Posts Tagged: Genetics


23
Feb 11

Milford Wolpoff And Razib Khan Discuss Multiregional Evolution

Milford Wolpoff and Razib Khan discuss multiregional evolution, including Neaderthal and Denisova contributions to modern humans.

(Link)


6
Feb 11

Kathryn Clancy and John Hawks talk Anthropology

Kathryn Clancy and John Hawks talk on BlogggingHeads about anthropology, genetics, blogging, and more.

(Link)


18
May 10

Monogamy, Polygyny and Mutations

A nice quote from Razib Khan

Mutations are as you know a double-edged sword. On the one hand mutations are the stuff of evolution [...] On the other hand mutations also tend to cause problems. In fact, mutations which are deleterious far outnumber those which are positive. It is much easier to break complex systems which are near a fitness optimum than it is to improve upon them through random chance.

[I]n a polygynous population a few healthy males with good genes could give rise to most of the next generation, and so providing the balance of selection to the background mutational rate. [While the rest of the males serve as a "dumping grounds of bad genes".]
[...]
In contrast monogamous populations will have less power to expunge mutations in this fashion because there is more genetic equality across males, the bad will reproduce along with the good, more or less.


8
May 10

Aspie Genotype?

AFAIK, no one currently knows what the Aspie genotype is. But it seems some people may have gotten closer to finding it.

From ScienceDaily: "Asperger Syndrome, Autism, And Empathy: Study Links 27 Genes"…

Scientists from the University of Cambridge have identified 27 genes that are associated with either Asperger Syndrome (AS) and/or autistic traits and/or empathy. The research will be published July 16 in the journal Autism Research. This is the first candidate gene study of its kind.

The research was led by Dr Bhismadev Chakrabarti and Professor Simon Baron-Cohen from the Autism Research Centre in Cambridge. 68 genes were chosen either because they were known to play a role in neural growth, social behaviour, or sex steroid hormones (e.g. testosterone and estrogen). The latter group of genes was included because AS occurs far more often in males than females, and because previous research from the Cambridge team has shown that foetal testosterone levels are associated with autistic traits and empathy in typically developing children.
[...]
The research found that single nucleotide polymorphisms (SNPs) in 27 out of the 68 genes were nominally associated with either AS and/or with autistic traits/empathy. 10 of these genes (such as CYP11B1) were involved with sex steroid function, providing support for the role of this class of genes in autism and autistic traits. 8 of these genes (such as NTRK1) were involved in neural growth, providing further support to the idea that autism and autistic traits could result from aberrant patterns of connectivity in the developing brain. The other 9 genes (such as OXTR) were involved in social behaviour, shedding light on the biology of social and emotional sensitivity.

From the paper: "Genes related to sex-steroids, neural growth and social-emotional behaviour are associated with autistic traits, empathy and Asperger Syndrome"…

Genes related to sex steroids, neural growth, and social-emotional behavior are associated with autistic traits, empathy, and Asperger syndrome

B. Chakrabarti, F. Dudbridge, L. Kent, S. Wheelwright, G. Hill-Cawthorne, C. Allison, S. Banerjee-Basu, S. Baron-Cohen
[...]

Abstract

Genetic studies of autism spectrum conditions (ASC) have mostly focused on the low functioning severe clinical subgroup, treating it as a rare disorder. However, ASC is now thought to be relatively common (1%), and representing one end of a quasi-normal distribution of autistic traits in the general population. Here we report a study of common genetic variation in candidate genes associated with autistic traits and Asperger syndrome (AS). We tested single nucleotide polymorphisms in 68 candidate genes in three functional groups (sex steroid synthesis/transport, neural connectivity, and social-emotional responsivity) in two experiments. These were (a) an association study of relevant behavioral traits (the Empathy Quotient (EQ), the Autism Spectrum Quotient (AQ)) in a population sample (n=349); and (b) a case-control association study on a sample of people with AS, a high-functioning subgroup of ASC (n=174). 27 genes showed a nominally significant association with autistic traits and/or ASC diagnosis. Of these, 19 genes showed nominally significant association with AQ/EQ. In the sex steroid group, this included ESR2 and CYP11B1. In the neural connectivity group, this included HOXA1, NTRK1, and NLGN4X. In the socio-responsivity behavior group, this included MAOB, AVPR1B, and WFS1. Fourteen genes showed nominally significant association with AS. In the sex steroid group, this included CYP17A1 and CYP19A1. In the socio-emotional behavior group, this included OXT. Six genes were nominally associated in both experiments, providing a partial replication. Eleven genes survived family wise error rate (FWER) correction using permutations across both experiments, which is greater than would be expected by chance. CYP11B1 and NTRK1 emerged as significantly associated genes in both experiments, after FWER correction (P<0.05). This is the first candidate-gene association study of AS and of autistic traits. The most promising candidate genes require independent replication and fine mapping.


8
May 10

Don’t Forget: DNA Evidence Can Be Fabricated!

A link a friend sent me made me want to remind people that: DNA evidence can be fabricated!

From The New York Times

Scientists in Israel have demonstrated that it is possible to fabricate DNA evidence, undermining the credibility of what has been considered the gold standard of proof in criminal cases.

The scientists fabricated blood and saliva samples containing DNA from a person other than the donor of the blood and saliva. They also showed that if they had access to a DNA profile in a database, they could construct a sample of DNA to match that profile without obtaining any tissue from that person.

“You can just engineer a crime scene,” said Dan Frumkin, lead author of the paper, which has been published online by the journal Forensic Science International: Genetics. “Any biology undergraduate could perform this.”
[...]
“DNA is a lot easier to plant at a crime scene than fingerprints,” she said. “We’re creating a criminal justice system that is increasingly relying on this technology.”

For those interested, the actual paper which this article is based on: "Authentication of forensic DNA samples", by Dan Frumkin, Adam Wasserstrom, Ariane Davidson, and Arnon Grafit.

(Of course, many people saw DNA evidence fabrication in the realm of possibility before this paper came out. But this paper gives people an example to point to.)

I should note though that one of the author’s of the paper (Dan Frumkin) has founded a company which claims to have developed a test which can detect fabricated DNA evidence using the techniques he describes.

Of course, one might wonder if there are any techniques for fabricating DNA evidence that this (or any other test) cannot detect? There could be a tactical advantage to being able to fabricate DNA evidence, in an undetectable manner, for some people. It’s just speculation on my part, but absence of evidence is not evidence of absence, of course.


2
May 10

Why Athletes Are Geniuses

An interesting article by Carl Zimmer on Why Athletes Are Geniuses. Here’s an excerpt….

Neuroscientists have found several ways in which the brains of top-notch athletes seem to function better than those of regular folks.

The qualities that set a great athlete apart from the rest of us lie not just in the muscles and the lungs but also between the ears. That’s because athletes need to make complicated decisions in a flash. [...]

In recent years neuroscientists have begun to catalog some fascinating differences between average brains and the brains of great athletes. By understanding what goes on in athletic heads, researchers hope to understand more about the workings of all brains—those of sports legends and couch potatoes alike.

[A]n athlete’s actions are much more than a set of automatic responses; they are part of a dynamic strategy to deal with an ever-changing mix of intricate challenges.
[...]
Good genes may account for some of the differences in ability, but even the most genetically well-endowed prodigy clearly needs practice—lots of it—to develop the brain of an athlete.

Some (but not all) of the research involved, for those interested…


14
Mar 10

Small Dogs Have Middle Eastern Origins

I’ll be blunt. I’m not a fan of small dogs. (I tend to consider them “large rats”.) However, I am a fan of dog genetics.

A genetic study has found that small domestic dogs probably originated in the Middle East more than 12,000 years ago. Researchers writing in the open access journal BMC Biology traced the evolutionary history of the IGF1 gene, finding that the version of the gene that is a major determinant of small size probably originated as a result of the domestication of the Middle Eastern gray wolf.

Melissa Gray and Robert Wayne, from the University of California, Los Angeles, led a team of researchers who surveyed a large sample of gray wolf populations. She said, “The mutation for small body size post-dates the domestication of dogs. However, because all small dogs possess this variant of IGF1, it probably arose early in their history. Our results show that the version of the IGF1 gene found in small dogs is closely related to that found in Middle Eastern wolves and is consistent with an ancient origin in this region of small domestic dogs.”

(Emphasis mine.)

(Link)


21
Feb 10

Making Life From Scratch

There is a hypothesis that there was a world filled with life based on RNA which predates our current world where life is based on DNA and protein. Given this hypothesis, this experiment in trying to make life from scratch, based on RNA, is an interesting one indeed.

For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes – that can replicate themselves without the help of any proteins or other cellular components.

What’s more, these simple nucleic acids can act as catalysts and continue the process indefinitely.
[...]
The researchers began with ribozymes known to occur naturally, and put these in a growth medium, heated them and allowed the ribozymes to replicate until they had exhausted their fuel – usually within an hour.

The team then extracted a random subset, and put them in a new medium: ribozymes then competed with each other to consume as much of the medium as possible.

Eventually more successful ribozymes came to dominate the culture, and as the process continued, the ribozymes – undergoing evolution – grew in complexity, blindly finding solutions that made them more successful.

“The key thing is it replicates itself, and passes information from parent to progeny down the line,” Joyce told Cosmos Online.

“There’s roughly 30 bits of information passed. Some functions are more fit than others, and those that are more fit ‘breed’ more, and are perpetuated more efficiently, and so it goes Darwinian.”

The ultimate goal is to create genetic systems that behave like life, and are for all intents ‘life’ as we know it, but arose without using biological systems.

“The aim is to create systems that have inventive capabilities, that can develop novel solutions to challenges posed by the environment. But that we don’t have yet,” he said.

“What we do have is a self-sustained chemical system that undergoes Darwinian evolution.
[...]
They are synthetic genetic systems, and they are evolving. But they’re not living because they don’t yet show the capacity to invent a whole cloth of functions.

(Emphasis mine.)

(Link)


17
Feb 10

Looks vs Genes

A nice excerpt from Razib Khan

For whatever reason many salient physical traits which we use to classify populations don’t exhibit the pattern of the total genome, whereby all non-Africans are a branch of the tree of H. sapiens, which mostly consists of African lineages which are much more variegated. Likely new environmental selection pressures once populations left Africa play a role in this.

But there may also be other factors. Biological anthropologist Henry Harpending once explained to me that even if populations exchange genes regularly so as to become indistinguishable on their total genome content, there may be social selection for particular traits correlated with group membership. Harpending explained that on many neutral markers, such as mtDNA lineages, the Bushmen and their Bantu neighbors seem to be relatively undifferentiated. But when it came to physical appearance there was a sharp distinction. Why? Harpending suggested that perhaps there is a strong fitness advantage for someone of mixed ancestry to look more like the group they’re born into. For example, imagine a Bushman man takes a Bantu wife, some of his children favor the father, some the mother. In terms of total genome content all the offspring reflect the parental populations, but on the subset of genes which control traits salient in marking Bushmen-Bantu differences (e.g., epicanthic eye fold) there may be greater fitness to those who carry genotypes which reflect the group into which they’re born.*

Obviously genetics is fascinating to me, and probably you if you’re reading this weblog. When applied to humans it has a very strong emotional impact, consider the popularity of genealogical companies which utilize genetic methods. But it is important to remember that our own intuitive model of our species is to some extent pre-scientific, and mapping colloquial concepts and preconceptions onto scientific findings can result is less than perfect clarity. In this, the 1980s hullabaloo over mitochondrial Eve served as simply a foretaste of what was to come.

* As a toy example, imagine that the epicanthic eye fold is monogenic, controlled by a locus which comes in two flavors, E & e. Those with EE have the fold, those with ee do not, while those with Ee are somewhere in the middle. Imagine that the Bushmen have very high frequencies of EE, while their Bantu neighbors have lower frequencies of the E allele, but not trivial. Imagine if a Bantu woman is of the genotype Ee, while her Bushmen husband is EE. 50% of the offspring would exhibit the Bushmen epicanthic eye fold phenotype. In terms of total genome content these individuals would be no more Bushmen than their Ee siblings, but they would look more Bushmen to others of the tribe, and so might have more success finding a mate due to lower levels of social exclusion. Extrapolate this process generally and you can see how genes which control outwardly salient traits may exhibit more between group difference than the overall genome.

(Link)


14
Feb 10

Dinosaur Comics: Genetics

T-Rex on Genetics :-)

(Link)