IHMC11 Wednesday afternoon session on ethics

The session's topic is 'ELSI', which I'm told is an acronym for ethical and philosophical issues...  The moderator repeated the acronym but didn't explain it.  (Later, ELSI=Ethical, Legal and Social Issues.)

Amy McGuire:  Identifiability of the human microbiome - Investigator perspectives.  Data sharing and identifiability (sounds dull but turns out to be really interesting, but she talks too fast!)

Policies favour data sharing and accessibility, developed out of large-scale consortium projects developing a community resource.

Problem:  It used to be enough to strip the personal identifiers from the sequence file and associated phenotype information, but now we realize that DNA sequences are themselves personal identifiers (30-80 SNP diplotypes are enough to identify anyone).

Now. dbGap- data is behind a firewall, includes phenotypic information but is only accessible by 'professionals'.  (Professionals are trusted with confidential information.)  Even aggregated sequence data is now being moved behind professional barriers.  Is this overkill?

HMP data should be public but personally identifiable data should be put at dbGap.  Effort to remove human sequences from the data sets.   Also collect human DNA form a blood sample - aggregate data is released but individual sequence data into dbGap.

Even the cleaned up microbiome sequence data contains some bits of human sequence missed by the clean-up screen against human genome.  Alternative would be to screen against bacterial genomes, but risk losing unknown bacteria.  Researchers asked, is this overkill, given that participants have signed consent forms and the risks of harm to a participant are very small?  Is it a waste of $ and resources?

Another, more philosophical issue, is whether your microbiome is part of you - do participants think their microbiome is apart from them?  Will they continue to think this?  And will our microbiomes come to be ways to identify us personally, as our DNA sequences now are?  (A test using bacteria on our keyboards - we leave our bacterial 'fingerprints' on our keyboards!)

Lots of concern about the scientific value of linking microbiome data to metadata about the person it's from, and about how concerns for privacy could compromise this.  Participants have a lot of trust of the researchers, and are quite comfortable with data sharing about clinical information (not names and addresses).  They care more about feeling respected as a contributor that about protecting their privacy.

Need strong penalties for misuse of the data.  Rather than compromising the science, put in place strong deterrents to misuse.

Keiran O'Doherty:  Social and philosophical ramifications of HMP.  Ahhh, he speaks much slower...  But his slide background has streaks that simulate failing to block out all the sunlight in the room!  He's reading a quote from a philosopher.

The main point:  Do we think our bacteria are part of us?  Does changing my microbiome change me?  My questions:  Does brushing my teeth change me?  What about getting a dental crown, or dentures?  My hair and fingernails are part of me, but does cutting them change me?  Yes but No.  We're comfortable with having the external bits of our bodies changed, and don't think that this change who we are.   He's talking about genetic engineering of embryos and about eugenics, to set a baseline.

Scientific questions:  How heritable and stable is a microbiome?  Is there a 'core' microbiome? Is there horizontal transfer of microbiomes between people?  When we modify an individual's microbiome, are we tampering with the human microbiome-poo, (like eugenics and the gene pool?  (Yikes, now he's talking much faster...)  Do we need to worry about preserving human microbiome biodiversity?

Could we do good by modifying microbiomes?  Good at the public level.  the microbial equivalent of fluoridating the water supply?

Bottom line:  we should be cautious.


Laura Achenbaum:  HMP ethics from the trenches.  She's part of Amy McGuire's group (speaker 1).  Now she's telling us stuff we already know, and details about their survey population (OK, that is what the talk is about).

The consent form is 15 pages - do people really read it?  The participants say it's OK, it reassures them that all the issues have been taken into consideration?  Can the participants really understand it?  Hard to say because so far they've only tested it on a med-school derived sample.

Trust is a big factor - the government/NIH is protecting me...(nasty stretched image of clasped hands).  (nasty stretched image of apples).  Participants liked the financial compensation, and appreciated that they were contributing to socially valued research.


Mark Sagoff: Ecological metaphors.  More philosophical - from interactionist credo (self interacting with environment, e.g. norm or reaction, genotype vs environment) to ecological credo (whatever that is).  He's clearly steeped in the philosophy of ecology.

(Oh dear, he's a bit rambling and he's just put up a slide full of text, and he's quoting the same source as speaker 2.)  He's pointing out how ecological terms are used  he seems to think these are metaphors, but I think they're the reality.  Microbiome research is inheriting a history of confused nature- nurture controversy and a muddle of ecological ideas.

In the past, ecologists have used the human body as a metaphor, but now human biologists are using ecology as a metaphor.

The 'individualist' concept in ecology.  ('individual' meaning, in this context, 'species'!).  Some ecologists now think there are no patterns ad principles in ecology of communities.  Instead any particular community is just whatever assemblage of species that live there.

Bottom line:  The science of ecology cannot offer a conceptual hand to microbiome research, nor a normative analogy.  Because ecology traditionally excludes humans.  He looks for comfort in Aristotle:  material cause - the molecules we're made of; (whoa, now he's gone weird...)  efficient cause: how microbiome causes differences in humans; formal cause:  oops, lost what this is and the last kind of cause.

I asked him, just to confirm:  he says yes, it's true that microbiome research is indeed ecology, but ecology won't help us understand the microbiome because ecology itself is theoretically bankrupt.  He says that humans should now be seen as the model system for ecology.