Monday, October 5, 2009

Inbreeding and a Genetics Lesson

Recently in a discussion about something completely unrelated, a person made some very incorrect statements about how inbreeding works. Their argument was that it actually benefits small populations, helping to eliminate disease- and disability-causing genes from the gene pool.

Um, no, that's not how genetics works. At least, not in people. See, breeders of all kinds, but especially those who deal with livestock, use some degree of inbreeding to produce the best traits in the largest proportion of animals. They tend to use quite a few females, but very few males. So a half a dozen males - let's say dairy breed bulls - that have historically produced daughters that calve easily and give lots of high-quality milk may be the fathers of hundreds of children (ah, the miracles of sperm production and freezing), and some of those children may be more males that are also excellent breeding stock and are bred to many of their own half-sisters in an attempt to make the grandchildren cows even better producers. This, in combination with a careful management program and the odd infusion of outside stock, is a very successful way to make a highly inbred, highly successful herd of dairy cattle.

But wait! We're not dairy cattle! The reason inbreeding works to remove less fit alleles from a cattle population is because we kill off all the ones that aren't good enough out of the offspring. We, as human beings, go looking for cows who have poor milk yields, diseases, or defects, and we cull them without letting them reproduce, or in conjunction with not breeding their existing offspring (i.e., selling them for veal). This is a very artificial environment with extremely unrealistic gene flow conditions. We certainly can't artificially inseminate women with sperm from a small group of men chosen to be the breeders and kill (or at least sterilize) all the other men, and we definitely can't selectively kill babies with disabilities and the women that gave birth to them!

Lesson One: We Are Not Dairy Cattle. Human populations cannot be assumed to produce the same results from inbreeding as livestock populations, because the mating system and selection pressures are completely different.

This person quote-mined an article on wild bird populations (of all things!) to try to support the argument that inbreeding makes things better. However, the context of the article was that inbreeding is a problem that can be compensated for by birds mating with non-relatives most of the time even if they mate with a half-sibling once in a while. That is true. However, by compensating for inbreeding the researchers mean "offsetting the likelihood of nest failure" in inbred bird pairs. In other words, birds are far less likely to have surviving offspring in the inbreeding year, but the impact of that on their general reproductive success is small, as long as they mate with non-relative birds in other years, producing live, healthy chicks.

Do humans have babies every year? Technically we're capable of it, but most people don't. And even among those that do, very very few (hopefully none) are mating with a different person every year, raising babies for a year and then getting rid of them only to start over again the next year with someone new.

Lesson Two: We Are Not Birds.

Getting away from the tongue-in-cheek a bit here, let's talk a little bit more about why the initial statement of "eliminate disease- and disability-causing genes from the gene pool" is ridiculous. Not only can we not kill (or forcibly sterilize) people that have disabilities or genetic flaws - hello eugenics movement - but doing so would not eliminate bad genes. Not only are a large number of genetic problems recessive - that is, they are only disease-causing in people with two copies of the bad gene, so carriers are totally healthy - but there are also a number of diseases that are cumulative, ones that are due to spontaneous mutations, and ones that are not fully penetrant.

To explain in more detail, cumulative genetic diseases includes many types of autism as well as Huntington's disease. What happens in these cases is that the bad gene in question is bad because it has an excessive number of repeats in the "junk" part of the gene, and this number often increases in each generation. So someone who has Huntington's disease but does not show symptoms until their 50s may have children with the disease that show symptoms in their late 40s and grandchildren with the disease that show symptoms in their early 40s. There can be many generations with no problems, but once the number of repeats passes a certain threshold, each subsequent generation is affected and over time the disease gets worse. But before that threshold is reached, there is no way to know that the family is carrying the possibility of developing that disease. So inbreeding wouldn't make any problems show up - the gene needs time to copy that section more times, and inbreeding won't make that happen any faster.

Diseases caused by spontaneous mutations are not something inbreeding can help "weed out" either. About a third of haemophilia cases are de novo (Latin: newly occurring) mutations where neither parent had a bad gene. Since there is no way to predict when these mutations will happen, they will occur at random and at the same rate regardless of what kind of breeding occurs. Not to mention spontaneous chromosomal disorders such as Down's Syndrome are also impossible to predict and can happen to any couple, related or not.

Many diseases generally labelled "dominant" do not behave like one would expect when that term is used. Normally, dominant genetic diseases mean that if you have the bad gene, you have the condition. But a few strange cases where diseases thought to be dominant seem to skip a generation helped geneticists discover that many of so-called "dominant" genetic diseases are not fully penetrant; that is, there is not a 100% chance that someone who has the bad gene will show any symptoms of the condition it's associated with. So, in some cases, a person with a genetic condition can have children that are totally unaffected, and yet they may go on to have affected children anyway. Again, so much for using inbreeding to draw out and eliminate genetic disorders.

So, we're not dairy cattle and we're not birds. We ethically can't kill off people that don't meet our standards of what is "normal", we can't produce offspring in litters, and we don't get a chance to start over every year. Not to mention that genetic diseases are not simple enough that we can just eliminate them by breeding - often they are phenotypically invisible, occur spontaneously, or build up over time. They are not something you can "weed out", nor, might I add, is it ethical to encourage people to try to produce fatally ill children just so those genes are exposed.

This idea of inbreeding to strengthen a population is a myth. It won't work and it has serious racist and ableist undertones that make me very nervous, not to mention the genetic problems it can cause. The Human Genome Project has taught us that each human being carries, on average, between 7 and 10 recessive genes that can cause fatal conditions when no dominant gene is present. So producing offspring with siblings and cousins brings with it a serious increased risk of those children being fatally ill. Diverse parental genes are also a benefit to children's immune systems due to a mixing of genes for immune proteins that protect us from disease.

With much increased risks, and no benefits, inbreeding is not a solution to any sort of problem, in any situation. Sometimes it is necessary because there are no other options, but in a world where it's not difficult to meet people outside the family, why anyone would advocate choosing to "keep the gene pool pure", for any reason, is totally beyond me.

Saturday, September 26, 2009

Yes, I Do Suck

I have seriously failed at updating lately. I'm in a very intense university program for the next 8 months that is seriously kicking my ass. Don't worry, I still have opinions, knitting projects, and recipes to share, but The Boyfriend is out of the country (so not much baking until he gets back), and I haven't had a chance to knit in over two weeks. After this week my workload should lighten up some and I should have a chance to get back to updating this regularly.

I'm trying to find time to read The God Delusion, and I am also now the proud owner of God Is Not Great and The Portable Atheist, so those should provide lots of atheist fodder. I also have a beautiful edition of On The Origin Of Species (a Boyfriend graduation gift!), The Selfish Gene, The Blind Watchmaker, and The Ancestor's Tale to help me cope with not being immersed in biology for the next little while. I do have at least one more Nintendo washcloth in the works, hopefully two will be done by the end of the year (poll to be posted soon on which one to do next!). The lace sweater I'm designing is past the bust now and the neckline appears to be working. If I get to the armpits and find it is screwed up yet again, there will be a Sweater Design Odyssey entry for sure. I have a scarf most of the way finished as well - I'm usually a fairly monogamous knitter, but the difficulty level of the sweater has me becoming poly to save my sanity. However, now I'm finding that I'm not finishing the sweater because the scarf is easier. I really need to finish the scarf so I can focus on the sweater again.

Just so this post has something more than lame excuses, here's a link to the cinnamon roll recipe I made last week. They turned out great - I took them to class for my turn to bring an afternoon snack and they disappeared so quickly that I felt badly for not making more! Do NOT be intimidated by the use of yeast. The instructions are really easy to follow and they were fun to make, if a little messy.

Not to worry - I'm still alive and I'll be back to at least weekly postings soon.

Monday, July 27, 2009

Toad Washcloth!

I know, it's about time I got this up, since I finished it about a month ago.

But here it is:
It's the Toad Washcloth!


The finished product is 44 stitches wide and 61 rows long, just like the others, and is also worked from right to left instead of from bottom to top.

CO 44 stitches. Knit three rows. The next row (row 4) will be a WS row and the first row of the pattern chart (click to enlarge):

Start and end every row with K2. For the 40 stitches in between the edge stitches, follow the chart. Blank spaces are knit stitches for RS rows and purl stitches for WS rows. Dots are purl stitches for RS rows and knit stitches for WS rows.

After the chart is finished, you should be about to start a RS row. Knit this row and the next two (three rows total), then BO with knit stitches.

Toad is just so helpless and lovable. He's so cute that you just want to pinch his cheeks!


(Psst! Looking for the other Mario-gang washcloth designs? There are also Mario, Luigi, Princess Peach, Bowser, Yoshi, and Boo patterns available!)

Monday, June 22, 2009

Atheist Quote of the Week 40

All religions, with their gods, demigods, prophets, messiahs and saints, are the product of the fancy and credulity of men who have not yet reached the full development and complete possession of their intellectual powers.
~Mikhail Bakunin

Saturday, June 20, 2009

Why the Anti-Vaccine Movement is Completely Illogical

Today I'd like to post some information about vaccines. This is, to me, a very important issue. Let me preface anything I rant about here by saying that I have a degree in biology and I studied virology, pathology, epidemiology, and statistics as part of my education. I am not just some opinionated person here - I have read the original research papers and evaluated both the methodology and the statistical analyses for myself. I understand how viruses and human bodies work better than most people.

Just thought I would point that out first.

In recent years, people have begun to distrust the vaccines that people cheered about just a generation or two ago. Mostly this began with a UK study about the MMR (measles, mumps, rubella) vaccine, which I will tear apart in detail further on, but it is partially a problem with visibility. Half a century ago, people died or were disabled due to polio, measles, rubella, etc. on a regular basis. No, scratch that - children died from those diseases at a predictable frequency. Many, many families lost children to measles encephalitis, had a child blinded by rubella, or had a child confined to a wheelchair (or worse, an iron lung) by polio. It was tragic, but it was not uncommon. Vaccines changed all that, and at first people were grateful. Those people who are now in their 50s and 60s all vaccinated their children (those of us born in the 1970s and 1980s) because they remembered losing a classmate or having a disabled relative from theses diseases and they knew that a few pinpricks were worth the protection.

Then people forgot - or, more accurately, never knew just how bad it had been.

Now is a good time to explain herd immunity. As an example, measles is highly contagious and requires well over 90% of the population to be vaccinated in order to prevent disease outbreak and protect the small percentage of people that react badly to vaccines or cannot get vaccines for whatever reason. We do not force people with certain allergies to the serum, or who have parents or siblings that have had a bad reaction to a vaccine, to get vaccinated. For those few people, vaccines are dangerous. But as long as enough other people are immune due to the vaccine, those people who are not immune are still safe because it's very unlikely that a sick person (say someone new to the country from a place where a vaccine is not available) will come in contact with a non-immune person. They are far more likely to only come into contact with immune people, who will not catch the disease and therefore there will be no outbreak to endanger the unvaccinated few. That is how herd immunity works.

So, as long as people felt a responsibility to protect their own families by getting vaccines, everything was fine. Most people were vaccinated and many childhood diseases became things of the past in developed countries. However, people are self-centred and so once the drive to protect your own children was not as strong because people didn't really know firsthand how dangerous the diseases were, the drive to protect your neighbours and your community was not very strong. As soon as people had an excuse not to vaccinate, and bad information splashed all over the newspapers about how "dangerous" vaccines are, they stopped.

As for where that bad information came from, at first it was just anecdotal - someone had a kid with autism (which begins to show as symptoms around the time vaccinations are being given - six to twelve months of age) and they decided that the symptoms were due to the MMR vaccine, and not some other genetic or environmental factor, and they would sue the doctor or shout to the media about the chemicals in vaccines. This earned some publicity, but the biggest problem was a paper published in the UK claiming that such a link truly existed. Now, it should have raised flags in the scientific community when every scientist collaborating on the paper refused to have their name associated with it except someone who was notoriously anti-vaccine, but it managed to get published somehow anyway (an embarrassment to the scientific community, as far as I'm concerned). It said that it found that getting vaccinated was a huge risk factor for autism, and this is what the papers all ran as the headline the next day. What they failed to mention, however, is that the study only looked at 12 children (a statistically useless sample size to start with), and these children were not chosen at random from the population to get a good sample. Instead, the researcher went out and found 12 infants who displayed the early musculature warning signs of autism, and asked if they had gotten the MMR vaccine. Most had by that point, which was to be expected at the time and with the existing vaccine schedule. Since they all had known possible early autism symptoms, it was no surprise that 8 of them presented with diagnosable autism as they got older, and since most of them had been vaccinated, it was also no surprise that most of those had been vaccinated before they started showing symptoms. There was no control group in the population to see how many kids without autism had been vaccinated versus unvaccinated (which would have at least shown whether the percentage of unvaccinated versus vaccinated in the autistic children was different from non-autistic children). The methodology was so poor that the bias in the study alone made the results totally confounded by other factors and utterly useless for drawing conclusions.

And yet, because all that information was missing from news reports, people believed it. And even after the researcher behind the study has been widely discredited and hundreds of studies showing he was wrong have been published, many people still think vaccines cause autism and so they put their children - and, due to herd immunity requirements, the children of other people with legitimate concerns about vaccines in their family - at risk for the diseases that twenty years ago were largely eliminated from their community.

Why is it that people are so much more willing to believe unscientific crap (even long after it's been thrown out and stomped on by every reputable scientific journal) than they are to believe actual science, like human evolution and early-universe physics? I don't get it. I don't know why people will cling like crazy to totally wrong information that puts their families and their communities at risk. It's totally ridiculous. People need to smarten up and realize that getting measles is not a hand-waving risk. Out of every 1000 cases of childhood measles, three of those sick kids die. Of measles. I don't know about everyone else, but if all the kids in my elementary school had've gotten measles, that means that one or two of them would be dead now rather than healthy, productive adults. And that's just my school. Multiply that by thousands and thousands of schools and the effect becomes clear: before the vaccine, thousands of children were dying of measles (not to mention the tens or hundreds of thousands that needed hospitalization), and now they're not. However, measles is extremely contagious and it doesn't take much of a gap in the herd immunity for it to get back in.

So, anti-vaccination advocates, those are your options: either vaccinate your kids with a vaccine that has been shown to be safe by all reputable research, or put them at risk of dying of a preventable disease. Choose to protect the kids who are actually at risk of a bad reaction to the vaccine, or leave them exposed to death as well through no fault of their own, because of your inability to think logically.

Your choice.

Monday, June 15, 2009

Atheist Quotes of the Week 38 and 39

Okay, I know, F for "you suck at updating your blog, for sure's on dat, eh". Here's another double atheist quote post to get me caught up, and I promise I have a really good rant in the works to post later in the week. I'm back in Canada now, so I'll be working on the sweater project and organizing some Nintendo washcloth designs in the next few weeks.

The greatest tragedy in mankind's entire history may be the hijacking of morality by religion.
~Arthur C. Clarke

The rash assertion that 'God made man in His own image' is ticking like a time bomb at the foundation of many faiths, and as the hierarchy of the universe is disclosed to us, we may have to recognize this chilling truth: if there are any gods whose chief concern is man, they cannot be very important gods.
~Arthur C. Clarke

Truly a brilliant man who could see beyond the past and the present to put the consequences of both into sharp focus by writing about the future. I particularly like the second quote, since it reminds us that we are completely insignificant on the spatial and temporal scales of the universe. It must be nice to think that some god is out there, totally concerned by human beings, but the fact is that even if there was a god that created the universe, people are not even a blip on the universe's radar. So reality is that we live in a universe that has no guiding force to care about us at all, and even if it did, it still wouldn't care about us at all. It's a cold dose of reality, but somehow it makes me appreciate the fact that I'm alive at all, considering how many cosmological phenomena could have wiped out life on Earth at any time (and still can), but we've been able to evolve for a few billion years. That's pretty impressive.

Monday, June 1, 2009

Atheist Quotes of the Week 36 and 37

I know I missed last week, but I was packing, then flying, then adjusting to jet lag so it just kept getting put off. Here are two quotes, one for last week and one for this week, to make up for the difference. While I'm in Europe there will be no new Nintendo washcloths (watch for one of those potentially in late June/early July, however) and no updates on the lace sweater project, which remains in Canada during my trip. I do have wifi though and will use it to rant if necessary alongside the atheist quotes each week.

But people ... don't even know what atheism is. It's not a negation of anything. You don't have to negate what no one can prove exists. No, atheism is a very positive affirmation of man's ability to think for himself, to do for himself, to find answers to his own problems. I'm thrilled to feel that I can rely on myself totally and absolutely; that my children are being brought up so that when they meet a problem they can't cop out by foisting it off on God. Madalyn Murray's going to solve her own problems, and nobody's going to intervene. It's about time the world got up off its knees and looked at itself in the mirror and said: "Well, we are men. Let's start acting like it."
~Madalyn Murray O'Hair

Agreed. One of my main complaints about religion is its ability to explain everything while solving nothing. Anyone having a problem can say that it was "God's will", as if that somehow makes it better, or they can give their god credit for their success, thereby negating the effort they put into their achievements, or they can even say that current problems facing society are their god's way of punishing us because some of us are doing something it doesn't approve of. Why is there HIV? Because God hates gays. Why did Katrina destroy New Orleans? Because people there were sinning. Why does a child die of starvation and disease in a poor country? Because God wanted it that way. It explains everything but offers no compassion, no solution, no nothing.

The main reason, I think, is because if you remove God from the equation, suddenly HIV exists because it jumped from primates and it spreads today at least in part because we fail to teach proper sex ed in North America and religious organizations denounce the use of condoms in Africa. Katrina destroyed New Orleans because the government of the country failed to maintain the levees and so many people died or were left homeless because that same government failed to act swiftly in the face of a natural disaster. Children starve to death in poor countries because greedy rich countries do not behave like the world is one community and we would rather have another widescreen TV than help provide the essentials of life to other human beings. Those explanations are hard truths, and demand action to improve things. That's much less simple than just hand-waving some deity into the mix. It scares some people to death that we might have to actually work hard and sacrifice some wealth and some superstitions in order to make life better for our fellow human beings. Why not blame them instead? That is just so much easier.

As Madalyn says, it's time to start acting like men.

Why am I an atheist? The short answer is that I cannot accept any of the alternatives. I simply don't find them believable. As for the accusation of intellectual pride, surely the boot is on the other foot. Atheists don't claim to know anything with certainty—it's the believers who know it all.
~Barbara Smoker

This is related to the above quote in that it also references the easy answers believers seem to need. Rather than using their brains, they prefer to have pre-packaged answers for questions that really require thought on an individual level. While it must be nice, in a way, to have simple answers to any and all questions about life and the universe, I wonder why we, as thinking human beings, should be content to just be fed answers to everything. We are able to think for ourselves, so, even if it creates more questions than answers and more uncertainty than reassurance, it's independent thought, critical thinking, and scientific truth that should be what we are looking to achieve, not soundbite "truths" that are really just bedtime stories to make us less unsure of ourselves.

Atheists are not afraid to say, "I don't know." We are not afraid to face constant uncertainty and a neverending set of questions that may never have satisfactory answers. It is the believers who are afraid to not have an instant answer to any question. It is the believers who are afraid of change, afraid of needing to adjust their worldview, and constantly clinging to comforting but completely incorrect ideas and insisting they are true.

So, then, who is it that is arrogant, closed-minded, and know-it-all? Not the atheists, who by definition go where the evidence goes and must therefore be open-minded, humble in the face of being wrong (which happens all the time), and able to freely admit when they do not know the answers. Those sorts of insults are the product of frantic defensiveness on the part of believers who are trying to discredit a point of view that is contrary to the easy answers that make them feel safe and keep them from needing to think too hard about anything. Atheism, despite the fact that it is not an organization and does not have goals or some kind of agenda, is extremely threatening to religion, but for an interesting reason: as a philosophy, it promotes thinking for yourself. And, as it turns out, thinking for yourself usually ends with people moving away from organized religion.

I wonder why that is? Maybe to a thinking person (which we all have the ability to be), those "easy" answers aren't so easy to swallow after all.