Why we didn't sequence HeLa

Recently, another paper about HeLa's genome sequence was published in Nature. Along with that came an article explaining how the ethical ramifications of publishing the sequence of HeLa were handled before this recent paper's release.

My friend Dr. Cuiping Pan asked about why, when we were deciding on a cell line to whole genome sequence and publish back in 2008, we chose U87MG rather than HeLa. Here is my response:

At the time, we had a big argument about whether to do HeLa. We all knew it would be higher profile to do HeLa, but even in 2007/8 we were aware that the cell line had been derived without Henrietta Lacks' informed consent. Meanwhile, obviously HeLa is the most commonly used cell line, so we knew it would be more useful generally than U87MG, which we identified as the most commonly used glioma cell line but also only around the twelfth most commonly used cell line generally. [A quick Pubmed search finds 1,110 papers with the term "U87MG" in them, compared with 78,343 for HeLa!]

So it came down to an ethical choice versus a utilitarian choice, and it happened that the ethical choice would also be less "rewarded" with references, high impact journals, et cetera. In fact, we spoke with Nature and were basically told it would be harder to publish U87MG than HeLa there (but it's a moot point because we also wanted to support open access and Plos, which is why we went for Plos Genetics at the time).

Anyway, looking back I think we made the right choice. Back then, Francis Collins was not head of NIH and the book on Henrietta Lacks had not been released yet. The [European] group who subsequently sequenced HeLa got in a lot of hot water.

As for U87MG, we looked into its history. It was an anonymously donated sample that had been consented as far as we could tell in Germany. [Note: This is all off the top of my head, so don't use that as a primary reference, please.] The particular individual it was derived from was not publicly known that we could see, though his identity is still likely in the medical records of the hospital where he was treated. We did not try to find out who he was, because keeping him anonymous and deidentified was the ethical choice.

Also, on a practical level, doing a male genome seemed interesting since it would get us Y chromosome, but that was a minor and not very compelling reason.

I am of the opinion that as geneticists and genomic scientists, we must do things above the board and be very careful about informed consent and protecting people's identities. There is literally nothing as identifying as the genome, so we must be cautious and considerate in all cases. This is why, before ever considering sequencing something, we always need to consider the ethical implications.

HeLa, the cell line, is something we simply cannot give up on now. It is too late, and it has done too much good and it has too much future potential to do good in the future for all of us. But even with that in mind, I still feel using it and even sequencing it is questionable. It's a hard feeling to shake and it's sourced at the fact that the person who the cell is derived from never consented. I think, over the past few years, the dialogue between health science and the Lacks family has been a very good change, and I'm very happy the Lacks have basically consented to use of HeLa generally.

Really, it goes to show why it is so important for us to do as much as possible to behave ethically from the start. To avoid these types of situations in the future.

Save the Square Watermelons

NO on 37! Think about it, Californians. Are you telling me you can't figure this one out, @carighttoknow? #prop37 twitter.com/mjcgenetics/st…

— Michael James Clark (@mjcgenetics) November 6, 2012

Also, I just realized I've had over 25,000 hits on this blog. Thanks for reading! I hope it's been useful and interesting!

Stop SOPA

I'm not a huge politics guy, so I don't want to go on a tirade about the Stop Online Piracy Act. Sufficed to say, it's a huge censorship bill parading as a bill to protect intellectual property. While I think the majority of us support protecting IP, I can't imagine the best way to do so is to monitor everything we do and censor websites based on some government-backed list of sensitive content.

As an example, if someone were to post copyrighted material in the comments section of my blog without my notice, my blog could potentially be shut down (censored) because of it. If I were to link to a site that had, somewhere on it, shared copyrighted material (even if I had no idea it was there and didn't intend for anyone to go there and see it or download it), my blog could be shut down (censored).

Moreover, the bill basically forces both providers and hosting services to strongly monitor content and shut down sites that potentially "infringe" on protected IP. Ever posted a picture of something that was copyrighted? Ever shared a link to a YouTube video with a copyrighted song in the background? That could be enough to get you shut down (because your host or provider doesn't want to be sued).

My wife and I often talk about the situation in Japan (she's Japanese) regarding the Fukushima nuclear reactor situation and how censorship and control of the media in Japan is so strong that the general public has no idea how dire the situation is. We even see that censorship and media control bleed over to here in America, where the general public is under the impression the nuclear situation isn't as bad as it is, in large part because the government and big media have an incentive to see nuclear power as an industry succeed.

Now here's the scary thing: If I were to start posting excerpts from copyrighted articles about that topic to respond to, if SOPA were to pass, my blog could potentially be shut down. I could personally be denied access. It's unclear to me exactly how much power this bill would give big media and the government. And that's the major problem.

In our field of genomics, a lot of us utilize freedom of sharing information and media to rapidly advance the science. I understand that this bill is meant to limit piracy of software and other digital media, but it represents a foot-in-the-door to all sorts of censorship. Could SEQanswers, for example, be sued for having a post up that contains the Illumina adaptor sequences? It certainly has been threatened in the past based on such things, but with SOPA passed, SEQanswers very well could have been shut down for that. What a detriment that would have been to the genomics and bioinformatics community.

Anyway, I just wanted to share this on my outlet to the world, as it is a very important issue generally and to our field in particular.

If you are an American and you do not support SOPA, please send a notice to your congresspeople telling them not to support it, either.

Rising gas prices and their effect

This post is in response to an article I read on CNNMoney.com. Now, let's be frank, CNN is in the business of "gotcha news", posting articles that are often inaccurate or misrepresented with the intent to draw views and reap chatter. Typically, I wouldn't let it bother me, but this particular article is heavily mis-representing things to make a point. That point is: "Stop whining, California."

Here's the article. It presents some data in an interesting fashion. It shows states shaded by the average cost for a gallon of gas and then it shows states shaded by the amount spent on gas as a percent of income. The conclusion? Despite having dramatically higher gas prices, Californians should "quit whining" because they on average spend a smaller percent of their income on gas.

Gas expenditure as a percent of income

Average gas price per gallon

The article accounts for this phenomenon in a series of theories about why it occurs (rather than, you know, going ahead and proving any of them). Example:

"When you live in California or New York, where things are close by and there's public transit, that's great -- but we don't have those options here," said Hilary Hamblin, a Tupelo, Miss. resident who said her family typically spends about 10% of their monthly income on gas alone.

That's not uncommon in the state. Mississippi families earn a median household income of about $37,000 -- the lowest in the country -- but spend a whopping $402 per month, or 13.2% on gas.

In contrast, Californians earn a median of $59,000 per household, and spend about $380, or 7.8% of their income on gas each month

What we see here is a way of manipulating the facts to put together a dramatic article that will piss off Californians and New Yorkers and rally red-staters. What we don't see is any semblance of meaning.

Here's a little tid-bit the article doesn't tell you: California is a major agricultural center, including significantly more farms than Mississippi (or, it appears, any other state). Check out this fun little tool from the US Government's Economic Research Service.

How does having the highest gas prices in America impact those rural workers? What percent of their income is spent on gas? Lumping all of California's 37M people together and calculating mean gas expenditure as a percent of income, then comparing to Mississippi's 3M people is like comparing apples to oranges.

Personally, my gas expenditure is very low. I usually ride a bike to work. I don't drive far or often. But I guarantee you farmers down in Kern County or in other rural counties of California are driving quite a bit and paying similarly inflated gas prices to what I pay. So myself and people like me in California are bringing down that "gas expenditure as a percent of income" mean value down quite a bit. That doesn't mean the cost to the farmers here in Cali is any lower, though!

I'm not saying Mississippi doesn't have it bad now. To the contrary. What I'm saying is that this article is misrepresenting facts to make a false point. Farmers and farm communities in California likely have just as much if not more reason to complain than those elsewhere because they're penalized by being in a state with huge urban areas that cause gas prices to be higher (due to increased taxes, more expensive gas blends to deal with urban air pollution, et cetera).

I grabbed the data from the ERS and played around a little bit with it. Here are some interesting stats:

Total number of farms:
California: 81,033
Mississippi: 41,959


Mean percent of land per county dedicated to agriculture:
California: 33.28%
Mississippi: 38.36%


Mean percent of farmland per county (for counties with >50% farmland)
California: 70.23%
Mississippi: 67.67%


Total Population Size
California: 36,961,664
Mississippi: 2,951,996


Population of rural counties (counties with >50% farmland)
California: 4,933,655 (13.35%)
Mississippi: 482,751 (16.35%)

Let these numbers settle in. Similar ratios of the population live in rural areas in both states. Rural counties appear very similar broken down by percentages here. But California has more than twelve times as many people as Mississippi. In rural counties, California has about ten times as many people. However, there are only about twice as many farms in California as there are in Mississippi.

But what does it all mean? It means there are ten times as many people in California paying significantly higher gas prices while doing the same job as those in Mississippi. Californians may on average make more than people in Mississippi, but does that mean the farmers in California make more than the farmers in Mississippi? This is a hard number to determine. We can use what the ESR calls the "average value of agricultural products sold". In this case, I'm taking those "rural counties" I talk about earlier with >50% farmland and then just calculating the straight mean of these valued.

Mean for rural counties of average value of agricultural products sold
California: 535,808
Mississippi: 291,167

In this light, Mississippi farmers appear to make much less on average than California farmers. But if we look on a county-by-county basis, we note that there are a few counties skewing California's rosy outlook. Let's look at that distribution to see if there aren't a lot of California farmers in more dire straits than simply taking a mean would show.

Mississippi is in blue, California is in red (didn't expect that, did you?). We can see pretty clearly here that there are two counties skewing the California number. These are Kings County and Monterey County. If we remove those, the value of farming in California counties is down to 373,475. Not exactly making up for the fact that ten times as many people live in those counties.

Now, I don't want to make generalizations. The only point I truly want to make is that an article telling Californians to "stop whining" because farmers in Mississippi have it bad is ignoring the fact that there are many farmers in California in the same situation as those ones in Mississippi. I don't want to say they have it worse, either, but my guess (emphasis on guess, as I'm not proving it) is that these folks spend a similar percent of their income on gas as well.

Basically, I'm going to go out on a limb and say that given the makeup of farming counties in California and Mississippi are very similar (despite a difference in scale, given California's much larger size), the California farmer has just as much a right to be distraught about rising gas prices as the Mississippi. In fact, the California farmer has to pay significantly more per gallon, so even if they do make ten thousand dollars a year more (an estimate based on mean income in Kings County, California, which is down around 44k per year at this point), they probably spend a similar percent of income.

All of that said, you won't find me complaining about gas prices. But I may end up complaining about produce prices, which is obviously directly tied to gas prices on the farmer's end.