What would we do without experts?

State crime lab analyst Kathryn Troyer was running tests on Arizona’s DNA database when she stumbled across two felons with remarkably similar genetic profiles.
The men matched at nine of the 13 locations on chromosomes, or loci, commonly used to distinguish people.
The FBI estimated the odds of unrelated people sharing those genetic markers to be as remote as 1 in 113 billion. But the mug shots of the two felons suggested that they were not related: One was black, the other white.
In the years after her 2001 discovery, Troyer found dozens of similar matches — each seeming to defy impossible odds.
As word spread, these findings by a little-known lab worker raised questions about the accuracy of the FBI’s DNA statistics and ignited a legal fight over whether the nation’s genetic databases ought to be opened to wider scrutiny.
[…]
Among about 65,000 felons [in the Arizona database], there were 122 pairs that matched at nine of 13 loci. Twenty pairs matched at 10 loci. One matched at 11 and one at 12, though both later proved to belong to relatives.

The American Kennel Club has run into similar issues with their own DNA typing of purebred dogs. Breeders may use now use two different sires on a single litter if they choose, providing they parentage test the offspring. However, problems can arise – sometimes two sires share so many of the same markers that it isn’t possible to know which dog fathered what puppy. This should have been forseeable, given that so many breeds are based on a mere handful of founders.
In much the same way, present day humans are thought to be the survivors of genetic bottlenecking events that reduced world populations to mere thousands in the not so distant past. Despite our large modern population, we have relatively low genetic diversity.

Indeed, there is substantially more genetic difference among individuals within chimpanzee troops in West Africa than among all living humans on earth. As shown in Figure 1, this is due to a series of bottlenecks in human evolutionary history. Geneticists studying many different parts of the human genome have concluded that the past effective population size (that is, the number of reproducing females) averaged only 10,000 individuals over the last one million years, and was as low as 5,000 around 70,000 years ago. Compare this to the approximately one billion reproducing females alive today, and it becomes clear just how narrow these bottlenecks were.

Why this was not factored in when probabilities were assigned to DNA profiling is anyone’s guess, but the actions of the FBI in attempting to block continued investigations of databases suggests their oft-cited figures arose not in the genetics lab, but in the bureaucracy.
DNA typing will always be a powerful tool in law enforcement. But should it have been touted as infallable in the way that it has? Absolutely not – too many genetic phenomenon break the “rules” for that. See tetragametic chimerism. The bizarre claims of the FBI and other law enforcement agencies about the mathematical rarity of DNA matches, (on samples using as few as 9 loci!) were as unprovable and as ridiculous as asserting that “no two snowflakes are alike”. Their attempts to elevate the confidence of the science beyond reasonable limits will likely end up producing the opposite result, giving defense lawyers an opening to undermine the integrity of legitimate DNA evidence in the minds of jurors.
ht

Science Daily;

A genetic variation which evolved to protect people of African descent against malaria has now been shown to increase their susceptibility to HIV infection by up to 40 per cent, according to new research. Conversely, the same variation also appears to prolong survival of those infected with HIV by approximately two years.
The discovery marks the first genetic risk factor for HIV found only in people of African descent, and sheds light on the differences in genetic makeup that play a crucial role in susceptibility to HIV and AIDS.
[…]
“In sub-Saharan Africa, the vast majority of people do not express DARC on their red blood cells and previous research has shown that this variation seems to have evolved to protect against a particular form of malaria. However, this protective effect actually leaves those with the variation more susceptible to HIV.”

Related: Aha!

In molecular DNA;

Three genes may play a strong role in determining why some young men raised in rough neighborhoods or deprived families become violent criminals, while others do not, U.S. researchers reported on Monday.
[…]
They found specific variations in three genes — the monoamine oxidase A (MAOA) gene, the dopamine transporter 1 (DAT1) gene and the dopamine D2 receptor (DRD2) gene — were associated with bad behavior, but only when the boys suffered some other stress, such as family issues, low popularity and failing school.
MAOA regulates several message-carrying chemicals called neurotransmitters that are important in aggression, emotion and cognition such as serotonin, dopamine and norepinephrine.
The links were very specific.
The effect of repeating a grade depended on whether a boy had a certain mutation in MAOA called a 2 repeat, they found.
And a certain mutation in DRD2 seemed to set off a young man if he did not have regular meals with his family.
“But if people with the same gene have a parent who has regular meals with them, then the risk is gone,” Guo said.
“Having a family meal is probably a proxy for parental involvement,” he added. “It suggests that parenting is very important.”

Wait for it…

Human beings may have had a brush with extinction 70,000 years ago, an extensive genetic study suggests. The human population at that time was reduced to small isolated groups in Africa, apparently because of drought, according to an analysis released Thursday.
The report notes that a separate study by researchers at Stanford University estimated the number of early humans may have shrunk as low as 2,000 before numbers began to expand again in the early Stone Age.

here it comes…

Eastern Africa experienced a series of severe droughts between 135,000 and 90,000 years ago and the researchers said this climatological shift may have contributed to the population changes, dividing into small, isolated groups which developed independently.
Paleontologist Meave Leakey, a Genographic adviser, commented: “Who would have thought that as recently as 70,000 years ago, extremes of climate had reduced our population to such small numbers that we were on the very edge of extinction.”

Must have been all the coal-fired power plants!

Biotech News;

An international team of researchers have reported that differences between discordant monozygotic twins – where one twin has a genetic disorder and the other does not – are probably due to copy number variations.
The researchers studied 19 pairs of monozygotic twins and found differences in copy number variations in DNA. Copy number variations (CNVs) occur when a set of coding letters in DNA are missing, or when extra copies of segments of DNA are produced.
[…]
“This could have a major impact on our understanding of genetically determined disorders.”
“By uncovering these small genetic differences in identical twins where one of them is sick, we have a way of tying specific genetic changes to the genesis of common diseases,” Bruder said.
Discordant twins are an interesting area of study as one twin might develop a particular disease such as Parkinson’s while the other does not. Previously, it was thought that environmental factors were the likely culprits, not genetics.

Until science threatens political correctness. Research into human dna…

… is slipping out of the laboratory and into everyday life, carrying with it the inescapable message that people of different races have different DNA. Ancestry tests tell customers what percent of their genes are from Asia, Europe, Africa and the Americas. The heart-disease drug BiDil is marketed exclusively to African Americans, who seem genetically predisposed to respond to it. Jews are offered prenatal tests for genetic disorders rarely found in other ethnic groups.
Such developments are providing some of the first tangible benefits of the genetic revolution. Yet some social critics fear they may also be giving long-discredited racial prejudices a new potency. The notion that race is more than skin-deep, they fear, could undermine principles of equal treatment and opportunity that have relied on the presumption that we are all created equal.

There isn’t an experienced domestic animal breeder on the planet who doesn’t acknowledge the profound influence of genetics on intelligence and behavior. Traits such as trainability, aggression, prey drive, docility, bite inhibition are highly heritable and difficult to modify. The realization that behavior could be selected for and fixed within a population is how breeds evolve out of species, and how identifiable family lines evolve out of breeds. It’s why retrievers retrieve, pointers point, border collies herd, and basenjis steal from the fridge. It’s why some family lines in Dobermans like to carry shoes in their mouths, generation after generation – and others don’t.
Yet, despite thousands of years of practical knowledge gained in the field of agriculture, despite mountains of published research generated in the lab, the very scientific community that accepts that animal sub-populations can be significantly distinct from one another is reflexively resistant to the possibility that that such differences may exist between sub-populations of humans.
And when the science finally forces them to face the evidence?

Although few of the bits of human genetic code that vary between individuals have yet been tied to physical or behavioral traits, scientists have found that roughly 10 percent of them are more common in certain continental groups, and can be used to distinguish people of different races. They say that studying the differences, which arose during the tens of thousands of years human populations evolved on separate continents following their ancestors’ dispersal from humanity’s birthplace in East Africa is crucial to mapping the genetic basis for disease.
Many geneticists are loath to discuss the social implications of their findings. Still, some acknowledge that as their data and methods are extended to non-medical traits, the field is at what one leading researcher recently called “a very delicate time and a dangerous time.”
“There are clear differences between people of different continental ancestries,” said Marcus Feldman, a professor of biological sciences at Stanford University. “It’s not there yet for things like IQ, but I can see it coming. And it has the potential to spark a new era of racism if we do not start explaining it better.” Feldman said any finding on intelligence was likely to be exceedingly hard to pin down. But given that some may emerge, he wants to create “ready response teams” of geneticists to put such socially fraught discoveries in perspective.

They should consider augmenting such teams with a dog breeder or two. We seem to have figured out how to identify and exploit genetic strengths and weaknesses “beneath the skin” without assigning global superiority to any one breed. We might be able to teach them something.

On the horizon – the Ultimate Wonderbra and a vehicle tow rope you can carry in your wallet;

The black widow spider’s dragline silk is a standout compared to other spider silks because of its superior strength and extensibility, a combination which enables black widow dragline silk to absorb enormous amounts of energy. These properties suggest that synthetically-produced silk might find applications as diverse as lightweight super-strong body armor, components of medical devices and high-tech athletic attire.
The researchers — Associate Professor of Biology Cheryl Hayashi, postdoctoral researchers Nadia Ayoub and Jessica Garb, and graduate students Robin Tinghitella and Matthew Collin — report their findings in the June 13 online edition of the journal PLoS ONE. In the article, they describe their work to identify the genes encoding the two key proteins, named MaSp1 and MaSp2, and determine the genes’ complete DNA sequences. The UCR Office of Technology Commercialization has filed a patent application on the gene sequences.
There are currently no products on the market based on the dragline silk of spiders. “There’s nothing quite as good yet as natural dragline silk, but we should get a lot closer now that we have the full genetic recipe,” Hayashi said.
With the ingredients and their genetic blueprint now known, it may be possible to synthetically produce the proteins by inserting the genetic sequences into host organisms such as bacteria, plants or animals, she said. Once the pure proteins are harvested, a manufacturing challenge will be spinning them into silk fibers that have the same remarkable properties as spider spun silk. But several advances have recently been made in artificial spinning methods.

This is certain to be followed by environanny demands for mandatory government regulation forcing manufacturers to label their products with “genetically modified material spider allergy alert” warning stickers.

Via Halls of Macadamia – a new angle on human smuggling, or an unhappy moment of family truth ?

— When the DNA results landed on Isaac Owusu’s dinner table here last year, they showed that only one of the four boys — the oldest — was his biological child.
Federal officials are increasingly turning to genetic testing to verify the biological bonds between new citizens and the overseas relatives they hope to bring here, particularly those from war-torn or developing countries where identity documents can be scarce or doctored.

Can the discovery of folks who are their “own grandpa” be far behind?;

Researchers have discovered a pair of twins who are identical through their mother’s side, but share only half their genes on their father’s side.
The ‘semi-identical’ twins are the result of two sperm cells fusing with a single egg — a previously unreported way for twins to come about, say the team that made the finding. The twins are chimaeras, meaning that their cells are not genetically uniform. Each sperm has contributed genes to each child.
“Their similarity is somewhere between identical and fraternal twins,” says geneticist Vivienne Souter, of the Banner Good Samaritan Medical Center in Phoenix, Arizona. “It makes me wonder whether the current classification of twins is an oversimplification.”
Such twins are probably very rare. Their existence and discovery relies on three unusual, and possibly unlinked, events: first, that an egg fertilized by two sperm develops into a viable embryo; second, that this embryo splits to form twins; and third, that the children come to the attention of science.
“There’s value in understanding that this can happen, but it’s extremely unlikely that we’ll ever see another case,” says Charles Boklage, an expert on twinning who works at Eastern Carolina University in Greenville, North Carolina.

…wears army boots.

It’s the topography!

The discovery has astonished scientists studying the human genome – the genetic recipe of man. Until now it was believed the variation between people was due largely to differences in the sequences of the individual “letters” of the genome.
It now appears much of the variation is explained instead by people having multiple copies of some key genes that make up the human genome.
Until now it was assumed that the human genome, or “book of life”, is largely the same for everyone, save for a few spelling differences in some of the words. Instead, the findings suggest that the book contains entire sentences, paragraphs or even whole pages that are repeated any number of times.
The findings mean that instead of humanity being 99.9 per cent identical, as previously believed, we are at least 10 times more different between one another than once thought – which could explain why some people are prone to serious diseases.

The Independent article is rather poorly explained. This isn’t really new information – it’s the prevalence of coding repeats that seems to have taken researchers by surprise, This article is brief, but more accurate in its description.

Their focus has been to dig out deletions or duplications of code among relatively long sequences of DNA and then compare these so-called copy number variations (CNVs) across a range of volunteers of different ancestry.
The researchers were astonished to locate 1,447 CNVs in nearly 2,900 genes, or around one eighth of the human genetic code.
“Each one of us has a unique pattern of gains and losses of complete sections of DNA,” said Matthew Hurles of Britain’s Wellcome Trust Sanger Institute, one of the project’s partners.
“The copy number variation that researchers had seen before was simply the tip of the iceberg, while the bulk lay submerged, undetected. We now appreciate the immense contribution of this phenomenon to genetic differences between individuals.”
All the same, there are widespread differences in CNVs according to the three geographical origins of the samples. This implies that, over the last 200,000 years or so, subtle variants have arisen in the genome to allow different populations of humans adapt to their different environments, according to the researchers.

All Headline News;

Lincoln, NE (AHN) – Researchers and political scientists from three universities have a new theory that politics may not be in blood but it could be in the genes.
Researchers and political scientists from University of Nebraska-Lincoln, Rice University and Virginia Commonwealth University came up with the theory.
In the research, about 8,000 sets of identical and fraternal twins answered a series of questions. Topics were diverse and included such things as school prayer, nuclear power, women’s liberation and the death penalty.
Researchers found that identical twins, who share their entire genetic code, answered more similarly than fraternal twins, who are no more similar than non-twin siblings.
Evan Charney, assistant professor of public policy and political science at Duke University, said: “The very idea that something like a political ideology could be heritable is incoherent. It doesn’t make any sense, and it’s historically inaccurate.”

Kate McMillan, dog breeder, retorted: “Associate professors of political science who would discount the possibility that inheritance might influence complex behavioral traits or general political tendencies, need to breed a few generations of show or hunting dogs before declaring that it “doesn’t make sense”.
Abstract.

MedIndia;

A child’s susceptibility to autism is increased with a single gene mutation according to research conducted by, a Vanderbilt-led research team.
This discovery has far-reaching implications because this gene, a variant form of a gene called MET, is not just specifically a brain gene but rather a gene which has its effect on multiple systems in the body such as immune function and gut repair.
Therefore researchers have concluded that autism which is complex set of behaviors and mental disabilities may not solely a problem with brain development but rather may also be linked to subtle developmental problems throughout the body.
[…]
Levitt and colleagues suggest, “We hypothesize that the common, functionally disruptive [MET gene variant] can, together with other vulnerability genes and [genetic] and environmental factors, precipitate the onset of autism.” According to Levitt and his colleagues the MET gene encodes an important enzyme called the MET receptor which sends out signals important for brain growth, brain maturation, immune function, and gut repair.
Most parents of autistic children report that their kids have digestive problems and differing immune responses. This has never been clearly linked directly or indirectly to their autism.

Women are different than men.
All joking aside, the report contains some interesting findings;

Scrutinizing more than 23,000 genes to measure their expression level in male and female tissue, the researchers found a direct correlation between gender and the amount of gene expressed.
In fact, more than half of the inspected genes have shown striking and measurable differences in expression patterns between males and females, the researchers reported.
Even in the same organ, the researchers identified scores of genes that varied in expression levels between the sexes. Gender consistently influenced the expression levels of thousands of genes in the liver, fat and muscle tissue.
Earlier studies have identified roughly 1,000 sex-biased genes in the liver and brain, but the new study is the first to uncover a gender difference in gene expression in fat and muscle tissue.
The gender differences in gene expression also varied by tissue. Affected genes were typically those most involved in the organ’s function, suggesting that gender influences important genes with specialized roles, not the rank-and-file.
In the liver, for example, the expression of genes involved in drug metabolism differed by sex. The findings mean that male and female livers function the same, but work at different rates.
“Our findings in the liver may explain why men and women respond differently to the same drug,” said Jake Lusis, co- investigator and professor of human genetics.

I know what you’re thinking – but no, it wasn’t obtained via search warrant *;

As we branched off on the evolutionary tree, our ancestors look to have made a messy break from those of chimpanzees. By comparing samples of chimp, gorilla and human DNA, scientists from MIT and Harvard say they see evidence of interspecies sex.
[…]
The geneticists rely on a molecular clock — a technique that estimates when two organisms shared a common ancestor by counting the number of genetic differences.
With more of the human and chimp genetic codes available, Reich examined several thousand stretches side by side.
To their surprise, they found some parts of the genetic code look like they diverged more recently than others — falling into a range of several million years. Alone it wasn’t enough to conclude intermixing occurred.
Their more shocking conclusion came from the X chromosome. There, our DNA seems to have diverged from chimps more than a million years later than DNA on other chromosomes.
In other creatures, sharing a similar X with another species can be a sign — a scarlet letter — pointing to interbreeding. This has to do with a connection between the X chromosome and infertility in hybrid offspring, said co-author Nick Patterson of the Broad Institute in Cambridge, Mass.
Most animals from different species can’t reproduce, he said. Some that are closely related can produce infertile offspring — as when donkeys and horses create mules. But in other cases some offspring might be fertile and not others, Patterson said. For reasons we don’t completely understand, he said, hybrid infertility in mammals seems to come from incompatible genes on the X chromosome.
Only hybrids with certain combinations of genes on the X would have the fertility necessary to pass them down, and that would dampen diversity in the X chromosome until the mixing stopped.
Patterson said these hybrid ape-creatures may have mated with each other or with members of either the human ancestral line or that of the chimps. They can’t say who ended up getting the hybrid genes.
The separation of one species from another is more than a matter of reproductive compatibility, said Montgomery Slatkin, a biologist from the University of California.
He said speciation starts with geographic separation between two groups of the same species. They acquire different traits as they adapt to different environments and at the same time also grow apart through random genetic changes..

The rest is here

Back in July of ’04, I mentioned that I’m probably the “first professionally trained commercial artist to have a peer reviewed paper on opthalmology on her resume”.
The research has been continuing, and the team has just published another, this time in Investigative Ophthalmology and Visual Science. If you have any background in molecular genetics, you may find the abstract rather interesting.;

White blood cells of affected dogs contained less than 30% of the normal amount of two specific mtDNA sequences, compared with the content of the nuclear-encoded glyceraldehyde-3-phosphate dehydrogenase (GA-3-PDH) reference gene. Retina and RPE tissue from affected dogs had reduced mRNA transcript levels for the two mitochondrial genes detected in the RDA experiment. Transcript levels for another mtDNA-encoded gene as well as the nuclear-encoded mitochondrial Tfam transcription factor were reduced in these tissues in affected dogs. Mitochondria from affected dogs were reduced in number and size and were unusually electron dense.

What’s interesting is that the retinal dysplasia affected dogs are lacking normal mitochondria DNA in all the cell types tested so far – and that they are not only alive, but otherwise healthy and fertile.

Reason;

The pharmaceutical company Schering-Plough is excluding African-American patients from the Phase II trial of its new Hepatitis C (HCV) anti-viral drug. Activist groups are denouncing this exclusion as racist. For its part, Schering-Plough argues that it has valid scientific grounds for limiting the research at this stage to other racial groups. Company researchers point out that for unknown reasons, black people do not respond as well to HCV treatments as do members of other racial groups. One prominent activist, Judith Dillard, told the Newark Star-Ledger, “The bottom line is that African-Americans have been left out of this study to make the drug look good.” Which is precisely the point.
In the past, drug trials would generally include members from diverse racial and ethnic groups. If the drug being tested was effective in all groups, then that was great; the company testing it had a potential blockbuster. If, however, some groups in the trial did not respond well to a treatment, then it would appear to be ineffective compared to placebo, and it would not be approved. Eventually researchers began to notice that not all groups respond the same way to the same medicines.

Researchers worry however, that the introduction of race-specific drug therapies may cause side effects in other groups, including the poorly-understood phenomenon known as “spontanious head explosion”.

So is the Schering-Plough HCV anti-viral study “racist”? Not really. The researchers have identified a patient subpopulation that they believe is more likely to benefit from the new treatment. If Schering-Plough can demonstrate that the medicine does work for whites, then the company can get it approved for sale by the FDA for that patient population. Admittedly race is a crude biomarker, but it would surely be bowing to political correctness about race to deny patients the benefit of treatments that are more likely to help them.

Of course. But that won’t stop some from trying.
Related.

Chickens who can chew their food;

Around 300 million years ago, the ancestor of all modern vertebrates gave rise to two lineages, the mammals and the reptiles/birds. The oldest reptiles, such as crocodiles and alligators, had cone-shaped teeth. So did the earliest birds, called archosaurs.
Then, around 80 million years ago, modern birds emerged without teeth.
[…]
The archosaurs had mouths similar in shape to a reptile’s. It turns out that developing a beak caused birds to lose their teeth.
“The reason that birds lost their teeth is that in forming a beak, the two tissues that �talk’ to each other to make a tooth become separated,” Fallon said. “They can’t have the conversation to make a tooth. In the mutant, these tissues are brought back together.”
[…]
By making a few changes to the expression of certain molecules in the pathway, the researchers were able to induce tooth growth in normal developing chickens. These teeth also looked like reptilian teeth and shared many of the same genetic traits, supporting the scientists’ hypothesis. None of these chickens were allowed to hatch.

The research is being touted as having a possible application in “re-growing teeth in people who have lost them through accident or disease.”
Hopefully, no wakes up one morning with a beak.
Via Drudge

Scotland On Sunday;

Four years ago in Salt Lake, the drug busters came up with a secret test for the blood booster Darbepoetin and caught out two cross-country skiers, Johann Muelegg of Spain and Larissa Lazutina of Russia. But if Repoxygen is used in Turin, the medics have got a headache. America’s Anti-doping Agency senior managing director, Larry Bowers, has already called it a “real threat”, while German biochemist Werner Franke said this week: “It is worse than in the GDR [former East Germany] and more brutal than Balco.”
The springboard for these dire pronouncements was an email German police found on the computer belonging to former east German coach to Katrin Krabbe, Thomas Springstein, who is on trial at the moment for doping under-age female athletes. The message complained how “difficult it is to get hold of Repoxygen. Please give me new instructions so that I can get hold of the product for Christmas”.
It was an historic moment: the moment that email was presented in open court was the exact moment when the latest stage of doping was officially confirmed. The era of genetic doping has arrived.

This stuff makes steroid use look like allowing your teenage daughter out wearing too much makeup.
I’ve never understood the reasoning of sports punditry who advocate opening wide the doors to atheletes to use whatever performance enhancing drugs they wish. While some of the regulations sound like overkill (caffeine?) what seems to be forgotten is the age at which elite atheletes begin training for Olympic careers.
It’s one thing to argue that a 24 year old NFL player has the right to fill his veins with Big Jim’s Extract of Bull Testicle – it’s quite another to give the chemical green light to a coach entrusted with the training of 11 year old gymnasts.

New hope for a cure for freckles!