetus in your womb through a very ingenious mechanism that filters out all antibodies that might otherwise kill your fetus (after all, the fetus is only half 'you' and half its dad). Your baby is therefore born with some immunity. Immediately after birth, babies' own immune system starts developing and reacting to everything it encounters. Mother's milk also contain antibodies and some immune cells that further protect your baby, but only temporarily (and only from whatever you're still immune for). Vaccination (and only vaccination!) at about 2 months will help your baby build lasting immunity against all those diseases you don't want your child to get.

Fruits, a healthy diet and life style, homeopathic medicine and prayers won't protect your child, since none of these things challenge the immune system with antigen. None of these things can help you build immunological memory for lasting protection. A healthy life style can fortify your immune system to some extent, but even a fortified immune system can only respond rapidly to what it encountered before. It would still need about a week to respond to something new and a week is plenty of time to die from a tetanus infection, for example, or for measles, HPV and many other viruses to make themselves at home in your body and dodge your immune system altogether.

To some extent, vaccination is your decision. You want to brave the Amazonian jungle and die of yellow fever? Fine, go ahead, be my guest. But you think about going back home with the virus and make us all sick! If you don't vaccinate your child against whooping cough, measles, polio or HPV, it isn't just you who runs the risk, it's others too! Newborns hardly have any protection at all against whooping cough, for example, and will die if they catch the disease. Is that what you want?

The Sense of Vaccines part II

In this post, I would like to focus on the potential adverse effects of vaccination. I've researching the issue and there seem to be several concerns among parents. First, there's the concern of illness caused by the vaccine. As I discussed in my previous post, there are several kinds of vaccines. Only the life, attenuated, vaccines can actually cause the disease they're supposed to protect against. Of those, only the measles and polio vaccines have been known to cause serious illness.

In 2005, a new combination vaccine for measles, mumps, rubella and varicella (chickenpox) was approved (MMRV) and this vaccine has been in general use ever since. Do you know how many cases of measles were caused by his vaccine? It's zero. None whatsoever. Some 5% of vaccinated children develop a fever, some 1% a rash. In a few cases, some of the younger children, the fever causes further problems, such as febrile seizures, but nothing major. The vaccine has been linked to more serious conditions (coma, brain damage) but these are so extremely rare that it is impossible to say whether they're an effect of the vaccine or have another cause. The MMRV vaccine should therefore be considered safe. New cases of measles in the developed world are exceptional and only occur in the non-vaccinated population. However, because measles has found a safe haven in those populations in the bible belt and among the tree-hugging hippies that do not get vaccinated, we have to keep vaccinating our children.

From Wikipedia

The polio vaccine is a different case. There are two vaccines for polio: an oral vaccine with life virus and an injection with killed virus. The injection is absolutely safe, the oral vaccine caries a (very minor) risk but offers better protection and is cheaper to produce and distribute. However, the number of cases the polio vaccine prevented far outweigh the number of cases it caused. In 1988, some 350,000 children world-wide got polio. In 2007, that number had dropped to 1,652 cases as a direct result of the world-wide vaccination campaign. Polio has been eradicated from almost all countries, with the exception of Nigeria, Pakistan and Afghanistan (WHO). Not the healthiest countries in general.

Another concern about vaccination was raised in 1998, when a study published in the high-ranking medical journal Lancet suggested a link between measles vaccination and autism. What the study actually reported were 12 cases of children with inflamed bowels who also had neurological diseases, including autism-like symptoms. The parents of the children thought their vaccination against measles caused the bowel infections and the bowel infections led to the neurological disorder. However, further study indicated no link whatsoever between the inflamed bowels and the measles vaccine and, as it turned, the parents were actually plotting a class-action law suit with some lawyers to sew the vaccine producers. They just needed a doctor to testify. Altogether, this proved to be a very bad idea, as the consequent vaccine-scare led to several outbreaks of measles, resulting in at least one fatality in the UK. When no evidence was found that measles vaccination caused the children's illness and the authors realized what severe consequences their report had, they retracted the publication in 2010. In other words, the only evidence that linked measles vaccination to autism was false and has been retracted. Further studies found no link. Find a free review here.

Finally, some concerns exist among parents about mercury in vaccines also causing autism. This is based on the fact that a mercury containing compound called thimerosal used to be added to vaccines as a preservative. Used to be. This compound is no longer added to vaccines. It has been absent from vaccines in Europe since 1992, and in the US and Canada since 1999. Also, thimerosal, which is metabolized to ethyl mercury in the body, is not a neurotoxin but a nephrotoxin; it causes damage to the kidneys, not the brain.

Has there been any change in the number of reported autism cases since thimerosal is no longer added to vaccines? Yes, in fact, the number has gone up. This is mostly due to the fact that more children are diagnosed with autism as a consequence of increased awareness and recognition of the disease, but it is safe to say that mercury in vaccines never caused autism. In addition, the occurrence of autism in the population that choose not to vaccinate as a consequence of the vaccine-scare in the late 1990's is no different from the general population. There is no link, in other words, between autism and vaccination.

In conclusion, modern vaccines are safe. Yes, they can cause some mild illness, but nothing really serious, while the consequences of not vaccinating are very severe indeed. So, if you care about your children and the children of others, get them vaccinated!

In the last part of this series, I'll finally focus on the mechanism of vaccination.

The Sense of Vaccines

Vaccination works. There's no real reason to doubt that. How many people do you know who suffered from small pox, polio or even measles? I don't think I know anyone who had any of these diseases. All thanks to vaccines. Still, it appears, there are many 'skeptics' on the internet who doubt the efficiency of vaccination. Mostly, I suppose, because they're afraid to harm their children by vaccinating them. Odd, since there is absolutely no evidence whatsoever that vaccination is harmful for children and tons of evidence that it is beneficial. Most of those 'discussions' end in shouting wars and I've had a look at some of the blogs about the topic, but I really can't be bothered reading them (this one hurts my eyes!). They're generally very badly written by people who don't seem to have a clue what they're talking about.

Fortunately for you, there's me. I'm a natural skeptic and I never stop asking questions, but if the data overwhelmingly show that vaccines work and there is no evidence (none!) to the contrary, what is there to be skeptic about? In this present post, I'll provide you with some evidence that vaccines really work (but seriously, why do you even doubt that?) but I'll also explain why and how they work. I know that true believers can not be convinced with evidence and I would normally leave them alone. However, in this case, the believers (that is the 'vaccines are evil' crowd) are actually endangering all the rest of us. Many infectious diseases besides small pox would have been extinct already if the viruses that caused these diseases hadn't found a safe harbor in the bible-belt.

As I mentioned, I don't really understand the anti-vaccine lobby. Their websites are horrible and the arguments against vaccines, as far as I've seen them, are mostly false. Let me start with a little graph that shows the efficacy of some common vaccines.

From Immuno Biology, 5th Edition, by Janeway et al.

Diphtheria, Polio and Measles have all virtually disappeared from the USA since the vaccination campaigns started against these diseases. Small pox and rinderpest have been eradicated world wide. These diseases have been around for a very long time. For over 10,000 years (!) people have suffered from small pox. Now it's gone. Completely gone. Is this just a coincidence or a consequence of the world-wide vaccination campaign?

Let me explain how vaccines work and why they work, if I haven't convinced you yet that they work. There are five basic types of vaccine: killed, attenuated, toxoid, subunit and conjugate. Plus there are some experimental vaccines still under development, that may be safer and more effective than existing vaccination strategies.

Killed vaccine is rather obvious: it's the virus or bacterium that causes the disease but killed so it can not multiply and cause disease anymore. Injection of the whole thing will fool your body into thinking it's infected and prepare the immune system for an actual infection. Killed vaccines are generally safe, but can make you a bit sick. This has to do with your innate immune system over-reacting to the contents of the vaccine and isn't really anything to worry about.

Attenuated vaccines are live vaccines. Those can be dangerous. It is essentially a mutant of the same virus as the one causing the disease. The attenuated mutant is not infectious anymore and should not make you sick (at least no more than the killed virus), however, there's a very small chance that the attenuated virus has mutated back to a wild type, active, virus. This is why large-scale vaccination against, for example, measles, can sometimes lead to a small, localized, outbreak of the disease. Attenuated vaccines are not ideal, but they generally generate a better immune response that the other vaccine variants.

For toxoid, subunit and conjugate vaccines, only a small portion of the pathogen, the virus or bacteria that causes the disease, is used. A small dose of toxin, for example tetanus toxin to protect against tetanus infection, can also make you a bit sick, but not as sick as the real deal and it certainly won't kill you. I can't really find any reliable numbers on vaccine-induced deaths, most of the claims are on the anti-vaccine sites that hurt my eyes and the sources are unclear. Attenuated vaccines can result in a lethal disease, true. But the odds are very small and they are obviously being avoided now. It's a bit of a trade off, really, what would you rather have? A small illness from the vaccine? Or death form the disease? If the disease does not occur in your region, there's obviously no reason to get vaccinated and risk vaccine-related illness. I never got vaccinated for yellow fever, since I've never traveled to South-America where this disease occurs. I would get vaccinated if I were to travel to South-America, since I'd rather risk illness from the vaccine than death from yellow fever. Plus, if I don't get vaccinated, there's a chance I'll bring the disease back with me and infect others! This brings me to the bible-belters.

In the bible-belt, and there's one in every country, people believe that diseases are punishments from their god and should be accepted. If god wants to kill their children, well, then he must surely be lonely in his heaven! This, at least, is an argument a certain pope used when the children of Rome were dying of small pox (or some other disease, I can't remember). The problem is, however, that is they don't get vaccinated, diseases like mumps and measles can hide out in their compounds and will every now and then rear their ugly heads. As a consequence, children outside the bible belt will have still have to be vaccinated. If that vaccine makes them sick; the actual disease is worse. If only everyone would just accept the vaccine, those diseases could be exterminated and with them, the need for population-wide vaccination!

Now, why is it, then, that we have to keep vaccinating against certain other diseases, such as the flue? The problem with some pathogens is that they don't just infect humans, but also certain animals. The flue virus hides in birds and pigs as well. If we want to get rid of flue, we would have to vaccinate not just all the humans, but also all the birds and pigs in the world. That's a bit much, isn't it? Especially since flue keeps re-combining, changing it's coat, inside those pigs and birds!

Below, I've posted a graph to demonstrate again that vaccination works.

From Immuno Biology, 5th Edition, by Janeway et al.

What this graph shows is that when you challenge an animal (a rabbit in this case, but it could be a mouse or a human too, same thing, really) with an antigen (in other words: when you vaccinate it!) you get a certain response after a lag phase of a few days. Now, if you challenge the animal again with the same antigen (in other words: when the animal encounters the actual pathogen after vaccination) the response is much faster and much higher. While the response to another antigen (B), that the animal did not encounter before, is much lower and slower. This proves that vaccination works and that is specific. The immune system has remembered antigen A and can now mount a faster, better response to it when it sees it again. I will explain how that works in the next update, since I feel that this one is quite long already and I'm afraid you might get bored if you have to read too much...

Arsenic and an Old Lake

Felisa Wolfe-Simon collecting samples at Mono Lake

About a year and a half ago, NASA announced a press conference "to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life." This led to wild speculations on the internet that NASA might have discovered extraterrestrial life, that they would finally admit that they had known about aliens all along! However, what it was really all about was a discovery by geomicrobiologist Felisa Wolfe-Simon, about to be published in the prestigious journal Science. What she claimed was that she found a bacterium in the sediment of Mono Lake in California that could incorporate arsenic instead of phosphorous in its DNA. In theory, life would therefore not be completely dependent on phosphorous (as we always thought it was) but could also grow in its absence and thus in extraterrestrial environments that we would normally consider to be devoid of life. A very exciting discovery in its own right!

Sunset at Mono Lake (my own picture)

Mono Lake is very, very old -about 760,000 years- and, because water goes in but doesn't really go out anymore, it is also very salty. It is not, however, devoid of life-as-we-know-it; brine shrimp live in the lake and migratory birds visit the lake to feed of the shrimp. Arsenic concentrations in the lake are higher than usual, but not toxic. Besides being geologically very interesting, famous for it's tufa towers, Mono Lake is also a very beautiful place and certainly worth a visit if you're in the area.

Arsenic-loving bacteria from the Wolfe-Simon paper

Now, when Felisa's paper came out a few days after the press release from NASA, I was highly disappointed and many other scientists with me. First, this new bacterium, GFAJ-1, did not represent a 'completely new form of life' but rather an old form of life that had adapted to survive at high concentrations of arsenic, such as found in Mono Lake. Second, the authors did not, in any way, conclusively demonstrate that GFAJ-1 could survive and replicate in the complete absence of phosphorous or that it incorporated arsenate, instead of phosphate, in its DNA. Trace amount of phosphate the bacterium's growth medium could easily account for its growth and they did not exclude that the arsenic they found in samples of DNA isolated from GFAJ-1 (through rather crude methods!) could simply be due to contamination of their sample. In addition, they showed no direct evidence that the arsenate was actually incorporated in the DNA of GFAJ-1. Canadian microbiologist Rosie Redfield extensively discussed these and other flaws in her blog, almost immediately after the paper was released.

Rosie Redfield

Redfield has subsequently attempted to culture GFAJ-1, as obtained from Wolfe-Simon, herself and perform the control experiments that Wolfe-Simon neglected to do. She has consistently posted her progress on her blog, responding to suggestions from readers in the process. Earlier this year, this led her to conclude that the Wolfe-Simon paper was indeed flawed; GFAJ-1 does not grow in the complete absence of phosphate and its DNA, even at high concentrations of arsenic in the medium, does not incorporate any arsenate. These findings have now been published in Science as well (also freely available here), back to back with a paper from another group that found the same thing. Redfield's experiment with 'open science', publication of her constant progress on her blog, was an interesting one in it's own right. Hopefully one that will be repeated more often, especially where controversial issues involved.

Redfield's evidence; no phosphate, no growth

An extraordinary claim requires extraordinary evidence and Wolfe-Simon did not provide this evidence for her claim. It's therefore hardly surprising that the entire scientific community fell over Wolfe-Simon like an avalanche and that this caused poor Felisa more than a little bit of stress. She admitted that the data presented in the Science paper were somewhat preliminary and that she hoped the paper would get her the help she needed from specialists outside her direct field to really determine whether or not the DNA of GFAJ-1 really incorporated arsenate instead of phosphate. I find that defense a bit weak. Why would you even submit a paper to a prestigious journal like Science if you're not absolutely, positively sure about the validity of your claims? I certainly wouldn't. Plus, if you are aware of the flaws in your paper, then why don't you connect to the specialists you need to clear up those flaws? It's really no excuse at all and the paper is just full of obvious flaws (as Redfield pointed out in her blog).

Someone should have stopped her from staking such claims without the evidence to support them. In part, NASA is to blame for hyping their press release and making it sound like they had discovered more than they had. The journal Science is to blame as well for their obvious over-eagerness in accepting this study for publication. Qualified peer-reviewers would have never allowed this. I wouldn't have allowed it. I'm guessing that the editor decided to publish in disregard of the peer-reviewers' criticisms, hoping to generate publicity (and they certainly did!). This case would certainly argue for the co-publication on-line of the reviewer reports of every publication. Some journals already do that, but it still isn't common.

Wolfe-Simon has staked the hypothesis that arsenate might replace phosphate in some organisms before and her Science paper was supposed to be the proof of the pudding. She apparently wanted to prove her hypothesis so badly that she forgot about the fundamentals of science, got over-excited, forgot to falsify her findings and got blinded by the positive evidence. Scientists are only human in the end, we see what we want to see, especially when we get excited about our findings. In theory, that's where peer review should step in. In this case, peer review failed, probably as a consequence of the Science editor looking for sensation (although the reviewers might have been incompetent too). I wouldn't go so far as to call Wolfe-Simon a fraud. She merely suffered from over-confidence and a certain dose of naivety. I hope this experience has not embittered her and that she has come to see that she was wrong. It is very hard to admit when you're wrong, especially about something you really believe in, but I really hope she will admit her mistake and emerge from this experience that much wiser.

Most of all, I hope that other scientists will learn from this scenario that they should always, always, question their own data and their own hypothesis! If the data leaves any room for doubt, get back in the lab and eliminate that doubt! It has become a worrisome trend among scientists to focus on positive data, data that supports their pet hypothesis, instead of looking for ways to refute the hypothesis. Could the data be explained in any other way? That is the question that should always be asked. If you find another explanation, exclude it. That is the way science is supposed to work, and if you can't think of a better explanation for your data, ask a colleague. There's something to be said for making bold claims and building hypotheses, but the top-tier journals are not the place for that. Please don't contaminate the literature with those half-supported claims! In the end, there's nothing wrong with rejecting your hypothesis as false. Better to admit you're wrong than to stubbornly defend an indefensible position.

Time Travel and Higgs

I wanted to write about vaccines, but nerd-news of the week is the potential discovery of the Higgs boson, so I'll write about time travel instead. What do the Higss boson and time travel have to do with one another, you ask? I'll get to that, don't worry, but first I must explain what this Higgs thing is all about.

To start: The Higgs boson has not been discovered yet as such. Something has been observed and that something has properties consistent with the properties a Higgs boson would have, if such a thing existed. Basically, they see a bump in a line and that bump is most definitely there. Could be a Higgs boson, could be something entirely unexpected. So really, no guarantees.

Second: What is this 'Higgs boson', then? In short: It's the particle that gives all other particles their mass. A while ago, the author of PhD Comics, Jorge Cham, made a nice little movie to explain what the people at CERN are doing with their Large Hadron Collider (LHC; it has not destroyed the world yet (if you're a nerd, view the source of that site)). I've posted it below.

 

So, the Higgs boson is evidence of the Higss field and it's the Higgs field that gives particles their mass because they have to move through it. Simple, really.Now what does that have to do with time travel? It's all in Einstein's famous formula: E=mc^2. That is: Energy=mass multiplied by speed squared. 'Speed' is in this case the speed of light in a vacuum, which is pretty fast, which is why, if you would convert a given mass into energy (say in a nuclear explosion) you would have lots of energy indeed. 'Speed', of course, is distance/time, and that's where time enters the mix.

Einstein's law in action

We could also write the formula like this: E=m*(distance/time)^2. In that case, time (t) would be distance divided by the square root of energy divided by mass (sorry, I don't know how to insert mathematical formulas in HTML). This already says it all, because, as you know, division by zero is impossible! So, no mass, no division, no time. You need mass to get time! This makes the Higgs field pretty important.

The interrelation of mass and time has been known for a while. Einstein reasoned that space-time was curved. Basically, a great big mass (like a planet) makes a dent in space time, much like a ball would in a suspended table cloth. The slope of that dent is the speed at which time flows. So if you move away from the mass, time would slow. This has been proven. If you move a atom clock away from  the Earth it moves slower than it's equivalent on Earth. Of course, you can never stop time, since you would also have mass and thus make a dent in space-time, no matter how small. 


However, the formula above does not allow for mass to be negative, nor for energy to be negative. There is no such thing as negative energy or negative mass in our universe as we know it. Distance can't be negative either, since whether you go forwards or backwards, you'll still have traveled a certain distance, so that's not the way to go. It has been suggested that if you would exceed the speed of light ('c'), you would be able to travel back in time. Why? Something to do with relativity. Time is relative to speed. The faster one travels, the slower the time. Light speed is the constant here, the turning point. If you would travel at the speed of light, time would stop. This is simply how our universe works. No special reason for it. But it also means that if you would go faster than light, time would move backwards relative to you!

From 'Fake Science'

Now, this is entirely impossible. There's a reason light travels at light speed: It can't go any faster. Universe doesn't allow it. If you want to go faster, I suggest you find yourself another universe. However, for the sake of argument, let us try to at least accelerate to the speed of light. This can be done, in theory. At a comfortable constant acceleration of 1g, that is Earths gravity (9.8 m/sec^2), we would reach light speed in about a year (354 days, to be exact, you can do the math). But! But! Mass is relative to speed, to acceleration. The more you accelerate, the more you 'weigh'. You'll notice when a plane accelerates just before take-off and you're pushed back in your chair. This is because mass is slow. You need to put energy in to get it up to speed, and the more you want to accelerate, the more energy you need. That's why your car simply won't go any faster at a certain stage; not enough power from your engine. This increase is exponential and the closer you get to light speed, the closer the amount of energy required reaches infinity. There isn't enough energy in the universe to accelerate even one mass bearing particle to light speed, let alone your whole body and the ship and fuel you'd require to keep you safe and reach those kinds of speed in the first place. That's why mass-bearing particles don't travel at light speed. They can't Not even the LHC can give them the energy required.

Back to the Higgs! The Higgs field gives us mass. Cancel out that Higgs field, we would have no mass. No mass, means no energy required to reach light speed! So there you go, get yourself an anti-Higgs generator and you would instantly reach light speed! And die in the process. You see, mass is a property of your matter. Take that away and what do have? A handful of photons. Try to re-assemble those! The explosion would be rather formidable, remember E=mc^2? Well, a mass of 78.4 kg (that's me) would therefore yield an energy of approximately 7 times 10 to the 20th joules. That's about 7 million nuclear bombs of the type used in Nagasaki. I don't think I'd volunteer for that experiment.

So, what good is that Higgs, really? And that whole LHC? Can't use the Higgs to travel through time, that will never work. The LHC won't destroy the world, sine the microscopic black holes it can theoretically produce would evaporate almost instantly. You can't even produce enough anti-matter with the LHC to blow up the Vatican (as per the plot of Dan Brown's 'Angels and Demons'). Sure, anti-matter is produced, but the anti-particles almost instantly react with their normal counterparts to explode into more photons. Useless!

Of course, that doesn't negate the fact that we've gotten one big step closer to understanding our universe. And that's a pretty big deal. We need to understand the place that we live in, if we want to live in it much longer. Higgs is an important step forward. Maybe now we can have those quantum computers they promised us, please?