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Study of protein folds adds to evidence that viruses are alive and ancient

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Re: Study of protein folds adds to evidence that viruses are alive and ancient

#11

Post by gus_massa »

chongli wrote: post #2

I thought the definition of life was a matter philosophical, not scientific, debate. How does one "find evidence" to support an open philosophical argument?

If you ignore the title, the article is interesting.

They identified 66 "types" of proteins that are unique to virus and are not presents in bacteria, archea or eukaryotes (animals, plant, fungi, ...).

They use 66 "types" of proteins to classify some of the virus, make a phylogenic tree, and see evolution in the tree. This evolution is independent of the evolution of the cells.

So they propose that this new phylogenic tree must be included in THE phylogenic tree along with the trees of the bacteria, archea or eukaryotes (animals, plant, fungi, ...).

The non-virus tress are connected, I'm not sure how this will connect this new tree.

I didn't look at the details and I'm not a biologist, but this sounds like good science. (I guess it's overhyped as usual, and I'd wait five year just to be sure, but I think this has only the standard overhype in a press release.)

Does it mind that the viruses are alive? Cows are alive, rocks are not alive. IIRC trees were classified as not alive until a few thousands years ago. Life is an arbitrary label for a set of atoms, it's useful but the threshold is arbitrary.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#12

Post by InclinedPlane »

chongli wrote: post #2

I thought the definition of life was a matter philosophical, not scientific, debate. How does one "find evidence" to support an open philosophical argument?

The problem is really a semantic one, I'd say. The issue is what is defined as "a virus". Typically a virion is used as the canonical representation of a virus, but this is no more accurate than calling an egg a chicken. This is merely an infectious particle, one part of the viral lifecycle. Properly, the virus when it is operating after infecting a host is just as much "the virus", and in that phase is very much easier to see as alive.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#13

Post by kpil »

danieltillett wrote: post #7
guelo wrote: post #4

Earlier quoted context omitted.

A lot of biology is dedicated to these taxonomic categorization debates that don't actually mean anything.

I would not be so harsh on biologists, but I do agree that we waste far too much time arguing over garbage like this. As I used to tell my students taxonomy is just a tool to help humans make some sense of all the complexity in living systems, but it is not real.

I think that if the taxonomy is based on evolutionary paths, it's somewhat more "real" compared to the "looks alike" sense. The evolutionary paths could potentially give some insights, while grouping similar but genetically unrelated species is just a confusion in that sense.

On the other hand - classifying things based on their genome does not really help us understand the biomes.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#14

Post by WhitneyLand »

mjburgess wrote: post #8
NhanH wrote: post #3

Earlier quoted context omitted.

Nothing specific to the article here, but in general I believe philosophical question tends to be explain or made obsolete by scientific discovery rather than philosophy itself. Look at the discussion on "life substance" (I forgot the term) before we learn how to synthesize organic compound as an example. Otherwise, the concurrent philosophical text on conscious and intelligence would be another case where answer wou…

This is a common view amongst people who have never studied philosophy. Everyone is engaged in philosophy, including scientists themselves, and mostly poorly. Scientists in considering what data signifies life are themselves taking as given some concept 'life' - ie. their first step is philosophical (as ever). You may say whatever a decision a scientist makes on concepts such as these is obviously the best - but then…

Comes across as pedantic and somewhat bitter, possibly after having read Neil deGrasse Tyson's comments on philosophy.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#16

Post by hyperpape »

chongli wrote: post #2

I thought the definition of life was a matter philosophical, not scientific, debate. How does one "find evidence" to support an open philosophical argument?

You are making two assumptions that are arguably false:

1) That it's an either/or. The question of whether viruses are living can be both philosophical and scientific.

2) That if it's philosophical, there's no (empirical?) evidence that can bear on it.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#18

Post by pohl »

cLeEOGPw wrote: post #15

Whether viruses are classified as life or not doesn't matter and wouldn't change anything. The important and interesting thing is that viruses probably evolved from cells.

We should probably just accept that life (a particular class of self replicating systems) is not the same concept as being alive.

Then one wouldn't have a problem with accepting that viruses are life, albeit not alive.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#19

Post by hyperpape »

frenchy wrote: post #9
NhanH wrote: post #3

Earlier quoted context omitted.

Nothing specific to the article here, but in general I believe philosophical question tends to be explain or made obsolete by scientific discovery rather than philosophy itself. Look at the discussion on "life substance" (I forgot the term) before we learn how to synthesize organic compound as an example. Otherwise, the concurrent philosophical text on conscious and intelligence would be another case where answer wou…

I think "vital force" is the term you might be looking for. While almost any scientist would just chuckle at the idea, remnants of it are still quite common in modern philosophy.

Who/what are you thinking of when you say it's common? There's exactly one[1] post 1950 Anglosphere philosopher I could credibly associate with the idea, out of literally hundreds I've read: John Searle. And arguably that's a dismissive appraisal of what he thinks (but I don't think his view makes any damn sense, so that's what I'm stuck with).

[1] Honorable mention to Trenton Merricks and Peter Van Inwagen who have strange beliefs that sound a bit like belief in a vital force, but aren't: https://en.wikipedia.org/wiki/Mereological_nihilism

Edit: I see you say remnants. I suppose a lot of this is open to interpretation about what a remnant is.

Re: Study of protein folds adds to evidence that viruses are alive and ancient

#20

Post by mjburgess »

NhanH wrote: post #10
mjburgess wrote: post #8

Earlier quoted context omitted.

This is a common view amongst people who have never studied philosophy. Everyone is engaged in philosophy, including scientists themselves, and mostly poorly. Scientists in considering what data signifies life are themselves taking as given some concept 'life' - ie. their first step is philosophical (as ever). You may say whatever a decision a scientist makes on concepts such as these is obviously the best - but then…

> This is a common view amongst people who have never studied philosophy I really should take offence here with this statement ;). >You may say whatever a decision a scientist makes on concepts such as these is obviously the best - but then history would show you totally incorrect. That wasn't what I meant at all. I meant it is normal for scientific evidence to be part of answer for philosophical question, and there…

> "is there anything fundamentally difference between life and non-life objects" is answered by scientific advancement

No it isnt. Science has only made one candidate for the meaning of "fundamental" trivial (in particular, that the physical substance of living things is the same substance of non-living things)- there are many other senses in which living things and non-livings things are fundamentally different. For example, all moral agents are necessarily alive. All non-living things are necessarily not moral agents.

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