Several parallel discussions inspire me to write this post partly in the hope that you will chime in.

The chance of life elsewhere in the universe just went to near zero. Or did it?

I was just hanging around minding my own business the other day when someone said to me, “you know, every single one of the five thousand or so exoplanet holding stars found to date have the gas giants in the inner, Goldilocks zone, and the smaller Earth-like planets are too far out to have life. So, the chance of life on other planets is way lower. Zero, basically.”

So, that was depressing.

Then, I went to the opening of the Bell Museum, and watched the planetarium show. After the show, I asked one of the people running the show, a somewhat snotty graduate student from the U, about this news. He got even snottier and told me that was ridiculous, that there are plenty of systems with Earth-like planets in the Goldilocks zone. I asked him how many. Plenty. I asked him if the number was double digit percentage or single digit percentage. He said may be single, but that was enough. I told him I had heard zero, which is not many. He said that was wrong.

Just a few minutes later, on visiting the rest of the newly opened museum, the penny dropped.

It turns out one of the major faculty members at the U in astronomy is one of the planet hunters, and a huge portion of the overall universe level exhibitry in the museum is devoted to showing this one guy’s work and talking about exoplanets and stuff. That must have been his student. Clearly, I had stepped in a pile of something.

My question is, a pile of what, exactly? Is there really recent research that suggests that the Earth’s solar system is unique among a sample of 5,000 or so? Or not? Or what?

The origin of life vs evolution

A long time ago, maybe 20 years now, some evolution-believing but sympathetic to religion people decided to say that the origin of life is not really in the purview of biology, and therefore should not be addressed in textbooks, high school courses, etc. You can think whatever you want about the origin of life, but it has nothing to do with evolution.

I’ve written about this. See:

“We can know nothing about the origin of life”
Is the origin of life different from evolution?

More recently, I find myself repeatedly being dragged into Twitter arguments between people saying that the origin of life is separate from evolution, vs. not.

The reason to say that they are separate is to allow religious people to have their god of the gaps, in this case, the ultimate gap. The pre-life gap.

The conception involves a very serious misconception about what the word “evolution” or the term “evolutionary biology” refer to. Most people misunderstand this.

I’ll give you an example. I was at a conference many years ago at the original Bell (not the one that just opened) and a well meaning but not well informed science teacher said to a room full of science teachers, “Evolution is simple. It is simple to teach. All evolution is…” then he proceeded to lay out the three Necessary and Sufficient conditions for Natural Selection.

Unfortunately, that is not what evolution is, and even more dramatically, it is not what evolutionary biology is about.

Evolution is the change over time in organisms, no matter how that happens.

Evolution is the idea of common ancestry and differentiation of lineages form common ancestors.

Evolution is increase of diversification over time, speciation, and extinction.

So that is three or four, maybe five things, depending on how you count them, that evolution is, and none of them need involve natural selection.

Oh, and natural selection is also part of evolution.

The point is this: If you think evolution is only this one thing, and define it very narrowly, then it is easy to figure that the origin of life is not part of evolution. But evolutionary biology is really the study of life in general, and all of it, in the context of evolutionary theory, and evolutionary theory involves everything from how molecules selectively interact (in primordial soup and in cells and other places) to how genes mutate, to how populations randomly drift genetically apart, or interact genetically, to how coeval lineages of organisms affect each other’s evolution (co-evolution), to how life and non life interact, to how natural selection creatively shapes life.

Evolution and evolutionary biology are two terms that refer to a thing and the study of a thing that is whopping big and complicated and wonderful and amazing and confusing and only barley understood.

To say that the origin of this thing is somehow separate is idiotic.

But to underscore the stupidity of this idea further, allow yourself to consider the following idea as possibly true.

Life evolved more than once.

Even more amazing an idea, and a very interesting hypothesis that we hope one day to test:

Under certain conditions, which are not uncommon in the universe, life almost inevitably arises, just as under certain conditions, a crystal is likely to form, rain is likely to fall, or a fire is likely to ignite. Life, in other words, happens.

If that is true, then the multiple origins of many life systems is clearly of no small interest to evolutionary biologists, and is very much part of “evolution.”

Which brings me to my third thought.

Life evolved independently on Mars, Earth’s Moon, Earth, and who knows where else. Or not.

There is a study just out published in Astrobiology, by Dirk Schulze-Makuch, that addresses part of this. I’ve asked for a copy of the paper, and if I get it, I’ll tell you about it. Without the paper, all I have is the breathless press release, and I’m not going to report on that.

But I can tell you that the basic idea seems to be that there is vague isotopic evidence of past life on the Earth’s Moon, and reconstructions of the Moon’s history suggest that at some point after its formation, and another time later when it was very volcanic, there would have been pools of water, an atmosphere, and some degree of protection from radiation, so life could have been there.

I’m of the belief that life is not that hard to get started. Why do I think that? Because it isn’t that hard to maintain it. Bacteria, especially, survive and do well under a wide range of conditions. A very simple virus can exploit cellular machinery pretty easily. Even though conditions on the early Earth were probably pretty tough, bacteria seem to have arisen early and held on — or perhaps re-started? — for a very long time. This is little more than a gut feeling, but it seems to me that life starting up isn’t that unlikely of an event, given the right conditions.

The reason we don’t see life originating again and again on our planet now may be because the startup does poorly in aerobic conditions. It may be because any molecules that start to form up in a way that leads to life are inevitably tasty food for existing life. Hell, there may be life almost starting up all the time in some places, and then being guzzled up by bacteria of some sort. And there are people looking for that sort of thing so maybe we’ll find that eventually.

Here’s my question on this. Which is harder to see happening, harder to believe, harder to accept, given what we know, and what we like to guess, about life?

1) Life started once, say, on Mars, and that’s it. Just that one time. Life found later on the Moon or on Earth came from Mars by a large rock hitting life-bearing mars, spreading rocks across the inner solar system, and some of those rocks eventually landed on the Moon and Earth, burning to a crisp in the atmosphere but somehow the bacteria on the rocks survive.

or

2) Life starts up easily and did so on Mars, the Moon, and Earth. For the first two, conditions for life were transient and have ended. For the Earth, conditions for life are a bit longer lived, and will end later.

Yes, yes, this all assumes there was life on Mars or the Moon, and we simply do not know that to be true at this time. This argument only matters if we pretend it was true, or at least possible. So this is speculation.

The Nuvvuagittuq belt in Quebec is a geological formation that includes such rock.

There are two basic ways to identify a tiny bacteria like life form. Well, sort of three. Method 1 is to find a physical structure that looks like the life form. So, little bacteria shaped do-dads might be bacteria fossils. Method 1a would be to find that, method 1b would be to find something slightly less direct, such as stramotlites, which is a kind of rock formed from the accumulation of bacteria byproducts. Method 2 is to look at the isotopes of key elements, usually carbon. There are a lot of ways for carbon to get mixed up in a rock. But, the non-life connected sequence of events that put carbon in a rock would sample the ambient carbon in a characteristic way. Since carbon comes in more than one stable isotope, the stable isotope ratio of the carbon in the abiogenic rock would reflect this pattern. But living systems tend to use carbon in a different way. The carbon atoms that get used by the tiny molecular processes involved in assembling molecules are biased in which carbon isotope they end up using. This results in a carbon isotope profile different than the expected ambient one, and suggests life.

Today in Nature, a paper by Matthew S. Dodd, Dominic Papineau, Tor Grenne, John F. Slack, Martin Rittner, Franco Pirajno, Jonathan O’Neil, and Crispin T. S. Little entitled “Evidence for early life in Earth’s oldest hydrothermal vent precipitates” (Nature 543, 60-64) reports, from the abstract:

… we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago.

I used to work down the hall from a guy who was involved in the search for early life. I won’t mention names, but at the time, I remember the fighting among scientists about whether or not this or that piece of evidence was legit was pretty intense. I think things have calmed down a bit. Back then, the battle was between Australia and Greenland. These days, apparently, Canada is in the act.

At present, the oldest evidence of life that is widely accepted is probably close to about 3.0 mya, with several older sites in contention. The newest find, as noted, dates to between 3.77 and 4.28 billion, and I understand the dates are somewhat controversial. If this site ends up as representing early life, it may well be the earliest, assuming the date is anywhere in this range. There are other cases that are close to 3.8 billion but the current study’s argument may be stronger. Over the last few years, the very nature of the study of early life on earth has gained a significant amount of perspective and methodological philosophy which I think will allow future work to be considered more sensibly. By this, I mean, that rather than asserting that this or that evidence is certainly indicative of early life vs. not conclusive (or not evidence of life) we will start seeing a more unified characterization of early environments and conditions, along side a better set of models for how life could originate. In that context we may never have an “earliest life” fossil, but we may have a much better story to tell about how early life could start.

I’ll add this: Consider the number of scientists working on a problem like aging in muscles, or how to attack a certain kind of cancer. Tens of thousands. Now, consider the number of scientists dedicated to working on the origin of life. Not many. Given the magnitude and difficulty of the problem — in the field, in the lab, and in the theories — there is no wonder it is taking science many decades to nail this problem down.

And, no, the origin of life is NOT different from evolution, no matter what the creationists tell you.

See: The Story Of Life in 25 Fossils by Don Prothero: Review

I’ve found that many people use the term “spite” incorrectly. Many assume it has to do with vitriol or nastiness, or otherwise, is motivated negative behavior of some kind. This is not even close to the scientific definition of the term. A daffodil plant can carry out an act of spite, and a daffodil plant is unlikely to engage in motivated behavior.

Spite involves carrying out an act where the ultimate cost to oneself exceeds the net benefit to oneself, at the same time the recipient of the behavior experiences a net cost.

Trump’s anti John Lewis tweeting is an example of spite. It was an attack on Lewis, but it caused huge problems for Trump, and strengthened his opposition.

Since Trump’s tweet may actually have benefited his victim and may have done very little harm to anyone else, it is actually possible that it was an act of altruism.

The pertinent theory comes from behavioral biology, which many years ago influenced economics theory, so you see the concept in both evolutionary theory and game theory today. (Because most people incorrectly assume that economists are smarter than everyone else, except possibly physicists, it is often assume that this set of theories comes from economics and then was borrowed by biology, but the reverse is actually true. See work by Sewall Wright and Robert Trivers.)

This classic theory can be classically represented by the following classic graphic:

The actor, called here the “donor,” can help or hurt the recipient. In this case, the potential act probably has to do with nuts, since these are squirrels. But it can be any act as long as the act itself incurs a cost for the actor. (The cost is part of the definition of acts.) Then, the actor and the recipient, eventually, count up the net result. The actor can expend energy and incur risk by taking a nut away from the recipient. The recipient runs away. This is an act of selfishness on the part of the actor. The actor can give a nut to the donor. That is an act of altruism. The actor and recipient can share the nuts under a tree, and thus share the job of keeping an eye out for predators. They are both losing because they need to share the nuts, but since there are a gazillion nuts the loss is very close to zero. Since two sets of eyes are more than twice as good as one set of eyes for feeding squirrels, both gain. That is cooperation. And so on.

Trup’s Attack on John Lewis was spite

Trump seems immune to the idea of forethought when he tweets. I sincerely — and this is not an ablist remark but a legitimate question — suggest he is a victim of Tourette’s. Even the most obvious degree of restraint is like water cast on granite. Alternatively, it is possible that Trump sees himself as invulnerable to legitimate criticism — all those who disagree with him are mere losers, he seems ready to declare. He does seem to have megalomaniac tendencies.

Whatever the reason, a pair of 140 character missives by Trump can be relatively benign or incredibly offensive, but this time were very self destructive.

John Lewis was up to the fight:

Lewis said in an interview on NBC News’ “Meet the Press” on Sunday, that he doesn’t believe Trump is a “legitimate president” and that he wouldn’t be attending the presidential inauguration for the first time in his 30-year political career, citing the intelligence community’s explosive findings over Russian hacking of the presidential election.

More here.

The material harm to Trump and his presidency from this act of spite is growing, as the tweet is causing a cascade of effects..

The number of Democratic members of Congress saying they will boycott Donald Trump’s inauguration on Friday has increased to 26.
Many have cited as a reason the president-elect’s recent attack on civil rights icon and fellow congressman John Lewis.

There is also a petition.

See also: BBC – Democratic Inauguration boycott grows

In the end, what started out as a harmful stab against an opponent caused more harm to Trump than benefit. If the tweets also harmed Lewis or Liberal Democrats, then this was probably an act of spite. If, and look at the squirrels above, this was an act that benefited Lewis, Liberals, and Democrats, and hurt Trump, then it was an act of altruism. Maybe the Democrats should send Trump a thank you note!

Trump vs. CIA chief

Everybody knows that in Washington, the story is usually the comment or reaction, not the thing. It is all very meta. The story is the story, not what the story is about. We have a new term these days bandied about to stand in for thinking about this: The narrative. You control the narrative. Just hope no one asks you to explain what a narrative is. This can all seem very senseless, but it is also a little bit complex, thus pretty much beyond the range of Trump’s level of thinking. And for this reason, perhaps, Trump has not learned when to shut up.

The result is that when a moderately interesting story comes along, Tump picks it up and bludgeons himself about he head and neck with it. Five year old’s do this. The John Lewis story is an example. Rather than ignoring a complaint from a liberal democrat, he victimized a widely loved civil rights leader on the eve of MLK celebrations.

With respect to the intelligence business, Trump is attacking the outgoing director of the CIA for absolutely no reason, and this is causing a reaction that will harm Trump far more than his comment could possibly have benefited him.

In a recent tweet, Trump accused the outgoing CIA chief of being behind the “leak” of the Trump Dossier. Meanwhile, the CIA chief notes that

…Trump lacks a full understanding of the threat Moscow poses to the United States, delivering a public lecture to the president-elect that further highlighted the bitter state of Trump’s relations with American intelligence agencies.

Trump’s reaction to the widespread acceptance of Russian influence on the election, and the as yet less widely accepted — but very credible — Trump Dossier is to elevate these problems to the level of international incident. In his effort to protect himself from political fire, he is holding up a baby in front of his attackers. Unfortunately, the baby is all of use, Americans, his country, and beyond.

Trump takes big risks with American security

This is yet another example of spite, and a good one, because it shows that spite does not require malice. It can arise from simple ignorance.

I think, and prove me wrong if you like, that the Trump transition team is, collectively, as dumb as a broken brick. When they saw all these “presidential appointments” on the list of things to consider, they assumed that they were to replace them all on the 20th of January. So, they fired everyone effective that day including all of the ambassadors around the world.

This is one of several examples of misunderstanding the system, and in this case, putting our nation at risk.

A plan by Donald Trump to toss out dozens of ambassadors on the day he takes office risks months of uncertainty in some of the most sensitive parts of the world, according to several experts.

More here.

You might argue that this is not spite because it was just stupid. But the evolutionary biological theory of behavior counts this as spite because motivation is not related to the definition. By keeping motivation out of the definition, the theory is more general. For example, a plant can carry out a spiteful act. That makes the theory a hell of a lot more useful.

In this case, the Trump team gained nothing from their decision, but they risk causing innumerable problems world wide, hopefully mostly small ones, that put them in the hole with respect to foreign policy literally on day one. Nay, minute one.

Spite ends things

Look again at the chart above, and consider examples of spite in nature.

You can’t easily find them. When you do see them, they usually end up being acts of altruism that are explained as acts of cooperation or selfishness by taking the analysis to the next level. A squirrel allows another squirrel to forage near itself even when there aren’t a gazillion nuts under the tree, and is taking a real hit on food access for this reason. That looks like altruism, which is even more stupid, evolutionarily, than spite. But it turns out that the recipient of that act it the actor-squirrel’s offspring. By benefiting an offspring even with a cost to herself, the mother squirrel gains an ultimate genetic benefit.

I do not see how any of Trump’s acts of spite benefit him other than to strengthen the love he receives from his relatively small base. His spite erodes his support at the softer end, invigorates (and increases funding for, I’ll guess) his opponents, causes problems for his administration that will make him and his entire presidency less effective. Ultimately, he will spite his way into impeachment.

We don’t see true acts of spite in nature very often because that sort of behavior, or more exactly, the behavioral facility to make the generation of such behavior even possible, is selected against.

If Donald Trump does not learn, or is not restrained, almost literally, by his staff, he will spite himself into the annals of the Darwin Awards, in a political sense. Spite ends things. Spite will end Trump.

This book is an interesting idea. Never mind the field guide part for a moment. This isn’t really set up like a field guide, though it is produced by the excellent producers of excellent field guides at Princeton. But think about the core idea here. Take every group of mammal, typically at the level of Order (Mammal is class, there are more than two dozen living orders with about 5,000 species) and ask for each one, “what does the fossil record look like.” In some cases, a very few living species are related to a huge diversity of extinct ones. In some cases, a highly diverse living fauna is related to a much smaller number of extinct ones. And each of these different relationships between the present and the past is a different and interesting evolutionary story.

If you looked only at the living mammals, you would miss a lot because there has been so much change in the past.

The giant sloths may be extinct, but Don Prothero himself is a giant of our age among fossil experts. His primary area of expertise includes the fossil mammals (especially but not at all limited to rhinos). I believe it is true that he has personally handled more fossil mammalian material, in terms of taxonomic breath and time depth, across more institutional collections, than anyone.

Don has written several different monographs on fossil mammal groups, and recently, a general fossil book for the masses, that have, I think added to his expertise on how to produce a book like this. Illustrations by Mary Persis Williams are excellent as well.

A typical entry focuses on an order, and the orders are arranged in a taxonomically logical manner. A living or classic fossil representative is depicted, along with some boney material, in the form of drawings. Artist’s reconstructions, photographs, maps, and other material, with phylogenetic charting where appropriate, fills out the overview of that order.

The text is expert and informative, and very interesting. the quality of the presentation is to notch. The format of the book is large enough to let the artistry of the production emerge, but it is not a big too heavy floppy monster like some coffee table books are. This is a very comforatable book to sit and read, or browse.

It turns out that if you combine living and fossil forms for a given group, you get a much bigger picture of the facts underlying any one of a number of interesting evolutionary stories.

In addition to the order by order entries, front matter provides background to the science of paleontology, including phylogenetic method, taphonomy, etc. There is a bit of functional anatomy, and extra detailed material on teeth because, after all, the evolutionary history of man mammal groups is known primarily by analysis of (and discovery almost exclusively of) teeth.

The end matter includes a discussion of mammalian diversification, extinction, and an excellent index.

If you wold like some background on how a scientist like Don Prothero writes a book like this, you can listen to this interview, in which we discuss this process in some detail.

One of the most important things about this book is that it is fully up to date, and thus, the only current mammalian evolutionary overview that is available, to my knowledge. In some areas of fossil mammal research (including in our own Order, Primates) there has been a lot of work over recent years, so this is important.

I highly recommend this excellent book.

The book as 240 pages, and 303 illustrations.

For your reference, I’ve pasted the TOC below.

TABLE OF CONTENTS:

Index (with Pronunciation Guide for Taxonomic Names) 234
]]> https://gregladen.com/blog/2016/11/15/prehistoric-mammals-by-don-prothero-review-of-excellent-new-book/feed/ 3 23314 https://gregladen.com/blog/2016/08/30/it-is-not-easy-being-green/ https://gregladen.com/blog/2016/08/30/it-is-not-easy-being-green/#comments Tue, 30 Aug 2016 15:27:21 +0000 http://scienceblogs.com/gregladen/?p=22799 The latest in GMO technology: Photosynthesizing Human Beans!

This is silly, but makes some good points. May be good for teachers in your biology class:

]]> https://gregladen.com/blog/2016/08/30/it-is-not-easy-being-green/feed/ 3 22799 https://gregladen.com/blog/2016/06/29/an-interview-with-don-prothero/ https://gregladen.com/blog/2016/06/29/an-interview-with-don-prothero/#respond Wed, 29 Jun 2016 12:28:21 +0000 http://scienceblogs.com/gregladen/?p=22684 Continue reading An Interview with Don Prothero →]]> Ikonokast interviews Don Prothero.

Don Prothero is the author of just over 30 books and a gazillion scientific papers covering a wide range of topics in paleontology and skepticism. Mike Haubrich and I spoke with Don about most of these topics, including the recent history of the skeptics movement, the conflict and potentials between DNA and fossil research, extinctions and impacts, evolution in general, and the interesting projects Don is working on now.

The interview is here. Please click through and give this fascinating conversation a listen!

]]> https://gregladen.com/blog/2016/06/29/an-interview-with-don-prothero/feed/ 0 22684 https://gregladen.com/blog/2016/05/16/how-the-venus-flytrap-evolved/ https://gregladen.com/blog/2016/05/16/how-the-venus-flytrap-evolved/#comments Mon, 16 May 2016 15:39:39 +0000 http://scienceblogs.com/gregladen/?p=22508 Continue reading How the Venus Flytrap Evolved →]]> The trick to understanding evolution is less about finding good answer to questions, but rather, finding good questions to answer.

Read that sentence twice, because it is very important.

Years ago, Niko Tinbergen developed a method of formulating questions about biology. I’m pretty sure the Tinbergenian method has not been integrated into most science standards and teaching curriculum. It should be.

There are four types of questions one could formulate about a biological system, trait, or observation.

1) Mechanistic. How does this thing work? What cellular processes are involved in a metabolic process, or how do the lever forces work in a joint, or how does a heterotroph get some food into its gut.

2) Ontogenetic. Given the various parts of an organism, how did they arise initially during development? Thinking only of multi-celled animals for a moment, all animals can be divided into large categories that have a common body plan, and that body plan is easily seen in the embryonic state. Looking at a fully formed adult, at any particular organ or part of an organ, we can ask, how did this thing form during the process of differentiating this particular taxonomic category? For example, mammalian pituitary glands are a combination of a bit of what would otherwise be brain, and a bit of what otherwise would be the roof of the mouth. This helps make sense of the pituitary gland.

3) Phylogenetic. How is a particular feature of an organism potentiated or constrained, in its development or function, by ancestry? Birds have either two or four wings (the four winged birds are all extinct). Birds with two wings have two legs. Why not have two legs, two arms, and two wings? Because birds evolve within a taxonomic group that have four limbs, so wings are modified versions of those limbs.

4) Functional. Sometimes called “ultimate” this category of question is largely (but not entirely) about natural selection. What is it about this trait, or this particular form of this train in this species (or sex of a given species) that enhances fitness. This is about the aspect of the trait that presumably caused the trait to spread and become typical, or that caused a particular population (the population with this specific trait) to become more representative over time, due to selection.

A simpler version of this divides all features into two categories, “proximate” and “ultimate.” The proximate stuff is the immediate description, what it looks like, how it works, etc. The “ultimate” bit is the functional question (number 4 above). I prefer to keep the four categories in mind.

By the way, there is a thing I call Greg’s Rule of Tinbergenian Inquisition (GROTI). This is not a hard and fast rule of nature or logic, but just a common occurrence. If you consider all four Tinbergenian questions in relation to a given trait, one of the four questions will produce a boring answer or a tautology. There are probably deep underlying philosophically interesting reasons for this, but the rule is more important as a guide to teachers. If you want to teach the Tinbergenian method of asking questions about evolution, by example, you will probably need to come up with two or more examples in order to not have one of the four approaches look silly. But I digress.

You want to know how the Venus Flytrap evolved, and some recent research sheds some light on this by looking at the ontogenetic and phyogenetic aspects of known traits.

Venus flytraps are plants that capture and then digest insects (or other small critters). The ultimate reason they do this may have to do with nutrients. Capturing and absorbing the tissues of insects provides nitrogen and some other often rare nutrients. So, the adaptation is to nutrient poor environments. One might guess that this is a trait that was selected for in nutrient poor environments, or one might guess that it is a trait that emerged largely by accident and then allows plants that do this to do better in nutrient poor environments. Or, one might not be too concerned by this distinction and guess that both features of the emergence of a trait are likely to be involved in the evolutionary history of a particular species and its adaptations. But, again, I digress.

So, the Venus flytrap has sensors on it that tell the plant that there is prey present. Then it snaps shut (that is the coolest ting about the plant, but we’re not actually going to go into that here). Then a liquid engulfs the prey and digestion happens, then a different liquid is exuded and this facilitates the transport of nutrients into the plant.

Now, think about plants, generally. Plants have all sorts of chemicals in them, or on them, that do all sorts of things. Is there anything about plants in general, about what they normally do, that could provide the genetic (and therefore metabolic or processual) basis for any of these things?

Yes.

Plants have hairs on the that detect the presence of possible herbivores.

Herbivores may use certain chemicals to break down plant tissue, for ingestion and digestion.

Plants have evolved chemicals that break down those chemicals.

The chemicals that counteract the breakdown of plant tissues probably scare off herbivores, or limit their success, but the can also break down some of the molecules that herbivores are made of.

Meanwhile, plants have genes that are expressed in roots that produce chemicals that facilitate the transport of nutrients from the roots into the rest of the plant.

So, from a recent write-up in Science:

To catch an invertebrate that has blundered into its snare, the flytrap relies on an ancient alarm system. It starts ringing when the victim jostles trigger hairs. The hairs in turn generate electrical impulses that somehow stimulate glands in the trap to produce jasmonic acid—the same signal that noncarnivorous plants use to initiate defensive action against herbivores. Patterns of gene expression in the two kinds of plants confirm the similarity…

…In noncarnivorous plants, jasmonic acid triggers the synthesis of self-defense toxins and molecules that inhibit hydrolases, enzymes that herbivores secrete to break down the plant’s proteins. As part of their counterattack, plants also produce their own hydrolases, which can destroy chitin and other components of insects or microbes. In the flytrap, … [t]ens of thousands of tiny glands make and secrete hydrolases. The trapped invertebrate is drenched in the same digestive enzymes that another plant might use in smaller quantities to ward off an enemy….

Then, plant genes code for chemicals that help absorb the nutrients from the insect.

Experiments showed that many of these genes are the same ones expressed in the roots of other plants. “We looked at each other and said, ‘Yes, it’s a root,’” Hedrich says. “It made immediate sense,” because the flytrap draws its nutrition not from soil, but from its prey.

We now have a phylogenetic look at a large part of the Venus flytrap’s unique insectivores adaptation. As is generally the case, these novel adaptations are reworkings of pre-existing adaptations.

And, ontogenetic questions arise (but are not directly addressed by this research). How did the genes and their products normally found in roots get into the “stomach” thingie of the flytrap? Did the site of differentiation of root structures move to elsewhere in the plant, or is it just the genes being expressed in different cells? This question came to my mind reading this story, but I’m more of an animal guy than a plant guy. Animals have homeobox genes that control the overall differentiation of tissues, and stem cells that determine and limit, at various levels, what the possible cell types are in a give part of the developing animal. Plants are different. This is one of the reasons that plants can propagate vegetatively and few animals do anything similar.

So I asked Dr. Rainer Hedrich, the flytrap guy who produced, with his team, this research, if this was a case of the movement of root tissue into the business end of the flytrap, or, alternatively, the expression of genes in tissue that are not normally expressed there in a plant.

He told me, “The flytrap develops from tips of Dionaea leaves. So, the trap is a leaf on one side. The inner surface of the trap is covered by a turf of glands, and these glands express genes one otherwise finds in roots. So, the trap is a leaf with root function. Most likely, to serve carnivory, Dionea modified a transcription foactor or promoter of root genes and so directed them into the glands.”

So, the story remains one of phylogeny, not ontogeny. The ontogeny part of the story is uninteresting, but the funcitonal, phyogenetic, and mechanistic parts of the story are fascinating.

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The paper:

Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. Felix Bemm, Dirk Becker, Christina Larisch, Ines Kreuzer, Maria Escalante-Perez, Waltraud X. Schulze, Markus Ankenbrand, Anna-Lena Van de Weyer, Elzbieta Krol, Khaled A. Al-Rasheid, Axel Mithöfer, Andreas P. Weber, Jörg Schultz, and Rainer Hedrich. Genome Res. Published in Advance May 4, 2016, doi:10.1101/gr.202200.115

Graphic at the top of the post from here. Caption: Venus flytrap with its turf of glands and some gland complexes under the microscope – color enhanced transmission electron micrograph (TEM). B) Cross section of a gland complex showing the three characteristic cell types (Picture: Dirk Becker, Sönke Scherzer, Christina Larisch)

]]> https://gregladen.com/blog/2016/05/16/how-the-venus-flytrap-evolved/feed/ 8 22508 https://gregladen.com/blog/2016/02/11/the-serengeti-rules-the-quest-to-discover-how-life-works-and-why-it-matters-book-review/ https://gregladen.com/blog/2016/02/11/the-serengeti-rules-the-quest-to-discover-how-life-works-and-why-it-matters-book-review/#respond Thu, 11 Feb 2016 18:00:11 +0000 http://scienceblogs.com/gregladen/?p=22129 Continue reading The Serengeti Rules: The Quest to Discover How Life Works and Why It Matters (Book Review) →]]> Sean B. Carroll is coming out with a new book called The Serengeti Rules: The Quest to Discover How Life Works and Why It Matters.

This is the molecular biologist Sean Carroll, as distinct from the physicist (who wrote this).

Homeostasis is one of the basic principles of biology. The term can be applied broadly to mean that certain numbers are maintained within a certain range. This could refer to energy flowing through a system, numbers of specific cellular products like enzymes, numbers of individual organisms in an ecological system, etc. It is not so much that numbers don’t change. Change in numbers is often central to a physiological process. But the change is either demanded by a system of regulating numbers, or is a perturbation in a system that is responded to by regulation. Regulation is one of those key concepts that can be applied across pretty much all systems, and provides a powerful point of view from which to understand what is happening in any living system.

Carroll is a molecular biologist, so much of his training and work is about regulation: identifying it, characterizing it, figuring it out. What Carroll has done in this book is to apply this point of view broadly to biological systems, looking at things inside cells and things inside major ecosystems. The title of the book comes from his own experience visiting the Serengeti as a safari-going tourist, in combination with the fact that this particular ecosystem is one of the best studied in the world. Many different scientists studying everything from grass to microbes to lions to antelopes have spent countless hours observing, characterizing, and trying to explain the dynamics of the Serengeti. As Carroll points out, this is true of a number of different ecosystems, and he could well have named his book, “The Lake Erie Rules,” but that would not have been as cool of a name.

So Carroll has done, then, something that is very dangerous and often does not go well. He’s taken insight derived from his expertise in small scale, mostly sub-cellular, biological systems, and using the touchstone of regulation, applied this insight to help observe, describe, and understand biological systems generally, with a strong focus on ecology. When a scientist steps out of their normal realm to do such a thing, we often get something better ignored, because, in fact, it is not easy or, in some cases, appropriate to make this leap. In this case, however, it worked beautifully. Carroll’s book is fantastic, a success story in going form the specific to the general.

It helps that Carroll is a gifted writer, captivating and thoughtful, and highly respectful of the reader.

Carroll brings in the history of thought and research in the relevant areas of physiology, ecology etc. His messages are framed in the larger context of the Earth’s overall health and important environmental issues. He links the subject matter to key central themes in biological theory (such as natural selection and evolution). And this is all done very well.

You’ve seen the synthetic overviews of life and evolution framed in chaos theory, complexity theory, even quantum physics. This is better.

This is a book to give to your favorite biology teacher (high school or college), and that teacher will take from it examples, connections, lessons, ways of telling, that will enrich their teaching immeasurably.

I don’t think the book is available yet, but you can pre-order it.

]]> https://gregladen.com/blog/2016/02/11/the-serengeti-rules-the-quest-to-discover-how-life-works-and-why-it-matters-book-review/feed/ 0 22129 https://gregladen.com/blog/2015/12/02/the-story-of-life-in-25-fossils-by-don-prothero-review/ https://gregladen.com/blog/2015/12/02/the-story-of-life-in-25-fossils-by-don-prothero-review/#comments Wed, 02 Dec 2015 18:38:39 +0000 http://scienceblogs.com/gregladen/?p=21798 Continue reading The Story Of Life in 25 Fossils by Don Prothero: Review →]]> This is a review of The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution.

Fossils are cool. Why? Two very big and complex reasons. First, fossils allow us to reconstruct species that don’t exist any more. This is usually done by studying species that do exist, and using the information we glean from living things to interpret the details of the fossil species, giving it life. Second, fossils tell us about evolutionary change, both by showing us what evolutionary events happened that we would not be able to see in living species, and by showing us change. In order to understand the evolutionary history of life on our planet, we need to look at a lot of different fossil species, to develop histories of change and adaptation.

(OK, there may be more than two reasons fossils are cool. Feel free to add your fossil are cool ideas in the comments section below. Please to not say “to grind them up to make aphrodisiacs.”)

So, what if you had to describe the history of life by focusing on a small number of fossils? And, why would you do that? Last year, Paul Taylor and Aaron O’Dea did this with 100 fossils in A History of Life in 100 Fossils. I’ve looked through that book, and it is nice. But here I’m going to review a somewhat more recent book, just out, by Don Prothero, which has at least as much information in it but by focusing on a smaller number of cases: The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution.

Several of the fossils Prothero chose to illustrate the story of life represent major events or changes in the planet’s evolutionary history and diversification. For example, the nature of the earliest life forms is represented by the stramotlite, which is really fossil scum. Others illustrate key transitions within major groups such as the origin of hard body parts, or the major divisions of animals, such as the origin of the amphibians. Others are exemplars chosen because they are spectacular and/or because they are touchstones to understanding very different times in the past, or important categories of living and extinct forms. These examples include the extremes, as well as good exemplars of the “diversity in adaptations to size, ecological niche, and habitat.” Generally, the chosen representatives are fossils with good preservation, detailed study, and in general, piles of information.

Prothero also provides rich detail about discovery, early interpretations, and the role of specific fossils (or extinct species) in the history of thought about evolution. In some ways this may be the most interesting parts of the discussion of several of the fossils. And, the book is chock full of excellent and interesting illustrations.

As a result, the chosen 25 are somewhat biased towards the more spectacular, and intentionally, towards those extinct forms that people tend to gravitate towards because they are either very interesting or very spectacular (generally, both). It would probably be difficult to develop a panoply of species that ignore the dinosaurs, but the history of life on Earth could probably have been written without humans, as long as “providing a viable existential threat to all known life forms” was not on your list of key attributes to do cover, but Prothero takes on human ancestors, and covers more than one, because most of the book’s readers are likely to be humans.

There are far more than 25 life forms in The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution, because the author makes use of a much richer body of information than just the key chapter-titling form.

Also, Prothero is a world renowned expert on certain fossil groups, found among the mammals. Well, actually, a lot of fossil groups. And, his expertise is applied richly here, with the selection of a disproportionate share of mammals.

The author writes excellent, readable prose, and vigorously makes connections between evolutionary questions and evolutionary data. It is hard to say if this book supplants or enhances his earlier major monograph for the public on evolution, Evolution: What the Fossils Say and Why It Matters. Either way, you can safely assume the more recent volume is more up to date in areas where research has been active.

I’m thinking of getting a copy of this book for the local school’s library, as a gift.

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A selection of other books by Donald Prothero:

• Abominable Science!: Origins of the Yeti, Nessie, and Other Famous Cryptids

• After the Dinosaurs: The Age of Mammals (Life of the Past)

• Catastrophes!: Earthquakes, Tsunamis, Tornadoes, and Other Earth-Shattering Disasters

• Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet

• Rhinoceros Giants: The Paleobiology of Indricotheres (Life of the Past)

• Evolution: What the Fossils Say and Why It Matters by Prothero, Donald R. 1st (first) Edition [Hardcover(2007)]

]]> https://gregladen.com/blog/2015/12/02/the-story-of-life-in-25-fossils-by-don-prothero-review/feed/ 6 21798 https://gregladen.com/blog/2015/11/25/books-on-fossils-and-evolution/ https://gregladen.com/blog/2015/11/25/books-on-fossils-and-evolution/#comments Wed, 25 Nov 2015 18:20:17 +0000 http://scienceblogs.com/gregladen/?p=21874 Continue reading Books On Fossils and Evolution →]]> Over the last several months, a lot of great books on fossils and evolution (as in paleontology) have come out. I’ve selected the best for your consideration. These are great gifts for your favorite science-loving nephew, life science teaching cousin, or local school library. Actually, you might like some of these yourself.

Let’s start off with a kid’s book: Grandmother Fish: a child’s first book of Evolution by Jonathan Tweet.

From the blurb:

Grandmother Fish is the first book to teach evolution to preschoolers. While listening to the story, the child mimics the motions and sounds of our ancestors, such as wiggling like a fish or hooting like an ape. Like magic, evolution becomes fun, accessible, and personal. Grandmother Fish will be a full-size (10 x 8), full-color, 32-page, hardback book full of appealing animal illustrations, perfect for your bookshelf. US publishers consider evolution to be too “hot” a topic for children, but with your help we can make this book happen ourselves.

I reviewed the book here before it first came out. This was a kickstarter project, and it may be currently unavailable commercially, but if you click through to the kickstarter project you can probably get a copy of it.

The most recent book to come across my desk is Don Prothero’s The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution. I’ve got a review of Prothero’s book in my draft file, so look for that post coming out over the next few days.

One might ask, “how do you choose 25 fossils, among so many choices, to represent evolution?” Well, Don cheated a little by mentioning more than 25 fossils. Also, you really can’t do this. Don selected fossils using several criteria, but one basis for his choice was the availability of rich historical information about a fossil’s discovery, interpretation, and effect on our thinking about evolution. And, he covers all of that.

Don is one of those rare authors who is both an expert scientist and a great writer, with a proven ability to explain things in a way that is not watered down yet totally accessible.

Here’s a selection of the many other books written by Prothero:

• Abominable Science!: Origins of the Yeti, Nessie, and Other Famous Cryptids

• After the Dinosaurs: The Age of Mammals (Life of the Past)

• Catastrophes!: Earthquakes, Tsunamis, Tornadoes, and Other Earth-Shattering Disasters

• Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet

• Rhinoceros Giants: The Paleobiology of Indricotheres (Life of the Past)

• Evolution: What the Fossils Say and Why It Matters by Prothero, Donald R. 1st (first) Edition [Hardcover(2007)]

Evolution: The Whole Story is an astonishing book that needs to be on the bookshelf of anyone interested in evolution. The work is edied by Steve Parker, but authored by nearly a dozen experts in various subfields of fossils and evolution, so it is authoritative and scholarly. At the same time, it is very accessible and enjoyable. This is not a book you read from cover to cover, though you could. Feel free to skip around, and you;ll find yourself looking stuff up all the time.

The book is divided into major sections, and each section has a series of short pieces on this or that fossil, group of fossils, type of life system, method for studying fossils, etc. There is a running sidebar on the bottom of many pages giving “key events” in evolutionary history of the group of life forms under consideration The book is VERY richly illustrated, with detailed keys to the illustrations. Many of the illustrations are broken down into “focal points” that expand significantly on the illustrations’ details. There are countless additional inserts with more information. The book itself is beautiful, intriguingly organized, and it is full of … well, everything. The book is very well indexed and sourced, and has helpful, up to date, phylogenies and chronological graphics.

The Biology Book: From the Origin of Life to Epigenetics, 250 Milestones in the History of Biology (Sterling Milestones) by Michael Gerald and Gloria Gerald is a compendium of biological topics and key moments in the history of biological science, organized in a sort of chronological framework. Major groups (the insects, the amphibians), major ideas (Pliny’s Natural History, Ongogeny and Phylogeny), key physiological and developmental concepts (meiosis, mitosis, many topics in endocrinology), key fossils (like the Coelocanth) and so on are discussed, very nicely illustrated. This is almost like having a gazillian short articles from Natural History Magazine (or similar) all in one book. There are 250 biological “milestones” in all. The charming part of the book is that a milestone can be an evolutionary event, an extinction episode, the emergence of a great idea, or a particular discover. And, as noted, these are ordered across time, as well as one can, from the beginning of life to a selection of the most recent discovery. The book effectively combines history of biology (and related sciences) and the biological history itself.

Life’s Greatest Secret: The Race to Crack the Genetic Code by the well respected scientist and historian Matthew Cobb is a carefully and clearly written history of the discovery of the nature of DNA, covering a lot more than, and since, Watson and Crick. It is extremely well sourced, indexed, and supported, and very readable.

This is the detailed and authoritative work on all the elements that came together to understand the genetic code. Don’t talk about the discovery and understanding of DNA any more until you’ve read this book. From the publisher:

Life’s Greatest Secret mixes remarkable insights, theoretical dead-ends, and ingenious experiments with the swift pace of a thriller. From New York to Paris, Cambridge, Massachusetts, to Cambridge, England, and London to Moscow, the greatest discovery of twentieth-century biology was truly a global feat. Biologist and historian of science Matthew Cobb gives the full and rich account of the cooperation and competition between the eccentric characters—mathematicians, physicists, information theorists, and biologists—who contributed to this revolutionary new science. And, while every new discovery was a leap forward for science, Cobb shows how every new answer inevitably led to new questions that were at least as difficult to answer: just ask anyone who had hoped that the successful completion of the Human Genome Project was going to truly yield the book of life, or that a better understanding of epigenetics or “junk DNA” was going to be the final piece of the puzzle. But the setbacks and unexpected discoveries are what make the science exciting, and it is Matthew Cobb’s telling that makes them worth reading. This is a riveting story of humans exploring what it is that makes us human and how the world works, and it is essential reading for anyone who’d like to explore those questions for themselves.

Extinction and Evolution: What Fossils Reveal About the History of Life is a an updated version of a classic book about evolution and extinction written by one of the scientists who developed our modern way of thinking about evolution and extinction (especially the extinction part).

Eldredge’s groundbreaking work is now accepted as the definitive statement of how life as we know it evolved on Earth. This book chronicles how Eldredge made his discoveries and traces the history of life through the lenses of paleontology, geology, ecology, anthropology, biology, genetics, zoology, mammalogy, herpetology, entomology and botany. While rigorously accurate, the text is accessible, engaging and free of jargon.

Honorable Mentions: Older books that are great and may now be avaialable for much reduced prices.

I really liked The Great Transition: Shifting from Fossil Fuels to Solar and Wind Energy as an expose of a particular time period and major event in geological history. Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet by Prothero is a classic, again, looking at a fairly narrowly defined moment in prehistory. You can get it used for about five bucks.

The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution by Dean Falk is a great book focusing on one key human fossil. This is a personal story as well as a scientific one. Again, available used for a song.

Have you read Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body yet? I’m sure you’ve heard about it. It is still a great read, and you can get it used cheap.

The only book I would recommend that uses the “paleolithic” to advise you on diet and exercise is The Paleolithic Prescription: A Program of Diet and Exercise and a Design for Living.

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