Kudos to you for refusing to be intimidated by name-calling, shaming, etc. It would seem we are agreed that science should be allowed to explore and speak for itself.
I read the article you linked at Sott.net. The title is catchy: “Why Darwin was wrong…” which I bet gets this article lots of hits. It starts off with a simple and true enough description of the tree concept. It goes on to suggest that the discovery of DNA, and then subsequent discoveries of how much HGT (Horizontal Gene Transfer) takes place have all made a big mess of the neat tree. The accuracy of their claims in that regard is best left to others here to evaluate. But what still caught my attention is that all the fuss addressed by this article seems to be confined to the eukaryotic / prokaryotic (i.e. ‘simple and early’) levels of life. But then I encountered this paragraph which speaks to my concern:
Hang on, you may be thinking. Microbes might be swapping genes left, right and centre, what does that matter? Surely the stuff we care about - animals and plants - can still be accurately represented by a tree, so what’s the problem?
Well, for a start, biology is the science of life, and to a first approximation life is unicellular. Microbes have been living on Earth for at least 3.8 billion years; multicellular organisms didn’t appear until about 630 million years ago. Even today bacteria, archaea and unicellular eukaryotes make up at least 90 per cent of all known species, and by sheer weight of numbers almost all of the living things on Earth are microbes. It would be perverse to claim that the evolution of life on Earth resembles a tree just because multicellular life evolved that way. “If there is a tree of life, it’s a small anomalous structure growing out of the web of life,” says John Dupré, a philosopher of biology at the University of Exeter, UK.
Okay – sure. If we go by linear time span, multi-cellular life is only a late-comer in the process and the bulk of life history on earth would only be observable under a microscope. And even today in terms of biomass, all the multicellular life, humans (and throw in all the animals!) are outweighed by the prokaryotes. Nothing new in any of that.
So my original simplistic concern about all this being relegated to one little singular “abiogenesis event” is given some proper perspective: it’s a billions of years long, messy, and (if the article is correct --which I’m provisionally open to accepting): little understood affair. So what? The “little bit” that interested Darwin and still captures much of our interest today is that branching out of life when it really started to get interesting. Isn’t most of the hoopla about the tree analogy (or bush or whatever people want to call it) forged from all the interesting stuff of the last few hundred millions of years?
So I read on to see if the authors would address this. Here is what they had to say (in their very next paragraph).
More fundamentally, recent research suggests that the evolution of animals and plants isn’t exactly tree-like either. “There are problems even in that little corner,” says Dupré. Having uprooted the tree of unicellular life, biologists are now taking their axes to the remaining branches.
Notice how the rhetoric changed here. Now instead of the rhetoric of "Darwin being wrong, or the whole tree being a mess or needing to be uprooted entirely; we hear instead: “There are problems …”. What? What happened to everything being a mess and not making any sense? Surely our rhetoricians aren’t falling down on the job here are they? Only a few problems? I was eager to see where they would go with this … and read on to see this paragraph.
Nobody is arguing - yet - that the tree concept has outlived its usefulness in animals and plants. While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another - a tree of 51 per cent, maybe. In that respect, Darwin’s vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him.
Did you miss that paragraph, Ashwin? This is from the article that you provided! It becomes apparent to me why you and so many others double down and focus so hard on the simple unicellular life (as dominant as it is in both time and mass). It is the only large canopy of refuge still available for those who want to hide behind problems and incomplete understandings. Not that they can’t also find many such remaining challenges in more recent evolutionary narratives too, but that picture is much more filled in (blurry as it still may be at some spots.) But the fact remains, if I see a photograph of the upper portion of a tree, I will recognize it for what it is regardless of the missing trunk that I can’t see because it’s not in my field of view. It could be a ten-thousand mile long trunk (or something else – not a trunk at all) for all I know. But what I do know is the bit of photo that is in view. And that’s the challenge you have to answer. It has problems – sure. But not near as many scientific problems as any competing narratives would create.
I’ll let the article have the last word in this conciliatory paragraph near the end of the article:
Even so, it is clear that the Darwinian tree is no longer an adequate description of how evolution in general works. “If you don’t have a tree of life, what does it mean for evolutionary biology?” asks Bapteste. “At first it’s very scary… but in the past couple of years people have begun to free their minds.” Both he and Doolittle are at pains to stress that downgrading the tree of life doesn’t mean that the theory of evolution is wrong - just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not. “We should relax a bit on this,” says Doolittle. “We understand evolution pretty well - it’s just that it is more complex than Darwin imagined. The tree isn’t the only pattern.”