{"id":376,"date":"2015-05-21T01:56:50","date_gmt":"2015-05-21T01:56:50","guid":{"rendered":"http:\/\/joshmitteldorf.peachpuff-wolverine-566518.hostingersite.com\/?p=376"},"modified":"2015-05-21T01:56:50","modified_gmt":"2015-05-21T01:56:50","slug":"vital-questions-part-2","status":"publish","type":"post","link":"https:\/\/scienceblog.com\/joshmitteldorf\/2015\/05\/21\/vital-questions-part-2\/","title":{"rendered":"Vital Questions, Part 2"},"content":{"rendered":"

Review of The Vital Question by Nick Lane, Part 2 of 3<\/p>\n

Last week<\/a>, I covered the fundamentals, the outline of the history of life on earth, including some unexpected findings and downright mysteries. \u00a0I\u2019ll continue here to talk about some of the broadbrush features in the history of eukaryotes as Lane paints the picture, and what he thinks the picture is telling us. \u00a0Next time, I’ll talk about sex and evolvability.<\/p>\n

\n

Eukaryotes encompass the full diversity of macroscopic life on earth, every animal and plant, from yeast cells to jellyfish to sequoia trees to you and me. \u00a0Strikingly, there are lots of things that all eukaryotes have in common (see last week\u2019s column) that no bacteria or archaeans have.<\/p>\n

It\u2019s Lane\u2019s ambition to explain some of the basic features of the eukaryotic lifestyle: birth and death, genetic recombination with two sexes, the association between sex and reproduction (which exists in almost all eukaryotes, but not in bacteria). \u00a0He begins with the event that\u00a0created the eukaryotes and gave them their advantage–the domestication of a sugar-burning bacterium that became universal energy source for all eukaryotic cells.<\/p>\n

This view of life\u2019s history, a 4-billion-year story, places the mitochondria right at the centre of the evolution of the eukaryotic cell…<\/p><\/blockquote>\n

This is the biggest new idea in the book. \u00a0How well does it hold up?<\/p>\n

 <\/p>\n

Linear chromosomes with Introns<\/b><\/p>\n

In prokaryotes, almost all the DNA comprises legitimate genes, that is, it codes for proteins. \u00a0In eukaryotes, less than 5% of the DNA codes for protein. \u00a0When this fact was first discovered in the 1970s<\/a>, non-coding DNA was called \u201cjunk\u201d or \u201cparasitic DNA\u201d. \u00a0The story was that it served no function except to replicate itself, along for a free ride. \u00a0Natural seleciton in prokaryotes is a race to the fastest reproducer, so they can\u2019t afford parasitic DNA, and it has been selected out. \u00a0But eukaryotes play a more sophisticated game (so the story goes), where \u201cfitness\u201d depends on survival strategies, and not raw speed of growth and reproduction. \u00a0Hence eukaryotes don\u2019t pay a high penalty for all this junk DNA, and it has accumulated in the genome.<\/p>\n

I have never bought into this story. \u00a0Just because we don\u2019t know the function of a stretch of DNA doesn\u2019t mean that there is none. \u00a0And indeed, over the years, functions have been discovered for non-coding DNA. \u00a0Some of it is translated into RNAs (ribozymes<\/a>) which biologically active in many of the same ways as proteins. \u00a0Some of it is \u201cgenetic capacitance<\/a>\u201d. \u00a0The genome has learned to behave like a packrate, holding on to genes that were useful in the evolutionary past but not now, because the genome has learned from long experience that conditions are likely to recur some generations in the future, and better to carry extra baggage for a few million years than to have to start all over and re-invent the wheel if the need should arise again.<\/p>\n

But all of it affects the way in which chromosomes spool and unspool along their length, opening as euchromatin<\/a> which is active and expressed, or closing up as heterochromatin<\/a> which is temporarily inactive. \u00a0This is epigenetic control, an intricate logic that determines which genes are expressed where and when. \u00a0Prokaryotes don\u2019t differentiate into diverse cell types, and they don\u2019t have life cycles that demand growth, maturation and development. \u00a0But eukaryotes do, and hence every cell needs to express just that subset of the genome that it needs to do its job at the moment. \u00a0I don\u2019t find it at all surprising that 95% of the genome is devolted to the decision when and where to deploy the other 5%. \u00a0An encyclopedia of human DNA by the ENCODE project<\/a> estimated that 80% of genetic material has a purpose.<\/p>\n

Lane believes that much of the non-coding DNA is indeed parasitic junk, and some of his argument about the origin of the cell nucleus, sex and aging hinge on this characterization. \u00a0Compellingly, he notes that the total quantity of DNA varies enormously from one plant or animal to another, and appears to bear no relationship to the complexity of what that species does or how it lives. \u00a0Looking at frogs alone, we see some species that have 100 times as much DNA as other frogs.<\/p>\n

It can\u2019t all be \u201cnecessary\u201d. \u00a0\u00a0But that doesn\u2019t mean it\u2019s parasitic. \u00a0Maybe there just isn\u2019t much incentive to do the job of epigenetic regulation efficiently, so some species use much more DNA than others.<\/p>\n

Lane describes a barrage of parasitic DNA that came with the mergers and invaders that formed the first eukaryotic cell. \u00a0It was to protect against this invasion that the cell\u2019s DNA was sequestered into a nucleus and surrounded by a membrane.<\/p>\n

Every time a eukaryotic gene is transcribed, DNA is first copied as messenger RNA, and the RNA is then translated into a unique protein. \u00a0But non-coding DNA is interspersed through as introns. \u00a0So the RNA must be edited, snipping out introns and re-attaching the free ends until just the coding portion remains, ready to be run through a ribosome<\/a> where it becomes blueprint for a protein. \u00a0The editing takes place inside th nucleus, and the ribosomes are outside the nucleus, assuring that no un-edited RNAs are transcribed to protein.<\/p>\n

In bacteria, it is efficient to have the DNA spread through the cell and conveniently interspersed with ribosomes. \u00a0But in eukaryotes, it would be a mistake to transcribe the RNA before the introns are snipped out. \u00a0So DNA is kept walled off in a nucleus, and RNA remains in the nucleus long enough for it to be snipped and edited.<\/p>\n

Lane documents the evolutionary origin of introns and gene splicing, demonstrating convincinginly that introns originated with parasitic DNA that lived within the bacterial genome and politely provided their own scissors<\/a>! \u00a0What he doesn\u2019t say is that this system of \u201cgenes in pieces\u201d has major advantages in complex organisms. \u00a0The self-splicing intron may have begun as a bacterial parasite and developed into a useful attribute in eukaryotes; or it may have evolved in eukaryotes as a useful innovation, and then crept back into bacteria as a parasite. \u00a0But the system has advantages for eukaryotes that make me think that it is the product of natural selection. \u00a0There is an economy in constructing genes from reusable modules that can be combined in different ways to perform different fuctions. \u00a0There is an advantage in efficiency of evolution, as it is easier to combine functional pieces for a new application than to design a new protein from scratch. \u00a0And, as I mentioned above, it may be that much of the DNA serves an epigenetic function, implementing a decision where and when to activate each particular gene.<\/p>\n

 <\/p>\n

One Wave of Cell Mergers, or Continuing Episodes?<\/b><\/p>\n

Eukaryotes encompass the full diversity of macroscopic life on earth, from yeast cells to jellyfish to sequoia trees. \u00a0Strikingly, there are lots of things that all eukaryotes have in common (see last week\u2019s column) that no bacteria or archaeans have. \u00a0There are also genes that clearly come from bacteria that characterize all eukaryotes, and so they were presumably present in LECA, the L<\/b>ast E<\/b>ukaryotic C<\/b>ommon A<\/b>ncestor, \u201cmother of us all\u201d. \u00a0And yet these genes come from at least 50 different bacteria, on widely separated bacterial taxa.<\/p>\n

In Lane\u2019s picture, all the merging of different genomes took place in an intense wave at the origin of eukaryotic life. \u00a0In support of this picture, he notes that most of this diverse genetic legacy is amazingly well conserved across the full range of different eukaryotes–protists, animals and plants.<\/p>\n

But I can\u2019t resist digressing to tell you about the alternative picture, as presented in Lynn Margulis\u2019s book with her son Dorion Sagan, Acquiring Genomes<\/a>. \u00a0They cite evidence that mergers and acquisitions have been continuing in an ongoing series of events that are rare only in a relative sense. \u00a0Many, many genome mergers have taken place in the history of eukaryotic life, continuing into the recent past.<\/p>\n

Many insects look entirely different in their larval form and their adult form.<\/p>\n

\"\"
House fly looks nothing like its larva or its pupa.<\/figcaption><\/figure>\n

The transition, for example from a caterpillar to a butterfly, is not a continuous change in shape. \u00a0Rather, inside the crysalis, the caterpillar dissolves and its biomass is reformed into a butterfly [ref<\/a>].<\/p>\n

\"Caterpillar<\/a>
Caterpillar looks nothing like the adult monarch. The caterpillar does not “grow into” a butterfly , but rather dissolves itself within the crysalis and starts over to build a new body.<\/figcaption><\/figure>\n

Margulis and Sagan take this as evidence that larva and adult were once different species, and that the two species became one when their genomes merged.<\/p>\n

But why? \u00a0What possible advantage can there be to making two species into one? \u00a0My answer has to do with stabilizing populations. \u00a0If the young and the mature form are in the same niche, competing directly with each other, then the larger, mature individuals have every advantage. \u00a0Predators or disease or famine–all of the common causes of death hit harder against the very young. \u00a0Very few of the young will have a chance to grow to maturity, and the population pyramid will be bottom-heavy with young \u2019uns, most of whom will never have a chance to grow up. \u00a0If the larvae and the adult are not in direct competition, then it is easier to establish a stable population structure.<\/p>\n

And how could it come about that a maggot\u2019s genome would merge with a housefly\u2019s, or a caterpillar\u2019s with a butterfly? \u00a0The answer is xenogenous fertilization<\/a>. \u00a0It is rare, but not all that rare, that an egg of one species can be fertilized by a completely different species.<\/p>\n

In the Liverpool University lab of Don Williamson, successful hybridizations were achieved between distant species to produce fertile offspring. \u00a0Sea urchins are echinoderms, ancient globes covered with spines. \u00a0Sea squirts are chordates, \u201calmost vertebrates\u201d like us. \u00a0This is one of the odd pairings that Williamson was able to hybridize.<\/p>\n

\"\"
Sea Squirt is a chordate<\/figcaption><\/figure>\n

 <\/p>\n

\"\"
Sea Urchin is an echinoderm.<\/figcaption><\/figure>\n

If Williamson could do it in a few years of futzing around in the lab, then\u00a0it\u2019s likely that over hundreds of millions of years in the vastness of the oceans and the air, it has happened dozens, maybe hundreds of times that an egg of one species has been fertilized by a sperm of a very different species.<\/p>\n

Williamson’s story is included in Acquiring Genomes<\/a>, and his\u00a0story of the Web of Life to replace the Tree was nicely summarized in a series of\u00a0New Scientist\u00a0articles<\/a> a few years ago.<\/p>\n

So what are we to make of these two very different stories about the Tree of Life? \u00a0Both pictures seem compelling to me, and I would guess there is truth in both stories. \u00a0Perhaps there was an intense wave of endosymbiosis around the time of the first eukaryotes. \u00a0Perhaps there were many different competing mosaics of different bacteria and archaeans, unlikely hybrid monsters that struggled to keep peace among their parts, and struggled with one another. \u00a0It seems that one of these won out, and the others died off without a trace. \u00a0Her name was LECA.<\/p>\n

This column is getting long, and there is more I have promised you: sex, parasitic DNA and a favorite topic of mine, the evolution of evolvability.<\/p>\n

\u2019Til next week…<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

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The surprising fact that our bodies are genetically programmed to age and to die offers an enormous opportunity for medical intervention. It may be that therapies to slow the progress of aging need not repair or regenerate anything, but only need to interfere with an existing program of self-destruction. Mitteldorf has taught a weekly yoga class for thirty years. He is an advocate for vigorous self care, including exercise, meditation and caloric restriction. After earning a PhD in astrophysicist, Mitteldorf moved to evolutionary biology as a primary field in 1996. He has taught at Harvard, Berkeley, Bryn Mawr, LaSalle and Temple University. He is presently affiliated with MIT as a visiting scholar. In private life, Mitteldorf is an advocate for election integrity as well as public health. He is an avid amateur musician, playing piano in chamber groups, French horn in community orchestras. His two daughters are among the first children adopted from China in the mid-1980s. Much to the surprise of evolutionary biologists, genetic experiments indicate that aging has been selected as an adaptation for its own sake. This poses a conundrum: the impact of aging on individual fitness is wholly negative, so aging must be regarded as a kind of evolutionary altruism. Unlike other forms of evolutionary altruism, aging offers benefits to the community that are weak, and not well focussed on near kin of the altruist. 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The surprising fact that our bodies are genetically programmed to age and to die offers an enormous opportunity for medical intervention. It may be that therapies to slow the progress of aging need not repair or regenerate anything, but only need to interfere with an existing program of self-destruction. Mitteldorf has taught a weekly yoga class for thirty years. He is an advocate for vigorous self care, including exercise, meditation and caloric restriction. After earning a PhD in astrophysicist, Mitteldorf moved to evolutionary biology as a primary field in 1996. He has taught at Harvard, Berkeley, Bryn Mawr, LaSalle and Temple University. He is presently affiliated with MIT as a visiting scholar. In private life, Mitteldorf is an advocate for election integrity as well as public health. He is an avid amateur musician, playing piano in chamber groups, French horn in community orchestras. His two daughters are among the first children adopted from China in the mid-1980s. Much to the surprise of evolutionary biologists, genetic experiments indicate that aging has been selected as an adaptation for its own sake. This poses a conundrum: the impact of aging on individual fitness is wholly negative, so aging must be regarded as a kind of evolutionary altruism. Unlike other forms of evolutionary altruism, aging offers benefits to the community that are weak, and not well focussed on near kin of the altruist. 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