Lynn Margulis, 73, dead

Posted on November 24, 2011 by Michael

Lynn Margulis was one of those scientists that biology needed. She forged the now universally accepted endosymbiotic theory only about 44 years ago, bringing it to the mainstream 30 years ago. I have heard her work compared to that of Watson & Crick insofar as it marked a significant turning point within the field. She really did have some great ideas and it’s a shame that she died so young.

Filed under: Biology, Evidence, Evolution, News | Tagged: , | Leave a comment »

Garuda wasp

Posted on September 1, 2011 by Michael

Biogeography and endemic species are two great pieces of evolution. The former refers to the distribution of species across the planet and only evolution adequately explains what we observe. Take for instance Australia. It is filled with marsupial mammals, yet it is off all by its lonesome in the ocean. Clearly mammals did not evolve twice, the second time taking an alternative path to being placental. We need an explanation. The one we have is that this marsupial subset of mammalian life migrated down the Americas, through Antarctica, and into Australia. Fossil and tectonic plate evidence independently confirm this hypothesis – marsupial fossils are found all through South America and into Antarctica (and, of course, Australia), dating back to the time when those continents were still all connected.

Endemic species also constitute a nice bit of evidence for Darwinists. The man himself, Charles Darwin, saw quite an array of species that are only present on the Galapagos Islands, their relatives residing back in South America for the most part. (One of my favorite Galapagos animals is the marine iguana.) But there are far greater islands out there. Madagascar has to be the first to come to mind (and, in turn, its lemurs come to mind next for me). There is also Alejandro Selkrik Island, a place I mention in the first link in this post. And then there is Sulawesi, an Indonesian Island a fair bit north of Australia. It’s a haven for researchers who want to study unique flora and fauna, including many large mammals. It has a lot of protected land and animals (especially its marine life), so it’s a prime location for many biologists. One such biologist is Lynn Kimsey, an entomologist who recently described a pretty striking find:

It sounds like the stuff of nightmares – a wasp that supplements a vicious sting with jaws longer than its front legs.

But this is a very real newly discovered warrior wasp found on the remote Indonesian island of Sulawesi.

Dubbed the ‘Komodo dragon’ of the wasp family, the males of the species measure two-and-a-half inches long…

Ms Kimsey, who is also director at the Bohart Museum of Entomology, said: ‘Its jaws are so large that they wrap up either side of the head when closed. When the jaws are open they are actually longer than the male’s front legs. I don’t know how it can walk.’

Luckily the species prefers to dine on insects, but if threatened it could leave a sizeable mark on human flesh too.

It’s a beast.

Whereas this is an insect which not only can fly, but can be carried away by strong winds, it may very well inhabit a number of other nearby islands. However, given its exceptional size, my suspicion is that it is the unique biosphere of Sulawesi itself which has given rise to such a monster. Perhaps the ‘Garuda wasp’, as it is to be known, can survive elsewhere, but my bet is that its currently only known island of habitat is where it can really thrive.

Of course, its current habitat is effectively random and haphazard without the framework of evolution to guide us. It is only with Darwin’s theory that we can really understand anything about the Garuda wasp or any other unique form of life around the globe.

Filed under: Evidence, Evolution | Tagged: , , , | 25 Comments »

Dawkins on Perry

Posted on August 27, 2011 by Michael

The good doctor nails this one:

There is nothing unusual about Governor Rick Perry. Uneducated fools can be found in every country and every period of history, and they are not unknown in high office. What is unusual about today’s Republican party (I disavow the ridiculous ‘GOP’ nickname, because the party of Lincoln and Theodore Roosevelt has lately forfeited all claim to be considered ‘grand’) is this: In any other party and in any other country, an individual may occasionally rise to the top in spite of being an uneducated ignoramus. In today’s Republican Party ‘in spite of’ is not the phrase we need. Ignorance and lack of education are positive qualifications, bordering on obligatory. Intellect, knowledge and linguistic mastery are mistrusted by Republican voters, who, when choosing a president, would apparently prefer someone like themselves over someone actually qualified for the job.

Let’s not forget that the likes of Palin, Bachmann, and Cain have also been bandied about as serious options. The Democrats may put out individuals deficient in charisma a la Gore and Kerry, but it is nothing like the Republicans where either stupid or ignorant people consistently rise to prominence. And, of all things, that is actually a point of pride for the party.

Filed under: Evolution, Politics and Social | Tagged: , , | 7 Comments »

The long reach of the gene

Posted on July 25, 2011 by Michael

An animal’s behaviour tends to maximize the survival of the genes ‘for’ that behaviour, whether or not those genes happen to be in the body of the particular animal performing it.

~Richard Dawkins, The Extended Phenotype

Filed under: Evolution | Tagged: , | 5 Comments »

Creationists cave to science

Posted on July 22, 2011 by Michael

Recognizing that they don’t have the facts on their side, the creationist members of the Texas State Board of Education gave in to science:

The Texas State Board of Education delivered a blow to social conservatives Friday, giving final approval to supplemental high school science materials after a brief flare-up over some lessons teaching the principles of evolution.

The lessons in question included a lab comparison on chimpanzee and human skulls, the fossil record and cell complexity.

A board-appointed reviewer had called the lessons errors and recommended changes, but a group of scientists objected on Friday, threatening to re-ignite a fierce debate over teaching evolution in Texas public schools.

There was some worry amongst those who understand and favor science that the recent appointment of Barbara Cargill spelled trouble for the teaching of biology. She “questions” evolution (which is code meaning she doesn’t understand it), so it was thought she might start a whole new round of creationist canards and bullshit in an effort to undermine a proper science education. That fortunately has not happened. I find this pleasing, especially considering just how frequently I will be sitting in one of my bio courses, learning something which only makes sense in the light of evolution. Anyone who denies the theory simply does not understand – nor desires to understand – biology.

So a tentative bravo to the Texas State Board of Education. Here’s hoping to see more votes for science.

Filed under: Evolution, News | Tagged: , | 2 Comments »

Hold your horses

Posted on July 9, 2011 by Michael

People like fast things. Our amusement park rides zip on their tracks. We jump from planes for fun. Our video games have names like Need for Speed. We’re even willing to watch bad movies so long as they’re called Speed. But that doesn’t mean there isn’t value in taking things at a pace reminiscent of the olden days. Sometimes we like to slow things down. Sometimes we like to take the time to smell the roses. And sometimes bloggers will engage in hackneyed stock expressions, both in title and content, in order to slowly build up a contrast between quickness and slowness.

As I’ve explained in the past, Richard Lenski is running a 20+ year evolutionary experiment with E. coli. He has published some fantastic results (much to the chagrin of overwhelmed creationists), and now his lab has utilized his bacterial lineages to further probe how evolution works.

[Co-author Tim] Cooper and his colleagues looked at two Escherichia coli clone lineages, sampled after 500, 1,000 and 1,500 generations of evolution. They came from a long-term bacterial evolution experiment running in the lab.

By looking for the presence of five beneficial mutations, the researchers found that ‘hare’ bacteria had more advantageous genetic changes than ‘tortoises’ after 500 generations, suggesting they were more likely to go on to successfully survive and reproduce, and to eventually wipe out their competitors altogether.

The terms “hare” and “tortoise” refer to the speed with which each group experienced mutation. The more quickly mutating group would change so rapidly that it was unable to achieve the same beneficial mutations as the more slowly mutating group. Here’s how I like to think of it.

In the late 90’s, several children were treated with gene therapy for various diseases. This is when a virus is used as a vector for a gene that has the ability (hopefully) to correct whatever is wrong with the child. It’s how researchers cured color blindness in monkeys in 2009. Basically, a gene is missing, resulting in some malady. When the virus is inserted, so is the missing gene. This usually helps or fixes the given problem. However, in a number of the children from the 90’s, insertional mutagenesis occurred. This is where the inserted gene causes a mutation (for reasons we can skip). In these cases, it caused a downstream mutation. The result was leukemia years after the fact.

The reason I’m seemingly rambling is that it was a complex interaction of genes that caused the cancer. It happens often enough that one gene is mutated and it is the loss of function of that gene that causes cancer, but that wasn’t the case in the 90’s. Think of mosquito genocide. Ultimately it’s all such a complex question that the specific results cannot be known ahead of time.

The reason Lenski’s lab found that the slower mutating group of E. coli out-competed the faster group was because the faster group had too many changes. The high number of mutations prevented it from obtaining other certain mutations. A change in one location can have long-reaching implications for future change in another location, in a way superficially similar to that of children from the 90’s, it turns out; it isn’t the case that just any gene can jump into a genome or population and be beneficial, or even work.

This research is important because it is generally assumed that high mutational rate means high evolvability. And that is still going to remain the assumption. But this gives factual credence to the idea that genetic background matters in a very deep way. In fact, Lenski’s earlier work with the same E. coli demonstrated that mutations themselves can be very much contingent. What this all means is that life doesn’t proceed with a single ‘strategy’. High mutation rates have their advantages, but just the same so do lower rates. It’s like driving through the city versus walking through the city. Plenty can be seen and much ground can be covered by car, sure, but a stroll by foot reveals doors and windows and alleys and other things that otherwise could have gone unnoticed.

Filed under: Evolution | Tagged: , , , , | Leave a comment »

Mosquito genocide

Posted on July 8, 2011 by Michael

Whenever I find myself under attack by mosquitoes, I will tend to remark to another person how much I would enjoy a mosquito genocide. Sure, a midge and/or horsefly genocide would be lovely as well – not to mention a whole host of other insect holocausts – but it’s the mosquito I really hate. I mean hate. I would eat raw onions and celery for the rest of my life if I could do away with the little bastards.

The natural response I get from people when I express my desire for mosquito eradication is, “Wouldn’t that really mess up the food chain?” I respond, half-jokingly, that I’m willing to make that sacrifice. Of course, along with most other people, I have always believed that the death of all mosquitoes, or at least the ones that bite humans, would have long-reaching ecological ramifications. And, again, along with most other people, I naturally don’t want to see that happen. But as it turns out, maybe it wouldn’t be such a bad thing after all:

Most mosquito-eating birds would probably switch to other insects that, post-mosquitoes, might emerge in large numbers to take their place. Other insectivores might not miss them at all: bats feed mostly on moths, and less than 2% of their gut content is mosquitoes. “If you’re expending energy,” says medical entomologist Janet McAllister of the Centers for Disease Control and Prevention in Fort Collins, Colorado, “are you going to eat the 22-ounce filet-mignon moth or the 6-ounce hamburger mosquito?”

With many options on the menu, it seems that most insect-eaters would not go hungry in a mosquito-free world. There is not enough evidence of ecosystem disruption here to give the eradicators pause for thought.

At this point in the evolution of life, any significant hole left open by one species will quickly be filled by another. Even when the world has seen mass extinctions, life has been quick to fill in the gaps. And that’s with broad gaps. The loss of mosquitoes would be a very narrow niche to cover.

But there are other mosquito-reliant organisms. The question, however, is, how reliant are they? Mosquitoes make up a lot of the biomass in both aquatic and summer arctic environments. In aquatic environments it’s their larvae that contribute to the ecosystem, bringing about greater variation in other organisms while also producing nutrients for plants. In the arctic, they are food for migratory birds. But in both cases other organisms could easily take their place. Though mosquitoes have co-evolved with so many other species, so have so many other insects and microorganisms. They aren’t unique except in their high level of annoyance.

Attempts at Genocide

When the French attempted to build a canal in Panama, one of their major setbacks was disease carried by mosquitoes. It wasn’t until shortly after they started construction that it was even known that mosquitoes were vectors for diseases such as malaria and dengue fever. And even then, it wouldn’t be for some time – about when the French gave up – that it was known just how much mosquitoes could spread disease.

Enter the Americans.

When the U.S. set to construct the canal, measures were taken to drastically cut down on the mosquito population in the area. Standing pools and ponds of water were drained near construction and living areas. High grasses were cut down to create fields mosquitoes were less likely to cross. Oils were added to difficult to drain ponds. Acids and caustic sodas were even spread in great quantity. And what effect did this have on the ecology of the surrounding area? Apparently none. (At least none as a result of the loss of the mosquito.) Of course, this wasn’t an eradication, and it didn’t impact all areas, but it was a massive effort and the mosquito population was reduced significantly.

So could we do something like that, but for all mosquitoes, in all areas? Probably not. Many places in the South have programs where standing buckets of water and other common mosquito breeding grounds are destroyed. Other places spread sprays which kill mosquito larvae. These methods help, but they aren’t enough to fix the problem. And in all likelihood, there are no practical methods available that could bring about the Great Mosquito Genocide. Really, I trust that if humans could get rid of this pest, we would have long, long, long ago.

But don’t let our inability to destroy these little bastards take anything away from the dream of mass mosquito murder:

“They don’t occupy an unassailable niche in the environment,” says entomologist Joe Conlon, of the American Mosquito Control Association in Jacksonville, Florida. “If we eradicated them tomorrow, the ecosystems where they are active will hiccup and then get on with life. Something better or worse would take over.”

Filed under: Evolution, Science | Tagged: , , , | 3 Comments »

Punching bags

Posted on July 1, 2011 by Michael

Whenever creationists get hold of a legitimate scientific paper, I groan a little bit for at least two reasons. First, I know whatever they have to say, they’re going to mangle the science. We saw that with Jack Hudson last year (and, actually on literally every post about science he has ever made). And, of course, we also saw that with all the other creationist sites from which Jack stole his material. Second, I know I’m going to have to devote some time to reading and blogging on a paper I would have otherwise missed. It isn’t that I don’t like to read these things – I do. The problem is that it’s a time-suck when the blogging is factored in. You see, unlike creationists I actually research and verify what I have to say on any given piece of science.

Let’s start with the paper in question:

Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized ‘bright zone’. These are the oldest non-biomineralized eyes known in such detail, with preservation quality exceeding that found in the Burgess Shale and Chengjiang deposits. Non-biomineralized eyes of similar complexity are otherwise unknown until about 85 million years later6, 7. The arrangement and size of the lenses indicate that these eyes belonged to an active predator that was capable of seeing in low light. The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event8.

The gist of the find is this. Researchers discovered very old fossils of arthropod eyes from the Early Cambrian. They do not predate complex eyes, but they do predate similar non-biomineralized eyes. That is, trilobite eyes are made of calcite, meaning the trilobites produce the minerals for their eyes themselves. In turn, their eyes are hardened (and thus more easily fossilized). So these new fossils show a different way in which eyes could become complex. Furthermore, they showed a tight packing in the lenses, much in the way that a fly’s lenses appear to be tightly packed. They also were curved to form binocular vision, meaning there was a visual overlap in front of the body. This helps for judging distances and discerning complicated backgrounds. This creature was a predator.

But here is where creationists draw issue:

Did you catch that? If you were a high school student who trusted your teachers, you’d think they had evidence for this unbelievably rapid amount of highly complex change. But they merely assume that it evolved, so it “had” to have been a great evolutionary event and another example of “rapid innovation.” [And is thus a tautology.]

This comes from Neil who, like many creationists, was taking his cue from another site. He believes that every paper that mentions evolution must provide a detailed description of why evolution is true.

His quote was a reference to this excerpt from the paper:

[The new fossils] provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event.

What this is referencing is the fact that until now advanced eye fossils were almost exclusively restricted to trilobites in the fossil record. These new fossils give evidence that, as suspected, there were other marine creatures swimming around with complex eyes. Furthermore, they show a quantitative change in the number of lenses, not the sudden appearance of these sort of lenses. (But note that we can’t expect to see a perfect fossil record. We can get a good outline, but it’s silly and really very ignorant for creationists to demand to see every intermediate organism. At some point things will have to “suddenly” appear. Of course, this is in geological terms, i.e., over millions of years.) These eyes are evidence that evolution was driven in part by the anatomical changes in vision during the Cambrian.

So it is clear that none of this is a tautology. This fossil find is further evidence of the nature of evolution and the role vision played in its creation of arms races. What we see from the creationist world, however, is an immature understanding of the science. There is no doubt that Neil never bothered to read the paper from Nature, nor have many of his creationist brethren. If any of these sort of non-academics bothered to look into the literature (or even take formal courses), they would see their obvious errors. Further, even if we are to understand this paper as Neil purports it to be, he’s still in error. That is, he believes the paper is a tautology because it assumes evolution without giving evidence for why evolution is true. This is like drawing issue with physics papers because they assume gravity is true without explaining general relativity. It’s a silly complaint to make and it only demonstrates how wildly over the head of creationists most scientific papers are.

Filed under: Creationism, Evidence, Evolution | Tagged: , , , , , | 1 Comment »

Re: Origins of vision

Posted on May 16, 2011 by Michael

I’m doing another repost, this time taking from an article I did about the origins of vision. Note that the quote coloring is reversed from how it normally appears.

Vision likely originated as simple eyespots in simple organisms. It also is traced back to jellyfish and their own simplistic eyespots, which are actually still present in some manner today. That is, jellyfish have areas of photoreceptor cells which don’t allow vision as we know it (they don’t even have brains), but they do allow a sensation of particular wavelengths of light to be perceived. These wavelengths often indicate depth (and maybe predators), which in turn may indicate food source (pelagic jellyfish don’t tend to get to plump).

Recent research has discovered the genetic pathway involved in light sensitivity in a close relative of the jellyfish.

“We determined which genetic ‘gateway,’ or ion channel, in the hydra is involved in light sensitivity,” said senior author Todd H. Oakley, assistant professor in UCSB’s Department of Ecology, Evolution and Marine Biology. “This is the same gateway that is used in human vision.”

This allows for a prediction using evolution: all organisms alive today which share a common ancestry with hydras will share this same genetic gateway. Organisms like flies, as the article points out, do not share this ancestry with vertebrates and as such do not share this genetic gateway. If they did share it, then wow. Creationists could actually trot out their improbability arguments.

“This work picks up on earlier studies of the hydra in my lab, and continues to challenge the misunderstanding that evolution represents a ladder-like march of progress, with humans at the pinnacle,” said Oakley. “Instead, it illustrates how all organisms — humans included — are a complex mix of ancient and new characteristics.”

(End different quote coloring.)

I looked this post up because I recently ran across a creationist who actually trotted out that old “the eye is irreducibly complex” bull and I was searching for some other links. But what’s interesting is what a different creationist was saying in the comment section:

You premised your claim of cnidarian relationship to vertebrates and humans on a gene they share in common. You said specifically, “This allows for a prediction using evolution: all organisms alive today which share a common ancestry with hydras will share this same genetic gateway.” I pointed out that certain beetles share certain genes with vertebrates and humans that other insects do not – and by your logic, that would mean these beetles share an ancestry with humans other insects do not.

As I pointed out at the time (and as the creationist failed to even come close to grasping), my claim was not based upon the sharing of individual genes, but rather on the sharing of complex genetic pathways. It is these pathways that ultimately allow for such a prediction. The creationist then confused the discussion on pathways with the article focus of a gateway. (I pointed out his error to him, but to no avail.) It is these pathways, by and large, which first get us to the point of where we can say that hydra and humans share a common ancestry in terms of vision. From that point we can look at the particular gateway in question and make the prediction I originally made. (One caveat: organisms which have lost their ability to see may not share the gateway.)

Filed under: Evidence, Evolution | Tagged: , , , , | 1 Comment »

Neil Shubin inducted into NAS

Posted on May 3, 2011 by Michael

This is satisfying:

The National Academy of Sciences today announced the election of 72 new members and 18 foreign associates from 15 countries in recognition of their distinguished and continuing achievements in original research…

Shubin, Neil H.; Robert R. Bensley Professor and associate dean, department of organismal biology and anatomy, University of Chicago, Chicago

Shubin is most famous for his evolution-utilizing research into Tiktaalik. I’m glad to see him inducted.

And congratulations to everyone else who was deemed worthy to be a member of such a prestigious institute.

Filed under: Evidence, Evolution, News, Science | Tagged: , , , | 1 Comment »

« Previous Page — Next Page »