"There is no two-word summary for the processes that go on in evolution" - Hate Mail

MY FAMILY affairs are at a critical point right now so this is being typed hastily and with transcription done on the fly.  The transcription is taken from the masterful lecture of James Shaprio posted here recently, What DNA Teaches About Evolution, given as the Linus Pauling Memorial Lecture 2012-13.  I would love to transcribe the whole thing and go over it, it is one of the best lectures on these topics I've ever listened to, finding more honesty and nuance than most lecturers present.

In the unusually well structured lecture, after a short exposition about the two formerly known types of cells, the eukaryotic cells, cells with a well-defined nucleolus within a membrane, such as our bodies and amoebas are made of and prokaryotic cells without a well defined nucleus and that there is also the archaea cell type discovered about half a century ago.  Dr. James Shapiro said:

Carl (Woese) set out to examine relationships (among cells) by looking at the ribosomal RNA.  And when he did he discovered, at the end of the 1970s, less than forty years ago, was that there are not two kinds of cells, there are actually three kinds of cells.  They found that bacteria which produce methane and live in certain extreme environments have ribosomes that are as different from those of (prokaryotic) bacteria and eukaryotes as bacteria and eukaryotes are from each other. So less than forty years ago we found out that our view of life was inadequate and there are actually three kinds of cells that make up life.  And that discovery has a lot of very important implications.  Among them is the implication that we really don't know what the early history of life was like. There might have been dozens, maybe hundreds or thousands of different kinds of cells which went extinct before they could leave any record that we can discern in fossils and in rocks today. And we just don't know how many types of cells there were and whether there was one single type of cell at the very beginning, which is what many people believe, or, in fact, there were multiple cell types. 

But this was a very important discovery and this put the study of relationships between organisms on a very firm molecular, empirical basis and it was hard to argue with this and identify organisms by extracting their RNA and looking at them. People use this today to go out and do what is called "meta-genomics,"  that is you just take a sample from the environment, this has been done in the oceans, in soils, on the human body, in different places on the human body, in our intestines, recently in the upper atmosphere and just take all of the DNA and ask what kinds of ribosomal DNAs are there. And in this way we can describe the organisms that are present even though they haven't been cultured in a particular environment.  And we've learned a lot about that, a lot that is relevant to our own health because we've learned a lot about the microorganisms that live with us and affect our health.  But one of the things we've learned that's very important and very humbling is that we've cultured in the laboratory about one percent of all the organisms that are present in nature. So, most of life is there, we can detect it but it's relatively unknown to us and we've got to do a lot of work to learn more about it.

I will point out to you what he says about very early life on Earth not being known to us BECAUSE THERE IS NO PHYSICAL EVIDENCE ON WHICH TO BASE THAT KNOWLEDGE. He didn't say it but if there was one kind of cell near the beginning of life as might be reasonable to surmise, it could have been of such a different type that we could never know what it was like.  As our ancient mammal and pre-mammal ancestors from much more recent epochs, so many of which are extinct as a species and of which we have no trace, so may that cell type. If there was one original organism from which all life now is evolved, that evolution would have included into those different cell types.  All current cells which these types are known from are almost certainly a product of an evolution far longer and far less in evidence. Modern single and multi-cellular animals are as evolved as we are, the relationship of their physiology to the earliest life on Earth is unknowable.

Considering that unknowable early life would have to be what was the basis of all later life which is available to us to study in fossils - though no where near even a hundredth of one-percent of the total of life before the rise of modern biology is actually known to us.  If not even one-percent of life on Earth now, when it is available for study, is known to science today, then that would be true for the entire period of life on Earth going back more than three billion years ago, so what is not known as opposed to what is known is an enormous though unknowable multiple of what is known today.  The farther back you go, the less fossil and other evidence is likely to have survived, very possibly that's true also of the resolvable genetic information these scientists can interpret to tell us what we can't see directly.

The idea that there is possibly even a general understanding of the evolution of life on Earth in hand is as absurd as the rantings of that wacky online flat-Earther, the parodying of whom I posted last week.  Wrong as she is, though, at least she is talking out of her own limited, uninformed and badly reasoned observation.  Which is evidence of a sort. Though you can certainly pretend evidence of the nature of early life is in hand and teach science at any modern university, today, the fact is it isn't.  Anyone who believes that natural selection is the sole mechanism of the evolution of species or even an important one does that without admitting that's what they're doing.  As James Shapiro also said, "It's not reducible to simple formulas.  There is no two-word summary for the processes that go on in evolution. We can't use just a phrase and say we've explained such an immense and important set of events that have occurred over such a long period of time."   I'm sure he knew that the most well known of those possible two-word phrases, "natural selection" would have come to many minds, though "genetic-drift," "Lamarckian evolution" "Mendelian genetics" or other such explanations of evolution would certainly have to be included in insufficient explanatory ideas.

I hope someday to get around to transcribing the subsequent parts of his lecture, especially the next section about the work of those like Lynn Margulis who figured out that eukaryotic cells are evolved from symbiotic combinations of previous independent cell types, one of the most important refutations (as I prefer to think of it) or modifications of the old neo-Darwinian synthesis.  The complexities of that certainly don't fit very well in to that just-so tale as I learned it in biology classes in high school and in college.

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I can't not talk about that without going through one of the questions and the brilliant answer given to a typical materialist ideological qualm about consciousness where only automatic, deterministic chemistry is supposed to operate. I will note, first that during just that section a drastic change in the sound quality of the video happened which makes coming up with a near verbatim transcript impossible with my equipment.  And I'll also point out that James Shaprio's masterful management of including both hard science and far more philosophical handling of the consequences of our own cognitive equipment and language  as it must mitigate what we find out and how we find that out which is certainly not good news for the old-fashioned automatic materialist causative ideology which is dominant in science and the general culture of 20th century style modernism.  I think James Shapiro must be one of the most brilliant and honest scientists I've ever encountered.

Questioner: About halfway through your lecture, where the use of the term "cells know"?

James Shapiro:  Well, I was quoting Barbara McClintock but. . .

Questioner:  Ok, but just the term, you know, I guess I have trouble with the idea of a cell being so self-directed.  I mean, fundamentally, it's all bio-chemistry.  That they would know in a cognitive sort of way, because that's kind of like I understand it.

James Shapiro: Well, "cognitive" is the word I like to use and cells are always sensing what's going on inside of them and outside of them and responding to that sensory information and they do it pretty well. I mean cell division is a pretty complicated process, more complex than any human manufacturing enterprise. Millions, hundreds of millions, billions of events have to be coordinated sometimes very quickly. E coli replicates DNA two thousand base-pairs a second and makes less than one in a billion mistakes because it has sequential proof-reading mechanisms which are based on monitoring the DNA and picking up those errors and directing them. So this is a form of cognitive behavior and I know we're taught not to anthropomorphize, although, I do it all the time, it's the only way I can understand what my bacteria are experiencing.

I will break in here to point out a post I once did in response to reading a casual statement by the geneticist Richard Lewontin about the experience of bacteria, in which he asserted that for a bacteria Brownian motions were far more relevant and for their experience gravity is non-existent, which makes sense but my question was how can we know what bacteria experience? Though even as sophisticated a materialist as Lewontin had to anthropomorphize a bacterium so as to come up with an understanding of it, which, in fact, any scientist of any kind has to do when trying to explain any animal's behavior because they are the only ones who could explain anything about their experience, and they don't. Even if they could explain it, for us to understand it they would have to bridge the chasm from their scale of experience to ours for us to understand them.  Even with the self-reporting of other humans in a language we share with them, you have no possible way to check to see if they're accurate about their own experience or if they are misrepresenting it in some way.

It is one of the biggest lies of materialist-scientism that that kind of interpretation of nature as if it is conscious doesn't lie at the very base or at least in the background of everything scientists discover and report. It is impossible for us to filter how we think out of our thinking apart from some very crude, very general, very unevenly and unreliably applied rules of thumb to get rid of only some of the most obvious of sources of distorting bias.  It is, from a small to complete extent the way we comprehend even the most inanimate of objects. I think Shapiro's admission that he does that about even the enormously complex organisms that bacteria are is shockingly honest.  It also goes pretty close to the whole way to answer why such ideological scientists as Jerry Coyne and his gang go totally nuts over the science he articulates.  It is a violation of another of those ways that humans think, out of our ideological preferences.  Admitting that you inevitably think the way you do is denied by that ideology.

And I think what McClintock is trying to tell us is we have to realize both the cell is a sensory, a sentient entity and it's using that sentience for its own needs and requirements and functions.  And sometimes that involves changing its genetics, changing its DNA.  

Breaking in again I'll point out that given the enormous survival and successful reproductive power given to perception, understanding and acting in accord with those which is an intrinsic part of Darwinism, which are taken as basic to the conception of natural selection, it's remarkable how that claim, especially among such Darwinian fundamentalists as Coyne, Dawkins, and especially all true believers in "smart genes" it's astonishing how they are the first to claim that all of life other than human beings and maybe a few other "highly evolved" multicellular creatures, probably by a huge percent the largest number of species that have ever existed, are unconscious. 

Given the claim for the Darwinian efficacity of not only consciousness but also the necessity of "superior" intelligence in human terms in escaping being selected out of the future by nature, you have to wonder how they explain the persistence of organisms, single cell as well as multicellular ones, if they aren't not only conscious but highly cognitive.  How do they explain that for not only the large majority of the history of life on Earth that signal aspect of Darwinian selection was absent from the entire epoch of life on Earth, in fact, the extreme fundamentalists of that faith hold that it would have to be irrelevant to the evolution of almost every species of life that has ever existed on Earth.   Yet all of those species survived Darwin's mechanism of culling.

When you consider what James Shapiro said about the working of the cell being more complex than the most complex human manufacturing enterprise, it's a lot harder for a materialist, Darwinian fundamentalist to explain why we shouldn't interpret that as consciousness and cognition. It's certainly more difficult for the school of the most extreme Darwinism such as Daniel Dennett became, he attributed natural selection to aspects of the univere outside of living organisms, who also is an eliminative reductionist denying the reality of consciousness even to human beings.  I would like to know from him how something which isn't real could, in the classical exposition of natural selection, then be a factor relevant to the working of natural selection.  His Darwinism might find itself in the embarrassing situation of being a Darwinism with no use for Darwin's thinking.

But, there's a whole school of study, one of the pioneers is in Seattle at the Fred Hutchinson Cancer Center, Lee Hartwell who got the Nobel Prize I think about seven or eight years ago for studying control of how the cell cycle progresses and you may know about that. And the cell cycle, the eukaryotic cell cycle involves lots of different things that have to happen and they all have to happen in a coordinated way.  And the cell is monitoring how all of those things are happening. The operation of the cell is being monitored, it sends out signals that says "stop, don't go through cell division." That's how we finished our [unintelligible] of DNA.[unintelligible]  If a chromosome doesn't line up in the right way cell division cannot occur because a signal is sent out that prevents it.  These are checkpoints, so they're based upon sensory, internal sensory information, I'm not talking about metabolic regulation or something that involves external sensing or morphogenesis which involves getting signals from other cells. There is all of this information coming in from other cells and its very common language now to talk about a cell making this decision or that decision. Sometimes cells decide to undergo cell death.  And that's conditioned by what cells find in the environment. A tumor necrosis factor. . .

I will leave it to you to try to hear more of the impressive reasoning BASED ON PHYSICAL EVIDENCE and some very impressive science that leads one of the finest biologists of our time to say what he does. His point that "anthropomorphizing" is essential to coming to an understanding of what's going on within and among cells, either independent organisms such as bacteria or cells within multi-cellular organisms, to understand what these scientists see as cognitive and sensory activity within them is certainly as central to that science as the just-so stories that, in fact, ALL OF EVOLUTIONARY LORE IS FOUNDED ON far more directly that than the mathematical analysis of subatomic particles. As I recently pointed out the entire theory of natural selection is based on telling stories about not only single organisms we imagine in the lost past but stories about their parents and children for many, many generations.  Only what James Shapiro is narrating is based on exactly what the theory of natural selection will never have, actual close, careful, rigorous direct observation and measurement and analysis of actual organisms and cells which are available.