Epigenetics: what is it and what isn't it? Part I: basic ideas

Epigenetics is a word that has had a variety of meanings historically, and it's sometimes unclearly employed, even by the user.  But these days, when people talk about epigenetics they generally mean the chemical modification of DNA sequence in a way that does not change the sequence itself but affects the expression of genes in or near the modified DNA region--that is why it is called 'epi' genetic. Such chemical modifications affect whether or not the cell uses a particular gene (only a subset of all genes is used in any particular cell, but that subset changes depending on the cell's local environment at any given time). That is, epigenetic changes essentially are regulatory; the epigenetically modified DNA sequences are not mutations of the coding of the structure of a particular protein (or a directly functional RNA), just how or when or how intensely it is used by the cell. Likewise, epigenetic modification doesn't change the affected sequence itself, but affects whether regulatory proteins can bind there to cause a nearby gene to be expressed, that is, transcribed into RNA.  The phenomenon of such DNA 'marking' itself isn't controversial, and a few of the means by which it happens in a cell are known.  Indeed, unlike mutations in the sequence itself, the marking is easily erased and there are known mechanisms that do that.

However, reports that epigenetic marking can be inherited are quite legitimately controversial.  There are a few reasons for this.

How can local gene usage be inherited?
Cells respond to their environment--to extra-cellular conditions--via cell-surface receptors or other similar means.  If they don't have receptors for a signal floating by, they can't detect or respond to that signal. But cells that do detect a signal change whether they start or stop using a particular set of genes. That's how complex multicellular, multi-organ system organisms become differentiated, as well as to respond to environmental conditions.  Most examples of epigenetic inheritance relate to experience that affects particular types of cells, though many 'housekeeping' genes, genes that carry on basic metabolism, are used by all cells, and any environmental change could in principle induce all cells to change their gene usage.

Unless there is subsequent environmentally-induced change, once modified, when they divide, cells transmit their particular expression state to their daughter cells. If an epigenetic modification causes a cell to respond to a particular environmental signal by turning on the expression of a particular gene, that 'use it!' state would be passed on when the cell divides to produce other cells in its lineage, unless or until another modification occurred to reverse the original change. Thus, if some particular cell, say a lung cell, is induced by some environmental factor like a nutrient to express some set of lung-related genes, the effect is local, specific to lung cells. How that works is complex but some of the mechanisms are known.  However, they have to do with how chromosomes specifically in lung cells are packaged; that is a local fact.  For example, it need not also affect nerve or vessel or skin or stomach cells.  Again, that is because in a differentiated organism different tissues are separated from each other so they can be different.

This raises a serious problem: Local effects on gene expression will be passed on to daughter cells in that tissue, but this is not the same as transmitting the effect to the next generation of organisms. Intergenerational transmission requires that the modification also be made in germline--sperm or egg cells--because the offspring organism starts out life just as a single fertilized egg (which has no lung cells!). Germline cells generally need to have genes switched on (or off) to enable them to make a new organism from scratch, from that single fertilized egg cell. Some temporary change that was important to the embryo's future lung cells would not likely be appropriate for the development of those cells in the first place during embryogenesis. So it is no surprise that there are active mechanisms to strip off epigenetic changes in germ cells' DNA, to reprogram those cells' gene usage to prepare them for their embryonic duties, this is done by erasing and re-setting DNA modification in the sperm or egg cell. If the embryo's lungs, when they eventually have them, need to modify what they due based on the air their exposed to, then new epigenetic changes will occur. Thus, the process of erasing and reprogramming removes those changes. Some bits of the genome are protected from this but it is not automatically true that even environmentally induced changes in housekeeping gene usage will be transmitted.

It was first systematically shown by Weismann in the 19th century and has been a theoretical bulwark against the idea of Lamarckian inheritance, that at least in most animals, somatic (body) and germline cells are separated, independent lineages isolated from each other (the situation is different in many or most plants).  That means that for epigenetic changes to become heritable--and hence affect evolution--modifications to particular body cells would have to be applied to germline cells and not be erased before fertilization.

Without some clear mechanism, there is no reason that future sperm or egg cells will even 'know' about, much less respond to, the signal that induces change in the lung or nerve or stomach cells.  So for epigenetic change to be inherited, there is the serious question of how the genomes in germline cells are specifically modified by signals that affect nerve or lung, etc.  If a lung cell alters its use of gene X related to how lungs work, when it detects some (say) pollutant in the air, how does that specific change also get imposed on the germ line?  Explanations that have been suggested so far are mainly not very convincing. That's why most reports of inherited epigenetic modification are properly received with skepticism.

Still, many investigators are seriously interested in epigenetic changes, especially when or if they are inherited, for a few reasons. This sort of inheritance, which modifies DNA usage differently among a person's many different localized tissues, threatens the degree to which traits can be predicted from a person's DNA sequence alone (obtained, for example, from a blood sample), and among other things that threatens realization of the promise of 'precision' genome-based medicine.  Secondly, accurate assessment of epigenetic effects could lead to a better understanding of important environmental exposures and/or what to do about them, so that newborns are not doomed by their parents' habits to live with pre-set epigenetic traits that they now cannot prevent.  And the least legitimate reason, but one important in the real world of today is that is a lucrative and sexy new finding that can be made to seem a melodramatic 'transformative' shift in our understanding of life.

An important criterion for claims of true epigenetic inheritance is that they must pass through at least to a 3d generation without the presence of the environmentally causal trigger.  That is, transgenerational transmission is evidence that the genome is in fact preserving the change rather than just each new individual learning it from environmental experience (such as in utero).  While there have been various generally convincing reports of true transgenerational inheritance in some species like the simple nematode (C. elegans) or plants, this hasn't clearly been shown in mammals (or humans), even if one or even two generational inheritance, usually through the maternal line, has been found.

Most of the literature consists of curious reports or claims of epigenetic inheritance, reviews of the germline erasure process and what areas of germline DNA could perhaps escape erasure of epigenetic marking, and some examples that seem to be truly transgenerational.  At present, the excitement seems generally far exceeding the reality.  But since epigenetics is potentially quite important, and the methods for understanding it rather new, it is being given serious attention.

A paper by Bohacek and Mansuy (November 2015 Nature Reviews Genetics), reviews what is known about the degree to which epigenetic 'marking' is inherited.  This is a very good, measured paper that in our reading of it makes it clear that claims of non-trivial multi-generational DNA modification effects still need careful documentation.  But if life-experience by parents can affect their offsprings' traits in substantial ways related to the offsprings' future life experience, even if they are not exposed to the risk factors that set their parents' genome usage patterns, then if we could understand how this works perhaps such modifications would not be destiny, and means of prevention or control could be developed if the phenomenon were to be better understood.

Gene usage isn't the same thing as gene structure
Epigenetic inheritance can also affect ideas about how evolution works, if they really have long-term (many generational) effects. The suggestion is now routinely being made that the phenotypic effects of epigenetics we are seeing introduces a Lamarckian view of evolution that may, after all, have to be melded with our Darwinian theory (e.g., see Skinner, MK, Gen Biol Evol. 7: 1296-1302, 2015).  But the idea that this is a genuine revival of Lamarckism is still treated with sneering.  Should it be?

We have written a 2015 series of posts about Lamarckian ideas.  Lamarck was interested in the evolution of adaptive traits, like flying or ocean-living mammals, not just some specific minor traits. He had some non-starter ideas, but so did Darwin and they had far less knowledge than we do!  So one can't defend his theory per se for various reasons.  Still, it's worth thinking about rather than just sneering at Lamarck.  That's for tomorrow's post.....

Remembrance of things past--in your genes? Part III: Was Lamarck so laughable?

A favorite sport of those holding to strict Darwinian views (to the extent they understand Darwin),  is to ridicule Jean Baptiste de Lamarck (1744-1829), he of the stretchy giraffe neck.

Lamarck

Lamarck has gotten a very bad name and at least partly undeservedly.  As are we all, he was a product of his time, his academic environment, and the knowledge then available.  He was apparently a quirky personality and got crosswise with other powerful French biologists, notably Georges Cuvier.  For various reasons it became important for Darwinians to distance themselves from Lamarck as an important intellectual ancestor, in particular, to avoid crediting him for his insight about evolution. Intentional PR-spinning to advance Darwinians (and British over French science)?

Lamarck did his best to clarify very explicitly that he was seeking material explanations not being mystical as he is essentially accused of being.  His basic idea of the inheritance of acquired characteristics was not even that new. It was the obvious thing to infer from the data available at the time, and the idea was commonly held as far back as Hippocrates (probably classics scholars can find it elsewhere as well).

In fact, Lamarck was very clear that he wanted a strictly materialistic explanation for species evolution and diversity. This is interesting, and if it weren't for the rather smug glee with which Lamarck is so universally ridiculed by biologists (whether or not they've read his actual work or even much of Darwin's), we might not want to make the following points.  But under the circumstances, we think it's merited, especially in light of the interpretations being given to widespread reports of various sorts of epigenetic inheritance, that is, of DNA marking rather than sequence change during life.

In our two prior posts in this series (here and here), we took the usual view and stated that any suggestion that epigenetic inheritance is Lamarckian inheritance is trying too hard to be revolutionary, because epigenetic inheritance is imposed by the environment, not by some mystic inner drive on the part of the organism as Lamarck is supposed to have suggested as the cause of adaptive evolutionary change. So, as the usual view has it, even if genome marking is inherited, it is not Lamarckian.  But is that actually so?

"Laws of Nature": who was right?

As we use the term, a Law of Nature is a concept that grew out of the so-called Enlightenment period in European culture history beginning around the mid-1600s.  Darwin's view of natural selection was that it was a Law of Nature that Isaac Newton might have been proud to recognize.  In the amended introduction to the 6th edition of the Origin of Species, Darwin added a review of the history of evolutionary thinking, and there he couldn't have expressed his views better: Darwin said that Lamarck "...did the eminent service of arousing attention to the probability of all change in the organic, as well as in the inorganic world, being the result of law, and not of miraculous interposition."  (italics mine).  

But in fact Darwin was quite wrong, reflecting his own ideological commitment, not Lamarck's. This is because Lamarck said something far more important in my view than the way Darwin thought, and in fact the exact opposite. Here's a fundamental point that Newton himself made very clear, about the central characteristic of a Law of Nature: Principia in 1687: 

"Those qualities of bodies that . . . belong to all bodies on which experiments can be made should be taken as qualities of all bodies universally."

That is, if you find something to be true in a local, restricted setting or 'sample', such as dropping an apple or the orbit of the moon around the earth, the same would be true everywhere else that you didn't or couldn't study.  That was the very essence of what it meant for some phenomenon to be a 'law'.   In his books and other writings it is repeatedly crystal clear that Darwin accepted this Newtonian view: natural selection is a law of nature the way the law of gravity is.  Indeed, in the autobiography he penned for his children near the end of his life, he couldn't have been more clear, writing "...now that the law of natural selection has been discovered..." and "Everything in nature is the result of fixed laws.”

Lamarck was closer to Newton in time than Darwin, but what were his views about laws of nature?  I know not, but Georges Cuvier gave a scathing 'eulogy' upon Lamarck's death, a bitter attack that poisoned posterity about Lamarck's reputation, and Cuvier notes of Lamarck "He had meditated on the general laws of physics and chemistry, on the phenomena of the atmosphere, on those of living bodies, and on the origin of the globe and its revolutions."  If accurate, Lamarck shared the prevailing idea of laws of Nature with Darwin.  Yet, when it came to life, Lamarck in his book said something very cogent, that Darwin and his intellectual descendants seem not fully to realize, even to this day: 

"In dealing with nature, nothing is more dangerous than generalizations, which are nearly always founded on isolated cases: nature varies her methods so greatly that it is difficult to set bounds to them."

Lamarck wrote this basically before the widespread development of statistical thinking, but it is a fact that has still not yet been absorbed by most biologists in evolutionary or biomedical genetics. Lamarck said that when the environment changes, that change in turn induces responses in behavior of organisms. His theory was about the consequent importance of (1) habit, (2) the use and disuse of traits, (3) the inheritance of acquired characters, and (4) the very slow process of adaptive evolution. 

As Lamarck described things, organisms have ways of life that depend on their circumstances.  They seek out resources, like food, that they are able to find, and the resulting 'habits' are essentially their ways of life.  Traits that are used seem to become more important over time but traits that are not used seem to wither or disappear.  Traits acquired during life are passed down to descendants.  The process is very slow, almost unimaginably so.

None of this seems to be at all forced, invented, or strange, and in fact, Darwin adopted all of these ideas in his own way.  As noted above, the idea that one's characteristics were controlled by some sort of transmitted substance is ancient, and the idea of evolution of species was hypothesized in classical times and here and there after that.

[If you are skeptical of our take on this, given Lamarck's clown-like image (due in large part to Darwin and his pals and Cuvier), that would not be surprising.  But that image is wrong, as you can see if you check his book itself and the Introductions by two highly respected evolutionary scholars (the 1984 U of Chicago Press English translation of Lamarck's Zoological Philosophy itself with very informative introductions by Hull and Burkhardt.), or Stephen Jay Gould's The Structure of Evolutionary Theory, or Ernst Mayr's The Growth of Biological Thought.]

So, what was so laughable about Lamarck?

Lamarck is routinely sneered at because, among other things, Darwin and his colleagues were motivated essentially to claim more credit for evolutionary ideas (I'm not the first to suggest this). Lamarck was a human with all the associated failings, but his work is derided because he suggested that the very striving or habits of life caused the associated heritable changes.  By contrast, the Darwinian idea is that new variation arises randomly relative to any need it might or might not have (one can debate how clearly Darwin understood or held such a view).  

However, Lamarck was trying to explain the same phenomena as Darwin, and to do so in terms of natural, historical evolutionary processes, rather than individual events of divine creation.

In our two previous posts in this series we basically took the Darwinian view, that Lamarck was laughable and any attempt to say that epigenetic inheritance was Lamarckian was equally wrong, trying too hard to challenge standard evolutionary theory. In fact, one can argue that epigenetic inheritance really is Lamarckian, based on what he actually said rather than what Darwin said about him, and adjusting for what was known in Lamarck's time.

(1) Habit: How do epigenetic changes arise?  
They arise because of the conditions and behavior of the organism: where they live, what they eat, stresses they are exposed, etc., and how their bodies respond to those exposures.  That is, they are the effects of the habits, as one could say, of the organisms.

And such changes are obviously adaptive if they allow the organism to persist and reproduce! If epigenetic changes are important and persist, over time they will be built into the characteristics of the species. Indeed, there are means by which such traits can eventually be built into the genome in the usual DNA-sequence way (one term for this is 'genetic assimilation').  Over time, nothing strange need be involved for epigenetic changes to be wholly compatible with our understanding of evolution.

(2) What about use and disuse?
In modern theory, 'disuse' means that eventually mutational or gene-expression changes (even if due to epigenetic mechanisms) lead a function or a gene to become more degenerate--as Darwinians would say, because there's no selection pressure to maintain it or even because it's costly if not useful and selection will favor its disappearance. And 'use', of course, would mean of adaptive value.  All perfectly compatible with Darwin (and part of his own theory).

(3) What is epigenetic inheritance?  
When and/or if it occurs, it is the modification of DNA (or the contents of cells) that arises in gametes (sperm or egg) during a parent's life and is transmitted to offspring.  The modifications of interest affect gene usage and hence the traits of the organism.  That is, this is the inheritance of acquired characteristics.

(4) What about the pace of evolution?
As to time, Lamarck was every bit as clear about the slow, gradual nature of evolution.  Both stressed this, recognizing the need to avoid creationist explanations.

So many of Lamarck's basic  ideas were similar to Darwin's (again, historians, not just I, have pointed this out).  What matters is not what someone said 200 years ago.  Instead, the bottom line is that if transgenerational inheritance by way of epigenetic changes acquired during life occurs and is functionally relevant, it is basically Lamarckian, but is also just a different form of 'mutation'.  And the differential proliferation of successful inherited traits, however acquired, will be a natural form of selection.

In that sense, it is Lamarck who is being misrepresented, and whose work in this context, given his context, is not risible.  It doesn't make Lamarckism entirely 'true'; there are wildly wrong things in Lamarck (but also in Darwin).  Cuvier, himself grossly wrong about life in many ways, cruelly portrayed Lamarck as a real nut case.  Despite Lamarck's sometimes free-wheeling ideas, that is not the judgment of history, and in any case, based on what Lamarck wrote in regard to the issues here, if epigenetic inheritance does turn out to have long-term relevance, which is not yet the case in terms of current evidence, it does not in any serious way undermine Darwin. What it does do, is to undermine ideological Darwinism.  And that is a very good thing for science.

Sperm, Meth, Rock'n'Roll

If you're interested in epigenetics at all--which  you should be if you're interested in how evolution works and if you're following any of this Lamarckian Renaissance--then you'll be interested in at least trying to read this paper: Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates by Molaro et al.

This is the "graphical abstract" and as you can see, all their findings are as crystal clear as their importance.

(That was sarcasm. Although, if you stare at this long enough it does start to make sense through the alien acronyms and jargon.)

The authors report, based on sperm studies, that methylation has evolved separately in chimps and humans and has diverged (as we'd expect) and they also explain how methylation changes can drive changes to the DNA sequence.

If you're interested in reading more into this topic, Eva Jablonka is just one scientist I know of who ascribes such evolutionary importance to methylation and maybe there are others (that I am unaware of because this is outside my area).  And she had a nice review in QRB about inheriting epigenetic changes.

Methylation as a force of evolution? Rock'n'roll!

Deep Time: The Movie

The online journal PaleoAnthropology has recently posted the longest boringest movie ever made!

Why would anyone do that? Well, hopefully, you'll see for yourself.

The movie begins with the earliest hominin fossil from between 7-6 million years ago and ....93 hours later... it ends with [SPOILER ALERT!] modern humans.

You can download the movie here and you can also check out the brief article that accompanies it called, "Deep time in perspective: An animated fossil hominin timeline."

(Notice the author's name?)

Because here on the Mermaid's Tale I can address a broader audience--and I'm also free to write about celestial bodies and microbes as much as I please--I thought I'd post about the movie here.

So stock up on raisinettes, nuke enough popcorn to last 93 hours, find a comfortable chair, and enjoy your journey through deep time....

Darwin and Deep Time
Darwin heavily stressed the concept of deep time in Origin of Species because he knew it was a major obstacle to understanding evolution.

It is hardly possible for me to recall to the reader who is not a practical geologist, the facts leading the mind feebly to comprehend the lapse of time. (Darwin 1872: 294)

Deep, geologic time is absolutely crucial to evolution but it is difficult to grasp let alone represent in a drawing.

Scientists, like everyone else, have no frame of reference and so the lapse of deep time is all but ignored in evolutionary trees, like this one that Darwin drew.

Mr. Croll, a Strip of Paper, and Deep Time
A colleague of Darwin’s, a "Mr. Croll" mentioned in Origin of Species, offered a crafty illustration of deep time.

Take a narrow strip of paper, 83 feet 4 inches in length, and stretch it along the wall of a large hall; then mark off at one end the tenth of an inch. This tenth of an inch will represent one hundred years and the entire strip a million years. But let it be borne in mind in relation to the subject of this work, what a hundred years implies, represented as it is by a measure utterly insignificant in a hall of the above dimensions. (Darwin 1872: 269)

Demonstrations like this offer a glimpse into the expanse of deep time and conjure up a feeling of awe. Everyone should try Mr. Croll’s exercise.

Wait. What? You don’t have 83 feet of paper? You’d like to experience more than one million years of deep time?

Well, here’s a solution for you. It’s an animated movie of Mr. Croll’s strip of paper and the inspiration to make it came from marking off the hominin fossil record on a long strip of register receipt paper in Alan Walker's paleoanthropology lab several years ago.

Making the Movie about Deep Time
Because a movie about the entire fossil record of life on Earth might take a lifetime to make and a lifetime to watch, we focused in on the last six and a half million years of human evolution. We built a database of the majority of significant fossil hominin specimens beginning with the late Miocene Sahelanthropus cranium and going up until about 40,000 years ago.

(This was back in 2005 so we could only include fossils that were published at that time. We could also only use the known dates/ages from that time. We also had to stop adding fossils near the end (the present day) because that part of the record gets enormous and the fossils overwhelmed the movie... you'll see if you watch it all the way through.)

Then, with help from our programmer friends, we created a movie using the software Shockwave® that turned the record of hominin fossil specimens and their ages into an animated timeline.

The movie pauses with each fossil to allow the viewer to see it. Skeleton icons represent complete and nearly complete skeletal remains. Skull icons represent complete and nearly complete skulls and crania. Partial skull icons represent skull fragments. Full tooth row icons represent nearly complete maxillae and mandibles. Partial tooth row icons stand for jaw fragments. A single molar icon stands for an isolated tooth.

Watching the Movie about Deep Time
To watch the movie, you need to go to this link, find my article and click on "PA20110013_S03.zip." Download it, unzip it or "extract" the files (crucial), and then click on the "timeline" which should run in Mozilla Firefox or another browser. Detailed instructions on how to do this are here.

Viewers of the movie may begin by following these steps:

1. When you open the movie, it starts rolling immediately. The movie can be stopped at any time by clicking on the red button, which, when clicked again, causes the movie to resume playing. The default rate is 20 years per second and at this rate time ticks by at one generation (20 years) per second.
2. When you watch the movie at the default rate for at least 2 minutes, you will experience onlyabout 2400 years and will see very few icons. At this rate, watching the entire 6.5 million yearsof the timeline would take about 93 hours!
3. For a different perspective, you can click on the drop down menu and set the pace to 50,000 years per second (same as 2,500 generations per second). At this pace you can witness the entire timeline of hominin evolution in a more practical length of time... with the film taking only several minutes to watch from beginning to end.

A Guide to the Movie about Deep Time
The clock starts at 6.5 Ma with the cranium from Chad (Sahelanthropus tchadensis). Time ticks by on the screen at the chosen rate until 6 Ma when symbols representing the next known specimens (belonging to the species called Orrorin tugenensis) flash into view. Then specimens belonging to Ardipithecus pop on the screen, and so on until the proliferation of anatomically modern humans in the Late Pleistocene. This movie offers a different perspective on the hominin fossil record from that of conventional evolutionary tree drawings, where the time span of a species is sometimes estimated based on a single specimen or very few specimens. See this diagram below for just one of the myriad examples (Dunsworth, 2007).


Gaps in the Fossil Record and Deep Time
There are literally tons of fossils in museums around the world, yet it is clear from watching the movie that there are more gaps than there are fossils. How can that be? Part of the answer has to do with the fact that not all creatures fossilize; and, of those that do fossilize, not all preserve to the present; and, of those that do preserve to the present, only a rare few are actually discovered by paleontologists. This enormous Earth is teeming with life. And it has been teeming with life for longer than we can comprehend from our limited perspective.

So not only is the fossil record spotty because of the rare conditions that are required for fossils to form, and the special conditions that enable paleontologists to find them, but the fossil record also has gaps simply because it is so long. The record covers so much deep time that it is taking generations upon generations of scientists to fill in those gaps.

Like your body, like the Milky Way, and like the universe, the fossil record is more empty space than matter.

However, that does not diminish the wealth of information that we can glean from the thousands of hominin fossils and artifacts that have been discovered so far.

In general, hominin fossils are more similar to others that share space and/or time than they are to those found further away in space and/or time. There are a few instances where different types or species of hominins were living practically side-by-side (e.g. robust australopiths and early Homo) and when that is discovered, the hominins are placed on separate evolutionary lineages, marked by separate species or generic designations. Noting similarities and making distinctions are all part of the process that paleontologists use to reconstruct evolutionary history.

In spite of the gaps in the hominin fossil record that are made obvious by the movie, scientists know a great deal about human evolution.

Overall Trends in Hominin Aanatomy and Behavior
The traits and behaviors that distinguish hominins at the genus level are evident in their teeth, their skulls, their bones and the artifacts that they leave behind such as stone tools and butchered bones.

Ardipithecus, Orrorin, and Sahelanthropus: As the fossil record stands now, the bipedal abilities and adaptations of the earliest hominins are disputed (as is their inclusion as hominins!). Some of the teeth of these small-bodied apes have thick enamel and their canines are relatively small—both trends that link them to later hominins.

Australopithecus: The main trend in the time of the australopiths is that of bipedal adaptation. It’s during this era that two separate lineages diverged: The robust australopiths (or Paranthropus) and the genus Homo to which humans belong.

Robust australopiths (a.k.a. Paranthropus): With their large molars and large jaws, these hominins adapted to hard, tough diets and then went extinct.

Homo: With their nearly modern (and, later, totally modern) skeleton, these hominins made and used stone tools as they added meat to their diet. It’s during this time that the brain makes a significant expansion. Species in the genus Homo are the only hominins to be discovered outside of Africa.

Lamarck and Deep Time
Prior to Darwin, Jean Baptiste Lamarck grappled with deep time and described how miniscule the present perspective is in comparison to the vast stretches of time that came before.

There is one strong reason that prevents us from recognizing the successive changes by which known animals have been diversified and been brought to the condition in which we observe them; it is this, that we can never witness these changes. Since we see only the finished work and never see it in course of execution, we are naturally prone to believe that things have always been as we see them rather than that they have gradually developed. Throughout the changes which nature is incessantly producing in every part without exception, she still remains always the same in her totality and her laws; such changes as do not need a period much longer than the duration of human life are easily recognized by an observer, but he could not perceive any of those whose occurrence consumes a long period of time. (Lamarck, 1809)

Thanks to controlled breeding experiments on organisms like bacteria and basset hounds we can witness evolutionary changes. What’s more, that you are not a clone of your parents, that your generation is different from the previous one, is evolution. However, the dramatic changes that occurred over thousands and millions of years before the present, and that will carry on for thousands and millions of years into the future, are beyond our imagination.

Deep Time is beyond Human Imagination
It is impossible to comprehend deep time. Even if we had a time machine and could visit an australopith 3 million years ago, we would only gain a snapshot of the past.

To gain a better perspective on deep time than we have now—that is, to really see evolution taking place—we would have to increase our life spans substantially, which would require a substantial increase in body size as well.

Being as large as Earth would certainly give us a better feel for the lapse of deep, geologic time. Being as big as the Milky Way would be even better. And so on.

This is why so many evolutionary biologists study microbes. To a microbe you are slow and absolutely enormous.

It’s from this present and human point of view that we must continue to work towards the scientific truth about the evolution of all life on Earth, from microbes to mammals. Our inability to truly comprehend deep time does not prevent us from understanding evolution. As long as we accept our limitations we can forge ahead.

Acknowledgments
Alan Walker was the inspiration behind this project which was carried out at Penn State University. Jessica Berry, Stephanie Kozakowski, Gail E. Krovitz, Maria Ochoa, Joseph D. Orkin, and Kelli L. Welker helped compile the fossil hominin database. Brian Shook and Patrick Besong creatively programmed our ideas into the computer. Kevin Stacey, Ken Weiss, and Michael Rogers provided helpful insights, comments, and discussion.

References
Darwin, C. 1872. Origin of Species, 6th edition. John Murray, London.
Dunsworth, HM. 2007. Human Origins 101. Greenwood Press, CT.
Dunsworth, HM. 2011. Deep time in perspective: An animated fossil hominin timeline. PaleoAnthropology 2011: 13-17.
Lamarck, JB. 1809. Additions to Part I, Zoological Philosophy. From 1914 translation.


P.S. Time's Deep, Man...

Should we cut Darwin out of parts of the human skin color story?

A great deal of my students seem to think so!

My freshmen students and I have just spent a semester reading through Nina Jablonski’s book Skin: A Natural History in which she lays out a hypothesis for the evolution of human skin color variation based on natural selection, a.k.a. Darwinian evolution.

[I think it's a fantastic book for introducing anthropology to freshmen (written by a dear friend who I happen to also greatly admire), so I built a class around it.]

The Darwinian explanation* for human skin color goes like this...

Where there is intense UV radiation (the tropics) people adapted to its destructive powers by evolving natural sunscreen, that is, lots of melanin in their skin.

Conversely, in areas where there is relatively little UV (away from the tropics, going towards the poles), people lost pigmentation in order to maximize the sun’s stimulation of Vitamin D synthesis in the skin (something that melanin inhibits).

Your skin color is about the UV environment of your ancestors. Thus, Seal and Heidi Klum are explained.

As all adaptive scenarios need be, these phenotypes are linked to reproductive success. Highly melanized skin is the primitive condition in humans, that our common ancestor in Sub-Saharan Africa evolved post-fur loss to prevent UV radiation from destroying folate—a process that can lead to death and birth defects of offspring. Once humans began dispersing around the globe, the ones to live in low UV environs evolved poorly melanized skin in order to allow enough vitamin D to be synthesized by a mother so that her fetus could form properly and then eventually grow up to reproduce successfully too. We're specifically talking about the development of the skeleton, since vitamin D is necessary for calcium to do its thing.

That women are lighter than men around the globe supports this notion that allowing UV to penetrate the skin during pregnancy is important.

Perhaps the strongest support for this hypothesis is the stunning map of the globe that Jablonski and Chaplin put together. With some exceptions, global distribution of UV intensity is positively correlated with the amount of melanin in indigenous humans so they were able to construct pretty accurate predictions of human skin color around the world based on UV.

Seal's ancestors are from Africa, while Heidi's are from Scandanavia.

[Of course, before that, Heidi's ancestors, like Seal's and yours and mine and everyone else's, lived in Africa.]

It’s an elegant explanation for the evolution of human skin color variation, and one that has gained a lot of support. But the vitamin D aspect of the story is definitely not a hypothesis preferred by all.

And then of course, as reported here on the MT recently, even a mega-study on vitamin D can't tell us for sure what levels are required to stave off health problems, or even what those health risks are!

But it's difficult to go into the details and nuance of these issues about skin color variation and vitamin D while introducing evolution to students. For many of my students, this is the first time that they’ve learned about evolution in a scholarly setting and we perform activities to illustrate the differences between Lamarckian evolution and Darwinian selection. Of course we also discuss all the known evolutionary forces—mutation, gene flow, drift, and selection—not just selection.

Few students are able to digest all of this the first time they learn it. And regardless of the explanations for why that may be (i.e. instruction quality, lack of effort, difficulty with the concepts, too much bias and misunderstanding brought into the classroom, etc…), it takes longer than a semester to understand how natural selection works and how it does not work.

For many students, the moment that they grasp natural selection, they begin to see the world through selection-colored spectacles. Everything has a reason, much like Dr. Pangloss's philosophy in Voltaire’s Candide. And it’s not just physical features... behaviors become adaptive by default as well.

It’s fine if these ideas are understood to be hypotheses, accounting for the complexities of the genes and physiological processes that lie behind the traits, and accounting for the limitations to testing them. But all too often students blindly assume that natural selection explains EVERYTHING.

[And this leads down the slippery slope to Social Darwinism so it's not something to take lightly.]

Now, even though the adaptationist perspective is rampant, that’s not at all the pattern that emerges when students interpret and explain human skin color.

They do the exact opposite! They take natural selection and adaptation out of half of the story!

Here’s (my paraphrasing of) how many of my freshmen students answer when they are asked to explain the Darwinian folate/Vitamin D hypothesis offered by Jablonski in her book:

Natural Selection explains melanized skin in the tropics because it acts as a natural sunscreen to protect against harmful UV. However, for the non-melanized people in regions with little UV exposure… well, they don't have much melanin because “they don’t need it.”

Depending on how you interpret that (aside from the possibilities that I'm not doing my job well enough, that they're not listening in class, or that they're not doing the reading), the students are invoking genetic drift, neutral theory, or Lamarckian principles! And Darwin is totally out.

I doubt many are aware of the theoretical significance of their answers. But by erroneously explaining a Darwinian concept, they're offering us a window into their intuition.

Just so we’re all on the same page, here’s a translation of the various scenarios for the loss of a trait, like pigmentation:

1. If losing it is beneficial, then those who have lost it will out-survive and out-reproduce others and future generations will have more have-nots than haves. If it’s crucial to survival and reproduction, then the loss will become fixed in the population as an adaptation. - Darwinian adaptation through natural (or sexual) selection
2. If you don’t need it then you can lose it without issue. Reproductive success does not depend on whether or not you have the trait or not, so chance alone will determine how prevalent haves or have-nots will be in any given generation. Relaxed selection plus chance can ultimately lead to the elimination of alleles all together! Furthermore, there is a constant and low mutation rate and while selection is weeding out deleterious mutations in some genes, or while it is favoring adaptive mutations in some genes, the mutations in genes for traits that do not affect evolutionary fitness can accumulate. As long as these mutations are not harmful and purged by selection, they can disrupt the gene and either damage the trait or cause complete loss. - Genetic drift and neutral theory (both with relaxed selection)
3. If you don’t use it, you’ll lose it, meaning that the trait can fade within a lifetime if it's neglected. That neglected trait is passed on to future generations which will continue to experience its decline if they also stop using it, and if that’s widespread throughout the population, then that trait disappears. (It’s assumed that if a trait is not used that it’s not "needed," which is why the casual wording of this scenario can be similar to #2.) - Lamarckian evolution

The first two scenarios, #1 and #2, are widely accepted as biological phenomena, so they are valid hypotheses for the loss of pigmentation in people who live far from the tropics. The third scenario is seen by the scientific community as a misconceived foil to “real” evolution, having fascinating historical interest and useful pedagogical appeal, but that is all.

Okay then, how can we interpret what I've called this "intuitive" response by my students?

First of all, tanning is certainly enabling this muddling of Darwin. That skin color changes in response to stimulation by UV (and hormones!) and is not static during life makes it complex and matches it to UV in a non-evolutionary way, a way that they're used to assuming. A way that people around the world assume to be! Some of my Kenyan friends think that my skin would look like theirs if only I stopped wearing sunscreen lotion while I visit Kenya.

And second, if students think of melanin as natural sunscreen, then it's probably easy for them to take that metaphor too far and liken it, conceptually, to sunscreen lotion.

You apply sunscreen lotion when you need it and you don't apply it when you don't need it. You need it on the Equator, yet you don't need it as much far from the Equator. This feeds back into their evolutionary story: Melanized skin evolves to be where it's needed and it evolves away where it's not needed. This is, I think, the intuitive rationale behind my students' answers. Relaxed selection, neutral theory, and genetic drift provide the backing scientific power. Plus, pigmentation loss in other animals is overwhelmingly explained this way.

But, additionally, "need" can be one way to casually express the concept of Lamarckian "striving." Are my students really Lamarckists when they say that white people are that way because their ancestors didn't need much melanin? It's hard to say.

But I also can't help but wonder, What if their confusion is not just due to their theoretical naivete? What if a totally Darwinian explanation for human skin color variation is hard to understand because it just isn't the best explanation?

Maybe my next class should be dedicated to testing and fleshing out how we could test the adaptive hypothesis for human pigmentation loss versus the alternatives.

But even if we did know the real scenario, there would still be lingering questions...

Maybe it's a horrible under appreciation of deep time and convergent evolution...Maybe it's a gross underestimation of mutation and genetic drift...

But why do so many animals in UV-limited habitats (caves and sea floor) lose pigment? Is it just one of the few visible traits that a constant accumulation of mutations can safely derail under the watchful eye of selection?

And what about epigenetics and pigmentation? Hmm?

Oh, I don't know, maybe Stephen Colbert had it right: Pale skin is best for hiding in a snowbank.

* The Darwinian explanation for skin color variation that I describe here (called "Darwinian" because it's about natural selection acting on melanin differently in different environments), is NOT the same as Darwin's which he discusses in Descent of Man.