Language

Posted on March 15, 2009 by Michael

Language is a dicey thing. It’s especially dicey for scientists. Take Einstein for example. He used to use the word “God” quite often. He usually did not mean anything related to the Christian god (or any other god concept). Let’s look at the Einstein phrase “Did God have a choice in creating the Universe?” He wasn’t literally asking if any particular god had a choice. He was asking if the Universe could have come into being in more than one way. Incidentally, the fact that the answer to this question is unknown should throw some light on that awful argument, the “anthropic principle“. Allow me to digress.

The anthropic principle is the creationist delusion that their particular god made the Universe with humans soley in mind. It’s likely the most arrogant concept ever presented. Beside that, it basically says “Humanity (or life in general) is too well adapted to the Universe for everything not to have been made for humans/life”. Humans are evolved to the Universe (at least one, insignifcant part of it that holds no special relevance). The whole argument ignores this fact. Of course, that is the creationist motif: hear no facts, see no facts, speak no facts. What’s more, it’s just an argument from personal incredulity: “The Universe is just too perfect to not be for me! I can’t believe anything else! It’s too much!” Mooks.

But I return. Language in biology can be difficult. In order to popularize the subject, scientists will use personifying terms. “Genes want to replicate”, or “Cuts and bruises want to heal”. There shouldn’t be anything wrong with this. It’s human nature to do this. We call computers stupid or say “the flowers danced in the sun” (for the more poetic among us). Of course, there is a contingent of people who hear these terms and think they are literal. They also happen to often be people who don’t realize the Bible is metaphoric in its entirety and therefore take it literally.

Take the comment section from a recent thread. Not to harp on a particular commenter, but the term “code” is taken wildly out of context. Rather than read for what it is, it is read as being something with intention at its root. Let’s examine.

Biologists may say “DNA codes for the genome”. This is true, but it has no connection to intentionality. What it means is simply that DNA is in one form until it is translated and transcribed into another form. In other words, it goes from being a series of amino acids into a series of proteins and enzymes. This does not require some grand creator or intelligence. It requires a slow, gradual process that provides for plenty of random variation while being governed by a non-random mechanism. Evolution by natural selection fits the bill.

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

Words from a 'respected' theologian

Posted on February 15, 2009 by Michael

Why we still respect theologians is beyond me. These people are nothing more than literay critics with a very narrow focus. At least this one only seems to have made headlines at a Christian site. On top of that, he actually said some things which aren’t batshit crazy.

“If you understand Christianity or even Theism – the belief of a sovereign creator God – and evolutionary theory in its dominant form , I find it impossible to reconcile the two,” Dr. R. Albert Mohler Jr., president of Southern Baptist Theological Seminary, said on his radio program Thursday, the 200th birthday anniversary of Charles Darwin.

I wouldn’t go so far as to say impossible, but it is tremendously difficult.

The seminary head went on to explain how the “originating mechanism of creation” is where theism runs right into collision with where modern evolutionary theory is.

Whereas the Biblical account of creation accepts the role of a Creator, the theory of evolution “suggests that natural selection is indeed the mechanism and that it is entirely natural and in no case supernatural,” said the theologian.

“There is no way for God to intervene in the process and for it to remain natural,” he asserted.

He’s sort of right. Theism and evolution can intersect. It’s just that the theism has to be precisely superfluous with evolution. That, of course, makes the theism rather useless, but it does solve the issue of being irreconcilable: a god just needs to match the established scientific fact. A religion like that would be a very powerful force, indeed. Aside from having the noteworthy property of being true, it would also have the worthwhile attribute of being beautiful.

Archbishop Gianfranco Ravasi, head of the Pontifical Council for Culture, said last week that the idea of evolution could be traced to St. Augustine and St. Thomas Aquinas, according to the Telegraph in London. Both theologians had observed that big fish eat smaller fish and that forms of life had been transformed slowly over time.

This is a bug creationists love. Attempting to discredit Darwin seems to give them a tingle up their legs. I don’t quite understand why this is so popular but let’s just state a fact: Charles Darwin and Alfred Wallace discovered evolution independently around the same time. No one else gets credit for this big discovery. That’s because no one else described what they observed (nor even observed the same things) like Darwin and Wallace. These two men get the credit. End of story, you filthy, lying creationists.

Although Mohler said he rejected evolution as a way to explain the origin of all things, he acknowledged that there are changes in animals that take place over time.

“No Conservative Christian should deny there is a process of change that is evident within the animal kingdom. And there is even a process of natural selection that appears at least to be natural,” he said, adding all one has to do is look at a herd of cattle to find evidence of adaptation and a competition of genes.

Apparently in la-la land principles of change stop applying once they become inconvenient. “Oh, sure, gravity applies to apples and such, but certainly not galaxies. I mean, that’s too much to fathom!”

A Gallup poll released on Feb. 11 found that 200 years after Darwin most Americans still don’t believe in evolution, with only 4 out of 10 Americans saying they accepted the theory.

“I believe the reason why they cannot believe in evolution is because when they look in the mirror they cannot see an accident,” remarked Mohler.

It is true many humans have quite the ego, but I’d also propose that the campaign of ignorance as waged by the Discovery Institute, Ben Stein, and other dishonest creationist organizations/creationists is a much larger factor.

Perhaps if this literary critic went to school for a real education, he’d have far less ignorance on which to rely. But whom am I to talk? Mohler has a Master of Divinity and Ph.D. in “Systematic and Historical Theology”.

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Words from a ‘respected’ theologian

Posted on February 15, 2009 by Michael

Why we still respect theologians is beyond me. These people are nothing more than literay critics with a very narrow focus. At least this one only seems to have made headlines at a Christian site. On top of that, he actually said some things which aren’t batshit crazy.

“If you understand Christianity or even Theism – the belief of a sovereign creator God – and evolutionary theory in its dominant form , I find it impossible to reconcile the two,” Dr. R. Albert Mohler Jr., president of Southern Baptist Theological Seminary, said on his radio program Thursday, the 200th birthday anniversary of Charles Darwin.

I wouldn’t go so far as to say impossible, but it is tremendously difficult.

The seminary head went on to explain how the “originating mechanism of creation” is where theism runs right into collision with where modern evolutionary theory is.

Whereas the Biblical account of creation accepts the role of a Creator, the theory of evolution “suggests that natural selection is indeed the mechanism and that it is entirely natural and in no case supernatural,” said the theologian.

“There is no way for God to intervene in the process and for it to remain natural,” he asserted.

He’s sort of right. Theism and evolution can intersect. It’s just that the theism has to be precisely superfluous with evolution. That, of course, makes the theism rather useless, but it does solve the issue of being irreconcilable: a god just needs to match the established scientific fact. A religion like that would be a very powerful force, indeed. Aside from having the noteworthy property of being true, it would also have the worthwhile attribute of being beautiful.

Archbishop Gianfranco Ravasi, head of the Pontifical Council for Culture, said last week that the idea of evolution could be traced to St. Augustine and St. Thomas Aquinas, according to the Telegraph in London. Both theologians had observed that big fish eat smaller fish and that forms of life had been transformed slowly over time.

This is a bug creationists love. Attempting to discredit Darwin seems to give them a tingle up their legs. I don’t quite understand why this is so popular but let’s just state a fact: Charles Darwin and Alfred Wallace discovered evolution independently around the same time. No one else gets credit for this big discovery. That’s because no one else described what they observed (nor even observed the same things) like Darwin and Wallace. These two men get the credit. End of story, you filthy, lying creationists.

Although Mohler said he rejected evolution as a way to explain the origin of all things, he acknowledged that there are changes in animals that take place over time.

“No Conservative Christian should deny there is a process of change that is evident within the animal kingdom. And there is even a process of natural selection that appears at least to be natural,” he said, adding all one has to do is look at a herd of cattle to find evidence of adaptation and a competition of genes.

Apparently in la-la land principles of change stop applying once they become inconvenient. “Oh, sure, gravity applies to apples and such, but certainly not galaxies. I mean, that’s too much to fathom!”

A Gallup poll released on Feb. 11 found that 200 years after Darwin most Americans still don’t believe in evolution, with only 4 out of 10 Americans saying they accepted the theory.

“I believe the reason why they cannot believe in evolution is because when they look in the mirror they cannot see an accident,” remarked Mohler.

It is true many humans have quite the ego, but I’d also propose that the campaign of ignorance as waged by the Discovery Institute, Ben Stein, and other dishonest creationist organizations/creationists is a much larger factor.

Perhaps if this literary critic went to school for a real education, he’d have far less ignorance on which to rely. But whom am I to talk? Mohler has a Master of Divinity and Ph.D. in “Systematic and Historical Theology”.

Filed under: Misc | Tagged: , , , , , | 1 Comment »

Happy Darwin Day

Posted on February 12, 2009 by Michael

Today is the 200th anniversary of the birth of Charles Darwin. The discover of the principles of the most important theory yet formulated, Darwin also wrote his landmark book, On the Origin of Species, 150 years ago this year (though not this day).

As more people are likely to note, it is also the 200th anniversary of the birth of Abraham Lincoln. Certainly a man of high significance, his contributions to humanity have been greatly smaller than those of the aforementioned great scientist. Evolutionary theory is the backbone of life itself. It goes to explain far more important things than Lincoln’s actions affected mankind.

I am tentative in the qualifiers and apologies within these statements because it is abundantly clear Darwin trumps in greatness most men, at least insofar as contributions to his fellow species are concerned. However, this post isn’t intended to tarnish the image of Lincoln. Rather, we recognize Lincoln as one of the great men in history, one of the great contributors. In contrasting and comparing the man with Darwin, the intention is to illuminate the significance of Darwin’s theory of evolution. Lincoln was great. I hope we agree. Darwin was greater.

Let’s not forget, however, that Darwin is great for his discovery, but greater still is the discovery itself. It explains so much.

Earth

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Ancestral environments and reverse evolution

Posted on January 14, 2009 by Michael

There’s been a long debate regarding whether evolution can be reversed or not. The general trend has been that it can not. The idea goes that once one evolutionary pathway has been crossed, it cannot be retraced back to its origins. It turns out that is not entirely true.

Says [researcher] Henrique, ‘In 2001 we showed that evolution is reversible in as far as phenotypes are concerned, but even then, only to a point. Indeed, not all the characteristics evolved back to the ancestral state. Furthermore, some characteristics reverse-evolved rapidly, while others took longer. Reverse evolution seems to stop when the populations of flies achieve adaptation to the ancestral environment, which may not coincide with the ancestral state.

What the researchers did was subject fruit flies to various selection pressure for multiple decades, i.e., they changed their environment over and over. The ‘end’ result was fruit flies that were markedly different in their traits as compared to the original specimens. That’s evolution. Children should understand that. What happened next was the researchers mimicked the original environment of the fruit flies from decades gone by. In response, the fruit flies adapted to those environments, possessing many of the same allele frequencies they originally had. What I find particularly interesting is that they did not evolve exactly the same, but they still evolved in a way that was similar to the original phenotypes. This helps to explain why sharks and horseshoe crabs remain so similar for so long: the gene pool of the population centers around certain allele frequencies because, well, they work. Change may happen – in fact, it certainly does – but ancestral pheno- and genotypes can evolve to such similar future counterparts as to make little difference in show, even though we know there to actually be differences, at least in contigency. It’s a bit like how two people of very different backgrounds and even different alleles can come to have the similar tones to their skin. Their evolutionary contigency, or histories, are different, but the result is virtually the same.

Another point of note here is that evolution can produce similar things, but it will almost never produce the exact same thing. The history of life, if rerun, would be much, much different in all likelihood. When exolife is discovered, we’ll have indirect confirmation of this. Until then, it should be important for people to realize that nothing in biology is inevitable – including humans.

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Artificial molecules

Posted on January 9, 2009 by Michael

Origins research is beginning to really heat up (hilarious pun intended). One team of researchers is working with RNA (but then again, who isn’t?)

A new molecule that performs the essential function of life – self-replication – could shed light on the origin of all living things.

If that wasn’t enough, the laboratory-born ribonucleic acid (RNA) strand evolves in a test tube to double itself ever more swiftly.

“Obviously what we’re trying to do is make a biology,” says Gerald Joyce, a biochemist at the Scripps Research Institute in La Jolla, California. He hopes to imbue his team’s molecule with all the fundamental properties of life: self-replication, evolution, and function.

By building a molecule that can self-replicate, Joyce’s team has shown a pretty solid principle of how scientists believe life began: begin with something simple which makes copies of itself, then…

Not content with achieving one hallmark of life in the lab, Joyce and Lincoln sought to evolve their molecule by natural selection. They did this by mutating sequences of the RNA building blocks, so that 288 possible ribozymes could be built by mixing and matching different pairs of shorter RNAs.

What came out bore an eerie resemblance to Darwin’s theory of survival of the fittest: a few sequences proved winners, most losers. The victors emerged because they could replicate fastest while surrounded by competition, Joyce says.

As Joyce notes, this isn’t truly life. It’s a very promising experiment, however, and that’s where the excitement lay. By inducing mutations, evolution began to take place. It’s so simple a child can understand it.

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The confusion over Steve Jones

Posted on January 6, 2009 by Michael

Steve Jones has, according to media reports, made the claim that human evolution has stopped, or is at least slowing down in the West. At times we see conflicting statements from Jones himself over this.

I really just know about snails, and the beauty of evolution is that it gives biology a structure, so the rules that apply to snails or to fruit flies to some extent apply to ourselves. Obviously there’s much more that applies to us. But if you ask the simple Darwinian question about natural selection, inherited differences in the ability to pass on genes (which is only part of the evolutionary argument) it’s pretty clear to me that at least for the time being and at least in the developed world, natural selection has stopped or at least slowed down.

First, snail evolution is quite beautiful. Second, we see here that Jones is referring to natural selection, not evolution. Some sort of argument can be made that there is much less selection pressure on humans in Western nations than there was in the past. Of course, that wouldn’t be a very satisfying argument since natural selection is still ‘weeding out’ people with certain diseases and predispositions. It’s just that some of them, depending upon their economic situation as well as their particular affliction, happen to have reduced overall selection pressure on their alleles. But even then, there are people with diseases which will kill them before they get a chance to reproduce.

At any rate, this whole argument becomes rather moot because Jones also goes on to specifically speak of evolution rather than just one of its mechanisms. In fact, his talk is titled “Human Evolution is over”. He is wrong. Even if we were to ignore all the problems involved with making an argument that natural selection is over in humans (in the West), the evolution-is-over argument still does not fly because evolution is not simply selection. Genetic drift and mutation are two other major mechanisms. While he seems to ignore drift, Jones does, however, argue that there are fewer mutations in the population. His argument goes like this.

Men are fathering children at far younger ages than they did in the past. Given the fact that mutations accumulate in a person over time, these young men have fewer mutations than older men. Thus, subsequent generations are inheriting fewer and fewer mutations.

Okay, the first question which comes to mind is “So what?” The mutation rate of younger fathers is still, by far, substantial enough to maintain the continuing of human evolution. There is no shortage of mutations in each and every person at birth. Jones probably was born with around 100 mutations. You, too.

The second thing which comes to mind is to wonder why Jones would first make this age-mutation argument, but then go on to argue this.

Similarly, child survival rates, abysmal in antiquity, have dramatically improved in much of the world, cutting natural selection pressures.

In other words, more people live to reproductive age. This means there are more people reproducing, which means more mutations. His argument is dreadfully weak.

One wonders why such a quality scientist would make such a poor proposition.

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

Discussing science

Posted on December 9, 2008 by Michael

I find I often subject myself to a surprising amount of anti-science misery, otherwise known as the Crosswalk forums (with alternative names such as ibelieve.com). If you dare to read that rubbish, you’ll actually find a thread linking to one of my posts. I was banned long ago (it’s lifelong; I’m so flattered!), so it was actually a friend who made the thread. Anyway, it has generated a good deal of traffic for me, as well as quite a few responses, even if a large number of them are wholly devoid of any education. One reason it has generated traffic is because this blog (and science) tends to be a tad abrasive toward creationism and I guess there’s a whole slew of other people who like subjecting themselves to material which disagrees with what they believe, too.

Here’s a sample of the rubbish which is put on these forums.

NS [natural selection] is just a filter. It doesn’t create anything, it just weeds out stuff. Contrary to Darwinism, it doesn’t necessarily keep stuff either. There is nothing that stops deleterious mutations from undoing neutral and/or good ones.

Natural selection is a filter, but it does not exist, apparently.

Well, just speculating here, but if the tooth of a little dinosaur was made into a necklace, would anyone necessarily think of it being a dinosaur? A lot of what we see in the museums are people’s ideas of what they may have looked like, so I’m not entirely sure that what we see in the pictures are what they really even looked like.

Those silly misleading fossils. Scientists just guess how they go together.

So the pattern, rather than gradual changes through incremental and incidental modification of ongoing mutation, appears to be a rapid appearance of various groups [of horseshoe crabs] followed by extreme stasis, presumably comprising in some cases hundreds of millions.

This would seem to directly contradict the fundamental notion of Neo-Darwinian evolution.

Please see Gould.

Ok so here are some of the major reasons why I believe Darwinism will collapse.
Darwinism will ultimately collapse as a valid theory of life origins because :

It fails to explain the origin of complex coded information contained in all living organisms
It fails to explain the origin of nano bio-machinery contained in all living organisms
It fails to account for irreducibly complex systems contained in all living organisms
It fails to account for the human moral sense and altruism
It fails to explain the general lack of transitional forms in the fossil record which should number in the multiple millions but don’t
Natural selection (originally a creationist concept) has failed as a sufficient explanatory mechanism for the level of complexity and diversity in nature
Random mutations can never account for the sophisticated, factory-like organization within the cell
It fails to account for how, in the midst of greater numbers nefarious mutations, any of the rare beneficial mutations could dominate bio history = see 1st quote below
… IDists and creationists are invited to add to this list if you have more reasons

My head hurts.

Okay, I’m sorry for posting this, but I wouldn’t do it if I didn’t have a redeeming link, I promise. For actual discussion on evolution where people have [i]actual[/i] educations, the Richard Dawkins forums are excellent. I don’t personally post very much, but simply reading good discussions about science is refreshing and wonderful. And it isn’t necessary that you be an atheist to post or enjoy the read.

Filed under: Creationism, Evolution, Misc | Tagged: , , , , , , , , , | 2 Comments »

Kin Discrimination and the Social Amoeba

Posted on November 27, 2008 by Michael

Research recently published in PLoS Biology indicates that amoebas which are close to starvation will seek out genetically similar relatives.

We tested how widely social amoebae cooperate by mixing isolates from different localities that cover most of their natural range. We show here that different isolates partially exclude one another during aggregation, and there is a positive relationship between the extent of this exclusion and the genetic distance between strains. Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals, suggesting the existence of a mechanism that discerns the degree of genetic similarity between individuals in this social microorganism.

It will be really interesting if/when a description of the mechanism discerning genetic similarity is given, and if there is any remnant of it still present in humans or to what extent it exists in other species.

Interestingly, this study seems to provide more evidence for the gene being the important unit of selection by nature. It is the very survival of these organisms that could explain what has been observed here on a genetic level: genes which are similar have evolved a mechanism for detecting one another because of the mutual (but ultimately selfish) benefit of doing so. The further from similarity they are, the more likely they are to discriminate in offering assistance, as was the case in this study. Aside from the reason of promoting different allelic versions of one’s self, one good reason for the evolution of this discrimination mechanism would be to weed out “cheaters”, or genes which take advantage of the ‘altruism’ of these genes to assist other amoebas in their time of need (starvation) by abusing their helpful nature. That is, if it is embedded in me, when I see a fellow organism of my species, ‘If starving, help fellow organism’, it will pay me to also have the command, ‘If distantly related, do not help’. In other words, if I see my brother and my 2nd cousin starving, it’s going to be worthwhile for my genes if I am able to detect which one is my brother since he shares more genetic material with me than my 2nd cousin. By helping him instead of the more distant relative, I am increasing the odds that my genes or genes very close to my own will be passed on to the next generation. My genes have limited interest in helping out other, distant genes.

By the by, the use of GFP makes this experiment all the more beautiful.

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Why we believe in gods

Posted on November 25, 2008 by Michael

I found this video on why we believe in gods to be very interesting and worth watching.

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

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