Chopra responds about HIV/AIDS

January 30, 2015 • 7:25 pm

Someone whom I think is Deepak Chopra (the email address makes me a bit unsure) has responded to my criticisms of his earlier interview, an interview in which he stated, among other dubious claims, that the HIV virus is not the cause of AIDS. He now seems have retracted tha claim t without actually doing so. You can see his long comment (I’m assuming it’s him) here.

I have responded right below it.

Readers can feel free to respond as well, but, as always, do not be aggressive or nasty when dealing with someone who responds to public criticism on my site.

 

A seven-pound nutball

January 30, 2015 • 3:36 pm

This video was posted three days ago and already has garnered nearly two million views. Such is the power of cat videos, which someone should find a way to harness for good.  Anyway, this cat, named Luna and described as a “7-lb. nutball,” is about the most hyperactive kitty I’ve ever seen.

h/t: Su

 

Stephen Fry on God

January 30, 2015 • 1:30 pm

Stephen Fry is one of my heroes, and I shouldn’t have to explain why. In this video Fry is interviewed by the famous Gay Byrne for Irish television, and stuns Byrne with some rational thoughts about God:

I love that man!

Oh, and as a relevant lagniappe, I’ll add this photo that I found on John Loftus’s Facebook page. It’s basically true, but when you see it laid out this way the consummate craziness of religion becomes clear:

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The Infinite Monkey Cage does a U.S. tour, and has a show in Chicago avec moi

January 30, 2015 • 12:02 pm

I’ve never listened to the BBC’s “Infinite Monkey Cage” show (I almost never have time to listen to podcasts), but I feel that I have, because Matthew Cobb, Brian Cox’s colleague at Manchester Uni, has been on the show several times and has told me a lot about it. Apparently it’s good, as I’ve never heard anything but praise for it, and perhaps the greatest praise is this: it’s been #1 on the iTunes chart for all podcasts from the UK. That is amazing for a show about science. As of this weekend I’m going to listen to the show, and I have a new reason as well.

The show (official website with more information here; BBC website here; Facebook here; and Twi**er site here) stars physicist (and former rock star) Brian Cox and comedian Robin Ince, who educate and entertain their audience by bantering with a panel of scientists and Famous People. The show is recorded before a live audience.

So far the shows have been limited to the UK, but now the crew is going on the road—for a four-city tour of the U.S. As they’ve just announced, those cities include New York on March 5, Chicago on March 7, Los Angeles on March 12, and San Francisco on March 13. The list of scientist-guests is here, and there are more participants to come (look for updates).

I know almost all the scientists announced so far: they include Neil deGrasse Tyson, Janna Levin, Sean Carroll (the physicist) and Carolyn Porco. The great thing for me is that I’ll get to be on the show in Chicago along with my paleontologist colleague Paul Sereno, often described as “the new Indiana Jones.” I’d better bone up (Sereno, who excavates and studies dinosaur fossils, is already boned up). All the shows, as they are in the UK, will also be broadcast on BBC Radio 4.

I have a feeling tickets will sell fast, as the interest is likely to be high and the venues are small. Ticket information is here, and I’ll post the direct links to the ticket pages.  If you’re going to the Chicago show, I’ll see you there.

Oh, and congrats to Dr. Cox, who has just been named the Royal Society’s first Professor for Public Engagement in Science.
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Should there be a “Third Way” of evolution? I think not.

January 30, 2015 • 9:45 am

Someone just called a fairly new “Evolution-Needs-a-New-Paradigm” website to my attention, and I wish they hadn’t. The site, “The Third Way of Evolution,” has been going for some time and, according to the its notes, was created last May by two biologists, James Shapiro (here at the University of Chicago) and Dennis Noble, a renowed physiologist who was formerly a professor at Oxford, as well as by Raju Pookottil, an engineer credited with creating the site. Pookottil, showing the distressingly common trait of many engineers to question evolution while at the same time showing profound ignorance of the data supporting it, has allowed this to appear in his profile:

While [Pookotti]  was always unconvinced about the idea that a supreme intelligence could have created all life on earth, life unquestionably carries the hallmarks of design. As a weeding out instrument, natural selection has a certain role to play in evolution. But it cannot be the fundamental mechanism and the creative force driving evolution.  Even after 150 years, there are only a handful of examples of selection in action; and they are not very convincing ones either.

Evolution, he believes, is more of a Lamarckian process. In his book, Pookottil proposes a mechanism that could potentially explain how the whole thing might be working. Organisms do not need to depend on accidental mutations and selection. They have built in capabilities that allow them to interact with the environment and devise clever solutions. If a panda is in the process of generating a new thumb, it has worked out exactly where it needs one and how to build it. The emerging field of epigenetics is spearheading a comeback for Lamarckian evolution. There is now a rapidly growing list of examples that demonstrate that acquired characteristics can be transmitted for many generations. If Lamarckism is the future, here is how it could be working; right from forming the very first cells, to generating novel proteins, all the way to building whole complex organisms.

Here we have both the misguided criticism of evolution that characterizes the  wholesite (really, few and “not very convincing” examples of selection in action?), as well as the invocation of “revolutionary” new processes for which there’s virtually no evidence—or at least no evidence that the processes had an important role in evolution and adaptation. (In Pookottil’s case, it’s a nebulous form of Lamarckian inheritance.) The scenario of a panda somehow working out where it needs a new thumb and then building it is laughable, even if it doesn’t involve a quizzical panda pondering what it might do to strip leaves from bamboo.

But what is “The Third Way of Evolution”? The site explains:

 The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis. Many scientists today see the need for a deeper and more complete exploration of all aspects of the evolutionary process.

As for the last sentence, who would deny that we need to explore more deeply how evolution works? After all, we don’t know everything about it. But what we do know is that the outlines of modern evolutionary theory, and the importance of natural selection, seem indisputably correct for now, and that there’s no pressing need for an overturning of that theory.

Given the site’s explicit denial of creationism, it’s a bit surprising that it has been touted by Denyse O’Leary, the reliably vacuous “reporter” on ingelligent design for the ID website Uncommon Descent. But of course ID advocates try to hide their creationism under a bushel, changing their tactics to assert simply that the modern theory of is fatally flawed. Once the theory is demolished, they hope, Jesus will then rush in to fill the gap.

But I digress. What is distressing about the “Third Way” site is that about 50 biologists, physicians, physicists, mathematicians, historians of science, and even an expert in semiotics have joined this anti-Darwinian chorus. As I read over the list, I recognized quite a few names, especially those in my field, and I’m pretty familiar with their views. Here are a few of them (all gave permission to be included on the “Third Way” site); and I’ll add links to critiques that I or others have written about their “revolutionary” ideas. At the end I’ll give my brief take on this “Third Way.

 

Shapiro
Shapiro has long been an advocate of “adaptive mutation”: the view that mutations are not “random” in the sense that evolutionists think (that is, that the relative probability of a mutation occurring is independent of how much it would boost an individual’s reproductive success, an idea that could also be called “indifferent” mutation). Rather, says Shapiro, adaptive mutations occur relatively more often than maladaptive ones when the environment changes. I’ve written about the lack of evidence for Shaprio’s view, and about Shapiro’s misunderstandings of evolution, several times before: go here to see the list of posts.
Noble
Noble has made many unevidenced claims that, he says, call for an overturning of neo-Darwinism. These include the idea that mutations aren’t random (Shapiro’s view), that adaptive traits in evolution can be acquired from the environment rather than produced by gene mutations, that the gene-centered view of evolution is wrong, and that important evolutionary change is not gradual but instantaneous.  I’ve criticized all of these claims hereJablonka
Jablonka, along with her colleague Marion Lamb, are perhaps the most vociferous promoters of the idea that adaptive evolution does not come from random mutations winnowed by the environment, but from “epigenetic changes”—modifications of the DNA, like methylation, that are produced by the environment itself and then inherited across generations. Suffice it to say that despite all the noise emitted by the epigenetics boosters, we have not a single case of evolution operating in that way. At most, DNA modifications induced by the environment are inherited for only one or a few generations, and are almost never adaptive. There is not a single adaptation we can point to that has evolved in the way these people propose. Yet that hasn’t stopped them from repeatedly telling us that their theory has been unduly neglected and that when we finally recognize how great it is, it will completely overturn our view of evolution.  My criticisms of the “epigenetics-is-important” view of evolution can be found here, and of Jablonka’s in particular here.
Newman
Newman believes that natural selection is insufficient to explain “macroevolution” (big changes between groups that are, for instance, involved in the creation of new phyla), and that evolution of that type involves “saltations” (big instantaneous leaps) involving not natural selection on genes, but changes in the “self-organization” of the matter and biochemical pathways that make up organisms. I have criticized his views at length here and showed that none of them, since they’re supported by no evidence, call for a radical revision of modern evolutionary theory.
Keller
Keller isn’t really a practicing physicist; she’s a historian and philosopher of science. But never mind; everyone is welcome to criticize evolution—so long as their criticisms are sound.  I haven’t followed Keller extensively but I did review one of her books—a book arguing that evolution was not only not centered on the gene, but that the gene itself was a virtually useless concept. My review is largely behind a paywall, so I’ll send a pdf to anyone who wants it. But here’s a short excerpt from it (Nature; 2004):

Unfortunately, the book is long on complaint and short on substance, and ultimately fails to make its case against the primacy of the gene. Despite her repeated claims that the recent history of genetics is replete with “major reversals”, “serious provocations” and “radical modifications”, the gene emerges unscathed. Many of the alleged problems highlighted by Keller turn out to be semantic issues likely to be of little interest to either working biologists or serious philosophers of science. Moreover, the level of analysis is disturbingly superficial: Keller seems more interested in forcing genetics into the Procrustean bed of her thesis.

Bejan
 I’m not well acquainted with Bejan’s work, since he doesn’t publish in evolution journals, but Joe Felsenstein has taken apart some of his and his collaborators’ evolutionary ideas (most notably a “constructural law”) over at Panda’s Thumb.
Odling-Smee

Odling-Smee is an exponent (along with my former Ph.D advisor Dick Lewontin) of the idea of “niche construction.” That’s the notion that the behavior of organisms themselves, since it affects their environments (“niches”), must affect their subsequent evolution. The classic example is the beaver: by evolving to adopt a lifestyle that creates a new habitat (the construction of ponds by felling trees that dam streams, as well as by building “lodges” as their homes), the beaver creates new selective pressures that can affect its evolution.

Now this idea is intriguing and sound in principle, and the process must have operated during the evolution of some species. But does it require our rethinking standard evolutionary theory (SET)? In this post (point #4), I argue “no”.  As I wrote last November:

While this idea is getting new attention, and deservedly so, it doesn’t call for a revolution in SET. First of all, it’s not particularly new. The idea of “gene-culture” coevolution has been around a long time. One example is pastoralism, in which humans changed their environment by keeping domestic animals that give milk.  And that has changed our evolution, for cultures that are pastoral have undergone evolution involving the use of lactose. Genes that break lactose down into digestible components are usually inactivated after weaning in humans, who, over most of our history, didn’t have a source of milk after they stopped suckling. That’s why many of us are “lactose intolerant.” When we suddenly got a rich source of nutrition from our sheep and cows, pastoral cultures evolved so that the genes metabolizing lactose weren’t inactivated,but were turned on for life. (Individuals with genes allowing them to digest milk had up to 10% more offspring on average than intolerant individuals!) Thus, our own culture affected our subsequent evolution. This did not cause us to dismantle SET; rather, it was an interesting sidelight on how culture itself caused genetic change.

Second, we don’t know how pervasive this process is. That is, while many organisms do affect their environments, we don’t know how often that environmental change feeds back to the organism to cause additional evolution. In some cases it probably doesn’t: fish adapt to an unchanging fluid medium, the coat color of polar bears cannot affect their environment of ice or snow, and the hooves of the chamois don’t affect the granitic structure of the Swiss Alps. So how often “niche construction” is important is an open question, albeit an interesting one. But I don’t see it overthrowing SET, for it’s simply a novel way that the environment can change and affect organismal evolution.

So what is the “Third Way” of evolution? As far as I can see, it’s basically a grab-bag of criticisms of evolution that are unfounded, as well as proposals of new mechanisms whose importance is yet to be established (or, in the case of adaptive mutation, has been shown to be unlikely by experiments), and of processes, like niche construction, that fit comfortably within modern evolutionary theory. The common theme of nearly every “Third Wave” member whose work I know is this: “Modern evolutionary theory is deficient because it has ignored my own view of what is important.” In other words, the whole site is solipsistic.  The “Third Way” of evolution boils down to what one colleague said to me: “All these views are wildly and incommensurably different, and some are in the category of ‘not even wrong’.”

The colleague added:

What many of [the adherents to “The Third Way”] do agree on is one thing: “Nobody’s paying enough attention to me!”

Too right!

Readers’ wildlife photographs

January 30, 2015 • 8:00 am

Reader Ed Kroc sent a passel of swell bird photos and some notes:

I haven’t sent along a batch of photos in awhile, so I thought it was high time to collect some of the better ones of the past couple months and pass them on. These are all from around the BC [British Columbia] Lower Mainland.

First up is a male Spotted Towhee (Pipilo maculatus), peering expectantly through the brush. These guys are closely related to the Eastern Towhee (P. erythrophthalmus), but the ranges of the two species are almost disjoint, split down the Great Plains. I’ve read that the glaciation events in the Pleistocene were likely responsible for the divergence of the two groups. Spotted Towhees usually ignore people around here, but this one in Stanley Park seemed to be rather interested in my camera.

Spotted Towhee

A Pied-billed Grebe (Podilymbus podiceps) hanging out on the lagoon in Stanley Park. This is one of a pair that has taken up winter residence on the lagoon. These small diving birds don’t fly much, and I’ve rarely seen them even leave the water.

Pied-billed Grebe
An honorary cat?

 

Next, a portrait of a Northwestern Crow (Corvus caurinus) from Blackie Spit in Surrey, BC. I’ve been reading more about speciation events in local birds, and it seems that there is debate about whether or not C. caurinus is really a separate species from the nearly ubiquitous American Crow (C. brachyrhynchos), or just a subspecies. Northwestern Crows are smaller and have a different language, but look identical and readily interbreed with American Crows where their ranges overlap in Washington. I’m not sure if any genetic work has been done to help resolve the controversy.

Northwestern Crow portrait
From Barnet Marine Park in Burnaby, BC, a happy Glaucous-winged Gull (Larus glaucescens) paddling furiously through the water with a Purple Sea Star (Pisaster ochraceus) catch. These large sea stars are a common staple of the GW Gull’s diet. Their bodies are so impenetrable, though, that the gulls have to swallow them whole, a process that looks quite uncomfortable and can take between 10 and 30 minutes to complete. I’m still collecting some good pictures of this behaviour and will send them along when I amass a decent set.

GW Gull with Sea Star at sea
A very common sparrow of North America, but also one of the less noted species: the Fox Sparrow (Passerella iliaca). These guys are known for spending most of their time on the ground. As you can tell from the size of the claws in this picture, they specialize in digging through ground debris for seeds and small insects, literally scraping and kicking through the undergrowth. This guy was photographed at Maplewood Flats in North Vancouver.

Fox Sparrow
From Stanley Park again, a female Green-winged Teal (Anas carolinensis), showing off her eponymous wing patch. Since I seem to have speciation on the brain right now, there is dispute over whether or not A. carolinensis should be considered a separate species from the Eurasian or Common Teal (A. crecca). The females of the two groups look identical, but the males have a few morphological differences. The groups also exhibit substantial behavioural and genetic differences (a cool paper by K. Johnson and M. Sorenson discusses this), so for my money they’re probably distinct species.

[In case you’re curious, the paper by Johnson and Sorenson is Phylogeny and biogeography of dabbling ducks (Genus: Anas): a comparison of molecular and morphological evidence, from The Auk, 116(3), 792-805, 1999.]

Green-winged Teal female
Finally, a sunset stop at Boundary Bay in Delta, BC. As the name suggests, this place is right near the Canada-US border. It’s also a great place to view local and migratory bird and marine life. The picture here is of a Greater Yellowlegs (Tringa melanoleuca) looking at peace on the tranquil shallows of the bay.

Greater Yellowlegs at sunset

 

Your morning Deepakities

January 30, 2015 • 6:37 am

Chopra had a bad attack of Maru’s Syndrome on Twi**er yesterday. In  tw**t on HIV/AIDS, he compounds his confusion:

AIDS

Umm. . . I don’t think so: it worked for smallpox. If the virus is eliminated, PRESTO—No more AIDS, regardless of people’s lifestyles.

In another tw**t, Chopra mentions “unprotected sex” as a factor contributing to AIDS. If that’s not “concentrating on the pathogen,” I don’t know what is. This man is a practicing doctor, and claims to push a purely scientific view.

In the meantime, the deepities continue. What distresses me more than the fact that this clown thinks he has wisdom is the fact that many people (see the comments on the right) actually lap up that faux wisdom.
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And a quiz. . .

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Any ideas?

Friday: Hili dialogue

January 30, 2015 • 4:49 am
Andrzej and Malgorzata are totally dedicated to their website, and are at the computer, with breaks only for meals and walkies with the beasts, from about 8 a.m. to 11 p.m. This explains why Cyrus is so surprised when Andrzej breaks that routine. Oh and it’s Friday—again!
Cyrus: Andrzej got up from his computer!
Hili: Cool it—he is just drifting around the house with that camera of his.
P1020269In Polish:
Cyrus: Andrzej wstał od komputera!
Hili: Spokojnie, on tylko włóczy się po domu z tym swoim aparatem fotograficznym.