Tag Archives: Evolution

Aug 22 2013

Cornelius “Common Creationist” Hunter



Cornelius Hunter has a history of struggling to understand simply concepts. Today is no different:

As with the so-called vestigial structures—another evolutionary construct—function is, ultimately, irrelevant. A structure is “vestigial,” or DNA is “junk,” not by virtue of any objective criterion dealing with function, but because evolutionists say so.

His post was primarily about so-called ‘junk DNA’, but I’ve addressed that topic in the past, so I will only mention it to note that it only ever betrays a deep ignorance when creationists talk about it. What I really want to discuss is Hunter’s mention of vestigial structures. First, let’s define our term:

[Vestigial] refers to an organ or part (for example, the human appendix) which is greatly reduced from the original ancestral form and is no longer functional or is of reduced or altered function.

Vestigial structures provide a clue to the evolutionary history of a species because they are remnants of structures found in the ancestral species.

It’s easy to see Hunter’s error. A vestigial structure need not be related to function whatsoever – and that doesn’t therefore mean that it is merely the say-so of biologists that makes it vestigial. The human ear, for instance, has vestigial muscles that don’t do anything; in our ancestors (and cousins), their function is to swivel the ear for better directional hearing. That’s vestigial, it’s evolutionary, and it’s science. DNA comparison can, does, and will show that when looked at. Furthermore, a vestigial structure can have a function while still being vestigial. For instance, whales have remnants of hind legs that clearly are not used for walking. However, they do play a role in where muscles are attached. Again, that’s vestigial, it’s evolutionary, and it’s science. Hunter just isn’t familiar with these things.

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Mar 14 2013

On evolution:

The fact that we all have the same genetic building blocks strongly suggests a single point of origin for all of life. That we can trace our genetic heritage and cousinships in a hierarchical and expanding way which matches morphology, behaviors, and the fossil record helps to make the case for evolution one of the strongest cases for any theory in the history of science.

Feb 3 2013

How should we treat cloned Neanderthals?

Harvard geneticist George Church was recently interviewed by a German magazine where he said that we need to start talking about the ethical and other implications of cloning a Neanderthal. He said that, whereas the technological possibility is foreseeable in the relatively near future, we need to start the conversation today. Unfortunately, English-based media sensationalized his comments and falsely claimed that he was looking for a surrogate mother:

Harvard geneticist George M. Church was quoted in the Daily Mail as looking for an “adventurous woman” to serve as a surrogate for a “cloned cave baby.” The shocking headline spread quickly across the media with no small amount of help from major news aggregators like the Drudge Report…

“I’m certainly not advocating it,” Church told the Herald. “I’m saying, if it is technically possible someday, we need to start talking about it today.”…

Church added that he wasn’t even involved in the particular aspects of the Human Genome Project focused on Neanderthals. Nonetheless, he hopes to use the mistake made by the media for the greater good. “I want to use it as an educational moment to talk about journalism and technology,” he said.

To compound the mistake made by the media, people like Arthur Caplan, writing for CNN, continues to spread falsehoods even after the correction has been made:

Despite a lot of frenzied attention to the intentionally provocative suggestion by a renowned Harvard scientist that new genetic technology makes it possible to splice together a complete set of Neanderthal genes, find an adventurous surrogate mother and use cloning to gin up a Neanderthal baby — it ain’t gonna happen anytime soon.

My beef is with the baseless accusation that Church was being intentionally provocative. Here is what he actually said:

SPIEGEL: Mr. Church, you predict that it will soon be possible to clone Neanderthals. What do you mean by “soon”? Will you witness the birth of a Neanderthal baby in your lifetime?…

SPIEGEL: Would cloning a Neanderthal be a desirable thing to do?

Church: Well, that’s another thing. I tend to decide on what is desirable based on societal consensus. My role is to determine what’s technologically feasible. All I can do is reduce the risk and increase the benefits.

In other words, the magazine asked him all these things. He gave pretty uncontroversial answers, even choosing to take a rather neutral stance when asked if we should clone a Neanderthal. I think the evidence is clear that not only was Church not being intentionally provocative, he was actually attempting to give benign answers.

At any rate, this all does raise the interesting question of how we would treat Neanderthals if we did clone them. Would we give them the same rights and protections? Would we develop a new application for the old scourge of apartheid? I’m not sure the answers to these questions, but I do have some input on how we should go about considering them.

Humans are awfully fond of talking about our special status in the animal kingdom. Indeed, many of us refuse to even consider ourselves animals, disregarding the affront to biology such a stance is. Of course, we have some good reasons for separating ourselves, at least in the context of morality and ethics. Though such practices, common across many taxa, are little more than game theory working itself out amongst genes and individuals, humans take it to another level. So while, for example, our ape cousins will show rudimentary understandings of right and wrong, we have far more complex rules for our society, rules that we can reason out and justify by way of our higher level of intelligence. We are different and that’s important.

How different, though, are Neanderthals? We know a fair amount about them, but they haven’t been around for 20 or 30 thousand years. No one has interacted with them, so a cloned baby would be an experiment in every sense of its life. How different would it be? Would we have criteria established that said, ‘If the Neanderthal is different in these certain ways, it will not enjoy the same rights afforded everyone else under our laws’? I don’t know, but the concern is an interesting one because it raises the issue of why we think we’re so special.

Evolution is a continuous process. We are descended from species which were not human, but at no point did one species give birth to a brand new one. Every mother gives birth to offspring that are categorized in the same way she is. However, when enough time has passed, we’re given the luxury of defining different groups as species within this or that Genus under one or another Family. But look over the tape of evolution and everything eventually converges and lines blur. Just think about human evolutionary history: Back things up 100,000 years and we’re largely the same. How about 150,000? 300,000? 1,000,000? At some arbitrary point we pick, we’re going to start defining significant differences, but if we continually shrink the window of time, the differences start to disappear. (This is all a huge problem, in my view, for the Catholic or other theistic evolutionist who believes only humans have souls.) So from 500,000 years ago to 100,000 years ago, there will be notable change, but that change will be smaller between 400,000 and 200,000 years ago. And the differences become less when we look at our history from 300,000 to 200,000. Keep going and we may be talking about how different our ancestors from 272,000 years ago were from our ancestors living 271,000 years ago. Forget that our investigations into the history of life can’t get that specific. What’s important is that we have to realize there is no line in the sand that says “Species A ends there and Species B begins here”.

So if we do decide that Neanderthals are less deserving of the rights given to humans, we have to admit that humans, at some point in our lineage, were also not deserving. That is, our intelligence and consciousness become more and more comparable to our cousin apes (and now extinct man-like cousins) as we go back in time; we eventually arrive to a point where we would not give our ancestors the same rights that we enjoy. That means we are not inherently special, and I think that’s a major blow to a lot of our assumptions. The supposedly humble Neanderthal shines light on our human arrogance.

Jul 17 2012

Evolution, fruit flies, and counting

Don’t let any creationist tell you complex things don’t come from simple precursors:

US and Canadian researchers have evolved a population of fruitflies that can count. The result, presented on 9 July at the First Joint Congress on Evolutionary Biology in Ottawa, Canada, supports the notion that the neural mechanisms underlying basic arithmetic skills first emerged hundreds of millions of years ago. It could also eventually offer a key to understanding why some people have problems with numbers…

During a 20-minute training period, flies were exposed to either two, three or four flashes of light — two and four flashes coincided with a vigorous shake administered by placing a electric toothbrush next to the box containing the flies. After a brief rest, the flies were returned to box and shown the light flashes. Despite a dislike for being shaken, most of the flies were not able to learn to associate the negative stimulus with the number of flashes. But 40 generations later, they could.

The researchers caution that the work is preliminary and that they do yet know what genetic changes are behind the insects’ evolved number sense.

What I find interesting is exactly how this constitutes selection pressure. The flies certainly don’t like being shaken, but that’s entirely irrelevant if there isn’t some sort of reproductive advantage to be had from recognizing when the shaking will occur. Clearly there is, and we could speculate all day long as to why flies that associate the flashes with negative stimulus pass on more of their genes than the other flies, but I would like to see some experimental data showing the details. Does shaking disorient the flies? Does it interrupt the mating process? Does it affect fertility? Perhaps the paper that comes from all this can shed some light.

Now excuse me while I go murder the fruit flies that appear to have evolved to make my kitchen just awful for the past week.

Jun 14 2012

Evidence of evolution: The shrinking of insect body size

Insects used to be enormous. Go back in time 300 million years and we would see dragonflies with 28-inch wingspans. The reason, of course, for these ridiculous sizes had to do with the oxygen level in the atmosphere. Whereas we enjoy about 21% of the air we breathe today as oxygen, it was once closer to 30%. Looking through the fossil record will bear out the case: As oxygen levels fluctuated up and down, so did insect body mass – and it did so in concert; as one went up, so did the other, and as one went down, so did the other. That is, until about 150 million years ago. At that point we see oxygen levels rise, but insects actually became smaller. Here’s a likely reason for that change:

Maximum insect size decreased even as atmospheric pO2 rose in the Early Cretaceous following the evolution and radiation of early birds, particularly as birds acquired adaptations that allowed more agile flight.

No one wants to be the big target.

What we have here is a tidbit of evidence for evolution. We see that there is a strong link between oxygen levels and insect body mass. We know this makes sense because insects today require strong levels of O2 in order to work efficiently (this, in addition to simple wind, is one reason insect bites decrease as one increases in elevation, such as during a hike). In other words, we have that part pretty well figured out. However, there is a kink in the idea. Insects stopped following their usual trend at a particular point. Fortunately, we know that this point was when birds started to evolve. As evolutionary theory predicts in its most basic form, increased predation resulted in changes in prey. And as further evidence:

A further decrease in maximum size during the Cenozoic may relate to the evolution of bats, the Cretaceous mass extinction, or further specialization of flying birds.

New selection pressure brought about a massive change in the direction of an entire class of animals, and it probably did so several times. Just as the asteroid that hit Earth 65 million years ago made it so the dinosaurs were no longer the most significant constraint on mammal size, the evolution of birds made it so oxygen levels were no longer the most vital force behind total insect body mass.

May 26 2011

Religion and the fear of death

One of the motivators for religious belief is the comfort it provides. For many people it provides an immediate comfort because it allows one to be a part of a bigger group, and people like to belong. For others, it provides a comfort of ‘knowing’. For instance, we all want to know the answer to a lot of basic questions like “How old is the Earth” and “How did humanity begin”. Religion – while it has either always been wrong or been forced to defer to science in order to be correct (and even then it usually mangles things) – makes strong claims that it has the answers. But for so many others, religion provides comfort against the fear of death. Many of us want to believe we keep on existing, that all we’ve done in our lives has some unending meaning, and maybe ultimately, that we are never alone. It is this final sort of comfort that indirectly forms the basis of some new research:

Researchers at the University of British Columbia and Union College (Schenectady, N.Y.) have found that people’s ‘death anxiety’ can influence them to support theories of intelligent design and reject evolutionary theory…

The researchers carried out five studies with 1,674 U.S. and Canadian participants of different ages and a broad range of educational, socioeconomic and religious backgrounds.

In each study, participants were asked to imagine their own death and write about their subsequent thoughts and feelings, or they were assigned to a control condition: imagining dental pain and writing about that.

The participants were then asked to read two similarly styled, 174-word excerpts from the writings of Behe and Dawkins, which make no mention of religion or belief, but describe the scientific and empirical support for their respective positions.

After going through these steps, participants who imagined their own death showed greater support for intelligent design and greater liking for [Michael] Behe, or a rejection of evolution theory coupled with disliking for [Richard] Dawkins, compared to participants in the control condition.

However, the research team saw reversed effects during the fourth study which had a new condition. Along with writings by Behe and Dawkins, there was an additional passage by Carl Sagan. A cosmologist and science writer, Sagan argues that naturalism — the scientific approach that underlies evolution, but not intelligent design — can also provide a sense of meaning. In response, these participants showed reduced belief in intelligent design after being reminded of their own mortality.

While it was creationism intelligent design that was chosen for this experiment, I see this study as representative of religion at large. When shown two different arguments, a sizable portion of the participants clearly chose to reject evolution on the basis that it provided them with no sense of meaning. It isn’t particularly relevant that the alternative was specifically creationism intelligent design since there is no science to be found within any religious idea anyway – nor is there any science supporting any religious claim of significance. Any relatively mainstream religious idea could have been presented in science-y terms – just as creationism intelligent design is – and then used as a tool for comparison.

This isn’t all to say that the primary motivator for religious belief is the fear of death. I suspect it’s actually culture and upbringing – the biggest indicator of what one’s religion will be is what his or her parent’s religion is. But the fear of death – the fear of the unknown – frightens people and makes them uncomfortable. Religion helps to ease that discomfort with its made-up stories and fairy tales, and so it acts as a tightly woven net that catches people before they can fall into reason or even momentary consideration of their beliefs.

While the results of this study are obvious (and while they will be distorted by believers), I think there is another interesting point here, albeit an obvious one. There are a lot of accomodationists (Collins, Giberson, Miller, etc) out there who will argue that religion and science are compatible. While their position is one that is in some ways a small improvement over the current situation, there is comfort in the fact that they aren’t winning over too many adherents. People still recognize that evolution does largely eliminate their particular, cultural god. The fact that we know humans were not inevitable (or any other animal, for that matter) means that most of the gods in which people believe are untenable. That is, the sort of gods people praise are almost always the ones that deemed the inevitably of humanity. That inevitably takes away the random components of life and gives credence to why a god would care about us at all. I think the recognition that evolution takes this all away is ultimately good because it shows that while these people do not understand evolution in its details, they do understand its implications. That is a good thing – even if they falsely associate those implications with a lack of meaning in life.

Source

May 16 2011

Re: Origins of vision

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.)

Nov 14 2010

Butchering science

Creationists hate science. They hate its conclusions, they hate its methods, they hate that it doesn’t support their silly beliefs. It’s that hatred that motivates them to butcher scientific articles and papers.

One recent butchering comes from Jack Hudson. I’m sure regulars here remember him. If not, it isn’t important. He’s a creationist with a background in introductory biology courses from 20 years ago. It’s doubtful he has much experience reading scientific papers, but that doesn’t stop him from trying.

In his post he butchers two articles. I’m going to focus on the first one, but I’ll briefly mention the second one. In that one researchers found that some negative mutations don’t change the protein sequence yet they are still negative. This one is simple. The entire sequence of a gene is not devoted to just the protein sequence. A mutation can therefore change one aspect of a gene without changing another – but it can still change another process that is important in forming proteins. Alter shape in one place and you have a good chance of seeing change somewhere else as a result. Biology is still all about shape.

The second paper, though. Woo. What a doozy of a butchering. First let me summarize the paper.

In asexual populations alleles can become fixed rather quickly. Their evolution is more straight forward because they aren’t mixing and matching genes. They produce offspring with the exact same genome, less there be a mutation. If there is a mutation, it can become fixed because things are generally less complicated with asexual populations and thus more black and white. Is this mutation good or bad? As the paper says and as Jack repeats upon hearing the term for the first time, alleles sweep through a population.

But when it comes to sexually reproducing populations, things become more complicated. And this is what the paper is about. The question is, do alleles sweep through populations in sexually reproducing populations like they do in asexual populations? The answer is no.

Now, if we’re to believe Jack, this means that evolution has failed because, why, evolution predicts an advantageous allele to reach 100% fixation, of course. Except it isn’t so black and white with sexually reproducing populations. (Nor does evolution predict that anyway.)

What the researchers did was study over 600 generations of fruit flies. They let them breed naturally, but then selected out the eggs which were produced the most quickly. This led to significantly faster reproducing populations. They then tracked specific alleles to see if they would become fixed. What they found was that they don’t.

Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.

The conclusion here is that selection for a particular trait in sexually reproducing populations acts upon many different aspects and genetic variants within the genome, not merely a single gene or SNP.

This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.

This is the actual conclusion of the paper. To put it another way (and to repeat myself), advantageous variants do not wipe out other genetic variants in a sexually reproducing population, instead acting on variation in a more subtle and complicated way. The big conclusion here is that there is a difference in how genes become fixed (or not fixed) in asexual populations versus sexually reproducing populations.

And Jack’s conclusion?

In short, if the activity failed to occur in the lab under optimal conditions, it is unlikely that traits are going to be transmitted this way in nature.

The traits are still being transmitted through natural selection working on variation. Jack’s conclusion has little to no connection to anything from the paper. In fact, it is abundantly clear that he read an article somewhere, figured out how to butcher it, and then went and read a few lines from the original paper.

I’ve said in the past that what takes a creationist 30 seconds to say takes an educated person 3 hours to correct. This post and the research required for it didn’t take that long, but the sentiment remains true – it’s a real hassle to untangle the carelessly mushed writings of a creationist.