04/28/14

Seeing evolution in action


Peter and Rosemary GrantThe pop-science notion is that evolution takes a long time. Millennia, many millennia; even millions of years. But is that always true? Can one actually see and measure evolution in action? Can it happen in such a short time as to be recorded?

Peter and Rosemary Grant say they have. And it’s the subject of a new book they co-authored based on their research.

Their story was reported in the April 23 issue of the Princeton Alumni Weekly. It’s a terrific read if for nothing more than their 40-year tale of dedication, science and adventure on the isolated Daphne Major Island, one of the smaller islands of the Galapagos chain.

Forty years studying finches together, away from human company, away from the comforts of civilization. The small birds that first gave Charles Darwin insight into the mechanics of natural selection were their focus. And the Grants report they have seen that mechanism in action on the island.

Scientists previously had reported seeing the processes of natural selection among bacteria, honeycreepers, cichlid fish, and fruit flies. As Peter Grant puts it, “Until we began, it was well understood that agricultural pests and bacteria could evolve rapidly, but I doubt that many people thought that about big, vertebrate animals.”

The Grants believe that hybridization is an important force in the rise of new species, and think this applies, too, to human evolution. For a long time, for example, paleontologists believed that Neanderthals and “modern homo sapiens” did not interbreed when they came into contact in prehistoric times, but recent research indicates that about 20 percent of Neanderthal genes have been preserved in our species. “It’s almost been a hobbyhorse of ours,” Peter says. “We were saying, ‘I bet there has been gene exchange between the lineages of homo sapiens throughout their evolution.’”

The Grants’ new book is targeted at both lay readers and scientists familiar with their work, and broadly discusses their findings about natural selection, hybridization, population variation (why do some populations of birds vary more dramatically in beak size?), the potential vanishing of a species through interbreeding, and, of course, the potential origin of a new species — the Big Bird lineage. They also touch on global warming and its possible effect on Darwin’s finches. Most of all, the book is an affirmation of the importance of long-term fieldwork as a way of capturing the true dynamism of evolution.

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02/11/14

Feb. 12: Happy Darwin Day


Charles DarwinFebruary 12 is international Darwin Day, the day when we collectively celebrate science and reason. And, of course, we recognize Charles Darwin’s birthday: February 12, 1809 (the same birthdate as Abraham Lincoln, by the way).

If Collingwood made such declarations, I would propose we recognize the day in our municipality. Other Canadian municipalities have done so. Maybe we could raise a flag with Darwin’s face on it outside town hall.

Darwin Day was first celebrated in 1995 and has been growing in recognition and popularity ever since. As Darwinday.org tells us the celebration was:

…initiated by Dr. Robert (“Bob”) Stephens and took place at Stanford University. The first EVENT sponsored by the Stanford Humanists student group and the Humanist Community, was held on April 22, 1995. The famous anthropologist Dr. Donald Johanson, who discovered the early fossil human called ‘Lucy’, gave a lecture entitled “Darwin and Human Origins” to over 600 people in the Kresge Auditorium.

In subsequent years the location and date of the celebration was changed to coincide with Darwin’s birthday and was held on, or near, February 12 each year. The success of the venture is reflected in the list of speakers which include Richard Dawkins, 1996; Paul Berg, 1997; Robert Sapolsky, 1998; Douglas Hofstadter, 1999; Michael Shermer, 2001; Robert Stephens and Arthur Jackson, 2003; Robert and Lola Stephens, 2004; and Eugenie Scott, 2005.

And, as the site also adds, “Celebrating Science and Humanity within our various cultures throughout the world is an idea that is overdue…”

I would hope, too, that people would take some time out of their busy days to read something of Darwin’s, even if only a few pages. He wrote beautifully, albeit rather obtusely at times.

Of course, I don’t expect creationists will break out of their cult mentality and celebrate science today: they haven’t in more than 150 years since Darwin’s Origin of Species was published. But while we celebrate Darwin, we should give some thought to creationism on this day, not just to critical thinking, if for nothing else than to remind us that we still have a long way to go to get universal appreciation of science and reason.

Especially, it seems, in the USA, where 43 percent of Americans believe in young-earth creationism. Not entirely bad news, given that figure has dropped from 54 percent in 2009. But still very, very scary.*

On Facebook today there were a couple of links to articles about creationism worth reading on this Darwin Day.

Creationism museum displayFirst is a cutely risible piece on Buzzfeed called “45 Things I Learned At The Creation Museum.” For those who don’t know it, the Creation Museum in Kentucky is where Bill Nye recently successfully debated creationist Ken Ham. It’s probably the most strenuous effort to rationalize away science ever constructed.

If I ever get to Kentucky, I will pay a visit, but I expect I’ll get escorted out for laughing too loudly at the exhibits. And if you’re like me, you will probably enjoy the virtual tour in the Buzzfeed article more than actually being there, because you don’t risk being ejected. After all, how can you keep a straight face when confronted with a sign that claims all dinosaurs were vegetarians before Adam?

Uh, and those razor-edged, pointed, cutting, slashing teeth were for… broccoli? Okay, stop snickering or they won’t let you in the museum either.

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10/15/13

We are Stardust… and Viral Genes


SupernovaIn her classic song, Woodstock, Joni Mitchell ended with the chorus:

We are stardust
Billion-year-old carbon
We are golden
Caught in the devil’s bargain
And we’ve got to get ourselves
Back to the garden

Which most people assume is merely poetic licence. Well, Joni wasn’t wrong: we – and every living thing on our planet – are made of stardust. As we learn at Physics Central:

If we know how many hydrogen atoms are in our body, then we can say that the rest is stardust. Our body is composed of roughly 7×1027 atoms. That is a lot of atoms! Try writing that number out on a piece of paper: 7 with 27 zeros behind it. We say roughly because if you pluck a hair or pick your nose there might be slightly less. Now it turns out that of those billion billion billion atoms, 4.2×1027 of them are hydrogen. Remember that hydrogen is bigbang dust and not stardust. This leaves 2.8×1027 atoms of stardust. Thus the amount of stardust atoms in our body is 40%.

Since stardust atoms are the heavier elements, the percentage of star mass in our body is much more impressive. Most of the hydrogen in our body floats around in the form of water. The human body is about 60% water and hydrogen only accounts for 11% of that water mass. Even though water consists of two hydrogen atoms for every oxygen, hydrogen has much less mass. We can conclude that 93% of the mass in our body is stardust. Just think, long ago someone may have wished upon a star that you are made of.

Mitchell’s theme was picked up by the late cosmologist, Carl Sagan, in his hit TV show, Cosmos. Live Science tells us:

In the early 1980s, astronomer Carl Sagan hosted and narrated a 13-part television series called “Cosmos” that aired on PBS. On the show, Sagan thoroughly explained many science-related topics, including Earth’s history, evolution, the origin of life and the solar system.

Since stardust atoms are the heavier elements, the percentage of star mass in our body is much more impressive. Most of the hydrogen in our body floats around in the form of water. The human body is about 60% water and hydrogen only accounts for 11% of that water mass. Even though water consists of two hydrogen atoms for every oxygen, hydrogen has much less mass. We can conclude that 93% of the mass in our body is stardust. Just think, long ago someone may have wished upon a star that you are made of.

“We are a way for the universe to know itself. Some part of our being knows this is where we came from. We long to return. And we can, because the cosmos is also within us. We’re made of star stuff,” Sagan famously stated in one episode.

His statement sums up the fact that the carbon, nitrogen and oxygen atoms in our bodies, as well as atoms of all other heavy elements, were created in previous generations of stars over 4.5 billion years ago. Because humans and every other animal as well as most of the matter on Earth contain these elements, we are literally made of star stuff, said Chris Impey, professor of astronomy at the University of Arizona.

“All organic matter containing carbon was produced originally in stars,” Impey told Life’s Little Mysteries. “The universe was originally hydrogen and helium, the carbon was made subsequently, over billions of years.”

So how did all this stardust get into out bodies? Supernovae, spewing heavy material into the vastness of space, scattering atoms and molecules at near lightspeed. Our “Garden of Eden” was the nuclear furnace of an exploding star.

We are made of the material created 13-plus billion years ago, We are, as Mitchell sang, stardust. Recycled and reused, but the stuff of the cosmos nonetheless. *

And we’re also built of viral genes, a product of the evolution of life, of the co-evolution of life and that strange creature, the virus. Viruses have helped shape us, and our adaptations to the environment. That’s the premise of Frank Ryan’s latest book, Virolution.**

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09/17/13

The Cosmic Origins of Life


CometHere’s one to confound the creationist crowd: life may have begun as a result of organic molecules resulting from impacts by comets or meteorites. No supernatural foundation, no invisible hand guiding the process. Just random crashes, a little physics, some chemistry, a while lot of time, and voila: life.

But wait, there’s more…

How did these molecules go from static organic molecules to self-reproducing you ask? Ah, therein lies another tale… that of enzymes, the little engines of life. More randomness, more chemistry. No intelligent design.

Let’s start with the comets.

According to a recent article in Science Daily,

Scientists … from Imperial College London, the University of Kent and Lawrence Livermore National Laboratory discovered that when icy comets collide into a planet, amino acids can be produced. These essential building blocks are also produced if a rocky meteorite crashes into a planet with an icy surface.

The researchers suggest that this process provides another piece to the puzzle of how life was kick-started on Earth, after a period of time between 4.5 and 3.8 billion years ago when the planet had been bombarded by comets and meteorites.

The intrepid researchers fired projectiles at comet-like speeds into icy surfaces similar to what we know comets are made from.  They discovered that the shock wave slams simple molecules together into more complex forms. The heat from the impact  then transforms these more complex molecules into amino acids such as glycine and D-and L-alanine.

Dr Mark Price, co-author from the University of Kent, adds: “This process demonstrates a very simple mechanism whereby we can go from a mix of simple molecules, such as water and carbon-dioxide ice, to a more complicated molecule, such as an amino acid. This is the first step towards life. The next step is to work out how to go from an amino acid to even more complex molecules such as proteins.”

In a similar experiment, published in July,2013, scientists simulated an icy comet-like snowball using carbon dioxide, ammonia, methane, ethane and propane. They zapped it with high-energy electrons to “simulate the cosmic rays in space” and discovered that the result was “complex, organic compounds, specifically dipeptides, essential to life.”

Chemists from the University of California, Berkeley, and the University of Hawaii, Manoa, showed that conditions in space are capable of creating complex dipeptides – linked pairs of amino acids – that are essential building blocks shared by all living things. The discovery opens the door to the possibility that these molecules were brought to Earth aboard a comet or possibly meteorites, catalyzing the formation of proteins (polypeptides), enzymes and even more complex molecules, such as sugars, that are necessary for life.

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07/23/13

The colonization of land by life pushed back in time


Fossile lifeA recent story on Science Daily made me stop and read with fascination. It’s about the discovery of fossils that showed life colonized land more than two billion years ago. That’s a shocker, because all indicators are that the Earth was a hostile place, land was barren, and life was a lot simpler.

But apparently we underestimated the ability and tenacity of life. This gives us hope that life may exist on other planets or moons.

Mars, at least its surface, is unlikely to harbour life now, but may have in its water-rich past. We may find fossils. Europa, Jupiter’s ice-covered moon, may have life in the oceans under its surface. Finding out will be tough. Titan? A remote possibility. But these fossils give us new hope: life can survive in very hostile conditions.*

Conventional scientific wisdom has it that plants and other creatures have only lived on land for about 500 million years, and that landscapes of the early Earth were as barren as Mars. A new study, led by geologist Gregory J. Retallack of the University of Oregon, now has presented evidence for life on land that is four times as old — at 2.2 billion years ago and almost half way back to the inception of the planet.hat landscapes of the early Earth were as barren as Mars.

That raises several interesting ideas. First, what sort of life was it? The researchers don’t know for sure, but it’s a bit like slime mold or some lichen. It was tiny, but rather complex given its age and a promising candidate for the oldest known eukaryote. Sci-news notes:

Diskagma buttonii are very small – about 0.3 – 1.8 mm long. They most resemble modern soil organisms called Geosiphon, a fungus with a central cavity filled with symbiotic cyanobacteria.

It was something not quite animal or plant – something simple. But not that simple: they appear to have had symbiotic cyanobacteria in their interiors. Cyanobacteria appeared about 3 billion years ago, and started photosynthesizing (with water as a reducing agent) and making oxygen between then and about 2.6 billion years ago (life itself first showed up about 3.5 billion years ago but some estimates push it much earlier, to 4.3 billion).**

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02/15/13

ID’s deep roots in creationism


Fundamentalist folliesProponents of creationism often try to deny that “intelligent” design (ID) is merely creationism wrapped in a fake lab coat to make it look like it’s pals with science. It isn’t. They’re not buddies, didn’t go to school together, and don’t ‘like’ each others Facebook pages.

ID is merely a tawdry, paper-thin attempt to hoodwink the gullible who can’t see past the plastic pocket protector that there’s a bible in the pocket. In part this is because the popular notion of what a theory is has devolved into a synonym for guess or an unproven assumption. But that’s not the scientific meaning of the word: “…a well-confirmed type of explanation of nature, made in a way consistent with scientific method, and fulfilling the criteria required by modern science… Scientific theories are the most reliable, rigorous, and comprehensive form of scientific knowledge.” Scientific method

ID is not even a hypothesis: it’s a statement of faith and its pseudo-scientific arguments have been well-debunked on better sites than this (i.e. Skeptico). It starts with belief and looks for ways to prove it, rejecting anything that counters that preconceived theology.
creationism masquerading as ID

The National Center of Science Education defines ID this way:

“Intelligent Design” creationism (IDC) is a successor to the “creation science” movement, which dates back to the 1960s. The IDC movement began in the middle 1980s as an antievolution movement which could include young earth, old earth, and progressive creationists; theistic evolutionists, however, were not welcome. The movement increased in popularity in the 1990s with the publication of books by law professor Phillip Johnson and the founding in 1996 of the Center for the Renewal of Science and Culture (now the Center for Science and Culture.) The term “intelligent design” was adopted as a replacement for “creation science,” which was ruled to represent a particular religious belief in the Supreme Court case Edwards v. Aguillard in 1987.
IDC proponents usually avoid explicit references to God, attempting to present a veneer of secular scientific inquiry. IDC proponents introduced some new phrases into anti-evolution rhetoric, such as “irreducible complexity” (Michael Behe: Darwin’s Black Box, 1996) and “specified complexity” (William Dembski: The Design Inference, 1998), but the basic principles behind these phrases have long histories in creationist attacks on evolution. Underlying both of these concepts, and foundational to IDC itself, is an early 19th century British theological view, the “argument from design.”

Despite angry denials from creationist supporters that ID is not the same, and instead ID is a form of scientific research, that’s balderdash. It’s the “wedge” strategy- the ID movement’s published methods for inserting their religious content into the secular world.
Creationist bingo

All they’ve done is use cut-n-paste to replace terms like creationism in their documents with scientific-sounding phrases like “intelligent” design. They haven’t changed the core religious nature of their argument. Common Sense Atheism documents this as a clumsy, but failed attempt to mislead the reader:

…consider how the term “intelligent design” was born. In 1987, the Supreme Court ruled that “creation science” could not be taught in public schools because it advances a particular religion. That same year, a Creationist textbook called Of Pandas and People had been published using terms like “creationism” over 150 times. But after the defeat of Creationism in court, the editors replaced every instance of “creationism” with “intelligent design” and every instance of “creationists” with “design proponents.” In one case, part of the original term, “creationists,” was left behind by the editing process, rendering “cdesign proponentsists”… That the editors merely replaced “creationism” with the new term “intelligent design” is abundantly obvious when one compares various drafts of Of Pandas and People (originally called Biology and Creation)…

ID supporters universally identify the need for a “designer” as the mechanic behind the curtain, and all say it’s their own particular Christian deity. Wikipedia notes:

Intelligent design (ID) is a form of creationism promulgated by the Discovery Institute, a politically conservative think tank. The Institute defines it as the proposition that “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” It is a contemporary adaptation of the traditional teleological argument for the existence of God, presented by its advocates as “an evidence-based scientific theory about life’s origins” rather than “a religious-based idea”. All the leading proponents of intelligent design are associated with the Discovery Institute and believe the designer to be the Christian deity.

A designer, logically, has to be a deity* but why only this particular one? I have yet to run across a single ID proponent who will say that designer is Shiva. Or Kali. Or Moloch. Or Ra. Or Odin. Or Zeus. Why not each one working as a team (because there’s no God in team)? All of the hundreds of other deities (thousands?) in world mythologies and religions are ignored and just one is elected as the only possible designer: the hairy thunderer of the New Testament. Not only are non-Christians excluded from ID, but so are Catholics. Only fundamentalist literalist Christians need apply.

Creationism poster

As Wikipedia also notes:

Scientific acceptance of Intelligent Design would require redefining science to allow supernatural explanations of observed phenomena, an approach its proponents describe as theistic realism or theistic science.

In other words, yes kids, Santa Claus really does put those presents under the Xmas trees of good children every year, millions of them simultaneously, all over the world, delivered from a sleigh that travels faster than light and, while seemingly small, actually has an infinite storage capacity. Never mind those wrapped boxes you found at the back of the closet last week. Those aren’t proof of another, more logical explanation of how the presents arrive. Belief is more important than observation, so don’t question our explanation. We’ll tell you what you need to know.
Creationist continuum
As noted in another article on the NSCE website:

Following creationist tradition, IDC proponents accept natural selection but deny that mutation and natural selection are adequate to explain the evolution of one kind to another, such as chordates from echinoderms or humans and chimps from a common ancestor. The emergence of major anatomical body types and the origin of life, to choose just two examples popular among IDC followers, are phenomena supposedly too complex to be explained naturally; thus, IDC demands that a role be left for the intelligent designer — God.

About.com sums it up very well:

Intelligent Design is, like all other creationist movements, more about politics and religion than about science. Where Intelligent Design differs is that it was originally and deliberately conceived in explicitly political terms whereas earlier creationist movements tended to acquire political goals and principles over time. This is very important to understand because it reveals as false the pretensions of Intelligent Design apologists that they are involved in a scientific enterprise.

The US judicial system recognized the similarity between the two, as well (see this article). Judge Jones noted in the Dover School case:

ID uses the same, or exceedingly similar arguments as were posited in support of creationism. One significant difference is that the words “God,” “creationism,” and “Genesis” have been systematically purged from ID explanations, and replaced by an unnamed “designer.”
Demonstrative charts introduced through Dr. [Barbara] Forrest show parallel arguments relating to the rejection of naturalism, evolution’s threat to culture and society, “abrupt appearance” implying divine creation, the exploitation of the same alleged gaps in the fossil record, the alleged inability of science to explain complex biological information like DNA, as well as the theme that proponents of each version of creationism merely aim to teach a scientific alternative to evolution to show its “strengths and weaknesses,” and to alert students to a supposed “controversy” in the scientific community. In addition, creationists made the same argument that the complexity of the bacterial flagellum supported creationism as Professors Behe and Minnich now make for ID.

ID cartoon
Talkreason.org has many good articles critiquing ID, but this one is particularly good because it deconstructs a description from the “Discovery Institute” (the political and religious organization that developed and promotes ID, and spreads the wedge):

Right away we are told that ID is a program conducted by “scientists, philosophers, and other scholars who seek evidence of design in nature.” Basically this is an admission that their program is not about gathering data and allowing the evidence to lead them wherever it may, but rather a mission to find evidence which supports a predetermined conclusion — that being that an intelligent agent created everything. In this way, the ID “researcher” confines himself to analysis of only those findings which he may have use for as a buttress for the conclusion he has already arrived at. It goes without saying that this is not science. To presuppose automatically the existence of a (perhaps supernatural) designer is to preclude real, thoughtful, scientific research in accordance with the scientific method, since science deals only with observable, measurable, phenomena.

You can’t research an act of god. Any god. What happens when you find something you can’t fully explain or understand? IDers would assign it to “the designer” then move on. Scientists would investigate further to try and provide an answer that doesn’t involve a supernatural cause. They would look to see what existing laws, theories or hypotheses are related and whether they apply. They would test, then retest, and test again until something made sense, long after IDers had shrugged their shoulders and given up looking.
ID trial arguments
ID is, like the notion of the flat earth, based not on observation, research and experimentation, but simply on blind faith.
Intelligent geography
Why would ID deserve any more research that, say, phrenology? ID has already decided the answer, so anything scientists find that explains outside that answer will be rejected by the IDers. They already start by rejecting science – evolution, cosmology, biology.
Common Sense Atheism does allow that creationism and ID are, semantically, different terms (although joined at the hip by their theological basis):

Here’s how I like to think of Creationism and Intelligent Design. I tend to use “Creationism” to refer to theories informed by the Bible or Christian (or Muslim) theology. For example, a theory including a 6,000 year old Earth is obviously Creationism.
In contrast, I tend to use “Intelligent Design” to refer to modern attempts at natural theology, which are not dependent on scripture or doctrine. The method of natural theology is to make an inference from observations of public, natural evidence to the existence of some kind of Designer or First Cause. This method does not allow you to assume any properties at all about the Designer that cannot be inferred from the observations of public, natural evidence… Remember, “intelligent design” and “creationism” are just words. They mean whatever we say they mean.

I agree, but I prefer to call it “ID creationism” so that the concept is not mis-identified by those who are not aware of the historical or political origins of the ID movement, and somehow mistakenly think that ID is actually something scientific.It isn’t. It’s claptrap masquerading as an “alternative” to science. Why should we pretend otherwise?

Watch Judgment Day: Intelligent Design on Trial on PBS. See more from NOVA.

~~~~~
* Clearly the whole argument fails if you don’t believe in this or any other deity. If it wasn’t Ganesh who made the world and all the cute bunnies and squirrels, then I ain’t buying it… but you don’t have to be an atheist to believe in evolution: a modest education, and an open mind are all you need.