Tuesday, January 31, 2012

Genesis Weak

Published by Steven Novella under Creationism/ID

I advise you to please turn off your irony meters before reading further or clicking the link to the video I will be discussing today. You may also want to take a couple of deep relaxing breaths to help preserve your neurons from the irrational assault they are about to suffer.

I was recently asked to take a look at Genesis Week with Ian Juby (Wazooloo), a slick YouTube series in which Juby takes us on a mystical journey through the looking glass of creationist nonsense. In his world science and reason are flipped completely upside down. It is, as they say, a “target rich environment” – too rich for any one blog post, so I will pick out a few gems.

The title of this episode is “I’m hooked on a feeling,” referring to new research showing that acceptance of evolution is strongly influenced by a gut “feeling of certainty” that people have about the theory. Juby makes much of this study (without, of course, putting it into any context) concluding that people believe in evolution despite the evidence (what he describes as overwhelming evidence for creation) rather than because of it.

The study itself reviews prior research on this question, summarizing it:

Despite the variety of studies that have been reported, there are no convincingly clear findings about the relationships among knowledge level, beliefs, and acceptance level regarding the theory of evolution. While some studies have provided evidence for a robust relationship between knowledge level and level of acceptance (Paz-y-Miño & Espinosa, 2009; Rutledge & Warden, 1999), others found no evidence of a straightforward relationship (Sinatra et al., 2003), and little evidence that instructional treatments affect acceptance levels (Chinsamy & Plagányi, 2007), even when learning gains have been substantiated (Nehm & Schonfeld, 2007). It has also been suggested that the nature of relationships change when acceptance of evolutionary theory is framed in the context of macroevolution rather than microevolution (Nadelson & Southerland, 2010).

So – it’s complicated. Results of research seem to depend upon how the study was conducted, meaning that confounding variables have not adequately been controlled for so they determine the outcome of individual studies, which therefore have conflicting results.

However, at least so far there does not appear to be a clear relationship between teaching students about evolutionary theory and their acceptance of it. This is actually not surprising and in line with the consensus of psychological research, which shows that people form opinions largely for emotional and ideological reasons, and then cherry pick the facts they need to support those opinions.

The findings of the current study are therefore nothing new, and there is no reason to think that this phenomenon is unique to belief in evolution.

But to put this study into its proper context – this is about affecting the opinions of students by confronting their emotional reactions to evolution. It is not about how scientists form their opinions about evolutionary theory.

This is a common logical error that creationists make – confusing public opinion with expert scientific opinion. Juby tries to make it seem that this study shows that acceptance of evolution in general (including among scientists and educators) is about feeling rather than evidence.

He then goes on to another common claim of creationists that reflects their astounding intellectual dishonesty. He lists a few biologists who are creationists – as if their opinions are evidence based, and contrasting them with the emotion-based acceptance of evolution.

Among scientists, however, >99% accept evolutionary theory – a relevant fact that Juby failed to mention. This is also in line with other research, showing that only at the highest levels of science education do facts trump emotion in forming our beliefs about controversial or emotional topics. Among the experts there is a strong consensus – the evidence overwhelmingly supports the conclusion that all life on earth is related through an evolutionary process. Juby, however, rattles off a couple of creationist exceptions as if they are the rule.

It is hard to imagine that Juby is not aware of these facts. We are left to conclude that he is either living in a creationist bubble or is flagrantly dishonest in dealing with the question of scientific acceptance of evolution.

Eventually Juby gets around to listing some of the alleged overwhelming evidence for creation, including irreducible complexity and lack of a mechanism for increasing genetic information. He lists a bunch of old long-discredited creationist canards, and that is his “overwhelming evidence.”

Creationists proposed the notion of irreducible complexity over a decade ago, and really it was just a reformulation of arguments they have been putting forward for a century and a half – since Darwin proposed his version of evolutionary theory. It has been debated and discussed among scientists, and found to be a fatally flawed idea. It’s flat out wrong – disproved by numerous counter examples. I first wrote about it myself in 1999, and the arguments haven’t changed.

The alleged lack of a mechanism for generating new genetic information is nonsense – not a serious scientific or even philosophical argument. (I first debunked this one in 2002.) The combination of random mutations and selective pressures, combined with gene duplication and other genetic mechanisms, are fully capable of increasing overall genetic information and creating new information.

Creationists like Juby have no counterarguments to the scientific consensus clearly demonstrating that irreducible complexity and creationist abuses of information theory are false. They simply trot out the same discarded claims over and over again with arrogance and casual dismissiveness of the scientific consensus – a consensus slowly built on a mountain of evidence.

I’m not bothered by the fact the people like Juby can promote their nonsense on an open forum like YouTube. He is unlikely to change anyone’s opinion. He also provides yet another opportunity to point out the terrible logic and questionable honesty of the creationists. They do make it easy in that they have nothing new to say. Science changes and new ideas and new evidence are brought to bare. Creationism is stuck in its prescientific conclusion, and continue to rely upon long discredited arguments – even when dressed up in a slick YouTube video.

Friday, January 27, 2012

Viral Attacks on Bacteria Reveal a Secret to Evolution by Wynne Parry, LiveScience Senior Writer

Evolution of a trait. An image of the protein, LamB, on the surface of the bacterial cell. Scientists examined what happened with the virus could no longer infect the bacteria through this protein.
An image of a protein, LamB, found on the surface of the bacterial cell. Scientists examined what happened when a virus could no longer infect the bacteria through this protein.
CREDIT: Justin Meyer 

The arms race between a virus and the bacteria it attacks has helped scientists better understand one of the mysteries of evolution: How new traits evolve.
In a series of experiments, the bacteria-infecting viruses repeatedly acquired the ability to attack their host bacteria through a different "doorway," or receptor on the bacteria's cellular membrane, explained Justin Meyer, the lead researcher and a graduate student at Michigan State University. [Video: The Virus Mutates]
Their results offer insight into a difficult question about evolution: Where do new traits come from?
According to evolutionary theorynatural selection can favor certain members of a population because of traits they possess, such as camouflage or an ability to get at food others can't reach. These favored organisms are more likely to reproduce, passing on the genes for their helpful traits to future generations. While it's clear how natural selection causes a population to change, or adapt, explaining how new traits arise has been trickier, Meyer said.
For instance, do random genetic mutations gradually accumulate until they produce new traits? Or, does natural selection drive the process from the start, favoring certain mutations as they arise, until a whole new trait appears?
To get an idea, he and others, including two undergraduate researchers, prompted a virus to evolve a new way to infect the bacteria, then looked at the genetic changes associated with this new ability. They also found that changes in the bacteria could prevent the virus from acquiring this new trait.
Evolution of a trait. An E. coli cell. In the experiment, these bacterial cells evolved resistance to the virus, prompting the virus to evolve.
An E. coli cell. In the experiment, bacterial cells like this one evolved resistance to a virus, prompting the virus to evolve a new way to attack..
CREDIT: Brian D. Wade and Alicia Pastor, Center for Advanced Microscopy, MSU
In 102 trials, they combined E. coli cells with the virus, called lambda. Lambda normally infects the bacteria by targeting a receptor, LamB, on the bacterium's outer membrane. The virus does this using a so-called J protein at the end of its tail; this protein unlocks the door into the bacterial cell, Meyer said.
When cultured under certain conditions, most E. colicells developed resistance to the virus by no longer producing LamB receptors. To infect the bacterial cells, then, the virus had to find another doorway into the cell. (Once inside, the virus hijacks the bacteria's cellular machinery to copy its own genetic code and reproduce.)
In 25 of the 102 trials, the virus acquired the ability to infect bacteria through another receptor, called OmpF. The viruses were genetically identical at the beginning of the experiment, so the researchers looked to see what genetic changes had occurred.
They found that all the strains that could infect the bacteria shared at least four changes, all of which were in the genetic code for the J protein, and which worked together, according to Meyer.
"When you have three of the four mutations, the virus is still unable to infect [the E. coli]," Meyer said. "When you have four of four, they all interact with each other. … In this case, the sum is much more than its component parts."
However, natural selection appears to have driven the rise of these individual mutations, he said, because the same mutations arose over and over again, and because they appear to affect the function of the J protein.
"The mutations are really centered on a small part of the gene and genome that would affect binding," he said. 
Evolution of a trait. Two lambda viruses. Mutations in viruses like these lead them to find a new way to attack their bacterial hosts.
Two lambda viruses. Four genetic mutations in viruses like these lead them to find a new way to attack their bacterial hosts.
CREDIT: Brian D. Wade and Alicia Pastor, Center for Advanced Microscopy, MSU
So, why, in most cases, did the virus fail to acquire the ability to enter through the OmpF doorway? The researchers looked to see if other changes in the virus, or changes in the bacteria, interfered.
They found that while other changes in the virus did not seem to interfere, a specific change found in the E. coli populations from 80 trials did.  Disruptions appeared in bacterial genes responsible for producing a protein complex, called ManXYZ, in the inner membrane. That change in the inner membrane meant the virus couldn't get all the way inside the cell, whether through LamB or OmpF.
"So there is this interesting co-evolutionary dance," Meyer said. "One mutation in the host and four mutations in the virus lead to a new virus. One mutation [in the host] and only a few mutations in the virus and a second mutation in the host, and the whole system shuts down."
You can follow LiveScience senior writer Wynne Parry on Twitter @Wynne_Parry. Follow LiveScience for the latest in science news and discoveries on Twitter @livescience and onFacebook.

Wednesday, January 25, 2012

Why Do So Many Have Trouble Believing In Evolution?

Why Do So Many Have Trouble Believing In Evolution?

Sometimes the fossil record comes with teeth: Mapusaurus roseae on display in the "Dinosaurs of Gondwana" exhibit in 2009 at the National Museum of Nature and Science in Tokyo.
EnlargeJunko Kimura/Getty Images
Sometimes the fossil record comes with teeth: Mapusaurus roseae on display in the "Dinosaurs of Gondwana" exhibit in 2009 at the National Museum of Nature and Science in Tokyo.
Updated on Thursday at 1:15 p.m.: After reading your comments, I feel it's important to clarify a couple of points concerning human hereditary descent and horizontal gene transfer. Please see the bracketed additions below.

The evidence is clear, as in a February 2009 Gallup Poll, taken on the eve of the 200th anniversary of Charles Darwin's birthday, that reported only 39 percent of Americans say they "believe in the theory of evolution," while a quarter say they do not believe in the theory, and another 36 percent don't have an opinion either way.
Go To Article

Thursday, January 19, 2012

Symphony of Science - The Greatest Show on 

Earth! A music video about Evolution

Climate Change, Disbelief, and the Collision between Human and Geologic Time by Peter H. Gleick

Climate Change, Disbelief, and the Collision between Human and Geologic Time

Geologic time scales are long – too long for the human mind to really comprehend. Over millions, and tens of millions, and hundreds of millions of years, the Earth has changed from something unrecognizable to the planet we see on maps, plastic globes, and photos from space. The Atlantic Ocean didn’t exist eons ago and it will literally disappear in the future as the continental plates continue to move inch by inch. A visitor from outer space millions of years ago would have looked down upon land masses and land forms unrecognizable today. As John McPhee notes in his book, Assembling California, “For an extremely large percentage of the history of the world, there was no California.” Or North America, China, Australia, Hawai’i, Mt. Everest, Grand Canyon, or any of the other landforms and natural symbols we think of as immutable.

Thursday, January 12, 2012

Also, the sharks are smarter than Eric Hovind by PZ Pyers

The news a few weeks ago was that hybrid sharks had been found off the coast of Australia. They looked like tropical Australian black-tip sharks, but genetic testing revealed that they’d hybridized with the common black-tip, which has a wider range; these hybrid black-tips were similarly extending their range and living in colder waters.
This is an excellent example of evolution: it’s a population shifting its range, correlated with an observation of novel genetic attributes. This is exactly the kind of gradual transition that we’d expect to be compatible with evolutionary theory.
Unless you’re a creationist, of course. Or an idiot. But I repeat myself.
I wonder if they ever considered that when you stand back and look at them, they are all sharks. That means they are the same kind of animal. That is not evolution taking place; there is no changing from one kind of animal into another kind of animal happening here. We started with a shark and now we have a shark. That is not evolution!
That’s Eric Hovind’s take on the story. First of all, “kind” is not a valid taxonomic unit; it makes no sense at all to demand that a “kind” turn into a different “kind” when “kind” is undefined, undefinable, and unmeasurable. What was seen was a population with a measurable change in their genetic characteristics, and a natural mechanism, hybridization, to explain the shift, and a possible selective force, climate change, to drive the process. That’s the science.
Secondly, what does he expect? That a shark would turn into a mouse?
Thirdly, Eric Hovind does not get to define what evolution means. Biologists get to do that. Eric Hovind does not qualify. Eric Hovind has qualifications equivalent to those of his father: he is a “graduate” of Jackson Hole Bible College, an unaccredited and glorified tourist lodge in the Rocky Mountains which offers a one year course leading to a Diploma of Biblical Foundations, whatever the hell that is. That diploma and an application might qualify him for a job at McDonald’s.
Especially since I looked at their class schedule: not one lick of biology, but lots of evangelism, acts of the apostles, church history, prophecy, mangled geology, apologetics, and most importantly of all, “Intro to Finance”.

Evolution of complexity recreated using 'molecular time travel'

Scientists find that small, high-probability mutations can produce complex system

Much of what living cells do is carried out by "molecular machines" – physical complexes of specialized proteins working together to carry out some biological function. How the minute steps of evolution produced these constructions has long puzzled scientists, and provided a favorite target for creationists.

In a study published early online on Sunday, January 8, in Nature, a team of scientists from the University of Chicago and the University of Oregon demonstrate how just a few small, high-probability mutations increased the complexity of a molecular machine more than 800 million years ago. By biochemically resurrecting ancient genes and testing their functions in modern organisms, the researchers showed that a new component was incorporated into the machine due to selective losses of function rather than the sudden appearance of new capabilities.

"Our strategy was to use 'molecular time travel' to reconstruct and experimentally characterize all the proteins in this molecular machine just before and after it increased in complexity," said the study's senior author Joe Thornton, PhD, professor of human genetics and evolution & ecology at the University of Chicago, professor of biology at the University of Oregon, and an Early Career Scientist of the Howard Hughes Medical Institute.

"By reconstructing the machine's components as they existed in the deep past," Thornton said, "we were able to establish exactly how each protein's function changed over time and identify the specific genetic mutations that caused the machine to become more elaborate."

The study – a collaboration of Thornton's molecular evolution laboratory with the biochemistry research group of the UO's Tom Stevens, professor of chemistry and member of the Institute of Molecular Biology – focused on a molecular complex called the V-ATPase proton pump, which helps maintain the proper acidity of compartments within the cell.

One of the pump's major components is a ring that transports hydrogen ions across membranes. In most species, the ring is made up of a total of six copies of two different proteins, but in fungi a third type of protein has been incorporated into the complex.

To understand how the ring increased in complexity, Thornton and his colleagues "resurrected" the ancestral versions of the ring proteins just before and just after the third subunit was incorporated. To do this, the researchers used a large cluster of computers to analyze the gene sequences of 139 modern-day ring proteins, tracing evolution backwards through time along the Tree of Life to identify the most likely ancestral sequences. They then used biochemical methods to synthesize those ancient genes and express them in modern yeast cells.

Thornton's research group has helped to pioneer this molecular time-travel approach for single genes; this is the first time it has been applied to all the components in a molecular machine.
The group found that the third component of the ring in Fungi originated when a gene coding for one of the subunits of the older two-protein ring was duplicated, and the daughter genes then diverged on their own evolutionary paths.

The pre-duplication ancestor turned out to be more versatile than either of its descendants: expressing the ancestral gene rescued modern yeast that otherwise failed to grow because either or both of the descendant ring protein genes had been deleted. In contrast, each resurrected gene from after the duplication could only compensate for the loss of a single ring protein gene.
The researchers concluded that the functions of the ancestral protein were partitioned among the duplicate copies, and the increase in complexity was due to complementary loss of ancestral functions rather than gaining new ones. By cleverly engineering a set of ancestral proteins fused to each other in specific orientations, the group showed that the duplicated proteins lost their capacity to interact with some of the other ring proteins. Whereas the pre-duplication ancestor could occupy five of the six possible positions within the ring, each duplicate gene lost the capacity to fill some of the slots occupied by the other, so both became obligate components for the complex to assemble and function.

"It's counterintuitive but simple: complexity increased because protein functions were lost, not gained," Thornton said. "Just as in society, complexity increases when individuals and institutions forget how to be generalists and come to depend on specialists with increasingly narrow capacities."
The research team's last goal was to identify the specific genetic mutations that caused the post-duplication descendants to functionally degenerate. By reintroducing historical mutations that occurred after the duplication into the ancestral protein, they found that it took only a single mutation from each of the two lineages to destroy the same specific functions and trigger the requirement for a three-protein ring.

"The mechanisms for this increase in complexity are incredibly simple, common occurrences," Thornton said. "Gene duplications happen frequently in cells, and it's easy for errors in copying to DNA to knock out a protein's ability to interact with certain partners. It's not as if evolution needed to happen upon some special combination of 100 mutations that created some complicated new function."
Thornton proposes that the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today. Such a mechanism argues against the intelligent design concept of "irreducible complexity," the claim that molecular machines are too complicated to have formed stepwise through evolution.
"I expect that when more studies like this are done, a similar dynamic will be observed for the evolution of many molecular complexes," Thornton said.

"These really aren't like precision-engineered machines at all," he added. "They're groups of molecules that happen to stick to each other, cobbled together during evolution by tinkering, degradation, and good luck, and preserved because they helped our ancestors to survive."
The paper, "Evolution of increased complexity in a molecular machine," appears in the January 18, 2012, issue of Nature [doi: 10.1038/nature10724]. The work was a collaboration of Thornton's molecular evolution lab with the research group of Tom Stevens, a yeast geneticist at the University of Oregon. Other authors include Gregory C. Finnigan and Victor Hanson-Smith, of the University of Oregon.
Funding for this work was provided by the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute.

Friday, January 6, 2012

Regardless, The Dead Sea Does by Brian Thomas

Regardless, The Dead Sea Does

It goes without saying that the title for Wednesday’s Daily (pseudo)Science Update is a bit of an exaggeration: Dead Sea Sediment Core Confirms Genesis.
The last time that style of title was used it was for Genetics Analysis of Jews Confirms Genesis, in which we were told that a genetic study showed that Jews had interbred to some degree with sub-Saharan Africans – which of course proves that one of the sons of Jacob married an Egyptian as reported in the bible, that Moses married an Ethiopian, and that Science has Confirmed Genesis.
Panorama of the Dead sea from Mount Sodom
The dead sea is a highly saline body of water located in the Middle East. It’s so saline that it was apparently previously believed that it could not shrink more than 150 metres below its present depth, a maximum of 377 metres.
However, a sediment core turned up, 235 metres down (corresponding to 120,000 years ago, I might add), a layer of pebbles probably corresponding to a time when that part of the lake was the shore, showing that at the time the lake all-but dried up.
How does this confirm Genesis? It’s a bit of a stretch, as you might expect. First, remember that the YECs compress the remaining thousands/millions of years after the sediments deposited by the Flood into the period of roughly 2500 BCE to 1 CE. They believe that the Flood caused an ice age, which produced the features we attribute to the various glaciations of the present ice age, but really fast. For some context, the Dead Sea (or whatever was there at the time) went up with the glaciations, and down with the warmer interglaciations – the drying that caused the pebble layer would have been particularly severe.
According to the Bible, in around 2000 B.C. what is now the Dead Sea used to be a plain that probably served as farmland for people of the nearby debauched city of Sodom. Genesis 14 first named the valley during the time of Abraham (then called Abram) as “the vale of Siddim, which is the salt sea.” So, the area was apparently a vale, or valley, but had been relabeled “the salt sea” by the time the original writings were edited and compiled, probably by Moses some 400 years after Abraham.
Which, aside from anything else, is a nice admittance of the bible not quite being the ‘unchanging word of God.’
Lake LisanThere are a few problems here. For one, around 25 thousand years ago the area was flooded by a ‘Lake Lisan’ to the extent that it filled the whole area all the way up to the Sea of Gallile. It’s a little odd that that was never mentioned in the bible, isn’t it? It would change a lot. For more information on the ‘limnological history’ of the Dead Sea try this pdf, from which I’ve stolen the map at right (you can’t read it? Click the link). Again, you’d think somebody would’ve noticed.
Additionally, the Science NOW article being used as a reference for all this mentions that:
Most of the core is a series of black and white layers of sediment, representing seasonal variations. Dark sediments containing mud and silt from winter floods alternate with summertime sediment rich with white calcium carbonate precipitated from a seasonally shrinking lake. “It’s an absolutely phenomenal record,” Goldstein said. Overprinted on those finely detailed, seasonal layers in the core is a similar but larger-scale variation between wetter ice ages and drier interglacial warm periods. “Salt represents the Dead Sea declining and precipitating out the salt, which wasn’t happening during the ice ages,” Goldstein said.
Woah there! Varves? If they make up ‘most’ of the core, and the core was a full kilometre long, then there is probably a few more than, oh, 6000 of them? If so, how would Mr Thomas explain them?
Finally, for all this talk of “a plain that probably served as farmland for people of the nearby debauched city of Sodom,” the layer of pebbles is on top of a layer of salt, forty metres thick! Could be difficult to farm there…
So, does it ‘confirm Genesis’? No. Frankly, it does a better job of contradicting the YEC story.