October 10, 2015


News Clips For The Day


http://www.npr.org/2015/10/09/447202433/-great-pause-among-forensic-scientists-as-dna-proves-fallible

'Great Pause' Among Prosecutors As DNA Proves Fallible
Martin Kaste
OCTOBER 09, 2015

Graphics -- Chromosomes and double helix over silhouettes of man
Lee Woodgate/Ikon Images/Getty Images
Related Article -- Wash. Lawmakers Fight For DNA Sampling At Arrest

Over the summer, the Texas Forensic Science Commission, which sets standards for physical evidence in state courts, came to an unsettling conclusion: There was something wrong with how state labs were analyzing DNA evidence.

It seemed the labs were using an outdated protocol for calculating the probability of DNA matches in "mixtures"; that is, crime scene samples that contain genetic material from several people. It may have affected thousands of cases going back to 1999.

At first, they assumed the update wouldn't make a big difference — just a refinement of the numbers.

But when a state lab reran the analysis of a DNA match from a murder case about to go to trial in Galveston, Texas, it discovered the numbers changed quite a bit.

Under the old protocol, says defense lawyer Roberto Torres, DNA from the crime scene was matched to his client with a certainty of more than a million to one. That is, you'd have to go through more than a million people to find somebody else who'd match the sample. But when the lab did the analysis again with the new protocol, things looked very different.

"When they retested it, the likelihood that it could be someone else was, I think, one in 30-something, one in 40. So it was a significant probability that it could be someone else," Torres says.

The change didn't affect the outcome of that case because there was other evidence against his client, but officials in Texas have just begun the process of correcting the mistake.

"We have to go back and identify which of those cases involved DNA mixtures where the lab may have given incorrect results," says Jack Roady, the district attorney in Galveston. "It's going to be a herculean task, but we're gonna do it."

Roady has been cooperating with the Texas Forensic Science Commission on fixing the problem, and he recalls the scene in September when he described the situation to a meeting of his fellow prosecutors.

"There was sometimes moments of collective gasps," he says. "The fact that this science may not have been done correctly in the past gives us great pause."

It's unsettling to find out DNA analysis can vary like this because it threatens to undermine the deep faith people have placed in the technology.

"And it's not faith they should not have had to begin with," says Keith Inman, who teaches forensic science at California State University, East Bay.

Inman has worked with DNA evidence since the 1980s. He says forensic DNA-matching is based on sound science, but sometimes labs can get ahead of themselves. What happened in Texas, he says, is that labs have been using cutting-edge "testing kits" that can extract tiny traces of DNA from crime scenes, but those samples were then analyzed with math that's not suited to "weak" samples that combine DNA from many people.

A Washington State Patrol crime lab technician opens DNA sample cards containing cheek swabs sent from jails and prisons. If the state Legislature approves pre-conviction DNA sampling, the number of cards the lab processes could double.

He says the problem isn't limited to Texas. He says the newest, best analysis method — called "probabilistic genotyping" — takes time to roll out, and that's put labs in a quandary.

Prosecutors said a project to review untested rape kits proved the innocence of Michael Phillips, who says he pleaded guilty to a 1990 rape because his attorney advised him to avoid trial.

"There's this interim time that cases are coming up and the analyst has to do something with it, and they know by definition that there is a better approach," Inman says.

Meanwhile, the justice system's hunger for DNA evidence just keeps growing. There are now police departments that have made swabbing for DNA part of their routine.

"We collect DNA evidence daily," says Jim Ferraris, deputy chief in Salem, Ore. His department has taken advantage of quicker testing provided by the state lab, and he says every officer in town is now trained to collect DNA. They even swab stolen cars and burgled homes.

"The doorjamb area, the point of entry — we'd swab that area," says Ferraris. "Let's say the dresser got rifled, we'd look on the handles. DNA has been folded into the fabric of what we do every day here."

All that swabbing has paid off. They've found DNA links between crimes, and they've found suspects. Ferraris believes the DNA-swabbing has led to a decrease in property crimes.

At the same time, these "touch samples" can be very challenging for the labs. When you take a sample from a doorjamb, the sample may include DNA from several people, in roughly equal proportions, all mixed together.

Faced with ambiguous samples like that, results can vary. A lab using one method may find a match, while another lab, using a more conservative analysis, may judge the same sample to be inconclusive.

In the world of scientific research, this would be seen as normal; scientific doubt is considered part of the process. But NYU law professor Erin Murphy says in the world of courts and lawyers, those doubts aren't always understood.

"We have this tendency in criminal justice to look for solutions to the most vexing problem, which is, 'How do we find dangerous people and stop them?' And when we look for those solutions, we like for them to be perfect," Murphy says.

I feel like we're clinging to a life raft of DNA, and saying, 'Well this one will save us!'
Erin Murphy, NYU law professor
Murphy has written a new book about this called Inside the Cell: the Dark Side of Forensic DNA. She says people should understand that DNA analysis can involve "subjectivity," and she worries about the tendency of juries to look past doubt.

"[Juries] are even willing to go a step further and say, 'We'll convict on the basis of DNA, even in the face of evidence — non-DNA evidence — that this isn't the perpetrator," Murphy says.

She has a pet theory about this. She says the public has seen other kinds of evidence discredited over the years, such as bite mark analysis and hair analysis. Even eyewitness testimony is now seen as unreliable. So we look to DNA.

"I feel like we're clinging to a life raft of DNA and saying, 'Well this one will save us!' " Murphy says. "But I think that both wrongly inflates DNA's capabilities, and it also is just overlooking the part of the story of these old techniques, where they were used in our system for decades without challenge."

If we now push this technology too hard — say, by prosecuting someone on nothing more than a genetic match — then DNA may also be headed for the kind of reassessment that has battered the reputation of older types of physical evidence.




“I feel like we're clinging to a life raft of DNA, and saying, 'Well this one will save us!' Erin Murphy, NYU law professor. Murphy has written a new book about this called Inside the Cell: the Dark Side of Forensic DNA. She says people should understand that DNA analysis can involve "subjectivity," and she worries about the tendency of juries to look past doubt. …. "But I think that both wrongly inflates DNA's capabilities, and it also is just overlooking the part of the story of these old techniques, where they were used in our system for decades without challenge."


People, including me, are always looking for the absolutely reliable “truth,” and it just doesn’t exist. We want everything to be easy. Laboratory work and scientific theory are not 100% perfect, as individual practitioners are not. Juries are just going to have to keep paying attention to the “reasonable doubt” and retain a healthy suspicion of the “certainty” of this or any other evidence. Sometimes police departments and attorneys even cheat, paying a coroner to falsify evidence so a wealthy local citizen is not convicted. More often they may mishandle biological material by accident or simple oversight, causing it to read results that are inaccurate, as with the tainted blood samples in the OJ Simpson trial which had been carried around for too long a time by an officer rather than his bothering to make a special trip to the lab.

I still think techniques of DNA evidence are better than the piecemeal tests that we have had in the past, but as Quincy would tell you, we mustn’t overlook any peculiar variance at all that might indicate an error. The courts can only do their best, and I’m sure they will continue to try to do that.





http://www.npr.org/sections/thetwo-way/2015/10/09/447236239/mexico-says-it-will-allow-international-experts-to-revisit-missing-students-case

Mexico Says It Will Allow International Experts To Revisit Missing Students Case
Eyder Peralta
OCTOBER 09, 2015

Photograph -- A man holds a banner that reads in Spanish "Justice," during a march by parents and relatives of 43 missing students who were killed, in Iguala, Mexico.
Rebecca Blackwell/AP


Mexico says that it will allow a team of international experts to revisit the case of 43 students who went missing last year.

NPR's Carrie Kahn reports that the United Nations' top human rights official recommended the move after a visit to the country.

Carrie filed this report for our Newscast unit:

"Zeid Ra'ad Al Hussein, the U.N.'s High Commissioner on Human Rights, recommended the experts re-examine the site where the government says the bodies of the students were burned.

"Authorities contend the 43 were kidnapped, then murdered by a local drug gang. All the bodies were allegedly burned in one night at a garbage dump. That version has been publicly challenged by relatives and international experts.

"Mexico says it will allow seven experts from five countries to re-review the crime area.

"During his visit, the UN commissioner criticized Mexico's police and prosecutors. Referring to the tens of thousands of unsolved murders and disappearances.

"'No one in Mexico can feel safe. They're not enjoying the protection of the law,' he said."

El Universal reports that Arely Gómez González, the country's attorney general, told senators today that it had assembled an international team to take part in the investigation.

"The case of Iguala is not closed," she said. "The investigations continue."

Back in January, Mexico declared all 43 students dead. The attorney general at the time made a multimedia presentation that said the students were kidnapped, taken to a trash dump, killed, set on fire, the remains put in bags and then thrown into a river.




"Zeid Ra'ad Al Hussein, the U.N.'s High Commissioner on Human Rights, recommended the experts re-examine the site where the government says the bodies of the students were burned. "Authorities contend the 43 were kidnapped, then murdered by a local drug gang. All the bodies were allegedly burned in one night at a garbage dump. That version has been publicly challenged by relatives and international experts. …. "During his visit, the UN commissioner criticized Mexico's police and prosecutors. Referring to the tens of thousands of unsolved murders and disappearances. "'No one in Mexico can feel safe. They're not enjoying the protection of the law,' he said."

“Back in January, Mexico declared all 43 students dead. The attorney general at the time made a multimedia presentation that said the students were kidnapped, taken to a trash dump, killed, set on fire, the remains put in bags and then thrown into a river.” How many gang members does it take to kill, burn, bag and discard in a river 43 people who were young and probably able to run away? I guess if they’re terrified enough to cause them to simply give up and accept “their fate,” maybe fifteen or twenty attackers with assault rifles could do it. How did the gang get them all rounded up in one spot like that, though? This story is really steeped in mystery.

Hopefully we’ll hear the results of this UN study. The very poor control exercised by Mexican police over the drug lords has been in the news for years, and according to Al Hussein there are “tens of thousands of unsolved murders and disappearances.” The police, meanwhile, have been heavily corrupted with bribes. A situation like this mass killing is too barbaric to fully imagine in modern times, but ISIS, Boko Haram, al-Qaeda and undoubtedly others whose names I haven’t heard mentioned are as ruthless and brutal in their actions. Oh, yes, Hitler’s Germany and other European nations have also committed mass murders complete with mass burials. A recently discovered grave of that kind in Eastern Ukraine, the Russian part, was in the news just a few weeks ago.

The name of the website for that story is http://www.cbsnews.com/news/hidden-holocaust-60-minutes/. The star of the story is a French priest who is researching the MANY such graves in Russia and other European nations. It’s moving and fascinating information. Hatred was an everyday thing in that time period, and in others down through history. Listen to the video as well. It is very moving.





http://www.npr.org/sections/13.7/2015/10/08/446877747/are-we-ex-apes-a-story-of-human-evolution

Are We Ex-Apes? A Story Of Human Evolution
Barbara J King
October 8, 2015

Photograph -- A beautiful profile of a chimpanzee or bonobo with what looks to be a “smile” on its lips



"We are biocultural ex-apes trying to understand ourselves," declares biological anthropologist Jonathan Marks in his new book Tales of the Ex-Apes:How We Think About Human Evolution.

That term — ex-apes — get emphasized in the book a lot by Marks, as does "human exceptionalism." Marks really doesn't want to be an ape — and he delivers his argument in a book that's fresh (in all senses of the word), funny and full of rigorous anthropological scholarship. His argument pushes back against my tendency — even while working within the same discipline as Marks's — to emphasize not ape-human boundaries but ape-human continuities.

There are two central themes, as I see it, in Marks's Tales.

Tales of the Ex-Apes
Tales of the Ex-Apes
How We Think about Human Evolution
by Jonathan Marks

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First, human meaning-making is centered on kinship. Unlike other animals, we decide to whom we're related based as much on our shared ideas as on the fact of our shared genes. Consider first cousins. In some societies, your mother's brother's offspring and your mother's sister's offspring, though equally genetically related to you, may be considered to be in two wildly different categories of kin, such that one is a perfectly acceptable mating partner and the other would be a scandalously incestuous choice.

Second, because science is everywhere and always a cultural enterprise, this meaning-making extends to the ways we make sense of human origins. It's notoriously hard to distinguish one extinct species from another, which means that species are units of cultural thought as much as of biological fact. The inevitable conclusion is that in studying human evolution, we impose upon fossil finds more than discover from them trees of relatedness that attempt to draw connections among various ancestral species.

Marks concludes that ancestry "is an origin myth. It takes the world of biological data and emphasizes some things, invents others, and relates the present to the past in a meaningful way."

So far, so good.

But what about that next step, the one that carries us firmly into the territory of human exceptionalism? Sure, humans make meaning in ways that chimpanzees don't. But why push hard to wall us off as ex-apes from these smart, savvy primates who make meaning in their own ways?

And push hard Marks does. Making a cultural decision of his own, he portrays chimpanzees as a kind of dumb cousin.

Chimpanzees don't speak. Instead, Marks notes, "one ape goes 'oo-oo-oo,' and the others join in." Lacking graveside rituals for their dead, when a companion is unresponsive, chimpanzees are limited to understanding only that "once Boo-Boo has ceased to move, he is not going to start moving again." Chimpanzees, in fact, "have small, weak brains."

Marks doesn't, of course, deny that this way of framing chimpanzees is a cultural framing — that would go against all his conclusions. I asked him this week by email if scientists who study chimpanzees might find his language to be pretty obviously biased, an explicit attempt to stretch the ape-human divide. He replied in this way:

"Yes, absolutely! My point is precisely that nobody can say 'You're being political/ideological/biased and I'm not.' Given the subject, it is all bio-political, and that is what we need to acknowledge — this is not like fruit-fly genetics."
So, then, what is my bio-political take on our "dumb" cousins?

Even though chimpanzees neither speak nor bury their dead, they're not so dumb at all. In their dynamic fission-fusion communities, chimpanzees communicate with meaningful vocalizations and gestures, express both lethal violence and also empathy and grief, and show nifty levels of cognition by keeping track of complex social relationships, hunting collaboratively and making tools (used in precise sequence) that increase their foraging success.

Aren't we apes, in the same way that we are mammals? On this point, Marks holds firm. He told me:

"Let's differentiate between taxonomic terms and descriptive ones. We are mammals, because that is a classificatory term whose defining properties we possess. We are also hominoids; that is a classificatory term and we have the defining properties (no tail, Y-5 molars, rotating shoulder, etc.). Those are statements about what kinds of animals we are most similar to, and are taxonomic.

Apes is not a taxonomic category, but a descriptive category. By exactly the same criteria that would lead you to say we are apes (i.e., phylogeny), you would also have to say that we are fish. But we don't say that we are fish (because it would be stupid). There are certainly thing we can learn about our biology by coming to grips with our fish ancestry, but we aren't fish. Rather, we say that our ancestors were fish, but they evolved into land-dwelling, air-breathing tetrapods. Likewise our ancestors were long-armed, small-brained, and hairy (i.e., "apes"), but they evolved into short-armed, big-brained, glabrous creatures.

If evolution is descent with modification, then to say that we are fish would be to invoke descent without modification — just descent. That is the same situation for apes."

Point to Marks: We don't want to invoke descent without modification. Biological anthropologist John Hawks stresses the value in invoking precise phylogeny when he says, too, that humans aren't apes.

Yet, seeing ourselves as apes (and mammals, and even as fish, too) invites us to acknowledge the trajectory by which humans evolved to be who we are. We carry — in a very non-deterministic fashion — parts of our ancestral past with us; today we aren't so far apart from other animals as people sometimes think.

Marks and I agree on the big things. Humans shared a common ancestor with today's apes. The human lineage evolved over the last 6 or 7 million years in unprecedentedly bio-cultural ways.

And in taking up different emphases when describing modern humans' relationships to the apes, we embody the very heart of Marks's book. The interpretation of our own origins is a profoundly cultural process.

Barbara J. King, an anthropology professor at the College of William and Mary, often writes about human evolution, primate behavior and the cognition and emotion of animals. Barbara's most recent book on animals is titled How Animals Grieve. You can keep up with what she is thinking on Twitter: @bjkingape




“His argument pushes back against my tendency — even while working within the same discipline as Marks's — to emphasize not ape-human boundaries but ape-human continuities. …. First, human meaning-making is centered on kinship. … Second, because science is everywhere and always a cultural enterprise, this meaning-making extends to the ways we make sense of human origins. It's notoriously hard to distinguish one extinct species from another, which means that species are units of cultural thought as much as of biological fact. …. Marks concludes that ancestry "is an origin myth. It takes the world of biological data and emphasizes some things, invents others, and relates the present to the past in a meaningful way." …. Sure, humans make meaning in ways that chimpanzees don't. But why push hard to wall us off as ex-apes from these smart, savvy primates who make meaning in their own ways? And push hard Marks does. Making a cultural decision of his own, he portrays chimpanzees as a kind of dumb cousin. …. . I asked him this week by email if scientists who study chimpanzees might find his language to be pretty obviously biased, an explicit attempt to stretch the ape-human divide. He replied in this way: "Yes, absolutely! My point is precisely that nobody can say 'You're being political/ideological/biased and I'm not.' Given the subject, it is all bio-political, and that is what we need to acknowledge — this is not like fruit-fly genetics." …. We carry — in a very non-deterministic fashion — parts of our ancestral past with us; today we aren't so far apart from other animals as people sometimes think. Marks and I agree on the big things. Humans shared a common ancestor with today's apes. The human lineage evolved over the last 6 or 7 million years in unprecedentedly bio-cultural ways.”


“The interpretation of our own origins is a profoundly cultural process.” In taking several comparative religion and anthropology courses in college, I was told that EVERY group of people who self-identify with others of their own kind, had in the past and usually still do today, a creation myth in which the earth, sky, and life forms are described as originating in a magical way. Ouranos “spilled his seed on the Earth, who was named Gaia, to create other offspring. Gaia happened to be the first Entity after Chaos, and the mother of all those to come after. You will note she was therefore also his mother, which today would be a deep and horrible sin. But from that line developed the Greeks, as the story goes. The Hebrew Bible has its own set of beliefs which are very different, but each groups holds to its own views and interpretations of reality. Painfully, we humans will even fight wars over such beliefs.

Who we are related to is therefore very important to people. Being related to an ape is abhorrent to Christians and maybe most modern religious groups, though the Hindu religion has some of those animal to human stories. I took a Siddha Yoga introductory course and went to a number of ceremonies at their Ashram. The chants we sang were composed of names of Hindu Gods. My friend, who was more seriously into the meditation and philosophy than I, did tell me that the modern Indians don’t really “believe” those stories in the literal way that Fundamentalist Christians or very conservative Jews believe theirs. They have emotional and spiritual value, but are not considered history. They do link large groups together under an umbrella of kinship.

I feel, along with the writer of this article, that our link with the apes (which is not direct descent, but rather as too offshoots on a much older tree) is very obviously a physical link. I do believe in genetics and change over time, thus adaptation to the ever challenging environment. I cannot watch videos of apes without marveling at the obvious kinship. They do, after all, share over 90% of our genetic material. I wouldn’t want one as a pet because they are not reliably docile and they are strong as well. You might as fight hand to hand with a cougar as to fight a chimpanzee. I have been told that though a male chimpanzee is only about five feet tall and not as bulky in their musculature as a male gorilla, he can literally grasp a man’s arm and pull it totally out of its socket.

The psychological studies dealing with their intelligence are many and various, and should be read in order to appreciate just how clever they really are. The famous gorilla Koko was given a non-verbal IQ test which gives the score of 80 as “low normal,” and Koko scored 80. Granted she has been living with her human handler her whole life with a house trailer of her own at the San Diego Zoo and learning sign continuously. She has been taught a modified human sign language used by the deaf and knows several thousand words. She was in the news a few years ago when she informed her owner with her hands that she had a very bad pain in her mouth, at which point Penny took her to a human dentist who put her to sleep and pulled that bad tooth. You can’t put that down to simple training. It was original thinking and putting the thought into understandable language. Apes cannot speak, but they can handle thoughts and, yes, words. They may be our “dumb cousins,” but they aren’t as dumb as many people choose to think. And why is that? Because humans want an excuse to use them in laboratory tests and even kill and eat them. Gorillas are still being killed in Africa by superstitious tribesmen because their large and powerful hands are considered magical. Mankind should realize that in doing things like that perhaps we are actually showing how “primitive” we are, as well.





http://www.npr.org/sections/goatsandsoda/2015/10/09/447211121/scottish-nurse-who-recovered-from-ebola-is-back-in-isolation

Scottish Nurse Who Recovered From Ebola Is Back In Isolation
Jason Beaubien
OCTOBER 09, 2015

Photograph -- Pauline Cafferkey is now in isolation at the Royal Free Hospital in North London, where she was treated in January for Ebola.
Justin Tallis/AFP/Getty Images


A Scottish nurse who recovered from Ebola in January has been medevaced from Glasgow to London in a Royal Air Force C-130 Hercules transport plane specially equipped for infection control.

Doctors say Pauline Cafferkey is suffering "an unusual late complication" from her previous Ebola infection. They note that "Pauline previously had the Ebola virus and this is therefore not a new infection."

Cafferkey is being treated in the isolation unit of the Royal Free Hospital in London, the same high-security, bio-safety ward where she was treated for Ebola in January.

Cafferkey came down with the virus in December of last year. After volunteering as a nurse at an Ebola treatment unit in Sierra Leone, she got sick soon after returning to the U.K.

Cafferkey was the first recorded Ebola case on British soil. Although she became critically ill, she made a full recovery and was released in late January.

Dr. Aneesh Mehta, who is part of a team of doctors at Emory University that treated four Ebola patients during the recent outbreak, says Cafferkey's readmission to the isolation unit is puzzling.

"If it truly does turn out that she has Ebola 10 months [later] without any further exposures, that would be surprising to us," Mehta says, "And I believe [it] would be the first time that we've ever found a relapsed case of Ebola."

Officials at the Royal Free Hospital have released limited details about Cafferkey's case but as of Friday listed her as being in "serious" condition.

Mehta at Emory says the virus is capable of lingering in some patients long after they've recovered. The two main reservoirs are the testicles and the eyes. But his team has only seen this happen in men.

"We had two female patients here. There has been no persistent site of Ebola found in any of the female patients that we've taken care of nor have we heard of any other sites of persistence [of the Ebola virus] in any women," Mehta says.

Sandro Galea, the dean of the school of public health at Boston University, says this case illustrates the mysteries of Ebola. "There's a lot that we don't understand about this particular disease," Galea says.

If the Ebola virus is capable of lying dormant inside survivors and then re-emerging, this could have major implications in West Africa. There are roughly 17,000 survivors in the region. Liberia has already had at least one case of a male survivor who still carried Ebola in his semen and sexually transmitted the virus to a woman, who later died.

That new case occurred six months after the original patient had been declared Ebola-free.

If Ebola is shown to be capable of re-emerging, life could become even more difficult for survivors. They could face future health concerns in addition to the stigma and discrimination they already have to deal with.




“Doctors say Pauline Cafferkey is suffering "an unusual late complication" from her previous Ebola infection. They note that "Pauline previously had the Ebola virus and this is therefore not a new infection." …. Dr. Aneesh Mehta, who is part of a team of doctors at Emory University that treated four Ebola patients during the recent outbreak, says Cafferkey's readmission to the isolation unit is puzzling. "If it truly does turn out that she has Ebola 10 months [later] without any further exposures, that would be surprising to us," Mehta says, "And I believe [it] would be the first time that we've ever found a relapsed case of Ebola." …. Mehta at Emory says the virus is capable of lingering in some patients long after they've recovered. The two main reservoirs are the testicles and the eyes. But his team has only seen this happen in men. …. Mehta at Emory says the virus is capable of lingering in some patients long after they've recovered. The two main reservoirs are the testicles and the eyes. But his team has only seen this happen in men.”

Perhaps physicians should “watch” patients who seem to have recovered for any alarming changes in their condition as they do survivors of cancer. You aren’t considered to be truly a survivor until five years is up. If these people are having recurring episodes with Ebola, that fact could help explain why certain parts of Africa have these frightening “pop-up” epidemics after some years have passed. Of course, there are also the large and meaty fruit bats which certain tribes eat as a delicacy. It’s very difficult, given the poverty and lack of education, to break long held habits like that. Besides, they do have to find something to eat, and many still love “bush meat.” Every now and then even I want a nice dish of homemade “from scratch” buttermilk biscuits drowned in lightly salted sausage gravy, and if I go to my local Famous Amos Restaurant I can get it.