For now, sulfites are able to kill the yeast that might spoil this wine.

Wine sometimes tastes a bit funky because it was contaminated during fermentation with a yeast called Brettanomyces bruxellensis. This yeast can give wine a variety of interesting flavors like “…horse sweat, Band Aids, barnyard, and burnt plastic…”

Winemakers usually keep this from happening by killing off the yeast with those dreaded sulfites. But for awhile now, people in the know have been worrying about the emergence of a sulfite-resistant form of this yeast. And this is a well-founded fear.

Yeast, like bacteria, are fast growing microorganisms with lots of variation in their DNA. If you hit a population like this with something that kills them (like sulfites for B. bruxellensis or antibiotics for bacteria), some small percentage are probably going to be resistant. These resistant strains can then grow and replace the sensitive ones. The end result is sulfite-resistant yeast ruining our wines.

To try to head off this problem, a group of scientists in Australia has figured out this yeast’s DNA. The hope is that scientists will be able to use this data to determine how B. bruxellensis might evolve into a more resistant form.

Note that despite much trumpeting online, they haven’t really solved any problems with this knowledge yet. They have merely created the tool that might let them solve a potential future problem. And given how cheap and easy DNA sequencing is these days, it isn’t necessarily even an impressive feat of technological prowess.

Still, it may one day prove useful in allowing winemakers to more quickly defeat a sulfite-resistant strain. Which can only be a good thing for wine making.

I don’t want to end this before saying a nice word or two about B. bruxellensis. This yeast can spoil wines but it isn’t all bad.

For example, it gives Belgian beers their special taste. And some winemakers actively seek it to give their wine a bit of a “brett” taste.

Still, a sulfite-resistant form would definitely be a bad thing for most winemakers. So scientists should definitely stay vigilant and be ready to come up with quick solutions using this new tool (and whatever other ones they can find) when sulfite-resistant B. bruxellensis begin to appear.

My favorite ones are those where women sniff the shirts of various men and pick out the ones that smell the best to them. The ones they like best are usually from men whose immune systems are most different from theirs.

This makes some sense if you think about it. The strongest immune system is a varied one. It can fight off lots of different kinds of bacteria, parasites, and viruses.

And since our immune system is programmed by our genes and our genes come from mom and dad, the more different mom and dad’s genes are, the more varied your immune system will be. So ideally you would choose a mate that would give your children the stronger immune system. That mate would have an immune system very different from yours.

One way you might be able to find that particular mate is if different immune systems have different odors. The stinky guys share your immune system; the pleasant smelling ones have a different one.

This seems to be what is happening in these armpit smelling experiments. So at least some amount of attraction between people is happening with the nose.

But what I found even more interesting was that oral contraceptives mess with this system. Women on the pill tend to prefer the smell of men with similar immune systems. Some scientists think this is because pregnant women prefer family around them and family tends to have a similar immune system.

When I first read this I thought, “Wow, this is going to really mess up future generations’ immune systems. Maybe it even helps to explain the recent rise in allergies and autoimmune diseases.”

But then I caught myself and thought a little harder. It is probably not that likely that the recent increases in allergies and autoimmune diseases would have happened so quickly if the pill were the main culprit. And besides, there is undoubtedly more to human mate selection than smell!

We are complicated. There are all sorts of cues that cause someone to fall in love. Pheromones may play a role but they are certainly not the whole story.

For example, some studies use photos and ask women which men are the most attractive. The women in these studies tend to pick men with more similar immune systems (apparently there is some correlation between facial symmetry and the immune system).

And when scientists look at couples who actually have children together, they get mixed results. An early study pointed to Europeans having children with partners with different immune system genes. But a deeper look at that data and looking at a larger group of couples showed that this didn’t seem to be the case. Differing immune systems had little impact on who women chose to have children with.

The most that could be said was that women tended to avoid men with really similar immune systems. A bit similar was OK.

Of course we could already be seeing the effects of the pill in these studies. Maybe if the women in these studies hadn’t been on the pill when they met their partners, they might have chosen someone with a more dissimilar immune system.

Scientists need to look at people who did not meet while women were on the pill. Then we will have a better idea of how big a role your nose plays in choosing your soul mate. And how worried we should be about the pill’s effect on that selection.

Nice PBS video about the t-shirt smelling experiments.

Or my eyes? Or my smile? Or…?

Part of the reason for this is that most traits have not been studied in very much detail. Which makes sense in a world of finite research dollars.

As is right, we spend most of the limited money on trying to understand and find cures for diseases. Very little goes toward figuring out the chances that Junior will have grandpa’s nose.

The other big reason we can’t make good predictions is that the genetics behind most traits are surprisingly complex. Except maybe red hair, there really aren’t any simple dominant-recessive traits. Which means we don’t even have the parents with recessive traits to fall back on!

As you probably already know, we have two copies of each of our genes – one from mom and one from dad. These genes can come in different versions and some versions are dominant and some recessive. The dominant ones trump the recessive ones.

What this means is that if you have a recessive trait, then both of your copies of the gene in question should be the recessive version. So if two parents each had a recessive trait, then their child should end up with a recessive trait too. Because that is all the parents have to share.

This is why we can predict that two red haired parents will pretty much always have red haired kids (J.K. Rowling got the Weasleys right!). None of the other traits out there are so simple though.

Numerous studies have shown that ear lobe attachment, cleft chin, tongue rolling and whatever else you learned in high school biology are way more complicated than advertised. None of them are a simple, single gene, dominant/recessive trait. Even eye color is complicated.

Pretty much everyone knows that blue eyes are recessive to brown eyes. And so blue-eyed parents can’t have a brown eyed-child. Heck, one group of scientists even used this as a basis for an evolutionary model. Too bad it is wrong.

Blue-eyed parents can have brown-eyed kids. It isn’t as common as the other way around but it can and does happen.

So it is hard to guess what a child will look like just by seeing the parents. But if we could look at their DNA we could predict what their child might look like, right? No. In fact, we couldn’t predict what they looked like from their DNA.

People are often surprised to learn that even if scientists are given a complete genetic readout of a person, they would not be able to predict what he or she looks like. We could guess ethnic background and have a good shot at predicting if they had red hair. And that is pretty much it. Oh, except for eye color.

Scientists are starting to make real progress on figuring out eye color from a person’s DNA. By looking at six different markers they can predict whether someone has blue or brown eyes around 90% of the time. They are only right about hazel, green and other colors about 75% of the time.

So you can see that even “simple” eye color takes six genes to make any good predictions. How can anyone make a good prediction just from looking at two brown eyed people? They can’t without a good family history and even then, they can be fooled.

And that is with a well-studied trait where we have the markers and understand what is going on. All bets are off for the other traits. For now anyway.

By reversing evolution, scientists may be able to transform chickens into dinosaurs one step at a time.

You may remember that in Jurassic Park, scientists sequenced some dinosaur DNA from a mosquito trapped in amber. They made a copy of this DNA, filled in the gaps with frog DNA and then created a dinosaur.

Although cool, we're not likely to get dinosaurs this way in the near future for a bunch of different reasons. The biggest for now (besides not having any dinosaur DNA) is that we can’t clone anything bigger than a bacterium with just a piece of DNA. To clone a multi-celled creature like a dinosaur, we need frozen or even better, live cells.

While this might be possible for some extinct animals including mammoths, 65 million years is just too long to find any frozen or viable cells. But there may be another way to one day create Jurassic Park. By messing with a chicken’s genes.

Current theories are that birds evolved from dinosaurs. This means that all the information for making a dinosaur was contained in bird DNA at one time. The trick is to figure out what this dinosaur DNA looked like and to change bird DNA accordingly and/or to unlock any hidden dinosaur DNA that may still be in bird DNA.

After 65 million years you might think all traces of dino-DNA would be lost in birds. Surprisingly, you’d be wrong. It looks like there is still some T-rex lurking in a chicken’s DNA.

In the last decade, scientists have been able to make chickens look a bit more dinosaur-like by changing how the chickens use the genes they already have. For example, they have been able to make a chicken’s tail look a bit more like a dinosaur’s.

A big difference between birds and dinosaurs is that dinosaurs have much longer tails. But this doesn’t hold up in a chicken embryo.

At a very early stage of development, chicken embryos have what looks like a very reptilian tail with 16 vertebrae. Later in development, though, most of the vertebrae disappear until only five are left.

What this means is that if scientists can figure out how to keep the vertebrae from disappearing, they might end up with a long tailed chicken. And they’ve actually managed to sort of do this already.

By changing when certain genes are turned on or off, they have managed to create a chicken with a tail that has eight vertebrae. Not quite a dinosaur but a step in that direction.

They have also been able to create a chicken with teeth. And even a snout! All of this without fundamentally changing a chicken’s genes but instead changing how they are used.

Now they probably won’t be able to make the chicken-dinosaur transition simply by changing how chicken genes are used. There are bound to have been some significant changes in certain key genes that will have to be replicated to really make a dinosaur. And for that we’ll need to figure out what dinosaur DNA looked like.

But still, we can make a lot of progress towards making a dinosaur by simply using the toolkit of current bird genes. In the end, we’ll probably be able to recreate something very much like a dinosaur. The question will then become whether we should.

QUEST story on how scientists can figure out ancient DNA from modern DNA.

Scientists studied twins like these to figure out that genetics accounts for about 37% of autism. Image courtesy of Jeff Balke.

Scientists have known that autism is a combination of genes and the environment for a long time. But the focus has been on genes because early twin studies suggested that autism was mostly genetic.

Scientists looked at sets of identical and fraternal twins to see how often both twins in a pair had autism. Remember, identical twins have the exact same DNA whereas fraternal twins only share as much DNA as any other siblings.

If autism were purely genetic, then both identical twins in a pair should either have it or not. It should be very rare for one twin in a pair to have autism and the other to not have autism. Fraternal twins should have it at about the same rate as any other siblings.

But if autism were purely environmental, then both twins in an identical or fraternal twin pair should get it at about the same rate. Depending on what part of the environment is causing the problem, this rate might be higher than that of siblings.

A study back in the 1970’s found that both twins in an identical pair had autism 72% of the time and that both fraternal twins never had it at the same time. This is where the 90% heritability for autism number came from.

The fact that fraternal twins never both had autism was weird from the start. Scientists knew that if one sibling had autism, the risk for the other siblings was anywhere from 3-14% which is higher than the general risk. Fraternal twins are siblings and so there should probably be some increased risk too.

In a new study, scientists did a more extensive study on 192 twin pairs and arrived at very different results. In this study, male identical twins both had autism 58% of the time and male fraternal twins both had autism 21% of the time. (Female numbers were similar.) These numbers suggest that genetics accounts for about 37% of autism. Still significant but nowhere near 90%!

If this study holds up, it means is that scientists can start looking at environmental effects. They’ve ruled out vaccines as a cause but there are lots of other possibilities. And many of these may happen before the child is even born.

For example, it may be that like Down syndrome or schizophrenia, parents’ age is a factor. Or it may be that diseases mom might have had or chemicals she might have been exposed to while pregnant could increase chances for autism. Or a host of other possibilities might be responsible.

What is important to keep in mind is that if scientists can identify an environmental cause, they can try to keep expectant mothers away. Or try to ameliorate the effects. In many cases, this will be much easier to deal with than genes.

For more, read

Sometimes autism that looks environmental can be genetic from Undestanding Genetics.

My lower risk for Alzheimer's may be the silver lining
to being e2/e2 at APOE.
Image courtesy of ImUnicke

When last I left you in my personal genomic journey, I had just discovered that I was e2/e2 at the APOE gene. I was quietly giddy* about this as it meant I was at a lower risk for getting Alzheimer’s. And even more importantly, it meant I didn’t have e4 which would have significantly increased my chances of getting this form of dementia.

Digging a bit deeper I found some more good news. People with e2/e2 usually have lower levels of LDL, the bad cholesterol that increases the risk for a heart attack. This is consistent with my low levels of LDL. Two good effects from one allele!

But there are no free lunches in genetics. For example, having two copies of the delta32 version of the CCR5 gene makes you pretty resistant to HIV infection. But it makes you more susceptible to the West Nile Virus. Having one copy of the sickle cell version of the hemoglobin gene makes you resistant to malaria. But your kids might end up with full blown sickle cell anemia. And so on.

The e2 version of the APOE gene is no different. It makes me less likely to get Alzheimer’s and, most of the time, to have a heart attack. But it means that I can end up with higher triglycerides from what I eat. This is consistent with what I have seen at the doctor’s.

Triglycerides are actually an independent predictor of heart attack risk. So even though my LDL is low, I need to watch my diet to keep the triglycerides down. If I am not careful, my increased triglycerides might cancel out my decreased LDL and so change my reduced heart attack risk to an increased one.

Being e2/e2 also puts me at risk for a relatively rare disease called hyperlipoproteinemia type III (HLP type 3). One reason this disease is rare is because being e2/e2 is rare. For example, only around 0.4% of people of European background have this genetic combination.

But HLP type 3 is obviously more common for me since I am in that 0.4% group already. Still, only 2% of e2/e2 people end up with HLP type 3 so it is a low risk for me. I decided to look into it anyway.

This disease has various symptoms but the most worrisome ones for me are increased risk of heart attack and abnormal glucose tolerance. My fasting glucose levels are stubbornly high whenever I take my yearly blood test. Which makes me wonder if this genetic difference is affecting my glucose tolerance and I am on my way to HLP type 3.

Of course, lots of genetic differences are involved in establishing someone’s glucose tolerance. And the environment plays a role too. So my glucose tolerance might have nothing to do with me starting to get HLP type 3.

Still, I am definitely going to ask my doctor about it at my next visit. It is rare but there are specific blood tests I can ask for that can tell me if I have this condition. Who’d have thought that a lowered risk of Alzheimer’s would only be a silver lining…

*Well, more of a measured giddiness. I know this is just one of the many genes involved in Alzheimer’s but still, it was good news.

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Can genetics help them be all they can be?

A new report commissioned by the Department of Defense recommends that everyone in the military eventually get their DNA sequenced. The idea is that scientists can use this treasure trove of information to quickly learn a lot about which bits of DNA lead to which traits or diseases. The military brass would then use this information to better care for soldiers and to make a more effective fighting force.

For example, maybe they will be able to find people who are more prone to suffer from post traumatic stress disorder. These folks could then be kept away from the front lines.

Or maybe they can find soldiers who are more likely to be resistant to certain diseases. These folks would be the ones sent to regions where those diseases are common. And so on.

Of course they will also find out many other things that may be more useful to society (and the soldier’s personal lives) like which bits of DNA predispose someone to diabetes, cancer, heart disease, etc. And which bits make someone more likely to be tall, strong, have dark hair or green eyes or anything else the scientists can measure.

This obviously has the potential for good but it still feels a bit creepy to me. Especially if the military misuses or abuses the information it gets.

Everyone (including the military) has to be careful not to over interpret the data. Just because a piece of DNA correlates with a lower risk of PTSD, that does not mean it is the only piece of DNA that does. It may just be one of many.

So you can imagine people who are at a higher risk for PTSD being moved to the front lines because an incomplete understanding of their DNA made them look like they were at a lower risk. These kinds of mistakes would be bad for the soldier and may eventually cost us a war.

There also needs to be some kind of oversight to prevent outright abuse by military officials who do not understand the limitations of our DNA knowledge. We need to make sure they don’t do what a railroad company did a few years ago.

Back in 2001 railroad workers brought a suit against BNSF railroad. The suit alleges that the company secretly tested 125 workers for a DNA snippet that increases someone’s risk for developing carpal tunnel syndrome. The story was that BNSF wanted to be able to deny worker’s compensation for any of these workers that developed carpal tunnel syndrome because they had a pre-existing condition.

Besides being against the law, this was also just plain stupid on the part of the railroad. They did not understand that the DNA snippet was not really predictive and that it was one of many genetic factors that can lead to an increased risk. They basically tried to figure out what the elephant looked like from just its tail.

The military may also use genetics to exclude some people from jobs they’d like to do or from the military entirely. I am not sure we will ever know DNA well enough to justify this sort of thing but at the very least we need to be sure that the generals understand what we can and can’t learn from our DNA. And that we update the military head honchos constantly.

Once the cost of reading our DNA drops to $1000 or less, we’ll all eventually be getting our DNA sequenced. And if the military follows the report’s recommendations, then the military will be testing the waters of our genetic pool. We can all learn from the mistakes they make along the way. I just hope the learning process doesn’t endanger any of our soldiers.

The 10 Most Outrageous Military Experiments

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Dr. Edwards got his Nobel Prize for getting this to work in a Petri dish.

The 2010 Nobel Prize in Physiology or Medicine was given to Dr. Robert Edwards for his work on in vitro fertilization (IVF). Basically, he pioneered the fertilization of human eggs with sperm in a Petri dish.

IVF has obviously had a huge impact on society. Millions of infertile couples have been able to have children. And families that have severe genetic diseases in their family tree have been able to have children without these diseases partly because of IVF. (Preimplantation Genetic Diagnosis or PGD is the other part of that equation.) IVF has also provided a steady supply of embryonic stem cells for research.

Of course, there have been some downsides as well. Millions of frozen embryos will eventually be thrown away. This is mass murder to people who believe these embryos are a life. And being able to select embryos without genetic disease opens up the possibility of selecting embryos for more troubling, trivial traits like gender or hair, skin, and eye color.

At first blush, though, the science itself might not seem to be all that Nobel-worthy. He put an egg and some sperm in a dish, let the sperm do their work and then put the embryo back into a mom. Sounds too simple for a Nobel Prize. But it wasn’t.

Getting eggs is hard. And getting eggs that can be successfully fertilized in a lab is really hard.

When they first tried IVF, his research group found that the fertilized egg would divide once and that was that. Hardly the bouncing baby the infertile parents were hoping for!

So Dr. Edwards and his lab had to research how eggs develop in order to get eggs that could be successfully fertilized. Among other things, they learned in incredible detail the cascade of hormones required to get an egg ready for fertilization. It was collateral knowledge like this on the way to IVF that was a big part of why Dr. Edwards earned his Nobel Prize.

All in all it looks like the Nobel committee made a good choice in finally giving Dr. Edwards the Nobel Prize. Click here to see if you think this Nobel Prize stacks up to others in this category.

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Current DNA tests could not have predicted that George W. Bush would be our 43rd President of the United States.

Time recently had a great article on helicopter parents. These are the parents who hover around their kids, protecting them from any harm. They are undoubtedly doing this to ensure their kids’ success in life.

I don’t want to get into the plusses and minuses of this parenting style…to each his own. What I do want to do is to warn them away from a new genetic testing company that seems designed to target them.

This testing company, called My Gene Profile, claims to be able to use genetics to help parents figure out where their child’s inborn talents lie. The idea, then, is for parents to point their children towards interests or careers that match up with what the genetic test says.

The talents the company is looking at are not simple ones like tongue rolling or bending your thumb back (neither of which we can yet determine genetically). They claim to be able to tell you if your child will be smart, creative, good at sports, and near as I can tell, five other similarly broad traits.

This is impossible given our current knowledge of genetics. And frankly, I am not sure we’ll ever be able to figure any of this out with a simple genetic test. Most of these traits are more than just the DNA we inherit.

Let’s take IQ as an example. Most of the studies I have seen point to about half of someone’s IQ coming from genes and the other half from the environment. Any test done right now won’t look at how the environment affected a child’s DNA. And they certainly won’t look at how the environment influenced the growth and development of the brain or how it affected synapse connections or about a million other things to do with intelligence and the brain.

Still, 50% from genes is a lot. If we could get a complete readout of how our genes influence our IQ that might be at the very least interesting. But we can’t.

Scientists believe there are at least 100 genes that contribute to IQ. So far they’ve only identified a handful and none of them have been shown to have reproducibly significant effects on IQ.

For example, scientists have found that having certain versions of the CHRM2 gene affects your ability to organize things in a logical way. The effects aren’t huge though. 23andMe (a company that I have tested with) reports that the variations that they look at in this gene can lead to a 6 point swing in IQ. Woopty doo.

If you drill down a bit farther, some scientists claim that you can get much larger differences. For example, at the furthest extremes, people with one set of variations in this gene averaged an IQ of 85 while people with a second set averaged an IQ of 103. Sounds impressive.

Except that a larger follow up study was not able to see the same effect. In this study, scientists weren’t able to find any connection between variations in the CHRM2 gene and IQ. And CHRM2 is by far the best characterized IQ gene.

Most likely the way that genetics contributes to IQ is that each of the 100 or so genes tweaks IQ a bit higher or lower. So to get a complete readout on IQ you’d need to look at all of these genes. This is difficult to do right now since we only know about a few of them.

And to make things even more complicated, the genetic contribution to IQ probably isn’t a simple summing up of these different variations. They don’t exist in a vacuum—these gene variations all interact with each other too.

What this means is that we may never be able to get an accurate prediction about genetic IQ from our genes. There are lots of possible combinations all with different outcomes. In other words, everyone’s IQ genetics may be unique which would make predictions impossible.

The bottom line is that there is not nearly enough data out there to figure out someone’s IQ or intellectual potential. And this goes for athletic ability, creativity and any other similarly complicated trait. We can’t even predict eye color yet very well from our DNA!

So consumers be aware of what a genetic test can and can’t deliver based on what scientists know. Testing for cystic fibrosis, pretty good. Testing for intelligence, not so much.

A final example. Imagine that Einstein’s parents had tested his genes for IQ with a company that looked at four or five IQ genes. And let’s say that he happened to have versions of these genes that lead to a lower IQ. Of course, since it is Einstein his other 95 or 96 or so IQ genes swamp out the effects of these few genes. But the testing company misses this and recommends that he not take an academic career. A little knowledge is a dangerous thing.

*This is common with genetic studies. There is a promising result with a small group that disappears when scientists look at a larger group.

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If a DNA testing company gets bought out, what happens to their customers' DNA? Image by Molly Eyres. / CC BY 2.0

One niggling worry I had when I decided to get some genetic testing from 23andMe was what would happen to my DNA if the company failed. By all accounts, 23andMe is a very healthy company* so it was more of a theoretical worry for me. Not so for deCODEme folks…

Like 23andMe, deCODEme looks at hundreds of thousands of different areas of a customer’s DNA in order to predict that customer’s future health and provide information about his or her ancestry and traits. This week deCODEme’s parent company, DeCode Genetics, filed for bankruptcy. Press reports indicate that parts of the company will go up for auction. I am not sure if that includes deCODEme but I am sure all of their customers are sweating it out right now.

The big question now isn’t whether these people will still get good service from deCODEme. Instead it is what the company that buys deCODEme will do with all those customers’ DNA. Will they maintain deCODEme’s previous privacy policies? Or, in the worst case scenario, will they connect DNA to name and sell the combination to the highest bidder?

I have to say that at first I was a little panicky when I started thinking about this. Especially when I started to contemplate what my health insurance company would do to me if they got a hold of my DNA.

Everyone has some genetic problems lurking in their DNA and I am sure that insurance companies would be happy to limit or even drop people’s coverage based on this. The new health care reform bills are supposed to prevent an insurance company from dropping someone based on a pre-existing condition but I am not sure if something like this counts. If it doesn’t, then I would probably end up with a policy that doesn’t cover conditions my DNA says that I am more likely to get. (Very useful insurance!)

If the new bill does consider potential risks from our DNA a pre-existing condition, then this isn’t really that big a worry. Except that I bet the new bills allow the insurance companies to jack up someone’s premiums based on their pre-existing conditions. In which case they’ll charge me so much I’ll have to drop my coverage anyway.

The other possible uses for my DNA that I could think of paled in comparison to this one. For example, I don’t think I’d mind if they sold my DNA to a pharmaceutical company so that the company could make a useful drug. Or to academics so that my DNA could be used to learn something about the human genome. It seems like those are sort of noble purposes for my DNA, kind of like donating it to science.

I couldn’t really think of much else that other companies might do with my DNA. Of course if the health insurance scenario were to happen, that would be plenty bad enough.

* Especially since one of the cofounders, Anne Wojcicki, is married to Sergey Brin, Google cofounder.

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