Viruses and the definition of “life”

One of the things we often debate here is the definition of “consciousness,” but consciousness is far from the only concept that is difficult to define.  Others include religion, democracy, free will, and biological life.

Life has a number of definitions, many of which are suitable for particular purposes.  If I recall correctly, NASA, for purposes of detecting it in extraterrestrial environments, defines life as anything that reproduces and undergoes evolution.  But many biologists insist that homeostasis is crucial aspect.

Cells are often referred to as the basic unit of life.  That certainly seems true for the homeostasis definition.

(Interestingly, cells may be the basic unit of life, but they’re not the basic unit of capability.  For that, we have to drop down to proteins, molecular nanomachines that do the actual work in biology.  A simple cell has tens of millions of proteins.  More complex cells, such as neurons, reportedly have tens of billions.  It pays to remember that life began as, and remains, a molecular enterprise, with even cells being vast ecosystems.)

But here’s a question.  Are viruses alive?  It depends on which definition we use.  They reproduce and undergo evolution, producing new species and strains all the time, as most of us are only too aware of these days.  But they don’t have homeostasis.

Outside of a cell, in their “virion” phase, they consist of some genetic material (RNA or DNA) surrounded by a protein coat, both for protection and containing penetration machinery to get through cellular membranes.  Once they’ve invaded the cell, they hijack that cell’s reproductive mechanisms for their own use, reproducing themselves.

Viruses appear to be evolutionarily ancient, perhaps co-evolving along with the earliest cells.  Both cells and viruses may have evolved from pre-cellular biology.  It’s tempting to think of the cells as farmers putting up a fence to protect their mechanisms and resources, and viruses as the raiders coming in to hijack and ransack those mechanisms and resources.

Thinking back to Aristotle’s three layers of soul, he would almost certainly have attributed a nutritive soul to cells.  But I’m not sure he necessarily would have for viruses.  He might have seen them as soulless parasites.

But is that entirely fair?  It seems like viruses simply use the resources available to propagate, just as all heterotrophic life consumes other life to survive and propagate.  In evolution, they also provide an important means of horizontal gene transfer, increasing genetic diversity in non-sexually reproducing species.  And they’re often used today as vehicles for delivery gene editing therapies.

It’s worth noting that viruses are not the smallest infectious agent.  Viroids are even smaller.  Composed of a short circle of RNA with no protein coat, they only infect plant cells.  Their existence seems to have inspired the idea that life began in an RNA world.  Viroids may be leftovers from the earliest primeval life, or proto-life forms.  If viruses are alive, then it seems hard to exclude viroids.

There are even smaller replicating agents: prions.  These are proteins that have become misfolded, with the disturbing ability to transmit their misfolding, leading to a number of neurodegenerative conditions, such as “mad cow” disease.  Are prions alive?  Most biologists say no.  They do reproduce, but I haven’t seen any assertions they undergo evolution.  They may be more like crystals or clay, albeit of a more organic variety.

So what is life?  Does it require a cell?  Or do viruses and viroids count?  Thinking in terms of extraterrestrial life, it seems possible to conceive of mechanisms we might discover that would challenge any definitions we come up with.  Suppose we encountered a sort of organic clay somewhere.

Reality often seems to delight in ruining our little categories.

All adults are vulnerable to COVID-19

The other day I urged you to take COVID-19 seriously.  But in that post, I said that if you were younger than 60 or didn’t have health problems, the virus probably wouldn’t do anything to you.  In retrospect, that was misleading.

A lot of people are saying that we should reopen the economy for people “not vulnerable” to the virus.  The thing is, all adults are vulnerable.  We’ve all fixated too much on the fatality rate.  We also need to look at the hospitalization rate, as well as the ICU rate.  This report from the CDC has that information.

What I want to call your attention to, is this chart from the report:

Bar chart showing high hospitalization rates for all adults
Image credit: US CDC (click through for original)

You can see it in terms of percentage of cases in a table format here.  The TL;DR is that if you’re an adult and get the virus, you have a 20% chance or higher of ending up in the hospital.

Young adults are far less likely to die from the virus, if they have good care.  But being in the ICU is nothing to be blasé about.  And if the virus is allowed to run rampant among the “non-vulnerable” and the health systems become overrun, good care may not be available.

Keep this in mind when considering the calls currently being made by politicians and business people to let up on the social distancing and shelter in place policies.  There’s a reason health professionals are opposed to those calls.

I get that the economic situation is agonizing.  But it’s not like the economy would be robust with an overrun health system.

Take COVID-19 seriously

Just got back from getting a haircut and a run to the grocery store (which had an atmosphere very similar to the one down here when a hurricane is imminent), during which time I think I heard enough crazy rumors to start my own conspiracy blog.  The worst, by far, were variations that this is all just people freaking out over the flu, or a liberal conspiracy, or some kind of con.  So, I’m sharing this Political Wire blog post, because I think it’s important.

Coronavirus Is Unlike Anything in Our Lifetime

Charles Ornstein: “As a longtime health care reporter, the unfolding coronavirus pandemic represents everything I’ve read about — from the early days of epidemiology to the staggering toll of the 1918 Spanish Flu pandemic — but had not covered in my lifetime.”

“And still, I have been caught off guard by the pushback from top elected officials and even some friends and acquaintances who keep comparing it to the flu.”

“Not one public health expert I trust — not one — has said this flu comparison is valid or that we’re overdoing it. Every single one, from former FDA Commissioner Scott Gottlieb to Harvard professor Ashish Jha, has said we’re not doing enough, that this is far more serious than it is being taken.”

I’m not an epidemiologist, but I listen to the experts.  If you’re younger than 60, this virus probably wouldn’t do much to you.  Congratulations.  Good for you.  (CORRECTION: Actually young adults still have a roughly 20% chance of ending up in the hospital.  Your chance of survival is just better.)  But you’d still be a carrier, a link in the chain threatening people who have a serious chance of being harmed by it: those over 60, or with chronic conditions like diabetes, asthma, heart conditions, etc.

Just about everyone knows and cares about someone in these categories.  (Maybe you’re in one yourself.)  It’s fine to risk your own safety, but don’t be one of those selfish chest thumping jerks who make a big deal about how brave they are while putting others at risk.

Maybe in three to six months we’ll all look back with hindsight knowing that this wasn’t as severe as the experts currently think it is.  Maybe.  But before accepting assurances from anyone who claims to know that right now, ask what evidence or information they have that the health professionals are missing.

AI: An Exercise in Analytical Philosophy

An excellent analysis of the issue! It seems like this is a problem for any interesting philosophical question. I’m always struck by how often philosophical disagreements are really just definitional disputes in disguise. It’s particularly troublesome for any discussion about the mind, about us at the most fundamental level, because people have intense emotions about the conclusions.

Blogging to Share Knowledge

The Question

I recently attended a computing group in which the following question was asked:

Can Software Achieve Human Level Intelligence?

We covered this question over the course of 3 meetings (7-9 hours total).  Those meetings didn’t go well.  We spent hours talking past each other, objecting to arguments, and accusing each other of missing the point.  In the end we gave up and agreed to talk about something else.

How can people spend hours talking about something without anything to show for it?Because we weren’t talking about the same thing and never settled on meanings first to discover that.

After reflecting on those meetings, I thought the following process would have been more productive:

  1. Each person precisely translates the sentence as they understand it.
  2. Replace any contentious terms to avoid arguing over semantics.
  3. Decide if there’s any basis for arguing.

So let’s continue by assuming two arguers: John and…

View original post 527 more words

An excellent explanation of quantum decoherence, and how it might lead to many worlds

Matt O’Dowd is a first class science communicator.  In this latest video, he does an excellent job explaining decoherence, and why the MWI (many worlds interpretation) ends up being so tempting when you see it through.

Of course, this doesn’t mean MWI is the right interpretation, but it does demonstrate why many find it tempting.  (At least once they get over the visceral reaction we all seem to initially have for it.)

But it’s worth noting that decoherence actually is compatible with pilot-wave and many other interpretations, and reportedly even some versions of Copenhagen.  So don’t let MWI cause you to dismiss it!

Islands of awareness

(Warning: neuroscience weeds)

An interesting paper by Tim Bayne, Anil Seth, and Marcello Massimi, which came up in my Twitter stream today, asks whether there can be islands of awareness.

Ordinary consciousness involves ongoing interaction with the environment, receiving sensory information, and producing motor output.  It has a functional role, enabling an organism to deal with novel situations, including dangers and opportunities.

However, it is possible, due to injury or pathology, for some or all of this interaction to be lost, for the consciousness to become isolated.  The authors start out discussing various medical situations where people can become almost completely disconnected on the output end, only able to communicate with the world by the twitching of an eyelid, or even worse, be completely locked in, unable to communicate at all.

It’s also possible to become disconnected on the input side.  Some of these cases are reversible, such as what happens in dreaming.  In that state, we’re generally disconnected from the outside world, although with a strong enough stimulus, that can usually quickly be reversed.  There is also the anesthesia drug ketamine, which apparently provides the same disconnection, but doesn’t always extinguish consciousness, sometimes leading to vivid and terrifying experiences.

But what the authors are most concerned about here are actual islands of awareness, where the system in question is completely isolated from the environment.  They explore three scenarios: ex cranio brains in a nutrient vat, hemispherotomy, and cerebral organoids.

An example of ex cranio brains were the disembodied pig brains which were kept alive in a nutrient delivery system.  The nutrient mix included a neural inhibitor to ensure that the brains wouldn’t regain consciousness, but suppose that inhibitor hadn’t been present?  Could such brains actually be conscious?  A lot of people would say no, that consciousness requires interaction with a body.  But if such a brain showed wide scale organized activity, it might “put pressure” on embodied cognition theories.

A hemispherotomy is sometimes performed on a patient with severe epileptic seizures.  It involves severing the connections between the damaged hemisphere and the other side, as well as its connections with the brainstem, thalamus, and other subcortical structures.  However, a hemispherotomy, unlike a hemispherectomy, leaves the tissue in place, with all of its vascular connections.

Could such a disconnected hemisphere be conscious?  The authors note that, under normal circumstances, without the activating signals coming up from the RAS (reticular activating system) in the brainstem, the activity in the disconnected tissue has very low firing rates, equivalent to a deep dreamless sleep.  But, they ask, what would happen if electrodes were inserted and used to stimulate the hemisphere?  Might it then regain some consciousness?

The authors discuss the role of subcortical regions in consciousness.  It’s well established that they provide crucial support, but what is the nature of that support?  Are they causal, constitutive, or both?  Causal means they just cause awareness in cortical tissue but don’t participate in generating or consuming the content.  Constitutive means they do.

Personally, I think with a disconnected thalamus, the question is somewhat moot.  Such a hemisphere’s ability to communicate with its disparate regions would be heavily compromised.  I tend to doubt any awareness is possible under those conditions.  Only if the subcortical connections were kept intact, with only the RAS disconnected, might it be possible to re-stimulate some form of consciousness.

The third scenario is cerebral organoids.  I did a post on these a few months ago.  The chances that any form of awareness exists in these largely random collection of neural cells is so close to zero that I find worrying about it counter-productive.  There’s simply nothing to indicate these small clumps of neural tissue are organized to have any sensory or affective functionality, and without that, it’s hard to call whatever is happening in them consciousness.  We might as well worry about whether brain tumors or other excised tissue are conscious.

The authors worry that as organoids continue to be developed, there may eventually be issues.  I guess that’s possible, but it only seems to be a significant possibility when enough of the various components of the brain start to be included, which still seems very remote.

The authors mention other possibilities, such as an in utero fetus with some pathology causing it to be completely disconnected.  Given how immature the brain is until well into the third trimester, this only becomes a possibility in the last few months of pregnancy, but it is a possibility.  Would such a system, with no history of sensory input, be conscious in anything like our understanding of the word?

But the most likely scenario is the ex cranio one, such as the pig brains.  It seems inevitable that someone will eventually try that experiment without the inhibitors.  What will it mean if the brains in that scenario do show wide scale organized activity?  The paper discusses the difficulty of detection in these scenarios, and of avoiding false positive and false negatives.

It’s worth noting that the major cognitive theories: global workspace (GWT), integrated information (IIT), and  higher order thought (HOT), are compatible with the ex cranio scenario.  But the more fragmented the tissue is, the less compatible these theories are, although IIT may posit even organoids as having some level of consciousness.  The theory that might be most compatible with small fragmentary islands is recurrent processing theory (RPT).

The paper finishes up by noting that neuroscientific progress increases the chances of producing these islands, and that they may already exist.  They call for careful consideration of the ethical issues involved.

What do you think?  Are conscious hemispheres or organoids more likely than I think?  Or are there solid reasons to conclude that disembodied cognition is impossible?

Daniel Dennett on why phenomenal consciousness is access consciousness

This old talk by Daniel Dennett touches on a lot of topics we’ve discussed recently.  Dennett explains why it’s wrong to regard phenomenal consciousness (the “what it’s likeness” or “raw experience” version) as separate from access consciousness (the cognitive access of information for decision making, memory, report, etc).

Note that Dennett doesn’t deny the existence of phenomenal consciousness here, just the idea that it’s something separate and apart from access.  He even passes up opportunities to dismiss qualia, although he does provide a reduction of them.

This video is about 66 minutes long.  Unfortunately the video and sound quality aren’t great, and the camera operation is annoying, but the talk is worth powering through.

I agree with just about everything in this talk, but I do feel a little compelled to defend Victor Lamme since I read his stuff recently and it’s still relatively fresh in my mind.  Dennett says that there’s no rational provided for why recurrent neural processing leads to phenomenality.  Lamme, to his credit, actually does take a stab at it, citing the enhanced synaptic plasticity associated with recurrent processing, leading to the formation of memories, albeit very brief ones in the cases he’s considering.  But as I noted in my post on that theory, it’s arguably more about the preconscious, pre-access sensory processing, than consciousness itself.

The main thrust of Dennett’s remarks are that phenomenal content isn’t something that access consciousness makes use of, phenomenal experience is a result of access processing.  Therefore, studying access consciousness is studying phenomenal consciousness.  They are one and the same, just seen from the outside or the inside respectively.

Dennett also talks about the element people often feel is missing from strictly information processing accounts, referring to it as “the juice” or “the sauce” (a cute acronym for “subjective aspect unique to conscious experience”) before, in politeness to his host, settling on “feeling”, but pointing out that feelings must be felt, and felt is a form of access.

There have also been some conversations recently about the hard problem of consciousness, particularly at James Cross’ blog.  It’s worth noting that phenomenal consciousness is the version typically associated with the Chalmers’ hard problem, while access consciousness is associated with his “easy problems” (discrimination, attention, reportability, etc).  But if phenomenal and access consciousness are one and the same, then the hard problem is simply an agglomeration of the easy problems.  Meaning that as the easy problems are solved, the hard problem will gradually be solved.

So, a lot of good information in this talk, which I’m sure won’t be controversial at all.  🙂

(via Richard Brown)

Stimulating the central lateral thalamus produces consciousness

(Warning: neuroscience weeds)

The thalamus.
Image credit: Wikipedia

A couple of people have asked me about this study, described in numerous popular science articles (such as this one).  A monkey had electrodes installed in its brain that allowed scientists to stimulate parts of its thalamus, the region at the center of the brain which links the cortex to the brainstem and other systems, as well as serves as a relay station for some inter-cortical communication.

Stimulating the monkey, while it was anesthetized, in the central lateral thalamus region caused it to wake up, look around, and reach for things.  Ceasing the stimulation caused the monkey to immediately lose consciousness.  Notably, this region is heavily interconnected with frontal and parietal regions.

Diagram showing the various regions of the thalamus
Image credit: Madhero88 via Wikipedia

Interestingly, stimulating the medial dorsal thalamus, which is heavily connected to the prefrontal cortex, “proved less effective”, and stimulating the central medial thalamus, which projects to the striatum, was also less effective.

In other words, consciousness seemed to be associated with the central lateral thalamus region and its projections to layers in the frontoparietal network.

Diagram showing the regions of the brain
Lobes of the brain
Image credit: BruceBlaus via Wikipedia

One interesting point about this study, is it seems to contradict another study from a year or two ago which ruled out the thalamus as having a role in wakefulness (favoring the basal ganglia instead, if I recall correctly), a reminder that it’s not a good idea to hang too tightly on the results of individual studies.  Another point is the demonstration that the frontoparietal network overall, not just the prefrontal cortex, seemed to be most important for stimulating consciousness.

What does it all mean?  Well, it seems like a dramatic experiment.  And it seems to re-establish the role of the thalamus in wakefulness.  The part about stimulating the regions projecting to the prefrontal cortex not being effective makes me wonder about implications for higher order theories that focus on that region.

All that said, I think we have to bear in mind the distinction between the state of consciousness, that is wakefulness or vigilance, and awareness.  A lot of the information in this experiment seems to be about the state more than awareness.  In that sense, some of the anatomical details are new, but the overall macroscopic picture doesn’t seem to be much affected.

But this is a technical paper and there are probably implications I’m missing.  In particular, the implications for anesthesiology  and other clinical situations may be very significant.

Alita: Battle Angel

Movie poster for Alita: Battle Angel

I’m pretty late to the party on this one, but today I finally watched Alita: Battle Angel.  The movie is set in the 26th century and involves a society with a lot of cyborgs in it, including many whose entire body other than their head or brain has been replaced by machinery.

It’s about 300 years after an event known as “the fall”, in which all the floating cities were destroyed in a war.  Only one of those floating sky cities remains: Zalem (apparently held up by some kind of anti-gravity technology).  Beneath and around Zalem is another city on the ground: Iron City.

Directly underneath Zalem is a scrapyard, where the detritus from the floating city lands, and where Dr. Dyson Ido finds the head and upper torso of a young girl, who is still alive.

Ido attaches the her to a cybernetic body.  When she awakens, she has no memory of her past life.  He gives her the name “Alita”.  What follows is a journey of discovery as Alita learns about her abilities, who she is, and where she comes from, and the society she has awoken in.

It’s a society with a sharp class division, with an affluent population living in the sky city Zalem, and the rest of the hardscrabble population living in Iron City.  The people of Iron City dream of finding a way to move up into Zalem, but the options for doing so are very limited.  Life is hard and brutal.

It’s difficult to go into much more detail without getting into spoilers.  I’ll just note that it’s chock full of action, with plenty of battles between cyborgs with all kinds of attached weaponry.  And there are lots of special effects.  A big part of the appeal is the imagery, which this movie handles very well.

I have to admit that I hadn’t heard much about this movie so I wasn’t expecting more than moderately entertaining fluff.  It surprised me by being more than that.  It wasn’t until after finishing it that I learned that it’s based on a classic manga and anime series, and that one of the producers is James Cameron.

It’s not clear if it did well enough financially for sequels.  I hope it did.  It’d be good to see more.  If not, I might have to dig up the anime or manga material.

So, if you’re looking for a couple hours of entertainment, and aren’t turned off by cybernetic body parts and human machine hybrids being ripped apart, and like me have somehow managed to miss this movie until now, I recommend checking it out.

Prefrontal activity associated with the contents of consciousness

The other day I bemoaned the fact that the Templeton competition between global workspace theory (GWT) and integrated information theory (IIT) would take so long, particularly the point about having to wait to see the role of the front and back of the brain in consciousness clarified.  Well, it looks like many aren’t waiting, and studies seem to be piling up showing that the frontal regions have a role.

In a preprint of a new study, the authors discuss how they exposed monkeys to a binocular rivalry type situation.  They monitored the monkeys using a no-report protocol, to minimize the possibility that the monitored activity was more about the need to report than perception.  In this case, the no-report was achieved by monitoring a reflexive eye movement that had been previously shown to correlate with conscious perception.  So the monkeys didn’t have to “report” by pressing a button or any other kind of volitional motor action.

The authors were able “decode the contents of consciousness from prefrontal ensemble activity”.  Importantly, they were able to find this activity when other studies hadn’t, because while those other studies had depended on fMRI scans using blood oxygen levels, this study used equipment physically implanted in the monkey’s brain.

These results add support for cognitive theories of consciousness, such as GWT and higher order theories (HOT), and seem to contradict the predictions made by IIT.

Of course, it doesn’t close off every loophole.  There was speculation on Twitter that Ned Block will likely point out that some variation of his no-post-perceptual-cognition protocol is necessary.  In other words, it can’t be ruled out that the activity wasn’t the monkeys having cognition about their perception after the perception itself.  (Which of course assumes that cognition about the perception and conscious perception are distinct things, something cognitive theories deny.)

And as I’ve noted before, I tend to doubt that the prefrontal cortex’s role will be the whole story, which seems necessary for strict HOT.  It seems possible that someone could have sensory consciousness without it, but probably not affect consciousness, and not introspective consciousness.

So, not the last word, but important results.  After the study last week calling into question the role of the P3b wave, it seems to get global neuronal workspace off the ropes.