[Merged] The Vital Question: Why Is Life the Way It Is? / The first branching event of life

[Generally Rational]

That is the title of Nick Lane's new book, that comes out in July in the U.S. and Canada but has been out since late April in the U.K. I have a copy of that version if anybody wants to bring up issues. I tried to give my best shot at summarizing the key issues in the best science and medicine book sticky thread:

http://www.internationalskeptics.com/forums/showthread.php?postid=10681442#post10681442

I'm probably shooting myself in the foot by revealing my key motivation but it is to get as many skeptics as possible to read this and his previous, award winning, book, Life Ascending, also mentioned in that post. Better yet would be one of the most popular skeptical podcasts talking about it or even better yet interviewing him when he's promoting the U.S. release. He's twice been a guest on Brian Cox's Infinite Monkey Cage as well as other radio programs with mp3 recordings of the show.

It is running across posts like this that are motivating me to post here right now:

http://www.internationalskeptics.com/forums/showthread.php?postid=10625564#post10625564

Really nice graphic, and "This is the End" has the right attitude, but the time scale of chemistry is wrong. As Lane points out, chemistry happens quickly or not at all. Without some process pushing the chemistry along it won't happen at a fast enough rate to build upon itself. Fortunately alkaline hydrothermal vents would have pushed chemistry along on early Earth.

Creationists are by and large more ignorant than skeptics (intentionally so) but they do love to attack any opening they can identify so as to discredit us in their eyes and whatever audience they think they have. We should be adopting the best current armor rather than relying on old stuff. At the very least, the hypotheses brought up in the books have testable elements, unlike many previous hand-waving attempts at the problem.

His website is http://www.nick-lane.net/

 

[jonesdave116]

That is the title of Nick Lane's new book, that comes out in July in the U.S. and Canada but has been out since late April in the U.K. I have a copy of that version if anybody wants to bring up issues. I tried to give my best shot at summarizing the key issues in the best science and medicine book sticky thread:

http://www.internationalskeptics.com/forums/showthread.php?postid=10681442#post10681442

I'm probably shooting myself in the foot by revealing my key motivation but it is to get as many skeptics as possible to read this and his previous, award winning, book, Life Ascending, also mentioned in that post. Better yet would be one of the most popular skeptical podcasts talking about it or even better yet interviewing him when he's promoting the U.S. release. He's twice been a guest on Brian Cox's Infinite Monkey Cage as well as other radio programs with mp3 recordings of the show.

It is running across posts like this that are motivating me to post here right now:

http://www.internationalskeptics.com/forums/showthread.php?postid=10625564#post10625564

Really nice graphic, and "This is the End" has the right attitude, but the time scale of chemistry is wrong. As Lane points out, chemistry happens quickly or not at all. Without some process pushing the chemistry along it won't happen at a fast enough rate to build upon itself. Fortunately alkaline hydrothermal vents would have pushed chemistry along on early Earth.

Creationists are by and large more ignorant than skeptics (intentionally so) but they do love to attack any opening they can identify so as to discredit us in their eyes and whatever audience they think they have. We should be adopting the best current armor rather than relying on old stuff. At the very least, the hypotheses brought up in the books have testable elements, unlike many previous hand-waving attempts at the problem.

His website is http://www.nick-lane.net/

Well, if he's been on with Brian Cox, then I may well have a butcher's at that. I do like The Infinite Monkey Cage, and I do like Brian Cox.
One of a number of people, in my humble opinion, who have set this particular country (UK) on the road it is on now, religion-wise. That is, it is even more atheistic/agnostic than it has ever been.
I would add to that; Sir David Attenborough, Richard Dawkins, Steve Jones and Chris Stringer, among many others.
There are others, but long may our freedom of speech give them the right to continue broadcasting on a publicly funded TV station without censure.
Getting the religious rubbish out of our schools may take longer, however

 

[Generally Rational]

Well, if he's been on with Brian Cox, then I may well have a butcher's at that. I do like The Infinite Monkey Cage, and I do like Brian Cox.

Series 5, episode 3 "The Origins of Life" and Series 8 Episode 1 "What is Death?", which happen to be the subjects of the first and last chapters of Life Ascending. Lane was also one of the two consultants for "Wonders of Life".

One of a number of people, in my humble opinion, who have set this particular country (UK) on the road it is on now, religion-wise. That is, it is even more atheistic/agnostic than it has ever been.
I would add to that; Sir David Attenborough, Richard Dawkins, Steve Jones and Chris Stringer, among many others.
There are others, but long may our freedom of speech give them the right to continue broadcasting on a publicly funded TV station without censure.
Getting the religious rubbish out of our schools may take longer, however

Good luck. We seem to be going backwards here in the United States because there never seems to be any political or financial cost to being the worst possible version of yourself. Most Americans will either reward you, not pay attention, or scapegoat people who have nothing to do with it.

 

[Generally Rational]

The first branching event of life

It's a cliche that the oldest deepest divide in life is between bacteria and archaea, but if you assume that it happened in an alkaline hydro-thermal vent (or at least someplace with natural proton gradients), we might have an answer.

One of the most enlightening parts of Nick Lane's "The Vital Question" (coming out in North America on July 20) is explaining the most elegant reason to date for that split, based on these two papers and yes he was a coauthor.

http://rstb.royalsocietypublishing.org/content/368/1622/20130088

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001926

The second one came later and I agree with David Marjanović posting at

http://freethoughtblogs.com/pharyngula/2014/10/04/dang-good-paper/

that it states the premise more clearly. Lane was undoubtedly already writing "The Vital Question" and uses diagrams from the latter paper in the book.

In short, LUCA developed a simple single protein Proton/Sodium antiporter which is still part of the energy converting hydrogenase (Ech) and Complex I of the respiratory chain. It should be called hydronium/Sodium antiporter because hydronium is a cation that forms from water in the presence of hydrogen ions and is nearly identical (115pm vs 117pm) in size to a Sodium ion and allows the antiporter to be indiscriminate. After this event, pumping Sodium ions using the existing proton gradient become advantageous. This led towards a tight modern membrane rather the leaky early one and more sophisticated pumping mechanisms.

From page 151 of the book:

"Yet the similarities and differences begin to make sense if we assume that LUCA did indeed depend on natural proton gradients. If so, the key to pumping could lie in the direction of proton flux through Ech - whether the natural flow of protons into the cell drives carbon fixation, or whether this flux is reversed, with the protein now acting as a membrane pump, pumping protons out of the cell."

The papers say much the same but not as clearly to a layman. As Lane says, it was a binary "choice" made by two lines of descendants. One became acetogens and other bacteria and the other became methanogens and other archaea, and much much later they merged to become Eukaryotes that led to us.

Yes, yes this has not yet become the consensus view, but it is slowly growing in adherents.

 

[Generally Rational]

Energy is far less forgiving than genes

The title is the first sentence of the third to last paragraph of Nick Lane's "The Vital Question".

The last sentence of that paragraph is "Genes are almost infinitely permissive: anything that can happen will happen." Lane goes on with two equally more eloquent paragraphs about the importance of energy to life.

But to me, the point of the book is that the Cold Equations of physics and chemistry are not at all permissive towards biology. If it can't happen it won't. Life as been straitjacketed by certain physical fundamentals for its entire existence. I think people who listen too much to biologists and not enough to chemists and physicists forget that.

 

[Reality Check]

I would say that the opposite is true: the laws of physics and chemistry almost demand biology. For example the physics and chemistry of lipids means that protocells will form if we have lipids in conditions that probably existed in the early Earth.
Concentrating on just the energy as Nick Lane seems to do in your quote, is missing the wider picture. Luckily reviews of the book suggest that this is not the case.

 

[Dinwar]

I'm not sure who you're talkinig to to gain your understanding of biology, but they've been fooling you.

First, it's most difinitively NOT true that with genes "anything that can happen will happen". There are several facinating restrictions. The first that springs to mind in any paleontologist is channalization, the tendency for disparity to decrease through time. We see nothing like the diversity of bauplans we saw in the Cambrian in today's world, and the reasons for that are very interesting. There's also the fact that no morphospace is completely filled, which has about as many explanations as there are morphospaces!

Second, energy flow through cells, organisms, and ecosystems is such an integral part of biology that to say biologists don't pay enough attention to it is insane. They obsess over that stuff! EVERY ecosystem analysis focuses on that issue. What do you think trophic levels are?

This sounds like someone in physics who has watched a few NOVA episodes and concludes that they know more about biology than biologists. I may be wrong, and his work may be more in-depth, but that's my sense given the OP's description.

 

[Beelzebuddy]

This sounds like someone in physics who has watched a few NOVA episodes and concludes that they know more about biology than biologists. I may be wrong, and his work may be more in-depth, but that's my sense given the OP's description.

From GR's half-dozen other posts about the book, I gathered that the author is a biophysicist (speculative work on early proton pump mechanisms), seen here grumbling that biologists of other subdisciplines don't pay enough attention to biophysics. While that's probably true, the opposite is also likely to be the case.

 

[mike3]

I'm not sure who you're talkinig to to gain your understanding of biology, but they've been fooling you.

First, it's most difinitively NOT true that with genes "anything that can happen will happen". There are several facinating restrictions. The first that springs to mind in any paleontologist is channalization, the tendency for disparity to decrease through time. We see nothing like the diversity of bauplans we saw in the Cambrian in today's world, and the reasons for that are very interesting. There's also the fact that no morphospace is completely filled, which has about as many explanations as there are morphospaces!

Second, energy flow through cells, organisms, and ecosystems is such an integral part of biology that to say biologists don't pay enough attention to it is insane. They obsess over that stuff! EVERY ecosystem analysis focuses on that issue. What do you think trophic levels are?

This sounds like someone in physics who has watched a few NOVA episodes and concludes that they know more about biology than biologists. I may be wrong, and his work may be more in-depth, but that's my sense given the OP's description.

This is really interesting. Where can I find out more?

 

[Dinwar]

This is really interesting. Where can I find out more?

Gould has a decent intro to the concept of channalization in "Wonderful Life" as I recall; Ward's "Future Evolution" and "The Madea Hypothesis" have better ones (though a bit more grim).

For energy flow through ecosystems any ecology textbook will have an in-depth discussion of it (it more or less defines the field). After that, Lovelock's original "The Gaia Hypothesis" has a decent discussion (the later stuff appended to that hypothesis gets very, very woo, but the original is fairly well grounded in scientific fact).

From GR's half-dozen other posts about the book, I gathered that the author is a biophysicist (speculative work on early proton pump mechanisms), seen here grumbling that biologists of other subdisciplines don't pay enough attention to biophysics. While that's probably true, the opposite is also likely to be the case.

Can't fault him for that--"You people don't pay enough attention to this important stuff!" is a common theme in science, and not always wrong. I'm more than a little guilty of this myself!

 

[Generally Rational]

I would say that the opposite is true: the laws of physics and chemistry almost demand biology. For example the physics and chemistry of lipids means that protocells will form if we have lipids in conditions that probably existed in the early Earth.

As with everything else, an alkaline hydrothermal vent would more than likely have created enough lipids to be incorporated into the first leaky membrane.

Lane has been promoting single celled life being an emergent property of wet rocky worlds for a decade now. So no, he isn't saying physics and chemistry preclude life, quite the opposite.

Concentrating on just the energy as Nick Lane seems to do in your quote, is missing the wider picture. Luckily reviews of the book suggest that this is not the case.

It isn't the case, though as a biochemist firmly in the "metabolism first" camp he puts energy usage before genes. If he's making it the horse before the cart and I'm emphasizing it, that's just because of the dominance of DNA and genes in the discussion of life, particularly on TV. "Wonders of Life", hosted by a physicist, is still the only program I've seen try to explain the importance of proton gradients.

 

[Generally Rational]

I'm not sure who you're talkinig to to gain your understanding of biology, but they've been fooling you.

You've completely baffled me about how my post could have prompted this.

First, it's most difinitively NOT true that with genes "anything that can happen will happen".

Heard of metaphor? I said nothing about Lane genuinely believing that literally. Should I type out all three of the last paragraphs to allow Lane to defend himself? Even if I do, you'll still jump to conclusions from not having read the rest of the book.

There are several facinating restrictions. The first that springs to mind in any paleontologist is channalization, the tendency for disparity to decrease through time. We see nothing like the diversity of bauplans we saw in the Cambrian in today's world, and the reasons for that are very interesting. There's also the fact that no morphospace is completely filled, which has about as many explanations as there are morphospaces!

Second, energy flow through cells, organisms, and ecosystems is such an integral part of biology that to say biologists don't pay enough attention to it is insane. They obsess over that stuff! EVERY ecosystem analysis focuses on that issue. What do you think trophic levels are?

You're missing the forest for the trees. The emphasis is that no matter how much has changed with life since bacteria and archaea split off from LUCA and since a small group merged to become Eukaryotes, they haven't been able escape the method of energy management that gave rise to them in the first place. The prokaryotes can't get bigger without running into the surface area to volume problem. Eukaryotes only got around it by making use of multiple mitochondria who themselves lowered their overhead by dropping genes that could be given up in the constant environment of the cell.

Next you'll be yawning and telling me this is old news, but I didn't get this from Gould or Dawkins or Coyne or Shubin or PZ Myers or any of the other standbys of the Skeptical community.

Actually, Myers had nice things to say about "Life Ascending".

This sounds like someone in physics who has watched a few NOVA episodes and concludes that they know more about biology than biologists. I may be wrong, and his work may be more in-depth, but that's my sense given the OP's description.

You're right. The winner of the 2015 Biochemical Society Award(1) couldn't possibly know anything about biology. It couldn't be possibly be the fact that I can't post the whole book here and didn't feel right about posting whole paragraphs or the defensiveness of regulars to outsiders.

I despair that when I recommended "Life Ascending" here and at the SGU Forum, nobody responded. When I recommended "Wonders of Life", nobody responded. Looks like people would prefer to jump to conclusions about "The Vital Question" rather than read it. Granted it isn't out in the U.S. until July 20, but people could ASK me questions first, rather than hitting me with a sledgehammer. This after I praised your energy in another thread, because you've done 15000 posts since you joined the month before I did. I've liked the posts I've seen from you, but perhaps I should read more of them to get a more rounded picture.

(1) For 'a sustained and diverse contribution to the molecular life sciences, with a special emphasis on education and/or the public understanding of science'

 

[Generally Rational]

From GR's half-dozen other posts about the book, I gathered that the author is a biophysicist (speculative work on early proton pump mechanisms), seen here grumbling that biologists of other subdisciplines don't pay enough attention to biophysics. While that's probably true, the opposite is also likely to be the case.

What Dinwar said in response to this. Why anybody would think what I've posted is the sum total of the contents of the book, I don't know. Lane defends himself quite well but you have to read the actual papers and books rather than my sentences.

Anybody want me to post links to relevant papers in this thread?

 

[ThunderChunky]

Certainly there are energy limitations on cells and the evolution of life, but there are also genetic limitations. Any comprehensive theory must account for both.

 

[Dinwar]

I had to stop to laugh when you said "the standbys of the Skeptic community". If THAT is where you are getting your understanding of biology, you are doomed to failure. You are right, this IS old news, and IS worth only a yawn. Take a university level biology course or two and you will learn more than from any number of skeptical books.

As for metaphor, sure, I know all about that. Doesn't matter. You are ignoring and dismissing Hugh issues, which directly impact your assessment. You have, for example, given no indication that channalization isn't to blame. We know other metabolic pathways can work (see the hypothesized Titan organisms), and it is likely that a disparity in metabolism occurred in the early Earth. This disparity, if it existed, was culled. Point is, you are talking about organisms in the absence of any real data, so any scenario not precluded by what little info we have is equally valid as any other.

I am not saying the book you have recommended is bad. Your representation of it is horrible, fraught with biases, and displays a lack of understanding of basic biology. I have a sufficiently long reading list; why should I, someone who knows biology and evolutionary theory, bother with this book? Thus far, I have no reason. Okay, they guy's a biochemist. Doesn't mean he knows what he's talking about outside the area of biochemistry. Why should I take his opinion over and above those of paleontologists, who deal daily with alien life? Until you answer those questions clearly, you have failed to convince me, at least to read your book.

That is not a criticism of you, by the way. It is good form in science to tell the other person what it would take to convince them, so that they can more efficiently present their data. I am trying to help you.

 

[Generally Rational]

I had to stop to laugh when you said "the standbys of the Skeptic community". If THAT is where you are getting your understanding of biology, you are doomed to failure. You are right, this IS old news, and IS worth only a yawn. Take a university level biology course or two and you will learn more than from any number of skeptical books.

That's the welcoming attitude that's resulted in my lack of participation in this forum. Fine if you want a clique, but if you want to actually draw more people.....

I suppose I deserve it for having a deliberately provocative title, but after "The First branching of life" garnered no response I began to see how the game is played here.

As for metaphor, sure, I know all about that. Doesn't matter. You are ignoring and dismissing Hugh issues, which directly impact your assessment.

Pot, kettle. Read Lane's books before you tell me I'm the one ignoring hugE issues.

You have, for example, given no indication that channalization isn't to blame.

Channelization is late. It's Cambrian. The book is dedicated to the dawn of life and the complex cell itself.

We know other metabolic pathways can work (see the hypothesized Titan organisms), and it is likely that a disparity in metabolism occurred in the early Earth. This disparity, if it existed, was culled.

You're bringing in hypothesized organisms to defend trashing a discussion of how life started on Earth? How anybody can say they know definitively what is possible elsewhere when they've not even begun to nail down how it happened here....

Point is, you are talking about organisms in the absence of any real data, so any scenario not precluded by what little info we have is equally valid as any other.

That's a postmodernist statement if I've ever read one.

I am not saying the book you have recommended is bad. Your representation of it is horrible, fraught with biases, and displays a lack of understanding of basic biology.

There's an incredibly biased statement.

I have a sufficiently long reading list; why should I, someone who knows biology and evolutionary theory, bother with this book? Thus far, I have no reason.

Because people better than I have lauded his books, but you've managed to miss that? Because if you were approaching this in a mature manner rather than going instantly into attack mode you'd care what that actual content of the book is.

Okay, they guy's a biochemist. Doesn't mean he knows what he's talking about outside the area of biochemistry.

Doesn't mean he doesn't. Remember that postmodern statement about things being "equally valid"?

Why should I take his opinion over and above those of paleontologists, who deal daily with alien life?

Paleontologists? Alien life? Do you mean Astrobiologists? Once again, this is *early*. Unless you're going to bring up the work of paleontologists that work with deep Precambrian life it isn't relevant. While astrobiology might have some value in organizing thoughts, it seems to trying to run before we've even begun to walk.

Until you answer those questions clearly, you have failed to convince me, at least to read your book.

Either you're going to give this line of inquiry a fair shake or you won't. It's not up to me.

That is not a criticism of you, by the way.

Really? I'm not a creationist. The attack, attack, attack response you were showing in those threads is doing more harm than good here.

It is good form in science to tell the other person what it would take to convince them, so that they can more efficiently present their data. I am trying to help you.

Your response so far doesn't make me confident that you wouldn't just move the goalpost.

I'm not a professional at this, I'm just a reader who grew up on the work of another biochemist, Isaac Asimov. I read something I thought would be useful to members in this forum and tried to pass it along. Turns out that there's few if any interested among the people who actually respond, at least in this thread. Perhaps I did some good with the others just reading.

 

[Reality Check]

You missed the point, Generally Rational.
You are asking us to buy and read a book because you find it interesting.
But other posters such as Dinwar and I read your description of the book and see that the book would not be interesting to us. You make the book look like a specialist in a field (biophysics) doing what some specialists do - overemphasis their specialty in a subject covering many specialties. There does not seem to be anything new in it. There may be flaws in it.

When a book on biology contains the sentence "Genes are almost infinitely permissive: anything that can happen will happen." as you quoted, we have to suspect that
* the author is ignorant of biology (unlikely for a biophysicist) or
* the author is dramatizing their position or
* there is more context to the sentence that is missing.

An nitpick: Multiple threads each based on that book hints of a advertising campaign .

 

[Dinwar]

That's the welcoming attitude that's resulted in my lack of participation in this forum. Fine if you want a clique, but if you want to actually draw more people.....

You missed my point entirely. My point is, you're trying to learn advanced biology by looking at popular-press articles written by folks attempting to be deliberately provocative. You're looking in the wrong place, for the wrong reasons, and often to the wrong people. Not a bad thing--certainly better than not learning at all--but you have to admit that your education on the topic, limited by your own admission to "the standbys of the Skeptic community", isn't exactly exhaustive. Furthermore, there's no reason to conclude that the Skeptic community is any better at evaluating biological research than any other organization--it is not a community focused on biological research, and while some biologists are included in that community there's no reason to assume that they'll have a better selection of standard books than anyone else.

Channelization is late. It's Cambrian. The book is dedicated to the dawn of life and the complex cell itself.

Prove it, hot shot. I look forward to the attempt. Honestly--I would love to see some argument showing that channalization is limited to bauplan. It would have implications you cannot imagine for pretty much every field that deals with living things. Given my understanding, channalization should have began LONG before multicellularity, perhaps at the very beginning of life.

You're bringing in hypothesized organisms to defend trashing a discussion of how life started on Earth?

Well, seeing as WE DO NOT KNOW WHAT EARLY LIFE WAS LIKE, hypothetical organisms are all we have to work with. (We have some ideas, but nothing definite.) But again, you missed my point. I'm not trashing any discussion--I'm raising the very relevant point that we cannot assume that modern metabolic pathways were the ones used in the early Earth; we can only say they were the ones that continued. We know other pathways are possible (we may even have found organisms that use one), so it is incumbant upon us to determine whether or not they were present here before we dismiss them. Again, this is basic scholarship.

That's a postmodernist statement if I've ever read one.

It's a rational evaluation of the data. This is, whether you or anyone else likes to believe it or not, a paleontological issue. The data will come from the rock. Modern experiments and studies can tell us what COULD HAVE happened, but paleontological studies are the only way to say what DID happen. Or at least, the only way to define, within the possibility space established by biological studies, the portion utilized by life on Earth. And the thing about paleontology is that it's all complicated by the existence of taphonomy. Various processes strip information from the rock record--and if it's not in the rock record, we don't have it. See Shipman's fantastic work "Life History of a Fossil" for an introduction to the topic.

You find this depressing? Imagine how I find it. Imagine knowing that at best you will ever see through the rocks darkly, that your entire life's work has limits established by nature that you cannot overcome. Still, there's a lot we can do within those limits, and we're always working out ways around them.

Because people better than I have lauded his books, but you've managed to miss that?

Why should I give a rat's furry butt what they laud? This is the Bandwaggon Fallacy, and I see no reason to submit to fallacious reasoning. Before you say "No it isn't, they're experts", let me remind you that I am too. Even the most rabid advocate of consensus science admits that once you reach my level, you look at the data, not who's saying it. I don't care of Steven J. Gould came back from the dead and handed me a book to read--I'd still ask "Why?"

Because if you were approaching this in a mature manner rather than going instantly into attack mode you'd care what that actual content of the book is.

Again, you have given me zero reason TO care. The sum total fo the information you've given me about this book is that there's a guy who advocates looking at energy pathways through cells in determining....something about life? I think? That's not enough.

I'm trying to extract from you some synopsis of the work. What questions does he address? In what manner? Why is this important? None of that is in evidence here.

Doesn't mean he doesn't.

True, but no one should bother wasting their time on someone who MIGHT have something useful to say.

Paleontologists? Alien life? Do you mean Astrobiologists?

We WISH our job was as easy as astrobiologists. And yes, I do mean paleontologsits working in the Hadean and the like--they DO exist. Biogeochemistry is a thing. Besides, paleontologists are the only folks who work with truly alien life--astrobiologists work with possible life forms, and the weirdest things biologists work with are normal compared to, say, the Ediacaran fauna (no, I don't think the guy in Australia has sufficiently evidenced his conclusions to accept them). We also are the only ones who routinely deal with ancient life--and therefore the difficulties inherent in taphonomy. You dismiss me presenting alternative possibilities as me trashing the discussion. In paleontology, asking what may have been stripped from our knowledge via taphonomic processes is one of the first questions you ask. So yeah, asking why I should accept his arguments over those of paleontologists is valid.

A valid response is something along the lines of "He addresses the loss of information about ancient organisms in Chapter 3". Or perhaps "He is dealing with potential early life forms, and includes a few of the best options from abiogenesis research".

The way you presented the book is an attack against biology and paleontology as a whole. While the author may or may not have, you certainly presented the book in the OP and ever since as a slap in the face of every biologist and paleontologist out there. Of course I'm going to be pretty brutal in my critique--science isn't for easily-offended people, and brutal critique is the norm. Attack us en mass and we get even worse. That said, if you carefully examine my statements you'll find that I've never strayed outside the bounds of scientific discourse. My tone, sure, it's hellfire and brimstone--but the content is pure science.

 

[Darwin123]

One of the earliest milestones was between cell and virus.

I would bet that some of our bacteriophages are probably unchanged from the day they first split from the prokaryotes that developed from them. I would bet the first bacteriophage was indistinguishable from plasmids or jumping genes, However, eventually they would develop a capsid and the rest would be history.

Viruses probably separated many times from cells, independently. These would be independent branching events. However, the first bacteriophage that branched off from a bacteria would certainly have altered the course of evolution forever.

The first bacteriophage may have appeared long before the split between prokaryote and archaea. This is my conjecture.

 

[Reality Check]

A nitpick, Generally Rational. The two papers are
Early bioenergetic evolution (10 June 2013)
A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria (August 12, 2014)

Dang good paper is a blog entry referring to the earlier (first in the OP and thus the nitpick) paper which is a description of the "metabolism first (and at smokers)" origin of life hypothesis. PZ Myers is a bit peeved D) that he finished teaching an origin of life unit then found out about this paper from Larry Moran's Sandwalk blog: Metabolism first and the origin of life

Smokers, on the other hand, promote an origin of life scenario that relies on the chemistry surrounding hydrothermal vents on the ocean floor. These environments favor reactions that build up organic molecules from inorganic substrates like hydrogen and carbon dioxide. In this case, the most primitive reactions are simple oxidation-reduction reactions and the most primitive pathways are biosynthesis pathways, not catabolism. This view is often referred to as "metabolism first" [Metabolism First and the Origin of Life].

I'm a big fan of metabolism first and especially the versions promoted by Bill Martin and Nick Lane. I think it's the only reasonable model for the origin of life.

As far as I can see Early bioenergetic evolution (10 June 2013) has only a small bit of relevance to the second paper. The only discussion of membranes I found does not distinguish between archaea and bacteria. The paper is basically a review covering existing work rather than presenting new work. It would be useful as background material for the second paper.

 

[Generally Rational]

One of the earliest milestones was between cell and virus.

I would bet that some of our bacteriophages are probably unchanged from the day they first split from the prokaryotes that developed from them. I would bet the first bacteriophage was indistinguishable from plasmids or jumping genes, However, eventually they would develop a capsid and the rest would be history.

Viruses probably separated many times from cells, independently. These would be independent branching events. However, the first bacteriophage that branched off from a bacteria would certainly have altered the course of evolution forever.

The first bacteriophage may have appeared long before the split between prokaryote and archaea. This is my conjecture.

I agree completely that bacteriophages and probably viruses are descended from the precursors. If bacteria and archaea started in an alkaline hydrothermal vent system, the bacteriophages would have had plenty of time to become proper parasites of those two before they moved out into the wider world. I should have said "free living life" since bacteriophages need the other two for the living portion of their life cycle.

 

[Puppycow]

What would the first lifeform be called? A virus? or something else?

I realize we don't know exactly what the first lifeform was.

Some kind of molecule that was able to make copies of itself?

 

[marplots]

What would the first lifeform be called? A virus? or something else?

I realize we don't know exactly what the first lifeform was.

Some kind of molecule that was able to make copies of itself?

The word "lifeform" gets slippery.

 

[BenBurch]

The word "lifeform" gets slippery.

Which is appropriate when you think about it...

 

[deaman]

Republican LGBT.....?

 

[ThunderChunky]

What would the first lifeform be called? A virus? or something else?

I realize we don't know exactly what the first lifeform was.

Some kind of molecule that was able to make copies of itself?

The field seems to have moved passed the self replicating molecule idea. In the article linked in the First Branching post they propose it is some kind of metabolism driven by pH gradients and that is encapsulated within mineral membranes. Basically biochemistry happening in the rocks of hydrothermal vents. They provide a rationale for how this thing could eventually gain lipid membranes and leave the vents. Others propose lipid-membrane protocells that can grown and divide (but don't necessarily have a metabolism) of their own as the starting point. These would look like a blob of lipids with catalysts and the basic building blocks of life inside.

 

[Generally Rational]

You missed the point, Generally Rational.
You are asking us to buy and read a book because you find it interesting.

Did I say anything about buy? It is possible to request a book at one's local library.

But other posters such as Dinwar and I read your description of the book and see that the book would not be interesting to us.

But interesting enough to trash in the thread without even reading reviews, rather than letting it go and allowing other readers of the thread make up their own mind.

You make the book look like a specialist in a field (biophysics) doing what some specialists do - overemphasis their specialty in a subject covering many specialties.

Which so does not accurately portray Lane's work. I'm not certain how I could correct that when you don't want me to post anymore on the subject and you won't read what professional reviewers of science books have to say about it.

There does not seem to be anything new in it. There may be flaws in it.

You can tell that just from what little I've written?

When a book on biology contains the sentence "Genes are almost infinitely permissive: anything that can happen will happen." as you quoted, we have to suspect that
* the author is ignorant of biology (unlikely for a biophysicist) or
* the author is dramatizing their position or
* there is more context to the sentence that is missing.

He's wrapping up the epilogue of the book, making the final summation to the jury and I didn't think it was my place to type out the last three long paragraphs of the book. So basically the last two.

An nitpick: Multiple threads each based on that book hints of a advertising campaign .

Or someone who tried to get people to read Life Ascending 5 years ago and is trying to get them to read the next one now. I gain absolutely no financial benefit from this whatsoever.

 

[Generally Rational]

A nitpick, Generally Rational. The two papers are
Early bioenergetic evolution (10 June 2013)
A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria (August 12, 2014)

As far as I can see Early bioenergetic evolution (10 June 2013) has only a small bit of relevance to the second paper. The only discussion of membranes I found does not distinguish between archaea and bacteria. The paper is basically a review covering existing work rather than presenting new work. It would be useful as background material for the second paper.

Thank you for that. I thought there was more overlap but I was concentrating in the first paper on section 9 "From Harnessing To Pumping: The Same Leap By Two Prokaryotes".

That said I'm not certain how you can say the book "Vital Question" is completely uninteresting since it is a much expanded version of the Bioenergetics paper in particular for the lay public. Granted, that might not be interesting for a biologist, but do only biologists post about biology here?

BTW another reply of mine is harsher than I wanted. It timed out when I was editing it. I was going to change my reply about specialties to this:

"Which so does not accurately portray Lane's work. I'm not certain how I could correct that short of plagiarizing the book. All my attempts to condense the ideas seem to have failed."

 

[Myriad]

I read the portion of the book that's readable in the Amazon "look inside" feature. That portion is mostly prologue, and does come across as over-simplified (perhaps necessarily) in some regards. I noticed one or two questionable points, such as something to the effect of "how can we do medicine if we don't understand why life is the way it is?" Um, we could accept that life is indeed the way it is and proceed from there. How can we send a space probe to Pluto if we don't understand why gravity works the way it does?

Still, it looks interesting. When I get home I'll see if my library system has a copy.

 

[ThunderChunky]

I read the portion of the book that's readable in the Amazon "look inside" feature. That portion is mostly prologue, and does come across as over-simplified (perhaps necessarily) in some regards. I noticed one or two questionable points, such as something to the effect of "how can we do medicine if we don't understand why life is the way it is?" Um, we could accept that life is indeed the way it is and proceed from there. How can we send a space probe to Pluto if we don't understand why gravity works the way it does?

Still, it looks interesting. When I get home I'll see if my library system has a copy.

Saying the research is relevant to medicine and exobiology is how stuff like this gets funding.

 

[Reality Check]

That said I'm not certain how you can say the book "Vital Question" is completely uninteresting ...

I am not saying that, Generally Rational.
I am saying that your descriptions of the contents of the book suggests that it is "completely uninteresting" in that it is covering well known ground.
Metabolism First has been around for decades.

I am saying that your quotes from the book make it look at least overly simple and maybe factually incorrect.
1 July 2015 Generally Rational: "Genes are almost infinitely permissive: anything that can happen will happen." is wrong.

It is your descriptions that make the book look like a specialist in a field (biophysics) doing what some specialists do - overemphasis their specialty in a subject covering many specialties.

We would have to buy that book or waste our time (and librarian time) asking for it at a library. Either way a waste of money or time judging by your description and quotes.

By getting close to demanding people read books by an author is advertising the books by that author! It does not matter whether "Life Ascending" by Nick Lane or "The Vital Question" by Nick Lane.
The better thing to do is mention the books in one thread each, describe their contents and leave it up to other posters as to whether they want to read the books. Links to reviews are good.

BTW I have read reviews of the book, e.g.
The Vital Question: Why Is Life the Way It Is? review – back to biological basics
The Vital Question: Why Is Life the Way It Is? by Nick Lane, review: 'astonishing and intriguing'
If I had no knowledge of abiogenesis then the book would be interesting to me as a primer to one specific theory of abiogenesis.

 

[Generally Rational]

[First I was going to let most of your post go unanswered out of concern for brevity, but then wondered if you'd think I'd just blown it off without giving it serious thought.]

suggests that it is "completely uninteresting" in that it is covering well known ground.
Metabolism First has been around for decades.

Well known to whom? I see plenty of "gene firsters" still posting as if energy manipulation was a later affectation rather than a fundamental part of life. If the biological community consensus has shifted to metabolism first there's been a poor job of communicating that.

I am saying that your quotes from the book make it look at least overly simple and maybe factually incorrect.

If we stop with those single quotes, that's certainly true. I have a brevity problem. I had hoped people would ask me to elaborate.

"Genes are almost infinitely permissive: anything that can happen will happen." is wrong.

Here's the entire paragraph (apologies for any missed misspellings):

"Energy is far less forgiving than genes. Look around you. This wonderful world reflects the power of mutations and recombination, genetic change - the basis for natural selection. You share some of your genes with the tree through the window, but you and that tree parted company very early in eukaryotic evolution, 1.5 billion years ago, each following a different course permitted by different genes, the product of mutations, recombination, and natural selection. You run around, and I hop still climb trees occasionally; they bend gently in the breeze and convert the air into more trees, the magic trick to end them all. All those differences are written in the genes, genes that derive from your common ancestor but have now mostly diverged beyond recognition. All those changes were permitted, selected, in the long course of evolution. Genes are almost infinitely permissive: anything that can happen will happen."

He then goes about how the mitochondria in you and the tree have been passed down as well dealing with the energy consumed. Want me to type out those paragraphs, too?

It is your descriptions that make the book look like a specialist in a field (biophysics) doing what some specialists do - overemphasis their specialty in a subject covering many specialties.

Funny how limited information can give that impression.

We would have to buy that book or waste our time (and librarian time) asking for it at a library. Either way a waste of money or time judging by your description and quotes.

I've never had a problem convincing the library systems around here to buy good books. Three of them have ordered the book unprompted by me. Your offense on the part of the librarian is misplaced.

By getting close to demanding people read books by an author is advertising the books by that author! It does not matter whether "Life Ascending" by Nick Lane or "The Vital Question" by Nick Lane.

I'm not in a position to demand anything. It's in the eye of the beholder to see my enthusiastic recommendations as such. Is the last line of my post in the "The best science and medicine books" sticky thread bad? "I am probably doing the book a disservice with this post. Read it anyway. "

The better thing to do is mention the books in one thread each, describe their contents and leave it up to other posters as to whether they want to read the books. Links to reviews are good.

Good advice, but surprisingly not done but once I think in the sticky thread. Plenty of links to Amazon though.

BTW I have read reviews of the book, e.g.

Good reviews to link to. Thanks.

If I had no knowledge of abiogenesis then the book would be interesting to me as a primer to one specific theory of abiogenesis.

To bookend my point on metabolism first at the top: not all theories on abiogenesis hone to the known facts equally well. There is only one currently that makes the proton gradients that power bacteria and archaea and therefore eukaryotes, a driving force towards the origin of life rather than a curious later adaptation.

 

[marplots]

To bookend my point on metabolism first at the top: not all theories on abiogenesis hone to the known facts equally well. There is only one currently that makes the proton gradients that power bacteria and archaea and therefore eukaryotes, a driving force towards the origin of life rather than a curious later adaptation.

This is the part that confuses me. I understand that asymmetry has to be in the picture somewhere, but why is proton gradient selected out as the critical one? Couldn't we just as well say that temperature, viscosity, oxygen concentration, or any other gradient would be the important thing?

I have in mind (without any real justification) a kind of electro-chemical bias derived from our preferred ("that's the way my teachers taught it") category-making for chemical reactions.

 

[Dinwar]

This is the part that confuses me. I understand that asymmetry has to be in the picture somewhere, but why is proton gradient selected out as the critical one? Couldn't we just as well say that temperature, viscosity, oxygen concentration, or any other gradient would be the important thing?

Fundamentally, the problem all this sort of thing runs into--and the reason I see no reason to take them seriously right now--is that they are limited to life as we know it. What that means is that the error of assuming what we see is the full extent of possible options is extremely difficult to avoid, and many simply fail to do so.

Basically, until we find some life-form that operates differently from our own, or we find enough other types of life-forms to form a general view of life as such, we're speculating. Sorry, but extrapolation from the limited possibility space we've explored cannot be termed otherwise.

 

[Generally Rational]

This is the part that confuses me. I understand that asymmetry has to be in the picture somewhere, but why is proton gradient selected out as the critical one? Couldn't we just as well say that temperature, viscosity, oxygen concentration, or any other gradient would be the important thing?

This is the part that confuses me as well because I don't know how to answer without appearing insulting. Most of it isn't even you on your own but this apocalyptic attachment to postmodernism these days where everything is an intellectual abstraction that we choose among ourselves to agree on, with no real world objective basis to use for rational choices. Most of the problems in the political sphere seem to be because people have rejected Daniel Patrick Moynihan and said that they are damn well entitled to their own facts.

We didn't select proton(1) gradients as the critical asymmetry, life did. No energy, no life. Bacteria and archaea without a gradient are either dead or in an inert stage. They aren't engaging in an active part of their life. Almost all eukaryotes have mitochondria churning away for the collective good of the cell. I haven't personally tracked down the exceptions but they seem to mostly be parasites and the rest and the parasites still had functional mitochondria at one point giving them time to develop other barely sufficient ATP generation techniques. Just claiming any other gradient is just as good as another isn't science. It has no connection with how we know life works on planet Earth now among the descendants of those original lifeforms.

I have in mind (without any real justification) a kind of electro-chemical bias derived from our preferred ("that's the way my teachers taught it") category-making for chemical reactions.

Good thing you said without any real justification. Before I had all the real facts laid out before me, I thought the massive early tides could have made billions of tidal petri dishes for trillions of experiments overtime. Lane knocks that down just fine. Part of a paragraph about the dilution problem:
"The only way out of this impasse is to concentrate the seawater somehow, and this has been the mainstay of prebiotic chemistry for a generation. Either freezing or evaporating to dryness could potentially increase the concentration of organics, but these are drastic methods, hardly congruent with the physically stable state that is a defining feature of all living cells." Living cells may exploit disequilibrium, they are not themselves unstable.

Somebody in this thread maintains that ignorance is strength. Because we can't know for a certainty which proposed origin of life is the right one, they are all equally valid. Because we can't prove a negative and say that non water and carbon based life is impossible, than any types of life is equally possible(2). This view apparently is okay, but genes being permissible is not.


(1) Some life uses sodium gradients, but the paper Lane and Martin makes adopting a sodium gradient alternative a key part in bacteria and archaea leaving the vent, and the different ways they did that the key part in the split between them.

(2) Never mind that carbon dioxide and water are two of the most common two element molecules in the universe and ultramafic minerals damn common as well.

 

[Reality Check]

Well known to whom?

Well known to people who read or read about abiogenesis.
Well known to people who can use Google even .

"Energy is far less forgiving than genes. Look around you. This wonderful world reflects the power of mutations and recombination, genetic change - the basis for natural selection. You share some of your genes with the tree through the window, but you and that tree parted company very early in eukaryotic evolution, 1.5 billion years ago, each following a different course permitted by different genes, the product of mutations, recombination, and natural selection. You run around, and I hop still climb trees occasionally; they bend gently in the breeze and convert the air into more trees, the magic trick to end them all. All those differences are written in the genes, genes that derive from your common ancestor but have now mostly diverged beyond recognition. All those changes were permitted, selected, in the long course of evolution. Genes are almost infinitely permissive: anything that can happen will happen."

This expanded quote still does not have any evidence that genes are "almost infinitely permissive". But then it may just be rhetoric in a popular science book - not actual science.
Otherwise maybe you can concentrate on citing his evidence for his assertion?

Funny how expanded information still gives the impression that we have a biophysicist specializing in how energy flows in cells thinking that his specialty solves a problem!

 

[Generally Rational]

Well known to people who read or read about abiogenesis.
Well known to people who can use Google even .

Noticed you cut off at the question mark. I told you precisely the sort of people who act as if it isn't well known to them.

This expanded quote still does not have any evidence that genes are "almost infinitely permissive". But then it may just be rhetoric in a popular science book - not actual science.

I've already provided links to relevant 'actual science' papers published in reputable 'actual science' publications. Other relevant papers can be found by 'people who can use Google even'.

Otherwise maybe you can concentrate on citing his evidence for his assertion?

You are still fixated on one sentence in one paragraph at the end of the epilogue of a 300+ page book. You've given no indication whatsoever what you'd consider 'evidence' for a rhetorical assertion.

Funny how expanded information still gives the impression that we have a biophysicist specializing in how energy flows in cells thinking that his specialty solves a problem!

By the way, he's a biochemist and a reader at UCL, which I gather is a full professor without a chair, but I don't really know the British university system.

From this interview:

http://www.radionz.co.nz/national/programmes/thiswayup/20150704

He would agree that he's bringing his day job to this research but then so does everybody else.

As Adam Rutherford says, he's asking the right questions, as is the rest of the 'metabolism first' community and what I'd call the proto-mitochondria first community. The rest of you haven't raised good evidence to support the open hostility to idea that a constant need for energy has been undervalued in this research. In the interview he mentions how it would take four lightning strikes every second per square kilometer to even begin to provide enough energy, and life doesn't get its energy from lightning. It does get it from an excess supply of protons on one side of a membrane.

Funny how I only get the impression objections are being raised as excuses for not exposing yourself to the actual arguments as he actually puts them. If you want the whole book download it illegally yourself. I've been seeing the digital version show up in search results. Until you give some sort of indication what you want I'm not going to just keep typing in whole pages for you to raise objections to. Nor am I going to try to condense it either since you've all convinced me I can't do that to your satisfaction.

 

[Reality Check]

Noticed you cut off at the question mark.

Ok:

Well known to whom? I see plenty of "gene firsters" still posting as if energy manipulation was a later affectation rather than a fundamental part of life.

Well known to people who read about abiogenesis despite your personal opinion about posters in forums. The fact that people support one model does not mean that they do not know about other models.

Well known to people who can use Google. despite your personal opinion about posters in forums. because they can read and so will find article about many abiogenesis models.
The first result will probably be Abiogenesis which lists many models .
ETA: Another result Metabolism First and the Origin of Life

There are several competing hypotheses about the origin of life. Most people know about the Primordial Soup scenario; that's the one where complex organic molecules are created by spontaneous chemical reactions. Over time these complex molecules, such as amino acids and nucleotides, accumulate in a warm little pond and eventually they come together to form proteins and nucleic acids.

The RNA World scenario is similar except that nucleic acids (RNA) are thought to form before proteins. For a while, RNA molecules are the main catalysts in the primordial soup. Later on, proteins take over some of the catalytic roles. One of the problems with the RNA world hypothesis is that you have to have a reasonable concentration of nucleotides before the process can begin.

The third hypothesis is called Metabolism First. In this scheme, the first reactions involve spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. Pathways leading to the synthesis of simple organic molecules might be promoted by natural catalysts such as minerals and porous surfaces in rocks. The point is that the origin of life is triggered by the accumulation of very simple organic molecules in thermodynamically favorable circumstances.
Simple organic molecules can then be combined in various ways that result in simple amino acids, lipids, etc. These, in turn, could act as catalysts for the formation of more organic molecules. This is the beginning of metabolism.

You need to read my question again, Generally Rational:

This expanded quote still does not have any evidence that genes are "almost infinitely permissive". But then it may just be rhetoric in a popular science book - not actual science.
Otherwise maybe you can concentrate on citing his evidence for his assertion?

That is a question about Lane's evidence to support Lane's assertion. Easily answered by listing it or acknowledging that he supplies no such evidence.

But now we have a claim by you!
Generally Rational: Can you list your citations in this thread that show that genes are "almost infinitely permissive"?

BTW, it is irrelevant that Nick Lane (his web site) is a biochemist and a reader at UCL. The implication of argument from authority does not make Lane's book correct.

 

[ThunderChunky]

In the interview he mentions how it would take four lightning strikes every second per square kilometer to even begin to provide enough energy, and life doesn't get its energy from lightning. It does get it from an excess supply of protons on one side of a membrane.

I don't think anyone actually thinks life acquires it's energy from lightning. At most, I've seen it put forth as one of many potential examples for how certain molecules could form that would be useful to life. Is there actually any known life form that derives it's energy from environmental proton gradients or even uses them to drive some chemistry?

 

[Generally Rational]

Well known to people who read about abiogenesis despite your personal opinion about posters in forums. The fact that people support one model does not mean that they do not know about other models.

Well known to people who can use Google. despite your personal opinion about posters in forums. because they can read and so will find article about many abiogenesis models.

You're deliberately conflating to score points. I know perfectly well that all those posters know about the existence of other abiogenesis models. I know they may know the general gist of those models.

What all the other models I've read seem to ignore is the laws of thermodynamics and how everything has to obey them all of the time one way or another. I'm saying that anybody who still thinks life is somehow magical and can ignore the laws is hiding from inconvenient facts.

That is a question about Lane's evidence to support Lane's assertion.

What assertion? The real assertion of the book is that bacteria and archaea didn't get big like eukaryotes because of the cube square problems of getting your energy from a proton gradient across a membrane and having to provide on the spot management of the respiratory chain maintaining the gradient. Only when they merged did the resulting organism break free of that restriction by having multiple internal power systems without the overhead. Most of the differences between eukaryotes and their progenitors stem from the need to get two genomes to work in concert, starting at the beginning. How did bacteria and archaea find themselves in this morphological (but NOT biochemical) dead end by getting their energy from proton gradients? Because they were born in an alkaline hydrothermal vent. Why are there two ancient lines? Because there was a binary 'choice' in how to start active pumping of protons. On the latter, I've already written a post that's been merged into this thread (by somebody else).

Easily answered by listing it or acknowledging that he supplies no such evidence.

Oh, he supplies plenty of evidence for the assertions I've listed above, however badly I've listed them.

But now we have a claim by you!

What claim?

Can you list your citations in this thread that show that genes are "almost infinitely permissive"?

Oh, the fixation on 'infinitely', for which 'almost' is an insufficient modifier. Fine, it's a rhetorical flourish. I think I admitted that a few posts back. Your fixation on it says much more about you than the contents of the rest of the book.

BTW, it is irrelevant that Nick Lane (his web site) is a biochemist and a reader at UCL.

It is when you call him a biophysicist.

The implication of argument from authority does not make Lane's book correct.

Never said it did. I'm aware of the list of logical fallacies.

The book doesn't rely solely on his work or his immediate colleagues. The bibliography stretches from page 306 to 333. I suppose you'll question the authority of every paper listed.

Yet, I get the feeling that the primordial soup and its variants are supported solely on the standing of Darwin and Haldane's speculations and Millers single experiment just because it has been around so long. Never mind that the soup is inert.

Still, you keep acting like I am Nick Lane and that my posts here are his arguments in total. I'm just somebody who read Life Ascending and gave up the odd notions I'd had before because I had better facts presented to me.