Friday, December 21, 2018

This year's Seasons Groanings....er, Greetings

As is my seasonal wont, herewith I will: this year's Christmas Groanings...er, Greetings. . . . . 
Have a great Holiday!



HOW DO I LURE THEE?  LET ME COUNT THE WAYS!
How do I lure thee? 23 the ways!
I lure thee to the depth and breadth and hype
My sales can reach, with feeling out of sight:
Fear the ends of being and ideas grim!
I lure thee to the level of every gene’s
Most coding dire: by spin and detail-light 
I lure not freely, as men strive for right: 
I lure thee puerilely, as thee turn to promise:
I lure thee with your passions put to use--
In thy old genes, and thus thy children’s fate.
I lure thee with a lust I scheme as love,
With my lost sense. I lure thee with the breath,
Smiles, tears, of all thy life; and, if genes cause,
I shall but lose thy business after death.

(After Elizabeth Barrett Browning (1806-61), Sonnet 43)





GRANTS RUSH YOU MONEY, GENTLEMEN
Grants rush you money, Gentlemen,
Let nothing you dismay,
For Genes comprise our savior:
Omics have borne this Day!
To save poor souls from Teaching's power,
Which long time were grantless strays,
Which brings tidings of funding and joy--funding and joy!
Oh, tidings of funding and joy!

(From traditional carol God rest ye merry, gentlemen; source unknown)




Image result for christmas wreath


'OMICS, TADA!   
‘Omics, tada!  to me it’s been so wonderful
‘Omics, tada! to me it’s been so good.
No trick could be so subtle and unprovable,
‘Omics, tada! For my grants always good!

(After Eddie Fisher’s classic hit record Oh, my Papa)





SAFE CRISPR'S WAY

Now surgeon’s cloak has covered all:
Searing the brain with traits so fell
Forget now the pledge we made in May
We were to win in safe CRISPR’s Way.
Oh what made allure
go astray:

We were to mend it on CRISPR's Day
Now the red blood has crossed our stars
Robbed our feeling of “Hip!”s and “Hurrah!”s
Let not your law turn wintery too
Icy as the seasons do
Now all the august b’liefs are shred
High hope's asleep in misled bed
Truth’s cold winds have blown my hypes away
And left me forlorn on sad CRISPR’s Day

(Modified from: see Amazing Blondel Evensong album, St Crispin's Day)


Thursday, December 20, 2018

Mr Darwin's new science

In his recent, marvelous must-read book, Naturalists in Paradise, about the major explorers of the Amazon (Wallace, Bates, and Spruce), John Hemming quotes Alfred Wallace lauding Darwin's Origin of Species in a letter to fellow explorer Henry Bates, saying that "Mr. Darwin has created a new science and a new philosophy."

I am no historian of science by any means, but I think that there is substance in this grand characterization.  Prior to Darwin--taking him as representative and perhaps the most explicit spokesperson for the view--western science had viewed life as the result of one or more divine creation events.  The inanimate, physical universe was also created 'In the beginning', but as a law-like place.  At least, by Galileo and Newton and others, it had come formally to be seen as following universal mathematical principles.  The key, in my view, is the 'universal' aspect of this view of existence.

Later, with various scientists leading up to them, Darwin, Wallace and a few others saw life itself as also having arisen at some 'beginning', but a natural one, and as a process, having diversified thereafter to what is here today.  That process has come to be called evolution.  The idea from Darwin's time to now, with no evidence of serious challenge, as he said, all life today has descended from some beginning in 'a few forms or into one' following universal 'laws acting all around us'.  In asserting his view, in terms of laws, Darwin reflected his essentially explicit Newtonian viewpoint.

These 'laws' were, as specified by Darwin in the elegant last paragraph in his Origin of Species:

  1. Growth with Reproduction
  2. Inheritance
  3. Variability 'from the indirect and direct action of the external conditions of life, and from use and disuse'
  4. Resource-limited rates of increase leading to a struggle for life
  5. Natural Selection, which led to divergence of Character and Extinction of less improved forms.

I often note my view that Darwin was a product of his times, that is, believing in 'laws' of Nature and a kind of determinism in evolution, and a poor sense of probabilism.  As I note in some recent posts, I think he held this view, expressed clearly in terms of barnacles, but I wonder what he would have said about primates and humans in particular, as recently mused about here.

We're now in the world of probabilism in science, with fundamental probabilistic notions (mutation, drift, quantum mechanics, and so on).  Darwin would certainly have understood the ideas, but I wonder what his view of the probabilistic aspects would be.  That they were just a nuisance on the 'real' selective signal?  That they challenged the idea of precise adaptation?  How would they have affected his analysis of barnacles, as we've discussed recently here?

But is evolution law-like the way physics is?  Physics' 'laws' are universals.  Yet evolution (including selection) happens probabilistically, in the context of specific local circumstances.  This seems at odds with Newtonian universality and its consequent determinism.  Is anything missing in our 'theory' of life and evolution, for example, that vitiates promises of 'precision' genomic medicine?  Or that could be used to derive such predictability?  Or is it just that such promises are Newtonian, and don't fit the evolutionary living world in which we live?

Mr Darwin (and some contemporaries, in particular Alfred Wallace) founded a new science, but we have to go beyond his times to understand where that science will, or should, take us.

Wednesday, December 19, 2018

Barnacles? What about, say, Primates?

On Nov 8, here, I wrote about Darwin's work on the forms and evolution of barnacles.  I asserted that he had a deterministic view of the process of evolution, that I think reflected the Newtonian legacy of science at the time.  Darwin described the mode of sexual reproduction in different species of barnacles, as observed today, as if they were at various stages along the way to a most 'mature' kind of final stage of fully separate adult males and females.   

Darwin wrote several books on barnacles, with typical detail and care, and I cited a fine book by Rebecca Stott (Darwin and the Barnacle) that summarized the story very well and which I highly recommend.  The idea, basically, was that various stages of barnacle reproduction in the past had led to fully separate sexual reproduction in the most advanced present-day barnacles.  Thus, various of today's barnacles that are in these intermediate states are on their evolutionary way to the final one--they're just eons behind their most advanced compatriot species.

In a sense, I think this is part of a more general issue, the equating of induction with deduction--using what we can observe from the present, to make predictions about the future--and a deterministic force-like view of evolution.  Sometimes this means assuming that the future will be like the past, so that, for example, (as in the case of Darwin's barnacles) the present can be viewed tacitly or explicitly, as a cross section of a stream of events, each contemporary state leading to some future state that is already achieved by the most 'advanced' instance observed.

I think a way to understand the point, at least as I see it, is to use an example closer to home.  After all, it's possible that most people don't really know anything about barnacles because they've not seen them or, if they have on some beach trip, they didn't pay any attention, certainly not a Darwinian kind of attention.  So Darwin's barnacle work, even for those who would care to read it or about it, might seem too abstract.  Perhaps there are other ways we might explore his same point, about animals evolving toward a more mature or final stage.

For example, we could just as easily posit that other primates--lemurs, monkeys, and apes (orang-utans, gorillas, chimps), are each on their separate way to--are in separate stages of--becoming human-like.  Perhaps an equivalent suggestion to Darwin's about barnacles would be that non-human-primates are in various states on the road to 'humanity', which we can assume they will eventually reach.  What would this mean, and how could we tell--or could we?  If not, can we say anything about them, or, rather, about their future in this regard?

The fossil record and comparative genomics clearly show that all contemporary apes share relatively recent monkey-like common ancestry. We can take the living descendants and look, comparatively, at their various structures and behaviors.  Nothing stops us from making what would seem to be an obvious statement that we, humans, are more 'advanced' than the other primates.  Yes, of course, they do well today in their own ways, but we are obviously superior.  In some senses, it can be argued that other apes are more human-like than monkeys as if, though they are all contemporary (as with Darwin's barnacles), they can all be viewed as on the 'road to humanity', one of progress that is often to be taken.  Isn't that implicit in the famous figure from TH Huxley's Man's Place in Nature (1863)?
Image result for human evolution timeline
From Frontispiece in Huxley
He showed contemporary primates aligned as if, in a sense, they reflect our evolutionary history, from most primitive to most advanced (us).  Similar figures have been shown based on fossils representing stages, or prior times, during human evolution, such as this famous one grabbed from Google images.

Related image
After Time-Life books' image

These images have something in common: they use reconstructions of a linear evolutionary past, based on fossils, or they do the same by equating current species to past stages in our ancestry.  Yet, obviously, the other apes living today are no more our ancestors than living barnacles are the ancestors of the most 'advanced' species today.  Nor are they "less evolved".

Evolutionary inevitabilities?
What we have is a subtle kind of theory of inevitability, one that implicitly at least and in a sense explicitly asserts that there is in evolution a particular, in a sense pre-determined path.  Some species living today have reached a more advanced stage along that path (their future of course not yet knowable).  But others, though alive today, are as yet only part-way along the path.

Is there any reason to think, much less assume, that chimps are (if we don't wantonly kill them all off first) 'on the way' to becoming humanlike?  This kind of thinking was, I believe, implicit in Darwin, as if evolution were a kind of 'Newtonian' force, like gravity.  But does such thinking still lurk around?  If we share that kind of worldview we can ask, for example, why there are still chimps, if one branch of our shared ancestors evolved to become us humans.  If today's chimps are not on the way to becoming 'human', why did (some of) our chimp-like ancestors do so? If from a common ancestor we could evolve as we did, why not them and why haven't they yet--or will they?

We may have outgrown Darwin's more literal linear thinking, but perhaps not entirely.  As noted in our earlier post, the 'rewind the tape' argument is still raised from time to time.  Is evolution a 'force' that cannot be denied, a kind of inevitability, or is it so local, ad hoc, and related to existing genotypes at a time and place that has no real parallelism?

These are perhaps literally unanswerable questions, but perhaps they are in fact glibly answered by evolutionary biology. Darwin seemed, to me, to assert a sense of replicable inevitabilism, while we seem to have ad hoc accounts that don't suggest that.  If today's apes are on their evolutionary way to something else, it is legitimate at least to ask, at least rhetorically, whether that will be something human-like.  Today we generally say that despite similarities, our common human-chimp ancestors branched into our two present-day species and because of the random nature of mutation and local circumstance, we each evolved our separate ways.  But we'd also say that because of the randomness of mutations, and of environmental changes and so on, they are not destined to become like us.  But then, in the future, if the root abilities are there, and we share so much of our genomes......?

A plausible, indeed basically irrefutable view--so, rather, an axiom of life--is that today's species will either become extinct without issue, or will evolve into forms different from today's.  But can we make any sort of rigorous inference of the sort that today's apes will become human-like?  We know they will not become beetles, or trees--or mermaids--because they are constrained by what they already are, their future forms contingent upon the present.  But is there any rigorous or knowable sense in which a cross-section at any given time is a montage of the evolutionary future?  How precisely does their present form determine their evolutionary future?  Must they evolve into human-like creatures because our primate ancestors did?  If the rewind-the-tape argument has relevance for understanding the past, is the tape being played before our eyes today?  If not, is the biological future predictable with any kind of precision?

These are long-term questions, and modern biology would either just say we can't know or that the idea of parallelism is nonsensical since each species today is unique, as are its circumstances.  But it a non-trivial sense, when we take a sample of human populations for, say, disease-genetic mapping, and extend that to other people or populations, are we not making similar assumptions of parallelism, or the even stronger one that different populations are at the same stage?