Just-so stories: why spiders don’t have necks

December 2, 2012 • 3:19 pm

Commenter Marella asked a question based on the post about scorpions just below:

Marella

What I’d like explained is why arachnids don’t have necks. Everyone else has one and finds it useful, but arachnids have to move their entire bodies to look around.

While having my walk, the answer suddenly came to me—in the form of a limerick. Or rather, the answer came to me as it would be given by a molecular biologist who denies the ubiquity of natural selection (e.g., two posts down). So:

An anti-selectionist lout
Was asked why all spiders are stout:
“Why, the gene for the neck
Is deleted, by heck,
And that’s why they can’t look about!”

And a related one just came to me in the shower (I swear: soon I’ll start dreaming about monkeys holding each other’s tails):

“The giraffe,” said this colleague last fall,
“Causes me no amazement at all;
“Why the gene for the neck
“Is repeated, by heck:
“And that’s why the damn thing’s so tall!”

Awww. . . a scorpion mom protects her kids

December 2, 2012 • 1:07 pm

According to both New Scientist and the GDT (Gesellschaft Deutscher Tierfotographen, or “Society of German Animal Photography”), this photo, by Ingo Arndt, was winner of the Fritz Pölking Award for 2012 (read about Pölking here):

Scorpion / Skorpion

Here’s the description from New Scientist:

WHAT’S not to love about this photo? In one fell swoop it inverts the reputation of a much-feared invertebrate. For the defenceless newborns sitting under the vicious sting are the scorpion’s own offspring, tended by their mother until they are big enough to survive on their own.

It’s not just me who likes the shot – it has won German photographer Ingo Arndt the Fritz Pölking award for the second time.

There’s a good reason why scorpions are one of the few instantly recognisable invertebrates: that bulb at the end of the abdomen is full of deadly venom. What is less well known is that unlike most other arachnids they are viviparous: rather than laying eggs they give birth to live young. The juveniles are unable to feed or defend themselves, or regulate their moisture levels – they need their mother’s protection. It’s all really quite cute.

Buthidae family – to which the animals pictured here belong – have venom that is deadly to humans. Cuddly they ain’t.

“The owner of the scorpion mentioned that the animal is very dangerous,” says Arndt. “I just kept a safe distance, around 10 centimetres. The good thing is that they can’t jump.”

h/t: Matthew Cobb

James Shapiro gets evolution wrong again

December 2, 2012 • 10:54 am

When is PuffHo going to realize that they’re publishing criticisms of evolutionary biology that are deeply misguided? Do they have no worries about misleading the public with bad science?

I refer to the recurring posts of my Chicago colleague James Shapiro, who is making a PuffHo blogging career out of attacking “neoDarwinism,” the modern theory of evolution.  Not that we haven’t a lot to learn yet about evolution, but Shapiro has repeatedly been going after the importance of natural selection (see screenshot below) without offering a viable alternative. That is, Shapiro sees organisms as “self organizing” units controlled by “natural genetic engineering”, which of course doesn’t explain in the slightest why those organisms are adapted to their environments.

I almost don’t have the heart to criticize his latest piece, “Why the ‘gene’ concept holds back evolutionary thinking“, except that there may be some people out there (including the science editor of PuffHo) who think that Shapiro’s lucubrations are scientifically supported. They aren’t: they’re the misguided ideas of a contrarian who thinks that he alone has the key to overturning the modern theory of evolution.

Now we do know a lot more about the genome than we did when Beadle and Tatum proposed their “one gene/one enzyme hypothesis.” We know now that there are more than just protein-producing units in the DNA: there are parts of those units that regulate their expression (though this was posited by Jacob and Monod in the early Sixties), there are non-coding regions within genes (“introns’) that get snipped out, there are “transcription factors” (protein-producing genes) that regulate the expression of many other genes (e.g., Hox genes), and now we know that there are “microRNAs”, small molecules that serve to shut off genes.

In other words, we’re starting to learn how genes (originally defined as “stretches of DNA that make proteins”) are regulated, and the definition of a “gene” has become somewhat blurry. But I still don’t see the harm in using its original definition so long as we realize that the genome comprises much more than just protein-coding units. (The ENCODE project, however, has drastically oversold the notion that what we thought of as “useless” DNA is really functional. There’s still a lot of junk in our genome that doesn’t seem to do anything.)

Anyway, Shapiro’s point is that our modern understanding of how genomes are constructed and regulated when building organisms has completely overturned the modern theory of evolution—including the importance of natural selection—by making the notion of a “gene” fuzzier.

He’s wrong, and he’s wrong because he doesn’t seem to understand how evolution works.

Shapiro notes:

The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term “gene.” In March 2009, I attended a workshop at the Santa Fe Institute entitled “Complexity of the Gene Concept.” Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term.

The modern concept of the genome has no basic units. It has literally become “systems all the way down.” There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other “DNA elements” (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.

. . .A particularly important novelty highlighted by the Genome Biology paper is the unexpected and burgeoning role of so-called “non-coding” RNAs (ncRNAs) in all aspects of genome function. Cells transcribe many functional ncRNAs from so-called “intergenic” regions that had no functional importance according to the genocentric theory.

From an EVO-DEVO point of view, it is important to note that many morphogenetic changes in evolution occur at regulatory sites rather than coding sequences. Moreover, we continue to discover how many of these changes occur “intergenically” and involve supposedly “selfish” mobile elements. . .

. . . Conventional thinkers may claim that molecular data only add details to a well-established evolutionary paradigm. But the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness. DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function.

I’m baffled. Yes, these new discoveries are exciting, but they have absolutely no bearing on two issues: 1) whether natural selection acts on these new bits of the genome, and 2) whether natural selection is the primary process that produces “adaptations” in organisms. After all, all these units of the genome are still bits of DNA residing within the genome (usually on chromosomes), and therefore must obey the laws of population genetics. And those laws say that if a bit of DNA helps the organisms’s reproduction, it proliferates. If it hurts the organisms’s reproduction, it gets expunged from the population. That’s natural selection. Ergo, all of those genomic things that regulate other genes are subject to natural selection (and, of course, genetic drift).

In fact, there’s little doubt (except in the mind of contrarians like Shapiro) that the mechanisms of gene regulation themselves evolved by natural selection.

Shapiro still hasn’t provided a credible alternative theory of how adaptive features of an organism arise. “Natural genetic engineering” certainly can’t.  And until he provides a credible theory, he will be a voice crying out in the wilderness, thinking himself a paradigm-changer but sounding more like a crank. For it is sentences like these—the last in Shapiro’s piece—that verge on the crankish:

Shortly before he passed away, Kurt Vonnegut told a radio interviewer that the public senses something amiss with what they have been told about evolution. Maybe the new, high-tech understanding of genomes will help reverse the disastrously low level in the U.S. of public understanding of evolutionary biology.

That is real hubris—to think that if evolutionists would only agree with your bogus biological notions, creationism would decline! Nope, it’s not misunderstanding of modern genetics that buttresses creationism—it’s religion. Only someone completely blinkered could think otherwise.

It isn’t the “gene concept” that holds back evolutionary thinking; it’s not only creationist opposition, but also people like Shapiro who, without any scientific support, mislead readers by arguing that the modern theory of evolution is fatally flawed.

Finally, from the comments, here’s Shapiro’s explanation about why I criticize him:

Picture 2

Sorry, Dr. Shaprio, but I’ve built my career on understanding the genetic basis of how species arise, not on “accepting the central role of natural selection as a creative force in evolution.” I do think natural selection is the only viable explanation for the adaptations of organisms, and we have plenty of evidence for that contention, but it’s hardly the cornerstone of my career.

And, thank Ceiling Cat, I haven’t aspired in my middle age to overturn well-established paradigms. The reason I defend natural selection is not because I’m somehow wedded to that idea to buttress my career, but because it is still the best explanation that we have for adaptations.

Unbelievable!

December 2, 2012 • 8:49 am

Yes, it’s the old Brewer and Shipley tune from 1970, “One toke over the line”—performed on the Lawrence Welk show!  Did they not know what the song is about? Apparently not (see below).

From Songfacts (my emphasis):

This song is about drugs, especially marijuana. A “Toke” is a puff from a marijuana cigarette or pipe. Tom Shipley explained: “When we wrote ‘One Toke Over the Line,’ I think we were one toke over the line. I considered marijuana a sort of a sacrament… If you listen to the lyrics of that song, ‘one toke’ was just a metaphor. It’s a song about excess. Too much of anything will probably kill you.”

Brewer says of the song’s origin: “We wrote that one night in the dressing room of a coffee house. We were literally just entertaining ourselves. The next day we got together to do some picking and said, ‘What was that we were messing with last night?’ We remembered it, and in about an hour, we’d written ‘One Toke Over the Line.’ Just making ourselves laugh, really. We had no idea that it would ever even be considered as a single, because it was just another song to us. Actually Tom and I always thought that our ballads were our forte.” (quotes from brewerandshipley.com)

Some radio stations refused to play this song because of the drug references, but not everyone got this meaning. In 1971 the song was performed on the Lawrence Welk Show by a wholesome looking couple Gail Farrell and Dick Dale, who clearly had NO clue what a toke was. Welk, at the conclusion of the performance of the song, remarked, without any hint of humor, “there you’ve heard a modern spiritual by Gail and Dale.” Brewer & Shipley heard about the performance and searched for the footage, but didn’t see it until the clip showed up on YouTube in 2007.

So much wrong: a reader’s comment:

December 2, 2012 • 5:25 am

A comment from reader agathosozoe, which I’ll put above the fold.  I don’t want to respond at length; I’ll allow the readers to do this as it was a comment addressed to the readers.  But be polite, as I ask when you address another commenter.

The more I read the comments here, the more I hear that from the atheist perspective, error has no rights. Thus, many that follow Jerry Coyne are convinced that I am in error.  You see, I am a theist of the ilk where my world view begins with “In the beginning, God created the heavens and the earth”. If there were no prohibitions, would you then begin to burn at the stake folks like me?  Will you ensure that I can’t teach my children, that I can’t get a job as a teacher?  So then, such evil practices have “evolved” from the religious community of the middle ages to the secular community of today? Think about such a world – I for one, would not want to live in such a world where error has no rights.

Historically, mankind has primarily been religious, spiritual, and accepting of metaphysical ideas.  Although Evolution does not properly deal with biopoiesis, I am confident that if you are an atheist this branch of science is also fully accepted as fact – it had to occur if there is no supernatural realm.  Granted – pure naturalism is the framework by which you start your analysis of reality.  However, how did you get here? As a theist I admit, easily enough, that major tragedy and evil has occurred in the name of God.  Yet, the principles of freedom, by which the political and scientific trajectory that that entire western world has jetted from, started from good, creative, and investigative aspects of theist.  Theistic scientist of the past may not have been Christians or Jews or Muslims (some were), but they practiced their craft and performed their investigation based on the belief that God gave the universe order and structure that can be discovered. If there is no God, they were wrong, BUT this is the perspective they had and this has given us the foundation of our modern society.

So, as you enjoy this supposed victory of mandating that evolution be taught as a “comprehensive and coherent scientific theory” and as Jerry as stated, you take this to mean “fact” (which I don’t – it’s strictly a comprehensive and coherent theory – valid science with valid questions, corollaries, and guidelines, but nonetheless, it is a theory), I ask you – take the high road.  Don’t become that which many atheists have despised in our shared history about religious oppressors. I don’t want a new dark-age where all of human life is forced to fit into some scientific, deterministic, calculated, complex set of scientific canons, creeds, and maxims. Love, relationship, care, compassion, empathy, grace, forgiveness and the like need the freedom to exist without being codified as some complex psychological outgrowth of evolutionary necessity.

Just three remarks:

1.  Who ever said we’d burn people at the stake for their beliefs, keep them from being teachers, or ensure that he can’t teach his children? It’s the religious people who do stuff like that!  We fight religion with words and writings, don’t prevent anyone from being teachers so long as they don’t foist their religious beliefs on others in the public schools, and feel (but don’t legislate) that it’s abusive to indoctrinate children with religion. And really, in an atheist world “error” would have  rights? (Well, there would be no right to teach creationism in public schools!) What about what religion does when, as in Iran or Saudi Arabia, it gets the upper hand? Do women have a right to drive in Saudi Arabia, a right to go to school in Afghanistan, or do Catholics have a “right” to engage in homosexual behavior?

2. Historically, “mankind” has oppressed women and minorities, killed strangers, and tortured animals.  What was characteristic of the past isn’t perforce correct. This person should read Pinker’s book The Better Angels of Our Nature.

3. If evolution isn’t a fact by this reader’s lights then neither are viruses and bacteria that cause disease, or atoms as a fundamental chemical unit of matter.

The reader’s concern is duly noted. I commend agathosozoe into your hands.

A cat

December 1, 2012 • 5:09 pm

Anybody with a cat and a piece of paper can do this. Try it at home and send me the results. There’s an autographed book for the winner IF the winner is really good. I reserve the right to determine that. Deadline: January 1, 2013.

yep (1)

Cool animals: Ctenophora and Cnidaria

December 1, 2012 • 1:05 pm

Earlier this week I reported having read Peter Holland’s lovely little book, The Animal Kingdom: A Very Short Introduction, which is larded with interesting facts about animals.  I highlighted some of them on the plane home, intending to check them out when I was back. And of course the facts did check out (the VSI guides are very reliable).  Today I’ll put up a few bits about the phyla  Ctenophora (comb jellies) and Cnidaria (jellyfish, coral, and sea anemones).

Ctenophores are some of the coolest animals around. They’re jewels of the sea, small transparent beasts of amazing shape and behavior. Some of them, as seen in the second video below, can pulsate with flashes of multicolored lights, like a neon sign flashing outside a diner (for many pictures of ctenophores, go here.)

One of Holland’s descriptions struck me, and made me want to look at the animal:

The best-known comb jellies are the grape-sized “sea gooseberries” such as Pleurobanchia found throughout Pacific and Atlantic oceans, and around the British coast.  But the most spectacular comb jelly is undoubtedly the giant 1-metre-long Cestum veneris, or Venus’s girdle, named after the Roman goddess of love. Instead of the usual egg-shape typical of ctenophores, this striking, iridescent animal has an elongated, ribbon-like body that shimmers in the sea as the sun’s rays are scattered by its rows of cilia. In Richard Dawkins’s words,Cestum is “too good for a goddess.”

Of course I wanted to see it, and found a video of the goddess from YouTube. The true beauty of this creature is seen beginning about 30 seconds in:

Here are more ctenophores; they’re amazing!

Another observation about jellyfish (Cnidaria) intrigued me:

Many rhizostomids [jellyfish in the order Rhizostomae, which has many mouths instead of a single one like many jellyfish], such as Mastigias papua, supplement their food intake by harbouring in their tissues millions of symbiotic algae capable of producing energy by photosynthesis.  This enables Mastigias to live at incredibly high densities. In “Jellyfish Lake” on the Pacific island of Eil Malk in Palau, intense aggregations of Mastigias papua can sometimes reach a thousand 6-centimetre animals per cubic meter of sea water.

Of course I found that hard to believe—such densities! But I checked it out and it’s true (well, I can’t verify the density figure). Here’s a video of Jellyfish Lake:

And a photo of the lake and a diver from echeng on Flickr: