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| Got Chimeras? |
Among the many "things" I can't find in the MetaSUB reporting is any discussion of how they mastered the "chimera problem".
Perhaps they didn't know there was such a problem (many experts don't) ?
Before I discuss the continuing tests I have done on their data, let's consider the chimera biosphere:
"DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remain poorly defined."
(Genomic landscape of oxidative DNA damage). Can you imagine then, any place more likely to have "constant chemical modification and damage" than city streets, sidewalks, public bathrooms, and "the great outdoors" where rain, vehicle exhaust, and pile upon pile of DNA of various and sundry types is relentlessly deposited?
Or can you imagine them being surprised/alarmed when this was declared:
"About 12,000 bacteria and viruses collected in a sampling from public transit systems and hospitals around the world from 2015 to 2017 had never before been identified, according to a study by the International MetaSUB Consortium, a global effort at tracking microbes that is led by Weill Cornell Medicine investigators."
(Global Microbiome Identifies Thousands of "New Species", emphasis added). Note that chimera samples are not "new species" they are usually 'unidentifiable'.
In the criminal prosecution arena, where one would suppose that the most delicate care would be utilized to avoid the horror of punishing innocent people, the DNA forensic process must be more than just "rolling the dice":
"Partial profiles will match up with many more people than a full profile. And even full profiles may match with a person other than the culprit. Further complicating matters, a single DNA profile might be mistakenly generated when samples from multiple people are accidentally combined. It’s a messy world."
(How Forensic DNA Evidence Can Lead to Wrongful Convictions). How do everyday honest, crime-free, mothers, fathers, uncles, aunts, and other family members feel when their life becomes a nightmare because unscientific practices ruined their everything:
"In one recent study, researchers asked 17 experienced DNA examiners to analyze a DNA mixture (a sample including DNA from more than one person) from an alleged gang rape; the examiners reached widely divergent conclusions about whether a particular suspect might have been involved in the rape. What is more, only one of the 17 examiners tendered a conclusion consistent with the analyst in the actual case in which the DNA mixture arose—a conclusion introduced at trial to convict a real-life suspect of the crime.
These divergent conclusions are possible, even for a well-grounded scientific endeavor like forensic DNA typing, because the DNA collected at real crime scenes is often unlike the pristine DNA samples that we provide to our doctors or that known arrestees and convicted persons provide through a cheek swab. Unlike samples taken in a controlled environment, ‘crime scene testing…is like seeking results from [a] dirty Band-Aid—after it has been in the trash for two weeks’. Such samples ‘may have been exposed to light, heat, moisture, or chemicals that can compromise the ability to get results’. A sample may also contain DNA from an unknown number of persons, not all of whom may have had direct contact with the tested object at all or contact in proportion to the number of their cells on the tested object.
Each of these complicating factors may be further compounded by recent extensions of forensic DNA analysis to so-called ‘touch’ DNA or ‘low copy number’ settings—those in which DNA analysis is performed on a very small number of cells or even a single cell. As Murphy explains, in these settings ‘the rules of thumb that help analysts interpret ordinary samples do not work as well…, and guided subjectivity risks becoming little more than self-justifying guesses’. Yet, of the few courts to adjudicate the admissibility of low copy number test results, most have deferred to prosecutors' assertions that such testing is just like ordinary forensic DNA analysis. Meanwhile, laboratories engaged in this envelope-pushing testing have frequently ‘refused to disclose the protocols and studies’ informing their analysis, claiming that this information is proprietary.
These difficulties may be present even if the crime scene investigators, lab analysts, and everyone in between perform their jobs flawlessly. But this is an unrealistic assumption. As Murphy documents, there are now dozens of known (and how many more still unknown?) scandals involving sloppy, mistaken, or fraudulent casework. All the while, forensic analysts decline or refuse to disclose error rates when reporting DNA match probabilities in court, perpetuating the notion that forensic DNA analysis is free from either scientific or human error.
Having enumerated how the processes for generating a DNA profile can mislead or give rise to error, Murphy casts her perspective more broadly, examining how the search for and report of forensic matches can similarly mislead jurors, judges, prosecutors, and even lab analysts. Different ways of calculating DNA match probabilities may give rise to widely divergent statistics and very different levels of certainty that a particular suspect or defendant ‘did it’. There are at least 10 different software packages on the market for decoding whether a particular suspect or defendant's DNA is present in a complex sample, like a mixture or low-quantity crime scene stain—each utilizing its own algorithm. Meanwhile, the FBI prohibited database research that threatened to complicate the one-in-several-trillion type of statistics on which prosecutors routinely rely in court. While differing statistical models and disagreements about whether a DNA match has been found would be inconvenient in a case in which DNA were just one piece of evidence against the defendant, these matters take on increased significance in the growing number of cases prosecuted based on a DNA match alone."
(Inside the Cell: The Dark Side of Forensic DNA). When caution is thrown to the wind, it disintegrates just like DNA out in public places does:
"In December 2012 a homeless man named Lukis Anderson was charged with the murder of Raveesh Kumra, a Silicon Valley multimillionaire, based on DNA evidence. The charge carried a possible death sentence. But Anderson was not guilty. He had a rock-solid alibi: drunk and nearly comatose, Anderson had been hospitalized—and under constant medical supervision—the night of the murder in November. Later his legal team learned his DNA made its way to the crime scene by way of the paramedics who had arrived at Kumra's residence. They had treated Anderson earlier on the same day—inadvertently “planting” the evidence at the crime scene more than three hours later. The case, presented in February at
the annual American Academy of Forensic Sciences meeting in Las Vegas, provides one of the few definitive examples of a DNA transfer implicating an innocent person and illustrates a growing opinion that the criminal justice system's reliance on DNA evidence, often treated as infallible, actually carries significant risks."
(Scientific American). Bad practices are just another example of firing a shotgun into a crowd at one suspect without concern for the innocent ones also in that crowd:
"Particularly concerning is that police and prosecutors now frequently talk of 'touch DNA' — genetic profiles of suspects and offenders that have been generated in a laboratory from just a handful of skin cells left behind in a fingerprint.
Research done by me and others at the University of Indianapolis in Indiana has highlighted how unreliable this kind of evidence can be. We have found that it is relatively straightforward for an innocent person's DNA to be inadvertently transferred to surfaces that he or she has never come into contact with. This could place people at crime scenes that they had never visited or link them to weapons they had never handled.
Such transfer could also dilute the statistics generated from DNA evidence, and thereby render strong genetic evidence almost insignificant.
We urgently need to review how DNA evidence is assessed, viewed and described. Everyone in the medico-legal community — forensic scientists and technicians, DNA analysts, potential jurors, judges and lawyers for both the prosecution and defence— must know and understand the potential for mistakes.
The term 'touch DNA' conveys to a courtroom that biological material found on an object is the result of direct contact. In fact, forensic scientists have no way of knowing whether the DNA was left behind through such primary, direct transfer. It could also have been deposited by secondary transfer, through an intermediary. (If I shake your hand then I could pass some of your skin cells onto something that I touch next.)"
(Nature, Forensic DNA evidence is not infallible). Many cases give new meaning to "firing a shotgun into a crowd to stop the escaping criminal":
(Shot Gun Sequencing, emphasis added). "Shotgun sequencing", all things considered, "Sounds like a plan."
Some of those who are aware of genetic chimeras are contemplating improvement, thus, it's becoming "not just for forensic scientists anymore":
"A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, and found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate. In all, 11 phyla contained obvious chimeras, accounting for 0.8 to 11% of the records for these phyla. Many chimeras (43.1%) were formed from parental sequences belonging to different phyla. While most comprised two fragments, 13.7% were composed of at least three fragments, often from three different sources. A separate analysis of the Bacteroidetes phylum (2,739 sequences) also revealed 5.8% records to be anomalous, of which 65.4% were apparently chimeric. Overall, we conclude that, as a conservative estimate, 1 in every 20 public database records is likely to be corrupt. Our results support concerns recently expressed over the quality of the public repositories. With 16S rRNA sequence data increasingly playing a dominant role in bacterial systematics and environmental biodiversity studies, it is vital that steps be taken to improve screening of sequences prior to submission."
(Records Currently Held in Public Repositories). The public scientific databases are used for various reasons, and if we can't trust them, what can we trust in the genetic realm?
Regular readers will remember that I tried to reason with them a while back
"I have been trying to persuade microbiologists, virologists, and government (e.g. NCBI GenBank) to change errors in the format used in
genome nucleotide (base pair) sequencing (It's In The GenBank, 2, 3; Small Things Considered)."
(It's In The GenBank - 4). To no avail (Desolation Row).
But I am not the only one urging more than a high bar of catastrophically unsound policies and practices in genetics:
"A handful of studies have investigated how factors such as time, surface type, and environmental conditions (e.g., temperature, humidity, ultraviolet light) affect the quantity and stability of touch DNA (TABLE 1). These studies generally focus on a specific scenario (i.e. a particular surface type or simulated, crime-related activity) and involve relatively small sample sizes with limited or no statistical analysis. The focused scope of these studies combined with significant differences in experimental design between studies makes it difficult to draw generalizable conclusions. Another factor confounding quantitative studies of touch DNA persistence is the fact that the amount of DNA deposited by touch varies significantly between donors. 6 Several studies have circumvented this challenge by depositing controlled amounts of purified DNA or cell suspensions on surfaces. However, it is unclear whether the stability of actual touch DNA samples is similar to that of purified DNA or cell suspensions. There is therefore a need for comprehensive well-controlled studies that provide practical data about the basic properties of touch DNA evidence in real-world environments to understand how long a touch DNA sample would be expected to persist in a particular environment. The current study was designed to address this need ... In conclusion, this study represents the largest systematic study to date of touch DNA persistence under controlled representative environmental conditions ... Overall, exposure to UV-B light had the biggest impact on the stability of control and touch DNA samples, resulting in decreased DNA quantities and increased degradation indices by 24-hours of exposure. In the absence of UV light, touch DNA samples were generally stable under the different temperature/humidity combinations up to a period of 7 days, regardless of substrate."
(Office of Justice, PDF, emphasis added). Is there any way to know how long a DNA drop has been covered over in a public setting, like leaves falling to the ground (and covering those that fell earlier) year after year?
But I digress.
Anyway, there is only one appendix to today's post (Appendix Numero Uno), just so you don't get bored with the usual Dredd Blog plethora of data in appendices.
The next post in this series is here, the previous post in this series is here.
What next, AI doing "shotgun DNA sequencing"? (Link)
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