Showing posts with label primates. Show all posts
Showing posts with label primates. Show all posts

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 Barnaclethat 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?

Thursday, February 4, 2016

The Primate Family Tree: A classroom activity in evolution, adaptable for all ages

Feel free to email me to request the document (with all this text and all these figures) which is easier to work with. holly_dunsworth@uri.edu

In this activity, students will…
Observe and describe the similarities and differences between primates and other familiar mammals, and also the similarities and differences among primates.
Classify primate species into groups (superfamily and above). 
Transform Linnaean classification into evolutionary theory by merely changing the question from How do primates look similar and different from one another? to Why do primates look similar and different from one another?
Build a primate “family” tree by turning Linnaean classification into phylogeny (or evolutionary tree-thinking) to describe how common ancestry and change over time explain both similarities and differences among primates.

How old are the students? 
5-105* 
*Prior to about age 8, teachers will need to riff quite creatively off track from this (for one, because reading the Primate Taxonomy Table may be very difficult for younger students), but I include those earlier ages because I believe that teachers of those age groups can find a way to use this lesson if they’d like to. It's possible that just knowing how to read is enough to do a stripped down version of this activity, which includes children even younger than 5. I have used this activity successfully with students aged 8-25. For upper-level anthropology courses I've used it as an ice-breaker to kick off the semester (with students who have a background in evolutionary thinking already).

How long will it take? 
30 minutes minimum (much more depending on detail you wish to cover)

What materials?
Color pictures of a diverse array of primates - approximately 3-5 times as many pictures as students. Too many is better than too few. Rip them out of old textbooks and laminate for durability. Print them off the Internet (arkive.org is one of the best sources) and laminate for durability. Make sure to have at least two different pictures of the same species for many of the species you include. Label most of them with the common names under “examples” on the chart for Part 2 (e.g. “baboon”). But a fraction may be only labeled with geographic region, scientific name, or nothing at all.  Explanation is in the instructions below. Specific sources of primate photos for printing are listed in Appendix A.
Pencil – 1 per student
Note cards -  1 per student (for them to draw a self-portrait or a symbol to represent themselves)
Poster paper, or large sheets of paper – 6, one for each superfamily on the Primate Taxonomy Table (below)
Tacky gum, reusable tape, or some other ingenious sticky tool that can both hold primate pictures to the posters and also be removed and moved to different posters when students change their minds. 
Handout for students (see options below; must at minimum include Part 2: Primate Taxonomy Table)

Teacher Instructions

Part 1. (3 MINUTES minimum) DISCUSS CLASSIFICATION
Using the resources under Part 1 of the materials below, hold a discussion about classification. Don’t talk about relatedness or common ancestry! And especially don’t talk about evolution! (Next, in Part 2, the taxonomic terminology they will use, like “family,” will encourage them to think evolutionarily, hopefully, and this will come into play later in the activity.)  They will already be familiar with how like is grouped with like—I often use sock and underwear drawer analogy, grocery store organization works too. Stick to primates if you’d like, but if you go broader, make sure to end your discussion with primates, including humans. Make sure to explain how (Linnaean) taxonomy/classification works. That is, simply/broadly (or complicated/specifically if you’d like) describe the methods—the use of comparative anatomy and homology and also the binomial species name for the smallest, most exclusive group within ever-more inclusive groups going up to the Kingdom level.

Part 2. (10 MINUTES minimum) CLASSIFY THE PRIMATES INTO SUPERFAMILIES
Hang a poster for each superfamily along the wall in no particular order, lay out a pile of the photos in no particular order. Students get up out of their chairs, and using the Primate Taxonomy Table (below) they stick each primate picture to a poster labeled with the superfamily to which they think it belongs. They are able to do this without any knowledge of primates because you have labeled most of the pictures with “baboon”, for example. They can go to the table on the handout and see that baboons belong in the superfamily “cercopithecoidea” and stick the photo to that poster. Unlabeled baboons should look similar to labeled ones and they should also be sticking those to the cercopithecoidea poster if they are carefully observing and are engaged in the activity. Make sure they stick their own “human” cards to a poster too.  Hopefully they will respectfully work together and move others’ around if they think they have a better case for a different classification of a particular primate.  

Primate Taxonomy Table (handout).
Email me for a file you can work with more easily (holly_dunsworth@uri.edu)

Part 3. (5 MINUTES minimum) STUDENTS SHARE THEIR REASONING FOR THEIR CLASSIFICATION
Lead the students through a tour of the features that unite the primates into each of the superfamilies. First ask them to describe the similarities among all the primate superfamilies (a quick review of Part 1). Then ask them to describe the differences they can see between the superfamilies: what makes hominoids separate from cercopithecoids, etc?  It’s not imperative, but I recommend starting with the primates that share the most with humans (hominoidea) then going to the cercopithecoidea, and so on. This may appear to be difficult because they may observe overall (super) family resemblance but not be able to describe any more detail than that, which is fine! Using the resources under Part 3 below, you can provide details of the differences between the superfamilies, both that are visible in the pictures and that are not. 

Part 4. (2 MINUTES minimum) CHANGE THE QUESTION FROM HOW DO PRIMATES VARY? TO WHY DO PRIMATES VARY? 
Challenge students to explain the patterns of similarities that make all these creatures primates and that, for example, unite the hominoids, the cercopithecoids, etc..., while also explaining the differences that make each species unique and each superfamily unique.  Hopefully, with very little help from you, they will arrive at the idea that relatedness explains it. Family history, on a larger scale than our own families, but the same kind of thing. Common ancestry and change over time since common ancestors. Evolution plain and simple.  

Part 5. (10 MINUTES minimum) BUILD A PRIMATE TREE and DISCUSS ITS MEANING. 
There are many ways to do this and showing more than one way would be great, but one way is to put the known phylogenetic structure, the branches of the tree for the superfamilies (see resources below) on the wall or board and have them deduce where the superfamilies go and stick the posters to those branches. Another way, for older students, is to have them figure out the relatedness of superfamilies first, starting with humans and hominoids and hypothesizing which are more and more distantly related based on increasing differences. Another is to merely show them how to walk through the table for Part 2, and change it into a hypothesis for phylogenetic/evolutionary history, with lineages diverging where each level of taxonomy divides things further into more exclusive groups. So show them how to draw time and descent lines around that evolution-free taxonomy (classification table for Part 2) that they already have and they’ll arrive at.. dun-dun-DUN evolution! I prefer to draw the students’ hypothesized tree like a big oak tree (with a streps/haplorhine split in the trunk deep down near the bottom) on the wall, and to stick the posters at the ends of the branches. But it’s obviously up to teachers and whether they have a big wall to draw on! I cover my wall in paper first so that I can draw the big tree. 


Teacher Resources and Optional Handout Materials
Teachers: Pick and choose what you’d like to include in your handout, depending on what you will cover with your particular students (depending on age, time, goals, etc…). Be careful not to share any handouts too soon and spoil the opportunity for students to think first, if that’s what you have time for and are going for. 

Part 1
  • Where do humans fit in the classification of life on Earth? (link)
  • How do we make these categories? We ask, ‘What’s similar” of the anatomy, when comparing different species.  That is we look to homologous structures.  A great example is the tetrapod forelimb. (link)

  • What makes a primate a primate? (link)

Part 2
Lemuroidea
Nose: wet (hence the name strepsirrhine)
Geographic region: Madagascar
Tail present: yes
Activity: Some nocturnal, some diurnal
Teeth: Many more than we have, some shaped like comb for grooming fur
Body size: Small but variable from the smallest primate alive (<< 1 lb.) to ones as big as big pet cats (20 lbs.)

Lorisoidea
Nose: wet (hence the name strepsirrhine)
Geographic region: Sub-Saharan Africa and Southeast Asia
Tail present: yes and no
Activity: nocturnal
Teeth: Many more than we have
Body size: small

Tarsioidea
Nose: dry (hence the name haplorhine) 
Geographic region: Southeast Asia
Tail present: yes
Activity: nocturnal
Teeth: Many more than we have
Body size: small

Ceboidea
Nose: dry (hence the name haplorhine) 
Nostrils: flat and facing out to the side (hence the name platyrrhine)
Geographic region: Central and South America
Tail present: yes (and some are even prehensile!)
Activity: Most diurnal, some nocturnal
Teeth: four more than humans (one extra premolar/bicuspid in each quadrant of mouth compared to us)
Body size: Variable, with some small (like pygmy marmosets) but the largest, the spider monkey, is 25 lbs.

Cercopithecoidea
Nose: dry (hence the name haplorhine) 
Nostrils: facing down (hence the name catarrhine)
Geographic region: Asia, Southeast Asia, and Africa (all sub-Saharan except the Barbary macaque of Morocco and Gibraltar)
Tail present: yes (but 2-3 species are no or have very small stubs)
Activity: diurnal
Teeth: same number as humans
Body size: Many, including most macaques and baboons, weigh more than any ceboids. Some mandrills weigh over 100 lbs.!

Hominoidea
Nose: dry (hence the name haplorhine) 
Nostrils: facing down (hence the name catarrhine)
Geographic region: Southeast Asia (gibbons, siamangs, orangutans); Sub-Saharan Africa (gorillas, chimpanzees, bonobos); Worldwide (humans)
Tail present:  no
Activity: diurnal
Teeth: same number as humans
Body size: Although gibbons and siamangs are the smallest of the group, this group is the largest in body size and weight of all primate superfamilies and includes gorillas, the largest of all primates which can weigh 400 lbs.!


Part 4

Evolution and phylogenetic thinking is just family history writ large.

Part 5. The Primate Family Tree

Here is an example (one hypothesis, if you will) of a primate phylogeny or phylogenetic tree or evolutionary tree. 



Here's guidance on how to turn Part 2’s table into a phylogeny with students.


Then here it is, stripped down and rotated...



Appendix A.
Sources for primate pictures

Lemuroidea

Lorisoidea

Tarsioidea

Ceboidea

Cercopithecoidea

Hominoidea
Humans: students draw a personal sign, symbol, or self-portrait

Sunday, August 16, 2009

Dr Livingstone, I presume? (Frank, that is!)

Malaria may have killed or harmed more people than any other single cause of disease in our species' history. A new article by Rich et al. in PNAS uses newly available DNA sequence data to date the origin of a common virulent type of malarial parasite and its transfer from an ancestral chimpanzee host to humans.

Prior work had suggested the transfer was from a bird host, but primates seem now to be the guilty party. The relevant strains are Plasmodium falciparum and its close relative P. reichenowi, the chimp parasite. The idea of a recent transfer was supported hypothetically by the assumption that it's not in a parasite's long-term interests to be too virulent, but that the P. falciparum parasite hadn't had time to adapt more chronic effects.

Sequences of several samples of these and other Plasmodia show clearly that the human and chimp sequences form a single evolutionary clade (the top big branch in the figure, reproduced from the paper). That also supports the recent transfer to humans from a chimp source that is considerably older and geographically widespread in Africa, but not a much more ancient bird clade.

This paper properly relates the authors' new findings to a classic, elegant, and incredibly perceptive and integrative American Anthropologist paper in 1958 by the late anthropologist Frank B Livingstone (Anthropological implications of sickle cell gene duplication in West Africa, American Anthropologist, New Series, Vol. 60, No. 3 (Jun., 1958), pp. 533-562). He looked at the distribution of malaria, the population genetics of malarial resistance including the frequency and distribution of sickle cell and other hemoglobin variants, and how long a mutation with a selective advantage due to protection from malaria would take to reach its present distribution. He elegantly integrated these data with known patterns of language and culture in the malarial areas of Africa.

Frank concluded that malaria arose roughly 10,000 years ago with the advent of settled agriculture, that encroached on the chimpanzees' forest habitats, the proximity providing opportunity for transfer to humans. Settled agriculture led to cleared, stationary fields in which ponds of water could develop, providing enhanced or stably localized breeding grounds for the larval stage of the mosquito life cycle.

Sequence divergence between the human vs chimp parasite genes, plus the low level of divergence within the human clade, suggest to Rich et al. that the initial transfer may have occurred hundreds of thousands or even a few million years ago. It may have conferred only benign malaria on the 'human' hosts -- actually our species as such is only about 100,000 to 200,000 years old, so the transfer would have been to our very non-agricultural antecedents whose population structure was probably much more patchy, sparse, and in these senses chimp-like, if probably also less arboreal.

Sometime post-agriculture, there may have been human and/or parasite mutations that made the parasite much more virulent, and it then spread rapidly with agriculture. Whether the virulence directly helped the spread or not would be debatable.

This is a very nice paper of science, one that leads us to a somewhat related topic about science. Given the relatively crude state of genetics at the time, Livingstone's paper was quickly recognized as a classic, and that judgment persists....if only people these days weren't too impatient to read it. Rich et al. did, but that's not so typically the case.

With much media and journal ballyhoo, a recent paper in Science by Tishkoff et al. (Haplotype Diversity and Linkage Disequilibrium at Human G6PD: Recent Origin of Alleles That Confer Malarial Resistance, Science 20 July 2001: Vol. 293. no. 5529, pp. 455 - 462) studied the origins of the human G6PD mutation, also related to malarial resistance. The authors used population genetic analysis conceptually similar to Livingstone's, and estimated that the protective mutation arose less than 10,000 years, compatible with the earlier estimates and reasoning. This was solid genetics, and Tishkoff et al. did refer to Livingstone's hypothesis, though in a rather buried instead of featured way. The finding was strongly confirmatory, but not the transformative discovery that media hype gave the impression it was.

Science generates enough solid, interesting work without the hyperbole that these days has come to serve many interests. That gives a misleading impression that we're making 'paradigm shifts' in human knowledge on an almost daily basis, which is not true. In many ways, this is a kind of crying 'wolf!'. In the long run, science would be better off if routine or incremental findings were recognized as such, because that is how science mainly works, and the public who support us should know that. Authors should insist on tempered claims in the media and by the journals.

It is easy of course for us to be over-critical, and in the nature of full disclosure, although he never worked on malaria, Ken's PhD advisor was Livingstone himself. So we naturally knew of Livingstone's work.

But that doesn't change the fact which is all too symptomatic of our credit-hungry times that we and the media give more credit to ourselves as if new technology has obsolesced all previous knowledge, and are unwilling or in too much of a hurry to do like Stanley and make treks required to identify the source of the News. In this case, that would be Dr Livingstone, we presume.