Birds, bees, etc.

Yesterday I was thinking about sex.

Not like that.  My intention is to keep this blog PG-13.  I meant sexual reproduction in general, and the topic comes up because I just finished reading Riley Black's lovely new book When the Earth Was Green: Plants, Animals, and Evolution's Greatest Romance, which looks at paleontology through the lens of botany.  It's a brilliant read, the writing is evocative and often lyrical, and it needs to be added to your TBR list if you've even the slightest bit more than a passing interest in the past.

One of the topics she looks at in some detail is how sexual reproduction in plants -- better known as pollination -- led to an inseparable relationship between flowering plants and their pollinators.  A famous example is Darwin's orchid (Angraecum sesquipedale), a Madagascar species with night-scented white flowers whose nectaries are at the base of an impossibly long tube:

[Image licensed under the Creative Commons Bernard DUPONT from France, Darwin's Orchid (Angraecum sesquipedale) (8562029223), CC BY-SA 2.0]

Its discovery prompted Charles Darwin to predict that there must be a moth on the island whose mouthparts fit the flower, and which was responsible for pollinating it.  Sure enough, in a few years, biologists discovered the Madagascar hawk moth (Xanthopan morganii):

[Image licensed under the Creative Commons Nesnad, Xanthopan morganii praedicta Sep 16 2021 03-58PM, CC BY 4.0]

The problem is, such dramatic specialization is risky.  If something happens to either member of the partnership, the other is out of luck.  In fact, sexual reproduction in general is a gamble, but its advantages outweigh the risk, and I'm not just talking about the fact that it's kind of fun.

Asexually-reproducing organisms, like many bacteria and protists, some plants and fungi, and a handful of animals, have the advantages that it's fast, and only requires one parent.  There's a major downside, however; a phenomenon called Muller's ratchet.  Muller's ratchet has to do with the fact that the copying of DNA, and the passing of those copies on to offspring, is not mistake-proof.  Errors -- called mutations -- do happen.  Fortunately, they're infrequent, and we even have enzymatic systems that do what amounts to proofreading and error-correction to take care of most of them.  A (very) few mutations actually lead to a code that works better than the original did, but the majority of the ones that slip by the safeguards cause the genetic message to malfunction.

It's called a "ratchet" because, like the handy tool, it only turns one way -- in this case, from order to chaos.  Consider a sentence in English -- space and punctuation removed:

TOBEORNOTTOBETHATISTHEQUESTION

Now, let's say there's a random mutation on the letter in the fourth position, which converts it to:

TOBGORNOTTOBETHATISTHEQUESTION

The message is still pretty much readable, although the second word is now spelled wrong.  But most of us would have been able to figure out what it was supposed to say.

Now, suppose a second mutation strikes.  There is a chance that it would affect the fourth position again, and purely by accident convert the erroneous g back to an e, but that likelihood is vanishingly small.  This is called a back mutation, and is more likely in DNA -- which, of course, is what this is an analogy to -- because there are only four letters (A, T, C, and G) in DNA's "alphabet," as compared to the 26 English letters.  But it's still unlikely, even so.  You can see that at each "generation," the mutations build up, every new one further corrupting the message, until you end up with a string of garbled letters from which not even a cryptographer could puzzle out what the original sentence had been.

Sexual reproduction is a step toward remedying Muller's ratchet.  Having two copies of each gene (a condition known as diploidy) makes it more likely that at least one of them still works.  Many genetic diseases -- especially the ones inherited as recessives -- are losses of function, where copying errors have caused that stretch of the DNA to malfunction.  But if you inherited a good copy from your other parent, then lucky you, you're healthy (although you can still pass your "hidden" faulty copy on to your children).

This, incidentally, is why inbreeding -- both parents coming from the same genetic stock -- is a bad idea.  It doesn't (in humans) cause problems in brain development, which a lot of people used to think.  But what it does mean is that if both parents have a recent common ancestor, the faulty genes one of them carries are very likely the same ones the other does, and the offspring has a higher chance of inheriting both damaged copies and thus showing the effects of the loss of function.  It's this mechanism that explains why a lot of human recessive genetic disorders are characteristic of particular ethnic groups, such as cystic fibrosis in northern Europeans, Tay-Sachs disease in Ashkenazic Jews, and malignant hyperthermia in French Canadians.  It only happens when both parents are from the same heritage -- which is why "miscegenation laws," preventing intermarriage between people of different races or ethnic backgrounds, are exactly backwards.  Mixed-race children are actually less likely to suffer from recessive genetic disorders -- the mom and dad each had their own "genetic load" of faulty genes, but there was no overlap between the two sets of errors.  Result: healthy kid.

The difficulty, of course, is that despite its genetic advantages, sexual reproduction requires a genetic contribution from two parents.  This is tough enough with mobile species, but with organisms that are stuck in place -- like plants -- it's a real problem.  Thus the hijacking of animals as carriers for pollen, and the evolution of a host of mechanisms for preventing self-pollination (which cancels out the advantage of higher variation, given that once again, both sets of genes come from the same parent).

What's most curious about sexual reproduction is that we don't know how it started.  Even some very simple organisms have genetic exchange mechanisms, such as conjugation in bacteria, which help them not to get clobbered by Muller's ratchet, and something like that is probably how it got going in the first place.  We know sexual reproduction is evolutionarily very old, given that it's shared by the majority of life on Earth, but how the process of splitting up and recombining genetic material every generation first started is still a mystery.

Anyhow, that's our consideration of birds, bees, and others for the day.  I'll end by saying again that you should buy Riley Black's book, because it's awesome, and gives you a vivid picture of life at various times on Earth, not from the usual Charismatic Megafauna viewpoint, but from the perspective of our green friends and neighbors.  It's refreshing to consider how life is experienced from an entirely different angle every once in a while.

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Gender bender

Sex is a pretty cool phenomenon, and it's not just because it's kinda fun.

How exactly sexual reproduction first evolved isn't well understood, but its advantages are clear.  Asexually-reproducing species, like most bacteria, a good many protists, and a handful of plants and animals, result in genetic copies -- clones, really -- of the parent organism.  

The problem with this is twofold.  First, clones (being identical) are susceptible to the same pathogens, so a communicable disease that is deadly to one of them will wipe them all out.  In a genetically-diverse population, chances are there'd be some that were resistant or entirely immune; in a monoculture, one epidemic and it's game over.  (That's basically what caused the Irish Potato Famine; a one-two punch of cold, rainy weather and an outbreak of late blight killed nearly all of the island's potato crop, resulting in massive starvation.)

The second problem, though, is subtler, and causes problems even if there's no external environmental risk involved.  It's called Muller's Ratchet, named after American geneticist Hermann Muller, who first described the phenomenon.  Asexual species still undergo variation because of random mutations; at each generation, the DNA picks up what amount to typos.  The whole thing is like a genetic game of Telephone.  Each time the genes pass on, there are minor replication errors that accrue and ultimately will turn the whole genome into unintelligible garbage.

Various asexual species have evolved mechanisms for coping with Muller's Ratchet.  Some bacteria have multiple copies of critical genes, so if one copy gets knocked out by a mutation, they have other copies that still work.  Some evolved conjugation, which is a primitive form of sexual reproduction in which cells pair up and exchange bits of DNA, with the goal being the sharing of undamaged copies of important genes (as well as copies of any novel beneficial mutations that may have occurred).

So asexual reproduction is fast, efficient, and doesn't require finding a partner, but ultimately makes the species susceptible to the double whammy of disease proneness and Muller's Ratchet; sexual reproduction requires finding a partner, but increases overall fitness by improving genetic diversity.

Is there any way to gain both advantages without picking up the disadvantages at the same time?

This is one of the main drivers of evolution in flowering plants.  Some flowering plants can reproduce both sexually (through flowers) and asexually (through rhizomes, bulbs, and so on).  Grasses, for example, are pretty good at both.  A very few -- the commercial variety of bananas is one of the only ones that comes to mind -- only reproduce asexually.  (Which is why bananas have no seeds, and also why growers are in a panic over the spread of fusarium wilt.)  A lot of plant species only reproduce sexually, and this brings up the problem of finding a partner of the opposite sex -- which is difficult when you are stuck in place.

This is where pollinators come in.  Some flowering plants are wind-pollinated, and rely on the air to carry the pollen (containing the male gametes) to the ovules (containing the female gametes).  Others use nectar or color lures to bring in insects, birds, and even a few mammals to act as couriers.  But this risks having the pollinator simply double back and fertilize a flower on the same plant, meaning that the offspring is (more or less) identical to the parent -- obviating the advantage of sexual reproduction.

So a great many species have evolved mechanisms for facilitating cross-pollination and avoiding self-pollination.  Some of the brightly-colored flowers of plants in the genus Salvia have evolved a mechanism where there's a spring-loaded trigger -- a visiting bee trips the trigger and gets smacked by the pollen-bearing stamen, with the intention of startling it enough that it decides to move along and visit a different individual of the same species.  Many orchids have wildly byzantine mechanisms for maximizing the likelihood of cross-pollination.  Other species, such as some of the fruiting trees of the rose family (including cherries, apricots, and peaches) have bisexual flowers, but the stamens of one tree mature at a different time than the ovules do -- making self-pollination impossible.  Apples have a genetic barrier to self-pollination -- if pollen from an apple flower is brought to another flower on the same tree, it recognizes the ovule as genetically identical and simply doesn't fuse.

The reason this comes up is a study that appeared last week in the journal Science, looking at the genetics of gender and pollination in walnuts.  Walnuts, and most of the other members of the family Juglandaceae (which also includes hickories and pecans), are pollinated by the wind.  

[Image licensed under the Creative Commons Juglans regia Broadview, CC BY-SA 3.0]

Wind-pollinated plants are most at risk for accidental self-pollination; the wind, after all, isn't going to be attracted or deterred by any kind of mechanical contrivance, and wind-pollinated plants often produce tons of pollen (to maximize the likelihood of at least some of it hitting the target, since inevitably a lot of it is simply blown away and wasted).  This is, incidentally, why most allergy-inducing pollen comes from wind-pollinated plants like grasses, willows, birch, oak, cedar, and (especially) ragweed.

Walnuts, it turns out, solve this problem by switching sex every few weeks -- a particular tree only produces male flowers during one interval, then only female ones the next.  The following year, they do it again -- but changing the order of who is male when.  This renders self-pollination not just unlikely, but impossible.  And the paper, which came out of research at the University of California - Davis, describes the genetic mechanism for how this is controlled.

Oh, but you bigots, do go on and explain to me how in the natural world sex and gender are simple and binary, they're both fixed at conception, male-and-female-He-made-them, and so on and so forth.

Even after years of studying biology, and evolutionary biology in particular, I'm still astonished by the diversity of life, and how many solutions species have evolved to solve the problems of survival, nutrition, and reproduction.  It seems fitting to end this with the final paragraph of Charles Darwin's Origin of Species, which echoes that same sense of wonder:

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us.  These laws, taken in the largest sense, being Growth with reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less improved forms.  Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.  There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.

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Genetic leapfrog

Barbara McClintock is one of the most inspiring figures in the history of biology.  She received her Ph.D. in Botany from Cornell University in 1927 -- in a time when few women chose to go to college, even fewer pursued a major in the sciences, and almost none made it all the way to doctoral-level work.

In the 1940s and 1950s, she was studying the genetics of maize, especially how genes regulate the expression of seed color in multicolored "Indian corn."  What she found, she said, could only be explained if the genes were moving around within the genome -- altering expression because of shifting position.  When she published preliminary papers on the topic, her discovery was derided as "jumping genes," and no one much paid attention.  This led to her decision to stop seeking publication in 1953.

[Image licensed under the Creative Commons Steve Snodgrass from Shreveport, USA, Indian Corn, CC BY 2.0]

What it didn't do was to slow down her determination to continue her research.  She doggedly pursued her idea -- genetic transposition -- and finally had amassed so much evidence in its favor that the scientific establishment had to pay attention.  "Jumping genes" were a fact -- and in fact, have been found in every species studied -- and the phenomenon of transposition turns out to be a major factor in gene expression across the board.

The discovery, and the body of work that led up to it, earned McClintock the Nobel Prize in Physiology and Medicine in 1983 -- and to this day she is the only woman who has earned an unshared Nobel in that category.

Barbara McClintock died in 1992 at the age of ninety.  So it's unfortunate that she didn't live long enough to learn that not only to genes move around within the genome of an organism...

... they can jump from organism to organism.

Called horizontal transfer, this was initially thought to occur only in bacteria, where it helps them to avoid the bane of asexually-reproducing species, "Muller's Ratchet."  Since in asexual species, the DNA doesn't combine -- i.e., the offspring are clones -- mutations tend to accrue each time the DNA replicates, because replication isn't 100% faithful (it's pretty damn good, but not perfect).  You can think of it as a genetic game of Telephone; each copying process results in errors, and after a few generations, the DNA would be turned into nonsense (it's called a "ratchet" because like the mechanical device, it only goes one way -- in this case, toward converting the DNA into garbage).  But if horizontal transfer occurs, bacteria can pick up extra working copies of genes from their friends, meaning that if Muller's Ratchet knocks out a gene, chances are they have another version of it hanging around somewhere.

What no one realized is that like genetic transposition, horizontal transfer turns out to be ubiquitous.  And in a new paper out of the University of Adelaide, geneticists Atma M. Ivancevic, R. Daniel Kortschak, Terry Bertozzi, and David L. Adelson have shown that horizontal transfer is not only everywhere you look, it also is a major driver for evolution.

They write:

Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations.  TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events. 

Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes.  We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog.  Given that these transposable elements have colonised more than half of the genome sequence in today’s mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms.

Which I find simultaneously fascinating and creepy.  That a mosquito bite could not only make me itch, but inject into me the DNA of another species -- which then would colonize my own DNA, like some kind of molecular virus -- is seriously bizarre.

"Jumping genes, properly called retrotransposons, copy and paste themselves around genomes, and in genomes of other species," said project leader David Adelson in a press release from the University of Adelaide.  "How they do this is not yet known although insects like ticks or mosquitoes or possibly viruses may be involved – it’s still a big puzzle...  Think of a jumping gene as a parasite.  What’s in the DNA is not so important – it’s the fact that they introduce themselves into other genomes and cause disruption of genes and how they are regulated...  We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years."

So much of what's in "your" genome probably wasn't originally yours, or necessarily even originally human.  Kind of humbling, isn't it?  But I better go wrap this up, because I've got a mosquito bite that's itching like hell.  I'm just hoping that mosquito hadn't bitten a rabbit previously, because the last thing I need is to have a sudden craving for carrots.  I freakin' hate carrots.

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The Skeptophilia book-of-the-week for this week is Brian Greene's The Fabric of the Cosmos.  If you've always wondered about such abstruse topics as quantum mechanics and Schrödinger's Cat and the General Theory of Relativity, but have been put off by the difficulty of the topic, this book is for you.  Greene has written an eloquent, lucid, mind-blowing description of some of the most counterintuitive discoveries of modern physics -- and all at a level the average layperson can comprehend.  It's a wild ride -- and a fun read.