What is ‘junk DNA’?

Posted on March 5, 2011 by Michael

I’m always hearing people bring up the modern understanding of ‘junk DNA’ as if it somehow lends evidence to the existence of God. It’s not an argument I really get. Whether most of an organism’s DNA is needed or not doesn’t magically disprove evolution. Maybe people just don’t get the concept, I don’t know. I’ll try and give a brief explanation.

About 30 or 40 years ago it was understood that most of the human genome was composed of DNA that served no discernible purpose. That understanding changed with time, morphing from a position of no purpose to one where most DNA was noncoding. This was partially a technical change. Most DNA is noncoding; it doesn’t produce proteins. “Junk” is a misnomer in this context. But we’re discovering more and more that previously deemed purposeless DNA actually does have a function. Often enough it is important in regulation. But still, some 95% of our DNA has no function at all. We may be finding that more of it serves some purpose than we previously thought, but the fact that most of it is useless remains.

I bring this up because of a recent post I saw on an anti-science website (better known as the inspiration for my still-new Punching Bags series – I use it as a hunting ground now). What I find so entertaining about these creationists and their infatuation with junk DNA is that one of the reasons biologists (not creationists, of course) are able to determine that DNA has a function is because of evolution. Sometimes we can directly determine a function through experiment and observation, but much of the time we rely upon inference. DNA which is noncoding yet none-the-less conserved is said to have some sort of function. It must. It makes no sense for a given sequence to exist over millions of years and across distant lineages if it doesn’t serve some function. Of course, this is no problem for those of us on the side of science. Everything really does make sense in the light of evolution. (And you thought that saying was just rhetoric.) But this does pose a problem for creationists. While they’re trying to inanely deny that most of our DNA is not usefully transcribed, they are necessarily relying upon the fact of evolution – the very thing they want to deny.

If it wasn’t for the harm to all of science they cause, I would more easily delight in pointing out how ill-considered creationist ideas really are.

Filed under: Evolution | Tagged: , | 10 Comments »

Punching bags

Posted on February 17, 2011 by Michael

Aaaand the very first winner of my new series Punching Bags is Wintery Knight. Congratulations, Mr. Knight! This is the probably the greatest thing you’re ever going to accomplish in your blogging career.

There’s a lot of silliness out there, but what really grabbed my attention by standing heads and shoulders above the rest was a series of posts by Wintery Knight about atheism and morality. It’s astonishing just how poorly pieced together it all is. Let’s take a peek at WK’s methods:

First of all, I wrote up a list of questions to use to interview atheists about their views.

Second, I posted the raw results of my survey.

Third, I listed the minimal requirements that any worldview must support for in order to ground rational morality.

Fourth, I argued that atheism does not ground any of these requirements.

Fifth, I argued that Christian theism does ground all of these requirements.

Sixth, I posted my own answers to the questions.

I really recommend taking a look at that first link; the arrogance and snobbery drip from every word:

Who is safe to talk to?

In this post, I am going to explain to you clearly how to engage your atheist friends on these issues. But be careful. Some atheists have fascist tendencies – when they feel offended, some of them want to bring state to bear against those who make them feel bad. Atheists struggle with morality, it just doesn’t sit well on their worldview, even though they sense God’s law on their hearts, like we do.

1) Thank goodness WK is here to help everyone know which atheists are okay. Some of us bite, don’t you know.

2) It’s good to know he has already defined morality when he declares that atheists struggle with it. Of course, we all know this is just another case of a theist assuming “objective” in front of “morality”.

3) Of course atheists sense God’s law in their hearts. Just like how Christians really hate science and reason deep down, amirite?

But WK’s interviews appear to be entirely irrelevant. They aren’t necessary to any of his further posts in any way. Besides that, his questions are statistically meaningless since he, um, doesn’t obtain any statistics; his ‘survey’ holds no value and is nothing more than an exercise in condescension. Let’s move on.

His next move (third link) is to try and tell us what is required for “rational moral behavior”. Gee, I wonder if he’s going to assume “objective” anywhere, gaming the issue in his favor.

1) Objective moral values

There needs to be a way to distinguish what is good from what is bad. For example, the moral standard might specify that being kind to children is good, but torturing them for fun is bad. If the standard is purely subjective, then people could believe anything and each person would be justified in doing right in their own eyes. Even a “social contract” is just based on people’s opinions. So we need a standard that applies regardless of what people’s individual and collective opinions are.

Whoa! My whole world view has been devastated! And in only 5 sentences. How could I have been missing something so obvious?!

Oh. Wait. Woulddya look at that. We need a way to tell good from bad. Well, wouldn’t that require that there is an objective good and bad in the first place? Or maybe WK is just making an assumption, causing him to beg the question. Could it be that our ideas of “good” and “bad” have a basis in our cultures and societies and human nature and our emotions and physical bodies and relationships and intelligence? And if so, couldn’t we use ethical and moral theories, applying them to the facts of the world and our derived definitions of “good” and “bad”, thus shaping how we behave? And wouldn’t this be the very definition of rational? (Hint: The answer to all of my questions is “yes”.)

But despite being so far off, WK trudges onward:

What difference does it make to you [an evil stupid dumb butt atheist] if you just go ahead and disregard your moral obligations to whomever? Is there any reward or punishment for your choice to do right or do wrong? What’s in it for you?

Bracketed clarification added.

I’m not so sure I would trust someone who thought the point of morality was to get something for himself. (Oh, who am I kidding. I trust a ton of Christians and they all necessarily believe that the point of being good is to get a big pretty prize at the end of the road.) I guess I just prefer to act out of genuine reasons, not for the sake of enriching myself in some unevidenced afterlife.

Anyway. WK goes on and on with his blog, sometimes saying dumb things about evolution, other times promoting science that makes him feel special. He’s an old Earth creationist, perhaps the most nebulous of all creationists (tell me again, when did humanity begin?), but in the end he’s just another punching bag.

Don’t forget to submit other potential punching bags.

Filed under: Religions | Tagged: , , , , , , , , , , | 3 Comments »

Our failing schools

Posted on February 14, 2011 by Michael

It isn’t possible to list and discuss every single problem public schools in America face today. It would probably even be unwieldy to discuss just a small percentage. But there are some big issues that need to be tackled.

Researchers found that only 28 percent of biology teachers consistently follow the recommendations of the National Research Council to describe straightforwardly the evidence for evolution and explain the ways in which it is a unifying theme in all of biology. At the other extreme, 13 percent explicitly advocate creationism, and spend at least an hour of class time presenting it in a positive light.

This presents an obvious issue: teachers aren’t telling students a fundamental truth about the world. That’s more than a shame and we need to correct it. First, fire every single biology teacher that professes creationism to students. Second, give the teachers that are too timid or ill-prepared on the topic better tools. (I don’t know why a biology teacher should be ill-prepared to teach something so basic to an entire field, but here we are.) There are plenty of computer programs, textbooks, popular books, videos, documentaries, etc out there that can bring evolution to life for students.

But there is a deeper issue here. We have national standards for education that just aren’t being implemented. Sometimes it’s because the standard is only recommended, other times it’s because of bad teachers, and still other times it’s because of conflicting local standards. I know how popular it is to claim that local governments should be putting forth their own ideas on education, but it isn’t that black and white. There are necessary levels students need to be obtaining in order to be prepared for higher education. When local governments are given too much power, we often see lower standards.

That’s no good.

There is an expectation on the higher education level that students often are not meeting. This either slows down introductory courses or forces students to take sub-100 level classes in order to catch up. It’s a waste of money and time. Part of the solution has to be better implementation of national standards. This is what colleges and universities across the country need. It is at that level that the tempo is being set; we need to force our primary and secondary schools to meet that challenge.

And if anyone wants local control, by all means, draft proposals that require students to exceed far beyond anything our national standards might demand.

The original study can be found here. Thanks to Nancy H for the links.

Filed under: News, Politics and Social | Tagged: , , , , , | 29 Comments »

A basic point about evolution

Posted on February 7, 2011 by Michael

Evolution is an entirely natural process. It occurs through well understood mechanisms for which we are gaining ever improving detail. The belief in theistic evolution runs counter to all this; it is not compatible with the theory. Yes, yes, there are people who say they accept both their interventionist god and evolution and therefore their views are not contradictory, but that holds no relevance here. Things don’t become compatible simply because a lot of people believe them simultaneously.

In order for one’s views to be consistent with evolution, one can only hold two positions: atheism or a sort of deism. By “a sort of deism” I mean either exactly deism or something where, okay, there is a god who intervenes in human affairs, dictates our morality, and does all that other magic bigoted thought-crime sort of thing, but this god does so incidentally. That is, since no particular form of life, much less characteristic, much less species, was ever destined to exist by any law of biology, a god which it is believed made humans (or intelligent life, a la Miller) inevitable is necessarily false. Only a god which had no part in evolution is tenable; evolution is a miracle free process.

So let’s break it down:

Atheism: Entirely compatible with the theory of evolution. The process of natural selection is miracle free and excludes all directed intervention.

Traditional Deism: Compatible, but likely unsatisfying. By “traditional” I mean the deism which says there was a creator with intention that began the Universe, but that creator’s interest ended there.

Other Deism: Compatible, but still unsatisfying. I use “other” because there is no particular name for this sort of deism as far as I am aware. This is the deism which says we have a moral lawgiver and all that swell BS, but it can only be incidental. The theory of evolution tells us that humans were not destined to exist, therefore we cannot say that this interventionist god planned on us, as if we’re somehow special.

Theistic evolution: Not compatible. No species are destined to exist. That includes humans.

Creationism: Moronic anti-science nonsense. It isn’t compatible with any major branch of science.

I have excluded agnosticism because it doesn’t mean much to say that this or that is or is not compatible with “idunno”.

Filed under: Evolution | Tagged: , , , , | 33 Comments »

‘What would change your view on evolution?’

Posted on January 27, 2011 by Michael

I hear that question posed from time to time. Sometimes it is directed at me, but more often I hear it directed towards established (and often famous) scientists. It’s usually a product of creationist rhetoric where the answer doesn’t really matter. Regardless, it is an interesting question.

What would change my view on evolution?

It depends what is meant by “change”. My view on evolution changes quite frequently, actually. Sometimes it’s a qualitative change: the relationships between our known ancestral cousins are always shifting ever so slightly. Often, there is little consensus about where to place certain members of the genus Homo on the evolutionary tree. As new evidence is found, as more research is done, as further facts come to light, my views are always changing on that aspect of evolution.

And then there are quantitative changes. One excellent example comes from the discovery of tetrapod footprints. That discovery pushed the evolution of tetrapods back about 18 million years. All the relationships between species of that general time period stayed the same, but our view of when tetrapods began to populate the land changed.

And then there are all sorts of other changes, like recently when it was shown that natural selection works differently on allele fixation in sexually reproducing populations versus more simple asexual populations. (That was also a qualitative change, but on the genetic, not taxonomic, level.)

So if that is what is meant by “change”, then there are all sorts of examples that show how my views on evolution are, well, evolving. The same can be said of biologists around the world. But what if by “change”, the real question being asked is, What would make me dismiss evolution? Then the answer is very different.

As I recently explained, a basic fact of science is that it does not tend to operate on individual studies. It requires a body of evidence to change views. For example, I reject a connection between cell phone use and cancer. Studies have shown possible links, but they have been far from conclusive, weak even. And more importantly, there is a body of evidence showing no significant link. I’m going with the evidence in bulk, not the individual packaging. This relates directly to the question of what it would take to get me to dismiss evolution because there is a famous quote by J.B.S. Haldane I had in mind when starting this post. When asked what it would take to change his mind, he retorted,

Fossil rabbits in the Precambrian.

But that wouldn’t change my mind. My very first suspicion would be fraud; I suspect little more from creationists (and we know how much they would be promoting such a discovery). But let’s say it came from a reputable research team, then what? I would admittedly be perplexed. There is no reason a fossil rabbit ought to be found in that era, but that doesn’t mean we get to throw out such a well established theory as evolution. We know evolution is true insomuch as we know gravity is true. It would necessarily take more than a few rabbit fossils to alter the unifying theory of biology, just as it would take more than an apple falling up for us to alter the theory of gravity. Even if we could never explain the fossils satisfactorily, I would have no doubts that evolution still formed the basis of my field of choice.

What would change my view would be the discovery of a number of fossils in all the wrong places. We would need to start finding mammals and birds dating back 800 million years; we would need to see dinosaur fossils embedded in the rocks of 20 million years ago; we would, yes, need to see rabbit fossils in the Precambrian. No, I don’t need these specific examples, but I do need these sort of examples. I don’t want just individual anomalies that fly in the face of modern theories. I need more than that: it takes a body of evidence to start changing my view. Because that’s how science works.

Filed under: Evolution | Tagged: , , , , , | 13 Comments »

If evolution worked like homeopathy

Posted on January 12, 2011 by Michael

via xkcd

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

Are humans “more advanced” than other organisms?

Posted on January 2, 2011 by Michael

I recently had a discussion with a friend where he asserted that he was more advanced than, say, a plant. By the common connotations that come from the word “advanced”, we would have to agree that his statement was true. But it asks an interesting question: What do we really mean when we say we’re advanced?

To put the discussion in a proper framework, think in evolutionary terms. That means we can’t compare Albert Einstein to Sarah Palin and say, “Why, yes, he was more intellectually advanced than she is.” Of course that is true, but if we’re going to discuss evolution and what it means to be advanced, we’re necessarily comparing species, not individuals. That is what makes my friend’s initial comparison to plants a reasonable starting point.

But it is only a starting point. Because what are we comparing exactly? In terms of brain development, yes, he beats that plant handily. But what about in terms of ability to photosynthesize? Well, the plant just got a knockout in that round. Clearly there is a difficulty in making useful (and, in my view for this discussion, any) comparisons between species. Maybe we need to find a species that is closer in relation to humans. (It certainly would help for it to have a brain in the first place.) The animal I chose for the discussion and the one I am choosing for this discussion is the skunk. Jerry Coyne is the inspiration.

It does not always [evolutionarily] pay to be smarter, either. For some years I had a pet skunk, who was lovable but dim. I mentioned this to my vet, who put me in my place: “Stupid? Hell, he’s perfectly adapted for being a skunk!” Intelligence comes with a cost: you need to produce and to carry that extra brain matter, and to crank up your metabolism to support it. And sometimes this cost exceeds the genetic payoff. A smarter skunk might not be a fitter skunk.

A skunk is vastly more well adapted to life as a skunk than any human ever could be. All the things it takes to be a skunk? A skunk has them nailed down pretty well. The counter to this point was to say that if humans decided to destroy all skunks, we could. True enough. But does that make us more advanced? Of course our intelligence allows us to wipe out many other species, but the whole point of bringing up a skunk and its adaptation is to say that a comparison of intelligence is not valid for purposes of this discussion in the first place! (As always, you know I mean it when I use the lazy-man’s exclamation point.)

When we choose to compare intelligence in order to define what it means to be advanced, we have two massive assumptions going on. First, we’re assuming that intelligence is better than toothiness or having sharp claws or any other characteristic we see in nature. This assumption is untenable because some environments might call for all or any of those characteristics over intelligence. To put things in perspective, try thinking on an evolutionary timescale. So far I have only been comparing humans to other extant organisms (plants and skunks). But what if we go back 100 million years? 200 million? 500? 600? Any human put into an ancient enough environment would die. We know this because the right foods would not be available or because there would be no proper shelter or because the atmosphere would be poisonous or because our immune systems would not be evolved to cope with the bacteria and viruses present at the time or because…and so on. The assumption that intelligence is better than anything else is clearly wrong once we recognize that evolution and the ability of a species to survive depends largely upon environment.

The second assumption in this whole discussion is that we can even say something in evolution is “advanced”. We can say more complex or better suited to a particular environment, but “advanced”? That implies evolution is on the march towards some goal, to some end. That is not true. Science has demonstrated this again and again by showing what a contingent process evolution is. Take the Lenski experiments, for example. (I’m rather disappointed I never wrote about them here.) Richard Lenski and his researchers followed several lineages of E. coli for 20 years (in fact, they’re still following them). They would freeze samples every 500 generations so they could go back and re-run the tape of evolution should some fundamental change occur. And, eventually, such change did occur. Some E. coli were able to consume a natural by-product of their environment after nearly 30,000 generations. Lenski et al. unfroze the old generations to see just what enabled the bacteria to obtain their new found skill. As it turned out, they had to go back many thousands of generations; it wasn’t just one mutation, but at least three. The first two were effectively random. But they were necessary in order to get to the third mutation – the one that opened up a new food product for the colonies. But in the re-running of the tape, not all lineages re-evolved the new mutations. The chance involved in the process was too great to be inevitable; evolution is contingent.

So my answer to the question, Are humans “more advanced” than other organisms?, is to say it is an inappropriate question in the first place. There are several things we should not be assuming:

  • Intelligence is the best trait (whether to this point or in terms of possibility)
  • Evolution is goal oriented
  • The ability to destroy other species and still survive is a mark of advancement

I mentioned the argument for point three, but I have yet to address it. This one is pretty straight-forward, I think: We may be able to destroy many species, but that really only applies for large organisms. The vast majority of life is microbial. Since we would never be able to destroy it all (or even a minute fraction of it), does that mean it is more advanced than we are? What about all the bacteria we need to keep us alive? We certainly could not destroy all the mitochondria of the world and still survive.

Evolution is a contingent process that has no march towards any end. It is about the ability to survive. Our genes are interested in propagating themselves and that is why we are here. Life may mostly (though not entirely) be more complex since it first sprung forth nearly 4 billion years ago, but it always depends upon its environment – and that makes some characteristics more valuable than others. Sometimes.

Filed under: Evolution | Tagged: , , , , , , , | 16 Comments »

Thought of the day

Posted on January 2, 2011 by Michael

Any news piece about a new scientific discovery which says some key aspect of evolution has been rewritten or radically changed is probably just a load of horseshit.

Filed under: Misc | Tagged: , | 7 Comments »

Butchering science

Posted on November 14, 2010 by Michael

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.

Filed under: Creationism, Evidence, Evolution | Tagged: , , , , , , , , , , | 3 Comments »

On the conflict between science and religion

Posted on October 31, 2010 by Michael

It’s often said, ‘Sure, other people’s religion conflicts with science, but they aren’t representative of the majority. Besides, my religion isn’t in conflict with science!”

Here’s a simple test to find out if your religion conflicts with science:

1) Do you believe in miracles?
2) Do you believe in a creator who directed evolution?
3) Do you believe prayers work? (And why doesn’t your god heal amputees?)
4) Do you think faith is a virtue?

If you answered “Yes” to any of these, and you derive your answer(s) from your religion, then your religion does conflict with science. Let me explain.

1) A miracle is a suspension or interruption of a physical law or constant. The whole idea in science is that physical laws and constants are true at all times and in all places. If you believe they can be arbitrarily interrupted, your belief is in conflict with science; science does not allow for the interruption of, say, the speed of light in a vacuum. You can believe that the speed of light in a vacuum can be changed by your god, but (aside from having no evidence for such a claim) your belief is one that is anti-scientific.

2) Evolution is a natural process that is based upon the changing of allelic frequencies within a population over time. It happens as a result of genetic change and interaction with the environment. It is a natural process that is contingent upon a long series of chance happening and natural selection; under the same environmental conditions, a re-running of the history of life would give different results. You can believe your god made it so humans (or any other animal) would be inevitable, but your belief is anti-scientific.

3) The science is in and prayer does not work. You can still believe it does, but your belief is anti-scientific.

4) Science is a valuing of reason, experiment, and, ultimately, evidence. Faith is the anti-thesis of this. You can still believe faith is a good thing, but your belief is anti-scientific; it is not a belief that is found within science.

Bonus conflict: Philosophy

Do you believe in the philosophical reasoning of the First Cause? This is the argument that says everything has a cause and thus the Universe has a cause. (And then it is randomly declared that God is eternal.) This goes against science because Newton told us that everything which has a force has an opposite and equal force. This is dependent upon observations made within the Universe. Your philosophy goes beyond this evidence and makes a conclusion which is independent of the sort of reasoning Newton used. In other words, if you say the Universe has a cause because everything else has a cause, you aren’t making sense. Everything within the Universe has a cause. That’s all science tells us. We can presume a reason for the Universe since it, well, exists, but we cannot use the scientific reasoning used by Newton; he was talking about forces within the Universe.

Filed under: Religions, Science | Tagged: , , , , , , , | 7 Comments »

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