November Edition

The November edition is here. It can be found scattered throughout the UMA campus and in the hands of anyone who wants to read something intelligent.

As seems to be par for the course, it is not without errors. The previous edition had an unfortunate number of typos. This one does not have that problem (as so far noticed), though one article (Arguing From Consequence) did have one of those weird errors where certain characters are changed to seemingly random code. It looks like it is an isolated incident only affecting a few commas, however.

On page 4 at the bottom middle is an attempt to list the email address for contacting Without Apology. It seems to have been cut off. The address is withoutapologyinmaine@gmail.com.

Enjoy this month’s edition.

Secret Creationist Document Discovered

By Michael Hawkins

The following is a recently discovered creationist manifesto.

It is the objective of us, the New Creationists, to undermine not simply evolutionary theory, but science as a whole. It is this form of inquiry which has caused the greatest damage to our version of events. It must be destroyed at all costs.

The primary method for attaining our goal is Reaching a Middle Ground. This means that we are to seek, purely in the eye of the layman public, a position which appears on the surface to be a reasonable compromise. To be sure, we want to tell the world we embrace evolution. We also want to tell the world we embrace a Creator.

We want to hide Our Creator in the nearly impossible to understand gaps of reality. Quantum mechanics will often be our realm, but much more can work. As stated, our goal is Reaching a Middle Ground with the layman public. We need not answer to scientists. Indeed, they are the enemy. What we are to do is wrench the very fruits of these enemies from their empirical hands. We are to show gaps in the understanding of the cell. We are to discuss unknowns in molecular biology. We are to contort the flaws of physics, cosmology, and astronomy to assist our goals. It is in these places that Our Creator resides. If it’s science, it is imperfect. We shall exploit, even invent, imperfections. All is justified in our goal. Science deserves nothing but lip service; It is the enemy.

Our first step is to put forth an army of Christian scientists. They will not be the supporters of fringe creationism. They shall not espouse views which deny any modern science. However, they shall put atop all modern science a sense of confusion and remote possibility. That remote possibility shall be where Our Creator resides.

Our goals at this point will rely upon American idiosyncrasies. Tired of divisive politics, Americans seek a Middle Ground. They crave a sense of wishy-washy – it sounds fair. We shall marginalize the New Atheists with paint brushes of extremism. While they fully embrace science and all its evils, we shall embrace it only superficially – we shall not fall into the evil of the enemy. We shall appeal to the American sense of fair play. We are the New Creationists.

The Worst Thing About Creationism

By Michael Hawkins

To believe species to be immutable is to believe a falsehood. To believe light from billions and billions of light years away could really only be 6,000 years old is an affront to reality. To believe two of every animal could fit into an ark has no basis in truth. There is nothing but an incredible poverty in such infantile ideas. Yet creationists fully embrace them.

But of all the things about creationism, perhaps the worst is simply its lack of beauty. It teaches – nay, encourages – people to be content with a small Universe. It teaches that it is okay, even good, to look up at that deep band of stars that comprise the Milky Way and to say, “Meh. What else is there?” This is what believers in special creation are taught. They believe, most arrogantly, that there is nothing greater out there than their concept of an ever-shrinking, ever-so-tiny god.

Reason, rationality, and science encourage one to sit outside on one of those warm summer nights, pure awe undaunted by the anonymous fears lurking in the dark. They say, Look! there’s so much to be known. Don’t ever be satisfied with the Universe you know. They teach us to say, “Wow! What else is there?” They teach that it is not good but stupendously great to wonder – and it is even greater to tear that wonder asunder and leave it in shattered little pieces so to discover that, yes, there are still deeper wonders. That is the prize of knowledge. Creationism rejects this beauty.

Of course, none of this says whether one or the other is true. Reality dictates that (and reality has a strong bias toward the truths of science). What this does suggest, however, is that something so vile, empty, and ugly as creationism and petty, little humanoid gods has no place among the robust beauty of science and reason and rationality.

The Liberal Cup and Shaw’s Lodging

By Michael Hawkins

There are some downright awful businesses out there. Most big box stores fall under this heading. Then there are smaller businesses like T’s Golf in Manchester. But one can only stand reading about these sort of disgraces for so long. It is far better, indeed, to read about the good places.

One such place, without any doubt, is The Liberal Cup. It has the best food, the best environment, and a great owner: the squash is amazing, the people are great, and the owner, Geoff Houghton (who, in the interest of full disclosure, is not a personal acquaintance), has an incredible business sense about him. There isn’t a thing I don’t like about the place.

The only establishment, I think, that can rival the Cup is Shaw’s. No, not that Shaw’s. This one is located in Monson and offers more than groceries.

Located in a town through which Appalachian Trail thru-hikers must pass, Shaw’s (www.shawslodging.com) is made for the hiker. After walking the 100 Mile Wilderness, I stopped here with friends. We found ourselves stuffed with the most satisfying all-you-can-eat breakfast ($7) we’ve ever had.

And the owners, my goodness. Dawn MacPherson-Allen and Susan Stevens bring an environment that is like visiting an almost overly hospitable relative. At no point can anyone feel like this is a business; Shaw’s is like a home.

The world needs more places like The Liberal Cup and Shaw’s Lodging.

Arguing From Consequence

By Michael Hawkins

It is a systematic lie you’ve heard about Hitler and evolution. He did not use evolutionary science to justify his beliefs. Indeed, the man was a creationist. The following is a quote from Mein Kampf.

“Walking about in the garden of Nature, most men have the self-conceit to think that they know everything; yet almost all are blind to one of the outstanding principles that Nature employs in her work. This principle may be called the inner isolation which characterizes each and every living species on this earth. Even a superficial glance is sufficient to show that all the innumerable forms in which the life-urge of Nature manifests itself are subject to a fundamental law–one may call it an iron law of Nature–which compels the various species to keep within the definite limits of their own life-forms when propagating and multiplying their kind.”

He believed in “kinds”, a term as poorly defined in his time as it is by modern creationists. He fully rejected evolution, just as did one of his biggest influences, Houston Stewart Chamberlain. In fact, Chamberlain believed evolution would be judged as men of his day judged (and still judge) alchemy.

Of course, the fact that Hitler was a creationist says nothing of creationism. An evil man believing something does not make it false. And this is where a point must be made. Public creationists such as Ray Comfort, Kirk Cameron, Ben Stein, and those who work for AnswersInGenesis will willfully make fallacious arguments trying to link Hitler to evolution. They suggest – coyly as ever – that evolution is wrong because it leads to bad things. Of course, they would never be so direct in their coy creationist lies, but it is the obvious implication. They seem to have no idea that an Argument From Consequence is entirely meaningless.

But, for a moment, pretend it does matter; pretend the argument actually makes sense. Hitler never used evolution for his hatred anyway. Indeed, he couldn’t! Writing in 1945, he says, “We use the term Jewish race merely for reasons of linguistic convenience, for in the real sense of the word, and from a genetic point of view, there is no Jewish race.” Insofar as there is no good biological basis for races, he was correct. (However, concentrated populations will tend to share traits. Ashkenazi Jews, for instance, have increased odds of getting breast cancer.)

At best, Hitler and his Nazi party used a distorted version of Social Darwinism, which itself was a distorted version of Darwinism. Indeed, the basic concepts behind Social Darwinism existed long before Darwin even hit the scene. Out of unfortunate convenience, its supporters brutalized real science when they got the opportunity.

It is the firm hope of this writer that nothing as ugly as creationism could possibly be true, but that isn’t good enough. It is through evidence and NOT using red herrings that such a case must be made. Creationists would do well to understand that. Of course, then there would be no creationists.

Madison, Jefferson, Rights, and Defintions

By Michael Hawkins

James Madison espoused a separation of church and state in much the same manner as Thomas Jefferson. The following is from Congressional minutes recorded in August of 1789.

“Mr. Madison said, he apprehended the meaning of the words to be, that Congress should not establish a religion, and enforce the legal observation of it by law, nor compel men to worship God in any manner contrary to their conscience.”

And we can go one step further into Madison’s mind with more recordings from the same session.

“Mr. Madison thought, if the word national was inserted before religion, it would satisfy the minds of honorable gentlemen. He believed that the people feared one sect might obtain a pre-eminence, or two combine together, and establish a religion to which they would compel others to conform. He thought if the word national was introduced, it would point the amendment directly to the object it was intended to prevent.”

It’s hard to see how a reasonable person could misinterpret this. Madison obviously rejected the notion that religious beliefs should be codified into law, thus establishing them as the moral directives of other individuals. That is, religious beliefs should not be made law because that essentially makes government an enforcer of religion – and that is far from its role. Good government does not dictate morality.

Moving beyond Madison, a discussion of the concept of rights needs to happen. What is a right? A succinct definition is hard to formulate, but I think a good idea can be created. Something which does not infringe upon another’s rights should be a right. This alone isn’t much of a definition because it assumes the existence of rights, the very thing we want to define. But within a certain context it does give a good approximation of what a right should be; we already have established rights (free speech, religious beliefs, protest, etc), so assuming we agree on those, we can ask ourselves, does X infringe upon these? If the answer is “no”, then there’s a good chance that X is a right.

I think it is eminently appropriate to also include safety and security as one defining piece of rights. Does X cause bodily harm to me or others? Does it cause undue financial hardships? Does it put someone at risk of life or health? If the answer is “no”, we again have another good indicator that X is a right.

I hope it hasn’t escaped anyone that the previous two paragraphs are speaking of natural rights. These are rights which extend to all peoples, not merely Americans or Europeans or Russians or any one particular group. They are effectually based upon the idea that rights are to be based upon humanity and the human condition.

So why are rights so important? I think it should be obvious. If a society goes about imposing restrictions upon minorities or the meek, then the statement that some people are not equal to others is being made. This seems like nothing less than a manifested superiority complex.

Yet restrictions go beyond this statement of superiority. They implicitly say any group can be superior to another. The reasoning behind the superiority isn’t important (whether from religious doctrine or philosophical notions). What matters is that (usually unknowingly) there are people who do not accept the idea that rights are universal. They can’t. They believe that the very concept of rights can be ignored if it runs counter to some other line of thought. Does Religion X say public prayer is immoral? If so and if Religion X’s followers are a majority, they can stampede the rights of those who wish to publicly pray. This can only be because the teachings of Religion X are being claimed to be superior to the rights of others. And this can only be a true claim if rights are not universal and if we agree that morality trumps individual rights.

I, for one, disagree.

Only in the Light of Evolution

The following also appears at For the Sake of Science. Presented here is that version rather than the version for the physical copy of Without Apology.

By Michael Hawkins

We should see fossils in a certain order if evolution is correct. They should go from simple to more complex overall, and the fossils we see in the most recent strata should resemble extant life much more than the fossils we see in old strata.

We should also see changes within lineages. We should be able to observe instances of gradual change in species that eventually leads up to either current species or at least to the time of extinction for these species.

Here’s a simple timeline of life’s history. Click it.

What the evidence shows is gradual change. First we find simple bacteria which survived off energy from the Sun, then we see more complicated cells known as eukaryotes arise. (You are a eukaryote.) Next we see a slew of multi-cellular animals arise. They’re still simple, but much more complex than the original bacteria. A few million years later more complicated life arrives. Early (and simple) plants begin to take hold. Soon the fossil record begins to show more plant complexity with low-lying shrub such as ferns, then conifers, then deciduous trees, and finally flowering plants. Gradual changes occur in the oceans and fresh waters which lead to fish and then tetrapods (Tiktaalik comes to mind).

One of my favorite fossils is trilobites. They’re extremely common due to their hard bodies. In fact, even their eyes are well-preserved because of their hard mineral make-up. I personally recall entering touristy-stores seeing countless fossils of these guys in the mid-west to the west (which, unsurprisingly, was once a shallow sea). This image shows the different lineages of this organism. Studies show that the ‘rib’ count has changed over time in each individual species, often without regard to how the other species changed. Going back further, there is less and less divergence in each species. Eventually, as evolution predicts, they all meet at a common ancestor.

So naturally the next step is to find fossils which show more significant changes. Let’s take birds and reptiles. They hold similarities between each other, both morphologically (certain shapes and structures) and phylogenetically (genetic sequence). A good hypothesis is that they came from one common ancestor. If this is true, the links between birds and its ancestors and reptiles and its ancestors should lead to the same point. They do. Dinosaurs are the ancestors of both. The links between birds and dinosaurs are so incredibly well established that I’d prefer to not go over them in detail. But for starters, some dinosaurs sported feathers and claws and had the same proteins for the feather-making process as extant birds. The links between reptiles and dinosaurs is easier just on intuition, so I’ll leave it at that for now.

Other transitional fossils include the already mentioned Tiktaalik. A view of the history of life can be see here. This shows the change in head and neck structure. Recent research on long-ago discovered Tiktaalik fossils has shown the importance in the gradual bone changes in the neck. These changes – a hallmark of evolution – were important to the ability to turn its head. This is a hallmark because natural selection only modifies what already exists. This is precisely what happened.

Going further with this example, evolution makes predictions as to how early fish evolved to survive on land. If there were lobe-finned fish 390 million years ago and obviously terrestrial organisms 360 million years ago (which is what the fossil record shows), then if scientists are to find transitional fossils, they should date in between that time frame. There should be an animal that shows both features of lobe-finned fish and terrestrial animals. Tiktaalik is that animal. It has fins, scales, and gills, but it also has a flat, salamander-like head with nostrils on top of its nose. This is a good indication that it could breathe air. Its eyes were also placed there, indicating that it swam in shallow waters. Furthermore, it was lobe-finned, but shows bones (which eventually evolved into the arm bones you used to get out of bed today) that were able to support its weight to prop itself up. And of course, it dates to 375 million years ago.

Next, evolution says the fossil record should show recent fossils being more closely related to extant species than are early fossils. This is precisely what happens. Sixty million years ago there were no whales. Fossils resembling modern whales only show up 30 million years ago. So, again, evolution makes a predication: if transitional fossils are to be found, they will be within this gap. And so it is.

We begin with Indohyus. It was an artiodactyl. This is important because extant whales have vestigial bones which indicate that they came from this order: scientists expected to find this because, again, evolution predicted it. It should be of no surprise that this fossil dates to about 48 million years ago, right in the predicted gap. From here there is a gradual evolution shown in the fossil record which leads up to modern whales.

The lac Operon

This article has appeared separately at For the Sake of Science.

By Michael Hawkins

The lac operon of E. coli is the classic example for describing inducible prokaryotic gene expression. One excellent video description of it can be found here.

The jist is this. Not all genes are turned on all the time. There are ones which are needed constantly, others which are only needed in specific types of cells, and then others which are ‘turned on’ in specific situations. It is on this last point which I will focus.

In order for a gene to be ‘turned on’, it must be ‘off’ in the first place. All this means is that an organism’s (relevant) DNA is not being transcribed, thus preventing translation and the manifestation of proteins. The way this occurs in E. coli by means of the lac operon is that the lac repressor is bound to a DNA sequence.

A repressor is itself a protein. It binds to an organism’s DNA, thus preventing RNA polymerase from transcribing anything. This is a physical blockade; the repressor prevents the RNA polymerase from physically attaching and running along a specific sequence of DNA. This is the default position for an inducible repressor.

The way the repressor is removed is simple to understand. It has a specific shape to it which enables it to bind to the DNA sequence. However, this shape can be changed if lactose is present. The lactose will bind to the repressor, thus causing an allosteric change in shape. This means the repressor is no longer the specific shape needed to attach to the DNA, so it releases its ‘grip’.

This release allows the RNA polymerase to continue with transcription. This, eventually, turns to translation. In this stage, enzymes are created, two of which are ß-galactoside permease and ß-galactosidase (there is a third which can be ignored here). The former of the two is membrane-bound. This means it becomes embedded in the cell membrane. This quickens the transport of lactose from outside to inside the cell. Think of it like a tunnel through which only specific shapes can fit.

Once these specific shapes (lactose molecules) pass into the cell, ß-galactosidase breaks them into their constituents, one of which is glucose. This is used as a key source of energy in many organisms, including E. coli.

Once concentration falls, lactose molecules are no longer bound to the repressor, making it free to resume its normal duties attached to DNA.

Question 1 and Respect

By Michael Hawkins

It is necessary to briefly address the ugliness of Question 1. The results were abysmal: 52% of Mainers are bigots.

It would be a mistake to forget the analogy consistently drawn by No on 1 supporters. That is, this is like the past denials of civil rights for racial minorities.

Yes on 1 supporters never bothered to show how same-sex marriage infringed upon anyone’s rights. From this reason it must be concluded that “bigot” is the most appropriate term for these people.

Yet there’s an unjustified apprehension surrounding this label. Those who fought for liberty would do well to remember that the aforementioned analogy was more than just words. It meant something.

Do away with the undue respect. A bigot is a bigot is a bigot. Declare it loudly.

RNAi: Watching Your Back

The following has appeared on For the Sake of Science. The article in the physical copy of Without Apology has slightly different wording for the sake of print.

By Michael Hawkins

RNAi is an arrestingly interesting little mechanism for protecting the health of cells. The “i” stands for interference, and with good reason. RNAi is made up of a series of molecules which work to detect and destroy possible viruses and RNA which could be viruses.

It was first detected in 1986 when an attempt was made to make a really, really purple flower. The reason was purely for aesthetics, but it would prove to be far more important.

Knowing the gene which coded for purple pigmentation in petunias, geneticists made the logical conclusion and figured adding a bunch of those genes to the flowers would increase the depth of purple coloring in them. But as it turned out, they were wrong. In fact, they were remarkably wrong. Instead of deep purple flowers, they produced white flowers. Not a hint of purple anywhere.

No one had an answer to why would be. It took 12 years until researchers came up with the answer (and another 8 until they were awarded a Nobel Prize).

When viruses invade a cell, they ‘seek’ to make copies of themselves by utilizing the available DNA source. Post-transcription, this comes out with a funny shape due to the RNA making a mirror image of itself. The RNAi then recognizes this strange shape and destroys it with dicers. But it doesn’t stop there. Any sequence which comes out of the nucleus thereafter is also destroyed. This prevents any of the viruses (hopefully) from being translated and replicating (thus exploding out of the cell and infecting other cells).

Something similar happened when the geneticists tried making the super purple flowers. There wasn’t a mirror-image RNA sequence, but there was a funny sort of shape created by all the extra purple pigmentation genes. The RNAi recognized this as a potential virus and began destroying it. All of it. This meant there were no genes for purple getting translated into proteins.

Example petunia plants in which genes for pigmentation are silenced by RNAi. (http://en.wikipedia.org/wiki/Rnai)

So far this is pretty exciting stuff. It’s a post-transcriptional defense mechanism against viruses no one ever knew existed. But it has so much more potential than just as a passing curiosity.

Think about it. If RNAi can essentially turn off genes by destroying them through a sort of sequence-detection, then what stops it from curing diseases? This discovery has the serious potential to cure all the major ailments facing the world today: AIDS, cancer, Alzheimer’s. There has already been success in treating macular degeneration. This is a disease where too many blood vessels are growing in the eye. It damages the retina over time and makes vision majorly cloudy and blurry. There are simply too many genes for blood vessels being produced. But one way to stop this disease is to stop that blood vessel growth. To achieve this, a patient is given an injection which contains a copy of the gene with its mirror image (two mirror strands of DNA). The RNAi detects this misshape and destroys it. It then destroys all other likewise sequences. The same principle could be applied to any number of diseases.

There is an excellent NOVA video on RNAi which can be viewed here. It’s certainly worth watching (and only 15 minutes long).