I haven’t looked into this much. According to Massei, Umani Ronchi, a court-appointed expert, testified that a farinaceous meal takes 6-7 hours for gastric emptying, and additionally that it’s possible some of the food passed into the duodenum but then, after death, slid into the small intestine. Massei also claims that even Vinci agreed with the range of 18:50 − 4:50 for time of death. Did the defence experts take into account the composition of the meal, or testify that sliding of the food after death is unlikely?
We’re talking here not about the time it takes for the stomach to emtpy completely, but rather the time it takes for ingesta to begin passing into the duodenum (“T_lag”). (At death, there was 500mL of ingesta in the stomach—consistent with the meal size—and nothing in the duodenum.) According to this paper, the median value of T_lag is 81.5 minutes, and the 75th percentile is 102 minutes. (Furthermore, the median time for half the contents to empty [“T_1/2″] is 127 minutes, and the 75th percentile is 168.3 minutes.) The prosecution scenario of death during the 11:00 pm hour would require a T_lag of more than 240 minutes, possibly more than 300. My understanding is that this is basically unheard of, whatever the composition of the meal.
Ronchi claimed that the coroner, Lalli, had failed to seal the duodenum via ligature, as is apparently the standard procedure; this was the basis for his claim that food could have slipped into the small intestine. However, video of the autopsy revealed that Ronchi was wrong, and that Lalli had indeed properly sealed the duodenum. (Sollecito appeal, p. 165)
OK, what are the odds that a small dna trace left by “stabbing + cleaning” would test positive for blood, and what are the odds a small dna contamination to the knife would test positive for blood? (By the way, do you have a specific contamination hypothesis in mind?) In both cases, keep in mind only one “small zone” of the striation was tested for blood, and the rest of the striation was consumed in DNA analysis.
There were four samples on the blade, B,C,E, and G that were tested for blood; the results were all negative. These traces were all presumed to be blood by Stefanoni; it seems reasonable to suppose that if there had been blood on the knife, these would have been the most likely spots in which to have found it.
A positive blood test result would require more than DNA from (white) blood cells—it would require hemoglobin. So it seems to me that the only way to get a positive blood test result from contamination would be to spill a blood sample on the knife. I estimate the probability of this having happened as being in the range of 0.001.
On the other hand, in the event that the knife had been used for stabbing, and that the victim’s DNA remained on the knife, I would estimate a probability northward of 0.9 that at least one of the “presumed blood” traces would have tested positive for blood. (Cf. ChrisHalkides’ comment below: “Two experts have publicly stated that the chances of cleaning a bloody knife to the point at which blood is no longer detected but DNA is detected, are small.” This agrees with my intuition, and “no more than 0.1” seems a reasonable interpretation of “small”.)
Sounds like she didn’t document everything;
It’s worse than that; what Conti and Vecchiotti describe is suggestive of deliberate misrepresentation if not outright fabrication of results. The “several hundred picograms” quantification result for Trace B appears to have been completely made up. She claimed in court that she had obtained this result using Real Time PCR, but this was not the case: records obtained by Conti and Vecchiotti show that another method (“Qubit Fluorometer”) was used, and that the result obtained was “too low”—the exact same as for Trace C. There was no justification for treating Trace B as a positive result and Trace C as a negative, and in particular no reason for subjecting Trace B to amplification.
The “amplification” (chemical copying of the sample in order to produce a large enough amount for analysis) was performed only once, despite the fact (admitted by Stefanoni) that it should be repeated in order to be considered reliable.
Can I get a source for Stefanoni’s admission? Is this from the report?
Yes (p.61).
Stefanoni did not perform negative controls, which could have indicated the presence of contamination.
Is this also from the report? Have you translated this part yet?
This is on p. 79. This section of the report, on Stefanoni’s knife results, is next in line to be translated (by my collaborator katy_did, while I’ll be simultaneuously doing the clasp section).
The sample was analyzed in the same laboratory at the same time as numerous samples containing Meredith Kercher’s DNA.
I gave a .05 chance that, if there was a cross-contamination, it would have been of Meredith’s DNA. Are you giving a different probability?
Substantially different. Stefanoni is quoted as follows on p. 102 of the report:
″...the knife was analyzed...in the course of these 50 samples attributed to the victim, some were prior to the analysis of the knife, of course, and others subsequent, so in these 50 I don’t know if the knife was, I don’t know now, a fourth, a third of the way through this flux of analyses...”
This puts me at 0.5 or more. Also note that the number 50 itself gives a probability of 0.1 if we use your estimate of 500 total samples in the lab.
Let’s talk about the dna some more once you guys have finished translating the relevant parts of the independent report, then, if your argument hinges on details of the independent report rather than just the conclusions.
We’re talking here not about the time it takes for the stomach to emtpy completely, but rather the time it takes for ingesta to begin passing into the duodenum (“T_lag”).
Sounds good. In your case, for one particular meal where the subjects had probably fasted beforehand, the lag is just under 2⁄3 of the half-time. If you accept Umani Rochi’s half-time of 360-420 minutes, then the lag could be 2⁄3 of that, or 240+ minutes. Of course, for all I know Umani Rochi could have been referring to the lag time, or the final gastric emptying time, rather than the half-time. Lags could easily be much smaller, or larger, than 2⁄3 of the half-time in this case.
It sounds like you might disagree with not just with Umani Rochi (a court-appointed expert), and Raffaele’s consultant Vinci, but also with another of Raffaele’s consultants, Introna, who placed the start of attack between 21:30 and 22:30.
Note that stress (such as being attacked) can increase lag time, so we might be talking about the time the attack started rather than the time of death.
In addition to the starchiness of the meal, I would claim that:
Alcohol (or drug use) may increase lag time, studies differ as to how significant this is though.
Subjects in studies usually fast before the study, which means in the real world I expect lag times to be longer. Meredith also returned home after the meal, which may be more physical activity than the subjects did, though I could be wrong about that.
Subjects in studies don’t usually go and eat a snack after the meal, as I believe Meredith did. I would expect this to also increase Meredith’s lag time.
Anyway, what’s your model here: What do you personally estimate the lag to be based solely on digestion (assuming no slippage)? Maybe you can give a mean and a standard deviation, and we can start by modeling it as a normal distribution?
Ronchi claimed that the coroner, Lalli, had failed to seal the duodenum via ligature, as is apparently the standard procedure; this was the basis for his claim that food could have slipped into the small intestine. However, video of the autopsy revealed that Ronchi was wrong, and that Lalli had indeed properly sealed the duodenum. (Sollecito appeal, p. 165)
How much does application of the ligatures reduce the probability of slippage? If ligatures were not applied, how likely do you think complete slippage would be? If they are applied, what are the odds that (1) the slippage occurs before the ligatures are applied, or (2) the slippage occurs anyway after the ligatures are applied, perhaps due to improper application?
Let’s talk about the dna some more once you guys have finished translating the relevant parts of the independent report, then, if your argument hinges on details of the independent report rather than just the conclusions.
The translation is now nearing completion (the clasp section is finished, and the knife section will be soon). Here, furthermore, are some relevant links:
Great, give me a top-level post when the knife translation is finished, or when you think it’s in a good enough state to back up your claims in the dna discussion.
In your case, for one particular meal where the subjects had probably fasted beforehand, the lag is just under 2⁄3 of the half-time. If you accept Umani Rochi’s half-time of 360-420 minutes, then the lag could be 2⁄3 of that, or 240+ minutes. Of course, for all I know Umani Rochi could have been referring to the lag time, or the final gastric emptying time, rather than the half-time. Lags could easily be much smaller, or larger, than 2⁄3 of the half-time in this case.
As best I can determine, Ronchi was talking about total emptying time, not half-time (let alone lag time). This is unquestionably what would make the most sense, given not only the term used (“gastric emptying”), but also the averages presented, for example, here:
50% of stomach contents emptied: 2.5 to 3 hours
Total emptying of the stomach: 4 to 5 hours
Given this, a total emptying time of 6-7 hours under some cirumstances doesn’t seem outside the bounds of possibility. Extrapolating in such a way as to preserve ratios, we could then imagine a half-time of up to 4.5 hours, say. But 2⁄3 of that would give us 3 hours, or 180 minutes—not the 4-5 hours we need for the prosecution theory.
It sounds like you might disagree with not just with Umani Rochi (a court-appointed expert), and Raffaele’s consultant Vinci, but also with another of Raffaele’s consultants, Introna, who placed the start of attack between 21:30 and 22:30.
Not according to p. 180 of Massei-Cristiani, where Introna is described as placing it between 21:00 and 21:30. Raffaele’s appeal document argues for 21:30 − 22:00; this is apparently obtained by averaging the 2-3 hour (from last meal) figure of Lalli and Introna, and the 3-4 hour figure of Ronchi (whose testimony was incorrectly interpreted by Massei and Cristiani, according to the appeal: Raffaele’s lawyers cite passages where he appeared to agree that 4 hours is the normal limit). My “disagreement” with Raffaele’s lawyers in this context is of little import, for several reasons: (1) I am in perfect agreement with Introna, as reported by Massei; (2) We’re talking about confidence intervals anyway; I think 21:00-21:30 is most likely, but 21:30-22:00 is not ruled out nearly as strongly in my model as anything after 22:00 is; (3) Ronchi, whose estimate figured into their calculation, was talking about total emptying time anyway, not lag time (or even half time).
As for Vinci, he was looking at different criteria for the time of death (not specifically gastric contents), and simply gave a wider range, not an incompatible one. No disagreement here that I am aware of.
Note that stress (such as being attacked) can increase lag time, so we might be talking about the time the attack started rather than the time of death.
Sure; just remember that the computer evidence provides an alibi up to nearly 21:30.
In addition to the starchiness of the meal, I would claim [various ways lag time could be increased beyond study results]
No doubt you’ve identified some of the ways Meredith’s digestive process could have been slowed (although there is no evidence of significant alcohol or drug consumption), in the event that there actually was a lag time of 4-5 hours. The question, however, is how likely such an extraordinary retardation is. According to standard data (see below), it should be a highly unusual event. So how does this information (the fact that a time of death—or, if you like, attack time—after 23:00 requires a lag time of over 4 hours) affect your probability of guilt? It seems to me that it should go down noticeably, unless your model was already incorporating both the studies on digestion and the fact that Meredith’s duodenum was empty (i.e. you weren’t surprised by either datum). (For what it’s worth, I think the Massei court erred in this regard by ignoring lag time, and also by using uncertainty as an excuse to smuggle in probability for their preferred conclusion.)
Anyway, what’s your model here: What do you personally estimate the lag to be based solely on digestion (assuming no slippage)? Maybe you can give a mean and a standard deviation, and we can start by modeling it as a normal distribution?
Although the paper I cited explicitly stated that the results did not fit to a normal distribution, the percentiles given are fairly well approximated by assuming a mean of 81.5 and a standard deviation of 30. Under these assumptions, the lag time required for the Massei guilt scenario would be at least a five- or six-sigma event.
Now I know you doubt that the conditions of the study hold here, but don’t you find this at least a little bit confusing? To make the Massei narrative reasonable, you would basically have to assume that (1) the 6-7 hours allowed by Ronchi for total emptying of farinaceous meals is typical rather than exceptional; (2) this extrapolates to a typical lag time of 3 hours or more, as in my calculation above; and (3) the variance is large enough to make a 4-5-hour lag time a reasonable exception (in which case we would probably be talking about a total emptying time of 8-9 hours or more). Each of these seems highly doubtful, to say nothing of their conjunction. Regarding (2) in particular, note that the study data suggests that the ratio of lag time to total emptying time is closer to 1⁄3 than to 1⁄2 (implying a more concave relationship between elapsed time and percentage of contents emptied; suggesting perhaps that lag time may be short even when total emptying time is long).
How much does application of the ligatures reduce the probability of slippage? If ligatures were not applied, how likely do you think complete slippage would be? If they are applied, what are the odds that (1) the slippage occurs before the ligatures are applied, or (2) the slippage occurs anyway after the ligatures are applied, perhaps due to improper application?
I imagine that preventing slippage is at least part of the purpose of the ligatures, and so I assume they reduce the probability significantly. But even in the worst-case scenario here, the amount of slippage can’t have been very large, because the stomach contents could easily have constituted the entire meal on their own. In the unlikely event that the ligatures were improperly applied, we can infer that Meredith may have just passed her lag time, and that a few pieces of food had just started to pass into her duodenum. This is of minimal help to the prosecution, because on their timeline, we should have been long into that stage, and the stomach should not have been nearly as full as it was—indeed, we should have expected with significant probability that the stomach would be completely empty.
To illustrate further, if as much as half of Meredith’s meal had passed into the duodenum, and we assume a normally-distributed half-time with median 127 minutes and standard deviation 40 (the median taken from the study), the finding would still have put her well within the slowest 1% under the prosecution theory (while only in the slowest 10% to 50% under the defense theory).
We’re talking here not about the time it takes for the stomach to emtpy completely, but rather the time it takes for ingesta to begin passing into the duodenum (“T_lag”). (At death, there was 500mL of ingesta in the stomach—consistent with the meal size—and nothing in the duodenum.) According to this paper, the median value of T_lag is 81.5 minutes, and the 75th percentile is 102 minutes. (Furthermore, the median time for half the contents to empty [“T_1/2″] is 127 minutes, and the 75th percentile is 168.3 minutes.) The prosecution scenario of death during the 11:00 pm hour would require a T_lag of more than 240 minutes, possibly more than 300. My understanding is that this is basically unheard of, whatever the composition of the meal.
Ronchi claimed that the coroner, Lalli, had failed to seal the duodenum via ligature, as is apparently the standard procedure; this was the basis for his claim that food could have slipped into the small intestine. However, video of the autopsy revealed that Ronchi was wrong, and that Lalli had indeed properly sealed the duodenum. (Sollecito appeal, p. 165)
There were four samples on the blade, B,C,E, and G that were tested for blood; the results were all negative. These traces were all presumed to be blood by Stefanoni; it seems reasonable to suppose that if there had been blood on the knife, these would have been the most likely spots in which to have found it.
A positive blood test result would require more than DNA from (white) blood cells—it would require hemoglobin. So it seems to me that the only way to get a positive blood test result from contamination would be to spill a blood sample on the knife. I estimate the probability of this having happened as being in the range of 0.001.
On the other hand, in the event that the knife had been used for stabbing, and that the victim’s DNA remained on the knife, I would estimate a probability northward of 0.9 that at least one of the “presumed blood” traces would have tested positive for blood. (Cf. ChrisHalkides’ comment below: “Two experts have publicly stated that the chances of cleaning a bloody knife to the point at which blood is no longer detected but DNA is detected, are small.” This agrees with my intuition, and “no more than 0.1” seems a reasonable interpretation of “small”.)
It’s worse than that; what Conti and Vecchiotti describe is suggestive of deliberate misrepresentation if not outright fabrication of results. The “several hundred picograms” quantification result for Trace B appears to have been completely made up. She claimed in court that she had obtained this result using Real Time PCR, but this was not the case: records obtained by Conti and Vecchiotti show that another method (“Qubit Fluorometer”) was used, and that the result obtained was “too low”—the exact same as for Trace C. There was no justification for treating Trace B as a positive result and Trace C as a negative, and in particular no reason for subjecting Trace B to amplification.
Yes (p.61).
This is on p. 79. This section of the report, on Stefanoni’s knife results, is next in line to be translated (by my collaborator katy_did, while I’ll be simultaneuously doing the clasp section).
Substantially different. Stefanoni is quoted as follows on p. 102 of the report:
″...the knife was analyzed...in the course of these 50 samples attributed to the victim, some were prior to the analysis of the knife, of course, and others subsequent, so in these 50 I don’t know if the knife was, I don’t know now, a fourth, a third of the way through this flux of analyses...”
This puts me at 0.5 or more. Also note that the number 50 itself gives a probability of 0.1 if we use your estimate of 500 total samples in the lab.
Let’s talk about the dna some more once you guys have finished translating the relevant parts of the independent report, then, if your argument hinges on details of the independent report rather than just the conclusions.
Sounds good. In your case, for one particular meal where the subjects had probably fasted beforehand, the lag is just under 2⁄3 of the half-time. If you accept Umani Rochi’s half-time of 360-420 minutes, then the lag could be 2⁄3 of that, or 240+ minutes. Of course, for all I know Umani Rochi could have been referring to the lag time, or the final gastric emptying time, rather than the half-time. Lags could easily be much smaller, or larger, than 2⁄3 of the half-time in this case.
It sounds like you might disagree with not just with Umani Rochi (a court-appointed expert), and Raffaele’s consultant Vinci, but also with another of Raffaele’s consultants, Introna, who placed the start of attack between 21:30 and 22:30.
Note that stress (such as being attacked) can increase lag time, so we might be talking about the time the attack started rather than the time of death.
In addition to the starchiness of the meal, I would claim that:
Alcohol (or drug use) may increase lag time, studies differ as to how significant this is though.
Subjects in studies usually fast before the study, which means in the real world I expect lag times to be longer. Meredith also returned home after the meal, which may be more physical activity than the subjects did, though I could be wrong about that.
Subjects in studies don’t usually go and eat a snack after the meal, as I believe Meredith did. I would expect this to also increase Meredith’s lag time.
Anyway, what’s your model here: What do you personally estimate the lag to be based solely on digestion (assuming no slippage)? Maybe you can give a mean and a standard deviation, and we can start by modeling it as a normal distribution?
How much does application of the ligatures reduce the probability of slippage? If ligatures were not applied, how likely do you think complete slippage would be? If they are applied, what are the odds that (1) the slippage occurs before the ligatures are applied, or (2) the slippage occurs anyway after the ligatures are applied, perhaps due to improper application?
The translation is now nearing completion (the clasp section is finished, and the knife section will be soon). Here, furthermore, are some relevant links:
Expert commentary on C-V report: http://forensicdnaconsulting.wordpress.com/2011/07/30/understanding-the-independent-dna-experts%E2%80%99-report-in-the-amanda-knox-case-part-i/
Article detailing contamination issues and other problems with DNA testing: http://www.nacdl.org/public.nsf/0/6285f6867724e1e685257124006f9177
Examples of laboratory fraud and how they were detected: http://www.bioforensics.com/conference05/FBS_Dayton_2005_Fraud.pdf
9 DNA experts sign open letter critiquing evidence near the end of the first trial: http://www.newscientist.com/article/dn18215-knox-murder-trial-evidence-flawed-say-dna-experts.html
Chris Halkides’ blog: http://viewfromwilmington.blogspot.com
Great, give me a top-level post when the knife translation is finished, or when you think it’s in a good enough state to back up your claims in the dna discussion.
As best I can determine, Ronchi was talking about total emptying time, not half-time (let alone lag time). This is unquestionably what would make the most sense, given not only the term used (“gastric emptying”), but also the averages presented, for example, here:
50% of stomach contents emptied: 2.5 to 3 hours
Total emptying of the stomach: 4 to 5 hours
Given this, a total emptying time of 6-7 hours under some cirumstances doesn’t seem outside the bounds of possibility. Extrapolating in such a way as to preserve ratios, we could then imagine a half-time of up to 4.5 hours, say. But 2⁄3 of that would give us 3 hours, or 180 minutes—not the 4-5 hours we need for the prosecution theory.
Not according to p. 180 of Massei-Cristiani, where Introna is described as placing it between 21:00 and 21:30. Raffaele’s appeal document argues for 21:30 − 22:00; this is apparently obtained by averaging the 2-3 hour (from last meal) figure of Lalli and Introna, and the 3-4 hour figure of Ronchi (whose testimony was incorrectly interpreted by Massei and Cristiani, according to the appeal: Raffaele’s lawyers cite passages where he appeared to agree that 4 hours is the normal limit). My “disagreement” with Raffaele’s lawyers in this context is of little import, for several reasons: (1) I am in perfect agreement with Introna, as reported by Massei; (2) We’re talking about confidence intervals anyway; I think 21:00-21:30 is most likely, but 21:30-22:00 is not ruled out nearly as strongly in my model as anything after 22:00 is; (3) Ronchi, whose estimate figured into their calculation, was talking about total emptying time anyway, not lag time (or even half time).
As for Vinci, he was looking at different criteria for the time of death (not specifically gastric contents), and simply gave a wider range, not an incompatible one. No disagreement here that I am aware of.
Sure; just remember that the computer evidence provides an alibi up to nearly 21:30.
No doubt you’ve identified some of the ways Meredith’s digestive process could have been slowed (although there is no evidence of significant alcohol or drug consumption), in the event that there actually was a lag time of 4-5 hours. The question, however, is how likely such an extraordinary retardation is. According to standard data (see below), it should be a highly unusual event. So how does this information (the fact that a time of death—or, if you like, attack time—after 23:00 requires a lag time of over 4 hours) affect your probability of guilt? It seems to me that it should go down noticeably, unless your model was already incorporating both the studies on digestion and the fact that Meredith’s duodenum was empty (i.e. you weren’t surprised by either datum). (For what it’s worth, I think the Massei court erred in this regard by ignoring lag time, and also by using uncertainty as an excuse to smuggle in probability for their preferred conclusion.)
Although the paper I cited explicitly stated that the results did not fit to a normal distribution, the percentiles given are fairly well approximated by assuming a mean of 81.5 and a standard deviation of 30. Under these assumptions, the lag time required for the Massei guilt scenario would be at least a five- or six-sigma event.
Now I know you doubt that the conditions of the study hold here, but don’t you find this at least a little bit confusing? To make the Massei narrative reasonable, you would basically have to assume that (1) the 6-7 hours allowed by Ronchi for total emptying of farinaceous meals is typical rather than exceptional; (2) this extrapolates to a typical lag time of 3 hours or more, as in my calculation above; and (3) the variance is large enough to make a 4-5-hour lag time a reasonable exception (in which case we would probably be talking about a total emptying time of 8-9 hours or more). Each of these seems highly doubtful, to say nothing of their conjunction. Regarding (2) in particular, note that the study data suggests that the ratio of lag time to total emptying time is closer to 1⁄3 than to 1⁄2 (implying a more concave relationship between elapsed time and percentage of contents emptied; suggesting perhaps that lag time may be short even when total emptying time is long).
I imagine that preventing slippage is at least part of the purpose of the ligatures, and so I assume they reduce the probability significantly. But even in the worst-case scenario here, the amount of slippage can’t have been very large, because the stomach contents could easily have constituted the entire meal on their own. In the unlikely event that the ligatures were improperly applied, we can infer that Meredith may have just passed her lag time, and that a few pieces of food had just started to pass into her duodenum. This is of minimal help to the prosecution, because on their timeline, we should have been long into that stage, and the stomach should not have been nearly as full as it was—indeed, we should have expected with significant probability that the stomach would be completely empty.
To illustrate further, if as much as half of Meredith’s meal had passed into the duodenum, and we assume a normally-distributed half-time with median 127 minutes and standard deviation 40 (the median taken from the study), the finding would still have put her well within the slowest 1% under the prosecution theory (while only in the slowest 10% to 50% under the defense theory).
Just replied here: http://lesswrong.com/r/discussion/lw/6k7/experiment_knox_case_debate_with_rolf_nelson/4liq