Continuation - Discussion of the Amanda Knox case

[LondonJohn]

oops, looks like Fiona got a triple whammy on that one.

That's cos all three of us are part of the grand conspiracy, and we were mistakenly all issued with "attack" instructions from David Marriott at the same time

(I hope I don't have to split my fee for that attack three ways...)

 

[Fiona]

Hmmmmm. Firstly, I think you may be fundamentally misunderstanding the necessary fusion of computing (first) and biology (second) that is more-or-less a pre-requisite for becoming an expert in DNA testing. Biologists know a lot about DNA (what it's made of, what its purpose is, how it's constructed, how it can be split and replicated, etc). Computer scientists know how to test for DNA's presence (how to build and operate machines that identify, measure and report DNA profiles).

Dr Gilder doesn't NEED to be an expert in DNA BIOLOGY to be an expert in DNA TESTING - this is the crucial point. Nobody has been arguing that he is an expert in the biology of DNA. But that's not the area that's the subject for debate. The area of potential controversy is exclusively about DNA TESTING methodology, where - to my mind - Dr Gilder IS an expert.

I honestly thought that you weren't prone to engaging in this sort of arguing by sophistry. I also think, for example, that you might also know very well what meaning you intended to convey when you "corrected" halides by mentioning that Dr Gilder was a computer scientist. The clear implication of that was that he was therefore unqualified to have an opinion on DNA testing. Otherwise there can't have been any reason for you to mention it - since coming from a computer science background is absolutely no impairment (and in fact is a positive advantage) to gaining expertise in DNA testing.

Still, you live and learn.......

As I said, you can read anything into my posts that you like. Gilder is a computer scientist. He applies his knowledge of computers to DNA testing, certainly. It is still computer knowledge. If no one was led to believe that he was competent to judge Stefanoni's work then that is fine. I was concerned that they might be.

 

[LondonJohn]

As I said, you can read anything into my posts that you like. Gilder is a computer scientist. He applies his knowledge of computers to DNA testing, certainly. It is still computer knowledge. If no one was led to believe that he was competent to judge Stefanoni's work then that is fine. I was concerned that they might be.

So, just to clarify: your position is that Dr Gilder is incompetent to judge Stefanoni's DNA testing work?

 

[Mary_H]

That's cos all three of us are part of the grand conspiracy, and we were mistakenly all issued with "attack" instructions from David Marriott at the same time

(I hope I don't have to split my fee for that attack three ways...)

I've been meaning to complain to them about that. I only get paid by the post, whereas you appear to be paid by the word.

 

[Fiona]

It is ridiculous to believe that someone who has a doctorate in the field he works in is not educated about the field he works in. If he studies DNA, he is educated about DNA, and he doesn't need a degree in biology to prove it. Your complaint is like saying an atmospheric scientist only knows about atmospheric sciences without also mentioning all the other disciplines they are versed in - physics, chemistry, biology, geology, seismology, astronomy, ecology and so on.

I see that at least one person was mislead.

He is educated in the field he works in. That field is computer science and he is an expert in that. He does not study DNA. He studies and works in making computer software (perhaps hardware) to interpret the results of DNA testing. That is his job. He is apparently very good at it.

 

[Mary_H]

I see that at least one person was mislead.

He is educated in the field he works in. That field is computer science and he is an expert in that. He does not study DNA. He studies and works in making computer software (perhaps hardware) to interpret the results of DNA testing. That is his job. He is apparently very good at it.

I-yi-yi, Fiona. You seem to have missed halides' post about this being a cross-disciplinary field.

No one can do what Gilder does without understanding and studying DNA. There are all kinds of computer scientists, working in all kinds of professions. Do you think the computer scientists at Lockheed would allow anyone to tell them they don't know aeronautics?

 

[LondonJohn]

I've been meaning to complain to them about that. I only get paid by the post, whereas you appear to be paid by the word.

Yes, but my threshold for payment is 500 words. Over and above that, I get $1 per word. That's why my posts are so long and boring.

And this also means that I'm throwing in these shorter, pithier posts free of charge - out of the goodness of my heart

 

[Fiona]

I-yi-yi, Fiona. You seem to have missed halides' post about this being a cross-disciplinary field.

No one can do what Gilder does without understanding and studying DNA. There are all kinds of computer scientists, working in all kinds of professions. Do you think the computer scientists at Lockheed would allow anyone to tell them they don't know aeronautics?

No, I did not miss it. Many of the papers Halides1 has used to sustain his point seem to me to support mine instead. Why do you think these papers are co-authored? Could it be because a cross disciplinary field involves collaboration between people with different areas of expertise? Because no one of them is an expert in all that you need? What do you think the computer scientists at Lockheed do? Do they build aeroplanes? I don't know what they do but I think it is probably writing software to do some job which someone else has defined for them. Someone who knows about aeronautics maybe

ETA: like this, perhaps

https://sjobs.brassring.com/1033/ASP/TG/cim_jobdetail.asp?jobId=168659&partnerid=25037&siteid=5010

There is a need for some knowledge of the particular field because it says

Plans, conducts, and coordinates scientific programming application activities in support of research, engineering, and other related technical activities. Analyzes scientific applications and writes computer programs that contain logical and mathematical solutions to scientific problems or questions. Develops statements of problems and codes into computer language for solution by means of data processing equipment. Applies knowledge of computer processes, scientific subject matter to be programmed, and input from various users to develop and test programs. Corrects program errors, prepares operating instructions, compiles documentation of program development, and analyzes system capabilities to resolve questions of program intent, output requirements, input data acquisition, programming techniques, and controls.

But it is tangential to the computer work and, as you see, the real job is to find ways of computerising the processes which lead to scientific progress. In the case of Forensic Bioinformatics the goal is to standardise the interpretation of dna testing so as to reduce or remove the need for specialised personnel and replacing them with their machine/computer analysis. Nothing wrong with that. But Gilder makes computer stuff which will do that: the information on which the machine acts is supplied by others.

 

[Mary_H]

No, I did not miss it. Many of the papers Halides1 has used to sustain his point seem to me to support mine instead. Why do you think these papers are co-authored? Could it be because a cross disciplinary field involves collaboration between people with different areas of expertise? Because no one of them is an expert in all that you need? What do you think the computer scientists at Lockheed do? Do they build aeroplanes? I don't know what they do but I think it is probably writing software to do some job which someone else has defined for them. Someone who knows about aeronautics maybe

Would you send a DNA computer scientist to work at Lockheed? If they are "just" computer scientists and not specialists, then every time someone gave them a job they would have to reinvent the wheel.

 

[Fiona]

As I said: some knowledge of the field is helpful and working in collaboration with others a computer scientist who works in one area will of course learn from those who do know. But they will not become experts in that field: they will become experts in computer applications in that field. Otherwise we wouldn't need the others, clearly. Would you employ a forensic biologist to work on aeroplanes at Lockheed? I don't think you would. But you might very well employ a computer expert who had previously been working in DNA analysis. You would probably prefer it if you could get someone who had been working in aeronautics, but in the absence of that you would still know they had transferable skills; so it is not reinventing the wheel at all.

 

[Mary_H]

As I said: some knowledge of the field is helpful and working in collaboration with others a computer scientist who works in one area will of course learn from those who do know. But they will not become experts in that field: they will become experts in computer applications in that field. Otherwise we wouldn't need the others, clearly. Would you employ a forensic biologist to work on aeroplanes at Lockheed? I don't think you would. But you might very well employ a computer expert who had previously been working in DNA analysis. You would probably prefer it if you could get someone who had been working in aeronautics, but in the absence of that you would still know they had transferable skills; so it is not reinventing the wheel at all.

I see your point. In this case, though, I think it is safe to say that Gilder's background is more than ample for the field he works in.

 

[Fiona]

Of course it is more than adequate for the field he works in. He is a computer scientist who works with computers.

There is quite a good and comprehensible article which is the first cite on the wiki article on Bioinformatics which you might be interested to read. It is a quick overview of what the field is about and what kinds of things this type of expert actually does. I can't link it because it downloads as an attachment, unfortunately. But it is not hard to find

 

[Chris_Halkides]

a master's thesis and a Ph.D. thesis are single-author works

I would like to draw everyone's attention to the titles of Dr. Gilder's master's thesis and Ph.D. thesis, both of which I previously posted:

Ph.D. (2004-2007) Computer Science and Engineering. Dissertation: Computational methods for the objective review of forensic DNA testing results

M.S. (2001-2003) Computer Science. Thesis: Developing an expert system and discovering new standards for forensic DNA analysis

I note that these are single-author works. I also posted a paragraph of his Ph.D. thesis, which can be found on p. 7 of this thread.

 

[Fiona]

Yes that is what he does and it is also why he has been a prime mover in the development of the genophiler automated analysis system. That is why he is important to Forensic Bioinformatics. It is a computer programme to interpret dna test results. That has nothing at all to do with dna expertise: it is an computer solution to problems of interpretation of data. The analysis of complex data is what computers are for no matter what field they are employed in. That is why it called information technology, sometimes

 

[stilicho]

I would like to draw everyone's attention to the titles of Dr. Gilder's master's thesis and Ph.D. thesis, both of which I previously posted:

Ph.D. (2004-2007) Computer Science and Engineering. Dissertation: Computational methods for the objective review of forensic DNA testing results

M.S. (2001-2003) Computer Science. Thesis: Developing an expert system and discovering new standards for forensic DNA analysis

I note that these are single-author works. I also posted a paragraph of his Ph.D. thesis, which can be found on p. 7 of this thread.

Yes, you've confirmed that he's a computer scientist. Our Information Systems department has people who write and modify accounting programmes and who evaluate the results but they are not accountants. They do not create the criteria for evaluations or processes. They are experts (in many cases holding advanced degrees) but not outside the fields in which they are experts.

The best examples of relevant cross-discipline degrees I could find combine criminal justice elements with DNA forensics and they are called B.S.F.S or M.S.F.S. I wasn't able to locate the doctorate degree but it's probably the same thing.

 

[stilicho]

1.) Why did Raffaele have to leave Amanda when the police took her back to the house? Did they want to be alone with Amanda? Was Amanda allowed to bring anyone with her, or was it just her and the cops, alone together, in the empty house? Is that why they asked her not to tell anybody about it?

There was at least the interpreter with her and Raffaele was not required to be there. It wasn't his house. Witnesses are frequently required to accept conditions of responsibility and confidentiality. I don't have a cite but I'm certain anyone here who has been a witness would provide you with the corroboration you need.

2.) Why did the police ask Amanda whether Meredith liked anal sex? Was there evidence that Meredith had been anally raped? Was Vaseline found on Meredith's body during the autopsy? I haven't heard of these possibilities mentioned before. Seems like a strange thing for the cops to be asking one of the female roommates about if they didn't have any reason to. Couldn't they have asked Meredith's boyfriend, with whom she was phyically intimate, instead of Amanda?

I don't know that they ever did ask her that. We'll have to await the translation of the Massei Report. It was Amanda who wanted everyone on her spam list to know her opinion of Meredith.

3.) Oh, and one more -- why couldn't these questions have simply been asked back at the station? Why did they require a visit to the cottage? Is this where the fantasies that eventually gelled in Mignini's mind started to form, when he was told by the cops about the visit?

I don't know any of that either.

I can understand your wish to deflect Amanda's own words with idle musings about police actions. The alibi email was hers alone and was not contingent upon any actions of the police or the PM. She alone was responsible for its contents and the method of its distribution.

You will see, once the Massei Report is available in translated form, that the court did take this communication into account.

 

[Mr.D]

However, Hampikian says he is appalled by the standard of DNA evidence used by the Italian courts to convict Knox in the case. ‘The amount of DNA present is far below the normal cut-off for many labs that I know of. A one off spurious piece of DNA evidence shouldn’t be treated as a gold standard profile from a high-profile source. The issue of this low-template DNA sample is really troubling me.’ Trying to obtain the evidence to have it retested, however, is proving difficult.

Bolding mine.

This part reads to me like Hampikian wants to retest the knife, not reanalyze the data, but that part isn't in quotes, so is that just a misunderstanding on the article writer's part, or is there in fact more than one issue here (the physical evidence and the data files)?

 

[Mr.D]

If you mean slightly move your upper body then yes, you can say turn.

This is a small area we are talking about. Rudy was within inches of the door when he locked it.

Is there anyone who asserts that the footprint evidence is consistent with turning and locking the door who can just diagram/model (ie with Poser-like software), photograph or draw the motion(s) they mean?

I don't doubt that such a motion is possible, but I'm having trouble with the assertion that it's "natural" (without pivoting the planted foot for example).

ETA: Didn't see this:

I will see if I can make a little video of this motion.

Thank you.

 

[Chris_Halkides]

low copy number (low copy number) DNA

Bolding mine.

This part reads to me like Hampikian wants to retest the knife, not reanalyze the data, but that part isn't in quotes, so is that just a misunderstanding on the article writer's part, or is there in fact more than one issue here (the physical evidence and the data files)?

It may be that Dr. Hampikian is referring to the problem in low copy number DNA analysis of alleles dropping in or dropping out. Standard LCN work uses least two tests (see the Nature article referenced in the earlier thread), and only those alleles that show up in both test are accepted. This is a separate problem from that of lack of release of the electronic data files.

I asked one anonymous DNA expert unaffiliated with this case about the lack of release, and the expert replied, "Honest differences of opinion by qualified experts should be welcomed by the Court. This can only be accomplished if the independent expert is provided full and complete discovery by the government.”

 

[christianahannah]

I apologize in advance if the questions I am about to ask have already been answered in previous posts (I have been away and upon my return to JREF there are now two threads to read - I am reading backwards but don't know how long I shall continue doing so).

1. In the appeal document of Amanda what DNA evidence is included and what is the argument made towards that evidence?

2. Is there mention of the electronic files not being given to the defense included in the appeal?

3. Are the statements of Amanda included in the appeal?

4. Is the defense asking for an independent review of the forensic evidence?

5. And last, is there a link to the appeal document or a summary of the document?