Is there a tree of life?: Gene transfer between fungal species

March 8, 2011 • 6:22 am

There is a group of what I call “postmodern evolutionists” who loudly claim that, for one reason or another, the modern synthetic theory of evolution has to be thrown out the window.  Epistasis, modularity, adaptive mutation, genetic assimilation—these are the buzzwords that will supposedly dismember modern Darwinism.  On closer examination, though, one always finds that the theory remains pretty much intact: that these phenomena, while interesting, hardly constitute a Kuhnian revolution in evolutionary thought.

One of the main claims of postmodern biology is that “horizontal gene transfer” (HGT), the movement of genes between distantly related species via ingestion, viral vectors, and so on, can not only serve as a previously unknown source of genetic variation, but will also, by blurring the true pattern of ancestry and descent, efface the tree of life.  The former claim is correct.  The latter claim, while probably wrong, is still quite popular, as evidenced by the cover of New Scientist last February:

Why was Darwin “wrong”? As I noted at the time, New Scientist claimed that HGT is so pervasive among species that “the tree of life is not a fact of nature.”  New Scientist’s claim was palpably wrong, since species do have ancestors, whether or not we can recover that ancestry, and their evolutionary history, via gene sequencing.  Too, there’s no evidence that HGT is pervasive in nature.  It’s fairly common in bacteria, and has been seen in a few multicellular species, including rotifers and even Drosophila, but it’s so rare in metazoans that in those groups it hardly constitutes a challenge to the tree of life.

HGT has now been found in fungi, previously thought to be largely immune to the phenomenon since fungi can’t digest entire cells—usually the way genes are passed among species. The new issue of Current Biology has a dispatch on the topic by Thomas H. Richards, “Genome evolution: horizontal movements in the fungi“, summarizing recent work in that group, including a nice new paper in the journal by Slot and Rokas (reference below).

As Richards notes, HGT is usually detected by reconstructing evolutionary trees using different genes.  Most of the trees will coincide, but occasionally the use of one gene gives a tree that’s wildly disparate, showing “relatedness” of species that we know from other data are pretty unrelated. That’s a clue that that gene has moved horizontally among the unrelated species, giving a false signal of close evolutionary ancestry.

Using this technique, Slot and Rokas found that an entire cluster of 23 genes, those involved in the metabolic pathway for making sterigmatocystin (a toxic compound that is a precursor for the deadly aflatoxins), had been horizontally transferred from Aspergillis to the distantly related Podospora.  That’s a lot of genes, and since genes involved in the same pathway are often physically linked on the DNA of fungi, there’s a potential for widespread transfer of entire metabolic pathways between species (metabolic genes appear to be horizontally transferred among all species much more often than “informational” genes involved in DNA replication and transcription).

How did this happen? Well, Aspergillis and Podospora often occupy the same niche: both are “saprotrophs“, or species that break down dead animals and plants.  Living cheek by jowl, some of the DNA of an Aspergillis could have been ingested by a Podospora in the stew of organic matter, and incorporated into its genome.  But we don’t know exactly how this happened.

Richards gives a nice diagram summarizing cases of HGT among fungal species. HGT events are shown as colored arrows superimposed on the family tree of species determined from sequencing other genes. (The Slot and Rokas finding is the blue arrow.)  Note that transfers often involve species that are quite distantly related (click to enlarge):

But Richards hastens to add that this transfer is not common enough to efface the fungal tree of life, which can easily be discerned by concordant patterns of ancestry among the many non-transferred genes:

The inventory of HGTs identified represents a relatively small fraction of any of the fungal genomes studied. Consequently, the scale of transfer is unlikely to prevent the accurate resolution of a fungal phylogeny, as some have suggested to be the case for the prokaryote phylogeny [1], but will provide an interesting source of future research as investigators compare trait evolution with the fungal species phylogeny.

Even with these fungi, then, Darwin wasn’t really “wrong,” But what is exciting is the manifestly non-orthodox idea that adaptive genetic change can involve not just mutations within a species, but the wholesale movement of genes between different species—often very different ones.  As Richards notes, fungi have acquired genes not just from other fungi, but from bacteria and even plants.

Look for more examples of bizarre and wide HGT as DNA sequencing becomes more common.  But don’t expect it to demonstrate that there’s no tree of life!

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Richards, Thomas A.  Genome evolution: horizontal movements in the fungi. Current Biology 21:R166-R167.

Slot, J.C., and Rokas, A. 2011. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol. 21, 134–139.

Kitteh contest: Mocha Java Hecht

March 8, 2011 • 5:38 am

Owner “LBBHecht” entered his lovely calico, Mocha Java Hecht, who seems to be a bit of a sycophant.

Presenting Mocha Java Hecht, a beautiful 15 year old calico! As you can see, she is quite the scientifically literate felid.. though she does prefer some authors to others! However, she makes sure to leave time to play (and sleep). One of her major vices is jealousy. She has outlived two younger pets, with whom – much to her chagrin – she had to compete for attention. Upon the recent death of her sister, she has become much more affectionate. Horrible, right? In her younger years, she was quite a hunter and a climber (her favorite spot was the top of the refrigerator), frequently ending up 30-50 feet off the ground in our huge oak tree, at which point an offering of catnip was necessary to coax her down.

Mocha also has a penchant for paper products – even more than most kittehs. Overall, she is more a ‘srs cat’ than she is a ‘LOLcat,’ but she has her moments. Most entertaining is when she messes up and then tries to save face and cover for herself. A couple of weeks ago, she dashed up the stairs wild-eyed. At first we thought she might be having a seizure. Quickly, however, we realized that she had somehow gotten a front claw buried in her tail! For all her pomposity, she is quite the coward, withdrawing to her mother whenever a competing felid enters her yard.

LBB adds:

I’m including a link to an album with a few more pictures of her.  They support her story, and you might find them interesting anyway. You can never have too many cat pictures!

Thirteen minutes with Hitch

March 7, 2011 • 12:53 pm

One of the three segments on last night’s 60 Minutes on CBS was an interview of Christopher Hitchens by Steve Kroft.  I didn’t learn a lot new, but watching the man talk is always mesmerizing.  There’s a salacious joke about Princess Diana, some self-assessment, a group interview of three of his pals (including Salman Rushdie and the editor of Vanity Fair), and a snippet of his appearance on The Daily Show on the evening after a serious health episode led doctors to tell Hitchens that he probably had metastasized cancer.

One thing that struck me about the interview was the physical resemblance between the young Oxfordian Hitchens:

and one of my rock heroes, Stephen Stills:

h/t: John Danley

A rabbi proves God

March 7, 2011 • 8:56 am

As a cultural Jew, I’m especially embarrassed when someone of my “faith tradition” (there, Dr. Ecklund, you can count me among the religious!) makes stupid arguments.  Evangelical Christians can be as moronic as they want, but when a rabbi says something dumb, well, that sets my DNA on edge.

Sadly, it happens all too often. Over at PuffHo, Rabbi Adam Jacobs offers “A reasonable argument for God’s existence.”  The good rabbi was prompted to post by repeated assertions that “most, if not all, religious systems rely solely on wholly unsubstantiated faith to support their beliefs.”  So he offers up what he sees as an airtight argument for god’s existence.

Here it is in one sentence:  Because we don’t understand how life originated on Earth, god must have done it.

The longer version:

And there’s the rub: There just is no evidence for it [the material origin of life on Earth]. Not one of them has the foggiest notion about how to answer life’s most fundamental question: How did life arise on our planet? The non-believer is thus faced with two choices: to accept as an article of faith that science will eventually arrive at a reasonable, naturalistic conclusion to this intellectual black box or to choose to believe in the vanishingly small odds that the astonishing complexity, intelligence and mystery of life came about as a result of chance, which of course presents its own problems:

“Suppose you took scrabble sets, or any word game sets, blocks with letters containing every language on Earth and you heap them together, and then you took a scoop and you scooped into that heap, and you flung it out on the lawn there and the letters fell into a line which contained the words, ‘to be or not to be that is the question,’ that is roughly the odds of an RNA molecule appearing on the Earth.” (Dr. Robert Shapiro, Professor Emeritus and Senior Research Scientist in the Department of Chemistry at New York University)

Ask yourself, do you believe in the RNA molecule? Do you accept Dr. Shapiro’s scrabble analogy as an actual possibility? Most people intuitively recognize that it’s not a reasonable position to hold. . .

. . . I posit to you that all the evidence points, in an obvious and inextricable way, to a supernatural explanation for the origin of life. If there are no known naturalistic explanations and the likelihood that “chance” played any role is wildly minute, then it is a perfectly reasonable position to take that a conscious super-intelligence (that some of us call God) was the architect of life on this planet. Everyone agrees to the appearance of design. It is illogical to assume its non-design in the absence of evidence to the contrary.

Ergo Moses.

Not only does Rabbi Jacobs make the common error that life’s origin was purely a “chance” event (once a molecule was capable of replicating, the manifestly non-chance scenario of natural selection would take hold), but he pulls the old creationist trick of taking a quote out of context to make it seem that a speaker said the opposite of what he really meant.  Jacobs gives this quote from Francis Crick to imply that that eminent scientist couldn’t accept a naturalistic origin of life:

“An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle.” (Francis Crick)

That snippet is soon to take its place in the pantheon of misused quotations of scientists, alongside Darwin’s truncated quote about the eye* whose use P.Z. Myers regards, correctly, as a touchstone of idiocy.  Let’s look at the full quote by Crick from Life Itself (p.88)

“An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going. But this should not be taken to imply that there are good reasons to believe that it could not have started on the earth by a perfectly reasonable sequence of fairly ordinary chemical reactions. The plain fact is that the time available was too long, the many microenvironments on the earth’s surface too diverse, the various chemical possibilities too numerous and our own knowledge and imagination too feeble to allow us to be able to unravel exactly how it might or might not have happened such a long time ago, especially as we have no experimental evidence from that era to check our ideas against.”

Notice how Jacobs not only truncates the first sentence (that’s terrible scholarship, and a bit dishonest), but, even more dishonestly, leaves out the last part, in which Crick cautions against taking our scientific ignorance as proof of a miracle.  That’s exactly the same kind of truncation that creationists perform with Darwin’s quote.  And Crick, by the way, was pretty much an atheist, though I think at times he described himself as agnostic.

Nope, we don’t yet understand how life originated on Earth, but we have good leads, and abiogenesis is a thriving field.  And we may never understand how life originated on Earth, because the traces of early life have vanished.  We know it happened at least once (and that all species descend from only one origin), but not how.  I’m pretty confident that within, say, 50 years we’ll be able to create life in a laboratory under the conditions of primitive Earth, but that, too, won’t tell us exactly how it did happen—only that it could.  And if it could, then we needn’t postulate a much less parsimonious celestial deity, especially one who forbids you to eat bacon, or enjoy meat and cheese at the same meal.

Rabbi Jacobs, you make me ashamed to be a cultural Jew.

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*”To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree”.  P.Z. Myers notes, “As everyone who has read the Origin knows, what he was doing there was setting up a rhetorical question, which he then followed by three pages of detailed description of exactly how such an eye could have evolved.”

Mimicry: polymorphism for camouflage in a caterpillar

March 7, 2011 • 7:07 am

This finding was published in 1989 by Erick Greene (reference and link below), who sent me these photos, but it’s such an astonishing case of mimicry that I showed it to my students last week.

It involves the caterpillar Nemoria arizonaria, the juvenile stage of a moth that lives in Arizona, New Mexico, northern Mexico, Texas and California.  It has two generations per year, one in the late winter/early spring and the other in the summer. In both cases the caterpillars, after hatching, live on oak trees and eat parts of them.

If the caterpillars hatch in the winter or early spring, they feed on oak “catkins” (flowers), and, sure enough, their bodies take on the appearance of a catkin, almost certainly to hide them from visual predators like birds. Here’s a “catkin morph” (to the right) next to some real catkins.

When the summer brood hatches, however, the catkins are long gone, and the caterpillars feed on the only food available: oak leaves.  This generation looks not like flowers, but like oak twigs:

It’s camouflage again, but a different type.  And it’s obviously adaptive, if you have several broods per year, to evolve an appearance that matches the environment in which you hatch. There are also differences not just in appearance, but in their heads and jaws: catkin morphs have smaller jaws suitable for eating the pollen grains, while twig morphs have larger mouthparts and jaws to nom the tougher leaves.  Finally, they differ in their behavior:  if you put the catkin morph on a twig, it moves back to the flowers, but the twig morph does the opposite.

The interesting thing about these two morphs is that they are genetically identical: a caterpillar of this species has genes that can make it look either like an oak flower, or like an oak twig.  Within its genome are two distinct developmental programs coding for its appearance, and which program is activated depends on the season (this temporally varying appearance of a single species is called a developmental polymorphism or a polyphenism).  How does the caterpillar know which set of genes to turn on, and when?

The two obvious environmental cues are photoperiod (which differs between winter/spring and summer) and diet.  Greene captured moths in the field and reared them on different diet and photoperiod regimes. It turned out that the only factor affecting appearance was diet: caterpillars reared on catkin diets assumed the catkin appearance; those raised on leaves turned into twig morphs.  Greene hypothesized that the critical chemical difference involved tannins (polyphenols), which are high in leaves and low in catkins.  Sure enough, caterpillars raised on artificial diets supplemented with polyphenols developed into twig morphs, even when they were also fed catkins.

The evolutionary advantage of producing two broods per year is obvious.  Although catkins seem to be a superior diet, they’re available only once a year during the short flowering period.  Any catkin morph that developed into a moth who was also able to produce twig morphs would leave many more copies of its genes than would a moth constrained to reproduce only once per year.

The precise evolutionary sequence of change, however, is unknown, since all we have is the endproducts.  Developmental polymorphisms are not unique to this species—they’re also found in aphids, rotifers, water striders and, of course, the social insects, where every female has the genes for becoming either a queen or a worker.

Despite our ignorance of the evolutionary path, the precision of the mimicry (to use a Stangroomism, look at them) tells us that when the proper mutations are available, natural selection can make an animal look almost identical to its background.  In this case we know the “targets” of selection: the appearance of a flower and a twig. And in both cases natural selection gets it spot on.  This precision also tells us that the predators—certainly birds—are sharp sighted. If they couldn’t see all that well, there would be no selective advantage to such a precise resemblance.  But we all know that birds have keen sight!

By the way, both forms of the caterpillar turn into this lovely geometrid moth, which itself seems to be a leaf mimic:

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Greene, E. 1989. A diet-induced developmental polymorphism in a caterpillar.  Science 243:643-646.

It feels so good when it stops

March 6, 2011 • 12:44 pm

Would you like the mental equivalent of hitting your head with a hammer? If so, here’s some fun courtesy of Denis Alexander at BioLogos.

First, another new reason to ignore the Gnu Atheists: they’re old, odd, and pointless:

“Yes,” I hear you say, “but isn’t it the case that today the UK is home to some fire-breathing scientist-atheists whose fame has spread throughout the world?” True, the way the media works does give huge scope for the dissemination of extremism, but the point in this case is that the number of such ultra-enthusiastic scientist-atheists is really small, to be counted on the fingers of one hand. They are retired elderly professors, with time on their hands, and to be frank my secular colleagues tend to treat them as slightly odd. What’s the point in getting all hot under the collar in crusading for a belief system that, in essence, just represents a disbelief in someone else’s belief system? That does seem a bit pointless.

And don’t miss Part 2!  Here we see true progress in theology: debates about angels on pins have been replaced by debates about precisely where in the hominin lineage we became sinful. (My money is on Homo erectus.)

Taking the corpus of Biblical literature as a whole, here we have a ‘grand narrative’ of creation, alienation from God due to human sin and disobedience, redemption through Christ, and a new heavens and a new earth.  We have the possibility of fellowship with God through freely willed choice. Our nearest cousins, chimps and bonobos, to the best of our knowledge, do not. So the curious Christian is likely to ask at least some time during their lives, “Well, when did that possibility first begin? When did people first start knowing the one true God in such a way that they could pray, walk with God, and be responsible to God? When could they first be judged by God because they had sinned?” It is those kinds of questions that the Retelling and Homo divinus type of models are interested in addressing. Did all this happen rather slowly, as in the first model, or rather fast, as in the second? Notice that the questions raised are not to do with the origins of religion (however defined), which is another kind of discussion altogether, but with the origins of spiritual life, knowledge of God, the time when humans first became answerable to God for their actions. . . .

. . . Think of the Retelling Model. Here in this context it is imagined that a population of early humans at some unspecified time come to an awareness of God as creator and of (at least some of) their responsibilities toward God, but reject the light that they have received. This is perceived to happen as a process over a long period of time, maybe thousands or even tens of thousands of years. In the case of the Homo divinus Model, such ‘spiritual enlightenment’ is seen as occurring less as a process, more as a saltation, again in a small human community or even in a single couple.

Are these “Models” really all that different from the “Flood Model” of Henry Morris and Duane Gish?  In all of these cases the models, unlike those of science, originate not from observations of nature but from a book of fiction.

See Eric MacDonald for the antidote.

Islam and science: cowed Muslim physicist cancels lecture on evolution

March 6, 2011 • 7:14 am

According to yesterday’s Independent, Dr. Usama Hasan, an imam who also happens to be a physicist at Middlesex University and a fellow of the Royal Astronomical Society, was forced to cancel a lecture on “Islam and the theory of evolution” because of death threats.  The lecture was to be held at Masjid al-Tawhid, a mosque in east London.  Sadly, he not only canceled the talk, but apologized for his heresy:

But according to his sister, police advised him not to attend after becoming concerned for his safety. Instead his father, Suhaib, head of the mosque’s committee of trustees, posted a notice on his behalf expressing regret over his comments. “I seek Allah’s forgiveness for my mistakes and apologise for any offence caused,” the statement read.

One hopes that he construed his “mistake” as giving a lecture where he might have been killed, not as talking favorably about evolution.  Hasan had given a pro-evolution lecture at the mosque in January, but was interrupted by leaflet-bearing fanatics who shouted him down (was there “forced laughter”?) and threatened his life.

Unfortunately, Hasan’s apology—which I’d normally dismiss as intellectual cowardice, but can perhaps be understood if he feared for his life—was not enough.  The mosque’s committee of trustees fired him as imam and vice-chairman of the mosque (which the Independent describes as running one of Britain’s largest sharia courts), and issued a statement characterizing Hasan’s views as a “source of antagonism in the Muslim community”.

This kind of thing is only going to increase as Britain and other countries of western Europe become more Islamicized.  The inimical effect of Islam on science is particularly worrisome in Britian’s odious institution of government-supported faith-based schools.  Watch part of these two videos by Richard Dawkins (the entire four-part series is here) on that topic.  The visit to an Islamic school, starting at 8:00, shows how religious instruction is used to undermine what the students learn in science classes. The upshot: none of the students wind up accepting evolution.

The discussion of Islam and evolution continues for the first minute and a half of the next video:

Granted, Islam is not the only faith that attacks science, and there are Islamic scholars who do accept evolution.  But, as Salman Hameed notes in a piece in Science on Islamic creationism, evolution appears to strike particularly hard at certain parts of Islamic dogma, especially the notion that humans are special.  Hameed gives a graph of acceptance of evolution in six Muslim countries (data gathered between 1996 and 2003).  It’s very low, much lower than in nearly all Western countries, with less than 25% of people accepting evolution except in Kazakhstan:

In a survey of 34 countries by Miller et al. in Science (ref. below), Turkey came dead last in accepting evolution (the U.S. was next to last):

Now this may have nothing to do with Islam, but I doubt it.  Of all the translations that I wanted for Why Evolution is True, the most important to me was Arabic.  Although evolution is formally taught in parts of the Muslim world, as far as I know there is no book in Arabic laying out all the evidence for evolution.  But I faced a lot of problems getting such a translation done, largely because no Arabic publisher wanted to touch it, even in countries like Kuwait.  (After some difficulties and the help of an Egyptian colleague, it may soon be translated in Egypt, although political troubles there may scotch that.)

So how do we fight the threats that Islam, like some other faiths, poses toward accepting science?

Alternative A: Convince the faithful that Islam is perfectly compatible with science.

Alternative B: Work to lessen the grip of Islam (and other faiths) on people’s minds.

Islamic scholars are already busy with the first alternative, but with little effect.  Alternative B, of course, is much harder, and will take much more time.  But think of the ancillary benefits: no more death threats to Dr. Hasan, no more sharia law, no more Muslim women being second-class citizens, no more jihad, no more stonings, no more acid thrown into the faces of Muslim schoolgirls, no more internecine killing between Sunni and Shiite Muslims—none of the pernicious and destructive behavior particularly associated with that faith.

I swear, sometimes I think that fellow atheists who want to foster the acceptance of evolution by making nice with religion are completely blinkered.  Their goal is to get people to accept any kind of evolution—including that driven or guided by gods—even if it conflicts with the notion of non-theistic and materialistic evolution held by scientists.  God made natural selection?  That’s fine.  God guided the process so that the evolution of god-worshiping humans was inevitable?  That’s okay too.  God inserted—as Catholic dogma asserts—a soul in the hominin lineage somewhere between Australopithecus and Homo? We’ll just keep quiet on that one.

And although those accommodationists are atheists, presumably aware of the the many destructive aspects of religion, you won’t hear them talking about that.  Nor will you hear them admit the obvious fact that the main impediment to accepting evolution in this world is not scientific ignorance, but religion.  Every anti-evolutionist I know, with the possible exception of David Berlinski, is motivated at bottom by faith.  Instead, faitheists yammer on about how important it is that Americans accept evolution, because otherwise, you know, we’ll fall way behind India and China. (So what?, I ask. A rising tide lifts all boats.)  They claim without proof that that evolution-acceptance will come only when atheists shut up about the incompatibility between science and religion, and when we get line with those accommodationists who osculate the rump of faith.  They assert that religion will always be with us and it’s useless to fight it—despite the fact that faith has largely disappeared in Europe.

They worry far more about an Alabama schoolchild accepting evolution than about an Afghan girl defaced with acid for daring to attend school at all.  For an atheist, that is a clear case of misplaced priorities, and it sickens me.

h/t: Malgorzata

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Hameed, S.  2008.  Bracing for Islamic creationism. Science 322:1637-1638.

Miller, J. D., E. C. Scott, et al. (2006). Public acceptance of evolution. Science 313: 765-766.