Richard C. Francis' "Epigenetics: The Ultimate Mystery of Inheritance"

This is an exciting topic and I had high hopes for this book. The book does include some wonderful "attention grabbing" stories of some biological facts that don't fit the traditional genetics story. It did introduce me to several areas of research where epigenetics his giving new insight into biology. But I felt the author could have provided more detail on the science and more a "lay of the land" review. The specific examples were interesting but without more background it is hard to appreciate them in the overall context of epigenetics as a scientific theory.

My lament may not be a fault of the author. I notice than when I look through the Wikipedia article on epigenetics I find much detail but not a solid sense of an over-arching scientific theory. I see many mechanisms discussed, but I feel the glue is missing, the stuff that makes these mechanisms all part of a coherent scientific theory. Maybe I'm asking for too much. But it feels as if "physics" is introduced as statics, dynamics, kinematics, etc. An assortment of subfields grouped under "physics". But what is the rational for physics as a scientific field and how do these subfields fit together into a whole? Presumably the glue and the coherent overarching theory is "epigenesis" but Francis' book doesn't make me comfortable that I understand this theory. I'm left seeing the trees but not the forest.

The author goes to great pains to make clear that epigenetics isn't just a new development in genetics. He wants to emphasize that the "genetics" in epigenetics derives from "genesis" and not "genes". It is a story of developmental biology. I especially enjoyed the section where he discussed "preformationism" and "epigenesis". I found this an excellent motivation for understanding why epigenetics as a new science is so important. It provides the scientific mechanisms to support epigenesis.

I found the material on "genetic imprinting" murky. He did labour mightily to make it clear, but I think I'm a victim of terminology. The word "imprinting" kept throwing me for a loop. There was nothing to imprint with imprinting. And it certainly has nothing to do with ethology's "imprinting". It is simply a deplorable lack of imagination in coming up with a technical term that adequately captures the concept.

The chapter on cancer and epigenetics was exciting. I can see great hope in dealing with cancer by changing the paradigm from genetics and disease to inter-cellular communication and control over gene expression.

He makes it very clear that the traditional story of genes are the blueprint and proteins are the resulting organism is far too shallow a story. The book makes it clear that something quite exciting is happening with discoveries of how inter-cellular communication is controlling gene expression through epigenetics and that the story of epigenetics is quite complex. I just wish he has expanded the book to cover more of the story.

I was disappointed in the book because it was written with a whiff of dry academic style. He needs to put more effort into using words to paint pictures and build up a story that can carry the average reader along. I found myself having to refer to the index far too often to keep straight terminology. Only specialists want to learn the opaque terminology of modern science. I'm happy to be acquainted with the words, but I need something more descriptive to hang my hat on. I need more of "tell me what you are going to say, say it, and then tell me what you just said to me" storyline so that I can get comfortable with new concepts and get confidence that I understand them.

You can get a sense of the dryness of the text from the postscript where he is reviewing the "themes" that his book covered:

The first theme concerns the nature of epigenetic processes: a form of gene regulation. Epigenetic gene regulation is long-term gene regulation, hence epigenetic alterations have long-term effects on gene behavior. Indeed, epigenetic alterations of gene behavior can be longer lasting than mutational alterations of gene behavior, epigenetic alterations of gene behavior are generally reversible.

I can vouch that the book supports the factual truth of all of the above, but you can see how turgid the style can be. That's a lot of dense prose that will put most readers to sleep with too much repetition of fairly opaque terms. You have to be motivated to want to wade through that kind of writing to understand what the author is trying to tell you. Sure, from an insider's viewpoint, all of that is obvious. But from an outsider's view there is that deadly repetition of $100 words labouring a point that is hard to discern.

I do recommend this book. It is an important field. You will find some interesting examples of epigenetics and get an appreciation of how it works. But it will mostly leave you desperate for a better text to more properly introduce you to the field. Something that goes beyond examples and presents a well rounded theory with all the examples safely embedded into a structure that makes sense of the field.

The New Biology

While creationists continue with their viselike grip on the minds of the young in America, real science marches forward.

Here is a UK Oxford collaboration called "e. chromi" that is playing with synthetic biology which moves past trying to "understand" life to actually engineering human-made life:



More info at the E. chromi home.

Basic Economics

Here are two bits from a fun article by Robert H. Frank in the NY Times. This looks at how female availability for marriage has ecomomic (and social) implications).

First, contemporary China where marriageable women are in short supply:

The Chinese government’s one-child policy, combined with a cultural preference for sons and technologies that permit selective abortion, have helped to create a large sex-ratio imbalance among young Chinese. For every 100 women in that group, there are now more than 120 men.

According to market models, the terms of trade in the Chinese marriage market should have shifted sharply in favor of women. And evidence suggests that young Chinese women and their families have in fact become much more selective in recent years.

They appear, for example, to focus more critically on the earnings potential of prospective mates. Because house size is often assumed to be a reliable signal of wealth, a family can enhance its son’s marriage prospects by spending a larger fraction of its income on housing. (Other families can follow the same strategy, of course, but when all families do so, the resulting homes are still reliable indicators of relative wealth.) Such a shift appears to have occurred.

For example, when Shang-Jin Wei, an economist at Columbia University, and Xiaobo Zhang of the International Food Policy Research Institute examined the size distribution of Chinese homes, they found that families with sons built houses that were significantly larger than those built by families with daughters, even after controlling for family income and other factors. They also generally found that the higher a city’s male-to-female ratio, the bigger the average house size of families that have sons.

Second, the US in the late 1960s when marriageable men were in short supply:

In the United States, the end of World War II and the return of millions of troops set off the baby boom. In the second half of the 1940s, the population swelled by almost 14 percent, versus growth of less than half of 1 percent during the first half of the decade. By the mid-1960s, many of those babies were reaching the traditional marriage age.

At the time, it was American custom for women to marry men several years older than themselves. In a typical wedding in 1969, for example, the bride might have been born in 1947 and the groom in 1943. Because of that custom, women at the leading edge of the baby boom confronted a significant shortfall of potential marriage partners.

Economics teaches us that when there is excess demand for a good, its price rises. According to this model, excess demand for grooms should have caused the terms of courtship to shift in favor of men.

Before the 1960s, cultural norms encouraged celibacy before marriage. The breakdown of those norms has been widely attributed to the introduction of oral contraception, which gave women an unintrusive way to protect themselves against an unwanted pregnancy. The pill no doubt played a role — perhaps a very big one — but skeptics object that effective alternative forms of contraception had long since been available.

The supply-and-demand model bolsters the skeptics’ concerns. Biologists describe a fundamental asymmetry in the sexual strategies favored by males and females in vertebrate species. Males, whose sex cells are cheap to produce, tend to favor more transient sexual relationships, whereas females, for whom pregnancy and birth are far more costly, tend to favor greater commitment. The sexual revolution, which bent cultural norms toward male preferences, may thus be partly explained by the excess demand for grooms in the 1960s.

My skeptical nature holds me back from saying "this explains everything". But I do think the above is a significant factor in these sociological changes. We are victims of larger social forces that swirl around us, just as our ancestors on the African plains were subject to the preditor-prey ratios between lions/leopards and humans. Our cultural/mental world is powerful, but not all-powerful. Outside forces still rattle our chain.

Science Through Song

Nothing like a nice song to make science more "accessible". From a blog at Smithsonian.com, a song about the Cambrian explosion:



Nothing deep about the song. You aren't going to learn anything surprising. But the melody is good and the performance is nicely done. I love the slide guitar.

... And I love the touch where they throw in the Canadian national anthem with a bit of "Oh Canada"! This national anthem isn't completely extraneous. The most famous example of Cambrian fossils is in Canada with the Burgess Shale.

Zimmer Talks about Viruses

Carl Zimmer write articles and books on biological topics. His latest book is titled A Planet of Viruses. Here is a recent talk he gave on that subject and is available as a video from FORA.tv:



Elsewhere Zimmer points out that we are more bacteria than human, i.e. we carry ten times the number of baterial cells in and on our bodies than we carry human cells. In this talk he astounds me with a new fact. We have roughly tens times as much endogenous retroviruses embedded in our genome than we have human genes in our genome! (This article by Zimmer gives examples of embedded viruses.)

To call yourself "human" is to be charitable. We are more bacteria than human and more virus than human. Who would have thought!

The Latest Dystopia to Fear

Here is a tongue-in-cheek look into the future where humans will be dominated by the birdbrained. From the Gawker blog:

There is not, as far as we know, a forum where we might place bets on which non-robot species is most likely to conquer and enslave the human race, but if there were, we would place our money on the African Grey Parrot, which, scientists have recently confirmed, has the capacity to reason, a skill that places it in the same category as chimpanzees, gorillas and humans.

[E]ach parrot watched a researcher hide a walnut under one opaque cup and a seed under another. Next the researcher hid the cups behind a screen, removed one of the treats and showed the bird which one had been taken. Finally, the screen was removed to see if the parrot could work out which treat must remain, and under which cup it must be.

Only one of the parrots, a female called Awisa, was able to do this, choosing correctly in three-quarters of the tests –- 23 out of 30. "So far, only great apes have been shown to master this task," says Mikolasch.

Obviously, not all African Greys are capable of logical reasoning—though neither are all chimpanzees or gorillas, or, we might argue, humans—but even if only one in seven are, that provides the frighteningly long-lived bird with an elite class to lead the rest into battle. As an added advantage, African Greys, unlike great apes, have the ability to mimic, and perhaps speak, human language; they are also, like all bird species, notorious liars. In any event, we are likely to be saved from a future under the booted talon of rational parrots only because robots will get there first, but in the spirit of planning for all eventualities we suggest being nice to all the African Greys you meet from here on out.

I might prefer the birds, but right now I'm still fixated on the singularity when the machines take over. I'm just hoping to be taken in as the pet of some kindly robot who will feed me and treat me well. In return I promise to act illogically and stupidly so that it will be amused.

The Science of Sleep

Here is an interesting panel from the June 2011 World Science Festival dealing with the issue of sleep and dreaming:



The web page with annotation introducing this panel can be found here.

I like the bit at 24:20 because it addresses the connundrum of why everybody finds their own dreams "meaningful" but find other people's dreams pretty boring.

The most fascinating bit is the section from 25:20 thru 49:20 where Matthew Wilson looks at his research on a rat's mind. First his has decoded the rat's experiencing the traversing of a maze and he can then follow the rat dreaming or rehearsing that traversal during sleep. What is especially fascinating is his interpretation of non-REM versus REM dreaming.

Long Lost Cousins

I've just discovered my long lost cousins...



That is, evolutionarily speaking.

The above sort of reminds me of this much closer relative of mine, a long-necked Karen with neck rings.

Christopher Ryan & Cacilda Jetha's "Sex at Dawn"

This was a fun read. Lots of sweeping generalizations. Lots of unique interpretations of facts. Lots of bold claims.

Previously I had written a review of this book and expressed some scepticism about the claims in this book. Now having read the book, I remain dubious about the more sweeping generalizations in this book. But I now will admit that the authors have gathered interesting facts to build their case. I simply think they make claims that go beyond the facts they have.

I'm willing to accept their argument that viewing monogamy as "natural" for humans is silly. But the same has been discovered for all those "virtuous" birds who were thought to be true to their mates but have been found cheating on the side. Sex and love are much more complicated than the standard account. This is amply demonstrated in this book.

I think variability in human societies and in human nature is wider than more standard presentations of "virtuous monogamy". But Christopher and Jethá see outliers and want to claim they represent the "true" nature of humans. I don't buy it. When they talk about wild sex and wife swapping among the pilots of WWII, I think -- but don't have the data to prove it -- that this was one reaction to the fear and stress of war and am willing to allow that this was a noticeable, sizable fraction of pilots, but I doubt it was anywhere near a majority. Christopher and Jethá go on to claim this was the birth of the wild swinger clubs of the 1960s. I can see it as a thread, one small feed-in to a movement that got popularized by the rise in interest in sex and "alternative" lifestyles during the 1960s. But I don't see it as evidence about the "true nature" of human sexuality.

What I do know is that the radical left in the late 19th century had their adherents to "free love". This was mostly men of status seeking access to impressionable women in "the movement". But that's the same old story of the alpha male getting access to concubines in Biblical days.

My simple-minded view is that monogamy is the choice of about 80% of the population. But within that 80% there is an unhappy half who fall into divorce, affairs, and serial monogamy to deal with their unhappiness. At the same time there is a peripheral 20% who evidence the variability in human sexuality. These are the swingers, the bi-sexuals, and the homosexuals and even the chastity fanatics of religion, the fetishists, and the mentally deranged sex killers.

Science of complex phenomena like people, institutions, and societies is not the hard science of physics and chemistry. The subject matter of the soft sciences is simply too complex to be nailed down with simplistic laws. The fact that you can find polygamous and polyandrous societies as well as group sex societies simply proves there is a lot of variability.

I do accept Christopher and Jethá's argument that sexuality changed as humans moved from foraging to agricultural societies.

Here are some bits from the book that I found interesting:

If it's true that multiple mating was common in human evolution, the apparent mismatch between the relatively quick male orgasmic response and the so-called "delayed" female response makes sense (note how the female response is "delayed" only if the male's is assumed to be "right on time"). The male's quick orgasm lessens the chances of being interrupted by predators or other males (survival of the quickest!), while the female and her child would benefit by exercising some preconscious control over which spermatozoa would be most likely to fertilize her ovum.

Prolactin and the other hormones released at orgasm appear to trigger very different responses in men and women. While a man is likely to require a prolonged refractory (or recovery) period immediately after an orgasm (and maybe a sandwich and a beer as well), thus getting him out of the way of other males, many women are willing and able to continue sexual activity well beyond a "starter orgasm."

It's worth repeating that primate species with orgasmic females tend to be promiscuous.

And this:

Before the war on drugs, the war on terror, or the war on cancer, there was the war on female sexual desire. It's a war that has been raging for longer than any other, and its victims number well into the billions by now. Like the others, it's a war that can never be won, as the declared enemy is a force of nature. We may as well declare war on the cycles of the moon.

There is a pathetic futility animating the centuries-long insistence -- against overwhelming evidence to the contrary -- that the human female is indifferent to the insistent urgings of libido. Recall the medical authorities in the antebellum South who assured plantation owners that slaves trying to break out of their chains were not human beings deserving of freedom and dignity, but sufferers of Drapetomania, a medical disorder best cured with a good lashing.

And this:

Our journey into deeper understanding of the "feminine soul" begins in a muddy field in the English countryside. In the early 1990s, neuroscietist Keith Kendrick and his colleagues exchanged that season's newborn sheep and goats (the baby sheep were raised by adult goats, and vice versa). Upon reaching sexual maturity a few years later, the animals were reunited with their own species and their mating behavior was observed. The females adopted a love-the-one-you're-with approach, showing themselves willing to mate with males of either species. But the males, even after being back with their own species for three years, would mate only with the species with which they were raised.

Research like this suggests strong differences in degrees of "erotic plasticity" (changeability) in the males and females of many species -- including ours. ... Greater erotic plasticity leads more women to experience more variation in their sexuality than men typically do, and women's sexual behavior is far more responsive to social pressure. This greater plasticity could manifest through changes in whom a woman wants, in how much she wants him/her/them, and in how she expresses her desire.

And this:

In Hierarchy in the Forest, primatologist Christopher Boehm argues that egalitarianism is an eminently rational, even hierarchical political system, writing, "Individuals who otherwise would be subordinated are clever enough to form a large and united political coalition, and they do so for the express purpose of keeping the strong from dominating the weak." According to Boehm, foragers are downright feline in refusing to follow orders, writing, "Nomadic foragers are universally -- and all but obsessively -- concerned with being free of the authority of others."

Prehistory must have been a frustrating time for megalomaniacs. "An individual endowed with the passion for control," writes psychologist Erich Fromm, "would have been a social failure and without influence."

This book is interesting and is well worth reading. I would simply warn the reader that the authors have an agenda that colours their presentation of the facts. They are right to attack narrow-minded "monogamous only" theories of human sexuality, but then they over-sell the idea that humans are built for wild group sex. I would agree that some are, but not everybody. They've identified variation and then latched onto an extreme to declare it the "new normal". It isn't.

Interesting Research Result on Autism

The NeuroLogica blog has an interesting post on ASD (Autism Spectrum Disorder). Here is the bit I found most interesting because it cites an interesting phenomenon of copy number variation which can act to turn up or down sociability:

Sanders et al studied 1124 families with one affected child with ASD and one unaffected child, with unaffected parents. They found that 6-8% of them could be explained by changes in copy number variants – how many copies of specific genes were present. Most intriguing, they found:

We find significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome, characterized by a highly social personality.

In other words – at one gene location where a deletion causes a syndrome characterized by a highly social personality, they found duplications associated with a decrease in sociability. This strongly suggests that the gene in question has a strong influence on sociability, and can be either turned up or down depending on the genetic change.

And this:

In another study in the same issue researchers find that large networks of genes are responsible for the ASD phenotype. Further they provide evidence that could explain the fact that males are at higher risk of ASD than females. They find that a much greater perterbation in the gene network is required for ASD to manifest in girls than in boys.

And it interesting that they are eliminating epigenetics as an explanation:

Genes evolve to respond to the environment, and increasingly scientists are identifying important epigenetic factors in disease. But the research to date suggests a highly dominant role for genetics in autism, and this recent research adds to the growing body of research supporting this.

Go read the original article to get the embedded links.

Know Your Sea Creatures

Here's a beautiful and informative video on the variety of sea creatures without backbones. This is a provocative video claiming "there is no such thing as a jellyfish":

By all accounts, jellyfish are creatures that kill people, eat microbes, grow to tens of meters, filter phytoplankton, take over ecosystems, and live forever. Because of the immense diversity of gelatinous plankton, jelly-like creatures can individually have each of these properties. However this way of looking at them both overstates and underestimates their true diversity. Taxonomically, they are far more varied than a handful of exemplars that are used to represent jellyfish or especially the so-called "true" jellyfish. Ecologically, they are even more adaptable than one would expect by looking only at the conspicuous bloom forming families and species that draw most of the attention. In reality, the most abundant and diverse gelatinous groups in the ocean are not the ones that anyone ever sees.

The above is from the Monterrey Bay Aquarium Research Institute.

You Are an Expression of Your Parasites

Here is a bit from a Scientific American article on how gut bacteria have been discovered to influence your mind:

How, then, do these single-celled intestinal denizens exert their influence on a complex multicellular organ such as the brain? Although the answer is unclear, there are several possibilities: the Vagus nerve, for example, connects the gut to the brain, and it’s known that infection with the Salmonella bacteria stimulates the expression of certain genes in the brain, which is blocked when the Vagus nerve is severed. This nerve may be stimulated as well by normal gut microbes, and serve as the link between them and the brain. Alternatively, those microbes may modulate the release of chemical signals by the gut into the bloodstream which ultimately reach the brain. These gut microbes, for example, are known to modulate stress hormones which may in turn influence the expression of genes in the brain.

Regardless of how these intestinal “guests” exert their influence, these studies suggest that brain-directed behaviors, which influence the manner in which animals interact with the external world, may be deeply influenced by that animal’s relationship with the microbial organisms living in its gut. And the discovery that gut bacteria exert their influence on the brain within a discrete developmental stage may have important implications for developmental brain disorders.

This reminds me of an ant whose mind is seized the parasite Dicrocoelium dendriticum and forced to go climb a grass stem and hang there waiting to be eaten by a grazing animal:

The second intermediate host, an ant (Formica fusca in the United States[5]), uses the trail of snail slime as a source of moisture. The ant then swallows a cyst loaded with hundreds of juvenile lancet flukes. The parasites enter the gut and then drift through its body. Most of the cercariae encyst in the haemocoel of the ant and mature into metacercariae, but one moves to the sub-esophageal ganglion (a cluster of nerve cells underneath the esophagus). There, the fluke takes control of the ant's actions by manipulating these nerves.[6] As evening approaches and the air cools, the infected ant is drawn away from other members of the colony and upward to the top of a blade of grass. Once there, it clamps its mandibles onto the top of the blade and stays there until dawn. Afterward, it goes back to its normal activity at the ant colony. If the host ant were to be subjected to the heat of the direct sun, it would die along with the parasite. Night after night, the ant goes back to the top of a blade of grass until a grazing animal comes along and eats the blade, ingesting the ant along with it, thus putting lancet flukes back inside their host. They live out their adult lives inside the animal, reproducing so that the cycle begins again.

To my mind, there is nothing quite as scary as being seized and turned into a helpless robot manipulated by alien life to satisfy its needs while you are trapped in your own body. It combines the horror of being paralyzed along with the horror of being used by another for their own benefit and at the expense of your own interests.

Here is a video of a fungus that seizes an ant and grows from its head. It gives me the shivers to watch:



You can read more about this brain-controlling, zombie ant making fungus here.

It's a jungle out there! Whoever can believe the soft soap story about gentle nature, of the lamb lying with the lion, about the noble primitive. No. The real world is fully of cruelly indifferent agents that sometimes cooperate but can also compete with or exploit their fellow creatures, cruelly exploit in the case of these parasites.

Is Deanimation in Your Future?

Here is an interesting TED talk by Mark Roth.



More information on Wikipedia.

Razzle Dazzle in Arachnid Land

This is a most impressive video of a spectacularly gorgeous spider, the peacock spider of Australia..



I can't help anthropomorphizing the video and believing it holds some "courting" cues for human males, i.e. spiff up with fancy duds, be sure to signal you intentions (not by swizzling your legs about, but by splashing money hither and yon), and be very careful in your approach to the female of the species. If she show disinterest, run like hell to avoid a bad outcome!

Confusing the Tool with the Object of Study

There is an interesting controversy in biology over the concepts of eusociality and inclusive fitness.

This blog posting by Carl Zimmer on the Discover magazine site sums up the state of the controversy and identifies the key paper that is driving the current intellectual battles. Zimmer sides with the mathematical modelers. The other side is led by E. O. Wilson and is represented by this paper "The Evolution of Eusociality" in the Nature journal.

But I worry that the argument of inclusive fitness is an example of science mistaking the tool for the object of the science. Sure, if you make the assumptions of inclusive fitness you "explain" a large number of eusocial species. But I fear that models, as tools to tweeze out principles and help understand complex phenomena, get reified into "solutions" when in fact they are idealizations and can't handle all cases.

Carl Zimmer is dismissive of the E. O. Wilson paper, but it appears to me that Wilson has a valid criticism of the modelers. His point is the eusociality, while being extremely successful as a strategy, is rare in nature because it requires some unlikely series of steps and especially because it requires multilevel selection (a viewpoint that is anathema to the inclusive fitness crowd and many geneticists). But nature is complex and the drive to find simple models boxes you in conceptually. It is as if physics only allowed ideal gas laws and ignored any explanatory mechanisms that went below the level of an idealized billiard ball (i.e. models that attempt to describe real gas behaviour).

In a multicellular organism you have "eusociality" at a level of cells. Clearly you have reproductive division of labour, overlapping generations, and cooperative care of the young. And in this case, this is a degenerate and simplistic case of "inclusive fitness" because the genes in all cells are exactly the same. The odd cells that don't fit this pattern, e.g. blood cells, in fact do have the same genes until late in their "maturation" where they discard the nucleus with the DNA and go into a robo-mode. So in fact they do fit exactly the assumptions of inclusive fitness. But what about symbionts? How do lichen flourish? How does this cooperation arise since the originating algae/cyanobacterium and the fungus share no DNA? It does despite no fitting the mathematical model of inclusive fitness.

I like Wilson's attempt to understand the rise of eusociality in five phases:

1. Formation of groups in a freely mixing population.


2. Historical accidents that lead to the accumulation of traits that make the change to eusociality more likely (i.e. preadaptions).


3. The rise of eusocial alleles.


4. Natural selection operating on emergent traits among the cooperating organisms in a eusocial group.


5. Natural selection operating on competing eusocial groups with their variant emerging eusocial traits.

That explanation has the richness to ring true to me. It is a much more credible account than the simplistic inclusive fitness model which is a simple calculation that can't explain how eusociality arises and changes over time.

I enjoy Carl Zimmer, but I think he has made a mistake in picking a "winner" in this controversy. Sure the inclusive fitness guys may have the "numbers" to be persuasive. But science isn't a political contest. Ultimately it is effectiveness of a theory in explaining the real world. It may take some time, but I expect that Wilson and his crowd will win this argument, not the simple modelers of the inclusive fitness crowd. They have a very useful tool for analysis, but (in my humble opinion) they've made the mistake of confusing the tool with their object of study.

Why is there World Hunger?

Superstitious, anti-science thinking is the simple answer. Here's a bit from a UK Guardian newspaper article:

Food prices worldwide were up by a whopping 25% in 2010, according to the UN's Food and Agriculture Organisation, and February marked the eighth consecutive month of rising global food prices. Within the past two months, food riots helped to trigger the ousting of ruling regimes in Tunisia and Egypt. (It is noteworthy that food prices increased 17% last year in Egypt, and the price of wheat, a critical staple there, soared by more than 50%.) For poor countries that are net importers of food, even small increases in food prices can be catastrophic, and recent bumps have been anything but small.

There are several causes of rising prices. First, large-scale disasters have precipitated localised crop failures, some of which have had broad ripple effects – for example, Russia's ban on grain exports through at least the end of this calendar year resulted from fires and drought. Second, deadly strains of an evolving wheat pathogen (a rust) named Ug99 are increasingly threatening yields in the major wheat-growing areas of southern and eastern Africa, the central Asian Republics, the Caucasus, the Indian subcontinent, South America, Australia and North America. Third, rising incomes in emerging markets like China and India have increased the ability of an expanding middle class to shift from a grain-based diet to one that contains more meat.

And fourth, against this backdrop of lessened supply and heightened demand, private investment in R&D on innovative practices and technologies has been discouraged by arbitrary and unscientific national and international regulatory barriers – against, in particular, new varieties of plants produced with modern genetic engineering (aka recombinant DNA technology or genetic modification, or GM). Genetic engineering offers plant breeders the tools to make crops do spectacular new things. In more than two dozen countries, farmers are using genetically engineered crop varieties to produce higher yields, with lower inputs and reduced impact on the environment.

And this:

In fact, the United States and Europe are diverting vast and increasing amounts of land and agricultural production into making ethanol. The United States is approaching the diversion of 40% of the corn harvest for fuel and the EU has a goal of 10% biofuel use by 2020. The implications are worrisome. On 9 February, the US department of agriculture reported that the ethanol industry's projected orders for 2011 rose 8.4%, to 13.01bn bushels, leaving the United States with about 675m bushels of corn left at the end of the year. That is the lowest surplus level since 1996.

So, what do we know? Bad weather and a virulent new plant pathogen. The weather will change. And science can help develop resistent strains to deal with the new pathogen.

Rising incomes is not a problem. It makes it tough for the world's poor, but rising incomes also gives them hopes that they too will earn more and eat better some day.

Anti-GM quackery is a real problem. This is anti-science at its worst. Mumbo jumbo about what is "natural" and how it goes "against God's will to move genes from one species to another" is nutty. And the lies these fanatics tell! They claim that new breeding programs based on GM need special scrutiny is the same nonsense as the belief that the tomato was a "poisonous food" back in 1590.

Worst of all are the doom-and-gloom crowd so worried about "global warming" that they are willing to sacrifice the poorest billion people so that the "global warming" crowd can tool around in their SUV's using ethanol. That's right. The "global warming" crowd burns food so they can enjoy their yuppie lifestyle and continue to spread malicious rumours about "global warming" while letting a billion or so people starve to death. Talk about misplaced values and skewed ethics! And these hypocrites dare to preach to the rest of the world and spread their vile propaganda, a lie about climate that isn't going to kill anybody. But they are willing to condemn a billion to painful starvation. Hypocrites!

The Mysteries of Life

When I was a kid, the world was simple. There were plants and animals. End of story.

Then it was rearranged to be little stuff versus big stuff, i.e. bacteria versus multi-cellular life.

But the story keeps getting more complicated. Here is the story from 30 years ago:

Click to Enlarge

Now there is the "web of life" and much more complicated story:

Click to Enlarge

Yep... now they claim "giant viruses" as a 4th domain of life. It just gets wierder and wierder the older I get. next thing you know they will add in a domain for Martian life and then we will be off to the races!

Carl Zimmer has an article in Discover magazine that argues that there are 4 domains of life, no the 3 domains of 30 years ago.

The Genesis Story

I like reading the Bible, but when I want to understand how the world works, I put that down and go read some science. If you want a real Genesis story, here's a bit from an article by Carl Zimmer in the NY Times:

The origin of animals is also one of the more mysterious episodes in the history of life. Changing from a single-celled organism to a trillion-cell collective demands a huge genetic overhaul. The intermediate species that might show how that transition took place have become extinct.

“We’re just missing the intervening steps,” said Nicole King, an evolutionary biologist at the University of California, Berkeley.

To understand how animals took on this peculiar way of life, scientists are gathering many lines of evidence. Some use rock hammers to push back the fossil record of animals by tens of millions of years. Others are finding chemical signatures of animals in ancient rocks. Still others are peering into the genomes of animals and their relatives like Capsaspora, to reconstruct the evolutionary tree of animals and their closest relatives. Surprisingly, they’ve found that a lot of the genetic equipment for building an animal was in place long before the animal kingdom even existed.

The trick of building a multicellular animal out of a single cell predecessor isn't in getting cells to stick together. It is in handling problems that single cells never face:

“When cells die in a group, they can poison each other,” said Dr. Michod. In animals, cells die in an orderly fashion, so that they release relatively few poisons. Instead, the dying cells can be recycled by their living brethren.

Another danger posed by multicellularity is the ability for a single cell to grow at the expense of others. Today that danger still looms large: cancer is the result of some cells refusing to play by the same rules as the other cells in our body.

Even simple multicellular organisms have evolved defenses to these cheaters. A group of green algae called volvox have evolved a limit to the number of times any cell can divide. “That helps reduce the potential for cells to become renegades,” said Dr. Michod.

To figure out the solutions that animals evolved, researchers are now sequencing the genomes of their single-celled relatives. They’re discovering a wealth of genes that were once thought to exist only in animals. Iñaki Ruiz-Trillo of the University of Barcelona and his colleagues searched Capsaspora’s genome for an important group of genes that encode proteins called transcription factors. Transcription factors switch other genes on and off, and some of them are vital for turning a fertilized egg into a complex animal body.

Fascinating stuff.

And for all those religious nuts who keep denying evolution because they want "intermediates", the fact is evolution is full of spandrels which lay the foundations for an evolutionary leap:

Studies by other scientists point to the same conclusion: a lot of the genes once thought to be unique to the animal kingdom were present in the single-celled ancestors of animals. “The origin of animals depended on genes that were already in place,” Dr. King said.

In the transition to full-blown animals, Dr. King argues, these genes were co-opted for controlling a multicellular body. Old genes began to take on new functions, like producing the glue for sticking cells together and guarding against runaway cells that could become tumors.

Meanwhile the origins of life get pushed back billions of years. And here's the latest thinking on the origin of animals:

Last year, Adam Maloof of Princeton and his colleagues published details of what they suggest are the oldest animal fossils yet found. The remains, found in Australia, date back 650 million years. They contain networks of pores inside of them, similar to the channels inside living sponges.

There's a lot more fascinating details in Carl Zimmer's article. Go read the whole thing.

Creepy Crawlies

I remember reading a science fiction story back in the 1960s that stuck with me. It was about an alien invasion that captured people, planted an egg inside them, and left them frozen, but conscious, as the egg grew within them to produce a new alien.

This world, our world, has such a nasty life form: fungi. Here's a newly discovered fungus taking control of an ant and using it for its own reproductive purposes. From Alex Wild's Myrmecos blog:


A Camponotus femoratus carcass sprouts an Ophiocordyceps stalk (Ecuador)
This week the biodiversity news is abuzz with tales of new Zombie-Ant Fungi. The sensationalized name aside, these are common rain forest fungi that infect an ant and convince it to walk to an area of optimal fungal growth conditions before killing it and consuming the carcass. It’s a classic case of parasites manipulating the behavior of the host for their own benefit.

If you click on the link in Alex Wild's posting you get to read the Wired article which starts:

Four new species of brain-manipulating fungi that turn ants into "zombies" have been discovered in the Brazilian rain forest.

These fungi control ant behavior with mind-altering chemicals, then kill them. They're part of a large family of fungi that create chemicals that mess with animal nervous systems.

...

Once infected by spores, the worker ants, normally dedicated to serving the colony, leave the nest, find a small shrub and start climbing. The fungi directs all ants to the same kind of leaf: about 25 centimeters above the ground and at a precise angle to the sun (though the favored angle varies between fungi). How the fungi do this is a mystery.

"It's related to the fungus that LSD comes from," Hughes said. "Obviously they are producing lots of interesting chemicals."

Before dying, ants anchor themselves to the leaf, clamping their jaws on the edge or a vein on the underside. The fungi then takes over, turning the ant's body into a spore-producing factory. It lives off the ant carcass, using it as a platform to launch spores, for up to a year.

"This is completely different from what we see in temperate zones where, if an insect dies from a fungal infection, the game's over in a few days," Hughes said. "The fungi rots the body of the insect and releases massive amounts of spores over two or three days. But in the tropics, where humidity and temperature are more stable, the fungi has this strategy for long-term release."

Of the four new species, two grow long, arrow-like spores which eject like missiles from the fungus, seeking to land on a passing ant. The other fungi propel shorter spores, which change shape in mid-air to become like boomerangs and land nearby. If these fail to land on an ant, the spores sprout stalks that can snag ants walking over them. Upon infecting the new ant, the cycle starts again.

Chemicals from this global group of fungi, known as Cordyceps, have been a part of traditional medicine for thousands years, and part of Western medicine for the last 50.

Organ transplant patients, for example, receive ciclosporin — a drug that suppresses the immune system, reducing the chance the body will reject the new tissue. Chemicals from this same fungal group are also used for antibiotic, antimalarial and anticancer drugs.

There's more with more pictures and text. Go read the whole article.

Experimental Science Denounces Right Wing Political "Theory"

For nearly 40 years a right wing politics has held sway that argues that humans are selfish and the only "glue" in society is through self-serving contracts. This philosophy argues that any government is a perversion because it claims to act on behalf of "the people" when in fact the only "real" values are greed and selfishness.

But experimental science denies this ridiculous view of human nature. Here is a bit from an interview with Frans Waal in the MDM Wonderlance on-line magazine:

For the past three decades, scientists and popularizers have tried to tell us that we and all other animals are inherently selfish, and that the evolution of morality is an almost impossible affair, since nature cannot provide the caring for others needed for morality. I call this "Veneer Theory," since it assumes that human morality and kindness is just a thin veneer over an otherwise nasty human nature. This is a position that goes back to Thomas Henry Huxley, a contemporary of Darwin, and has been repeated over and over even though Darwin himself disagreed. Darwin saw human morality as continuous with animal social instincts, and my own work is a return to Darwinian thinking. I am supported in this now by many recent studies that indicate that humans (and other animals) are far more altruistic and cooperative than was assumed. The field has radically changed in recent years. Psychologists stress the intuitive way we arrive at moral judgments while activating emotional brain areas, and economists and anthropologists have shown humanity to be far more cooperative, altruistic, and fair than predicted by self-interest models. Similarly, the latest experiments in primatology reveal that our close relatives will do each other favors even if there's nothing in it for themselves.

Chimpanzees and bonobos will voluntarily open a door to offer a companion access to food, even if they lose part of it in the process. And capuchin monkeys are prepared to seek rewards for others, such as when we place two of them side by side, while one of them barters with us with differently colored tokens. One token is ‘selfish,’ and the other ‘prosocial.’ If the bartering monkey selects the selfish token, it receives a small piece of apple for returning it, but its partner gets nothing. The prosocial token, on the other hand, rewards both monkeys. Most monkeys develop an overwhelming preference for the prosocial token, which preference is not due to fear of repercussions, because dominant monkeys (who have least to fear) are the most generous.

And he makes this comment:

I study chimpanzees, bonobos and other primates mainly to learn more about them, but of course they also tell us something about ourselves. We are primates, after all. So, a second goal over the years has become to understand human society and how many aspects that we consider complex -- such as culture, morality, politics -- actually have roots that can be illustrated by the behavior of other primates.

For example, chimpanzee males form a hierarchy in which the smallest male may be the leader. How is such a thing possible? It is based on deal making by this male: he is probably more diplomatic than the others, grooms his supporters, gives them bribes and favors, so that when he is challenged by a bigger male he has coalition partners that help him. Such coalitions are part and parcel of human politics, and are now very well documented in chimpanzees both in the field and in zoo settings.

They are not necessarily based on kinship, because -- as in humans -- chimpanzees often strike these deals with non-relatives, so long as both parties stand to gain. This is why I read Machiavelli in the time that I wrote Chimpanzee Politics, now almost thirty years ago: the old Florentine philosopher had more to offer than most books on animal intelligence.

OK, to be honest, De Waal isn't making the claim I headed this post with, but the reality is that the politics of the last 40 years has seen the biggest resurgence of right wing thinking since the 1930s leading into WWII. The good news is that all the demostrations around the world imply a reawakening of the democratic spirit to push back the false values sold to the public by right wing extremists.

For those horrified by violent demonstrations, a look at early democracy in Greece indicates that at the very roots of democracy lies a bloody struggle between tyrants and oligarchies composed of aristocrats versus the politics of the street that would rise up as democratic revolts from time to time. So violence goes deep and it goes far back into the past. Ideally there would be no violence, but the right is unwilling to give up power when their "politics" fails and the people become unhappy.

Violence is tragic, it is to be avoided unless you are like the Libyan people, trapped with no way out and your own crazed leader bombing you from the air and unleashing mercenaries to shell and shoot at you from the streets. In that case, democratic revolt -- even bloody revolt -- is justified to get the hand of the mad killer off your throat.