Mike May had a successful corneal transplant and forty-two years later, his eye was healthy again. But his vision was still impaired.

In this week's radio story, we profile Mike May, who lives in Davis, California. Mike's the founder of a GPS-services company called Sendero Group and the author of a memoir, Crashing Through

Mike grew up in a rural part of New Mexico, on land that had once been owned by miners. When Mike was three years old, he opened up a jar containing an explosive chemical that the miners had left behind. The accident left him nearly blind.

Forty-two years later, doctors fixed one of his eyes (the other was too damaged) in a series of two procedures.

First they performed limbal stem cell transplant – an early, fairly-well established stem-cell procedure. Donor limbal cells, removed from a cadaver, were placed onto Mike's eye, where they repaired the scarred tissue. This made Mike a candidate for a successful corneal transplant. Forty-two years after his injury, Mike's eye was healthy again. But his vision was still impaired.

During those decades of blindness, it seemed that Mike's brain had essentially lost the ability to see detail, to make out faces. Our story looks at the research Mike's case has inspired, in particular a recent paper, published in the journal Neuron by Stanford Psychology Professor Brian Wandell. We also hear from Ione Fine, who was one of the first scientists to study Mike.

Fine shared with us this image of two brain scans.

Mike's brain is on the left; a seeing person's brain is on the right. You can see how much less of Mike's brain becomes active when presented with images of objects (in blue) or faces (in red).

This Powerpoint lecture, also provided by Ione Fine, takes a closer look at Mike’s brain and its ability to process visual information. Download the Power Point Presentation here.

Listen to Teaching A Brain To See radio report online.

It can be hard to tell which science is good, bad, or ugly on the web.

I have often thought that the percentage of good scientific information on the web must be pretty low. So I decided to test the idea out on a question I was recently working on.

Someone asked me if humans started out with O blood type and then only later developed A and B.  A quick look at PubMed showed that this was not the case.  Most of the recent genetics studies point to A coming first, followed by B about 3.5 million years ago and then, finally, about 1 million years ago, O.

This makes some intuitive sense if we think about what A, B, and O are.  O is a form of A that doesn’t work any more because of a mutation*.  This makes the idea that a broken gene came before a working one pretty unlikely.  Not impossible, just not all that likely.

Now I researched this answer the way I usually do—I headed straight for PubMed to get the hard scientific data.  I can do that because I work for Stanford and so have access to lots of journal articles and I have the scientific background to decipher the geneticsese these reports are written in.

What I also did this time was to try to find the answer without PubMed.  I started out on Yahoo searching for human blood type evolution.  Yikes.

Links 1, 2, and 7 talk about primate A and B blood types.  Gorillas have B and chimpanzees have A and a bit of O.  From this the authors try to conclude that we are somehow a mix of these two…perhaps gorillas and Neanderthals are closely related to each other and so are chimps and Cro Magnon.  In this scenario, humans come from a mix of Cro Magnon and Neanderthals.

This is certainly not the case.  Gorillas do have a blood type similar to B but it isn’t the same as ours at the gene level.  And if current evolutionary history is to be believed, we split from gorillas way before our B blood type was born.  So we did not get our B from gorillas.

Also, chimpanzee O is not the same as our O…it developed well after we split as well.  We even know that Neanderthals have our O blood type and not a chimp’s (and certainly not a gorilla’s!).

Links 3, 5, and 9 use blood type genetics to show that Adam and Eve could have founded the human race.  Links 4, 6, and 8 talk about the blood type diet.  And link 10 connects blood groups to aliens.

Google does a bit better.  You get eight similar links but you also get an NPR piece that does pretty well and a Dawkins forum comments piece that can get you to the answer eventually.  However, you have to wade through a lot of stuff to get there and you only know to home in on the comment with the correct information if you already know the right answer.

Obviously what is popular isn’t always what is right.  (And the prize for stating the obvious goes to Dr. Starr!)  I thought I’d try Wikipedia next.  Wikipedia can have many factual errors but it often gets the overall story line correct.  Unfortunately there isn’t an article on this subject.  There is on one the blood type diet though…

So what is a non-scientist to do?  There don’t seem to be a lot of options.

There are websites like mine at Understanding Genetics that try to give the real scoop on what current science says about various issues.  But they tend to focus on a single topic and don’t often appear at the top of a website search.  (Understanding Genetics is an exception in that it gets enough hits to often be on the first or second page if the query is worded in the right way.)

I am not sure what the answer is to getting better science via the web.  Maybe we need a web based encyclopedia about science written by scientists.

The tricky part will be to get them to do it.  And to have it make sense to anyone but another scientist in that particular field.  And for them to do it impartially.

I’m curious how other people find their science online.  And how they make sure it is reliable.

* This isn’t weird, blue eyes and red hair work the same way.

When choosing an embryo, a little bit of knowledge is a dangerous thing.

People often think about certain versions of a gene as either good or bad. One that leads to depression is bad while one that protects you from HIV infection is good.

For most genes this is almost certainly too simplistic a view. Many versions of genes can be good or bad depending on your situation.

For example, the delta 32 version of the CCR5 gene can make you more resistant to HIV infection. But it also makes you more susceptible to infection by the West Nile Virus.

Which version is best for you depends on where and how you live. If you’re an IV drug user who lives somewhere up north, then you would probably benefit most from the delta 32 version. But if you are a faithfully monogamous man in Africa or Central America, then you might do better with the more common version of the CCR5 gene.

As I talk about in a recent GeneWatch article, the same is true for the SERT gene and depression. This gene comes in two versions, long and short.

Studies have shown that people who only have the short version are at a higher risk for depression. A deeper look at the data shows that this is only the case if these people had a traumatic childhood. People with two short versions who had a happy childhood are actually more resistant to depression than people with the longer gene versions.

This all matters because we are at the point where you can choose some of your child’s gene versions. And too simplistic a view of genes could cause you to make the wrong choice.

People who undergo in vitro fertilization (IVF) can go through an additional procedure called preimplantation genetic diagnosis (PGD). Basically PGD allows you to look at an embryo’s DNA before it is placed in the womb. This means that when multiple embryos are created, you can choose which one to implant based on its genes.

Fortunately we can’t really change the embryo’s DNA for the foreseeable future so you’re stuck with whatever genes you and your partner can contribute. But as we are able to look at more and more genes with less and less DNA, we are getting very close to a Gattaca-like future where we can choose many of our children’s genes.

And as the two previous examples showed, this won’t be a simple choice! There are undoubtedly hundreds of genes just like these where what effect they have on someone depends on how and where that person lives, how they were raised, etc. It might be best to restrict this sort of thing except for cases where the child might end up with a devastating illness like cystic fibrosis or sickle cell anemia.

In some ways, this sort of thing is already being restricted. For example, when a fertility doctor in L.A. suggested that he might offer parents a chance to choose what eye, hair, and skin color their children might have, the public uproar shut down the service before it even began.

I’m not sure that less politically sensitive gene selection would cause such a furor. It may be that we need some sort of government regulation to protect people from what they don’t know. Or maybe parents need to take a course before selecting which embryo they want…

For most of us, avoiding these is just as important as the genes we inherit.

As someone who studies genes, I tend to give the environment short shrift. I have to watch out for that because it can cause a blind spot in how I think about biology. And how I live my life.

As readers of this blog might remember, I was recently diagnosed with metabolic syndrome just as I was undergoing DNA testing. This was a wake up call in a couple of different ways.

First off, it confirmed my belief that we can’t get a lot out of genetic testing for complicated diseases right now. I couldn’t look at my DNA and predict that I would end up with high cholesterol, triglycerides and glucose levels. We just don’t know enough yet about our genes to be able to figure this out from any available DNA test.

But I could have guessed this might be a problem from my lifestyle and family history. All four of my grandparents developed Type 2 diabetes which put me at a pretty high risk. Of course I thought I could beat the odds and so lived a life filled with couch sitting, Haagen Dazs, and Double Western Bacon Cheeseburgers (cue Homer Simpson drool). Until my diagnosis.

Then I decided to see if all this talk of diet and exercise actually can have a significant impact on me. Or was I destined to high cholesterol, triglycerides and glucose levels because of the genes I got from my parents.

The doctor told me to lose weight, exercise more and eat better. So I did.

I lost 30 pounds by changing my diet and walking 30 minutes a day. This dropped my body mass index (BMI) from overweight (27.8) to normal (23.5).

I also stopped eating most sweets, and cut my saturated fats down to 15 grams per day. And the effects on my blood work have been amazing.

Here are a few of the stats:

As you can see, everything is now in the normal range except for glucose which is still a bit worrisome. Now I just need to maintain this regimen which, in America, won’t be easy.

I probably panicked and went overboard anyway. I should have tried to just add exercise and see if that was good enough. If not, then cut back on sweets and saturated fats. I did bad science on myself by changing too many variables at once.

I think what I can conclude is that my set of genes makes me particularly susceptible to my lifestyle choices. Some lucky people are born with genes that let them get away with poor diet and no exercise.

I am not one of those lucky ones. Although perhaps more lucky than those people who make these changes and still have these health issues.

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.

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.

Could the cosmetics in your purse be harmful to your health? Image from Wikimedia Commons. / CC BY-NC 3.0

Each October, within Breast Cancer Awareness Month, my friends and I get into a flurry organizing and putting on Beats for Boobs. Beats for Boobs is an annual fundraiser started by my friend Juliana Cochnar after finding out her mother was diagnosed with Breast Cancer. The Beats for Boobs mission is to educate the community on breast cancer through a collaborative celebration of art, fashion, food and music.

This year the fundraiser welcomed 1200 people through its doors and raised over $20,000 for local Breast Cancer organizations. The theme this year was Green is the new Pink. The education team, which I have been a member of for three years, now, was tasked with educating the public on ways to prevent breast cancer. We set up a prize wheel and gave everyone a chance to win; all they had to do was answer a question about Breast Cancer correctly.

Some of the questions posed were:

Question: Synthetic Chemicals can accumulate in body fat and remain in breast tissue for decades- some that can cause mammary tumors.

TRUE/FALSE

Answer: TRUE

Question: 80,000 chemicals have been registered for use in the United States in the last 40 years, yet _________ of them have been fully tested for their effects on our health.

10%
25%
50%
5%

Answer: 10%

Question: No more than _______ women who have Breast Cancer have a genetic history of the disease.

1:5
1:3
1:8
1:10

Answer: 1:10

Question: Which of the everyday products below can contain chemicals linked to breast cancer?

Shampoo
Deodorant
Face Cream and Make-Up
Sunscreen
All of the above

Answer: All of the above

Most of the night, I was stationed at the What’s in Your Purse Table, which used the Skin Deep: Cosmetic Safety Database Website to access the hazard of everyday products. “Now in its fourth year and third major update… Skin Deep database provides you with easy-to-navigate safety ratings for nearly a quarter of all products on the market — 52,099 products with 8,799 ingredients. At about one million page views per month, Skin Deep is the world's largest and most popular product safety guide. The database rates items on a 1 to 10 scale – 0-2 is low hazard, 3-6 is a moderate hazard, 7-10 is a high hazard. After the fundraiser, I became very well acquainted with the Skin Deep website. I went through every cosmetic item in my house and as a girl with a love of make-up that meant quite a few items! Most of the items I was using on my face were a moderate to high hazard rating. The toothpaste I used had a rating of 7. The eyeliner I used on a daily basis had a rating of 9 and the lip-gloss I wore nearly everyday had a rating of 6. At the end of my research, I had found out that my mineral make-up was low hazard but my eye shadows, sunscreen, soap and toothpaste had to go. I got rid of a full shopping bag of products that all rated 5 and above. I called my mom and told her what I found out. I am bringing over my laptop and we are going through her bathroom and toiletries next week.

Each year, on the education committee for Beats for Boobs we try to make the education fun and accessible so we can instill ways to prevent Breast Cancer. The Skin Deep website was an excellent resource to do just that. Only one person was able to get something out of it this year but I am hoping that with this blog and a new approach next year, that number will continue to rise.

This blog is in honor to my Aunt who is surviving Breast Cancer.

"Mysteries of DNA" image courtesy Mark H. Adams. Full-size version.

As anyone who follows this blog knows, I recently took a 23andMe genetic test and have been blogging about it ever since. Today I thought I would focus on one of the fun parts of the service: traits.

Lots of our traits are at least partly dependent on our genes. So a genetic test should be able to tell me a bit about what I’ll look and even be like in the future. It may even tell me what I can expect for my kids.

Here is what is available on the 23andMe test (click on the image for a larger version):

As you can see, some of this is pretty obvious…I know my eye color for example. It is kind of cool to see my blue eyes written in my DNA but not necessarily that helpful. When I click on eye color, I find out that people with this particular bit of DNA have a 72% chance for blue eyes, a 27% chance for green and a 1% for brown. (Incidentally, this 1% brown is probably a big reason why blue-eyed parents can have a brown-eyed child.)

What would have made this report more interesting for me is what it meant for my kids’ eye color. Does it mean I’ll have blue-eyed kids? This of course depends on my wife’s genes but it would be cool to have the option of including my wife’s data to find out.

Other less obvious traits were very interesting to me. The results say that like most mammals, I should be lactose intolerant. Which I am not—I’m fine drinking milk. So did 23andMe get it wrong?

Probably not. The science is pretty good on this topic. People with a certain difference in their lactase gene almost always lose the ability to make lactase as adults. No lactase means lactose intolerance.

When I dug deeper on the website I got some hand waving about other genetic influences or the environment. A better explanation is that I will probably become lactose intolerant at some point in my adult life—it just hasn’t happened yet.

Losing the ability to make lactase is a gradual thing. It happens to some people early in adulthood and others later on. I am probably one of the “later ons.” Something to look forward to…

One trait that I’ve always been a bit interested in is HIV resistance. Some people are more resistant to infection by HIV (the virus that causes AIDS). If these people do become infected, they tend to develop AIDS symptoms much more slowly as well.

In Europeans at least, this resistance has been tied to a DNA difference called CCR5-delta32. The people who are resistant to infection and who develop AIDS more gradually tend to have two copies of this DNA difference.

This DNA difference has been proposed to have become common in Europeans because it also makes people resistant to either the plague or smallpox. If true, my ancestors must have died like flies from the plague or smallpox because I don’t have the DNA difference.

I also now know about what my DNA tells me about my earwax, how I respond to a certain bitter chemical, and whether I flush from alcohol. These are sort of interesting but not very.

This part of the 23andMe experience is kind of fun though. I really enjoy it when genetic theory matches up with what I can see about me. It sort of validates genetics…

What can genetic testing tell you?

A while back I took a 23andMe genetic test that looks at over 600,000 different spots on my DNA. The last few blogs I have been going over my genetic test results with an eye on how useful they are. And how well the results are explained.

Last blog I wrote about how current genetic tests aren’t that great at predicting your risk for common, complicated diseases like diabetes or Alzheimer’s. This time I thought I’d focus on what today’s genetic tests can be very good at and whether or not 23andMe does a good job with these.

Current genetic tests are very good at predicting your risk for rare, simple genetic diseases like cystic fibrosis (CF) or Huntington’s disease (HD). And at predicting the chances that your kids will get these diseases too.

Genetic tests for these diseases work because most of them are caused by a single gene gone awry. Testing for a single gene is relatively easy.

For example, most cases of CF happen because of known differences in the CFTR gene. A genetic test can look for these differences and tell you if you and/or your spouse have any of them. If you both do, they can also give you a pretty good idea about the chances that your kids will get them too.

Of course, we don’t know all of the differences in the CFTR gene that can cause CF. And some differences only cause CF some of the time. And there are people with everyday, run-of-the-mill CFTR genes who get CF because of differences in different genes.

Still, as genetic tests go, these are pretty good. If a test comes up with a known CFTR difference that causes CF, then you have a pretty good idea of what your chances for developing CF are. If your spouse gets tested too, then your kids’ chances can be determined as well.

So how does 23andMe do? OK, I guess…

First off, they look at eight of these sorts of diseases under a category called Carrier Status. The diseases they look at are shown in this image:

For me, the first big result is that I am a carrier for a variant that can lead to hemochromatosis. This isn’t surprising since 1 in 8-12 people of Northern European descent in the U.S. are too, but it is definitely something to watch out for. It may be important for my wife to be checked too so we can make sure none of our kids got two copies. (Luckily hemochromatosis is easily treated by giving blood on a regular basis.)

Some of the other results are less illuminating. For example, I do not carry the CF difference they test for (delta F508). This is of course great news. Unfortunately, this variant only accounts for about half of the CF cases out there. Which means I could be a carrier for CF, just not a carrier of the most common variant that they happen to test for.

The same thing goes for most if not all of the other carrier status diseases (sickle cell anemia is an exception). Some like BRCA (breast cancer) are as poorly covered as CF while others like Bloom’s disease cover a larger percentage of cases.

23andMe is pretty upfront about the limitations of their testing once you dig a bit into the results. But still, if they’re going to look at 600,000 different parts of my DNA, you’d think they could add a few more to give me a stronger answer about whether or not I am a CF carrier.

Luis Medellin and Karl Tupper set up a drift catcher in Lindsay, CA.

My radio story on pesticide drift looks at how residents in the citrus town of Lindsay are monitoring pesticides in the air and in their bodies. They are using a device called a Drift Catcher, modeled after technology used by the California Air Resources Board and the Department of Pesticide Regulation.

The pesticide drift catcher has a vacuum pump that sucks air into a glass test tube, where pesticide residues are trapped in a resin. Community members change out the test tubes and send them to a lab, where scientists crack them open, extract the residues with an organic solvent, and then analyze those extracts through gas chromatography.

The Lindsay study measures Chlorpyrifos, a pesticide that can cause headaches, blurred vision, and muscle weakness when people breathe in the air from a recently-sprayed orchard or field. Studies also show prenatal exposure MAY have effects on children's cognitive and motor skills.

Environmental lawyers are using preliminary data from the Lindsay drift catchers in a petition asking the EPA to create pesticide buffer zones around schools, child care centers, and hospitals.

Listen to the Catching the Drift – Part Two radio report online.