Tag Archives: Genetics

The Three Necessary and Sufficient Conditions of Natural Selection

Natural Selection is the key creative force in evolution. Natural selection, together with specific histories of populations (species) and adaptations, is responsible for the design of organisms. Most people have some idea of what Natural Selection is. However, it is easy to make conceptual errors when thinking about this important force of nature. One way to improve how we think about a concept like this is to carefully exam its formal definition.

In this post, we will do the following:

  • Discuss historical and contextual aspects of the term “Natural Selection” in order to make clear exactly what it might mean (and not mean).
  • Provide what I feel is the best exact set of terms to use for these “three conditions,” because the words one uses are very important (there are probably some wrong ways to do it one would like to avoid).
  • Discuss why the terms should be put in a certain order (for pedagogical reasons, mainly) and how they relate and don’t related to each other.

When you are done reading this post you should be able to:

  • Make erudite and opaque comments to creationists that will get you points with your web friends.
  • Write really tricky Multiple Choice Exam Questions if you are a teacher.
  • Evolve more efficiently towards your ultimate goal because you will be more in control of the Random Evolutionary Process (only kidding on this third one…)

Continue reading The Three Necessary and Sufficient Conditions of Natural Selection

Is Human Behavior Genetic Or Learned?

Imagine that there is a trait observed among people that seems to occur more frequently in some families and not others. One might suspect that the trait is inherited genetically. Imagine researchers looking for the genetic underpinning of this trait and at first, not finding it. What might you conclude? It could be reasonable to conclude that the genetic underpinning of the trait is elusive, perhaps complicated with multiple genes, or that there is a non-genetic component, also not yet identified, that makes finding the genetic component harder. Eventually, you might assume, the gene will be found. Continue reading Is Human Behavior Genetic Or Learned?

A Possible Problem with CRISPR

Viruses use the DNA of their hosts to help themselves reproduce. Bacteria have counter-attacked viruses by grabbing some of the DNA from viruses and using this to identify them and kill them back. That as an oversimplified description of an eons old arms race between viruses and bacteria.

Among the DNA sequences co-opted by bacteria is the famous gene-frag-family known as CRISPR. You’ve heard of it, and you probably know what it does. Briefly, genetic scientists can use the innate power of CRISPR to manipulate other DNA to “repair” or modify in situ DNA sequences in living organisms. Got a genetic disease? No problem. We get the good genetic sequence, and then use the CRISPR based technology to replace all your bad DNA with the good DNA.

Now, of course, that doesn’t really work this way, and CRISPR technology has had fairly limited success so far. But there have been successes, and CRISPR is generally regarded as the Next Great Hope in the future of genetic therapy.

But now there may be a problem. Among the bacteria that use a CRISPER sort of sequence are two that are fairly nasty and common human pathogens. These are Staphylococcus aureus and Streptococcus pyogenes. In fact, the specific CRISPER sequences that genetic scientists use to do the CRISPR thing, come from these specific bacteria.

So, think about this for a moment. If CRISPER is used by bacteria to do any of their dirty work, and the bacteria are common human pathogens, is it possible that some humans have built up an immunity to the CRISPER sequences, perhaps putting them off limits for future CRISPR therapy? Continue reading A Possible Problem with CRISPR

Some good science and thinking related books for you

screen-shot-2017-01-12-at-9-07-03-amA Fortunate Universe: Life in a Finely Tuned Cosmos

This is a concept that has always fascinated me, ever since reading some stuff about the Periodic Table of Elements. Check it out:

Over the last forty years, scientists have uncovered evidence that if the Universe had been forged with even slightly different properties, life as we know it – and life as we can imagine it – would be impossible. Join us on a journey through how we understand the Universe, from its most basic particles and forces, to planets, stars and galaxies, and back through cosmic history to the birth of the cosmos. Conflicting notions about our place in the Universe are defined, defended and critiqued from scientific, philosophical and religious viewpoints. The authors’ engaging and witty style addresses what fine-tuning might mean for the future of physics and the search for the ultimate laws of nature. Tackling difficult questions and providing thought-provoking answers, this volumes challenges us to consider our place in the cosmos, regardless of our initial convictions.

screen-shot-2017-01-12-at-9-12-09-amGetting Risk Right: Understanding the Science of Elusive Health Risks

Understanding risk, and misunderstanding it, became a major topic of discussion, initially in economics, about the time that I was working in a major think tank where much of this discussion was happening. Risk perception had been there as a topic for a while (the head risk-thinker where I worked had already won a Nobel on the topic) but it became a popular topic when a couple of economists figured out how to get the message out to the general public.

In my view, the modern analsyis of risk perception is deeply flawed in certain ways, but very valuable in other ways. This book is very relevant, and very current, and is the go to place to assess health related risk issues, and I think it is very good. I do not agree with everything in it, but smart people reading a smart book … that’s OK, right?

Do cell phones cause brain cancer? Does BPA threaten our health? How safe are certain dietary supplements, especially those containing exotic herbs or small amounts of toxic substances? Is the HPV vaccine safe? We depend on science and medicine as never before, yet there is widespread misinformation and confusion, amplified by the media, regarding what influences our health. In Getting Risk Right, Geoffrey C. Kabat shows how science works?and sometimes doesn’t?and what separates these two very different outcomes.

Kabat seeks to help us distinguish between claims that are supported by solid science and those that are the result of poorly designed or misinterpreted studies. By exploring different examples, he explains why certain risks are worth worrying about, while others are not. He emphasizes the variable quality of research in contested areas of health risks, as well as the professional, political, and methodological factors that can distort the research process. Drawing on recent systematic critiques of biomedical research and on insights from behavioral psychology, Getting Risk Right examines factors both internal and external to the science that can influence what results get attention and how questionable results can be used to support a particular narrative concerning an alleged public health threat. In this book, Kabat provides a much-needed antidote to what has been called “an epidemic of false claims.”

screen-shot-2017-01-12-at-9-19-43-amFeeding the World: Agricultural Research in the Twenty-First Century (Texas A&M AgriLife Research and Extension Service Series)

In the not too distant past, it was understood that we, the humans, were going to run out of food within a certain defined time range. This actually happened several times, this estaimte, followed by the drop-dead date coming and going, and the species continued. Kind of embarassing.

Historically, that estimate of when we would run out of food has been wrong for one, two, or all of three reasons. First, the rate of population increase can be misestimated. We now know a lot more about how that works, and still probably can’t get it right, but in the past, this has been difficult to guess. Second, it hasn’t always been about food production, but rather, distribution or other aspects of the food supply. Right now, the two big factors that need to be addressed in the future are probably commitment to meat and waste. Third, and this is the one factor that people usually think of first, is how much food is produced given the current agricultural technology. That third factor has changed, in the past, several times, usually increasing but sometimes decreasing, depending on the region or crop. Sadly, this is probably also the factor that will change least (in a positive direction) in the future, even given the supposed promise of GMOs, which have so far had almost no effect.

Anyway, this book is about this topic:

The astounding success of agricultural research has enabled farmers to produce increasingly more—and more kinds—of food throughout the world. But with a projected 9 billion people to feed by 2050, veteran researcher Gale Buchanan fears that human confidence in this ample supply, especially in the US, has created unrealistic expectations for the future. Without a working knowledge of what types and amounts of research produced the bounty we enjoy today, we will not be prepared to support the research necessary to face the challenges ahead, including population growth, climate change, and water and energy scarcity.

In this book, Buchanan describes the historical commitment to research and the phenomenal changes it brought to our ability to feed ourselves. He also prescribes a path for the future, pointing the way toward an adequately funded, more creative agricultural research system that involves scientists, administrators, educators, farmers, politicians, and consumers; resides in one “stand alone” agency; enjoys a consistent funding stream; and operates internationally.

screen-shot-2017-01-12-at-9-22-54-amModern Prometheus: Editing the Human Genome with Crispr-Cas9

Gene editing and manipulation has come a long way. We may actually be coming to the point where methods have started to catch up with desire, and applications may start taking up more of the news cycle. We’ll see. Anyway:

Would you change your genes if you could? As we confront the ‘industrial revolution of the genome’, the recent discoveries of Crispr-Cas9 technologies are offering, for the first time, cheap and effective methods for editing the human genome. This opens up startling new opportunities as well as significant ethical uncertainty. Tracing events across a fifty-year period, from the first gene splicing techniques to the present day, this is the story of gene editing – the science, the impact and the potential. Kozubek weaves together the fascinating stories of many of the scientists involved in the development of gene editing technology. Along the way, he demystifies how the technology really works and provides vivid and thought-provoking reflections on the continuing ethical debate. Ultimately, Kozubek places the debate in its historical and scientific context to consider both what drives scientific discovery and the implications of the ‘commodification’ of life.

Genetics and Food Security

There is a food crisis sneaking up on us right now. A lot of them, actually. A lot of little one, some big ones. There are always places in the world where food has become scarce for at time, and people starve or move. You’ve heard of the “”Syrian refugee crisis,” and the often extreme reactions to it in Europe and among some in the US. That started out as a food crisis, brought on by human pollution induced global warming in an already arid agricultural zone.

Nearly similar levels of climate change related pressure on agricultural systems elsewhere has led to very different outcomes, sometimes more adaptive outcomes that won’t (at least for now) lead to major geopolitical catastrophes as we have now in the Levant and elsewhere in West Asia. What’s the difference? The difference is how agriculture is done.

Are GMOs a solution? Are GMOs safe, and can the produce a small or medium size revolution in crop productivity? What about upgrading traditional agriculture to “industrial agriculture”?

And speaking of GMOs, what is the latest in GMO research? How should GMOs be regulated, by the method they are produced, or by the novel or altered traits they have? How do we communicate about GMO research and GMO crops? What about labeling?

These and many other questions are addressed ad Mike Haubrich, me, and Anastasia Bodnar talk about “Genetics and Food Security” on the latest installment of the Ikonokast Podcast. GO HERE to listen to the podcast. Also, if you go there, you can see a picture of Anastasia holding her latest GMO product, a corn plant that can see and talk!

Also, Iknokast has a Facebook Group. Please click here to go and joint it!

And, if you have not yet listened to our first podcast, with author and science advocate Shawn Otto, click here to catch up!

Micro-Evolution In Greenland: Inuit Diet, Weight, and Stature

There is a new paper in Science linking genetic variation in people living in Greenland with long term selection for managing a marine-oriented diet, affecting stature, weight, and probably, physiological processing of omega-3 polyunsaturated fatty acids (PUFAs).

The vast majority of the variation we seen in stature (height) among humans is not genetic. That is a fact hard to swallow by so many of us who were told in biology class that “height is a complex genetic trait with many genes affecting it.” It also seems wrong because the classic examples of variation in stature, the Pygmies of Central Africa (short) and the Maasai of East Africa (tall) are assumed to be populations under selection that caused them to be outliers. Of course, the Maasai are really not that tall by modern Western standards, but the story about them being tall, first told by relatively short European travelers who met them in the 19th century, persists, despite the fact that those travelers’ offspring, such as Modern Americans and Brits, are in many cases significantly taller than their own ancestors without natural selection being the cause.

But there are some genetic factors that control height and weight and account for some percentage of variation in those phenotypes. Pygmies taken from their homeland and raised among people with unlimited food supply do not grow tall. They may become obese, but not tall, because one of the main genes that regulates growth in almost all humans simply does not function in Pygmies. (One individual Efe Pygmy I’ve met who was raised among Italian nuns, in Italy, was short but rather wide.) There may be other short statured populations with a similar genetically determined stature. But as far as we can tell, something like 20% (and that is probably an overestimate) of variation in stature in living humans over the last century or so can be accounted for by genetic variation. The rest is a combination of diet and, I suspect, an epigenetic effect linked to maternal size and diet. When a population of relatively short people get unlimited food the next generation is taller. But then, the next generation is taller still. It is as though mothers won’t give birth to maximally sized offspring, just somewhat larger offspring, who then give birth to somewhat larger offspring, so the part of the demographic transition where everyone gets taller happens over a few generations. This is a well documented but not very well explained phenomenon, and the explanation I suggest here is merely a hypothesis.

A new study in Science looks at the Inuit people, and some Europeans living in the same place they live, in this case Greenland, and finds a genetic component to Inuit stature and weight. There are also other differences having to do with processing elements of their relatively unusual diet.

The key result with respect to weight and height is shown in the graph at the top of the post. The letters (GG, GT, TT) are the alleles (T is the derived allele). Homozygotes for the derived allele are quite a bit less massive, and a small amount shorter, than those without the allele, and heterozygotes are in between.

Here is the abstract from the paper:

The indigenous people of Greenland, the Inuit, have lived for a long time in the extreme conditions of the Arctic, including low annual temperatures, and with a specialized diet rich in protein and fatty acids, particularly omega-3 polyunsaturated fatty acids (PUFAs). A scan of Inuit genomes for signatures of adaptation revealed signals at several loci, with the strongest signal located in a cluster of fatty acid desaturases that determine PUFA levels. The selected alleles are associated with multiple metabolic and anthropometric phenotypes and have large effect sizes for weight and height, with the effect on height replicated in Europeans. By analyzing membrane lipids, we found that the selected alleles modulate fatty acid composition, which may affect the regulation of growth hormones. Thus, the Inuit have genetic and physiological adaptations to a diet rich in PUFAs.

How long have the Inuit been living this lifeway, in this environment? Actually, not that long. The researchers, in their supplemental information, suggest that it could be as long as 30,000 years, but this is unlikely, or at least, the story is more complicated.

There are several complications to understanding the history of the selective environment of the Inuit, the environment that would have shaped this genetic adaptation. First, the environment has changed. Not only have we gone from an ice age to no ice age during this 30,000 year time period, but with sea level rise during the Holocene, the ecology of the arctic has changed considerably. Large areas of the continent have been inundated by the sea. Prior to that, most of the ocean adjoining land was immediately deep. With the inundation of the continent, vast relatively shallow areas of ocean would exist. Nutrients well up along the continental shelf, but shallow areas are also potentially nutrient rich because of sediments coming off shore. During glacial melt periods, there may have been frequent large scale fresh water incursions which would have had occasional disastrous effects on the local ecology. The position of estuarine settings, which can be very productive, would change. As sea level rise slowed, near shore sediments may have had a chance to build up, causing regional increases in productivity.

The migratory patterns, overall distribution, and abundance of marine mammals and common shoaling fish would have changed dramatically, and multiple times, during the last several thousand years. It would not have been until about five thousand years ago that things would have settled down allowing long term regional foraging adaptations to emerge. Prior to that there may have been periods when the marine environment was significantly more, or significantly less, productive.

Meanwhile, the ancestors of the Inuit themselves moved a great deal during this period. They were not in Greenland, or anywhere in North America, 30,000 years ago, but rather, in an unknown location in Asia. The Inuit ancestors were part of a later migration into the New World. The association (population wise) of true Arctic people and others living farther south is not known.

A second factor is cultural adaptation. When we look at the traditional Inuit foraging patterns and associated technology, together with the preceding prehistoric Thule adaptations, we can’t help but to be impressed with the highly specialized effective approaches, both strategically and technologically, to acquiring marine resources. Boats, lamps, harpoons, and processing tools are highly refined and efficient. That material culture and strategic approach, however, is only a few thousand years old. Before that, in the region, were the Dorset, who simply lacked many of these tools. It is possible that the Thule and Inuit had sled and sled dogs, but earlier people in the Arctic did not. And so on. The ancestors of the Inuit, just a few thousand years ago, could not have had as specialized a diet as the traditional (modern ethnohistoric) Inuit. Cultural adaptations changing over time is as important as, if not more important than, the afore mentioned likely changes in environment.

So, I’m not going to argue that these adaptations are not 30,000 years in the making. Rather, I’ll argue that strong selection for these alleles could be as recent a few thousand years or even less, and that prior selective environments (the combination of the natural environment and human cultural adaptations to it) may have different and the situation may have been rather complicated for many years. In other words, the new, and very interesting, results looking at the Inuit genome need to be integrated with a better understanding of Inuit history, which is probably going to require a lot more research in the region.

There is a second point I want to make about this paper. We see research suggesting a genetic explanation for a lot of things, but often, in the past, that has involved finding a correlation between this or that genetic variation and a presumed phenotypic feature. Often, the next key step to establish the link isn’t, perhaps sometimes can’t be, taken. This is the link between the observed genetic variation and a good physiological story. The present research finds genetic variation associated with physiological features that seem to be associated with a marine-oriented diet in an Arctic or Sub Arctic setting. That makes this research really valuable.

Greenlandic Inuit show genetic signatures of diet and climate adaptation
Matteo Fumagalli, Ida Moltke, Niels Grarup, Fernando Racimo, Peter Bjerregaard, Marit E. Jørgensen, Thorfinn S. Korneliussen, Pascale Gerbault, Line Skotte, Allan Linneberg, Cramer Christensen, Ivan Brandslund, Torben Jørgensen, Emilia Huerta-Sánchez, Erik B. Schmidt, Oluf Pedersen, Torben Hansen, Anders Albrechtsen, and Rasmus Nielsen
Science 18 September 2015: 349 (6254), 1343-1347. [DOI:10.1126/science.aab2319]

Temperature and sex determination

Some interesting new research. The paper is, unfortunately, behind a paywall but they made a video, so it is worth posting.

Here’s the press release for the paper:

Scientists know that temperature determines sex in certain reptiles—alligators, lizards, turtles, and possibly dinosaurs. In many turtles, warm temperatures during incubation create females. Cold temperatures, males. But no one understands why.

A recent study sheds further light on this question. The findings of researchers Kayla Bieser, assistant professor at Northland College, and Thane Wibbels, professor of reproductive biology at the University of Alabama at Birmingham, will be published this month in the primary research journal “Sexual Development,” and is now available online.

This study represents the most comprehensive, simultaneous evaluation of the chronology of how sex-determining genes express themselves during embryonic development and and looks at the impacts of estrogen.

Bieser and Wibbels followed five different genes and what was going on in the exact same turtle. To date, scientists have looked at a number of turtles and pooled the data but Bieser is the first to follow individual turtles. She wanted to know when and how they “express” themselves. For an example, Bieser describes expression as the physical manifestation of those genes such as blue or brown eye color.

She looked at turtle eggs incubated at male and female temperatures and documented what the genes were doing while sex is being determined. “Which genes ‘turn on’ and when, could be an indication of what is triggering sex,” Bieser said.

According to Bieser, temperature-dependent sex determination species may be unable to evolve rapidly enough to offset the increases in temperature, which may ultimately result in their extinction.

“It’s critical that we understand the genetic mechanisms for which temperature acts and incorporate this knowledge into management plans for the conservation of these vulnerable species.”

Secondly, Bieser applied estrogen to eggs at a male-producing temperature. The purpose she said is to help determine the triggers for sex determination and how hormones, such as estrogen, can override the temperature signal.

In other words, would temperature or estrogen win out in deciding sex? The answer: in short, neither. What she found — and this is new information — is when estrogen is applied to eggs incubating at a male temperature, gonads—or sexual parts—do not develop. Or, if they do, they barely develop.

Why? “We don’t know yet,” Bieser said.

Scientists have been doing this experiment for some time but never reported these results. She suspects the reason is because scientists did not dissect the gonadal area specifically and that they took the general area but may have not analyzed the gonads to the same detailed level. In fact, this was a sticking point for one of the reviewers of this study—so Bieser provided photos of her findings.

“This research provides a critical understanding of how temperature acts on and above the genes in species where temperature determines sex—this is particularly critical in light of global climate change,” Bieser said.

Here’s the video:

The original paper:
Bieser K.L. · Wibbels T. 2014. Chronology, Magnitude and Duration of Expression of Putative Sex-Determining/Differentiation Genes in a Turtle with Temperature-Dependent Sex Determination. Sexual Development 8(6).

It turns out that coffee is special

But you knew that already.

The Coffea canephora Genome has been sequenced. This is probably more important than the Human Genome project because humans are completely useless first thing in the morning, but coffee is very important first thing in the morning.

Some important plant evolution involves wholesale duplication of large parts of the genome. This does not appear to be the case with coffee. Rather, diversification of single genes characterizes the genome, so, according to the paper reporting these results in Science, “…the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis.”

Also of great interest is the apparent fact that caffeine related genes either evolved separately from, or engaged in the important work of making caffeine separately from similarly functioning sets of genes in tea and cacao (chocolate). I had always suspected tea was … different.

So, not at all unexpectedly, the most important molecule on earth evolved more than once!

Elizabeth Pennisi also has a writeup here.

Reviews of Nicholas Wade's "A Troublesome Inheritance"

A list of reviews of Nicholas Wade’s book “A Troublesome Inheritance,” mainly by anthropologists and others who have investigated issues surrounding the concept of “race” in humans.

Bethune, Brian: Inheritance battles

Daniels, Anthony: Genetic disorder

Dobbs, David: The Fault in Our DNA

Fuentes, Augustín: The Troublesome Ignorance of Nicholas Wade

Geneticists, Lotsofthem: An Open Letter

Goodman, Alan: A Troublesome Racial Smog

Johnson, Eric Michael: On the Origin of White Power

Laden, Greg: A Troubling Tome

Marks, Jonathan: The Genes Made Us Do It

Marks, Jonathan: Review of A Troublesome Inheritance

Myers, PZ: The hbd delusion

O, Josyln (AAA): Is Cultural Anthropology Really Disembodied?

Orr, Allen H.: Stretch Genes

Raff, Jennifer: Nicholas Wade and race: building a scientific façade

Steadman, Ian: “Jews are adapted to capitalism”, and other nonsenses of the new scientific racism

Terrell, John Edward: A Troublesome Ghost

Yoder, Jeremy: Cluster-struck

Yoder, Jeremy: How A Troublesome Inheritance gets human genetics wrong

My Review of Nicholas Wade's Book, A Troublesome Inheritance: Genes, Race, and Human History.

I first heard about Wade’s book when a colleague started talking about bits and pieces of it. He was reading it pursuant to a writing a review. I asked the publisher for a review copy, which they kindly supplied, and started tracking the pre-publication reactions. After reading the first couple of chapters, I realized that I needed to write a review of this book, but I wanted to do something a bit more than a blog post. So, I contacted American Scientist. I had reviewed two books for them earlier. American Scientist is actually my very favorite science magazine (among magazines that are not peer reviewed research outlets). It is a bit higher level than Scientific American (which is also a good mag) in its treatment of subjects.

The book review editor told me that American Scientist had shifted its book review approach to be more of a notice section, mainly talking about books that they recommended to their readers without intensive critical reviews. But they felt that my review of this particular book would be important so they agreed to try out a more extensive review to feature in the next issue.

For this reason I’ve been mainly quiet about Wade’s book. I did attend an online seminar with him and Agustín Fuentes, during which I asked a few questions, but for the most part I decided to focus only on this printed review which would come out after the dust had settled around Wade’s publication date. Keeping my mouth shut has been painful (as some of you know from our private conversations).

And now that review is done, in print, and thankfully, available on line.

You can read it here.

My original plan was to point to the American Scientists review and at the same time provide a longer blog post with all the stuff that would not fit in the printed review. But as I wrote the review and interacted with the editors at American Scientist, the phrase “Normally our reviews are under 800 words” evolved into something more like “This is important, don’t worry about length. We’ll figure it out.” This is not something you hear from editors very often, especially in print media! In the end, the review that got published is the review I’d write on my blog, significantly improved with editorial input form Scientists’ Nightstand editor Dianne Timblin and the American Scientist’s Editor in Chief.

Note: The online review is one of those muti-page web pages, so don’t forget to read all of it!!!

Enjoy. Or rage. As you wish.

How to do any genetic research you want without getting permission.

Let’s say you want to do a market-related study in which you gain entry to one thousand homes representing sets of people defined by the usual variables of income, ethnicity, urban-suburban lifestyle etc. The first thing you do is to ask a few people, real nice like, if you can go through their stuff and take a lot of photographs and notes. Most of them say no, and you perhaps even discover that the one or two who actually agree to this are odd ducks. So you go to Plan B. This involves breaking into the homes when the people are out so you can get your data despite the fact that they don’t want to participate. But you get caught and can’t do that any more. So, now you are faced with the reality that your research plans are done for.

But wait, there is a way to get similar data without needing any permission from anyone and it is not illegal, and in fact, it could actually be cheaper and easier than your original proposal and, while it may not provide the same exact results, it could even provide BETTER results. Let’s call it Plan C.

Plan C involves looking at every iteration of every single Google Street View picture ever taken anywhere in the US at any time. All of them. The vast majority of these photographs will show you nothing, but every here and there, you will get some data. There will be a shot that shows a thing in an open window, or an open door, or an open garage, or being carried into our out of a person’s house, being delivered, thrown out on the curb, sold in a garage sale, sitting on the lawn after an explosion or fire, or in use (especially yard and garden implements). This is not the same thing as sampling hundreds of houses once each, looking at all contents. But it is sampling the homes lived in by hundreds of millions of people, and sampling them dozens of times over a few years. That could be some amazing data.

And nobody can stop you from studying this source of information or doing this research. If someone does try to stop you with silly regulations from a University or something, just change into a Journalist. Then you’re golden. It would be WRONG to stop a journalist from using this information!

Turns out that this works with genes, but even better. One might want to study the relationship between a putative genetic marker and a possible behavioral thing, like maybe a psychiatric disorder or something, in a genetically bottle necked tribal group somewhere. You can try to get permission to do this, and maybe you’ll get it. Maybe you won’t get permission but you can certainly steal the genetic data from some place and do the research anyway. But people will get mad at you and you’ll not get any more research money.

Or, you can go to Plan C.

Here’s how Plan C works with genes. We have a good idea of the distribution of many genetic markers that have to do with geographical patterns over time. (Some people would use the term “race” in that sentence but that’s incorrect and unnecessary.) So, something like “East Asian” or “Native South American” or “Central African” or whatever has a list of genetic markers that go with it. Genes are supposed to “independently assort” and act all random and all, but they don’t. At the finest level, on chromosomes, genetic markers that are near each other travel together because of “linkage.” More importantly, genes move in populations. So, those East Asian genetic markers are not going to get all mixed up with the Central African genetic markers too often. Also, if you have enough samples, some mixing up doesn’t matter all that much.

So, if you want to study a disease-related “gene” (allele, a variant of a gene, really), if you think such a thing exists, you can effectively study it in a small population of repressed brown people who, tired of repression and exploitation decided to be totally unfair to you and not give you their blood, by looking at the association of LBP (“little brown people”) markers and the alleles of interest. It does not even matter if many of those marker associations are found in totally non LBP people. They are still associated. Genetic lineages are the thing, not human lineages. Humans are merely reasonable approximations of genes, really. Or at least, you can make a case for the associations and get your research funded and published without asking anybody any permissions for anything, just using giant available genetic databases. OK, so, maybe this is not “any genetic research you want.” But it is without permission!

This all sounds very nefarious but may not be. Or maybe it is. I’ll leave that to the ethicists.

By the way, if you are interesting in a big fight on the Internet about genetic research, ethics, “IRB” permissions, LBP’s and science and so on and so forth, I recommend the following, in the order suggested.

First, read this blog post: Is the Havasupai Indian Case a Fairy Tale? by Ricki Lewis (and if you have time, along with it, this related blog post)


Then, read this blog post: The Empire Strikes Back by Jonathan Marks

Then, go back to the first blog post (Is the Havasupai Indian Case a Fairy Tale?) and read the comments.

Then, report back here and tell me what you think. Especially about that last comment on the PLOS blog post.

Have a nice evening!

Photo Credit: tapasparida via Compfight cc

Regenesis: Taking over biology using readily available materials from your kitchen

I might be exaggerating slightly about the ready availability of the materials…

Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves by George Church and Ed Regis looks like a futurist tome on what could happen when technology finally catches up with human imagination and everything changes. Except it isn’t. Most futurists are people with some knowledge of technology, a fertile imagination, and a publicist. Regenesis is by a scientist (working with a writer) who is busy making a different future and who has been involved in every stage of development of the technology under discussion, and for this reason is one of the more important new science-related books you can read right now. Regis is a multiply published science author (his most recent book is What Is Life?: Investigating the Nature of Life in the Age of Synthetic Biology) and George Church is Professor of Genetics at Harvard Medical School who is one of the key players in the Personal Genome Project. He directs Personal Genomics.org, which curates the only OpenAccess human “Genomic, Environmental and Trait database. His work led to the first commercial genome sequence (for apathogen) and he has been involved in both genome sequencing (reading the genes) and synthesis (making new ones) in both the academic and private milieu. He is also director of the NIH “Center for Excellence in Genomic Science” which places him at the center of biosafety, gene privacy, and security policy development.

Church was finishing is PhD work at Harvard the same year that I started mine. We never met to my knowledge, but I remember the construction in those days of the new genetic research facility there. Cambridge, Massachusetts was the first and only city (and still maybe the only one) to write zoning and building regulations for genetic research facilities, and the building was right across from the museum I worked in. People were afraid of what might happen if some of the genes, or genetically modified organisms, they were working on in that building got out. That was a valid concern given the unknowns, but it would eventually happen that the details of what people needed to worry about shifted considerably over time. Had George Church been sent back in a time capsule and put in charge of that project, his understanding of and commitment to safety in genetic research would have been more than a little reassuring. Of course, this would have then affected his own future and thus … oh never mind, that damn Time Paradox is too confusing…

Regenesis covers the history and current status of some of the most innovative and interesting research in genetic engineering, and it is organized in a way that I really liked. The book is written as a time line. The chapters run as follows:

  • -3,800 Myr, Late Hadan
  • -3,500 Myr, Archean
  • -500 Myr, Cambrian
  • -360 Myr, Carboniferous
  • -60 Myr, Paleocene
  • -30,000 YR, Pleistocene Park
  • -10,000 YR, Neolithic
  • -100 Yr, Anthropocene
  • -1 Yr, Holocene
  • +1 Yr, The End of the Beginning, Transhumanis, and the Panspermia Era

See what they did there?

Each of these past eras represents a change in the genetics, cellular biology, evolutionary stage, or environmental context in which live existed, with the human role coming along in a big way near the end. This allows the authors to discuss the nature of life at each stage, and related the last 20 or so years of genomic and genetic research to different levels of organization of life. This causes this book to be different from the average run of the mill futurist book in two ways: 1) You learn stuff about how things are and have been, detailed stuff, interesting stuff; and 2) There is a solid road map imposed on the discussion of what is being done now and what could be done in the future, which allows the authors to avoid the messing around we see in a lot of futurist books. In other words, this is not futurist manifest; It is a history of life and a detailed discussion of what humans are actually doing with life these days and what we seem poised to be able to do based on a solid grounding in actual ongoing research.

One of the most interesting themes that helps underscore the nature of this discussion is left- vs right-handedness in biology. Most complex biological molecules could be built with the structure and symmetry organized in a left handed vs right handed way. It is quite possible that we could encounter a planet (if we could get there) rich in life that is all built on molecules that are the opposite in orientation from what we have here on Earth. Not only that, but it is possible to build such a life form now. We could construct a human that is left-handed, and thus, fundamentally different from all other humans. Such a human could not be infected by many, perhaps most, cell-level pathogens because those pathogens would not be able to interact with the left-handed body. Obviously, this is a complex issue and there is a lot too it…you’ll have to read the book to find out what the implications and complications of such a thing might be.

The most important theme in the book, and also very interesting, is the concept of synthetic biology. The goal of synthetic biology is to create an organism or set of organisms that use the standard biological machinery (proteins and enzymes and stuff building other molecules in a certain way) that will be instructed with their DNA to produce a certain product, such as oil, a house, a cute little furry organism that will replace your Roomba. Well, maybe not that last one. We use lots of synthetic biology now but we are at the chipped-stone tool phase. The basics are in place, the research is progressing, the market for the products is there. Synthetic biology is one of those “technologies” that many hope will come along and solve many of our problems. It should be relatively straight forward to create a thing that will make hydrocarbon based fuels, which one must admit are a very handy way of storing energy, from raw materials that do not include fossil carbon. My personal fantasy is to build large flat factories on the sea surface or in open arid regions that will produce a solid that we just pile up somewhere to contain carbon taken from the atmosphere, and a steady stream of a clean burning liquid. Down the street, I want to see a factory that consist of a giant, 30 acre leaf surface under which is constantly being built a layer of genetically engineered wood, with whatever properties are needed. Imagine 2X4s of just the right strength and flexibility, but indurated with anti-fungicidal and other preservative chemicals. A combination of balsa, ebony, maple, cedar and hickory. Left-handed, of course. Who needs plastic and concrete when we have Frankewood! Bwahahaha!

I interviewed George Church a couple of weeks ago on the radio. The podcast of that interview is located hare on iTunes
icon, or you can find out other ways to get it or listen to it directly here.

From the official description of the book:

Imagine a future in which human beings have become immune to all viruses, in which bacteria can custom-produce everyday items, like a drinking cup, or generate enough electricity to end oil dependency. Building a house would entail no more work than planting a seed in the ground. These scenarios may seem far-fetched, but pioneering geneticist George Church and science writer Ed Regis show that synthetic biology is bringing us ever closer to making such visions a reality.

In Regenesis, Church and Regis explorethe possibilities—and perils—of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. Until now, nature has been the exclusive arbiter of life, death, and evolution; with synthetic biology, we now have the potential to write our own biological future. Indeed, as Church and Regis show, it even enables us to revisit crucial points in the evolution of life and, through synthetic biological techniques, choose different paths from those nature originally took.

Do you hate or like Cilantro? Turns out, it's genetic. Science Teachers Take Note!

A number of lines of evidence have converged on the apparent fact that how you feel about Cilantro is a relatively simple genetic system. That Cilantro hatred is inherited genetically and not culturally has long been suspected, but now it is becoming clear enough that this could be a new module in the Science Classroom where kids are forced to taste it and record their level of disgust. It’s all written up here, in Nature.

In hopes of identifying the genetic basis for these traits, researchers led by Nicholas Eriksson at the consumer genetics firm 23andMe, based in Mountain View, California, asked customers whether coriander tasted like soap and whether or not they liked the herb. The researchers identified two common genetic variants linked to people’s “soap” perceptions. A follow-up study in a separate sub-set of customers confirmed the associations.

The strongest-linked variant lies within a cluster of olfactory-receptor genes, which influence sense of smell. One of those genes, OR6A2, encodes a receptor that is highly sensitive to aldehyde chemicals, which contribute to the flavour of coriander. This makes OR6A2 “a compelling candidate gene for the detection of the odours that give it its divisive flavour”, the researchers write.

Go to the source to get all the info. See also the I Hate Cilantro site.

Personally, I simultaneously think it tastes like soap and I like it.

The Genetics of Pesticide Resistant Bedbugs

ResearchBlogging.orgBedbugs (Insects of the Cimicidae family, commonly Cimex lectularius) are annoying, might carry diseases (though this is unclear, so probably nothing importat1, and are apparently becoming more common in the US. Interestingly, there has been very little study done of their genetics. A new study just out in PLoS ONE looks at the bedbug genome in an effort to better understand pesticide resistance in these pesky critters.

Continue reading The Genetics of Pesticide Resistant Bedbugs